4D Nucleome (4DN)
4D Nucleome (4DN)
Program Publications
Publications Search by Program
Search Results
The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Author | Journal Name | PubMedID | Journal Abbreviation | Publication Date |
|---|---|---|---|---|---|
| Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer. | Stackpole ML, Zeng W, Li S, Liu CC, Zhou Y, He S, Yeh A, Wang Z, Sun F, Li Q, Yuan Z, Yildirim A, Chen PJ, Winograd P, Tran B, Lee YT, Li PS, Noor Z, Yokomizo M, Ahuja P, Zhu Y, Tseng HR, Tomlinson JS, Garon E, French S, Magyar CE, Dry S, Lajonchere C, Geschwind D, Choi G, Saab S, Alber F, Wong WH, Dubinett SM, Aberle DR, Agopian V, Han SB, Ni X, Li W, Zhou XJ | Nature communications | 36175411 | Nat Commun | 2022 Sep 29 |
| The 3D Genome Structure of Single Cells. | Zhou T, Zhang R, Ma J | Annual review of biomedical data science | 34465168 | Annu Rev Biomed Data Sci | 2021 Jul 20 |
| UNADON: transformer-based model to predict genome-wide chromosome spatial position. | Yang M, Ma J | Bioinformatics (Oxford, England) | 37387176 | Bioinformatics | 2023 Jun 30 |
| UNADON: Transformer-based model to predict genome-wide chromosome spatial position. | Yang M, Ma J | ArXiv | 37163136 | ArXiv | 2023 Jul 1 |
| Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi. | Zhang R, Zhou T, Ma J | Cell systems | 36265466 | Cell Syst | 2022 Oct 19 |
| Computational methods for analysing multiscale 3D genome organization. | Zhang Y, Boninsegna L, Yang M, Misteli T, Alber F, Ma J | Nature reviews. Genetics | 37673975 | Nat Rev Genet | 2024 Feb |
| Interpretable representation learning for 3D multi-piece intracellular structures using point clouds. | Vasan R, Ferrante AJ, Borensztejn A, Frick CL, Gaudreault N, Mogre SS, Morris B, Pires GG, Rafelski SM, Theriot JA, Viana MP | bioRxiv : the preprint server for biology | 39091871 | bioRxiv | 2024 Aug 13 |
| Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues. | Stein J, Ericsson M, Nofal M, Magni L, Aufmkolk S, McMillan RB, Breimann L, Herlihy CP, Lee SD, Willemin A, Wohlmann J, Arguedas-Jimenez L, Yin P, Pombo A, Church GM, Wu CT | bioRxiv : the preprint server for biology | 38370628 | bioRxiv | 2025 Feb 13 |
| scGHOST: identifying single-cell 3D genome subcompartments. | Xiong K, Zhang R, Ma J | Nature methods | 38589516 | Nat Methods | 2024 May |
| L2G: Repurposing Language Models for Genomics Tasks. | Cheng W, Shen J, Khodak M, Ma J, Talwalkar A | bioRxiv : the preprint server for biology | 39713364 | bioRxiv | 2024 Dec 10 |
| Uncovering the Principles of Genome Folding by 3D Chromatin Modeling. | Yildirim A, Boninsegna L, Zhan Y, Alber F | Cold Spring Harbor perspectives in biology | 34400556 | Cold Spring Harb Perspect Biol | 2022 Jun 14 |
| Nuclear Compartments: An Incomplete Primer to Nuclear Compartments, Bodies, and Genome Organization Relative to Nuclear Architecture. | Belmont AS | Cold Spring Harbor perspectives in biology | 34400557 | Cold Spring Harb Perspect Biol | 2022 Jul 1 |
| Integrative approaches in genome structure analysis. | Boninsegna L, Yildirim A, Zhan Y, Alber F | Structure (London, England : 1993) | 34963059 | Structure | 2022 Jan 6 |
| Nucleome Browser: an integrative and multimodal data navigation platform for 4D Nucleome. | Zhu X, Zhang Y, Wang Y, Tian D, Belmont AS, Swedlow JR, Ma J | Nature methods | 35864167 | Nat Methods | 2022 Aug |
| Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells. | Zhou T, Zhang R, Jia D, Doty RT, Munday AD, Gao D, Xin L, Abkowitz JL, Duan Z, Ma J | bioRxiv : the preprint server for biology | 37546900 | bioRxiv | 2023 Jul 25 |
| Conformational analysis of chromosome structures reveals vital role of chromosome morphology in gene function. | Zhan Y, Yildirim A, Boninsegna L, Alber F | bioRxiv : the preprint server for biology | 36824908 | bioRxiv | 2023 Feb 19 |
| scGHOST: Identifying single-cell 3D genome subcompartments. | Xiong K, Zhang R, Ma J | bioRxiv : the preprint server for biology | 37292994 | bioRxiv | 2023 May 25 |
| Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells. | Calandrelli R, Wen X, Charles Richard JL, Luo Z, Nguyen TC, Chen CJ, Qi Z, Xue S, Chen W, Yan Z, Wu W, Zaleta-Rivera K, Hu R, Yu M, Wang Y, Li W, Ma J, Ren B, Zhong S | Nature communications | 37845234 | Nat Commun | 2023 Oct 16 |
| SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells. | Zhang M, Ehmann ME, Matukumalli S, Boob AG, Gilbert DM, Zhao H | Nature communications | 37699958 | Nat Commun | 2023 Sep 12 |
| Applying interpretable machine learning in computational biology-pitfalls, recommendations and opportunities for new developments. | Chen V, Yang M, Cui W, Kim JS, Talwalkar A, Ma J | Nature methods | 39122941 | Nat Methods | 2024 Aug |
| Nuclear speckle biology: At the cross-roads of discovery and functional analysis. | Chaturvedi P, Belmont AS | Current opinion in cell biology | 39340981 | Curr Opin Cell Biol | 2024 Dec |
| DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks. | Cheng W, Song Z, Zhang Y, Wang S, Wang D, Yang M, Li L, Ma J | bioRxiv : the preprint server for biology | 39829833 | bioRxiv | 2025 Jan 8 |
| Mapping Replication Timing in Single Mammalian Cells. | Bartlett DA, Dileep V, Baslan T, Gilbert DM | Current protocols | 34986273 | Curr Protoc | 2022 Jan |
| Phase separation in genome organization across evolution. | Feric M, Misteli T | Trends in cell biology | 33771451 | Trends Cell Biol | 2021 Aug |
| SPICEMIX enables integrative single-cell spatial modeling of cell identity. | Chidester B, Zhou T, Alam S, Ma J | Nature genetics | 36624346 | Nat Genet | 2023 Jan |
| OME-Zarr: a cloud-optimized bioimaging file format with international community support. | Moore J, Basurto-Lozada D, Besson S, Bogovic J, Bragantini J, Brown EM, Burel JM, Moreno XC, de Medeiros G, Diel EE, Gault D, Ghosh SS, Gold I, Halchenko YO, Hartley M, Horsfall D, Keller MS, Kittisopikul M, Kovacs G, Yoldaş AK, Kyoda K, de la Villegeorges ALT, Li T, Liberali P, Lindner D, Linkert M, Lüthi J, Maitin-Shepard J, Manz T, Marconato L, McCormick M, Lange M, Mohamed K, Moore W, Norlin N, Ouyang W, Özdemir B, Palla G, Pape C, Pelkmans L, Pietzsch T, Preibisch S, Prete M, Rzepka N, Samee S, Schaub N, Sidky H, Solak AC, Stirling DR, Striebel J, Tischer C, Toloudis D, Virshup I, Walczysko P, Watson AM, Weisbart E, Wong F, Yamauchi KA, Bayraktar O, Cimini BA, Gehlenborg N, Haniffa M, Hotaling N, Onami S, Royer LA, Saalfeld S, Stegle O, Theis FJ, Swedlow JR | bioRxiv : the preprint server for biology | 36865282 | bioRxiv | 2023 May 7 |
| Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories. | Dixon JC, Frick CL, Leveille CL, Garrison P, Lee PA, Mogre SS, Morris B, Nivedita N, Vasan R, Chen J, Fraser CL, Gamlin CR, Harris LK, Hendershott MC, Johnson GT, Klein KN, Oluoch SA, Thirstrup DJ, Sluzewski MF, Wilhelm L, Yang R, Toloudis DM, Viana MP, Theriot JA, Rafelski SM | bioRxiv : the preprint server for biology | 38979140 | bioRxiv | 2024 Jun 30 |
| An integrated view of the structure and function of the human 4D nucleome. | 4D Nucleome Consortium, Dekker J, Oksuz BA, Zhang Y, Wang Y, Minsk MK, Kuang S, Yang L, Gibcus JH, Krietenstein N, Rando OJ, Xu J, Janssens DH, Henikoff S, Kukalev A, Willemin A, Winick-Ng W, Kempfer R, Pombo A, Yu M, Kumar P, Zhang L, Belmont AS, Sasaki T, van Schaik T, Brueckner L, Peric-Hupkes D, van Steensel B, Wang P, Chai H, Kim M, Ruan Y, Zhang R, Quinodoz SA, Bhat P, Guttman M, Zhao W, Chien S, Liu Y, Venev SV, Plewczynski D, Azcarate II, Szabó D, Thieme CJ, Szczepińska T, Chiliński M, Sengupta K, Conte M, Esposito A, Abraham A, Zhang R, Wang Y, Wen X, Wu Q, Yang Y, Liu J, Boninsegna L, Yildirim A, Zhan Y, Chiariello AM, Bianco S, Lee L, Hu M, Li Y, Barnett RJ, Cook AL, Emerson DJ, Marchal C, Zhao P, Park P, Alver BH, Schroeder A, Navelkar R, Bakker C, Ronchetti W, Ehmsen S, Veit A, Gehlenborg N, Wang T, Li D, Wang X, Nicodemi M, Ren B, Zhong S, Phillips-Cremins JE, Gilbert DM, Pollard KS, Alber F, Ma J, Noble WS, Yue F | bioRxiv : the preprint server for biology | 39484446 | bioRxiv | 2024 Oct 27 |
| Nucleolus and centromere Tyramide Signal Amplification-Seq reveals variable localization of heterochromatin in different cell types. | Kumar P, Gholamalamdari O, Zhang Y, Zhang L, Vertii A, van Schaik T, Peric-Hupkes D, Sasaki T, Gilbert DM, van Steensel B, Ma J, Kaufman PD, Belmont AS | Communications biology | 39271748 | Commun Biol | 2024 Sep 13 |
| SPIN reveals genome-wide landscape of nuclear compartmentalization. | Wang Y, Zhang Y, Zhang R, van Schaik T, Zhang L, Sasaki T, Peric-Hupkes D, Chen Y, Gilbert DM, van Steensel B, Belmont AS, Ma J | Genome biology | 33446254 | Genome Biol | 2021 Jan 14 |
| Compartmentalization with nuclear landmarks yields random, yet precise, genome organization. | Kamat K, Lao Z, Qi Y, Wang Y, Ma J, Zhang B | Biophysical journal | 36871158 | Biophys J | 2023 Apr 4 |
| Multiscale and integrative single-cell Hi-C analysis with Higashi. | Zhang R, Zhou T, Ma J | Nature biotechnology | 34635838 | Nat Biotechnol | 2022 Feb |
| Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations. | Boninsegna L, Yildirim A, Polles G, Zhan Y, Quinodoz SA, Finn EH, Guttman M, Zhou XJ, Alber F | Nature methods | 35817938 | Nat Methods | 2022 Aug |
| GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. | Zhou T, Zhang R, Jia D, Doty RT, Munday AD, Gao D, Xin L, Abkowitz JL, Duan Z, Ma J | Nature genetics | 38744973 | Nat Genet | 2024 Aug |
| PhyGCN: Pre-trained Hypergraph Convolutional Neural Networks with Self-supervised Learning. | Deng Y, Zhang R, Xu P, Ma J, Gu Q | bioRxiv : the preprint server for biology | 37873233 | bioRxiv | 2023 Oct 2 |
| Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. | Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S | Molecular cell | 37419111 | Mol Cell | 2023 Aug 3 |
| Evaluating the role of the nuclear microenvironment in gene function by population-based modeling. | Yildirim A, Hua N, Boninsegna L, Zhan Y, Polles G, Gong K, Hao S, Li W, Zhou XJ, Alber F | Nature structural & molecular biology | 37580627 | Nat Struct Mol Biol | 2023 Aug |
| Single-Cell Multiomics Integration by SCOT. | Demetci P, Santorella R, Sandstede B, Noble WS, Singh R | Journal of computational biology : a journal of computational molecular cell biology | 34985990 | J Comput Biol | 2022 Jan |
| A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup. | Qiu C, Martin BK, Welsh IC, Daza RM, Le TM, Huang X, Nichols EK, Taylor ML, Fulton O, O'Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, Noble WS, Hamazaki N, Moens CB, Kimelman D, Cao J, Schier AF, Spielmann M, Murray SA, Trapnell C, Shendure J | bioRxiv : the preprint server for biology | 37066300 | bioRxiv | 2023 Apr 5 |
| Inference of 3D genome architecture by modeling overdispersion of Hi-C data. | Varoquaux N, Noble WS, Vert JP | Bioinformatics (Oxford, England) | 36594573 | Bioinformatics | 2023 Jan 1 |
| High-Capacity Sample Multiplexing for Single Cell Chromatin Accessibility Profiling. | Booth GT, Daza RM, Srivatsan SR, McFaline-Figueroa JL, Gladden RG, Furlan SN, Shendure J, Trapnell C | bioRxiv : the preprint server for biology | 36945538 | bioRxiv | 2023 Mar 6 |
| A molecular proximity sensor based on an engineered, dual-component guide RNA. | Choi J, Chen W, Liao H, Li X, Shendure J | bioRxiv : the preprint server for biology | 37645782 | bioRxiv | 2024 Aug 27 |
| High-capacity sample multiplexing for single cell chromatin accessibility profiling. | Booth GT, Daza RM, Srivatsan SR, McFaline-Figueroa JL, Gladden RG, Mullen AC, Furlan SN, Shendure J, Trapnell C | BMC genomics | 38049719 | BMC Genomics | 2023 Dec 4 |
| Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin. | Aman AJ, Saunders LM, Carr AA, Srivatasan S, Eberhard C, Carrington B, Watkins-Chow D, Pavan WJ, Trapnell C, Parichy DM | eLife | 37695017 | Elife | 2023 Sep 11 |
| CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation. | Fang H, Tronco AR, Bonora G, Nguyen T, Thakur J, Berletch JB, Filippova GN, Henikoff S, Shendure J, Noble WS, Duan Z, Disteche CM, Deng X | BMC biology | 40025499 | BMC Biol | 2025 Mar 3 |
| A molecular proximity sensor based on an engineered, dual-component guide RNA. | Choi J, Chen W, Liao H, Li X, Shendure J | eLife | 39937081 | Elife | 2025 Feb 12 |
| HiCRep.py: fast comparison of Hi-C contact matrices in Python. | Lin D, Sanders J, Noble WS | Bioinformatics (Oxford, England) | 33576390 | Bioinformatics | 2021 Sep 29 |
| X-factors in human disease: impact of gene content and dosage regulation. | Fang H, Deng X, Disteche CM | Human molecular genetics | 34387327 | Hum Mol Genet | 2021 Oct 1 |
| Optimized single-nucleus transcriptional profiling by combinatorial indexing. | Martin BK, Qiu C, Nichols E, Phung M, Green-Gladden R, Srivatsan S, Blecher-Gonen R, Beliveau BJ, Trapnell C, Cao J, Shendure J | Nature protocols | 36261634 | Nat Protoc | 2023 Jan |
| Embryo model completes gastrulation to neurulation and organogenesis. | Amadei G, Handford CE, Qiu C, De Jonghe J, Greenfeld H, Tran M, Martin BK, Chen DY, Aguilera-Castrejon A, Hanna JH, Elowitz MB, Hollfelder F, Shendure J, Glover DM, Zernicka-Goetz M | Nature | 36007540 | Nature | 2022 Oct |
| A time-resolved, multi-symbol molecular recorder via sequential genome editing. | Choi J, Chen W, Minkina A, Chardon FM, Suiter CC, Regalado SG, Domcke S, Hamazaki N, Lee C, Martin B, Daza RM, Shendure J | Nature | 35794474 | Nature | 2022 Aug |
| Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation. | Alavattam KG, Mitzelfelt KA, Bonora G, Fields PA, Yang X, Chiu HS, Pabon L, Bertero A, Palpant NJ, Noble WS, Murry CE | Stem cell reports | 36493778 | Stem Cell Reports | 2023 Jan 10 |
| Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation. | Bonora G, Ramani V, Singh R, Fang H, Jackson DL, Srivatsan S, Qiu R, Lee C, Trapnell C, Shendure J, Duan Z, Deng X, Noble WS, Disteche CM | Genome biology | 34579774 | Genome Biol | 2021 Sep 27 |
| Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes. | Aguilar R, Camplisson CK, Lin Q, Miga KH, Noble WS, Beliveau BJ | Nature communications | 38310092 | Nat Commun | 2024 Feb 3 |
| Symbolic recording of signalling and cis-regulatory element activity to DNA. | Chen W, Choi J, Li X, Nathans JF, Martin B, Yang W, Hamazaki N, Qiu C, Lalanne JB, Regalado S, Kim H, Agarwal V, Nichols E, Leith A, Lee C, Shendure J | Nature | 39020177 | Nature | 2024 Aug |
| Multiomic characterization of RNA microenvironments by oligonucleotide-mediated proximity-interactome mapping. | Tsue AF, Kania EE, Lei DQ, Fields R, McGann CD, Marciniak DM, Hershberg EA, Deng X, Kihiu M, Ong SE, Disteche CM, Kugel S, Beliveau BJ, Schweppe DK, Shechner DM | Nature methods | 39468212 | Nat Methods | 2024 Nov |
| Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells. | Swygert SG, Lin D, Portillo-Ledesma S, Lin PY, Hunt DR, Kao CF, Schlick T, Noble WS, Tsukiyama T | eLife | 34734806 | Elife | 2021 Nov 4 |
| Targeted DNase Hi-C. | Duan Z | Methods in molecular biology (Clifton, N.J.) | 32820399 | Methods Mol Biol | 2021 |
| Systematic reconstruction of cellular trajectories across mouse embryogenesis. | Qiu C, Cao J, Martin BK, Li T, Welsh IC, Srivatsan S, Huang X, Calderon D, Noble WS, Disteche CM, Murray SA, Spielmann M, Moens CB, Trapnell C, Shendure J | Nature genetics | 35288709 | Nat Genet | 2022 Mar |
| Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome. | Fang H, Bonora G, Lewandowski JP, Thakur J, Filippova GN, Henikoff S, Shendure J, Duan Z, Rinn JL, Deng X, Noble WS, Disteche CM | Nature communications | 33247132 | Nat Commun | 2020 Nov 27 |
| CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation. | Fang H, Tronco AR, Bonora G, Nguyen T, Thakur J, Berletch JB, Filippova GN, Henikoff S, Shendure J, Noble WS, Disteche CM, Deng X | bioRxiv : the preprint server for biology | 37205597 | bioRxiv | 2023 May 4 |
| Embryo-scale, single-cell spatial transcriptomics. | Srivatsan SR, Regier MC, Barkan E, Franks JM, Packer JS, Grosjean P, Duran M, Saxton S, Ladd JJ, Spielmann M, Lois C, Lampe PD, Shendure J, Stevens KR, Trapnell C | Science (New York, N.Y.) | 34210887 | Science | 2021 Jul 2 |
| LSMMD-MA: scaling multimodal data integration for single-cell genomics data analysis. | Meng-Papaxanthos L, Zhang R, Li G, Cuturi M, Noble WS, Vert JP | Bioinformatics (Oxford, England) | 37421399 | Bioinformatics | 2023 Jul 1 |
| Sex-biased and parental allele-specific gene regulation by KDM6A. | Ma W, Fang H, Pease N, Filippova GN, Disteche CM, Berletch JB | Biology of sex differences | 35871105 | Biol Sex Differ | 2022 Jul 23 |
| Single-cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes. | Shi T, Beaulieu MO, Saunders LM, Fabian P, Trapnell C, Segil N, Crump JG, Raible DW | eLife | 36598134 | Elife | 2023 Jan 4 |
| Cross-species imputation and comparison of single-cell transcriptomic profiles. | Zhang R, Yang M, Schreiber J, O'Day DR, Turner JMA, Shendure J, Disteche CM, Deng X, Noble WS | bioRxiv : the preprint server for biology | 37905060 | bioRxiv | 2024 Aug 12 |
| Proteostasis governs differential temperature sensitivity across embryonic cell types. | Dorrity MW, Saunders LM, Duran M, Srivatsan SR, Barkan E, Jackson DL, Sattler SM, Ewing B, Queitsch C, Shendure J, Raible DW, Kimelman D, Trapnell C | Cell | 37949057 | Cell | 2023 Nov 9 |
| Cross-species imputation and comparison of single-cell transcriptomic profiles. | Zhang R, Yang M, Schreiber J, O'Day DR, Turner JMA, Shendure J, Noble WS, Disteche CM, Deng X | Genome biology | 40012008 | Genome Biol | 2025 Feb 26 |
| Unsupervised manifold alignment for single-cell multi-omics data. | Singh R, Demetci P, Bonora G, Ramani V, Lee C, Fang H, Duan Z, Deng X, Shendure J, Disteche C, Noble WS | ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine | 33954299 | ACM BCB | 2020 Sep |
| X-chromosome regulation and sex differences in brain anatomy. | Raznahan A, Disteche CM | Neuroscience and biobehavioral reviews | 33171144 | Neurosci Biobehav Rev | 2021 Jan |
| SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport. | Demetci P, Santorella R, Sandstede B, Noble WS, Singh R | Journal of computational biology : a journal of computational molecular cell biology | 35050714 | J Comput Biol | 2022 Jan |
| Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning. | Zhang R, Meng-Papaxanthos L, Vert JP, Noble WS | Journal of computational biology : a journal of computational molecular cell biology | 36251758 | J Comput Biol | 2022 Nov |
| Multi-condition and multi-modal temporal profile inference during mouse embryonic development. | Zhang R, Qiu C, Filippova G, Li G, Shendure J, Vert JP, Deng X, Disteche C, Noble WS | bioRxiv : the preprint server for biology | 38496477 | bioRxiv | 2024 Sep 13 |
| Retinoic acid induces human gastruloids with posterior embryo-like structures. | Hamazaki N, Yang W, Kubo CA, Qiu C, Martin BK, Garge RK, Regalado SG, Nichols EK, Pendyala S, Bradley N, Fowler DM, Lee C, Daza RM, Srivatsan S, Shendure J | Nature cell biology | 39164488 | Nat Cell Biol | 2024 Oct |
| Induction and in silico staging of human gastruloids with neural tube, segmented somites & advanced cell types. | Hamazaki N, Yang W, Kubo C, Qiu C, Martin BK, Garge RK, Regalado SG, Nichols E, Lee C, Daza RM, Srivatsan S, Shendure J | bioRxiv : the preprint server for biology | 38405970 | bioRxiv | 2024 Feb 12 |
| A single-cell time-lapse of mouse prenatal development from gastrula to birth. | Qiu C, Martin BK, Welsh IC, Daza RM, Le TM, Huang X, Nichols EK, Taylor ML, Fulton O, O'Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, Noble WS, Hamazaki N, Moens CB, Kimelman D, Cao J, Schier AF, Spielmann M, Murray SA, Trapnell C, Shendure J | Nature | 38355799 | Nature | 2024 Feb |
| A systematic evaluation of Hi-C data enhancement methods for enhancing PLAC-seq and HiChIP data. | Huang L, Yang Y, Li G, Jiang M, Wen J, Abnousi A, Rosen JD, Hu M, Li Y | Briefings in bioinformatics | 35488276 | Brief Bioinform | 2022 May 13 |
| WashU Epigenome Browser update 2022. | Li D, Purushotham D, Harrison JK, Hsu S, Zhuo X, Fan C, Liu S, Xu V, Chen S, Xu J, Ouyang S, Wu AS, Wang T | Nucleic acids research | 35412637 | Nucleic Acids Res | 2022 Jul 5 |
| SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data. | Yu M, Abnousi A, Zhang Y, Li G, Lee L, Chen Z, Fang R, Lagler TM, Yang Y, Wen J, Sun Q, Li Y, Ren B, Hu M | Nature methods | 34446921 | Nat Methods | 2021 Sep |
| The dynamics of chromatin architecture in brain development and function. | Harabula I, Pombo A | Current opinion in genetics & development | 33421764 | Curr Opin Genet Dev | 2021 Apr |
| Phase separation of ecDNA aggregates establishes in-trans contact domains boosting selective MYC regulatory interactions. | Conte M, Matteuzzi T, Esposito A, Chiariello AM, Bianco S, Vercellone F, Nicodemi M | bioRxiv : the preprint server for biology | 37503084 | bioRxiv | 2023 Jul 17 |
| Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells. | Chiariello AM, Abraham A, Bianco S, Esposito A, Vercellone F, Conte M, Fontana A, Nicodemi M | bioRxiv : the preprint server for biology | 37546924 | bioRxiv | 2023 Jul 28 |
| A fast, scalable and versatile tool for analysis of single-cell omics data. | Zhang K, Zemke NR, Armand EJ, Ren B | Nature methods | 38191932 | Nat Methods | 2024 Feb |
| Epigenetic regulatory layers in the 3D nucleus. | Willemin A, Szabó D, Pombo A | Molecular cell | 38242127 | Mol Cell | 2024 Feb 1 |
| Sensory Input, Sex, and Function Shape Hypothalamic Cell Type Development. | Kaplan HS, Logeman BL, Zhang K, Santiago C, Sohail N, Naumenko S, Ho Sui SJ, Ginty DD, Ren B, Dulac C | bioRxiv : the preprint server for biology | 38328205 | bioRxiv | 2024 Jan 23 |
| Droplet Hi-C for Fast and Scalable Profiling of Chromatin Architecture in Single Cells. | Chang L, Xie Y, Taylor B, Wang Z, Sun J, Tan TR, Bejar R, Chen CC, Furnari FB, Hu M, Ren B | bioRxiv : the preprint server for biology | 38712075 | bioRxiv | 2024 Apr 22 |
| Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells. | Chiariello AM, Abraham A, Bianco S, Esposito A, Fontana A, Vercellone F, Conte M, Nicodemi M | Nature communications | 38740770 | Nat Commun | 2024 May 13 |
| Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations. | Conte M, Abraham A, Esposito A, Yang L, Gibcus JH, Parsi KM, Vercellone F, Fontana A, Di Pierno F, Dekker J, Nicodemi M | International journal of molecular sciences | 39337699 | Int J Mol Sci | 2024 Sep 23 |
| H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation. | Kubo N, Chen PB, Hu R, Ye Z, Sasaki H, Ren B | Molecular cell | 38513661 | Mol Cell | 2024 May 2 |
| Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina. | Yuan Y, Biswas P, Zemke N, Dang K, Wu Y, D Antonio M, Xie Y, Yang Q, Dong K, Lau PK, Li D, Seng C, Bartosik W, Buchanan J, Lin L, Lancione R, Wang K, Lee S, Gibbs Z, Ecker J, Frazer K, Wang T, Preissl S, Wang A, Ayyagari R, Ren B | bioRxiv : the preprint server for biology | 39764062 | bioRxiv | 2025 Apr 2 |
| Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. | Kubo N, Ishii H, Xiong X, Bianco S, Meitinger F, Hu R, Hocker JD, Conte M, Gorkin D, Yu M, Li B, Dixon JR, Hu M, Nicodemi M, Zhao H, Ren B | Nature structural & molecular biology | 33398174 | Nat Struct Mol Biol | 2021 Feb |
| The Need for a Human Pangenome Reference Sequence. | Miga KH, Wang T | Annual review of genomics and human genetics | 33929893 | Annu Rev Genomics Hum Genet | 2021 Aug 31 |
| Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin. | Fiorillo L, Musella F, Conte M, Kempfer R, Chiariello AM, Bianco S, Kukalev A, Irastorza-Azcarate I, Esposito A, Abraham A, Prisco A, Pombo A, Nicodemi M | Nature methods | 33963348 | Nat Methods | 2021 May |
| Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser. | Li D, Harrison JK, Purushotham D, Wang T | Nature methods | 35864166 | Nat Methods | 2022 Aug |
| Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C. | Beagrie RA, Thieme CJ, Annunziatella C, Baugher C, Zhang Y, Schueler M, Kukalev A, Kempfer R, Chiariello AM, Bianco S, Li Y, Davis T, Scialdone A, Welch LR, Nicodemi M, Pombo A | Nature methods | 37336949 | Nat Methods | 2023 Jul |
| Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding. | Conte M, Irani E, Chiariello AM, Abraham A, Bianco S, Esposito A, Nicodemi M | Nature communications | 35831310 | Nat Commun | 2022 Jul 13 |
| Role of H3K4 monomethylation in gene regulation. | Wang Z, Ren B | Current opinion in genetics & development | 38278054 | Curr Opin Genet Dev | 2024 Feb |
| Modbed track: Visualization of modified bases in single-molecule sequencing. | Li D, Zhuo X, Harrison JK, Liu S, Wang T | Cell genomics | 38116122 | Cell Genom | 2023 Dec 13 |
| Conserved and divergent gene regulatory programs of the mammalian neocortex. | Zemke NR, Armand EJ, Wang W, Lee S, Zhou J, Li YE, Liu H, Tian W, Nery JR, Castanon RG, Bartlett A, Osteen JK, Li D, Zhuo X, Xu V, Chang L, Dong K, Indralingam HS, Rink JA, Xie Y, Miller M, Krienen FM, Zhang Q, Taskin N, Ting J, Feng G, McCarroll SA, Callaway EM, Wang T, Lein ES, Behrens MM, Ecker JR, Ren B | Nature | 38092918 | Nature | 2023 Dec |
| Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues. | Yu M, Zemke NR, Chen Z, Juric I, Hu R, Raviram R, Abnousi A, Fang R, Zhang Y, Gorkin DU, Li YE, Zhao Y, Lee L, Mishra S, Schmitt AD, Qiu Y, Dickel DE, Visel A, Pennacchio LA, Hu M, Ren B | Nature structural & molecular biology | 39681766 | Nat Struct Mol Biol | 2025 Mar |
| Dose-dependent sensitivity of human 3D chromatin to a heart disease-linked transcription factor. | Grant ZL, Kuang S, Zhang S, Horrillo AJ, Rao KS, Kameswaran V, Joubran C, Lau PK, Dong K, Yang B, Bartosik WM, Zemke NR, Ren B, Kathiriya IS, Pollard KS, Bruneau BG | bioRxiv : the preprint server for biology | 39829922 | bioRxiv | 2025 Jan 12 |
| HPRep: Quantifying Reproducibility in HiChIP and PLAC-Seq Datasets. | Rosen JD, Yang Y, Abnousi A, Chen J, Song M, Jones IR, Shen Y, Hu M, Li Y | Current issues in molecular biology | 34563051 | Curr Issues Mol Biol | 2021 Sep 17 |
| Cell-type specialization is encoded by specific chromatin topologies. | Winick-Ng W, Kukalev A, Harabula I, Zea-Redondo L, Szabó D, Meijer M, Serebreni L, Zhang Y, Bianco S, Chiariello AM, Irastorza-Azcarate I, Thieme CJ, Sparks TM, Carvalho S, Fiorillo L, Musella F, Irani E, Torlai Triglia E, Kolodziejczyk AA, Abentung A, Apostolova G, Paul EJ, Franke V, Kempfer R, Akalin A, Teichmann SA, Dechant G, Ungless MA, Nicodemi M, Welch L, Castelo-Branco G, Pombo A | Nature | 34789882 | Nature | 2021 Nov |
| Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data. | Shao W, Wang T | Genome research | 33355230 | Genome Res | 2021 Jan |
| Physical mechanisms of chromatin spatial organization. | Chiariello AM, Bianco S, Esposito A, Fiorillo L, Conte M, Irani E, Musella F, Abraham A, Prisco A, Nicodemi M | The FEBS journal | 33583147 | FEBS J | 2022 Mar |
| CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains. | Huang H, Zhu Q, Jussila A, Han Y, Bintu B, Kern C, Conte M, Zhang Y, Bianco S, Chiariello AM, Yu M, Hu R, Tastemel M, Juric I, Hu M, Nicodemi M, Zhuang X, Ren B | Nature genetics | 34002095 | Nat Genet | 2021 Jul |
| Spatially resolved epigenomic profiling of single cells in complex tissues. | Lu T, Ang CE, Zhuang X | Cell | 37172568 | Cell | 2023 May 11 |
| The dynseq browser track shows context-specific features at nucleotide resolution. | Nair S, Barrett A, Li D, Raney BJ, Lee BT, Kerpedjiev P, Ramalingam V, Pampari A, Lekschas F, Wang T, Haeussler M, Kundaje A | Nature genetics | 36241719 | Nat Genet | 2022 Nov |
| A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH. | Jia BB, Jussila A, Kern C, Zhu Q, Ren B | Nature biotechnology | 36593410 | Nat Biotechnol | 2023 Jul |
| Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser. | Zhuo X, Hsu S, Purushotham D, Kuntala PK, Harrison JK, Du AY, Chen S, Li D, Wang T | Genome research | 37156621 | Genome Res | 2023 May |
| Cell-type-specific 3D-genome organization and transcription regulation in the brain. | Liu S, Zheng P, Wang CY, Jia BB, Zemke NR, Ren B, Zhuang X | bioRxiv : the preprint server for biology | 38105994 | bioRxiv | 2023 Dec 5 |
| Spatially resolved epigenomic profiling of single cells in complex tissues. | Lu T, Ang CE, Zhuang X | Cell | 36272405 | Cell | 2022 Nov 10 |
| SnapHiC-D: a computational pipeline to identify differential chromatin contacts from single-cell Hi-C data. | Lee L, Yu M, Li X, Zhu C, Zhang Y, Yu H, Chen Z, Mishra S, Ren B, Li Y, Hu M | Briefings in bioinformatics | 37649383 | Brief Bioinform | 2023 Sep 20 |
| SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data. | Lee L, Yu H, Jia BB, Jussila A, Zhu C, Chen J, Xie L, Hafner A, Mishra S, Wang DD, Strambio-De-Castillia C, Boettiger A, Ren B, Li Y, Hu M | Nature communications | 37573342 | Nat Commun | 2023 Aug 12 |
| SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data. | Yu H, Wu D, Mishra S, Shen G, Sun H, Hu M, Li Y | Communications biology | 38982263 | Commun Biol | 2024 Jul 9 |
| Polymer models are a versatile tool to study chromatin 3D organization. | Esposito A, Bianco S, Fiorillo L, Conte M, Abraham A, Musella F, Nicodemi M, Prisco A, Chiariello AM | Biochemical Society transactions | 34282837 | Biochem Soc Trans | 2021 Aug 27 |
| HiC-ACT: improved detection of chromatin interactions from Hi-C data via aggregated Cauchy test. | Lagler TM, Abnousi A, Hu M, Yang Y, Li Y | American journal of human genetics | 33545029 | Am J Hum Genet | 2021 Feb 4 |
| Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes. | Choudhary MNK, Quaid K, Xing X, Schmidt H, Wang T | Nature communications | 36746940 | Nat Commun | 2023 Feb 6 |
| Interpreting non-coding disease-associated human variants using single-cell epigenomics. | Gaulton KJ, Preissl S, Ren B | Nature reviews. Genetics | 37161089 | Nat Rev Genet | 2023 Aug |
| Characterizing cis-regulatory elements using single-cell epigenomics. | Preissl S, Gaulton KJ, Ren B | Nature reviews. Genetics | 35840754 | Nat Rev Genet | 2023 Jan |
| Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states. | Esposito A, Bianco S, Chiariello AM, Abraham A, Fiorillo L, Conte M, Campanile R, Nicodemi M | Cell reports | 35354035 | Cell Rep | 2022 Mar 29 |
| TWO-SIGMA-G: a new competitive gene set testing framework for scRNA-seq data accounting for inter-gene and cell-cell correlation. | Van Buren E, Hu M, Cheng L, Wrobel J, Wilhelmsen K, Su L, Li Y, Wu D | Briefings in bioinformatics | 35325048 | Brief Bioinform | 2022 May 13 |
| Developmental Pathways Are Epigenetically Reprogrammed during Lung Cancer Brain Metastasis. | Karlow JA, Devarakonda S, Xing X, Jang HS, Govindan R, Watson M, Wang T | Cancer research | 35706127 | Cancer Res | 2022 Aug 3 |
| Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations. | Conte M, Abraham A, Esposito A, Yang L, Gibcus JH, Parsi KM, Vercellone F, Fontana A, Pierno FD, Dekker J, Nicodemi M | bioRxiv : the preprint server for biology | 39071404 | bioRxiv | 2024 Jul 16 |
| RNA-mediated symmetry breaking enables singular olfactory receptor choice. | Pourmorady AD, Bashkirova EV, Chiariello AM, Belagzhal H, Kodra A, Duffié R, Kahiapo J, Monahan K, Pulupa J, Schieren I, Osterhoudt A, Dekker J, Nicodemi M, Lomvardas S | Nature | 38123679 | Nature | 2024 Jan |
| Nuclear morphology is shaped by loop-extrusion programs. | Patta I, Zand M, Lee L, Mishra S, Bortnick A, Lu H, Prusty A, McArdle S, Mikulski Z, Wang HY, Cheng CS, Fisch KM, Hu M, Murre C | Nature | 38355805 | Nature | 2024 Mar |
| SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data. | Yu H, Wu D, Shen G, Hu M, Li Y | bioRxiv : the preprint server for biology | 38293083 | bioRxiv | 2024 Jan 15 |
| A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons. | Szabó D, Franke V, Bianco S, Batiuk MY, Paul EJ, Kukalev A, Pfisterer UG, Irastorza-Azcarate I, Chiariello AM, Demharter S, Zea-Redondo L, Lopez-Atalaya JP, Nicodemi M, Akalin A, Khodosevich K, Ungless MA, Winick-Ng W, Pombo A | bioRxiv : the preprint server for biology | 38766140 | bioRxiv | 2024 May 12 |
| Cell type-specific 3D-genome organization and transcription regulation in the brain. | Liu S, Wang CY, Zheng P, Jia BB, Zemke NR, Ren P, Park HL, Ren B, Zhuang X | Science advances | 40009678 | Sci Adv | 2025 Feb 28 |
| Efficient, scalable, and near-nucleotide-resolution profiling of protein occupancy in the genome with deaminases. | Chang L, Ren B | Proceedings of the National Academy of Sciences of the United States of America | 39869813 | Proc Natl Acad Sci U S A | 2025 Feb 4 |
| HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics. | Strom AR, Biggs RJ, Banigan EJ, Wang X, Chiu K, Herman C, Collado J, Yue F, Ritland Politz JC, Tait LJ, Scalzo D, Telling A, Groudine M, Brangwynne CP, Marko JF, Stephens AD | eLife | 34106828 | Elife | 2021 Jun 9 |
| Single-molecule micromanipulation studies of methylated DNA. | Zaichuk T, Marko JF | Biophysical journal | 33838135 | Biophys J | 2021 Jun 1 |
| Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. | Gabriele M, Brandão HB, Grosse-Holz S, Jha A, Dailey GM, Cattoglio C, Hsieh TS, Mirny L, Zechner C, Hansen AS | Science (New York, N.Y.) | 35420890 | Science | 2022 Apr 29 |
| Reeling it in: how DNA topology drives loop extrusion by condensin. | Narducci DN, Hansen AS | Nature structural & molecular biology | 35835869 | Nat Struct Mol Biol | 2022 Jul |
| Spatial organization of transcribed eukaryotic genes. | Leidescher S, Ribisel J, Ullrich S, Feodorova Y, Hildebrand E, Galitsyna A, Bultmann S, Link S, Thanisch K, Mulholland C, Dekker J, Leonhardt H, Mirny L, Solovei I | Nature cell biology | 35177821 | Nat Cell Biol | 2022 Mar |
| CTCF is essential for proper mitotic spindle structure and anaphase segregation. | Chiu K, Berrada Y, Eskndir N, Song D, Fong C, Naughton S, Chen T, Moy S, Gyurmey S, James L, Ezeiruaku C, Capistran C, Lowey D, Diwanji V, Peterson S, Parakh H, Burgess AR, Probert C, Zhu A, Anderson B, Levi N, Gerlitz G, Packard MC, Dorfman KA, Bahiru MS, Stephens AD | bioRxiv : the preprint server for biology | 36712070 | bioRxiv | 2023 Jan 10 |
| Design principles of 3D epigenetic memory systems. | Owen JA, Osmanović D, Mirny L | Science (New York, N.Y.) | 37972190 | Science | 2023 Nov 17 |
| Rules of engagement for condensins and cohesins guide mitotic chromosome formation. | Samejima K, Gibcus JH, Abraham S, Cisneros-Soberanis F, Samejima I, Beckett AJ, Pučeková N, Abad MA, Medina-Pritchard B, Paulson JR, Xie L, Jeyaprakash AA, Prior IA, Mirny LA, Dekker J, Goloborodko A, Earnshaw WC | bioRxiv : the preprint server for biology | 38659940 | bioRxiv | 2024 Apr 30 |
| Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation. | Yang JH, Hansen AS | Nature reviews. Molecular cell biology | 38413840 | Nat Rev Mol Cell Biol | 2024 Jul |
| Crumpled polymer with loops recapitulates key features of chromosome organization. | Polovnikov KE, Slavov B, Belan S, Imakaev M, Brandão HB, Mirny LA | Physical review. X | 38774252 | Phys Rev X | 2023 Oct-Dec |
| An autoinhibitory switch of the LSD1 disordered region controls enhancer silencing. | Waterbury AL, Kwok HS, Lee C, Narducci DN, Freedy AM, Su C, Raval S, Reiter AH, Hawkins W, Lee K, Li J, Hoenig SM, Vinyard ME, Cole PA, Hansen AS, Carr SA, Papanastasiou M, Liau BB | Molecular cell | 38870936 | Mol Cell | 2024 Jun 20 |
| Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics. | Belaghzal H, Borrman T, Stephens AD, Lafontaine DL, Venev SV, Weng Z, Marko JF, Dekker J | Nature genetics | 33574602 | Nat Genet | 2021 Mar |
| DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations. | Nomidis SK, Carlon E, Gruber S, Marko JF | Nucleic acids research | 35474142 | Nucleic Acids Res | 2022 May 20 |
| Pairtools: from sequencing data to chromosome contacts. | Open2C, Abdennur N, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Venev SV | bioRxiv : the preprint server for biology | 36824968 | bioRxiv | 2023 Feb 15 |
| Mechanics and functional consequences of nuclear deformations. | Kalukula Y, Stephens AD, Lammerding J, Gabriele S | Nature reviews. Molecular cell biology | 35513718 | Nat Rev Mol Cell Biol | 2022 Sep |
| Multi-View Design Patterns and Responsive Visualization for Genomics Data. | LYi S, Gehlenborg N | IEEE transactions on visualization and computer graphics | 36166553 | IEEE Trans Vis Comput Graph | 2023 Jan |
| GenoREC: A Recommendation System for Interactive Genomics Data Visualization. | Pandey A, L'Yi S, Wang Q, Borkin MA, Gehlenborg N | IEEE transactions on visualization and computer graphics | 36191105 | IEEE Trans Vis Comput Graph | 2023 Jan |
| Dynamics of endogenous PARP1 and PARP2 during DNA damage revealed by live-cell single-molecule imaging. | Mahadevan J, Jha A, Rudolph J, Bowerman S, Narducci D, Hansen AS, Luger K | iScience | 36594010 | iScience | 2023 Jan 20 |
| Measuring Inaccessible Chromatin Genome-Wide Using Protect-seq. | Spracklin G, Yang L, Pradhan S, Dekker J | Methods in molecular biology (Clifton, N.J.) | 36807063 | Methods Mol Biol | 2023 |
| Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization. | L'Yi S, Wang Q, Lekschas F, Gehlenborg N | IEEE transactions on visualization and computer graphics | 34596551 | IEEE Trans Vis Comput Graph | 2022 Jan |
| Cooltools: Enabling high-resolution Hi-C analysis in Python. | Open2C, Abdennur N, Abraham S, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Oksuz BA, Venev SV, Xiao Y | PLoS computational biology | 38709825 | PLoS Comput Biol | 2024 May |
| Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus. | Attar AG, Paturej J, Banigan EJ, Erbaş A | Nucleus (Austin, Tex.) | 38753956 | Nucleus | 2024 Dec |
| DRAVA: Aligning Human Concepts with Machine Learning Latent Dimensions for the Visual Exploration of Small Multiples. | Wang Q, L'Yi S, Gehlenborg N | Proceedings of the SIGCHI conference on human factors in computing systems. CHI Conference | 38074525 | Proc SIGCHI Conf Hum Factor Comput Syst | 2023 Apr |
| Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus. | Girard M, de la Cruz MO, Marko JF, Erbaş A | Physical review. E | 39160964 | Phys Rev E | 2024 Jul |
| Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells. | Adams NM, Galitsyna A, Tiniakou I, Esteva E, Lau CM, Reyes J, Abdennur N, Shkolikov A, Yap GS, Khodadadi-Jamayran A, Mirny LA, Reizis B | bioRxiv : the preprint server for biology | 39345451 | bioRxiv | 2024 Oct 30 |
| Independence of Centromeric and Pericentromeric Chromatin Stability on CCAN Components. | Biggs RJ, Sundararajan K, Sun M, Hendrix E, Straight AF, Marko JF | bioRxiv : the preprint server for biology | 39763731 | bioRxiv | 2024 Dec 19 |
| Genome-wide absolute quantification of chromatin looping. | Jusuf JM, Grosse-Holz S, Gabriele M, Mach P, Flyamer IM, Zechner C, Giorgetti L, Mirny LA, Hansen AS | bioRxiv : the preprint server for biology | 39935886 | bioRxiv | 2025 Jan 15 |
| Actin contraction controls nuclear blebbing and rupture independent of actin confinement. | Pho M, Berrada Y, Gunda A, Lavallee A, Chiu K, Padam A, Currey ML, Stephens AD | Molecular biology of the cell | 38088876 | Mol Biol Cell | 2024 Feb 1 |
| Cohesin-mediated loop anchors confine the locations of human replication origins. | Emerson DJ, Zhao PA, Cook AL, Barnett RJ, Klein KN, Saulebekova D, Ge C, Zhou L, Simandi Z, Minsk MK, Titus KR, Wang W, Gong W, Zhang D, Yang L, Venev SV, Gibcus JH, Yang H, Sasaki T, Kanemaki MT, Yue F, Dekker J, Chen CL, Gilbert DM, Phillips-Cremins JE | Nature | 35676475 | Nature | 2022 Jun |
| Polyphony: an Interactive Transfer Learning Framework for Single-Cell Data Analysis. | Cheng F, Keller MS, Qu H, Gehlenborg N, Wang Q | IEEE transactions on visualization and computer graphics | 36155452 | IEEE Trans Vis Comput Graph | 2023 Jan |
| Gos: a declarative library for interactive genomics visualization in Python. | Manz T, L'Yi S, Gehlenborg N | Bioinformatics (Oxford, England) | 36688709 | Bioinformatics | 2023 Jan 1 |
| Development and implementation of a metaphase DNA model for ionizing radiation induced DNA damage calculation. | Sitmukhambetov S, Dinh B, Lai Y, Banigan EJ, Pan Z, Jia X, Chi Y | Physics in medicine and biology | 36533598 | Phys Med Biol | 2022 Dec 19 |
| Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments. | Goel VY, Huseyin MK, Hansen AS | Nature genetics | 37157000 | Nat Genet | 2023 Jun |
| mRNA initiation and termination are spatially coordinated. | Calvo-Roitberg E, Carroll CL, Venev SV, Kim G, Mick ST, Dekker J, Fiszbein A, Pai AA | bioRxiv : the preprint server for biology | 38260419 | bioRxiv | 2024 Jan 7 |
| A Versatile Micromanipulation Apparatus for Biophysical Assays of the Cell Nucleus. | Currey ML, Kandula V, Biggs R, Marko JF, Stephens AD | Cellular and molecular bioengineering | 36119136 | Cell Mol Bioeng | 2022 Aug |
| Nuclear shape is affected differentially by loss of lamin A, lamin C, or both lamin A and C. | Pho M, Berrada Y, Gunda A, Stephens AD | microPublication biology | 38440331 | MicroPubl Biol | 2024 |
| CTCF and R-loops are boundaries of cohesin-mediated DNA looping. | Zhang H, Shi Z, Banigan EJ, Kim Y, Yu H, Bai XC, Finkelstein IJ | Molecular cell | 37536339 | Mol Cell | 2023 Aug 17 |
| CTCF is essential for proper mitotic spindle structure and anaphase segregation. | Chiu K, Berrada Y, Eskndir N, Song D, Fong C, Naughton S, Chen T, Moy S, Gyurmey S, James L, Ezeiruaku C, Capistran C, Lowey D, Diwanji V, Peterson S, Parakh H, Burgess AR, Probert C, Zhu A, Anderson B, Levi N, Gerlitz G, Packard MC, Dorfman KA, Bahiru MS, Stephens AD | Chromosoma | 37728741 | Chromosoma | 2024 Jul |
| Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis. | Hildebrand EM, Polovnikov K, Dekker B, Liu Y, Lafontaine DL, Fox AN, Li Y, Venev SV, Mirny LA, Dekker J | Molecular cell | 38521067 | Mol Cell | 2024 Apr 18 |
| Brain and cancer associated binding domain mutations provide insight into CTCF's relationship with chromatin and its ability to act as a chromatin organizer. | Do C, Jiang G, Cova G, Katsifis CC, Narducci DN, Yang J, Sakellaropoulos T, Vidal R, Lhoumaud P, Tsirigos A, Regis FFD, Kakabadze N, Nora EP, Noyes M, Cheng X, Hansen AS, Skok JA | Research square | 39070636 | Res Sq | 2024 Jul 19 |
| DNA damage causes ATM-dependent heterochromatin loss leading to nuclear softening, blebbing, and rupture. | Eskndir N, Hossain M, Currey ML, Pho M, Berrada Y, Stephens AD | bioRxiv : the preprint server for biology | 38853925 | bioRxiv | 2024 May 29 |
| The chromosome folding problem and how cells solve it. | Dekker J, Mirny LA | Cell | 39547207 | Cell | 2024 Nov 14 |
| Isolation and manipulation of meiotic spindles from mouse oocytes reveals migration regulated by pulling force during asymmetric division. | Liu N, Kawamura R, Qiang W, Balboula A, Marko JF, Qiao H | bioRxiv : the preprint server for biology | 39677774 | bioRxiv | 2024 Dec 8 |
| A General Framework for Comparing Embedding Visualizations Across Class-Label Hierarchies. | Manz T, Lekschas F, Greene E, Finak G, Gehlenborg N | IEEE transactions on visualization and computer graphics | 39255153 | IEEE Trans Vis Comput Graph | 2025 Jan |
| The crucial role of bioimage analysts in scientific research and publication. | Cimini BA, Bankhead P, D'Antuono R, Fazeli E, Fernandez-Rodriguez J, Fuster-Barceló C, Haase R, Jambor HK, Jones ML, Jug F, Klemm AH, Kreshuk A, Marcotti S, Martins GG, McArdle S, Miura K, Muñoz-Barrutia A, Murphy LC, Nelson MS, Nørrelykke SF, Paul-Gilloteaux P, Pengo T, Pylvänäinen JW, Pytowski L, Ravera A, Reinke A, Rekik Y, Strambio-De-Castillia C, Thédié D, Uhlmann V, Umney O, Wiggins L, Eliceiri KW | Journal of cell science | 39475207 | J Cell Sci | 2024 Oct 15 |
| Dynamics of microcompartment formation at the mitosis-to-G1 transition. | Goel VY, Aboreden NG, Jusuf JM, Zhang H, Mori LP, Mirny LA, Blobel GA, Banigan EJ, Hansen AS | bioRxiv : the preprint server for biology | 39345388 | bioRxiv | 2024 Sep 16 |
| Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm. | Schooley A, Venev SV, Aksenova V, Navarrete E, Dasso M, Dekker J | bioRxiv : the preprint server for biology | 39345587 | bioRxiv | 2024 Sep 16 |
| High-resolution, genome-wide mapping of positive supercoiling in chromosomes. | Guo MS, Kawamura R, Littlehale ML, Marko JF, Laub MT | eLife | 34279217 | Elife | 2021 Jul 19 |
| Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers. | Spracklin G, Abdennur N, Imakaev M, Chowdhury N, Pradhan S, Mirny LA, Dekker J | Nature structural & molecular biology | 36550219 | Nat Struct Mol Biol | 2023 Jan |
| Systematic evaluation of chromosome conformation capture assays. | Akgol Oksuz B, Yang L, Abraham S, Venev SV, Krietenstein N, Parsi KM, Ozadam H, Oomen ME, Nand A, Mao H, Genga RMJ, Maehr R, Rando OJ, Mirny LA, Gibcus JH, Dekker J | Nature methods | 34480151 | Nat Methods | 2021 Sep |
| Right on target: Chromatin jets arise from targeted cohesin loading in wild-type cells. | Drayton JA, Hansen AS | Molecular cell | 36270244 | Mol Cell | 2022 Oct 20 |
| CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity. | Liu Y, Dekker J | Nature cell biology | 36202971 | Nat Cell Biol | 2022 Oct |
| Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. | Mirny L, Dekker J | Cold Spring Harbor perspectives in biology | 34518339 | Cold Spring Harb Perspect Biol | 2022 Jul 1 |
| DNA density is a better indicator of a nuclear bleb than lamin B loss. | Bunner S, Prince K, Srikrishna K, Pujadas EM, McCarthy AA, Kuklinski A, Jackson O, Pellegrino P, Jagtap S, Eweka I, Lawlor C, Eastin E, Yas G, Aiello J, LaPointe N, von Blucher IS, Hardy J, Chen J, Backman V, Janssen A, Packard M, Dorfman K, Almassalha L, Bahiru MS, Stephens AD | bioRxiv : the preprint server for biology | 38370828 | bioRxiv | 2024 Feb 7 |
| Capturing Chromosome Conformation Across Length Scales. | Yang L, Akgol Oksuz B, Dekker J, Gibcus JH | Journal of visualized experiments : JoVE | 36744801 | J Vis Exp | 2023 Jan 20 |
| Cell cycle and Age-Related Modulations of Mouse Chromosome Stiffness. | Liu N, Qiang W, Jordan P, Marko JF, Qiao H | bioRxiv : the preprint server for biology | 38559262 | bioRxiv | 2025 Mar 10 |
| Transcription inhibition suppresses nuclear blebbing and rupture independently of nuclear rigidity. | Berg IK, Currey ML, Gupta S, Berrada Y, Nguyen BV, Pho M, Patteson AE, Schwarz JM, Banigan EJ, Stephens AD | Journal of cell science | 37756607 | J Cell Sci | 2023 Oct 15 |
| Chromosome and protein folding: In search for unified principles. | Mirny LA | Current opinion in structural biology | 37327690 | Curr Opin Struct Biol | 2023 Aug |
| Transcription shapes 3D chromatin organization by interacting with loop extrusion. | Banigan EJ, Tang W, van den Berg AA, Stocsits RR, Wutz G, Brandão HB, Busslinger GA, Peters JM, Mirny LA | Proceedings of the National Academy of Sciences of the United States of America | 36897969 | Proc Natl Acad Sci U S A | 2023 Mar 14 |
| Pairtools: From sequencing data to chromosome contacts. | Open2C, Abdennur N, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Venev SV | PLoS computational biology | 38809952 | PLoS Comput Biol | 2024 May |
| Bigtools: a high-performance BigWig and BigBed library in Rust. | Huey JD, Abdennur N | Bioinformatics (Oxford, England) | 38837370 | Bioinformatics | 2024 Jun 3 |
| PRC1.6 localizes on chromatin with the human silencing hub (HUSH) complex for promoter-specific silencing. | Rodríguez TC, Yurkovetskiy L, Nagalekshmi K, Lam CHO, Jazbec E, Maitland SA, Wolfe SA, Sontheimer EJ, Luban J | bioRxiv : the preprint server for biology | 39026796 | bioRxiv | 2024 Jul 13 |
| Nuclear blebs are associated with destabilized chromatin-packing domains. | Pujadas Liwag EM, Acosta N, Almassalha LM, Su YP, Gong R, Kanemaki MT, Stephens AD, Backman V | Journal of cell science | 39878045 | J Cell Sci | 2025 Feb 1 |
| Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities. | Dai C, Li W, Tjong H, Hao S, Zhou Y, Li Q, Chen L, Zhu B, Alber F, Jasmine Zhou X | Nature communications | 27240697 | Nat Commun | 2016 May 31 |
| TopDom: an efficient and deterministic method for identifying topological domains in genomes. | Shin H, Shi Y, Dai C, Tjong H, Gong K, Alber F, Zhou XJ | Nucleic acids research | 26704975 | Nucleic Acids Res | 2016 Apr 20 |
| Affinity Isolation of Endogenous Saccharomyces Cerevisiae Nuclear Pore Complexes. | Nudelman I, Fernandez-Martinez J, Rout MP | Methods in molecular biology (Clifton, N.J.) | 35412228 | Methods Mol Biol | 2022 |
| The three-dimensional genome organization of Drosophila melanogaster through data integration. | Li Q, Tjong H, Li X, Gong K, Zhou XJ, Chiolo I, Alber F | Genome biology | 28760140 | Genome Biol | 2017 Jul 31 |
| Integrative modelling of cellular assemblies. | Joseph AP, Polles G, Alber F, Topf M | Current opinion in structural biology | 28735107 | Curr Opin Struct Biol | 2017 Oct |
| Crystal Structure of the FGFR4/LY2874455 Complex Reveals Insights into the Pan-FGFR Selectivity of LY2874455. | Wu D, Guo M, Philips MA, Qu L, Jiang L, Li J, Chen X, Chen Z, Chen L, Chen Y | PloS one | 27618313 | PLoS One | 2016 |
| Quantitative Methods to Investigate the 4D Dynamics of Heterochromatic Repair Sites in Drosophila Cells. | Caridi CP, Delabaere L, Tjong H, Hopp H, Das D, Alber F, Chiolo I | Methods in enzymology | 29523239 | Methods Enzymol | 2018 |
| Integrative structure and functional anatomy of a nuclear pore complex. | Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP | Nature | 29539637 | Nature | 2018 Mar 22 |
| Producing genome structure populations with the dynamic and automated PGS software. | Hua N, Tjong H, Shin H, Gong K, Zhou XJ, Alber F | Nature protocols | 29622804 | Nat Protoc | 2018 May |
| Crystal Structure of Apo MEF2B Reveals New Insights in DNA Binding and Cofactor Interaction. | Lei X, Shi H, Kou Y, Rajashekar N, Wu F, Sen C, Xu J, Chen L | Biochemistry | 29944822 | Biochemistry | 2018 Jul 17 |
| Comprehensive characterization of neutrophil genome topology. | Zhu Y, Gong K, Denholtz M, Chandra V, Kamps MP, Alber F, Murre C | Genes & development | 28167501 | Genes Dev | 2017 Jan 15 |
| Principles for Integrative Structural Biology Studies. | Rout MP, Sali A | Cell | 31150619 | Cell | 2019 May 30 |
| Quantitative imaging of chromatin decompaction in living cells. | Dultz E, Mancini R, Polles G, Vallotton P, Alber F, Weis K | Molecular biology of the cell | 29771637 | Mol Biol Cell | 2018 Jul 15 |
| From integrative structural biology to cell biology. | Sali A | The Journal of biological chemistry | 33957123 | J Biol Chem | 2021 Jan-Jun |
| Archiving and disseminating integrative structure models. | Vallat B, Webb B, Westbrook J, Sali A, Berman HM | Journal of biomolecular NMR | 31278630 | J Biomol NMR | 2019 Jul |
| Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. | Tjong H, Li W, Kalhor R, Dai C, Hao S, Gong K, Zhou Y, Li H, Zhou XJ, Le Gros MA, Larabell CA, Chen L, Alber F | Proceedings of the National Academy of Sciences of the United States of America | 26951677 | Proc Natl Acad Sci U S A | 2016 Mar 22 |
| Spatial Principles of Chromatin Architecture Associated With Organ-Specific Gene Regulation. | Chapski DJ, Rosa-Garrido M, Hua N, Alber F, Vondriska TM | Frontiers in cardiovascular medicine | 30697540 | Front Cardiovasc Med | 2018 |
| Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface. | Lei X, Zhao J, Sagendorf JM, Rajashekar N, Xu J, Dantas Machado AC, Sen C, Rohs R, Feng P, Chen L | Journal of molecular biology | 32681840 | J Mol Biol | 2020 Sep 4 |
| Mechanics and Buckling of Biopolymeric Shells and Cell Nuclei. | Banigan EJ, Stephens AD, Marko JF | Biophysical journal | 29045860 | Biophys J | 2017 Oct 17 |
| Robust model-based analysis of single-particle tracking experiments with Spot-On. | Hansen AS, Woringer M, Grimm JB, Lavis LD, Tjian R, Darzacq X | eLife | 29300163 | Elife | 2018 Jan 4 |
| CTCF and cohesin regulate chromatin loop stability with distinct dynamics. | Hansen AS, Pustova I, Cattoglio C, Tjian R, Darzacq X | eLife | 28467304 | Elife | 2017 May 3 |
| Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition. | Flyamer IM, Gassler J, Imakaev M, Brandão HB, Ulianov SV, Abdennur N, Razin SV, Mirny LA, Tachibana-Konwalski K | Nature | 28355183 | Nature | 2017 Apr 6 |
| Comparative analysis of 2D and 3D distance measurements to study spatial genome organization. | Finn EH, Pegoraro G, Shachar S, Misteli T | Methods (San Diego, Calif.) | 28179124 | Methods | 2017 Jul 1 |
| Causes and consequences of nuclear gene positioning. | Shachar S, Misteli T | Journal of cell science | 28404786 | J Cell Sci | 2017 May 1 |
| Determining cellular CTCF and cohesin abundances to constrain 3D genome models. | Cattoglio C, Pustova I, Walther N, Ho JJ, Hantsche-Grininger M, Inouye CJ, Hossain MJ, Dailey GM, Ellenberg J, Darzacq X, Tjian R, Hansen AS | eLife | 31205001 | Elife | 2019 Jun 17 |
| C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2. | Gao XD, Tu LC, Mir A, Rodriguez T, Ding Y, Leszyk J, Dekker J, Shaffer SA, Zhu LJ, Wolfe SA, Sontheimer EJ | Nature methods | 29735996 | Nat Methods | 2018 Jun |
| Molecular basis and biological function of variability in spatial genome organization. | Finn EH, Misteli T | Science (New York, N.Y.) | 31488662 | Science | 2019 Sep 6 |
| A supervised learning framework for chromatin loop detection in genome-wide contact maps. | Salameh TJ, Wang X, Song F, Zhang B, Wright SM, Khunsriraksakul C, Ruan Y, Yue F | Nature communications | 32647330 | Nat Commun | 2020 Jul 9 |
| Bend-Induced Twist Waves and the Structure of Nucleosomal DNA. | Skoruppa E, Nomidis SK, Marko JF, Carlon E | Physical review letters | 30192578 | Phys Rev Lett | 2018 Aug 24 |
| Effects of altering histone posttranslational modifications on mitotic chromosome structure and mechanics. | Biggs R, Liu PZ, Stephens AD, Marko JF | Molecular biology of the cell | 30625026 | Mol Biol Cell | 2019 Mar 21 |
| Adapting dCas9-APEX2 for subnuclear proteomic profiling. | Gao XD, Rodríguez TC, Sontheimer EJ | Methods in enzymology | 30691651 | Methods Enzymol | 2019 |
| Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation. | McSwiggen DT, Hansen AS, Teves SS, Marie-Nelly H, Hao Y, Heckert AB, Umemoto KK, Dugast-Darzacq C, Tjian R, Darzacq X | eLife | 31038454 | Elife | 2019 May 7 |
| Nucleation of Multiple Buckled Structures in Intertwined DNA Double Helices. | Brahmachari S, Gunn KH, Giuntoli RD, Mondragón A, Marko JF | Physical review letters | 29219598 | Phys Rev Lett | 2017 Nov 3 |
| Dense Bicoid hubs accentuate binding along the morphogen gradient. | Mir M, Reimer A, Haines JE, Li XY, Stadler M, Garcia H, Eisen MB, Darzacq X | Genes & development | 28982761 | Genes Dev | 2017 Sep 1 |
| Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond. | Nomidis SK, Skoruppa E, Carlon E, Marko JF | Physical review. E | 30999490 | Phys Rev E | 2019 Mar |
| Ultrastructural Details of Mammalian Chromosome Architecture. | Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh TS, Parsi KM, Yang L, Maehr R, Mirny LA, Dekker J, Rando OJ | Molecular cell | 32213324 | Mol Cell | 2020 May 7 |
| Building momentum through networks: Bioimaging across the Americas. | De Niz M, Escobedo García R, Terán Ramirez C, Pakowski Y, Abonza Y, Bialy N, Orr VL, Olivera A, Abonza V, Alleva K, Allodi S, Almeida MF, Becerril Cuevas AR, Bonnet F, Burgos Solorio A, Chew TL, Chiabrando G, Cimini B, Cleret-Buhot A, Contreras Jiménez G, Daza L, De Sá V, De Val N, Delgado-Álvarez DL, Eliceiri K, Fiolka R, Grecco H, Hanein D, Hernández Herrera P, Hockberger P, Hernandez HO, Hernandez Guadarrama Y, Itano M, Jacobs CA, Jiménez-García LF, Jiménez Sabinina V, Kamaid A, Keppler A, Kumar A, Lacoste J, Lovy A, Luby-Phelps K, Mahadevan-Jansen A, Malacrida L, Mehta SB, Miller C, Miranda K, Moore JA, North A, O'Toole P, Olivares Urbano M, Pietrasanta LI, Portugal RV, Rossi AH, Sanchez Contreras J, Strambio-De-Castilla C, Soldevila G, Vale B, Vazquez D, Wood C, Brown CM, Guerrero A | Journal of microscopy | 38747464 | J Microsc | 2024 Jun |
| Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. | Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG | Cell | 28525758 | Cell | 2017 May 18 |
| Chromosome organization by one-sided and two-sided loop extrusion. | Banigan EJ, van den Berg AA, Brandão HB, Marko JF, Mirny LA | eLife | 32250245 | Elife | 2020 Apr 6 |
| Structural organization of the inactive X chromosome in the mouse. | Giorgetti L, Lajoie BR, Carter AC, Attia M, Zhan Y, Xu J, Chen CJ, Kaplan N, Chang HY, Heard E, Dekker J | Nature | 27437574 | Nature | 2016 Jul 28 |
| Two independent modes of chromatin organization revealed by cohesin removal. | Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, Haering CH, Mirny L, Spitz F | Nature | 29094699 | Nature | 2017 Nov 2 |
| A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture. | Gassler J, Brandão HB, Imakaev M, Flyamer IM, Ladstätter S, Bickmore WA, Peters JM, Mirny LA, Tachibana K | The EMBO journal | 29217590 | EMBO J | 2017 Dec 15 |
| Effects of electrostatic interactions on ligand dissociation kinetics. | Erbaş A, de la Cruz MO, Marko JF | Physical review. E | 29548245 | Phys Rev E | 2018 Feb |
| Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization. | Finn EH, Pegoraro G, Brandão HB, Valton AL, Oomen ME, Dekker J, Mirny L, Misteli T | Cell | 30799036 | Cell | 2019 Mar 7 |
| Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos. | Mir M, Stadler MR, Ortiz SA, Hannon CE, Harrison MM, Darzacq X, Eisen MB | eLife | 30589412 | Elife | 2018 Dec 27 |
| Higher-Order Organization Principles of Pre-translational mRNPs. | Metkar M, Ozadam H, Lajoie BR, Imakaev M, Mirny LA, Dekker J, Moore MJ | Molecular cell | 30415953 | Mol Cell | 2018 Nov 15 |
| Integrative detection and analysis of structural variation in cancer genomes. | Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F | Nature genetics | 30202056 | Nat Genet | 2018 Oct |
| Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences. | McSwiggen DT, Mir M, Darzacq X, Tjian R | Genes & development | 31594803 | Genes Dev | 2019 Dec 1 |
| Multi-contact 3C reveals that the human genome during interphase is largely not entangled. | Tavares-Cadete F, Norouzi D, Dekker B, Liu Y, Dekker J | Nature structural & molecular biology | 32929283 | Nat Struct Mol Biol | 2020 Dec |
| Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals. | Feodorova Y, Falk M, Mirny LA, Solovei I | Trends in cell biology | 31980345 | Trends Cell Biol | 2020 Apr |
| Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation. | Stephens AD, Liu PZ, Kandula V, Chen H, Almassalha LM, Herman C, Backman V, O'Halloran T, Adam SA, Goldman RD, Banigan EJ, Marko JF | Molecular biology of the cell | 31365328 | Mol Biol Cell | 2019 Aug 1 |
| Facilitated dissociation of transcription factors from single DNA binding sites. | Kamar RI, Banigan EJ, Erbas A, Giuntoli RD, Olvera de la Cruz M, Johnson RC, Marko JF | Proceedings of the National Academy of Sciences of the United States of America | 28364020 | Proc Natl Acad Sci U S A | 2017 Apr 18 |
| The 4D nucleome project. | Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S, 4D Nucleome Network | Nature | 28905911 | Nature | 2017 Sep 13 |
| SMC complexes differentially compact mitotic chromosomes according to genomic context. | Schalbetter SA, Goloborodko A, Fudenberg G, Belton JM, Miles C, Yu M, Dekker J, Mirny L, Baxter J | Nature cell biology | 28825700 | Nat Cell Biol | 2017 Sep |
| Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. | Kundu S, Ji F, Sunwoo H, Jain G, Lee JT, Sadreyev RI, Dekker J, Kingston RE | Molecular cell | 28157505 | Mol Cell | 2017 Feb 2 |
| Phase separation drives heterochromatin domain formation. | Strom AR, Emelyanov AV, Mir M, Fyodorov DV, Darzacq X, Karpen GH | Nature | 28636597 | Nature | 2017 Jul 13 |
| FISH-ing for captured contacts: towards reconciling FISH and 3C. | Fudenberg G, Imakaev M | Nature methods | 28604723 | Nat Methods | 2017 Jul |
| Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. | Kundu S, Ji F, Sunwoo H, Jain G, Lee JT, Sadreyev RI, Dekker J, Kingston RE | Molecular cell | 29979966 | Mol Cell | 2018 Jul 5 |
| Defect-facilitated buckling in supercoiled double-helix DNA. | Brahmachari S, Dittmore A, Takagi Y, Neuman KC, Marko JF | Physical review. E | 29548184 | Phys Rev E | 2018 Feb |
| Imaging dynamic and selective low-complexity domain interactions that control gene transcription. | Chong S, Dugast-Darzacq C, Liu Z, Dong P, Dailey GM, Cattoglio C, Heckert A, Banala S, Lavis L, Darzacq X, Tjian R | Science (New York, N.Y.) | 29930090 | Science | 2018 Jul 27 |
| Supercoiling DNA Locates Mismatches. | Dittmore A, Brahmachari S, Takagi Y, Marko JF, Neuman KC | Physical review letters | 29053317 | Phys Rev Lett | 2017 Oct 6 |
| History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. | Khrameeva EE, Fudenberg G, Gelfand MS, Mirny LA | Journal of bioinformatics and computational biology | 27021249 | J Bioinform Comput Biol | 2016 Apr |
| Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines. | Eastland A, Hornick J, Kawamura R, Nanavati D, Marko JF | Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology | 27145786 | Chromosome Res | 2016 Sep |
| TAD disruption as oncogenic driver. | Valton AL, Dekker J | Current opinion in genetics & development | 27111891 | Curr Opin Genet Dev | 2016 Feb |
| Formation of Chromosomal Domains by Loop Extrusion. | Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny LA | Cell reports | 27210764 | Cell Rep | 2016 May 31 |
| Chromosome Compaction by Active Loop Extrusion. | Goloborodko A, Marko JF, Mirny LA | Biophysical journal | 27224481 | Biophys J | 2016 May 24 |
| Measuring the reproducibility and quality of Hi-C data. | Yardımcı GG, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, Taylor J, Yue F, Dekker J, Noble WS | Genome biology | 30890172 | Genome Biol | 2019 Mar 19 |
| Physics and Biology (of Chromosomes). | Marko JF | Journal of molecular biology | 31866291 | J Mol Biol | 2020 Jan 17 |
| Multiomics characterization of mouse hepatoblastoma identifies yes-associated protein 1 target genes. | Rodríguez TC, Kwan SY, Smith JL, Dadafarin S, Wu CH, Sontheimer EJ, Xue W | Hepatology (Baltimore, Md.) | 35932276 | Hepatology | 2023 Jul 1 |
| Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffold. | Sun M, Biggs R, Hornick J, Marko JF | Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology | 30143891 | Chromosome Res | 2018 Dec |
| Highly structured homolog pairing reflects functional organization of the Drosophila genome. | AlHaj Abed J, Erceg J, Goloborodko A, Nguyen SC, McCole RB, Saylor W, Fudenberg G, Lajoie BR, Dekker J, Mirny LA, Wu CT | Nature communications | 31582763 | Nat Commun | 2019 Oct 3 |
| How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation. | Erbaş A, Marko JF | Current opinion in chemical biology | 31586479 | Curr Opin Chem Biol | 2019 Dec |
| Guided nuclear exploration increases CTCF target search efficiency. | Hansen AS, Amitai A, Cattoglio C, Tjian R, Darzacq X | Nature chemical biology | 31792445 | Nat Chem Biol | 2020 Mar |
| Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding. | Hsieh TS, Cattoglio C, Slobodyanyuk E, Hansen AS, Rando OJ, Tjian R, Darzacq X | Molecular cell | 32213323 | Mol Cell | 2020 May 7 |
| The Smc5/6 Core Complex Is a Structure-Specific DNA Binding and Compacting Machine. | Serrano D, Cordero G, Kawamura R, Sverzhinsky A, Sarker M, Roy S, Malo C, Pascal JM, Marko JF, D'Amours D | Molecular cell | 33301731 | Mol Cell | 2020 Dec 17 |
| Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches. | Desai PR, Brahmachari S, Marko JF, Das S, Neuman KC | Nucleic acids research | 33045724 | Nucleic Acids Res | 2020 Nov 4 |
| MCM complexes are barriers that restrict cohesin-mediated loop extrusion. | Dequeker BJH, Scherr MJ, Brandão HB, Gassler J, Powell S, Gaspar I, Flyamer IM, Lalic A, Tang W, Stocsits R, Davidson IF, Peters JM, Duderstadt KE, Mirny LA, Tachibana K | Nature | 35585235 | Nature | 2022 Jun |
| The Histone Chaperone FACT Induces Cas9 Multi-turnover Behavior and Modifies Genome Manipulation in Human Cells. | Wang AS, Chen LC, Wu RA, Hao Y, McSwiggen DT, Heckert AB, Richardson CD, Gowen BG, Kazane KR, Vu JT, Wyman SK, Shin JJ, Darzacq X, Walter JC, Corn JE | Molecular cell | 32603710 | Mol Cell | 2020 Jul 16 |
| Loop extrusion: theory meets single-molecule experiments. | Banigan EJ, Mirny LA | Current opinion in cell biology | 32534241 | Curr Opin Cell Biol | 2020 Jun |
| The interplay between asymmetric and symmetric DNA loop extrusion. | Banigan EJ, Mirny LA | eLife | 33295869 | Elife | 2020 Dec 9 |
| Assessing Self-interaction of Mammalian Nuclear Proteins by Co-immunoprecipitation. | Cattoglio C, Pustova I, Darzacq X, Tjian R, Hansen AS | Bio-protocol | 33654750 | Bio Protoc | 2020 Feb 20 |
| CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning. | Oomen ME, Hansen AS, Liu Y, Darzacq X, Dekker J | Genome research | 30655336 | Genome Res | 2019 Feb |
| Heterochromatin drives compartmentalization of inverted and conventional nuclei. | Falk M, Feodorova Y, Naumova N, Imakaev M, Lajoie BR, Leonhardt H, Joffe B, Dekker J, Fudenberg G, Solovei I, Mirny LA | Nature | 31168090 | Nature | 2019 Jun |
| Receptor-Ligand Rebinding Kinetics in Confinement. | Erbaş A, Olvera de la Cruz M, Marko JF | Biophysical journal | 31029377 | Biophys J | 2019 May 7 |
| qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells. | Andrews JO, Conway W, Cho WK, Narayanan A, Spille JH, Jayanth N, Inoue T, Mullen S, Thaler J, Cissé II | Scientific reports | 29743503 | Sci Rep | 2018 May 9 |
| Blank spots on the map: some current questions on nuclear organization and genome architecture. | Adriaens C, Serebryannyy LA, Feric M, Schibler A, Meaburn KJ, Kubben N, Trzaskoma P, Shachar S, Vidak S, Finn EH, Sood V, Pegoraro G, Misteli T | Histochemistry and cell biology | 30238154 | Histochem Cell Biol | 2018 Dec |
| Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy. | Mir M, Reimer A, Stadler M, Tangara A, Hansen AS, Hockemeyer D, Eisen MB, Garcia H, Darzacq X | Methods in molecular biology (Clifton, N.J.) | 29956254 | Methods Mol Biol | 2018 |
| Chromatin organization by an interplay of loop extrusion and compartmental segregation. | Nuebler J, Fudenberg G, Imakaev M, Abdennur N, Mirny LA | Proceedings of the National Academy of Sciences of the United States of America | 29967174 | Proc Natl Acad Sci U S A | 2018 Jul 17 |
| Emerging Evidence of Chromosome Folding by Loop Extrusion. | Fudenberg G, Abdennur N, Imakaev M, Goloborodko A, Mirny LA | Cold Spring Harbor symposia on quantitative biology | 29728444 | Cold Spring Harb Symp Quant Biol | 2017 |
| Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. | Belaghzal H, Dekker J, Gibcus JH | Methods (San Diego, Calif.) | 28435001 | Methods | 2017 Jul 1 |
| Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins. | Stephens AD, Liu PZ, Banigan EJ, Almassalha LM, Backman V, Adam SA, Goldman RD, Marko JF | Molecular biology of the cell | 29142071 | Mol Biol Cell | 2018 Jan 15 |
| An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerases. | Gunn KH, Marko JF, Mondragón A | Nature structural & molecular biology | 28414321 | Nat Struct Mol Biol | 2017 May |
| Erratum: Torque correlation length and stochastic twist dynamics of DNA [Phys. Rev. E 89, 062706 (2014)]. | Banigan EJ, Marko JF | Physical review. E | 27182590 | Phys Rev E | 2016 Apr |
| Epigenetic characteristics of the mitotic chromosome in 1D and 3D. | Oomen ME, Dekker J | Critical reviews in biochemistry and molecular biology | 28228067 | Crit Rev Biochem Mol Biol | 2017 Apr |
| Activation of proto-oncogenes by disruption of chromosome neighborhoods. | Hnisz D, Weintraub AS, Day DS, Valton AL, Bak RO, Li CH, Goldmann J, Lajoie BR, Fan ZP, Sigova AA, Reddy J, Borges-Rivera D, Lee TI, Jaenisch R, Porteus MH, Dekker J, Young RA | Science (New York, N.Y.) | 26940867 | Science | 2016 Mar 25 |
| The 3D Genome as Moderator of Chromosomal Communication. | Dekker J, Mirny L | Cell | 26967279 | Cell | 2016 Mar 10 |
| Bioframe: operations on genomic intervals in Pandas dataframes. | Open2C, Abdennur N, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Venev S | Bioinformatics (Oxford, England) | 38402507 | Bioinformatics | 2024 Feb 1 |
| HiGlass: web-based visual exploration and analysis of genome interaction maps. | Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber JM, Ouellette SB, Azhir A, Kumar N, Hwang J, Lee S, Alver BH, Pfister H, Mirny LA, Park PJ, Gehlenborg N | Genome biology | 30143029 | Genome Biol | 2018 Aug 24 |
| Recent evidence that TADs and chromatin loops are dynamic structures. | Hansen AS, Cattoglio C, Darzacq X, Tjian R | Nucleus (Austin, Tex.) | 29077530 | Nucleus | 2018 Jan 1 |
| Oligomerization and ATP stimulate condensin-mediated DNA compaction. | Keenholtz RA, Dhanaraman T, Palou R, Yu J, D'Amours D, Marko JF | Scientific reports | 29079757 | Sci Rep | 2017 Oct 27 |
| A pathway for mitotic chromosome formation. | Gibcus JH, Samejima K, Goloborodko A, Samejima I, Naumova N, Nuebler J, Kanemaki MT, Xie L, Paulson JR, Earnshaw WC, Mirny LA, Dekker J | Science (New York, N.Y.) | 29348367 | Science | 2018 Feb 9 |
| Micromanipulation of prophase I chromosomes from mouse spermatocytes reveals high stiffness and gel-like chromatin organization. | Biggs RJ, Liu N, Peng Y, Marko JF, Qiao H | Communications biology | 32999386 | Commun Biol | 2020 Sep 30 |
| Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture. | Lafontaine DL, Yang L, Dekker J, Gibcus JH | Current protocols | 34286910 | Curr Protoc | 2021 Jul |
| Cooler: scalable storage for Hi-C data and other genomically labeled arrays. | Abdennur N, Mirny LA | Bioinformatics (Oxford, England) | 31290943 | Bioinformatics | 2020 Jan 1 |
| Chromatin and lamin A determine two different mechanical response regimes of the cell nucleus. | Stephens AD, Banigan EJ, Adam SA, Goldman RD, Marko JF | Molecular biology of the cell | 28057760 | Mol Biol Cell | 2017 Jul 7 |
| Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma. | McGeachie MJ, Yates KP, Zhou X, Guo F, Sternberg AL, Van Natta ML, Wise RA, Szefler SJ, Sharma S, Kho AT, Cho MH, Croteau-Chonka DC, Castaldi PJ, Jain G, Sanyal A, Zhan Y, Lajoie BR, Dekker J, Stamatoyannopoulos J, Covar RA, Zeiger RS, Adkinson NF, Williams PV, Kelly HW, Grasemann H, Vonk JM, Koppelman GH, Postma DS, Raby BA, Houston I, Lu Q, Fuhlbrigge AL, Tantisira KG, Silverman EK, Tonascia J, Strunk RC, Weiss ST, CAMP Research Group | American journal of respiratory and critical care medicine | 27367781 | Am J Respir Crit Care Med | 2016 Dec 15 |
| Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. | Beagan JA, Gilgenast TG, Kim J, Plona Z, Norton HK, Hu G, Hsu SC, Shields EJ, Lyu X, Apostolou E, Hochedlinger K, Corces VG, Dekker J, Phillips-Cremins JE | Cell stem cell | 27152443 | Cell Stem Cell | 2016 May 5 |
| Two major mechanisms of chromosome organization. | Mirny LA, Imakaev M, Abdennur N | Current opinion in cell biology | 31228682 | Curr Opin Cell Biol | 2019 Jun |
| A chromosome folding intermediate at the condensin-to-cohesin transition during telophase. | Abramo K, Valton AL, Venev SV, Ozadam H, Fox AN, Dekker J | Nature cell biology | 31685986 | Nat Cell Biol | 2019 Nov |
| The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. | Erceg J, AlHaj Abed J, Goloborodko A, Lajoie BR, Fudenberg G, Abdennur N, Imakaev M, McCole RB, Nguyen SC, Saylor W, Joyce EF, Senaratne TN, Hannan MA, Nir G, Dekker J, Mirny LA, Wu CT | Nature communications | 31582744 | Nat Commun | 2019 Oct 3 |
| OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries. | An L, Yang T, Yang J, Nuebler J, Xiang G, Hardison RC, Li Q, Zhang Y | Genome biology | 31847870 | Genome Biol | 2019 Dec 18 |
| Torque and buckling in stretched intertwined double-helix DNAs. | Brahmachari S, Marko JF | Physical review. E | 28618488 | Phys Rev E | 2017 May |
| Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF. | Hansen AS, Hsieh TS, Cattoglio C, Pustova I, Saldaña-Meyer R, Reinberg D, Darzacq X, Tjian R | Molecular cell | 31522987 | Mol Cell | 2019 Nov 7 |
| Compaction and segregation of sister chromatids via active loop extrusion. | Goloborodko A, Imakaev MV, Marko JF, Mirny L | eLife | 27192037 | Elife | 2016 May 18 |
| Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds. | Dahlke K, Zhao J, Sing CE, Banigan EJ | Biophysical journal | 31427067 | Biophys J | 2019 Sep 17 |
| Molecular basis of CTCF binding polarity in genome folding. | Nora EP, Caccianini L, Fudenberg G, So K, Kameswaran V, Nagle A, Uebersohn A, Hajj B, Saux AL, Coulon A, Mirny LA, Pollard KS, Dahan M, Bruneau BG | Nature communications | 33154377 | Nat Commun | 2020 Nov 5 |
| Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures. | Brahmachari S, Marko JF | Proceedings of the National Academy of Sciences of the United States of America | 31757850 | Proc Natl Acad Sci U S A | 2019 Dec 10 |
| DNA-loop-extruding SMC complexes can traverse one another in vivo. | Brandão HB, Ren Z, Karaboja X, Mirny LA, Wang X | Nature structural & molecular biology | 34312537 | Nat Struct Mol Biol | 2021 Aug |
| Fast and efficient DNA replication with purified human proteins. | Baris Y, Taylor MRG, Aria V, Yeeles JTP | Nature | 35585232 | Nature | 2022 Jun |
| Tuning levels of low-complexity domain interactions to modulate endogenous oncogenic transcription. | Chong S, Graham TGW, Dugast-Darzacq C, Dailey GM, Darzacq X, Tjian R | Molecular cell | 35483357 | Mol Cell | 2022 Jun 2 |
| Bigtools: a high-performance BigWig and BigBed library in Rust. | Huey JD, Abdennur N | bioRxiv : the preprint server for biology | 38370777 | bioRxiv | 2024 Feb 8 |
| Massively multiplex single-cell Hi-C. | Ramani V, Deng X, Qiu R, Gunderson KL, Steemers FJ, Disteche CM, Noble WS, Duan Z, Shendure J | Nature methods | 28135255 | Nat Methods | 2017 Mar |
| The K219T-Lamin mutation induces conduction defects through epigenetic inhibition of SCN5A in human cardiac laminopathy. | Salvarani N, Crasto S, Miragoli M, Bertero A, Paulis M, Kunderfranco P, Serio S, Forni A, Lucarelli C, Dal Ferro M, Larcher V, Sinagra G, Vezzoni P, Murry CE, Faggian G, Condorelli G, Di Pasquale E | Nature communications | 31118417 | Nat Commun | 2019 May 22 |
| Comprehensive single-cell transcriptional profiling of a multicellular organism. | Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J | Science (New York, N.Y.) | 28818938 | Science | 2017 Aug 18 |
| Fatty Acids Enhance the Maturation of Cardiomyocytes Derived from Human Pluripotent Stem Cells. | Yang X, Rodriguez ML, Leonard A, Sun L, Fischer KA, Wang Y, Ritterhoff J, Zhao L, Kolwicz SC Jr, Pabon L, Reinecke H, Sniadecki NJ, Tian R, Ruohola-Baker H, Xu H, Murry CE | Stem cell reports | 31564645 | Stem Cell Reports | 2019 Oct 8 |
| A Proteomic Perspective on Cardiomyocyte Maturation. | Muraoka N, Sun B, Murry CE | Circulation research | 31697629 | Circ Res | 2019 Nov 8 |
| Computational methods for analyzing and modeling genome structure and organization. | Lin D, Bonora G, Yardımcı GG, Noble WS | Wiley interdisciplinary reviews. Systems biology and medicine | 30022617 | Wiley Interdiscip Rev Syst Biol Med | 2019 Jan |
| Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana. | Jean-Baptiste K, McFaline-Figueroa JL, Alexandre CM, Dorrity MW, Saunders L, Bubb KL, Trapnell C, Fields S, Queitsch C, Cuperus JT | The Plant cell | 30923229 | Plant Cell | 2019 May |
| The accessible chromatin landscape of the murine hippocampus at single-cell resolution. | Sinnamon JR, Torkenczy KA, Linhoff MW, Vitak SA, Mulqueen RM, Pliner HA, Trapnell C, Steemers FJ, Mandel G, Adey AC | Genome research | 30936163 | Genome Res | 2019 May |
| Understanding the 3D genome: Emerging impacts on human disease. | Krumm A, Duan Z | Seminars in cell & developmental biology | 29990539 | Semin Cell Dev Biol | 2019 Jun |
| Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome. | Schreiber J, Durham T, Bilmes J, Noble WS | Genome biology | 32228704 | Genome Biol | 2020 Mar 30 |
| Sarcomere function activates a p53-dependent DNA damage response that promotes polyploidization and limits in vivo cell engraftment. | Pettinato AM, Yoo D, VanOudenhove J, Chen YS, Cohn R, Ladha FA, Yang X, Thakar K, Romano R, Legere N, Meredith E, Robson P, Regnier M, Cotney JL, Murry CE, Hinson JT | Cell reports | 33951429 | Cell Rep | 2021 May 4 |
| High-resolution 3D fluorescent imaging of intact tissues. | El-Nachef D, Martinson AM, Yang X, Murry CE, MacLellan WR | International journal of cardiology and cardiovascular diseases | 35243481 | Int J Cardiol Cardiovasc Dis | 2021 |
| Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. | Fenix AM, Miyaoka Y, Bertero A, Blue SM, Spindler MJ, Tan KKB, Perez-Bermejo JA, Chan AH, Mayerl SJ, Nguyen TD, Russell CR, Lizarraga PP, Truong A, So PL, Kulkarni A, Chetal K, Sathe S, Sniadecki NJ, Yeo GW, Murry CE, Conklin BR, Salomonis N | Nature communications | 34732726 | Nat Commun | 2021 Nov 3 |
| Epiphany: predicting Hi-C contact maps from 1D epigenomic signals. | Yang R, Das A, Gao VR, Karbalayghareh A, Noble WS, Bilmes JA, Leslie CS | Genome biology | 37280678 | Genome Biol | 2023 Jun 6 |
| Understanding Spatial Genome Organization: Methods and Insights. | Ramani V, Shendure J, Duan Z | Genomics, proteomics & bioinformatics | 26876719 | Genomics Proteomics Bioinformatics | 2016 Feb |
| A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets. | Sharon N, Chawla R, Mueller J, Vanderhooft J, Whitehorn LJ, Rosenthal B, Gürtler M, Estanboulieh RR, Shvartsman D, Gifford DK, Trapnell C, Melton D | Cell | 30661759 | Cell | 2019 Feb 7 |
| Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation. | Packer J, Trapnell C | Trends in genetics : TIG | 30007833 | Trends Genet | 2018 Sep |
| Activated CARD11 accelerates germinal center kinetics, promoting mTORC1 and terminal differentiation. | Wray-Dutra MN, Chawla R, Thomas KR, Seymour BJ, Arkatkar T, Sommer KM, Khim S, Trapnell C, James RG, Rawlings DJ | The Journal of experimental medicine | 30127060 | J Exp Med | 2018 Sep 3 |
| Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. | Pliner HA, Packer JS, McFaline-Figueroa JL, Cusanovich DA, Daza RM, Aghamirzaie D, Srivatsan S, Qiu X, Jackson D, Minkina A, Adey AC, Steemers FJ, Shendure J, Trapnell C | Molecular cell | 30078726 | Mol Cell | 2018 Sep 6 |
| Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing factors and RNA-binding proteins required for mitotic progression. | Kim JS, He X, Liu J, Duan Z, Kim T, Gerard J, Kim B, Pillai MM, Lane WS, Noble WS, Budnik B, Waldman T | The Journal of biological chemistry | 31010829 | J Biol Chem | 2019 May 31 |
| A combination of transcription factors mediates inducible interchromosomal contacts. | Kim S, Dunham MJ, Shendure J | eLife | 31081754 | Elife | 2019 May 13 |
| High-Throughput Single-Cell Sequencing with Linear Amplification. | Yin Y, Jiang Y, Lam KG, Berletch JB, Disteche CM, Noble WS, Steemers FJ, Camerini-Otero RD, Adey AC, Shendure J | Molecular cell | 31495564 | Mol Cell | 2019 Nov 21 |
| Supervised classification enables rapid annotation of cell atlases. | Pliner HA, Shendure J, Trapnell C | Nature methods | 31501545 | Nat Methods | 2019 Oct |
| Sonic Hedgehog upregulation does not enhance the survival and engraftment of stem cell-derived cardiomyocytes in infarcted hearts. | Weyers JJ, Gunaje JJ, Van Biber B, Martinson A, Reinecke H, Mahoney WM, Schwartz SM, Cox TC, Murry CE | PloS one | 31945113 | PLoS One | 2020 |
| A Rainbow Reporter Tracks Single Cells and Reveals Heterogeneous Cellular Dynamics among Pluripotent Stem Cells and Their Differentiated Derivatives. | El-Nachef D, Shi K, Beussman KM, Martinez R, Regier MC, Everett GW, Murry CE, Stevens KR, Young JE, Sniadecki NJ, Davis J | Stem cell reports | 32619493 | Stem Cell Reports | 2020 Jul 14 |
| Cronos Titin Is Expressed in Human Cardiomyocytes and Necessary for Normal Sarcomere Function. | Zaunbrecher RJ, Abel AN, Beussman K, Leonard A, von Frieling-Salewsky M, Fields PA, Pabon L, Reinecke H, Yang X, Macadangdang J, Kim DH, Linke WA, Sniadecki NJ, Regnier M, Murry CE | Circulation | 31587567 | Circulation | 2019 Nov 12 |
| Delta-1 Functionalized Hydrogel Promotes hESC-Cardiomyocyte Graft Proliferation and Maintains Heart Function Post-Injury. | Gerbin KA, Mitzelfelt KA, Guan X, Martinson AM, Murry CE | Molecular therapy. Methods & clinical development | 32426414 | Mol Ther Methods Clin Dev | 2020 Jun 12 |
| Reversed graph embedding resolves complex single-cell trajectories. | Qiu X, Mao Q, Tang Y, Wang L, Chawla R, Pliner HA, Trapnell C | Nature methods | 28825705 | Nat Methods | 2017 Oct |
| Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome. | Bonora G, Deng X, Fang H, Ramani V, Qiu R, Berletch JB, Filippova GN, Duan Z, Shendure J, Noble WS, Disteche CM | Nature communications | 29654302 | Nat Commun | 2018 Apr 13 |
| Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells. | Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, Shendure J, Duan Z | Methods (San Diego, Calif.) | 31536770 | Methods | 2020 Jan 1 |
| The dynamic three-dimensional organization of the diploid yeast genome. | Kim S, Liachko I, Brickner DG, Cook K, Noble WS, Brickner JH, Shendure J, Dunham MJ | eLife | 28537556 | Elife | 2017 May 24 |
| Learn from Your Elders: Developmental Biology Lessons to Guide Maturation of Stem Cell-Derived Cardiomyocytes. | Marchianò S, Bertero A, Murry CE | Pediatric cardiology | 31388700 | Pediatr Cardiol | 2019 Oct |
| Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy. | Bertero A, Fields PA, Smith AST, Leonard A, Beussman K, Sniadecki NJ, Kim DH, Tse HF, Pabon L, Shendure J, Noble WS, Murry CE | The Journal of cell biology | 31395619 | J Cell Biol | 2019 Sep 2 |
| Three-dimensional chromatin organization in cardiac development and disease. | Bertero A, Rosa-Garrido M | Journal of molecular and cellular cardiology | 33242466 | J Mol Cell Cardiol | 2021 Feb |
| RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture. | Bertero A | Frontiers in genetics | 33732290 | Front Genet | 2021 |
| Replication Timing Becomes Intertwined with 3D Genome Organization. | Ma J, Duan Z | Cell | 30735630 | Cell | 2019 Feb 7 |
| Human Pluripotent Stem Cell-Derived Engineered Tissues: Clinical Considerations. | Stevens KR, Murry CE | Cell stem cell | 29499147 | Cell Stem Cell | 2018 Mar 1 |
| X-Chromosome Inactivation and Escape from X Inactivation in Mouse. | Ma W, Bonora G, Berletch JB, Deng X, Noble WS, Disteche CM | Methods in molecular biology (Clifton, N.J.) | 30218369 | Methods Mol Biol | 2018 |
| Single-cell mRNA quantification and differential analysis with Census. | Qiu X, Hill A, Packer J, Lin D, Ma YA, Trapnell C | Nature methods | 28114287 | Nat Methods | 2017 Mar |
| Software tools for visualizing Hi-C data. | Yardımcı GG, Noble WS | Genome biology | 28159004 | Genome Biol | 2017 Feb 3 |
| Form and function of topologically associating genomic domains in budding yeast. | Eser U, Chandler-Brown D, Ay F, Straight AF, Duan Z, Noble WS, Skotheim JM | Proceedings of the National Academy of Sciences of the United States of America | 28348222 | Proc Natl Acad Sci U S A | 2017 Apr 11 |
| Unsupervised embedding of single-cell Hi-C data. | Liu J, Lin D, Yardimci GG, Noble WS | Bioinformatics (Oxford, England) | 29950005 | Bioinformatics | 2018 Jul 1 |
| Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution. | Ma W, Ay F, Lee C, Gulsoy G, Deng X, Cook S, Hesson J, Cavanaugh C, Ware CB, Krumm A, Shendure J, Blau CA, Disteche CM, Noble WS, Duan Z | Methods (San Diego, Calif.) | 29382556 | Methods | 2018 Jun 1 |
| A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility. | Cusanovich DA, Hill AJ, Aghamirzaie D, Daza RM, Pliner HA, Berletch JB, Filippova GN, Huang X, Christiansen L, DeWitt WS, Lee C, Regalado SG, Read DF, Steemers FJ, Disteche CM, Trapnell C, Shendure J | Cell | 30078704 | Cell | 2018 Aug 23 |
| The single-cell transcriptional landscape of mammalian organogenesis. | Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C, Shendure J | Nature | 30787437 | Nature | 2019 Feb |
| Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory. | Bertero A, Fields PA, Ramani V, Bonora G, Yardimci GG, Reinecke H, Pabon L, Noble WS, Shendure J, Murry CE | Nature communications | 30948719 | Nat Commun | 2019 Apr 4 |
| Engrafted Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Undergo Clonal Expansion In Vivo. | El-Nachef D, Bugg D, Beussman KM, Steczina S, Martinson AM, Murry CE, Sniadecki NJ, Davis J | Circulation | 33872080 | Circulation | 2021 Apr 20 |
| Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. | Kim HJ, Yardımcı GG, Bonora G, Ramani V, Liu J, Qiu R, Lee C, Hesson J, Ware CB, Shendure J, Duan Z, Noble WS | PLoS computational biology | 32946435 | PLoS Comput Biol | 2020 Sep |
| Cardiomyocyte maturation: advances in knowledge and implications for regenerative medicine. | Karbassi E, Fenix A, Marchiano S, Muraoka N, Nakamura K, Yang X, Murry CE | Nature reviews. Cardiology | 32015528 | Nat Rev Cardiol | 2020 Jun |
| Sci-fate characterizes the dynamics of gene expression in single cells. | Cao J, Zhou W, Steemers F, Trapnell C, Shendure J | Nature biotechnology | 32284584 | Nat Biotechnol | 2020 Aug |
| Dosage compensation of the sex chromosomes and autosomes. | Disteche CM | Seminars in cell & developmental biology | 27112542 | Semin Cell Dev Biol | 2016 Aug |
| Mapping 3D genome architecture through in situ DNase Hi-C. | Ramani V, Cusanovich DA, Hause RJ, Ma W, Qiu R, Deng X, Blau CA, Disteche CM, Noble WS, Shendure J, Duan Z | Nature protocols | 27685100 | Nat Protoc | 2016 Nov |
| Structural aspects of the inactive X chromosome. | Bonora G, Disteche CM | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 28947656 | Philos Trans R Soc Lond B Biol Sci | 2017 Nov 5 |
| X Inactivation and Escape: Epigenetic and Structural Features. | Fang H, Disteche CM, Berletch JB | Frontiers in cell and developmental biology | 31632970 | Front Cell Dev Biol | 2019 |
| Jointly Embedding Multiple Single-Cell Omics Measurements. | Liu J, Huang Y, Singh R, Vert JP, Noble WS | Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop) | 34632462 | Algorithms Bioinform | 2019 Sep 3 |
| Polymer physics of chromosome large-scale 3D organisation. | Chiariello AM, Annunziatella C, Bianco S, Esposito A, Nicodemi M | Scientific reports | 27405443 | Sci Rep | 2016 Jul 13 |
| DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data. | Sun Z, Wang T, Deng K, Wang XF, Lafyatis R, Ding Y, Hu M, Chen W | Bioinformatics (Oxford, England) | 29036318 | Bioinformatics | 2018 Jan 1 |
| Predicting chromatin architecture from models of polymer physics. | Bianco S, Chiariello AM, Annunziatella C, Esposito A, Nicodemi M | Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology | 28070687 | Chromosome Res | 2017 Mar |
| Gene regulation in the 3D genome. | Li Y, Hu M, Shen Y | Human molecular genetics | 29767704 | Hum Mol Genet | 2018 Aug 1 |
| Models of polymer physics for the architecture of the cell nucleus. | Esposito A, Annunziatella C, Bianco S, Chiariello AM, Fiorillo L, Nicodemi M | Wiley interdisciplinary reviews. Systems biology and medicine | 30566285 | Wiley Interdiscip Rev Syst Biol Med | 2019 Jul |
| MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. | Juric I, Yu M, Abnousi A, Raviram R, Fang R, Zhao Y, Zhang Y, Qiu Y, Yang Y, Li Y, Ren B, Hu M | PLoS computational biology | 30986246 | PLoS Comput Biol | 2019 Apr |
| Joint analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes. | Yu J, Hu M, Li C | BMC genetics | 31039743 | BMC Genet | 2019 Apr 30 |
| Freestanding Emergency Critical Care During the Aftermath of Hurricane Sandy: Implications for Disaster Preparedness and Response. | Smith SW, Jamin CT, Malik S, Abrukin L, Tupchong KM, Portelli I, Asaeda G, Prezant DJ, Wang B, Hu M, Goldfrank LR, Meyers CM | Disaster medicine and public health preparedness | 27174171 | Disaster Med Public Health Prep | 2016 Jun |
| Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation. | Proserpio V, Piccolo A, Haim-Vilmovsky L, Kar G, Lönnberg T, Svensson V, Pramanik J, Natarajan KN, Zhai W, Zhang X, Donati G, Kayikci M, Kotar J, McKenzie AN, Montandon R, Billker O, Woodhouse S, Cicuta P, Nicodemi M, Teichmann SA | Genome biology | 27176874 | Genome Biol | 2016 May 12 |
| Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate. | Isoda T, Moore AJ, He Z, Chandra V, Aida M, Denholtz M, Piet van Hamburg J, Fisch KM, Chang AN, Fahl SP, Wiest DL, Murre C | Cell | 28938112 | Cell | 2017 Sep 21 |
| Sensory experience remodels genome architecture in neural circuit to drive motor learning. | Yamada T, Yang Y, Valnegri P, Juric I, Abnousi A, Markwalter KH, Guthrie AN, Godec A, Oldenborg A, Hu M, Holy TE, Bonni A | Nature | 31068695 | Nature | 2019 May |
| Computational approaches from polymer physics to investigate chromatin folding. | Bianco S, Chiariello AM, Conte M, Esposito A, Fiorillo L, Musella F, Nicodemi M | Current opinion in cell biology | 32045823 | Curr Opin Cell Biol | 2020 Jun |
| TWO-SIGMA: A novel two-component single cell model-based association method for single-cell RNA-seq data. | Van Buren E, Hu M, Weng C, Jin F, Li Y, Wu D, Li Y | Genetic epidemiology | 32989764 | Genet Epidemiol | 2021 Mar |
| Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. | Fang R, Yu M, Li G, Chee S, Liu T, Schmitt AD, Ren B | Cell research | 27886167 | Cell Res | 2016 Dec |
| Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis. | Kragesteen BK, Spielmann M, Paliou C, Heinrich V, Schöpflin R, Esposito A, Annunziatella C, Bianco S, Chiariello AM, Jerković I, Harabula I, Guckelberger P, Pechstein M, Wittler L, Chan WL, Franke M, Lupiáñez DG, Kraft K, Timmermann B, Vingron M, Visel A, Nicodemi M, Mundlos S, Andrey G | Nature genetics | 30262816 | Nat Genet | 2018 Oct |
| Inferring Spatial Organization of Individual Topologically Associated Domains via Piecewise Helical Model. | Zhang R, Hu M, Zhu Y, Qin Z, Deng K, Liu JS | IEEE/ACM transactions on computational biology and bioinformatics | 30113897 | IEEE/ACM Trans Comput Biol Bioinform | 2020 Mar-Apr |
| Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. | Zhang Y, Li T, Preissl S, Amaral ML, Grinstein JD, Farah EN, Destici E, Qiu Y, Hu R, Lee AY, Chee S, Ma K, Ye Z, Zhu Q, Huang H, Fang R, Yu L, Izpisua Belmonte JC, Wu J, Evans SM, Chi NC, Ren B | Nature genetics | 31427791 | Nat Genet | 2019 Sep |
| Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation. | Conte M, Fiorillo L, Bianco S, Chiariello AM, Esposito A, Nicodemi M | Nature communications | 32620890 | Nat Commun | 2020 Jul 3 |
| Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. | Yang Y, Gu Q, Zhang Y, Sasaki T, Crivello J, O'Neill RJ, Gilbert DM, Ma J | Cell systems | 29936186 | Cell Syst | 2018 Aug 22 |
| A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. | Xu Z, Zhang G, Jin F, Chen M, Furey TS, Sullivan PF, Qin Z, Hu M, Li Y | Bioinformatics (Oxford, England) | 26543175 | Bioinformatics | 2016 Mar 1 |
| Transcriptional network orchestrating regional patterning of cortical progenitors. | Ypsilanti AR, Pattabiraman K, Catta-Preta R, Golonzhka O, Lindtner S, Tang K, Jones IR, Abnousi A, Juric I, Hu M, Shen Y, Dickel DE, Visel A, Pennachio LA, Hawrylycz M, Thompson CL, Zeng H, Barozzi I, Nord AS, Rubenstein JL | Proceedings of the National Academy of Sciences of the United States of America | 34921112 | Proc Natl Acad Sci U S A | 2021 Dec 21 |
| Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data. | Miko H, Qiu Y, Gaertner B, Sander M, Ohler U | BMC genomics | 33509077 | BMC Genomics | 2021 Jan 28 |
| Comparison of OCT Angiography Review Strategies to Identify Vascular Abnormalities in the AVATAR Study. | Babiuch AS, Khan M, Hu M, Kaiser PK, Srivastava SK, Singh RP, Watts A, Reese JL, Ehlers JP | Ophthalmology. Retina | 30035246 | Ophthalmol Retina | 2018 Jun |
| A Dynamic Folded Hairpin Conformation Is Associated with α-Globin Activation in Erythroid Cells. | Chiariello AM, Bianco S, Oudelaar AM, Esposito A, Annunziatella C, Fiorillo L, Conte M, Corrado A, Prisco A, Larke MSC, Telenius JM, Sciarretta R, Musella F, Buckle VJ, Higgs DR, Hughes JR, Nicodemi M | Cell reports | 32075757 | Cell Rep | 2020 Feb 18 |
| LAIT: a local ancestry inference toolkit. | Hui D, Fang Z, Lin J, Duan Q, Li Y, Hu M, Chen W | BMC genetics | 28877673 | BMC Genet | 2017 Sep 6 |
| HUGIn: Hi-C Unifying Genomic Interrogator. | Martin JS, Xu Z, Reiner AP, Mohlke KL, Sullivan P, Ren B, Hu M, Li Y | Bioinformatics (Oxford, England) | 28582503 | Bioinformatics | 2017 Dec 1 |
| Inference of chromosome 3D structures from GAM data by a physics computational approach. | Fiorillo L, Bianco S, Chiariello AM, Barbieri M, Esposito A, Annunziatella C, Conte M, Corrado A, Prisco A, Pombo A, Nicodemi M | Methods (San Diego, Calif.) | 31604121 | Methods | 2020 Oct 1 |
| Joint profiling of DNA methylation and chromatin architecture in single cells. | Li G, Liu Y, Zhang Y, Kubo N, Yu M, Fang R, Kellis M, Ren B | Nature methods | 31384045 | Nat Methods | 2019 Oct |
| Modeling Single-Molecule Conformations of the HoxD Region in Mouse Embryonic Stem and Cortical Neuronal Cells. | Bianco S, Annunziatella C, Andrey G, Chiariello AM, Esposito A, Fiorillo L, Prisco A, Conte M, Campanile R, Nicodemi M | Cell reports | 31390570 | Cell Rep | 2019 Aug 6 |
| Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors. | Geusz RJ, Wang A, Lam DK, Vinckier NK, Alysandratos KD, Roberts DA, Wang J, Kefalopoulou S, Ramirez A, Qiu Y, Chiou J, Gaulton KJ, Ren B, Kotton DN, Sander M | Nature communications | 34789735 | Nat Commun | 2021 Nov 17 |
| GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data. | Markowski J, Kempfer R, Kukalev A, Irastorza-Azcarate I, Loof G, Kehr B, Pombo A, Rahmann S, Schwarz RF | Bioinformatics (Oxford, England) | 33830196 | Bioinformatics | 2021 Oct 11 |
| Chromosome dynamics near the sol-gel phase transition dictate the timing of remote genomic interactions. | Khanna N, Zhang Y, Lucas JS, Dudko OK, Murre C | Nature communications | 31235807 | Nat Commun | 2019 Jun 24 |
| The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. | Wang Y, Song F, Zhang B, Zhang L, Xu J, Kuang D, Li D, Choudhary MNK, Li Y, Hu M, Hardison R, Wang T, Yue F | Genome biology | 30286773 | Genome Biol | 2018 Oct 4 |
| FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data. | Xu Z, Zhang G, Wu C, Li Y, Hu M | Bioinformatics (Oxford, England) | 27153668 | Bioinformatics | 2016 Sep 1 |
| Evolving methodologies and concepts in 4D nucleome research. | Sparks TM, Harabula I, Pombo A | Current opinion in cell biology | 32473574 | Curr Opin Cell Biol | 2020 Jun |
| A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis. | Xiong X, Zhang Y, Yan J, Jain S, Chee S, Ren B, Zhao H | ACS synthetic biology | 28215080 | ACS Synth Biol | 2017 Jun 16 |
| A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. | Schmitt AD, Hu M, Jung I, Xu Z, Qiu Y, Tan CL, Li Y, Lin S, Lin Y, Barr CL, Ren B | Cell reports | 27851967 | Cell Rep | 2016 Nov 15 |
| Removing unwanted variation between samples in Hi-C experiments. | Fletez-Brant K, Qiu Y, Gorkin DU, Hu M, Hansen KD | Briefings in bioinformatics | 38711367 | Brief Bioinform | 2024 Mar 27 |
| Extrusion without a motor: a new take on the loop extrusion model of genome organization. | Brackley CA, Johnson J, Michieletto D, Morozov AN, Nicodemi M, Cook PR, Marenduzzo D | Nucleus (Austin, Tex.) | 29300120 | Nucleus | 2018 Jan 1 |
| Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers. | Yan J, Chen SA, Local A, Liu T, Qiu Y, Dorighi KM, Preissl S, Rivera CM, Wang C, Ye Z, Ge K, Hu M, Wysocka J, Ren B | Cell research | 29313530 | Cell Res | 2018 Feb |
| Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq). | Yu M, Juric I, Abnousi A, Hu M, Ren B | Methods in molecular biology (Clifton, N.J.) | 34382190 | Methods Mol Biol | 2021 |
| Global analysis of histone modifications and long-range chromatin interactions revealed the differential cistrome changes and novel transcriptional players in human dilated cardiomyopathy. | Liu CF, Abnousi A, Bazeley P, Ni Y, Morley M, Moravec CS, Hu M, Tang WHW | Journal of molecular and cellular cardiology | 32533974 | J Mol Cell Cardiol | 2020 Aug |
| Preformed chromatin topology assists transcriptional robustness of Shh during limb development. | Paliou C, Guckelberger P, Schöpflin R, Heinrich V, Esposito A, Chiariello AM, Bianco S, Annunziatella C, Helmuth J, Haas S, Jerković I, Brieske N, Wittler L, Timmermann B, Nicodemi M, Vingron M, Mundlos S, Andrey G | Proceedings of the National Academy of Sciences of the United States of America | 31147463 | Proc Natl Acad Sci U S A | 2019 Jun 18 |
| HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. | Xu Z, Zhang G, Duan Q, Chai S, Zhang B, Wu C, Jin F, Yue F, Li Y, Hu M | BMC research notes | 26969411 | BMC Res Notes | 2016 Mar 11 |
| Genome-wide mapping and analysis of chromosome architecture. | Schmitt AD, Hu M, Ren B | Nature reviews. Molecular cell biology | 27580841 | Nat Rev Mol Cell Biol | 2016 Dec |
| Chromatin Domains: The Unit of Chromosome Organization. | Dixon JR, Gorkin DU, Ren B | Molecular cell | 27259200 | Mol Cell | 2016 Jun 2 |
| Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription. | Beagrie RA, Pombo A | BioEssays : news and reviews in molecular, cellular and developmental biology | 27452946 | Bioessays | 2016 Sep |
| Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. | Yang Y, Zhang Y, Ren B, Dixon JR, Ma J | Cell systems | 31229558 | Cell Syst | 2019 Jun 26 |
| Common DNA sequence variation influences 3-dimensional conformation of the human genome. | Gorkin DU, Qiu Y, Hu M, Fletez-Brant K, Liu T, Schmitt AD, Noor A, Chiou J, Gaulton KJ, Sebat J, Li Y, Hansen KD, Ren B | Genome biology | 31779666 | Genome Biol | 2019 Nov 28 |
| The Three-Dimensional Organization of Mammalian Genomes. | Yu M, Ren B | Annual review of cell and developmental biology | 28783961 | Annu Rev Cell Dev Biol | 2017 Oct 6 |
| Molecular Dynamics simulations of the Strings and Binders Switch model of chromatin. | Annunziatella C, Chiariello AM, Esposito A, Bianco S, Fiorillo L, Nicodemi M | Methods (San Diego, Calif.) | 29522804 | Methods | 2018 Jun 1 |
| CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. | Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ, Szalaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, Michalski P, Piecuch E, Wang P, Wang D, Tian SZ, Penrad-Mobayed M, Sachs LM, Ruan X, Wei CL, Liu ET, Wilczynski GM, Plewczynski D, Li G, Ruan Y | Cell | 26686651 | Cell | 2015 Dec 17 |
| FunPred 3.0: improved protein function prediction using protein interaction network. | Saha S, Chatterjee P, Basu S, Nasipuri M, Plewczynski D | PeerJ | 31198622 | PeerJ | 2019 |
| Evolutionarily Conserved Principles Predict 3D Chromatin Organization. | Rowley MJ, Nichols MH, Lyu X, Ando-Kuri M, Rivera ISM, Hermetz K, Wang P, Ruan Y, Corces VG | Molecular cell | 28826674 | Mol Cell | 2017 Sep 7 |
| Methods for comparative ChIA-PET and Hi-C data analysis. | Capurso D, Tang Z, Ruan Y | Methods (San Diego, Calif.) | 31629084 | Methods | 2020 Jan 1 |
| The Mixture of Autoregressive Hidden Markov Models of Morphology for Dentritic Spines During Activation Process. | Urban P, Rezaei Tabar V, Denkiewicz M, Bokota G, Das N, Basu S, Plewczynski D | Journal of computational biology : a journal of computational molecular cell biology | 32175768 | J Comput Biol | 2020 Sep |
| Free energy-based model of CTCF-mediated chromatin looping in the human genome. | Dawson WK, Lazniewski M, Plewczynski D | Methods (San Diego, Calif.) | 32645447 | Methods | 2020 Oct 1 |
| 3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome. | Wlasnowolski M, Sadowski M, Czarnota T, Jodkowska K, Szalaj P, Tang Z, Ruan Y, Plewczynski D | Nucleic acids research | 32442297 | Nucleic Acids Res | 2020 Jul 2 |
| Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization. | Trzaskoma P, Ruszczycki B, Lee B, Pels KK, Krawczyk K, Bokota G, Szczepankiewicz AA, Aaron J, Walczak A, Śliwińska MA, Magalska A, Kadlof M, Wolny A, Parteka Z, Arabasz S, Kiss-Arabasz M, Plewczyński D, Ruan Y, Wilczyński GM | Nature communications | 32358536 | Nat Commun | 2020 May 1 |
| Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions. | Li X, Luo OJ, Wang P, Zheng M, Wang D, Piecuch E, Zhu JJ, Tian SZ, Tang Z, Li G, Ruan Y | Nature protocols | 28358394 | Nat Protoc | 2017 May |
| Three-dimensional organization and dynamics of the genome. | Szalaj P, Plewczynski D | Cell biology and toxicology | 29568981 | Cell Biol Toxicol | 2018 Oct |
| Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction. | Al Bkhetan Z, Plewczynski D | Scientific reports | 29581440 | Sci Rep | 2018 Mar 26 |
| Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. | Zhu Y, Gujar AD, Wong CH, Tjong H, Ngan CY, Gong L, Chen YA, Kim H, Liu J, Li M, Mil-Homens A, Maurya R, Kuhlberg C, Sun F, Yi E, deCarvalho AC, Ruan Y, Verhaak RGW, Wei CL | Cancer cell | 33836152 | Cancer Cell | 2021 May 10 |
| Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions. | Chiliński M, Lipiński J, Agarwal A, Ruan Y, Plewczynski D | bioRxiv : the preprint server for biology | 37066361 | bioRxiv | 2023 Apr 6 |
| ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs. | Chai H, Tjong H, Li P, Liao W, Wang P, Wong CH, Ngan CY, Leonard WJ, Wei CL, Ruan Y | Nature communications | 36639381 | Nat Commun | 2023 Jan 13 |
| Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions. | Chiliński M, Lipiński J, Agarwal A, Ruan Y, Plewczynski D | Scientific reports | 37474564 | Sci Rep | 2023 Jul 20 |
| HiCDiffusion - diffusion-enhanced, transformer-based prediction of chromatin interactions from DNA sequences. | Chiliński M, Plewczynski D | BMC genomics | 39407104 | BMC Genomics | 2024 Oct 15 |
| The Energetics and Physiological Impact of Cohesin Extrusion. | Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, Sanborn AL, Canela A, Maman Y, Oksanen A, Resch W, Li X, Lee B, Kovalchuk AL, Tang Z, Nelson S, Di Pierro M, Cheng RR, Machol I, St Hilaire BG, Durand NC, Shamim MS, Stamenova EK, Onuchic JN, Ruan Y, Nussenzweig A, Levens D, Aiden EL, Casellas R | Cell | 29706548 | Cell | 2018 May 17 |
| Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development. | Ngan CY, Wong CH, Tjong H, Wang W, Goldfeder RL, Choi C, He H, Gong L, Lin J, Urban B, Chow J, Li M, Lim J, Philip V, Murray SA, Wang H, Wei CL | Nature genetics | 32094912 | Nat Genet | 2020 Mar |
| Identification of miRNA Biomarkers for Diverse Cancer Types Using Statistical Learning Methods at the Whole-Genome Scale. | Sarkar JP, Saha I, Lancucki A, Ghosh N, Wlasnowolski M, Bokota G, Dey A, Lipinski P, Plewczynski D | Frontiers in genetics | 33281862 | Front Genet | 2020 |
| High-throughput automated microfluidic sample preparation for accurate microbial genomics. | Kim S, De Jonghe J, Kulesa AB, Feldman D, Vatanen T, Bhattacharyya RP, Berdy B, Gomez J, Nolan J, Epstein S, Blainey PC | Nature communications | 28128213 | Nat Commun | 2017 Jan 27 |
| Cohesin Loss Eliminates All Loop Domains. | Rao SSP, Huang SC, Glenn St Hilaire B, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, Huang X, Shamim MS, Shin J, Turner D, Ye Z, Omer AD, Robinson JT, Schlick T, Bernstein BE, Casellas R, Lander ES, Aiden EL | Cell | 28985562 | Cell | 2017 Oct 5 |
| One protein to rule them all: The role of CCCTC-binding factor in shaping human genome in health and disease. | Lazniewski M, Dawson WK, Rusek AM, Plewczynski D | Seminars in cell & developmental biology | 30096365 | Semin Cell Dev Biol | 2019 Jun |
| Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia. | Wang P, Tang Z, Lee B, Zhu JJ, Cai L, Szalaj P, Tian SZ, Zheng M, Plewczynski D, Ruan X, Liu ET, Wei CL, Ruan Y | Genome biology | 32393309 | Genome Biol | 2020 May 11 |
| Genome Organization Drives Chromosome Fragility. | Canela A, Maman Y, Jung S, Wong N, Callen E, Day A, Kieffer-Kwon KR, Pekowska A, Zhang H, Rao SSP, Huang SC, Mckinnon PJ, Aplan PD, Pommier Y, Aiden EL, Casellas R, Nussenzweig A | Cell | 28735753 | Cell | 2017 Jul 27 |
| ASXL1 interacts with the cohesin complex to maintain chromatid separation and gene expression for normal hematopoiesis. | Li Z, Zhang P, Yan A, Guo Z, Ban Y, Li J, Chen S, Yang H, He Y, Li J, Guo Y, Zhang W, Hajiramezanali E, An H, Fajardo D, Harbour JW, Ruan Y, Nimer SD, Yu P, Chen X, Xu M, Yang FC | Science advances | 28116354 | Sci Adv | 2017 Jan |
| ML-DTD: Machine Learning-Based Drug Target Discovery for the Potential Treatment of COVID-19. | Saha S, Chatterjee P, Halder AK, Nasipuri M, Basu S, Plewczynski D | Vaccines | 36298508 | Vaccines (Basel) | 2022 Sep 30 |
| Rule-Based Pruning and In Silico Identification of Essential Proteins in Yeast PPIN. | Banik A, Podder S, Saha S, Chatterjee P, Halder AK, Nasipuri M, Basu S, Plewczynski D | Cells | 36078056 | Cells | 2022 Aug 25 |
| Unveiling epigenetic regulatory elements associated with breast cancer development. | Jardanowska-Kotuniak M, Dramiński M, Własnowolski M, Łapiński M, Sengupta K, Agarwal A, Filip A, Ghosh N, Pancaldi V, Grynberg M, Saha I, Plewczynski D, Dąbrowski MJ | bioRxiv : the preprint server for biology | 39605637 | bioRxiv | 2024 Nov 15 |
| pyBedGraph: a python package for fast operations on 1D genomic signal tracks. | Zhang HB, Kim M, Chuang JH, Ruan Y | Bioinformatics (Oxford, England) | 32044918 | Bioinformatics | 2020 May 1 |
| Sox2-Dependent 3D Chromatin Interactomes in Transcription, Neural Stem Cell Proliferation and Neurodevelopmental Diseases. | Wei CL, Nicolis SK, Zhu Y, Pagin M | Journal of experimental neuroscience | 31431802 | J Exp Neurosci | 2019 |
| MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms. | Kim M, Zheng M, Tian SZ, Lee B, Chuang JH, Ruan Y | Genome biology | 31767038 | Genome Biol | 2019 Nov 25 |
| Spring Model - Chromatin Modeling Tool Based on OpenMM. | Kadlof M, Rozycka J, Plewczynski D | Methods (San Diego, Calif.) | 31790732 | Methods | 2020 Oct 1 |
| Aggregated network centrality shows non-random structure of genomic and proteomic networks. | Halder AK, Denkiewicz M, Sengupta K, Basu S, Plewczynski D | Methods (San Diego, Calif.) | 31740366 | Methods | 2020 Oct 1 |
| RNA structure interactions and ribonucleoprotein processes of the influenza A virus. | Dawson WK, Lazniewski M, Plewczynski D | Briefings in functional genomics | 29040388 | Brief Funct Genomics | 2018 Nov 26 |
| The structural variability of the influenza A hemagglutinin receptor-binding site. | Lazniewski M, Dawson WK, Szczepinska T, Plewczynski D | Briefings in functional genomics | 29253080 | Brief Funct Genomics | 2018 Nov 26 |
| Dendritic Spines Taxonomy: The Functional and Structural Classification • Time-Dependent Probabilistic Model of Neuronal Activation. | Urban P, Rezaei V, Bokota G, Denkiewicz M, Basu S, Plewczyński D | Journal of computational biology : a journal of computational molecular cell biology | 30810368 | J Comput Biol | 2019 Apr |
| Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance. | Bertolini JA, Favaro R, Zhu Y, Pagin M, Ngan CY, Wong CH, Tjong H, Vermunt MW, Martynoga B, Barone C, Mariani J, Cardozo MJ, Tabanera N, Zambelli F, Mercurio S, Ottolenghi S, Robson P, Creyghton MP, Bovolenta P, Pavesi G, Guillemot F, Nicolis SK, Wei CL | Cell stem cell | 30849367 | Cell Stem Cell | 2019 Mar 7 |
| Machine learning polymer models of three-dimensional chromatin organization in human lymphoblastoid cells. | Al Bkhetan Z, Kadlof M, Kraft A, Plewczynski D | Methods (San Diego, Calif.) | 30853548 | Methods | 2019 Aug 15 |
| Quantitative 3-D morphometric analysis of individual dendritic spines. | Basu S, Saha PK, Roszkowska M, Magnowska M, Baczynska E, Das N, Plewczynski D, Wlodarczyk J | Scientific reports | 29476060 | Sci Rep | 2018 Feb 23 |
| STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the Il2ra gene locus. | Li P, Mitra S, Spolski R, Oh J, Liao W, Tang Z, Mo F, Li X, West EE, Gromer D, Lin JX, Liu C, Ruan Y, Leonard WJ | Proceedings of the National Academy of Sciences of the United States of America | 29078395 | Proc Natl Acad Sci U S A | 2017 Nov 14 |
| Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. | Kieffer-Kwon KR, Nimura K, Rao SSP, Xu J, Jung S, Pekowska A, Dose M, Stevens E, Mathe E, Dong P, Huang SC, Ricci MA, Baranello L, Zheng Y, Tomassoni Ardori F, Resch W, Stavreva D, Nelson S, McAndrew M, Casellas A, Finn E, Gregory C, St Hilaire BG, Johnson SM, Dubois W, Cosma MP, Batchelor E, Levens D, Phair RD, Misteli T, Tessarollo L, Hager G, Lakadamyali M, Liu Z, Floer M, Shroff H, Aiden EL, Casellas R | Molecular cell | 28803781 | Mol Cell | 2017 Aug 17 |
| An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization. | Szałaj P, Tang Z, Michalski P, Pietal MJ, Luo OJ, Sadowski M, Li X, Radew K, Ruan Y, Plewczynski D | Genome research | 27789526 | Genome Res | 2016 Dec |
| Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy. | Parteka-Tojek Z, Zhu JJ, Lee B, Jodkowska K, Wang P, Aaron J, Chew TL, Banecki K, Plewczynski D, Ruan Y | Scientific reports | 35595799 | Sci Rep | 2022 May 20 |
| The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations. | Menghi F, Barthel FP, Yadav V, Tang M, Ji B, Tang Z, Carter GW, Ruan Y, Scully R, Verhaak RGW, Jonkers J, Liu ET | Cancer cell | 30017478 | Cancer Cell | 2018 Aug 13 |
| Multiplex chromatin interactions with single-molecule precision. | Zheng M, Tian SZ, Capurso D, Kim M, Maurya R, Lee B, Piecuch E, Gong L, Zhu JJ, Li Z, Wong CH, Ngan CY, Wang P, Ruan X, Wei CL, Ruan Y | Nature | 30778195 | Nature | 2019 Feb |
| Intermingling of chromosome territories. | Szczepińska T, Rusek AM, Plewczynski D | Genes, chromosomes & cancer | 30828902 | Genes Chromosomes Cancer | 2019 Jul |
| PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies. | Bokota G, Sroka J, Basu S, Das N, Trzaskoma P, Yushkevich Y, Grabowska A, Magalska A, Plewczynski D | BMC bioinformatics | 33596823 | BMC Bioinformatics | 2021 Feb 17 |
| ChIA-PIPE: A fully automated pipeline for comprehensive ChIA-PET data analysis and visualization. | Lee B, Wang J, Cai L, Kim M, Namburi S, Tjong H, Feng Y, Wang P, Tang Z, Abbas A, Wei CL, Ruan Y, Li S | Science advances | 32832596 | Sci Adv | 2020 Jul |
| Spatial chromatin architecture alteration by structural variations in human genomes at the population scale. | Sadowski M, Kraft A, Szalaj P, Wlasnowolski M, Tang Z, Ruan Y, Plewczynski D | Genome biology | 31362752 | Genome Biol | 2019 Jul 30 |
| Guilt by association: EcDNA as a mobile transactivator in cancer. | Zhu Y, Gong L, Wei CL | Trends in cancer | 35753910 | Trends Cancer | 2022 Sep |
| Multifaceted roles of cohesin in regulating transcriptional loops. | Kim M, Wang P, Clow PA, Chien IE, Wang X, Peng J, Chai H, Liu X, Lee B, Ngan CY, Yue F, Milenkovic O, Chuang JH, Wei CL, Casellas R, Cheng AW, Ruan Y | bioRxiv : the preprint server for biology | 38585764 | bioRxiv | 2024 Mar 27 |
| Identifying gene regulatory network rewiring using latent differential graphical models. | Tian D, Gu Q, Ma J | Nucleic acids research | 27378774 | Nucleic Acids Res | 2016 Sep 30 |
| A New Era of Genome Integration-Simply Cut and Paste! | Liu Z, Liang Y, Ang EL, Zhao H | ACS synthetic biology | 28073246 | ACS Synth Biol | 2017 Apr 21 |
| Use of genome-editing tools to treat sickle cell disease. | Tasan I, Jain S, Zhao H | Human genetics | 27250347 | Hum Genet | 2016 Sep |
| An efficient gene knock-in strategy using 5'-modified double-stranded DNA donors with short homology arms. | Yu Y, Guo Y, Tian Q, Lan Y, Yeh H, Zhang M, Tasan I, Jain S, Zhao H | Nature chemical biology | 31873222 | Nat Chem Biol | 2020 Apr |
| Exploiting sequence-based features for predicting enhancer-promoter interactions. | Yang Y, Zhang R, Singh S, Ma J | Bioinformatics (Oxford, England) | 28881991 | Bioinformatics | 2017 Jul 15 |
| Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. | Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM | Cell | 30595451 | Cell | 2019 Feb 7 |
| Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs. | Leemans C, van der Zwalm MCH, Brueckner L, Comoglio F, van Schaik T, Pagie L, van Arensbergen J, van Steensel B | Cell | 30982597 | Cell | 2019 May 2 |
| Predicting CTCF-mediated chromatin loops using CTCF-MP. | Zhang R, Wang Y, Yang Y, Zhang Y, Ma J | Bioinformatics (Oxford, England) | 29949986 | Bioinformatics | 2018 Jul 1 |
| Predicting enhancer-promoter interaction from genomic sequence with deep neural networks. | Singh S, Yang Y, Póczos B, Ma J | Quantitative biology (Beijing, China) | 34113473 | Quant Biol | 2019 Jun |
| p53 mediates target gene association with nuclear speckles for amplified RNA expression. | Alexander KA, Coté A, Nguyen SC, Zhang L, Gholamalamdari O, Agudelo-Garcia P, Lin-Shiao E, Tanim KMA, Lim J, Biddle N, Dunagin MC, Good CR, Mendoza MR, Little SC, Belmont A, Joyce EF, Raj A, Berger SL | Molecular cell | 33823140 | Mol Cell | 2021 Apr 15 |
| TALEN outperforms Cas9 in editing heterochromatin target sites. | Jain S, Shukla S, Yang C, Zhang M, Fatma Z, Lingamaneni M, Abesteh S, Lane ST, Xiong X, Wang Y, Schroeder CM, Selvin PR, Zhao H | Nature communications | 33504770 | Nat Commun | 2021 Jan 27 |
| Imaging Method Using CRISPR/dCas9 and Engineered gRNA Scaffolds Can Perturb Replication Timing at the HSPA1 Locus. | Xiong X, Tasan I, Yang C, Zhang M, Hernandez Gonzalez GA, Liu S, Chaturvedi P, Belmont AS, Zhao H | ACS synthetic biology | 37058298 | ACS Synth Biol | 2023 May 19 |
| The sound of silence: Transgene silencing in mammalian cell engineering. | Cabrera A, Edelstein HI, Glykofrydis F, Love KS, Palacios S, Tycko J, Zhang M, Lensch S, Shields CE, Livingston M, Weiss R, Zhao H, Haynes KA, Morsut L, Chen YY, Khalil AS, Wong WW, Collins JJ, Rosser SJ, Polizzi K, Elowitz MB, Fussenegger M, Hilton IB, Leonard JN, Bintu L, Galloway KE, Deans TL | Cell systems | 36549273 | Cell Syst | 2022 Dec 21 |
| Widespread chromatin context-dependencies of DNA double-strand break repair proteins. | Vergara X, Manjón AG, de Haas M, Morris B, Schep R, Leemans C, Friskes A, Beijersbergen RL, Sanders MA, Medema RH, van Steensel B | Nature communications | 38909016 | Nat Commun | 2024 Jun 22 |
| Transcription can be sufficient, but is not necessary, to advance replication timing. | Vouzas AE, Sasaki T, Rivera-Mulia JC, Turner JL, Brown AN, Alexander KE, Brueckner L, van Steensel B, Gilbert DM | bioRxiv : the preprint server for biology | 39975371 | bioRxiv | 2025 Feb 5 |
| Fully Automated One-Step Synthesis of Single-Transcript TALEN Pairs Using a Biological Foundry. | Chao R, Liang J, Tasan I, Si T, Ju L, Zhao H | ACS synthetic biology | 28103009 | ACS Synth Biol | 2017 Apr 21 |
| High-throughput assessment of context-dependent effects of chromatin proteins. | Brueckner L, van Arensbergen J, Akhtar W, Pagie L, van Steensel B | Epigenetics & chromatin | 27777628 | Epigenetics Chromatin | 2016 |
| Two-Color Imaging of Nonrepetitive Endogenous Loci in Human Cells. | Tasan I, Su CJ, Enghiad B, Zhang M, Mishra S, Zhao H | ACS synthetic biology | 32822529 | ACS Synth Biol | 2020 Sep 18 |
| MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome. | Tian D, Zhang R, Zhang Y, Zhu X, Ma J | Genome research | 31907193 | Genome Res | 2020 Feb |
| MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning. | Zhang R, Ma J | Cell systems | 32550271 | Cell Syst | 2020 May 20 |
| Engineering biological systems using automated biofoundries. | Chao R, Mishra S, Si T, Zhao H | Metabolic engineering | 28602523 | Metab Eng | 2017 Jul |
| Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression. | van Steensel B, Belmont AS | Cell | 28525751 | Cell | 2017 May 18 |
| 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. | Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Sedeño Cacciatore Á, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire BG, Weisz D, Omer AD, Pham M, Colaric Z, Yang Z, Rao SSP, Mitra N, Lui C, Yao W, Khan R, Moroz LL, Kohn A, St Leger J, Mena A, Holcroft K, Gambetta MC, Lim F, Farley E, Stein N, Haddad A, Chauss D, Mutlu AS, Wang MC, Young ND, Hildebrandt E, Cheng HH, Knight CJ, Burnham TLU, Hovel KA, Beel AJ, Mattei PJ, Kornberg RD, Warren WC, Cary G, Gómez-Skarmeta JL, Hinman V, Lindblad-Toh K, Di Palma F, Maeshima K, Multani AS, Pathak S, Nel-Themaat L, Behringer RR, Kaur P, Medema RH, van Steensel B, de Wit E, Onuchic JN, Di Pierro M, Lieberman Aiden E, Rowland BD | Science (New York, N.Y.) | 34045355 | Science | 2021 May 28 |
| CTCF and cohesin promote focal detachment of DNA from the nuclear lamina. | van Schaik T, Liu NQ, Manzo SG, Peric-Hupkes D, de Wit E, van Steensel B | Genome biology | 36050765 | Genome Biol | 2022 Sep 1 |
| To Cut or not to Cut: Next-generation Genome Editors for Precision Genome Engineering. | Zhang M, Zhu Z, Xun G, Zhao H | Current opinion in biomedical engineering | 37593347 | Curr Opin Biomed Eng | 2023 Dec |
| Measuring Cytological Proximity of Chromosomal Loci to Defined Nuclear Compartments with TSA-seq. | Zhang L, Chen Y, Belmont AS | Methods in molecular biology (Clifton, N.J.) | 35867249 | Methods Mol Biol | 2022 |
| Perturbations in 3D genome organization can promote acquired drug resistance. | Manjón AG, Manzo SG, Prekovic S, Potgeter L, van Schaik T, Liu NQ, Flach K, Peric-Hupkes D, Joosten S, Teunissen H, Friskes A, Ilic M, Hintzen D, Franceschini-Santos VH, Zwart W, de Wit E, van Steensel B, Medema RH | Cell reports | 37733591 | Cell Rep | 2023 Oct 31 |
| Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. | Chen Y, Zhang Y, Wang Y, Zhang L, Brinkman EK, Adam SA, Goldman R, van Steensel B, Ma J, Belmont AS | The Journal of cell biology | 30154186 | J Cell Biol | 2018 Nov 5 |
| Scientific honesty and publicly shared lab notebooks: Sharing lab notebooks along with publication would increase transparency and help to improve honesty when reporting results. | van Steensel B | EMBO reports | 30158143 | EMBO Rep | 2018 Oct |
| Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions. | Xiong K, Ma J | Nature communications | 31699985 | Nat Commun | 2019 Nov 7 |
| Gene expression amplification by nuclear speckle association. | Kim J, Venkata NC, Hernandez Gonzalez GA, Khanna N, Belmont AS | The Journal of cell biology | 31757787 | J Cell Biol | 2020 Jan 6 |
| Expanding the Potential of Mammalian Genome Engineering via Targeted DNA Integration. | Zhang M, Yang C, Tasan I, Zhao H | ACS synthetic biology | 33596056 | ACS Synth Biol | 2021 Mar 19 |
| CHRAC/ACF contribute to the repressive ground state of chromatin. | Scacchetti A, Brueckner L, Jain D, Schauer T, Zhang X, Schnorrer F, van Steensel B, Straub T, Becker PB | Life science alliance | 30456345 | Life Sci Alliance | 2018 Jan |
| CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. | Tasan I, Sustackova G, Zhang L, Kim J, Sivaguru M, HamediRad M, Wang Y, Genova J, Ma J, Belmont AS, Zhao H | Nucleic acids research | 29912475 | Nucleic Acids Res | 2018 Sep 28 |
| Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. | Marchal C, Sasaki T, Vera D, Wilson K, Sima J, Rivera-Mulia JC, Trevilla-García C, Nogues C, Nafie E, Gilbert DM | Nature protocols | 29599440 | Nat Protoc | 2018 May |
| Single-cell replication profiling to measure stochastic variation in mammalian replication timing. | Dileep V, Gilbert DM | Nature communications | 29382831 | Nat Commun | 2018 Jan 30 |
| Corrigendum: The 4D nucleome project. | Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S, 4D Nucleome Network | Nature | 29168505 | Nature | 2017 Dec 14 |
| Engineering inducible biomolecular assemblies for genome imaging and manipulation in living cells. | Peng Q, Huang Z, Sun K, Liu Y, Yoon CW, Harrison RES, Schmitt DL, Zhu L, Wu Y, Tasan I, Zhao H, Zhang J, Zhong S, Chien S, Wang Y | Nature communications | 36566209 | Nat Commun | 2022 Dec 24 |
| Allele-specific control of replication timing and genome organization during development. | Rivera-Mulia JC, Dimond A, Vera D, Trevilla-Garcia C, Sasaki T, Zimmerman J, Dupont C, Gribnau J, Fraser P, Gilbert DM | Genome research | 29735606 | Genome Res | 2018 Jun |
| High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells. | Zhao PA, Sasaki T, Gilbert DM | Genome biology | 32209126 | Genome Biol | 2020 Mar 24 |
| Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance. | Schep R, Brinkman EK, Leemans C, Vergara X, van der Weide RH, Morris B, van Schaik T, Manzo SG, Peric-Hupkes D, van den Berg J, Beijersbergen RL, Medema RH, van Steensel B | Molecular cell | 33848455 | Mol Cell | 2021 May 20 |
| Precise Regulation of Cas9-Mediated Genome Engineering by Anti-CRISPR-Based Inducible CRISPR Controllers. | Jain S, Xun G, Abesteh S, Ho S, Lingamaneni M, Martin TA, Tasan I, Yang C, Zhao H | ACS synthetic biology | 34006094 | ACS Synth Biol | 2021 Jun 18 |
| TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes. | Zhang L, Zhang Y, Chen Y, Gholamalamdari O, Wang Y, Ma J, Belmont AS | Genome research | 33355299 | Genome Res | 2021 Feb |
| Cell cycle dynamics of lamina-associated DNA. | van Schaik T, Vos M, Peric-Hupkes D, Hn Celie P, van Steensel B | EMBO reports | 32893442 | EMBO Rep | 2020 Nov 5 |
| Mammalian DNA Replication Timing. | Vouzas AE, Gilbert DM | Cold Spring Harbor perspectives in biology | 33558366 | Cold Spring Harb Perspect Biol | 2021 Jul 1 |
| Efficient and Reproducible Multigene Expression after Single-Step Transfection Using Improved BAC Transgenesis and Engineering Toolkit. | Zhao B, Chaturvedi P, Zimmerman DL, Belmont AS | ACS synthetic biology | 32216371 | ACS Synth Biol | 2020 May 15 |
| Local rewiring of genome-nuclear lamina interactions by transcription. | Brueckner L, Zhao PA, van Schaik T, Leemans C, Sima J, Peric-Hupkes D, Gilbert DM, van Steensel B | The EMBO journal | 32080885 | EMBO J | 2020 Mar 16 |
| Unearthing worm replication origins. | Sasaki T, Gilbert DM | Nature structural & molecular biology | 28257138 | Nat Struct Mol Biol | 2017 Mar 3 |
| A new correlation clustering method for cancer mutation analysis. | Hou JP, Emad A, Puleo GJ, Ma J, Milenkovic O | Bioinformatics (Oxford, England) | 27540270 | Bioinformatics | 2016 Dec 15 |
| Allele-Specific Quantification of Structural Variations in Cancer Genomes. | Li Y, Zhou S, Schwartz DC, Ma J | Cell systems | 27453446 | Cell Syst | 2016 Jul |
| Biosystems Design by Machine Learning. | Volk MJ, Lourentzou I, Mishra S, Vo LT, Zhai C, Zhao H | ACS synthetic biology | 32485108 | ACS Synth Biol | 2020 Jul 17 |
| Targeting Specificity of the CRISPR/Cas9 System. | Tasan I, Zhao H | ACS synthetic biology | 28911233 | ACS Synth Biol | 2017 Sep 15 |
| Genome organization around nuclear speckles. | Chen Y, Belmont AS | Current opinion in genetics & development | 31394307 | Curr Opin Genet Dev | 2019 Apr |
| Incorporation of noncanonical base Z yields modified mRNA with minimal immunogenicity and improved translational capacity in mammalian cells. | Zhang M, Singh N, Ehmann ME, Zheng L, Zhao H | iScience | 37720088 | iScience | 2023 Oct 20 |
| ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization. | Gunsalus LM, Keiser MJ, Pollard KS | bioRxiv : the preprint server for biology | 38045231 | bioRxiv | 2023 Nov 22 |
| SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models. | Gjoni K, Pollard KS | Bioinformatics (Oxford, England) | 38796686 | Bioinformatics | 2024 Jun 3 |
| Comparing chromatin contact maps at scale: methods and insights. | Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS | bioRxiv : the preprint server for biology | 37066196 | bioRxiv | 2023 Apr 4 |
| Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning. | Kuang S, Pollard KS | bioRxiv : the preprint server for biology | 37961712 | bioRxiv | 2023 Oct 24 |
| SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models. | Gjoni K, Pollard KS | bioRxiv : the preprint server for biology | 37961123 | bioRxiv | 2023 Nov 5 |
| Machine learning reveals the diversity of human 3D chromatin contact patterns. | Gilbertson EN, Brand CM, McArthur E, Rinker DC, Kuang S, Pollard KS, Capra JA | bioRxiv : the preprint server for biology | 38187606 | bioRxiv | 2023 Dec 23 |
| Exploring the roles of RNAs in chromatin architecture using deep learning. | Kuang S, Pollard KS | Nature communications | 39075082 | Nat Commun | 2024 Jul 29 |
| Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. | Mowery CT, Freimer JW, Chen Z, Casaní-Galdón S, Umhoefer JM, Arce MM, Gjoni K, Daniel B, Sandor K, Gowen BG, Nguyen V, Simeonov DR, Garrido CM, Curie GL, Schmidt R, Steinhart Z, Satpathy AT, Pollard KS, Corn JE, Bernstein BE, Ye CJ, Marson A | Nature genetics | 38811842 | Nat Genet | 2024 Jun |
| ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization. | Gunsalus LM, Keiser MJ, Pollard KS | PLoS computational biology | 39965010 | PLoS Comput Biol | 2025 Feb |
| Cell Layers: uncovering clustering structure in unsupervised single-cell transcriptomic analysis. | Blair AP, Hu RK, Farah EN, Chi NC, Pollard KS, Przytycki PF, Kathiriya IS, Bruneau BG | Bioinformatics advances | 35967929 | Bioinform Adv | 2022 |
| In silico discovery of repetitive elements as key sequence determinants of 3D genome folding. | Gunsalus LM, Keiser MJ, Pollard KS | Cell genomics | 37868032 | Cell Genom | 2023 Oct 11 |
| Machine Learning Reveals the Diversity of Human 3D Chromatin Contact Patterns. | Gilbertson EN, Brand CM, McArthur E, Rinker DC, Kuang S, Pollard KS, Capra JA | Molecular biology and evolution | 39404010 | Mol Biol Evol | 2024 Oct 4 |
| Comparing chromatin contact maps at scale: methods and insights. | Gjoni K, Gunsalus LM, Kuang S, McArthur E, Pittman M, Capra JA, Pollard KS | Nature methods | 40108448 | Nat Methods | 2025 Apr |
| An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. | Shah PP, Keough KC, Gjoni K, Santini GT, Abdill RJ, Wickramasinghe NM, Dundes CE, Karnay A, Chen A, Salomon REA, Walsh PJ, Nguyen SC, Whalen S, Joyce EF, Loh KM, Dubois N, Pollard KS, Jain R | Genome biology | 36691074 | Genome Biol | 2023 Jan 23 |
| De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes. | Gjoni K, Ren X, Everitt A, Shen Y, Pollard KS | bioRxiv : the preprint server for biology | 39574698 | bioRxiv | 2024 Nov 7 |
| Comparing chromatin contact maps at scale: methods and insights. | Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS | Research square | 37292728 | Res Sq | 2023 May 23 |
| TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons. | Zhao S, Lu J, Pan B, Fan H, Byrum SD, Xu C, Kim A, Guo Y, Kanchi KL, Gong W, Sun T, Storey AJ, Burkholder NT, Mackintosh SG, Kuhlers PC, Edmondson RD, Strahl BD, Diao Y, Tackett AJ, Raab JR, Cai L, Song J, Wang GG | Nature | 37938770 | Nature | 2023 Nov |
| Skeletal muscle regeneration failure in ischemic-damaged limbs is associated with pro-inflammatory macrophages and premature differentiation of satellite cells. | Southerland KW, Xu Y, Peters DT, Lin X, Wei X, Xiang Y, Fei K, Olivere LA, Morowitz JM, Otto J, Dai Q, Kontos CD, Diao Y | Genome medicine | 37950327 | Genome Med | 2023 Nov 10 |
| Maf family transcription factors are required for nutrient uptake in the mouse neonatal gut. | Bara AM, Chen L, Ma C, Underwood J, Moreci RS, Sumigray K, Sun T, Diao Y, Verzi M, Lechler T | Development (Cambridge, England) | 36504079 | Development | 2022 Dec 1 |
| Crosstalk between RNA m(6)A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells. | Sun T, Xu Y, Xiang Y, Ou J, Soderblom EJ, Diao Y | Nature genetics | 37474847 | Nat Genet | 2023 Aug |
| HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization. | Wei X, Xiang Y, Peters DT, Marius C, Sun T, Shan R, Ou J, Lin X, Yue F, Li W, Southerland KW, Diao Y | Molecular cell | 35196517 | Mol Cell | 2022 Mar 17 |
| HiCAR: Analysis of Open Chromatin Associated Long-range Chromatin Interaction Using Low-Input Materials. | Wei X, Tran D, Diao Y | Current protocols | 37818863 | Curr Protoc | 2023 Oct |
| Vcam1+ Fibro-adipogenic Progenitors Mark Fatty Infiltration in Chronic Limb Threatening Ischemia. | Dai Q, Wan C, Xu Y, Fei K, Olivere LA, Garrett B, Akers L, Peters D, Otto J, Kontos CD, Ji Z, Diao Y, Southerland KW | bioRxiv : the preprint server for biology | 39026697 | bioRxiv | 2024 Jul 11 |
| RNA m(6)A modification orchestrates a LINE-1-host interaction that facilitates retrotransposition and contributes to long gene vulnerability. | Xiong F, Wang R, Lee JH, Li S, Chen SF, Liao Z, Hasani LA, Nguyen PT, Zhu X, Krakowiak J, Lee DF, Han L, Tsai KL, Liu Y, Li W | Cell research | 34108665 | Cell Res | 2021 Aug |
| NANOG prion-like assembly mediates DNA bridging to facilitate chromatin reorganization and activation of pluripotency. | Choi KJ, Quan MD, Qi C, Lee JH, Tsoi PS, Zahabiyon M, Bajic A, Hu L, Prasad BVV, Liao SJ, Li W, Ferreon ACM, Ferreon JC | Nature cell biology | 35484250 | Nat Cell Biol | 2022 May |
| SARS-CoV-2 restructures host chromatin architecture. | Wang R, Lee JH, Kim J, Xiong F, Hasani LA, Shi Y, Simpson EN, Zhu X, Chen YT, Shivshankar P, Krakowiak J, Wang Y, Gilbert DM, Yuan X, Eltzschig HK, Li W | Nature microbiology | 36959507 | Nat Microbiol | 2023 Apr |
| Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization. | Zhu X, Qi C, Wang R, Lee JH, Shao J, Bei L, Xiong F, Nguyen PT, Li G, Krakowiak J, Koh SP, Simon LM, Han L, Moore TI, Li W | Cell reports | 36323253 | Cell Rep | 2022 Nov 1 |
| SARS-CoV-2 Restructures the Host Chromatin Architecture. | Wang R, Lee JH, Xiong F, Kim J, Al Hasani L, Yuan X, Shivshankar P, Krakowiak J, Qi C, Wang Y, Eltzschig HK, Li W | bioRxiv : the preprint server for biology | 34312624 | bioRxiv | 2021 Jul 21 |
| Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. | Sanborn AL, Yeh BT, Feigerle JT, Hao CV, Townshend RJ, Lieberman Aiden E, Dror RO, Kornberg RD | eLife | 33904398 | Elife | 2021 Apr 27 |
| Enhancer release and retargeting activates disease-susceptibility genes. | Oh S, Shao J, Mitra J, Xiong F, D'Antonio M, Wang R, Garcia-Bassets I, Ma Q, Zhu X, Lee JH, Nair SJ, Yang F, Ohgi K, Frazer KA, Zhang ZD, Li W, Rosenfeld MG | Nature | 34040254 | Nature | 2021 Jul |
| Transcriptomic and Epigenetic Profiling of Fibroblasts in Idiopathic Pulmonary Fibrosis. | Hanmandlu A, Zhu L, Mertens TCJ, Collum S, Bi W, Xiong F, Wang R, Amirthalingam RT, Ren D, Han L, Jyothula SSSK, Li W, Zheng WJ, Karmouty-Quintana H | American journal of respiratory cell and molecular biology | 34370624 | Am J Respir Cell Mol Biol | 2022 Jan |
| Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation. | Lee JH, Wang R, Xiong F, Krakowiak J, Liao Z, Nguyen PT, Moroz-Omori EV, Shao J, Zhu X, Bolt MJ, Wu H, Singh PK, Bi M, Shi CJ, Jamal N, Li G, Mistry R, Jung SY, Tsai KL, Ferreon JC, Stossi F, Caflisch A, Liu Z, Mancini MA, Li W | Molecular cell | 34375583 | Mol Cell | 2021 Aug 19 |
| The Australian dingo is an early offshoot of modern breed dogs. | Field MA, Yadav S, Dudchenko O, Esvaran M, Rosen BD, Skvortsova K, Edwards RJ, Keilwagen J, Cochran BJ, Manandhar B, Bustamante S, Rasmussen JA, Melvin RG, Chernoff B, Omer A, Colaric Z, Chan EKF, Minoche AE, Smith TPL, Gilbert MTP, Bogdanovic O, Zammit RA, Thomas T, Aiden EL, Ballard JWO | Science advances | 35452284 | Sci Adv | 2022 Apr 22 |
| Reconstructing Progenitor State Hierarchy and Dynamics Using Lineage Barcoding Data. | Fang W, Yang Y, Ji H, Kalhor R | Methods in molecular biology (Clifton, N.J.) | 39745641 | Methods Mol Biol | 2025 |
| Quantitative fate mapping: A general framework for analyzing progenitor state dynamics via retrospective lineage barcoding. | Fang W, Bell CM, Sapirstein A, Asami S, Leeper K, Zack DJ, Ji H, Kalhor R | Cell | 36423582 | Cell | 2022 Nov 23 |
| Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites. | Zou RS, Marin-Gonzalez A, Liu Y, Liu HB, Shen L, Dveirin RK, Luo JXJ, Kalhor R, Ha T | Nature cell biology | 36064968 | Nat Cell Biol | 2022 Sep |
| Deconvolving organogenesis in space and time via spatial transcriptomics in thick tissues. | Asami S, Yin C, Garza LA, Kalhor R | bioRxiv : the preprint server for biology | 39386671 | bioRxiv | 2024 Sep 24 |
| A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. | Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL | Cell | 25497547 | Cell | 2014 Dec 18 |
| Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map. | Eagen KP, Aiden EL, Kornberg RD | Proceedings of the National Academy of Sciences of the United States of America | 28765367 | Proc Natl Acad Sci U S A | 2017 Aug 15 |
| Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity. | Zhang X, Jeong M, Huang X, Wang XQ, Wang X, Zhou W, Shamim MS, Gore H, Himadewi P, Liu Y, Bochkov ID, Reyes J, Doty M, Huang YH, Jung H, Heikamp E, Aiden AP, Li W, Su J, Aiden EL, Goodell MA | Molecular cell | 32386543 | Mol Cell | 2020 May 7 |
| ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesin(STAG1) from WAPL. | Wutz G, Ladurner R, St Hilaire BG, Stocsits RR, Nagasaka K, Pignard B, Sanborn A, Tang W, Várnai C, Ivanov MP, Schoenfelder S, van der Lelij P, Huang X, Dürnberger G, Roitinger E, Mechtler K, Davidson IF, Fraser P, Lieberman-Aiden E, Peters JM | eLife | 32065581 | Elife | 2020 Feb 17 |
| Exploring chromosomal structural heterogeneity across multiple cell lines. | Cheng RR, Contessoto VG, Lieberman Aiden E, Wolynes PG, Di Pierro M, Onuchic JN | eLife | 33047670 | Elife | 2020 Oct 13 |
| Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. | Field MA, Rosen BD, Dudchenko O, Chan EKF, Minoche AE, Edwards RJ, Barton K, Lyons RJ, Tuipulotu DE, Hayes VM, D Omer A, Colaric Z, Keilwagen J, Skvortsova K, Bogdanovic O, Smith MA, Aiden EL, Smith TPL, Zammit RA, Ballard JWO | GigaScience | 32236524 | Gigascience | 2020 Apr 1 |
| Transferable model for chromosome architecture. | Di Pierro M, Zhang B, Aiden EL, Wolynes PG, Onuchic JN | Proceedings of the National Academy of Sciences of the United States of America | 27688758 | Proc Natl Acad Sci U S A | 2016 Oct 25 |
| De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. | Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL | Science (New York, N.Y.) | 28336562 | Science | 2017 Apr 7 |
| Chromatin Is Frequently Unknotted at the Megabase Scale. | Goundaroulis D, Lieberman Aiden E, Stasiak A | Biophysical journal | 31818464 | Biophys J | 2020 May 5 |
| The fundamental role of chromatin loop extrusion in physiological V(D)J recombination. | Zhang Y, Zhang X, Ba Z, Liang Z, Dring EW, Hu H, Lou J, Kyritsis N, Zurita J, Shamim MS, Presser Aiden A, Lieberman Aiden E, Alt FW | Nature | 31511698 | Nature | 2019 Sep |
| Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly. | Kaur P, Lui C, Dudchenko O, Nandety RS, Hurgobin B, Pham M, Lieberman Aiden E, Wen J, Mysore K | International journal of molecular sciences | 33919286 | Int J Mol Sci | 2021 Apr 21 |
| Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development. | Phanstiel DH, Van Bortle K, Spacek D, Hess GT, Shamim MS, Machol I, Love MI, Aiden EL, Bassik MC, Snyder MP | Molecular cell | 28890333 | Mol Cell | 2017 Sep 21 |
| Cohesin depleted cells rebuild functional nuclear compartments after endomitosis. | Cremer M, Brandstetter K, Maiser A, Rao SSP, Schmid VJ, Guirao-Ortiz M, Mitra N, Mamberti S, Klein KN, Gilbert DM, Leonhardt H, Cardoso MC, Aiden EL, Harz H, Cremer T | Nature communications | 33262376 | Nat Commun | 2020 Dec 1 |
| Improved reference genome of Aedes aegypti informs arbovirus vector control. | Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gloria-Soria A, Hall R, Joardar VS, Jones AK, Kay RGG, Kodali VK, Lee J, Lycett GJ, Mitchell SN, Muehling J, Murphy MR, Omer AD, Partridge FA, Peluso P, Aiden AP, Ramasamy V, Rašić G, Roy S, Saavedra-Rodriguez K, Sharan S, Sharma A, Smith ML, Turner J, Weakley AM, Zhao Z, Akbari OS, Black WC 4th, Cao H, Darby AC, Hill CA, Johnston JS, Murphy TD, Raikhel AS, Sattelle DB, Sharakhov IV, White BJ, Zhao L, Aiden EL, Mann RS, Lambrechts L, Powell JR, Sharakhova MV, Tu Z, Robertson HM, McBride CS, Hastie AR, Korlach J, Neafsey DE, Phillippy AM, Vosshall LB | Nature | 30429615 | Nature | 2018 Nov |
| Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture. | Darrow EM, Huntley MH, Dudchenko O, Stamenova EK, Durand NC, Sun Z, Huang SC, Sanborn AL, Machol I, Shamim M, Seberg AP, Lander ES, Chadwick BP, Aiden EL | Proceedings of the National Academy of Sciences of the United States of America | 27432957 | Proc Natl Acad Sci U S A | 2016 Aug 2 |
| Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. | Sanborn AL, Rao SS, Huang SC, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D, Cutkosky A, Li J, Geeting KP, Gnirke A, Melnikov A, McKenna D, Stamenova EK, Lander ES, Aiden EL | Proceedings of the National Academy of Sciences of the United States of America | 26499245 | Proc Natl Acad Sci U S A | 2015 Nov 24 |
| De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture. | Di Pierro M, Cheng RR, Lieberman Aiden E, Wolynes PG, Onuchic JN | Proceedings of the National Academy of Sciences of the United States of America | 29087948 | Proc Natl Acad Sci U S A | 2017 Nov 14 |
| Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function. | Lawlor N, Márquez EJ, Orchard P, Narisu N, Shamim MS, Thibodeau A, Varshney A, Kursawe R, Erdos MR, Kanke M, Gu H, Pak E, Dutra A, Russell S, Li X, Piecuch E, Luo O, Chines PS, Fuchbserger C, NIH Intramural Sequencing Center, Sethupathy P, Aiden AP, Ruan Y, Aiden EL, Collins FS, Ucar D, Parker SCJ, Stitzel ML | Cell reports | 30650367 | Cell Rep | 2019 Jan 15 |
| Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. | Durand NC, Shamim MS, Machol I, Rao SS, Huntley MH, Lander ES, Aiden EL | Cell systems | 27467249 | Cell Syst | 2016 Jul |
| Chromatin Viscoelasticity Measured by Local Dynamic Analysis. | Vivante A, Bronshtein I, Garini Y | Biophysical journal | 32320676 | Biophys J | 2020 May 5 |
| The gene-rich genome of the scallop Pecten maximus. | Kenny NJ, McCarthy SA, Dudchenko O, James K, Betteridge E, Corton C, Dolucan J, Mead D, Oliver K, Omer AD, Pelan S, Ryan Y, Sims Y, Skelton J, Smith M, Torrance J, Weisz D, Wipat A, Aiden EL, Howe K, Williams ST | GigaScience | 32352532 | Gigascience | 2020 May 1 |
| Chromosomal-level genome assembly of the scimitar-horned oryx: Insights into diversity and demography of a species extinct in the wild. | Humble E, Dobrynin P, Senn H, Chuven J, Scott AF, Mohr DW, Dudchenko O, Omer AD, Colaric Z, Lieberman Aiden E, Al Dhaheri SS, Wildt D, Oliaji S, Tamazian G, Pukazhenthi B, Ogden R, Koepfli KP | Molecular ecology resources | 32365406 | Mol Ecol Resour | 2020 Nov |
| Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. | Fulco CP, Nasser J, Jones TR, Munson G, Bergman DT, Subramanian V, Grossman SR, Anyoha R, Doughty BR, Patwardhan TA, Nguyen TH, Kane M, Perez EM, Durand NC, Lareau CA, Stamenova EK, Aiden EL, Lander ES, Engreitz JM | Nature genetics | 31784727 | Nat Genet | 2019 Dec |
| Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. | Nir G, Farabella I, Pérez Estrada C, Ebeling CG, Beliveau BJ, Sasaki HM, Lee SD, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, Russell S, Durand NC, Rao SSP, Kishi JY, Soler-Vila P, Di Pierro M, Onuchic JN, Callahan SP, Schreiner JM, Stuckey JA, Yin P, Aiden EL, Marti-Renom MA, Wu CT | PLoS genetics | 30586358 | PLoS Genet | 2018 Dec |
| Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data. | Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, Aiden EL | Cell systems | 29428417 | Cell Syst | 2018 Feb 28 |
| Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription. | Goronzy IN, Quinodoz SA, Jachowicz JW, Ollikainen N, Bhat P, Guttman M | Cell reports | 36450242 | Cell Rep | 2022 Nov 29 |
| Single-cell measurement of higher-order 3D genome organization with scSPRITE. | Arrastia MV, Jachowicz JW, Ollikainen N, Curtis MS, Lai C, Quinodoz SA, Selck DA, Ismagilov RF, Guttman M | Nature biotechnology | 34426703 | Nat Biotechnol | 2022 Jan |
| RNA promotes the formation of spatial compartments in the nucleus. | Quinodoz SA, Jachowicz JW, Bhat P, Ollikainen N, Banerjee AK, Goronzy IN, Blanco MR, Chovanec P, Chow A, Markaki Y, Thai J, Plath K, Guttman M | Cell | 34739832 | Cell | 2021 Nov 11 |
| High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection. | Vangala P, Murphy R, Quinodoz SA, Gellatly K, McDonel P, Guttman M, Garber M | Molecular cell | 32991830 | Mol Cell | 2020 Oct 15 |
| SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses. | Banerjee AK, Blanco MR, Bruce EA, Honson DD, Chen LM, Chow A, Bhat P, Ollikainen N, Quinodoz SA, Loney C, Thai J, Miller ZD, Lin AE, Schmidt MM, Stewart DG, Goldfarb D, De Lorenzo G, Rihn SJ, Voorhees RM, Botten JW, Majumdar D, Guttman M | Cell | 33080218 | Cell | 2020 Nov 25 |
| Xist spatially amplifies SHARP/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome. | Jachowicz JW, Strehle M, Banerjee AK, Blanco MR, Thai J, Guttman M | Nature structural & molecular biology | 35301492 | Nat Struct Mol Biol | 2022 Mar |
| The NORAD lncRNA assembles a topoisomerase complex critical for genome stability. | Munschauer M, Nguyen CT, Sirokman K, Hartigan CR, Hogstrom L, Engreitz JM, Ulirsch JC, Fulco CP, Subramanian V, Chen J, Schenone M, Guttman M, Carr SA, Lander ES | Nature | 30150775 | Nature | 2018 Sep |
| Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus. | Quinodoz SA, Ollikainen N, Tabak B, Palla A, Schmidt JM, Detmar E, Lai MM, Shishkin AA, Bhat P, Takei Y, Trinh V, Aznauryan E, Russell P, Cheng C, Jovanovic M, Chow A, Cai L, McDonel P, Garber M, Guttman M | Cell | 29887377 | Cell | 2018 Jul 26 |
| Xist drives spatial compartmentalization of DNA and protein to orchestrate initiation and maintenance of X inactivation. | Strehle M, Guttman M | Current opinion in cell biology | 32535328 | Curr Opin Cell Biol | 2020 Jun |
| SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding. | Quinodoz SA, Bhat P, Chovanec P, Jachowicz JW, Ollikainen N, Detmar E, Soehalim E, Guttman M | Nature protocols | 35013617 | Nat Protoc | 2022 Jan |
| A Dementia-Associated Risk Variant near TMEM106B Alters Chromatin Architecture and Gene Expression. | Gallagher MD, Posavi M, Huang P, Unger TL, Berlyand Y, Gruenewald AL, Chesi A, Manduchi E, Wells AD, Grant SFA, Blobel GA, Brown CD, Chen-Plotkin AS | American journal of human genetics | 29056226 | Am J Hum Genet | 2017 Nov 2 |
| Detecting hierarchical genome folding with network modularity. | Norton HK, Emerson DJ, Huang H, Kim J, Titus KR, Gu S, Bassett DS, Phillips-Cremins JE | Nature methods | 29334377 | Nat Methods | 2018 Feb |
| The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. | Hsu SC, Gilgenast TG, Bartman CR, Edwards CR, Stonestrom AJ, Huang P, Emerson DJ, Evans P, Werner MT, Keller CA, Giardine B, Hardison RC, Raj A, Phillips-Cremins JE, Blobel GA | Molecular cell | 28388437 | Mol Cell | 2017 Apr 6 |
| Crossed wires: 3D genome misfolding in human disease. | Norton HK, Phillips-Cremins JE | The Journal of cell biology | 28855250 | J Cell Biol | 2017 Nov 6 |
| The interdependence of gene-regulatory elements and the 3D genome. | Vermunt MW, Zhang D, Blobel GA | The Journal of cell biology | 30442643 | J Cell Biol | 2019 Jan 7 |
| Variability within rare cell states enables multiple paths toward drug resistance. | Emert BL, Cote CJ, Torre EA, Dardani IP, Jiang CL, Jain N, Shaffer SM, Raj A | Nature biotechnology | 33619394 | Nat Biotechnol | 2021 Jul |
| Genome folding dynamics during the M-to-G1-phase transition. | Zhang H, Blobel GA | Current opinion in genetics & development | 37099832 | Curr Opin Genet Dev | 2023 Jun |
| Post-transcriptional splicing can occur in a slow-moving zone around the gene. | Coté A, O'Farrell A, Dardani I, Dunagin M, Coté C, Wan Y, Bayatpour S, Drexler HL, Alexander KA, Chen F, Wassie AT, Patel R, Pham K, Boyden ES, Berger S, Phillips-Cremins J, Churchman LS, Raj A | eLife | 38577979 | Elife | 2024 Apr 5 |
| Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals. | Sanford EM, Emert BL, Coté A, Raj A | eLife | 33284110 | Elife | 2020 Dec 7 |
| Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant. | Ginart P, Kalish JM, Jiang CL, Yu AC, Bartolomei MS, Raj A | Genes & development | 26944681 | Genes Dev | 2016 Mar 1 |
| A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition. | Hsiung CC, Bartman CR, Huang P, Ginart P, Stonestrom AJ, Keller CA, Face C, Jahn KS, Evans P, Sankaranarayanan L, Giardine B, Hardison RC, Raj A, Blobel GA | Genes & development | 27340175 | Genes Dev | 2016 Jun 15 |
| Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting. | Symmons O, Chang M, Mellis IA, Kalish JM, Park J, Suszták K, Bartolomei MS, Raj A | PLoS genetics | 30625149 | PLoS Genet | 2019 Jan |
| ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. | Rouhanifard SH, Mellis IA, Dunagin M, Bayatpour S, Jiang CL, Dardani I, Symmons O, Emert B, Torre E, Cote A, Sullivan A, Stamatoyannopoulos JA, Raj A | Nature biotechnology | 30418432 | Nat Biotechnol | 2018 Nov 12 |
| Alteration of genome folding via contact domain boundary insertion. | Zhang D, Huang P, Sharma M, Keller CA, Giardine B, Zhang H, Gilgenast TG, Phillips-Cremins JE, Hardison RC, Blobel GA | Nature genetics | 32868908 | Nat Genet | 2020 Oct |
| Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors. | Shaffer SM, Emert BL, Reyes Hueros RA, Cote C, Harmange G, Schaff DL, Sizemore AE, Gupte R, Torre E, Singh A, Bassett DS, Raj A | Cell | 32735851 | Cell | 2020 Aug 20 |
| 3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data. | Fernandez LR, Gilgenast TG, Phillips-Cremins JE | Genome biology | 32859248 | Genome Biol | 2020 Aug 28 |
| Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. | Huang P, Keller CA, Giardine B, Grevet JD, Davies JOJ, Hughes JR, Kurita R, Nakamura Y, Hardison RC, Blobel GA | Genes & development | 28916711 | Genes Dev | 2017 Aug 15 |
| CRISPR/Cas9 genome editing throws descriptive 3-D genome folding studies for a loop. | Beagan JA, Phillips-Cremins JE | Wiley interdisciplinary reviews. Systems biology and medicine | 27265842 | Wiley Interdiscip Rev Syst Biol Med | 2016 Jul |
| Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries. | Sun JH, Zhou L, Emerson DJ, Phyo SA, Titus KR, Gong W, Gilgenast TG, Beagan JA, Davidson BL, Tassone F, Phillips-Cremins JE | Cell | 30173918 | Cell | 2018 Sep 20 |
| Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation. | Bartman CR, Hamagami N, Keller CA, Giardine B, Hardison RC, Blobel GA, Raj A | Molecular cell | 30554946 | Mol Cell | 2019 Feb 7 |
| FISHing Out the Details of CRISPR Genome Tracks. | Coté AJ, Raj A | Biophysical journal | 28355532 | Biophys J | 2017 Mar 28 |
| Chromatin structure dynamics during the mitosis-to-G1 phase transition. | Zhang H, Emerson DJ, Gilgenast TG, Titus KR, Lan Y, Huang P, Zhang D, Wang H, Keller CA, Giardine B, Hardison RC, Phillips-Cremins JE, Blobel GA | Nature | 31776509 | Nature | 2019 Dec |
| On the existence and functionality of topologically associating domains. | Beagan JA, Phillips-Cremins JE | Nature genetics | 31925403 | Nat Genet | 2020 Jan |
| Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data. | Gilgenast TG, Phillips-Cremins JE | Cell systems | 30904376 | Cell Syst | 2019 Mar 27 |
| LADL: light-activated dynamic looping for endogenous gene expression control. | Kim JH, Rege M, Valeri J, Dunagin MC, Metzger A, Titus KR, Gilgenast TG, Gong W, Beagan JA, Raj A, Phillips-Cremins JE | Nature methods | 31235883 | Nat Methods | 2019 Jul |
| SAVER: gene expression recovery for single-cell RNA sequencing. | Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, Zhang NR | Nature methods | 29941873 | Nat Methods | 2018 Jul |
| Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. | Torre E, Dueck H, Shaffer S, Gospocic J, Gupte R, Bonasio R, Kim J, Murray J, Raj A | Cell systems | 29454938 | Cell Syst | 2018 Feb 28 |
| Visualizing adenosine-to-inosine RNA editing in single mammalian cells. | Mellis IA, Gupte R, Raj A, Rouhanifard SH | Nature methods | 28604724 | Nat Methods | 2017 Aug |
| A magnetic micropore chip for rapid (<1 hour) unbiased circulating tumor cell isolation and in situ RNA analysis. | Ko J, Bhagwat N, Yee SS, Black T, Redlinger C, Romeo J, O'Hara M, Raj A, Carpenter EL, Stanger BZ, Issadore D | Lab on a chip | 28809985 | Lab Chip | 2017 Sep 12 |
| Nanoscale imaging of RNA with expansion microscopy. | Chen F, Wassie AT, Cote AJ, Sinha A, Alon S, Asano S, Daugharthy ER, Chang JB, Marblestone A, Church GM, Raj A, Boyden ES | Nature methods | 27376770 | Nat Methods | 2016 Aug |
| Systematically quantifying morphological features reveals constraints on organoid phenotypes. | Beck LE, Lee J, Coté C, Dunagin MC, Lukonin I, Salla N, Chang MK, Hughes AJ, Mornin JD, Gartner ZJ, Liberali P, Raj A | Cell systems | 35705097 | Cell Syst | 2022 Jul 20 |
| YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment. | Beagan JA, Duong MT, Titus KR, Zhou L, Cao Z, Ma J, Lachanski CV, Gillis DR, Phillips-Cremins JE | Genome research | 28536180 | Genome Res | 2017 Jul |
| 5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design. | Kim JH, Titus KR, Gong W, Beagan JA, Cao Z, Phillips-Cremins JE | Methods (San Diego, Calif.) | 29772275 | Methods | 2018 Jun 1 |
| Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro. | Mellis IA, Edelstein HI, Truitt R, Goyal Y, Beck LE, Symmons O, Dunagin MC, Linares Saldana RA, Shah PP, Pérez-Bermejo JA, Padmanabhan A, Yang W, Jain R, Raj A | Cell systems | 34352221 | Cell Syst | 2021 Sep 22 |
| Genetic screening for single-cell variability modulators driving therapy resistance. | Torre EA, Arai E, Bayatpour S, Jiang CL, Beck LE, Emert BL, Shaffer SM, Mellis IA, Fane ME, Alicea GM, Budinich KA, Weeraratna AT, Shi J, Raj A | Nature genetics | 33398196 | Nat Genet | 2021 Jan |
| See(quence) and ye shall find: higher-order genome folding in intact single cells. | Pham K, Nikish A, Phillips-Cremins JE | Molecular cell | 33740473 | Mol Cell | 2021 Mar 18 |
| Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer. | Schuh L, Saint-Antoine M, Sanford EM, Emert BL, Singh A, Marr C, Raj A, Goyal Y | Cell systems | 32325034 | Cell Syst | 2020 Apr 22 |
| A subset of topologically associating domains fold into mesoscale core-periphery networks. | Huang H, Chen ST, Titus KR, Emerson DJ, Bassett DS, Phillips-Cremins JE | Scientific reports | 31266973 | Sci Rep | 2019 Jul 2 |
| Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping. | Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA | Molecular cell | 27067601 | Mol Cell | 2016 Apr 21 |
| What's Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism. | Symmons O, Raj A | Molecular cell | 27259209 | Mol Cell | 2016 Jun 2 |
| Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression. | Beagan JA, Pastuzyn ED, Fernandez LR, Guo MH, Feng K, Titus KR, Chandrashekar H, Shepherd JD, Phillips-Cremins JE | Nature neuroscience | 32451484 | Nat Neurosci | 2020 Jun |
| Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells. | Chen C, Yu W, Tober J, Gao P, He B, Lee K, Trieu T, Blobel GA, Speck NA, Tan K | Cell reports | 31851943 | Cell Rep | 2019 Dec 17 |
| Dynamic Looping Interactions: Setting the 3D Stage for the Macrophage. | Rege M, Phillips-Cremins JE | Molecular cell | 28938095 | Mol Cell | 2017 Sep 21 |
| ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ. | Dardani I, Emert BL, Goyal Y, Jiang CL, Kaur A, Lee J, Rouhanifard SH, Alicea GM, Fane ME, Xiao M, Herlyn M, Weeraratna AT, Raj A | Nature methods | 36280724 | Nat Methods | 2022 Nov |
| Cell-cycle dynamics of chromosomal organization at single-cell resolution. | Nagano T, Lubling Y, Várnai C, Dudley C, Leung W, Baran Y, Mendelson Cohen N, Wingett S, Fraser P, Tanay A | Nature | 28682332 | Nature | 2017 Jul 5 |
| Long-range enhancer-promoter contacts in gene expression control. | Schoenfelder S, Fraser P | Nature reviews. Genetics | 31086298 | Nat Rev Genet | 2019 Aug |
| De novo missense variants disrupting protein-protein interactions affect risk for autism through gene co-expression and protein networks in neuronal cell types. | Chen S, Wang J, Cicek E, Roeder K, Yu H, Devlin B | Molecular autism | 33032641 | Mol Autism | 2020 Oct 8 |
| Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock. | Ray J, Munn PR, Vihervaara A, Lewis JJ, Ozer A, Danko CG, Lis JT | Proceedings of the National Academy of Sciences of the United States of America | 31506350 | Proc Natl Acad Sci U S A | 2019 Sep 24 |
| Stress-induced transcriptional memory accelerates promoter-proximal pause release and decelerates termination over mitotic divisions. | Vihervaara A, Mahat DB, Himanen SV, Blom MAH, Lis JT, Sistonen L | Molecular cell | 33784494 | Mol Cell | 2021 Apr 15 |
| An improved 4'-aminomethyltrioxsalen-based nucleic acid crosslinker for biotinylation of double-stranded DNA or RNA. | Wielenberg K, Wang M, Yang M, Ozer A, Lis JT, Lin H | RSC advances | 35515418 | RSC Adv | 2020 Oct 27 |
| Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone. | Lewis JJ, Van Belleghem SM, Papa R, Danko CG, Reed RD | Science advances | 32978147 | Sci Adv | 2020 Sep |
| Dynamic evolution of regulatory element ensembles in primate CD4(+) T cells. | Danko CG, Choate LA, Marks BA, Rice EJ, Wang Z, Chu T, Martins AL, Dukler N, Coonrod SA, Tait Wojno ED, Lis JT, Kraus WL, Siepel A | Nature ecology & evolution | 29379187 | Nat Ecol Evol | 2018 Mar |
| RTFBSDB: an integrated framework for transcription factor binding site analysis. | Wang Z, Martins AL, Danko CG | Bioinformatics (Oxford, England) | 27288497 | Bioinformatics | 2016 Oct 1 |
| Nanoscale photobiotinylation, pulldown and sequencing of region-specific DNA from intact cells. | Roberts TC, Kushner M, Crowley JC, Ozer A, Wang J, Ray J, Lis JT, Zipfel WR | bioRxiv : the preprint server for biology | 38105945 | bioRxiv | 2023 Dec 6 |
| Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution. | Blumberg A, Rice EJ, Kundaje A, Danko CG, Mishmar D | Genome research | 28049628 | Genome Res | 2017 Mar |
| An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells. | Zhang Z, Chng KR, Lingadahalli S, Chen Z, Liu MH, Do HH, Cai S, Rinaldi N, Poh HM, Li G, Sung YY, Heng CL, Core LJ, Tan SK, Ruan X, Lis JT, Kellis M, Ruan Y, Sung WK, Cheung E | Genome research | 30606742 | Genome Res | 2019 Feb |
| ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. | Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, O'Shea CC | Science (New York, N.Y.) | 28751582 | Science | 2017 Jul 28 |
| CRISPR-mediated live imaging of genome editing and transcription. | Wang H, Nakamura M, Abbott TR, Zhao D, Luo K, Yu C, Nguyen CM, Lo A, Daley TP, La Russa M, Liu Y, Qi LS | Science (New York, N.Y.) | 31488703 | Science | 2019 Sep 20 |
| CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens. | Daley TP, Lin Z, Lin X, Liu Y, Wong WH, Qi LS | Genome biology | 30296940 | Genome Biol | 2018 Oct 8 |
| CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization. | Wang H, Xu X, Nguyen CM, Liu Y, Gao Y, Lin X, Daley T, Kipniss NH, La Russa M, Qi LS | Cell | 30318144 | Cell | 2018 Nov 15 |
| Engineering 3D genome organization. | Wang H, Han M, Qi LS | Nature reviews. Genetics | 33558716 | Nat Rev Genet | 2021 Jun |
| Enhanced Cas12a multi-gene regulation using a CRISPR array separator. | Magnusson JP, Rios AR, Wu L, Qi LS | eLife | 34499031 | Elife | 2021 Sep 9 |
| The adult human testis transcriptional cell atlas. | Guo J, Grow EJ, Mlcochova H, Maher GJ, Lindskog C, Nie X, Guo Y, Takei Y, Yun J, Cai L, Kim R, Carrell DT, Goriely A, Hotaling JM, Cairns BR | Cell research | 30315278 | Cell Res | 2018 Dec |
| Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. | Gao Y, Xiong X, Wong S, Charles EJ, Lim WA, Qi LS | Nature methods | 27776111 | Nat Methods | 2016 Dec |
| Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH. | Takei Y, Shah S, Harvey S, Qi LS, Cai L | Biophysical journal | 28427715 | Biophys J | 2017 May 9 |
| Genetic interaction mapping in mammalian cells using CRISPR interference. | Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ | Nature methods | 28481362 | Nat Methods | 2017 Jun |
| High-content CRISPR screening. | Bock C, Datlinger P, Chardon F, Coelho MA, Dong MB, Lawson KA, Lu T, Maroc L, Norman TM, Song B, Stanley G, Chen S, Garnett M, Li W, Moffat J, Qi LS, Shapiro RS, Shendure J, Weissman JS, Zhuang X | Nature reviews. Methods primers | 37214176 | Nat Rev Methods Primers | 2022 |
| Interrogation of the dynamic properties of higher-order heterochromatin using CRISPR-dCas9. | Gao Y, Han M, Shang S, Wang H, Qi LS | Molecular cell | 34428454 | Mol Cell | 2021 Oct 21 |
| Integrated spatial genomics reveals global architecture of single nuclei. | Takei Y, Yun J, Zheng S, Ollikainen N, Pierson N, White J, Shah S, Thomassie J, Suo S, Eng CL, Guttman M, Yuan GC, Cai L | Nature | 33505024 | Nature | 2021 Feb |
| CRISPRi/a Screening with Human iPSCs. | Nishiga M, Qi LS, Wu JC | Methods in molecular biology (Clifton, N.J.) | 34302664 | Methods Mol Biol | 2021 |
| CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming. | Liu Y, Yu C, Daley TP, Wang F, Cao WS, Bhate S, Lin X, Still C 2nd, Liu H, Zhao D, Wang H, Xie XS, Ding S, Wong WH, Wernig M, Qi LS | Cell stem cell | 30318302 | Cell Stem Cell | 2018 Nov 1 |
| Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH. | Shah S, Takei Y, Zhou W, Lubeck E, Yun J, Eng CL, Koulena N, Cronin C, Karp C, Liaw EJ, Amin M, Cai L | Cell | 29887381 | Cell | 2018 Jul 12 |
| A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria. | Peters JM, Colavin A, Shi H, Czarny TL, Larson MH, Wong S, Hawkins JS, Lu CHS, Koo BM, Marta E, Shiver AL, Whitehead EH, Weissman JS, Brown ED, Qi LS, Huang KC, Gross CA | Cell | 27238023 | Cell | 2016 Jun 2 |
| Therapeutic genome editing in cardiovascular diseases. | Nishiga M, Qi LS, Wu JC | Advanced drug delivery reviews | 32092381 | Adv Drug Deliv Rev | 2021 Jan |
| Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. | Eng CL, Lawson M, Zhu Q, Dries R, Koulena N, Takei Y, Yun J, Cronin C, Karp C, Yuan GC, Cai L | Nature | 30911168 | Nature | 2019 Apr |
| CRISPR/Cas9 for Human Genome Engineering and Disease Research. | Xiong X, Chen M, Lim WA, Zhao D, Qi LS | Annual review of genomics and human genetics | 27216776 | Annu Rev Genomics Hum Genet | 2016 Aug 31 |
| Visualization of Transvection in Living Drosophila Embryos. | Lim B, Heist T, Levine M, Fukaya T | Molecular cell | 29606591 | Mol Cell | 2018 Apr 19 |
| Enhancer Control of Transcriptional Bursting. | Fukaya T, Lim B, Levine M | Cell | 27293191 | Cell | 2016 Jul 14 |
| Using RNA Tags for Multicolor Live Imaging of Chromatin Loci and Transcription in Drosophila Embryos. | Chen H, Gregor T | Methods in molecular biology (Clifton, N.J.) | 32710421 | Methods Mol Biol | 2020 |
| Live Imaging of mRNA Synthesis in Drosophila. | Garcia HG, Gregor T | Methods in molecular biology (Clifton, N.J.) | 29130209 | Methods Mol Biol | 2018 |
| The Impact of Space and Time on the Functional Output of the Genome. | Nollmann M, Bennabi I, Götz M, Gregor T | Cold Spring Harbor perspectives in biology | 34230036 | Cold Spring Harb Perspect Biol | 2022 May 17 |
| Rapid Rates of Pol II Elongation in the Drosophila Embryo. | Fukaya T, Lim B, Levine M | Current biology : CB | 28457866 | Curr Biol | 2017 May 8 |
| Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting. | Zoller B, Little SC, Gregor T | Cell | 30340044 | Cell | 2018 Oct 18 |
| Dynamic interplay between enhancer-promoter topology and gene activity. | Chen H, Levo M, Barinov L, Fujioka M, Jaynes JB, Gregor T | Nature genetics | 30038397 | Nat Genet | 2018 Sep |
| Temporal dynamics of pair-rule stripes in living Drosophila embryos. | Lim B, Fukaya T, Heist T, Levine M | Proceedings of the National Academy of Sciences of the United States of America | 30061421 | Proc Natl Acad Sci U S A | 2018 Aug 14 |
| Trading bits in the readout from a genetic network. | Bauer M, Petkova MD, Gregor T, Wieschaus EF, Bialek W | Proceedings of the National Academy of Sciences of the United States of America | 34772813 | Proc Natl Acad Sci U S A | 2021 Nov 16 |
| Transcriptional coupling of distant regulatory genes in living embryos. | Levo M, Raimundo J, Bing XY, Sisco Z, Batut PJ, Ryabichko S, Gregor T, Levine MS | Nature | 35508662 | Nature | 2022 May |
| Simultaneous measurement of emission color and 3D position of single molecules. | Smith C, Huisman M, Siemons M, Grünwald D, Stallinga S | Optics express | 29092328 | Opt Express | 2016 Mar 7 |
| Localization microscopy at doubled precision with patterned illumination. | Cnossen J, Hinsdale T, Thorsen RØ, Siemons M, Schueder F, Jungmann R, Smith CS, Rieger B, Stallinga S | Nature methods | 31819263 | Nat Methods | 2020 Jan |
| Simultaneous orientation and 3D localization microscopy with a Vortex point spread function. | Hulleman CN, Thorsen RØ, Kim E, Dekker C, Stallinga S, Rieger B | Nature communications | 34635658 | Nat Commun | 2021 Oct 11 |
| Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. | Hammer M, Huisman M, Rigano A, Boehm U, Chambers JJ, Gaudreault N, North AJ, Pimentel JA, Sudar D, Bajcsy P, Brown CM, Corbett AD, Faklaris O, Lacoste J, Laude A, Nelson G, Nitschke R, Farzam F, Smith CS, Grunwald D, Strambio-De-Castillia C | Nature methods | 34862501 | Nat Methods | 2021 Dec |
| Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications. | Rigano A, Ehmsen S, Öztürk SU, Ryan J, Balashov A, Hammer M, Kirli K, Boehm U, Brown CM, Bellve K, Chambers JJ, Cosolo A, Coleman RA, Faklaris O, Fogarty KE, Guilbert T, Hamacher AB, Itano MS, Keeley DP, Kunis S, Lacoste J, Laude A, Ma WY, Marcello M, Montero-Llopis P, Nelson G, Nitschke R, Pimentel JA, Weidtkamp-Peters S, Park PJ, Alver BH, Grunwald D, Strambio-De-Castillia C | Nature methods | 34862503 | Nat Methods | 2021 Dec |
| Advanced 3D Analysis and Optimization of Single-Molecule FISH in Drosophila Muscle. | Noma A, Smith CS, Huisman M, Martin RM, Moore MJ, Grunwald D | Small methods | 32158910 | Small Methods | 2018 Sep 11 |
| MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text. | Ryan J, Pengo T, Rigano A, Llopis PM, Itano MS, Cameron LA, Marqués G, Strambio-De-Castillia C, Sanders MA, Brown CM | Nature methods | 34654919 | Nat Methods | 2021 Dec |
| QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. | Nelson G, Boehm U, Bagley S, Bajcsy P, Bischof J, Brown CM, Dauphin A, Dobbie IM, Eriksson JE, Faklaris O, Fernandez-Rodriguez J, Ferrand A, Gelman L, Gheisari A, Hartmann H, Kukat C, Laude A, Mitkovski M, Munck S, North AJ, Rasse TM, Resch-Genger U, Schuetz LC, Seitz A, Strambio-De-Castillia C, Swedlow JR, Alexopoulos I, Aumayr K, Avilov S, Bakker GJ, Bammann RR, Bassi A, Beckert H, Beer S, Belyaev Y, Bierwagen J, Birngruber KA, Bosch M, Breitlow J, Cameron LA, Chalfoun J, Chambers JJ, Chen CL, Conde-Sousa E, Corbett AD, Cordelieres FP, Nery ED, Dietzel R, Eismann F, Fazeli E, Felscher A, Fried H, Gaudreault N, Goh WI, Guilbert T, Hadleigh R, Hemmerich P, Holst GA, Itano MS, Jaffe CB, Jambor HK, Jarvis SC, Keppler A, Kirchenbuechler D, Kirchner M, Kobayashi N, Krens G, Kunis S, Lacoste J, Marcello M, Martins GG, Metcalf DJ, Mitchell CA, Moore J, Mueller T, Nelson MS, Ogg S, Onami S, Palmer AL, Paul-Gilloteaux P, Pimentel JA, Plantard L, Podder S, Rexhepaj E, Royon A, Saari MA, Schapman D, Schoonderwoert V, Schroth-Diez B, Schwartz S, Shaw M, Spitaler M, Stoeckl MT, Sudar D, Teillon J, Terjung S, Thuenauer R, Wilms CD, Wright GD, Nitschke R | Journal of microscopy | 34214188 | J Microsc | 2021 Oct |
| Impact of optical aberrations on axial position determination by photometry. | Thorsen RØ, Hulleman CN, Hammer M, Grünwald D, Stallinga S, Rieger B | Nature methods | 30504865 | Nat Methods | 2018 Dec |
| Cell cycle- and genomic distance-dependent dynamics of a discrete chromosomal region. | Ma H, Tu LC, Chung YC, Naseri A, Grunwald D, Zhang S, Pederson T | The Journal of cell biology | 30846483 | J Cell Biol | 2019 May 6 |
| CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging. | Ma H, Tu LC, Naseri A, Chung YC, Grunwald D, Zhang S, Pederson T | Nature methods | 30377374 | Nat Methods | 2018 Nov |
| Deconstructing transport-distribution reconstruction in the nuclear-pore complex. | Tu LC, Huisman M, Chung YC, Smith CS, Grunwald D | Nature structural & molecular biology | 30518848 | Nat Struct Mol Biol | 2018 Dec |
| CRISPR-Cas9 nuclear dynamics and target recognition in living cells. | Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T | The Journal of cell biology | 27551060 | J Cell Biol | 2016 Aug 29 |
| Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. | Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T | Nature biotechnology | 27088723 | Nat Biotechnol | 2016 May |
| Fluorescence Polarization Control for On-Off Switching of Single Molecules at Cryogenic Temperatures. | Hulleman CN, Huisman M, Moerland RJ, Grünwald D, Stallinga S, Rieger B | Small methods | 31240238 | Small Methods | 2018 Sep 11 |
| Live-Cell Imaging of mRNP-NPC Interactions in Budding Yeast. | Lari A, Farzam F, Bensidoun P, Oeffinger M, Zenklusen D, Grunwald D, Montpetit B | Methods in molecular biology (Clifton, N.J.) | 31407282 | Methods Mol Biol | 2019 |
| ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. | Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, Satpathy AT, Carter AC, Ghosh RP, East-Seletsky A, Doudna JA, Greenleaf WJ, Liphardt JT, Chang HY | Nature methods | 27749837 | Nat Methods | 2016 Dec |
| 3D single-molecule super-resolution microscopy with a tilted light sheet. | Gustavsson AK, Petrov PN, Lee MY, Shechtman Y, Moerner WE | Nature communications | 29317629 | Nat Commun | 2018 Jan 9 |
| Concerted localization-resets precede YAP-dependent transcription. | Franklin JM, Ghosh RP, Shi Q, Reddick MP, Liphardt JT | Nature communications | 32917893 | Nat Commun | 2020 Sep 11 |
| NuSeT: A deep learning tool for reliably separating and analyzing crowded cells. | Yang L, Ghosh RP, Franklin JM, Chen S, You C, Narayan RR, Melcher ML, Liphardt JT | PLoS computational biology | 32925919 | PLoS Comput Biol | 2020 Sep |
| Fast and parallel nanoscale three-dimensional tracking of heterogeneous mammalian chromatin dynamics. | Gustavsson AK, Ghosh RP, Petrov PN, Liphardt JT, Moerner WE | Molecular biology of the cell | 35352962 | Mol Biol Cell | 2022 May 15 |
| Tilted Light Sheet Microscopy with 3D Point Spread Functions for Single-Molecule Super-Resolution Imaging in Mammalian Cells. | Gustavsson AK, Petrov PN, Lee MY, Shechtman Y, Moerner WE | Proceedings of SPIE--the International Society for Optical Engineering | 29681676 | Proc SPIE Int Soc Opt Eng | 2018 Feb |
| Quantitative Super-Resolution Microscopy of the Mammalian Glycocalyx. | Möckl L, Pedram K, Roy AR, Krishnan V, Gustavsson AK, Dorigo O, Bertozzi CR, Moerner WE | Developmental cell | 31105009 | Dev Cell | 2019 Jul 1 |
| Light sheet approaches for improved precision in 3D localization-based super-resolution imaging in mammalian cells [Invited]. | Gustavsson AK, Petrov PN, Moerner WE | Optics express | 29801343 | Opt Express | 2018 May 14 |
| Observation of live chromatin dynamics in cells via 3D localization microscopy using Tetrapod point spread functions. | Shechtman Y, Gustavsson AK, Petrov PN, Dultz E, Lee MY, Weis K, Moerner WE | Biomedical optics express | 29296501 | Biomed Opt Express | 2017 Dec 1 |
| Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments. | Chen Z, Shaw A, Wilson H, Woringer M, Darzacq X, Marqusee S, Wang Q, Bustamante C | Proceedings of the National Academy of Sciences of the United States of America | 32817484 | Proc Natl Acad Sci U S A | 2020 Sep 1 |
| Performing Quantitative Imaging Acquisition, Analysis and Visualization Using the Best of Open Source and Commercial Software Solutions. | Shenoy SM | Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada | 27516727 | Microsc Microanal | 2016 Jul |
| Bidirectional Analysis of Cryba4-Crybb1 Nascent Transcription and Nuclear Accumulation of Crybb3 mRNAs in Lens Fibers. | Limi S, Zhao Y, Guo P, Lopez-Jones M, Zheng D, Singer RH, Skoultchi AI, Cvekl A | Investigative ophthalmology & visual science | 30646012 | Invest Ophthalmol Vis Sci | 2019 Jan 2 |
| Protein motion in the nucleus: from anomalous diffusion to weak interactions. | Woringer M, Darzacq X | Biochemical Society transactions | 30065106 | Biochem Soc Trans | 2018 Aug 20 |
| Rational Design of Fluorogenic and Spontaneously Blinking Labels for Super-Resolution Imaging. | Zheng Q, Ayala AX, Chung I, Weigel AV, Ranjan A, Falco N, Grimm JB, Tkachuk AN, Wu C, Lippincott-Schwartz J, Singer RH, Lavis LD | ACS central science | 31572787 | ACS Cent Sci | 2019 Sep 25 |
| p53 Dynamically Directs TFIID Assembly on Target Gene Promoters. | Coleman RA, Qiao Z, Singh SK, Peng CS, Cianfrocco M, Zhang Z, Piasecka A, Aldeborgh H, Basishvili G, Liu WL | Molecular and cellular biology | 28416636 | Mol Cell Biol | 2017 Jul 1 |
| A new era of studying p53-mediated transcription activation. | Liu WL, Coleman RA, Singh SK | Transcription | 28795863 | Transcription | 2018 |
| Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9. | Qin P, Parlak M, Kuscu C, Bandaria J, Mir M, Szlachta K, Singh R, Darzacq X, Yildiz A, Adli M | Nature communications | 28290446 | Nat Commun | 2017 Mar 14 |
| Nuclear microenvironments modulate transcription from low-affinity enhancers. | Tsai A, Muthusamy AK, Alves MR, Lavis LD, Singer RH, Stern DL, Crocker J | eLife | 29095143 | Elife | 2017 Nov 2 |
| Dual inhibition of MDMX and MDM2 as a therapeutic strategy in leukemia. | Carvajal LA, Neriah DB, Senecal A, Benard L, Thiruthuvanathan V, Yatsenko T, Narayanagari SR, Wheat JC, Todorova TI, Mitchell K, Kenworthy C, Guerlavais V, Annis DA, Bartholdy B, Will B, Anampa JD, Mantzaris I, Aivado M, Singer RH, Coleman RA, Verma A, Steidl U | Science translational medicine | 29643228 | Sci Transl Med | 2018 Apr 11 |
| Transcriptional burst fraction and size dynamics during lens fiber cell differentiation and detailed insights into the denucleation process. | Limi S, Senecal A, Coleman R, Lopez-Jones M, Guo P, Polumbo C, Singer RH, Skoultchi AI, Cvekl A | The Journal of biological chemistry | 29959226 | J Biol Chem | 2018 Aug 24 |
| Transvection Goes Live-Visualizing Enhancer-Promoter Communication between Chromosomes. | Tsai A, Singer RH, Crocker J | Molecular cell | 29677489 | Mol Cell | 2018 Apr 19 |
| Imaging Transcription: Past, Present, and Future. | Coleman RA, Liu Z, Darzacq X, Tjian R, Singer RH, Lionnet T | Cold Spring Harbor symposia on quantitative biology | 26763984 | Cold Spring Harb Symp Quant Biol | 2015 |
| A dynamic mode of mitotic bookmarking by transcription factors. | Teves SS, An L, Hansen AS, Xie L, Darzacq X, Tjian R | eLife | 27855781 | Elife | 2016 Nov 19 |
| Biological Insight from Super-Resolution Microscopy: What We Can Learn from Localization-Based Images. | Baddeley D, Bewersdorf J | Annual review of biochemistry | 29272143 | Annu Rev Biochem | 2018 Jun 20 |
| PYMEVisualize: an open-source tool for exploring 3D super-resolution data. | Marin Z, Graff M, Barentine AES, Soeller C, Chung KKH, Fuentes LA, Baddeley D | Nature methods | 34002092 | Nat Methods | 2021 Jun |
| Chemically activatable viral capsid functionalized for cancer targeting. | Chen CC, Xing L, Stark M, Ou T, Holla P, Xiao K, Kamita SG, Hammock BD, Lam K, Cheng RH | Nanomedicine (London, England) | 26786134 | Nanomedicine (Lond) | 2016 Feb |
| Development of (68)Ga-Labeled Hepatitis E Virus Nanoparticles for Targeted Drug Delivery and Diagnostics with PET. | Lambidis E, Chen CC, Baikoghli M, Imlimthan S, Khng YC, Sarparanta M, Cheng RH, Airaksinen AJ | Molecular pharmaceutics | 35857429 | Mol Pharm | 2022 Aug 1 |
| Determining of canine position by multiple facial landmarks to achieve natural esthetics in complete denture treatment. | Srimaneekarn N, Arayapisit T, Pooktuantong O, Cheng HR, Soonsawad P | The Journal of prosthetic dentistry | 33468316 | J Prosthet Dent | 2022 Jun |
| Nanodelivery of a functional membrane receptor to manipulate cellular phenotype. | Patriarchi T, Shen A, He W, Baikoghli M, Cheng RH, Xiang YK, Coleman MA, Tian L | Scientific reports | 29476125 | Sci Rep | 2018 Feb 23 |
| Surface Functionalization of Hepatitis E Virus Nanoparticles Using Chemical Conjugation Methods. | Chen CC, Stark M, Baikoghli M, Cheng RH | Journal of visualized experiments : JoVE | 29806824 | J Vis Exp | 2018 May 11 |
| Structural characterization of site-modified nanocapsid with monodispersed gold clusters. | Stark MC, Baikoghli MA, Lahtinen T, Malola S, Xing L, Nguyen M, Nguyen M, Sikaroudi A, Marjomäki V, Häkkinen H, Cheng RH | Scientific reports | 29213060 | Sci Rep | 2017 Dec 6 |
| Synthesis and ex vivo biodistribution of two (68)Ga-labeled tetrazine tracers: Comparison of pharmacokinetics. | Lambidis E, Lumén D, Koskipahta E, Imlimthan S, Lopez BB, Sánchez AIF, Sarparanta M, Cheng RH, Airaksinen AJ | Nuclear medicine and biology | 35680503 | Nucl Med Biol | 2022 Nov-Dec |
| Combinatorial chemistry in drug discovery. | Liu R, Li X, Lam KS | Current opinion in chemical biology | 28494316 | Curr Opin Chem Biol | 2017 Jun |
| Toxicologic Concerns with Current Medical Nanoparticles. | Cheng TM, Chu HY, Huang HM, Li ZL, Chen CY, Shih YJ, Whang-Peng J, Cheng RH, Mo JK, Lin HY, Wang K | International journal of molecular sciences | 35886945 | Int J Mol Sci | 2022 Jul 8 |
| Surface modulatable nanocapsids for targeting and tracking toward nanotheranostic delivery. | Stark M, Cheng RH | Pharmaceutical patent analyst | 27610752 | Pharm Pat Anal | 2016 Sep |
| ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy. | Barton C, Morganella S, Ødegård-Fougner Ø, Alexander S, Ries J, Fitzgerald T, Ellenberg J, Birney E | PLoS computational biology | 29522506 | PLoS Comput Biol | 2018 Mar |
| Photoactivation of silicon rhodamines via a light-induced protonation. | Frei MS, Hoess P, Lampe M, Nijmeijer B, Kueblbeck M, Ellenberg J, Wadepohl H, Ries J, Pitsch S, Reymond L, Johnsson K | Nature communications | 31594948 | Nat Commun | 2019 Oct 8 |
| Generation and validation of homozygous fluorescent knock-in cells using CRISPR-Cas9 genome editing. | Koch B, Nijmeijer B, Kueblbeck M, Cai Y, Walther N, Ellenberg J | Nature protocols | 29844520 | Nat Protoc | 2018 Jun |
| Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells. | Popovic D, Koch B, Kueblbeck M, Ellenberg J, Pelkmans L | Cell systems | 30342881 | Cell Syst | 2018 Oct 24 |
| Experimental and computational framework for a dynamic protein atlas of human cell division. | Cai Y, Hossain MJ, Hériché JK, Politi AZ, Walther N, Koch B, Wachsmuth M, Nijmeijer B, Kueblbeck M, Martinic-Kavur M, Ladurner R, Alexander S, Peters JM, Ellenberg J | Nature | 30202089 | Nature | 2018 Sep |
| Maximum-likelihood model fitting for quantitative analysis of SMLM data. | Wu YL, Hoess P, Tschanz A, Matti U, Mund M, Ries J | Nature methods | 36522500 | Nat Methods | 2023 Jan |
| EMU: reconfigurable graphical user interfaces for Micro-Manager. | Deschamps J, Ries J | BMC bioinformatics | 33059591 | BMC Bioinformatics | 2020 Oct 15 |
| Real-Time Imaging of a Single Gene Reveals Transcription-Initiated Local Confinement. | Germier T, Kocanova S, Walther N, Bancaud A, Shaban HA, Sellou H, Politi AZ, Ellenberg J, Gallardo F, Bystricky K | Biophysical journal | 28978433 | Biophys J | 2017 Oct 3 |
| Correlative live and super-resolution imaging reveals the dynamic structure of replication domains. | Xiang W, Roberti MJ, Hériché JK, Huet S, Alexander S, Ellenberg J | The Journal of cell biology | 29572382 | J Cell Biol | 2018 Jun 4 |
| Correction: Correlative live and super-resolution imaging reveals the dynamic structure of replication domains. | Xiang W, Roberti MJ, Hériché JK, Huet S, Alexander S, Ellenberg J | The Journal of cell biology | 30135095 | J Cell Biol | 2018 Sep 3 |
| A quantitative map of human Condensins provides new insights into mitotic chromosome architecture. | Walther N, Hossain MJ, Politi AZ, Koch B, Kueblbeck M, Ødegård-Fougner Ø, Lampe M, Ellenberg J | The Journal of cell biology | 29632028 | J Cell Biol | 2018 Jul 2 |
| Direct Visualization of Single Nuclear Pore Complex Proteins Using Genetically-Encoded Probes for DNA-PAINT. | Schlichthaerle T, Strauss MT, Schueder F, Auer A, Nijmeijer B, Kueblbeck M, Jimenez Sabinina V, Thevathasan JV, Ries J, Ellenberg J, Jungmann R | Angewandte Chemie (International ed. in English) | 31314157 | Angew Chem Int Ed Engl | 2019 Sep 9 |
| Global fitting for high-accuracy multi-channel single-molecule localization. | Li Y, Shi W, Liu S, Cavka I, Wu YL, Matti U, Wu D, Koehler S, Ries J | Nature communications | 35668089 | Nat Commun | 2022 Jun 6 |
| Quantitative imaging of loop extruders rebuilding interphase genome architecture after mitosis. | Brunner A, Morero NR, Zhang W, Hossain MJ, Lampe M, Pflaumer H, Halavatyi A, Peters JM, Beckwith KS, Ellenberg J | bioRxiv : the preprint server for biology | 38854067 | bioRxiv | 2024 May 30 |
| Chemogenetic Control of Nanobodies. | Farrants H, Tarnawski M, Müller TG, Otsuka S, Hiblot J, Koch B, Kueblbeck M, Kräusslich HG, Ellenberg J, Johnsson K | Nature methods | 32066961 | Nat Methods | 2020 Mar |
| Nuclear pores as versatile reference standards for quantitative superresolution microscopy. | Thevathasan JV, Kahnwald M, Cieśliński K, Hoess P, Peneti SK, Reitberger M, Heid D, Kasuba KC, Hoerner SJ, Li Y, Wu YL, Mund M, Matti U, Pereira PM, Henriques R, Nijmeijer B, Kueblbeck M, Sabinina VJ, Ellenberg J, Ries J | Nature methods | 31562488 | Nat Methods | 2019 Oct |
| Cost-efficient open source laser engine for microscopy. | Schröder D, Deschamps J, Dasgupta A, Matti U, Ries J | Biomedical optics express | 32206389 | Biomed Opt Express | 2020 Feb 1 |
| Deep learning enables fast and dense single-molecule localization with high accuracy. | Speiser A, Müller LR, Hoess P, Matti U, Obara CJ, Legant WR, Kreshuk A, Macke JH, Ries J, Turaga SC | Nature methods | 34480155 | Nat Methods | 2021 Sep |
| Direct supercritical angle localization microscopy for nanometer 3D superresolution. | Dasgupta A, Deschamps J, Matti U, Hübner U, Becker J, Strauss S, Jungmann R, Heintzmann R, Ries J | Nature communications | 33608524 | Nat Commun | 2021 Feb 19 |
| Quantitative mapping of fluorescently tagged cellular proteins using FCS-calibrated four-dimensional imaging. | Politi AZ, Cai Y, Walther N, Hossain MJ, Koch B, Wachsmuth M, Ellenberg J | Nature protocols | 29844523 | Nat Protoc | 2018 Jun |
| Optimizing imaging speed and excitation intensity for single-molecule localization microscopy. | Diekmann R, Kahnwald M, Schoenit A, Deschamps J, Matti U, Ries J | Nature methods | 32807954 | Nat Methods | 2020 Sep |
| Three-dimensional superresolution fluorescence microscopy maps the variable molecular architecture of the nuclear pore complex. | Sabinina VJ, Hossain MJ, Hériché JK, Hoess P, Nijmeijer B, Mosalaganti S, Kueblbeck M, Callegari A, Szymborska A, Beck M, Ries J, Ellenberg J | Molecular biology of the cell | 34191541 | Mol Biol Cell | 2021 Aug 15 |
| Photon-free (s)CMOS camera characterization for artifact reduction in high- and super-resolution microscopy. | Diekmann R, Deschamps J, Li Y, Deguchi T, Tschanz A, Kahnwald M, Matti U, Ries J | Nature communications | 35690614 | Nat Commun | 2022 Jun 11 |
| Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency. | Pękowska A, Klaus B, Xiang W, Severino J, Daigle N, Klein FA, Oleś M, Casellas R, Ellenberg J, Steinmetz LM, Bertone P, Huber W | Cell systems | 30414923 | Cell Syst | 2018 Nov 28 |
| Real-time 3D single-molecule localization using experimental point spread functions. | Li Y, Mund M, Hoess P, Deschamps J, Matti U, Nijmeijer B, Sabinina VJ, Ellenberg J, Schoen I, Ries J | Nature methods | 29630062 | Nat Methods | 2018 May |
| Quantitative live and super-resolution microscopy of mitotic chromosomes. | Walther N, Ellenberg J | Methods in cell biology | 29957216 | Methods Cell Biol | 2018 |
| Absolute quantification of cohesin, CTCF and their regulators in human cells. | Holzmann J, Politi AZ, Nagasaka K, Hantsche-Grininger M, Walther N, Koch B, Fuchs J, Dürnberger G, Tang W, Ladurner R, Stocsits RR, Busslinger GA, Novák B, Mechtler K, Davidson IF, Ellenberg J, Peters JM | eLife | 31204999 | Elife | 2019 Jun 17 |
| Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. | Wutz G, Várnai C, Nagasaka K, Cisneros DA, Stocsits RR, Tang W, Schoenfelder S, Jessberger G, Muhar M, Hossain MJ, Walther N, Koch B, Kueblbeck M, Ellenberg J, Zuber J, Fraser P, Peters JM | The EMBO journal | 29217591 | EMBO J | 2017 Dec 15 |
| Implementation of a 4Pi-SMS super-resolution microscope. | Wang J, Allgeyer ES, Sirinakis G, Zhang Y, Hu K, Lessard MD, Li Y, Diekmann R, Phillips MA, Dobbie IM, Ries J, Booth MJ, Bewersdorf J | Nature protocols | 33328610 | Nat Protoc | 2021 Feb |
| Publisher Correction: Deep learning enables fast and dense single-molecule localization with high accuracy. | Speiser A, Müller LR, Hoess P, Matti U, Obara CJ, Legant WR, Kreshuk A, Macke JH, Ries J, Turaga SC | Nature methods | 34548656 | Nat Methods | 2021 Nov |
| Nanoscale 3D DNA tracing reveals the mechanism of self-organization of mitotic chromosomes. | Beckwith KS, Brunner A, Morero NR, Jungmann R, Ellenberg J | bioRxiv : the preprint server for biology | 39554202 | bioRxiv | 2024 Oct 29 |
| HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. | Sahin M, Wong W, Zhan Y, Van Deynze K, Koche R, Leslie CS | Nature communications | 34099725 | Nat Commun | 2021 Jun 7 |
| Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression. | Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E | bioRxiv : the preprint server for biology | 37577543 | bioRxiv | 2023 Jul 19 |
| CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant. | Kaplan SJ, Wong W, Yan J, Pulecio J, Cho HS, Li Q, Zhao J, Leslie-Iyer J, Kazakov J, Murphy D, Luo R, Dey KK, Apostolou E, Leslie CS, Huangfu D | Cell reports | 39163202 | Cell Rep | 2024 Aug 27 |
| Epigenome rewiring in human pluripotent stem cells. | Yan J, Huangfu D | Trends in cell biology | 34955367 | Trends Cell Biol | 2022 Mar |
| 3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles. | Uyehara CM, Apostolou E | Cell reports | 37059094 | Cell Rep | 2023 Apr 25 |
| ChromaFold predicts the 3D contact map from single-cell chromatin accessibility. | Gao VR, Yang R, Das A, Luo R, Luo H, McNally DR, Karagiannidis I, Rivas MA, Wang ZM, Barisic D, Karbalayghareh A, Wong W, Zhan YA, Chin CR, Noble WS, Bilmes JA, Apostolou E, Kharas MG, Béguelin W, Viny AD, Huangfu D, Rudensky AY, Melnick AM, Leslie CS | Nature communications | 39487131 | Nat Commun | 2024 Nov 1 |
| Assessing Specific Networks of Chromatin Interactions with HiChIP. | Di Giammartino DC, Polyzos A, Apostolou E | Methods in molecular biology (Clifton, N.J.) | 35867248 | Methods Mol Biol | 2022 |
| Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions. | Luo R, Yan J, Oh JW, Xi W, Shigaki D, Wong W, Cho HS, Murphy D, Cutler R, Rosen BP, Pulecio J, Yang D, Glenn RA, Chen T, Li QV, Vierbuchen T, Sidoli S, Apostolou E, Huangfu D, Beer MA | Nature genetics | 37488417 | Nat Genet | 2023 Aug |
| Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies. | Scourzic L, Salataj E, Apostolou E | Frontiers in immunology | 34054841 | Front Immunol | 2021 |
| Chromatin interaction-aware gene regulatory modeling with graph attention networks. | Karbalayghareh A, Sahin M, Leslie CS | Genome research | 35396274 | Genome Res | 2022 May |
| ChromaFold predicts the 3D contact map from single-cell chromatin accessibility. | Gao VR, Yang R, Das A, Luo R, Luo H, McNally DR, Karagiannidis I, Rivas MA, Wang ZM, Barisic D, Karbalayghareh A, Wong W, Zhan YA, Chin CR, Noble W, Bilmes JA, Apostolou E, Kharas MG, Béguelin W, Viny AD, Huangfu D, Rudensky AY, Melnick AM, Leslie CS | bioRxiv : the preprint server for biology | 37546906 | bioRxiv | 2023 Jul 28 |
| 3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages. | Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E | Nature structural & molecular biology | 38053013 | Nat Struct Mol Biol | 2024 Jan |
| Genome oligopaint via local denaturation fluorescence in situ hybridization. | Wang Y, Cottle WT, Wang H, Feng XA, Mallon J, Gavrilov M, Bailey S, Ha T | Molecular cell | 33657402 | Mol Cell | 2021 Apr 1 |
| Mapping cellular responses to DNA double-strand breaks using CRISPR technologies. | Liu Y, Cottle WT, Ha T | Trends in genetics : TIG | 36967246 | Trends Genet | 2023 Jul |
| SIKs Regulate HDAC7 Stabilization and Cytokine Recall in Late-Stage T Cell Effector Differentiation. | Helms RS, Marin-Gonzalez A, Patel CH, Sun IH, Wen J, Leone RD, Duvall B, Gao RD, Ha T, Tsukamoto T, Slusher BS, Pomerantz JL, Powell JD | Journal of immunology (Baltimore, Md. : 1950) | 37947442 | J Immunol | 2023 Dec 15 |
| Cohesin drives chromatin scanning during the RAD51-mediated homology search. | Marin-Gonzalez A, Rybczynski AT, Nilavar NM, Nguyen D, Karwacki-Neisius V, Li AG, Zou RS, Avilés-Vázquez FJ, Kanemaki MT, Scully R, Ha T | bioRxiv : the preprint server for biology | 39990468 | bioRxiv | 2025 Feb 11 |
| GAGA-associated factor fosters loop formation in the Drosophila genome. | Li X, Tang X, Bing X, Catalano C, Li T, Dolsten G, Wu C, Levine M | Molecular cell | 37003261 | Mol Cell | 2023 May 4 |
| Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq. | Zou RS, Liu Y, Gaido OER, Konig MF, Mog BJ, Shen LL, Aviles-Vazquez F, Marin-Gonzalez A, Ha T | Nature methods | 37024653 | Nat Methods | 2023 May |
| Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization. | Sang M, Johnson ME | bioRxiv : the preprint server for biology | 40027831 | bioRxiv | 2025 Feb 23 |
| Light activation and deactivation of Cas9 for DNA repair studies. | Zou RS, Ha T | Methods in enzymology | 34776214 | Methods Enzymol | 2021 |
| Cas9 deactivation with photocleavable guide RNAs. | Zou RS, Liu Y, Wu B, Ha T | Molecular cell | 33662274 | Mol Cell | 2021 Apr 1 |
| Kinetic principles underlying pioneer function of GAGA transcription factor in live cells. | Tang X, Li T, Liu S, Wisniewski J, Zheng Q, Rong Y, Lavis LD, Wu C | Nature structural & molecular biology | 35835866 | Nat Struct Mol Biol | 2022 Jul |
| Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice. | Deshpande RA, Marin-Gonzalez A, Barnes HK, Woolley PR, Ha T, Paull TT | Nature communications | 37717054 | Nat Commun | 2023 Sep 16 |
| Electrostatic encoding of genome organization principles within single native nucleosomes. | Park S, Athreya A, Carrizo GE, Benning NA, Mitchener MM, Bhanu NV, Garcia BA, Zhang B, Muir TW, Pearce EL, Ha T | bioRxiv : the preprint server for biology | 38106048 | bioRxiv | 2023 Dec 9 |
| Latent space of a small genetic network: Geometry of dynamics and information. | Seyboldt R, Lavoie J, Henry A, Vanaret J, Petkova MD, Gregor T, François P | Proceedings of the National Academy of Sciences of the United States of America | 35737842 | Proc Natl Acad Sci U S A | 2022 Jun 28 |
| Efficient prime editing in two-cell mouse embryos using PEmbryo. | Kim-Yip RP, McNulty R, Joyce B, Mollica A, Chen PJ, Ravisankar P, Law BK, Liu DR, Toettcher JE, Ivakine EA, Posfai E, Adamson B | Nature biotechnology | 38321114 | Nat Biotechnol | 2024 Dec |
| Transcription factor clusters as information transfer agents. | Munshi R, Ling J, Ryabichko S, Wieschaus E, Gregor T | ArXiv | 38495568 | ArXiv | 2024 Nov 6 |
| Chromosome structure in Drosophila is determined by boundary pairing not loop extrusion. | Bing X, Ke W, Fujioka M, Kurbidaeva A, Levitt S, Levine M, Schedl P, Jaynes JB | eLife | 39110499 | Elife | 2024 Aug 7 |
| Recording morphogen signals reveals mechanisms underlying gastruloid symmetry breaking. | McNamara HM, Solley SC, Adamson B, Chan MM, Toettcher JE | Nature cell biology | 39358450 | Nat Cell Biol | 2024 Nov |
| Gene activity fully predicts transcriptional bursting dynamics. | Chen PT, Levo M, Zoller B, Gregor T | ArXiv | 37131882 | ArXiv | 2024 Jun 28 |
| Eukaryotic gene regulation at equilibrium, or non? | Zoller B, Gregor T, Tkačik G | Current opinion in systems biology | 36590072 | Curr Opin Syst Biol | 2022 Sep |
| What are tethering elements? | Li X, Levine M | Current opinion in genetics & development | 38237456 | Curr Opin Genet Dev | 2024 Feb |
| Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag. | Brumbaugh-Reed EH, Gao Y, Aoki K, Toettcher JE | Nature communications | 39112465 | Nat Commun | 2024 Aug 7 |
| Transcription factor clusters as information transfer agents. | Munshi R, Ling J, Ryabichko S, Wieschaus EF, Gregor T | Science advances | 39742495 | Sci Adv | 2025 Jan 3 |
| Deriving a genetic regulatory network from an optimization principle. | Sokolowski TR, Gregor T, Bialek W, Tkačik G | Proceedings of the National Academy of Sciences of the United States of America | 39752518 | Proc Natl Acad Sci U S A | 2025 Jan 7 |
| Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulation. | Singh AP, Wu P, Ryabichko S, Raimundo J, Swan M, Wieschaus E, Gregor T, Toettcher JE | Cell reports | 35320726 | Cell Rep | 2022 Mar 22 |
| Synthetic developmental biology: New tools to deconstruct and rebuild developmental systems. | McNamara HM, Ramm B, Toettcher JE | Seminars in cell & developmental biology | 35484026 | Semin Cell Dev Biol | 2023 May 30 |
| Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. | Brückner DB, Chen H, Barinov L, Zoller B, Gregor T | bioRxiv : the preprint server for biology | 36711618 | bioRxiv | 2023 Feb 13 |
| Recording morphogen signals reveals origins of gastruloid symmetry breaking. | McNamara HM, Solley SC, Adamson B, Chan MM, Toettcher JE | bioRxiv : the preprint server for biology | 37333235 | bioRxiv | 2023 Jun 5 |
| Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies. | Voortman L, Anderson C, Urban E, Yuan L, Tran S, Neuhaus-Follini A, Derrick J, Gregor T, Johnston RJ Jr | Developmental cell | 35835116 | Dev Cell | 2022 Aug 8 |
| Control of gastruloid patterning and morphogenesis by the Erk and Akt signaling pathways. | Underhill EJ, Toettcher JE | Development (Cambridge, England) | 37590131 | Development | 2023 Aug 15 |
| Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo. | Ho EK, Oatman HR, McFann SE, Yang L, Johnson HE, Shvartsman SY, Toettcher JE | Development (Cambridge, England) | 37602510 | Development | 2023 Sep 1 |
| Efficient Genome Editing with Chimeric Oligonucleotide-Directed Editing. | Nguyen LT, Rakestraw NR, Pizzano BLM, Young CB, Huang Y, Beerensson KT, Fang A, Antal SG, Anamisis KV, Peggs CMD, Yan J, Jing Y, Burdine RD, Adamson B, Toettcher JE, Myhrvold C, Jain PK | bioRxiv : the preprint server for biology | 39026836 | bioRxiv | 2024 Jul 10 |
| Light-switchable transcription factors obtained by direct screening in mammalian cells. | Zhu L, McNamara HM, Toettcher JE | Nature communications | 37268649 | Nat Commun | 2023 Jun 2 |
| Chromosome-level organization of the regulatory genome in the Drosophila nervous system. | Mohana G, Dorier J, Li X, Mouginot M, Smith RC, Malek H, Leleu M, Rodriguez D, Khadka J, Rosa P, Cousin P, Iseli C, Restrepo S, Guex N, McCabe BD, Jankowski A, Levine MS, Gambetta MC | Cell | 37536338 | Cell | 2023 Aug 31 |
| Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. | Brückner DB, Chen H, Barinov L, Zoller B, Gregor T | Science (New York, N.Y.) | 37384691 | Science | 2023 Jun 30 |
| Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo. | Ho EK, Oatman HR, McFann SE, Yang L, Johnson HE, Shvartsman SY, Toettcher JE | bioRxiv : the preprint server for biology | 36945584 | bioRxiv | 2023 Mar 10 |
| Functional analysis of the Drosophila eve locus in response to non-canonical combinations of gap gene expression levels. | Haroush N, Levo M, Wieschaus EF, Gregor T | Developmental cell | 37890488 | Dev Cell | 2023 Dec 4 |
| Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag. | Brumbaugh-Reed EH, Aoki K, Toettcher JE | bioRxiv : the preprint server for biology | 38293146 | bioRxiv | 2024 Jan 17 |
| In vivo measurements of receptor tyrosine kinase activity reveal feedback regulation of a developmental gradient. | Ho EK, Kim-Yip RP, Simpkins AG, Farahani PE, Oatman HR, Posfai E, Shvartsman SY, Toettcher JE | bioRxiv : the preprint server for biology | 39829924 | bioRxiv | 2025 Jan 7 |
| Utilizing flow cytometry sorting signal width to enrich for cells positive to endogenous gene integration of fluorescent proteins. | Faber GP, Hauschner H, Atrash MK, Bilinsky L, Shav-Tal Y | Cytometry. Part A : the journal of the International Society for Analytical Cytology | 37158244 | Cytometry A | 2023 Aug |
| Photonic lantern TIRF microscopy for highly efficient, uniform, artifact-free imaging. | Husain A, Yerolatsitis S, Amezcua Correa R, Han KY | Optics express | 39573578 | Opt Express | 2024 Oct 7 |
| Deep learning enables fast, gentle STED microscopy. | Ebrahimi V, Stephan T, Kim J, Carravilla P, Eggeling C, Jakobs S, Han KY | bioRxiv : the preprint server for biology | 36747618 | bioRxiv | 2023 Jan 27 |
| Nuclear speckles - a driving force in gene expression. | Faber GP, Nadav-Eliyahu S, Shav-Tal Y | Journal of cell science | 35788677 | J Cell Sci | 2022 Jul 1 |
| The Association of MEG3 lncRNA with Nuclear Speckles in Living Cells. | Hasenson SE, Alkalay E, Atrash MK, Boocholez A, Gershbaum J, Hochberg-Laufer H, Shav-Tal Y | Cells | 35741072 | Cells | 2022 Jun 16 |
| HLH-30/TFEB rewires the chaperone network to promote proteostasis under conditions of Coenzyme A and Iron-Sulfur Cluster Deficiency. | Shalash R, Levi-Ferber M, von Chrzanowski H, Atrash MK, Shav-Tal Y, Henis-Korenblit S | bioRxiv : the preprint server for biology | 38895373 | bioRxiv | 2024 Jun 6 |
| Deep learning enables fast, gentle STED microscopy. | Ebrahimi V, Stephan T, Kim J, Carravilla P, Eggeling C, Jakobs S, Han KY | Communications biology | 37369761 | Commun Biol | 2023 Jun 27 |
| Versatile Labeling and Detection of Endogenous Proteins Using Tag-Assisted Split Enzyme Complementation. | Makhija S, Brown D, Rudlaff RM, Doh JK, Bourke S, Wang Y, Zhou S, Cheloor-Kovilakam R, Huang B | ACS chemical biology | 33734687 | ACS Chem Biol | 2021 Apr 16 |
| Understanding Regulatory Mechanisms of Brain Function and Disease through 3D Genome Organization. | Liu W, Zhong W, Chen J, Huang B, Hu M, Li Y | Genes | 35456393 | Genes (Basel) | 2022 Mar 25 |
| Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler. | Abdulhay NJ, Hsieh LJ, McNally CP, Ostrowski MS, Moore CM, Ketavarapu M, Kasinathan S, Nanda AS, Wu K, Chio US, Zhou Z, Goodarzi H, Narlikar GJ, Ramani V | Nature structural & molecular biology | 37696956 | Nat Struct Mol Biol | 2023 Oct |
| YAP charge patterning mediates signal integration through transcriptional co-condensates. | Meyer K, Yserentant K, Cheloor-Kovilakam R, Ruff KM, Chung CI, Shu X, Huang B, Weiner OD | bioRxiv : the preprint server for biology | 39149273 | bioRxiv | 2024 Aug 10 |
| MYC phase separation selectively modulates the transcriptome. | Yang J, Chung CI, Koach J, Liu H, Navalkar A, He H, Ma Z, Zhao Q, Yang X, He L, Mittag T, Shen Y, Weiss WA, Shu X | Nature structural & molecular biology | 38811792 | Nat Struct Mol Biol | 2024 Oct |
| ATP-dependent remodeling of chromatin condensates uncovers distinct mesoscale effects of two remodelers. | Moore C, Wong E, Kaur U, Chio US, Zhou Z, Ostrowski M, Wu K, Irkliyenko I, Wang S, Ramani V, Narlikar GJ | bioRxiv : the preprint server for biology | 39314305 | bioRxiv | 2024 Sep 10 |
| HMGB1 restores a dynamic chromatin environment in the presence of linker histone by deforming nucleosomal DNA. | Saunders HS, Chio US, Moore CM, Ramani V, Cheng Y, Narlikar GJ | bioRxiv : the preprint server for biology | 39229246 | bioRxiv | 2024 Aug 24 |
| HybriSeq: Probe-based Device-free Single-cell RNA Profiling. | Foyt D, Brown D, Zhou S, Huang B | bioRxiv : the preprint server for biology | 37808850 | bioRxiv | 2024 Sep 18 |
| Chemogenetic Minitool for Dissecting the Roles of Protein Phase Separation. | Chung CI, Yang J, Shu X | ACS central science | 37521779 | ACS Cent Sci | 2023 Jul 26 |
| Phase separation of YAP-MAML2 differentially regulates the transcriptome. | Chung CI, Yang J, Yang X, Liu H, Ma Z, Szulzewsky F, Holland EC, Shen Y, Shu X | Proceedings of the National Academy of Sciences of the United States of America | 38315854 | Proc Natl Acad Sci U S A | 2024 Feb 13 |
| Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers. | Yang MG, Richter HJ, Wang S, McNally CP, Harris N, Dhillon S, Maresca M, de Wit E, Willenbring H, Maher J, Goodarzi H, Ramani V | bioRxiv : the preprint server for biology | 39896524 | bioRxiv | 2025 Jan 22 |
| SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress. | Wolin E, Guo JK, Blanco MR, Perez AA, Goronzy IN, Abdou AA, Gorhe D, Guttman M, Jovanovic M | bioRxiv : the preprint server for biology | 37333139 | bioRxiv | 2023 Jun 7 |
| Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo. | Guo JK, Blanco MR, Walkup WG 4th, Bonesteele G, Urbinati CR, Banerjee AK, Chow A, Ettlin O, Strehle M, Peyda P, Amaya E, Trinh V, Guttman M | Molecular cell | 38387462 | Mol Cell | 2024 Apr 4 |
| ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements. | Perez AA, Goronzy IN, Blanco MR, Yeh BT, Guo JK, Lopes CS, Ettlin O, Burr A, Guttman M | Nature genetics | 39587360 | Nat Genet | 2024 Dec |
| Genome organization around nuclear speckles drives mRNA splicing efficiency. | Bhat P, Chow A, Emert B, Ettlin O, Quinodoz SA, Strehle M, Takei Y, Burr A, Goronzy IN, Chen AW, Huang W, Ferrer JLM, Soehalim E, Goh ST, Chari T, Sullivan DK, Blanco MR, Guttman M | Nature | 38720076 | Nature | 2024 May |
| High-resolution spatial multi-omics reveals cell-type specific nuclear compartments. | Takei Y, Yang Y, White J, Yun J, Prasad M, Ombelets LJ, Schindler S, Cai L | bioRxiv : the preprint server for biology | 37214923 | bioRxiv | 2023 May 9 |
| How subtle changes in 3D structure can create large changes in transcription. | Xiao JY, Hafner A, Boettiger AN | eLife | 34240703 | Elife | 2021 Jul 9 |
| Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition. | Murphy SE, Boettiger AN | Nature genetics | 38361032 | Nat Genet | 2024 Mar |
| Loop stacking organizes genome folding from TADs to chromosomes. | Hafner A, Park M, Berger SE, Murphy SE, Nora EP, Boettiger AN | Molecular cell | 37146570 | Mol Cell | 2023 May 4 |
| NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells. | Chen AF, Parks B, Kathiria AS, Ober-Reynolds B, Goronzy JJ, Greenleaf WJ | Nature methods | 35501385 | Nat Methods | 2022 May |
| Two unrelated distal genes activated by a shared enhancer benefit from localizing inside the same small topological domain. | Huang Y, Verstegen MJAM, Tjalsma SJD, Krijger PHL, Gupta K, Park M, Boettiger A, de Laat W | Genes & development | 39870429 | Genes Dev | 2025 Mar 3 |
| Single-cell chromatin state transitions during epigenetic memory formation. | Fujimori T, Rios-Martinez C, Thurm AR, Hinks MM, Doughty BR, Sinha J, Le D, Hafner A, Greenleaf WJ, Boettiger AN, Bintu L | bioRxiv : the preprint server for biology | 37873344 | bioRxiv | 2023 Oct 5 |
| The H3.3 K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation. | Sinha J, Nickels JF, Thurm AR, Ludwig CH, Archibald BN, Hinks MM, Wan J, Fang D, Bintu L | bioRxiv : the preprint server for biology | 37873347 | bioRxiv | 2023 Oct 14 |
| Super-enhancer interactomes from single cells link clustering and transcription. | Le DJ, Hafner A, Gaddam S, Wang KC, Boettiger AN | bioRxiv : the preprint server for biology | 38766104 | bioRxiv | 2024 May 10 |
| Physical modeling of nucleosome clustering in euchromatin resulting from interactions between epigenetic reader proteins. | Wakim JG, Spakowitz AJ | Proceedings of the National Academy of Sciences of the United States of America | 38900792 | Proc Natl Acad Sci U S A | 2024 Jun 25 |
| Long-range regulation of transcription scales with genomic distance in a gene-specific manner. | Jensen CL, Chen LF, Swigut T, Crocker OJ, Yao D, Bassik MC, Ferrell JE Jr, Boettiger AN, Wysocka J | Molecular cell | 39626660 | Mol Cell | 2025 Jan 16 |
| Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer-promoter contact. | Rajpurkar AR, Mateo LJ, Murphy SE, Boettiger AN | Nature communications | 34103507 | Nat Commun | 2021 Jun 8 |
| The H3.3K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation. | Sinha J, Nickels JF, Thurm AR, Ludwig CH, Archibald BN, Hinks MM, Wan J, Fang D, Bintu L | Molecular cell | 39368466 | Mol Cell | 2024 Oct 17 |
| Cohesin-dependence of neuronal gene expression relates to chromatin loop length. | Calderon L, Weiss FD, Beagan JA, Oliveira MS, Georgieva R, Wang YF, Carroll TS, Dharmalingam G, Gong W, Tossell K, de Paola V, Whilding C, Ungless MA, Fisher AG, Phillips-Cremins JE, Merkenschlager M | eLife | 35471149 | Elife | 2022 Apr 26 |
| CTCF and transcription influence chromatin structure re-configuration after mitosis. | Zhang H, Lam J, Zhang D, Lan Y, Vermunt MW, Keller CA, Giardine B, Hardison RC, Blobel GA | Nature communications | 34453048 | Nat Commun | 2021 Aug 27 |
| Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome. | Malachowski T, Chandradoss KR, Boya R, Zhou L, Cook AL, Su C, Pham K, Haws SA, Kim JH, Ryu HS, Ge C, Luppino JM, Nguyen SC, Titus KR, Gong W, Wallace O, Joyce EF, Wu H, Rojas LA, Phillips-Cremins JE | Cell | 38134876 | Cell | 2023 Dec 21 |
| Genome folding principles revealed in condensin-depleted mitotic chromosomes. | Zhao H, Lin Y, Lin E, Liu F, Shu L, Jing D, Wang B, Wang M, Shan F, Zhang L, Lam JC, Midla SC, Giardine BM, Keller CA, Hardison RC, Blobel GA, Zhang H | bioRxiv : the preprint server for biology | 38014261 | bioRxiv | 2023 Nov 13 |
| Genome folding principles uncovered in condensin-depleted mitotic chromosomes. | Zhao H, Lin Y, Lin E, Liu F, Shu L, Jing D, Wang B, Wang M, Shan F, Zhang L, Lam JC, Midla SC, Giardine BM, Keller CA, Hardison RC, Blobel GA, Zhang H | Nature genetics | 38802567 | Nat Genet | 2024 Jun |
| AP-1 Mediates Cellular Adaptation and Memory Formation During Therapy Resistance. | Li J, Ravindran PT, O'Farrell A, Busch GT, Boe RH, Niu Z, Woo S, Dunagin MC, Jain N, Goyal Y, Sarma K, Herlyn M, Raj A | bioRxiv : the preprint server for biology | 39091739 | bioRxiv | 2024 Jul 25 |
| LDB1 establishes multi-enhancer networks to regulate gene expression. | Aboreden NG, Lam JC, Goel VY, Wang S, Wang X, Midla SC, Quijano A, Keller CA, Giardine BM, Hardison RC, Zhang H, Hansen AS, Blobel GA | bioRxiv : the preprint server for biology | 39229045 | bioRxiv | 2024 Aug 24 |
| Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells. | Jain N, Goyal Y, Dunagin MC, Cote CJ, Mellis IA, Emert B, Jiang CL, Dardani IP, Reffsin S, Raj A | bioRxiv : the preprint server for biology | 36798299 | bioRxiv | 2023 Feb 10 |
| Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states. | Reffsin S, Miller J, Ayyanathan K, Dunagin MC, Jain N, Schultz DC, Cherry S, Raj A | bioRxiv : the preprint server for biology | 37461472 | bioRxiv | 2023 Jul 7 |
| Scalable biological signal recording in mammalian cells using Cas12a base editors. | Kempton HR, Love KS, Guo LY, Qi LS | Nature chemical biology | 35637351 | Nat Chem Biol | 2022 Jul |
| 3D genome, on repeat: Higher-order folding principles of the heterochromatinized repetitive genome. | Haws SA, Simandi Z, Barnett RJ, Phillips-Cremins JE | Cell | 35868274 | Cell | 2022 Jul 21 |
| FISHnet: Detecting chromatin domains in single-cell sequential Oligopaints imaging data. | Patel R, Pham K, Chandrashekar H, Phillips-Cremins JE | bioRxiv : the preprint server for biology | 38948824 | bioRxiv | 2024 Jun 18 |
| Spatial transcriptomics reveals influence of microenvironment on intrinsic fates in melanoma therapy resistance. | Boe RH, Triandafillou CG, Lazcano R, Wargo JA, Raj A | bioRxiv : the preprint server for biology | 39005406 | bioRxiv | 2024 Jul 2 |
| Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells. | Jain N, Goyal Y, Dunagin MC, Cote CJ, Mellis IA, Emert B, Jiang CL, Dardani IP, Reffsin S, Arnett M, Yang W, Raj A | Cell systems | 38335955 | Cell Syst | 2024 Feb 21 |
| LDB1 establishes multi-enhancer networks to regulate gene expression. | Aboreden NG, Lam JC, Goel VY, Wang S, Wang X, Midla SC, Quijano A, Keller CA, Giardine BM, Hardison RC, Zhang H, Hansen AS, Blobel GA | Molecular cell | 39721581 | Mol Cell | 2025 Jan 16 |
| Cis-regulatory chromatin contacts form de novo in the absence of loop extrusion. | Aboreden NG, Zhao H, Shan F, Liu F, Zhang H, Blobel GA | bioRxiv : the preprint server for biology | 39975341 | bioRxiv | 2025 Feb 8 |
| Innate Immune Memory is Stimulus Specific. | O'Farrell A, Niu Z, Li J, Van Eyndhoven LC, Sarma K, Raj A | bioRxiv : the preprint server for biology | 39896612 | bioRxiv | 2025 Jan 24 |
| A multi-looping chromatin signature predicts dysregulated gene expression in neurons with familial Alzheimer's disease mutations. | Chandrashekar H, Simandi Z, Choi H, Ryu HS, Waldman AJ, Nikish A, Muppidi SS, Gong W, Paquet D, Phillips-Cremins JE | bioRxiv : the preprint server for biology | 38463966 | bioRxiv | 2024 Feb 27 |
| Multi-color super-resolution imaging to study human coronavirus RNA during cellular infection. | Wang J, Han M, Roy AR, Wang H, Möckl L, Zeng L, Moerner WE, Qi LS | Cell reports methods | 35128513 | Cell Rep Methods | 2022 Feb 28 |
| Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks. | Boe RH, Ayyappan V, Schuh L, Raj A | Cell systems | 36450286 | Cell Syst | 2022 Dec 21 |
| MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing. | Su C, Chandradoss KR, Malachowski T, Boya R, Ryu HS, Brennand KJ, Phillips-Cremins JE | bioRxiv : the preprint server for biology | 38746155 | bioRxiv | 2024 May 2 |
| Piscis: a novel loss estimator of the F1 score enables accurate spot detection in fluorescence microscopy images via deep learning. | Niu Z, O'Farrell A, Li J, Reffsin S, Jain N, Dardani I, Goyal Y, Raj A | bioRxiv : the preprint server for biology | 38352551 | bioRxiv | 2025 Jan 15 |
| CTCF blocks antisense transcription initiation at divergent promoters. | Luan J, Vermunt MW, Syrett CM, Coté A, Tome JM, Zhang H, Huang A, Luppino JM, Keller CA, Giardine BM, Zhang S, Dunagin MC, Zhang Z, Joyce EF, Lis JT, Raj A, Hardison RC, Blobel GA | Nature structural & molecular biology | 36369346 | Nat Struct Mol Biol | 2022 Nov |
| CRISPR-Mediated Synergistic Epigenetic and Transcriptional Control. | Dominguez AA, Chavez MG, Urke A, Gao Y, Wang L, Qi LS | The CRISPR journal | 35271371 | CRISPR J | 2022 Apr |
| The use of new CRISPR tools in cardiovascular research and medicine. | Nishiga M, Liu C, Qi LS, Wu JC | Nature reviews. Cardiology | 35145236 | Nat Rev Cardiol | 2022 Aug |
| A nuclear architecture screen in Drosophila identifies Stonewall as a link between chromatin position at the nuclear periphery and germline stem cell fate. | Chavan A, Isenhart R, Nguyen SC, Kotb NM, Harke J, Sintsova A, Ulukaya G, Uliana F, Ashiono C, Kutay U, Pegoraro G, Rangan P, Joyce EF, Jagannathan M | Genes & development | 38866555 | Genes Dev | 2024 Jun 25 |
| Multi-color super-resolution imaging to study human coronavirus RNA during cellular infection. | Wang J, Han M, Roy AR, Wang H, Möckl L, Zeng L, Moerner WE, Qi LS | bioRxiv : the preprint server for biology | 34127974 | bioRxiv | 2022 Jan 12 |
| Heterogeneity of fetal hemoglobin production in adult red blood cells. | Khandros E, Blobel GA | Current opinion in hematology | 33631783 | Curr Opin Hematol | 2021 May 1 |
| High-throughput Oligopaint screen identifies druggable 3D genome regulators. | Park DS, Nguyen SC, Isenhart R, Shah PP, Kim W, Barnett RJ, Chandra A, Luppino JM, Harke J, Wai M, Walsh PJ, Abdill RJ, Yang R, Lan Y, Yoon S, Yunker R, Kanemaki MT, Vahedi G, Phillips-Cremins JE, Jain R, Joyce EF | Nature | 37438531 | Nature | 2023 Aug |
| Advances in CRISPR therapeutics. | Chavez M, Chen X, Finn PB, Qi LS | Nature reviews. Nephrology | 36280707 | Nat Rev Nephrol | 2023 Jan |
| CRISPR technologies for precise epigenome editing. | Nakamura M, Gao Y, Dominguez AA, Qi LS | Nature cell biology | 33420494 | Nat Cell Biol | 2021 Jan |
| Cell type determination for cardiac differentiation occurs soon after seeding of human-induced pluripotent stem cells. | Jiang CL, Goyal Y, Jain N, Wang Q, Truitt RE, Coté AJ, Emert B, Mellis IA, Kiani K, Yang W, Jain R, Raj A | Genome biology | 35382863 | Genome Biol | 2022 Apr 5 |
| Multiplexed genome regulation in vivo with hyper-efficient Cas12a. | Guo LY, Bian J, Davis AE, Liu P, Kempton HR, Zhang X, Chemparathy A, Gu B, Lin X, Rane DA, Xu X, Jamiolkowski RM, Hu Y, Wang S, Qi LS | Nature cell biology | 35414015 | Nat Cell Biol | 2022 Apr |
| Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation. | Titus KR, Simandi Z, Chandrashekar H, Paquet D, Phillips-Cremins JE | bioRxiv : the preprint server for biology | 38106199 | bioRxiv | 2023 Dec 5 |
| Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles. | Andronov L, Han M, Zhu Y, Balaji A, Roy AR, Barentine AES, Patel P, Garhyan J, Qi LS, Moerner WE | bioRxiv : the preprint server for biology | 37986994 | bioRxiv | 2024 Apr 1 |
| Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles. | Andronov L, Han M, Zhu Y, Balaji A, Roy AR, Barentine AES, Patel P, Garhyan J, Qi LS, Moerner WE | Nature communications | 38821943 | Nat Commun | 2024 May 31 |
| YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle. | Lam JC, Aboreden NG, Midla SC, Wang S, Huang A, Keller CA, Giardine B, Henderson KA, Hardison RC, Zhang H, Blobel GA | Nature genetics | 39210046 | Nat Genet | 2024 Sep |
| Regulation of mammalian totipotency: a molecular perspective from in vivo and in vitro studies. | Nakatani T, Torres-Padilla ME | Current opinion in genetics & development | 37421903 | Curr Opin Genet Dev | 2023 Aug |
| Dynamics of nuclear architecture during early embryonic development and lessons from liveimaging. | Pecori F, Torres-Padilla ME | Developmental cell | 36977375 | Dev Cell | 2023 Mar 27 |
| Emergence of replication timing during early mammalian development. | Nakatani T, Schauer T, Altamirano-Pacheco L, Klein KN, Ettinger A, Pal M, Gilbert DM, Torres-Padilla ME | Nature | 38123678 | Nature | 2024 Jan |
| Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo. | Oomen ME, Torres-Padilla ME | EMBO reports | 38528171 | EMBO Rep | 2024 Apr |
| Reorganization of lamina-associated domains in early mouse embryos is regulated by RNA polymerase II activity. | Pal M, Altamirano-Pacheco L, Schauer T, Torres-Padilla ME | Genes & development | 37914351 | Genes Dev | 2023 Oct 1 |
| Subtype-specific 3D genome alteration in acute myeloid leukaemia. | Xu J, Song F, Lyu H, Kobayashi M, Zhang B, Zhao Z, Hou Y, Wang X, Luan Y, Jia B, Stasiak L, Wong JH, Wang Q, Jin Q, Jin Q, Fu Y, Yang H, Hardison RC, Dovat S, Platanias LC, Diao Y, Yang Y, Yamada T, Viny AD, Levine RL, Claxton D, Broach JR, Zheng H, Yue F | Nature | 36289338 | Nature | 2022 Nov |
| A functional cellular framework for sex and estrous cycle-dependent gene expression and behavior. | Knoedler JR, Inoue S, Bayless DW, Yang T, Tantry A, Davis CH, Leung NY, Parthasarathy S, Wang G, Alvarado M, Rizvi AH, Fenno LE, Ramakrishnan C, Deisseroth K, Shah NM | Cell | 38810647 | Cell | 2024 Jul 11 |
| A functional cellular framework for sex and estrous cycle-dependent gene expression and behavior. | Knoedler JR, Inoue S, Bayless DW, Yang T, Tantry A, Davis CH, Leung NY, Parthasarathy S, Wang G, Alvarado M, Rizvi AH, Fenno LE, Ramakrishnan C, Deisseroth K, Shah NM | Cell | 35065713 | Cell | 2022 Feb 17 |
| Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice. | Bashkirova EV, Klimpert N, Monahan K, Campbell CE, Osinski J, Tan L, Schieren I, Pourmorady A, Stecky B, Barnea G, Xie XS, Abdus-Saboor I, Shykind BM, Marlin BJ, Gronostajski RM, Fleischmann A, Lomvardas S | eLife | 38108811 | Elife | 2023 Dec 18 |
| Olfactory receptor choice: a case study for gene regulation in a multi-enhancer system. | Pourmorady A, Lomvardas S | Current opinion in genetics & development | 34896807 | Curr Opin Genet Dev | 2022 Feb |
| Disruption of nuclear architecture as a cause of COVID-19 induced anosmia. | Zazhytska M, Kodra A, Hoagland DA, Fullard JF, Shayya H, Omer A, Firestein S, Gong Q, Canoll PD, Goldman JE, Roussos P, tenOever BR, Overdevest JB, Lomvardas S | bioRxiv : the preprint server for biology | 33594368 | bioRxiv | 2021 Feb 9 |
| Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia. | Zazhytska M, Kodra A, Hoagland DA, Frere J, Fullard JF, Shayya H, McArthur NG, Moeller R, Uhl S, Omer AD, Gottesman ME, Firestein S, Gong Q, Canoll PD, Goldman JE, Roussos P, tenOever BR, Jonathan B Overdevest, Lomvardas S | Cell | 35180380 | Cell | 2022 Mar 17 |
| Probing neural circuit mechanisms in Alzheimer's disease using novel technologies. | Grieco SF, Holmes TC, Xu X | Molecular psychiatry | 36959497 | Mol Psychiatry | 2023 Oct |
| PHGDH expression increases with progression of Alzheimer's disease pathology and symptoms. | Chen X, Calandrelli R, Girardini J, Yan Z, Tan Z, Xu X, Hiniker A, Zhong S | Cell metabolism | 35508105 | Cell Metab | 2022 May 3 |
| Epigenetic and 3D genome reprogramming during the aging of human hippocampus. | Zemke NR, Lee S, Mamde S, Yang B, Berchtold N, Maximiliano Garduño B, Indralingam HS, Bartosik WM, Lau PK, Dong K, Yang A, Tani Y, Chen C, Zeng Q, Ajith V, Tong L, Seng C, Li D, Wang T, Xu X, Ren B | bioRxiv : the preprint server for biology | 39463924 | bioRxiv | 2024 Oct 17 |
| Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain. | Zhang Y, Amaral ML, Zhu C, Grieco SF, Hou X, Lin L, Buchanan J, Tong L, Preissl S, Xu X, Ren B | Cell research | 36207411 | Cell Res | 2022 Nov |
| Psychedelics and Neural Plasticity: Therapeutic Implications. | Grieco SF, Castrén E, Knudsen GM, Kwan AC, Olson DE, Zuo Y, Holmes TC, Xu X | The Journal of neuroscience : the official journal of the Society for Neuroscience | 36351821 | J Neurosci | 2022 Nov 9 |
| ULV: A robust statistical method for clustered data, with applications to multi-subject, single-cell omics data. | Du M, Johnston K, Berrocal V, Li W, Xu X, Yu Z | ArXiv | 38947924 | ArXiv | 2024 Jun 10 |
| Stripenn detects architectural stripes from chromatin conformation data using computer vision. | Yoon S, Chandra A, Vahedi G | Nature communications | 35332165 | Nat Commun | 2022 Mar 24 |
| Dissecting gene activation and chromatin remodeling dynamics in single human cells undergoing reprogramming. | Martinez-Sarmiento JA, Cosma MP, Lakadamyali M | Cell reports | 38700983 | Cell Rep | 2024 May 28 |
| Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity. | Goldman N, Chandra A, Johnson I, Sullivan MA, Patil AR, Vanderbeck A, Jay A, Zhou Y, Ferrari EK, Mayne L, Aguilan J, Xue HH, Faryabi RB, John Wherry E, Sidoli S, Maillard I, Vahedi G | Nature immunology | 37592014 | Nat Immunol | 2023 Oct |
| Single-cell expression profiling of islets generated by the Human Pancreas Analysis Program. | Patil AR, Schug J, Naji A, Kaestner KH, Faryabi RB, Vahedi G | Nature metabolism | 37188822 | Nat Metab | 2023 May |
| Remodeling the chromatin landscape in T lymphocytes by a division of labor among transcription factors. | Vahedi G | Immunological reviews | 33452686 | Immunol Rev | 2021 Mar |
| Technological advances in super-resolution microscopy to study cellular processes. | Bond C, Santiago-Ruiz AN, Tang Q, Lakadamyali M | Molecular cell | 35063099 | Mol Cell | 2022 Jan 20 |
| Quantitative control of Ets1 dosage by a multi-enhancer hub promotes Th1 cell differentiation and protects from allergic inflammation. | Chandra A, Yoon S, Michieletto MF, Goldman N, Ferrari EK, Abedi M, Johnson I, Fasolino M, Pham K, Joannas L, Kee BL, Henao-Mejia J, Vahedi G | Immunity | 37263273 | Immunity | 2023 Jul 11 |
| TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors. | Wang W, Chandra A, Goldman N, Yoon S, Ferrari EK, Nguyen SC, Joyce EF, Vahedi G | Nature immunology | 35726060 | Nat Immunol | 2022 Jul |
| Toward a comprehensive view of gene architecture during transcription. | Woodworth MA, Lakadamyali M | Current opinion in genetics & development | 38309073 | Curr Opin Genet Dev | 2024 Apr |
| Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes. | Fasolino M, Schwartz GW, Patil AR, Mongia A, Golson ML, Wang YJ, Morgan A, Liu C, Schug J, Liu J, Wu M, Traum D, Kondo A, May CL, Goldman N, Wang W, Feldman M, Moore JH, Japp AS, Betts MR, HPAP Consortium, Faryabi RB, Naji A, Kaestner KH, Vahedi G | Nature metabolism | 35228745 | Nat Metab | 2022 Feb |
| Single nucleosome tracking to study chromatin plasticity. | Lakadamyali M | Current opinion in cell biology | 35033775 | Curr Opin Cell Biol | 2022 Feb |
| BRD4 orchestrates genome folding to promote neural crest differentiation. | Linares-Saldana R, Kim W, Bolar NA, Zhang H, Koch-Bojalad BA, Yoon S, Shah PP, Karnay A, Park DS, Luppino JM, Nguyen SC, Padmanabhan A, Smith CL, Poleshko A, Wang Q, Li L, Srivastava D, Vahedi G, Eom GH, Blobel GA, Joyce EF, Jain R | Nature genetics | 34611363 | Nat Genet | 2021 Oct |
| Multiple allelic configurations govern long-range Shh enhancer-promoter communication in the embryonic forebrain. | Harke J, Lee JR, Nguyen SC, Arab A, Rakowiecki SM, Hugelier S, Paliou C, Rauseo A, Yunker R, Xu K, Yao Y, Lakadamyali M, Andrey G, Epstein DJ, Joyce EF | Molecular cell | 39579767 | Mol Cell | 2024 Dec 19 |
| Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries. | Chang LH, Ghosh S, Papale A, Luppino JM, Miranda M, Piras V, Degrouard J, Edouard J, Poncelet M, Lecouvreur N, Bloyer S, Leforestier A, Joyce EF, Holcman D, Noordermeer D | Nature communications | 37699887 | Nat Commun | 2023 Sep 12 |
| Aberrant chromatin reorganization in cells from diseased fibrous connective tissue in response to altered chemomechanical cues. | Heo SJ, Thakur S, Chen X, Loebel C, Xia B, McBeath R, Burdick JA, Shenoy VB, Mauck RL, Lakadamyali M | Nature biomedical engineering | 35996026 | Nat Biomed Eng | 2023 Feb |
| Multiscale 3D genome organization underlies ILC2 ontogenesis and allergic airway inflammation. | Michieletto MF, Tello-Cajiao JJ, Mowel WK, Chandra A, Yoon S, Joannas L, Clark ML, Jimenez MT, Wright JM, Lundgren P, Williams A, Thaiss CA, Vahedi G, Henao-Mejia J | Nature immunology | 36050414 | Nat Immunol | 2023 Jan |
| Co-depletion of NIPBL and WAPL balance cohesin activity to correct gene misexpression. | Luppino JM, Field A, Nguyen SC, Park DS, Shah PP, Abdill RJ, Lan Y, Yunker R, Jain R, Adelman K, Joyce EF | PLoS genetics | 36449519 | PLoS Genet | 2022 Nov |
| Aberrant chromatin organization at the nexus of laminopathy disease pathways. | Santini GT, Shah PP, Karnay A, Jain R | Nucleus (Austin, Tex.) | 36503349 | Nucleus | 2022 Dec |
| From feulgen to modern methods: marking a century of DNA imaging advances. | Lakadamyali M | Histochemistry and cell biology | 38753186 | Histochem Cell Biol | 2024 Jul |
| FMRP regulates MFF translation to locally direct mitochondrial fission in neurons. | Fenton AR, Peng R, Bond C, Hugelier S, Lakadamyali M, Chang YW, Holzbaur ELF, Jongens TA | Nature cell biology | 39548330 | Nat Cell Biol | 2024 Dec |
| ECLiPSE: a versatile classification technique for structural and morphological analysis of 2D and 3D single-molecule localization microscopy data. | Hugelier S, Tang Q, Kim HH, Gyparaki MT, Bond C, Santiago-Ruiz AN, Porta S, Lakadamyali M | Nature methods | 39256629 | Nat Methods | 2024 Oct |
| Generalized multi-SNP mediation intersection-union test. | Zhong W, Darville T, Zheng X, Fine J, Li Y | Biometrics | 33316078 | Biometrics | 2022 Mar |
| TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data. | Huang L, Rosen JD, Sun Q, Chen J, Wheeler MM, Zhou Y, Min YI, Kooperberg C, Conomos MP, Stilp AM, Rich SS, Rotter JI, Manichaikul A, Loos RJF, Kenny EE, Blackwell TW, Smith AV, Jun G, Sedlazeck FJ, Metcalf G, Boerwinkle E, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Raffield LM, Reiner AP, Auer PL, Li Y | American journal of human genetics | 35504290 | Am J Hum Genet | 2022 Jun 2 |
| High-throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases. | Jones IR, Ren X, Shen Y | Human molecular genetics | 35972825 | Hum Mol Genet | 2022 Oct 20 |
| A conserved molecular logic for neurogenesis to gliogenesis switch in the cerebral cortex. | Liang XG, Hoang K, Meyerink BL, Kc P, Paraiso K, Wang L, Jones IR, Zhang Y, Katzman S, Finn TS, Tsyporin J, Qu F, Chen Z, Visel A, Kriegstein A, Shen Y, Pilaz LJ, Chen B | Proceedings of the National Academy of Sciences of the United States of America | 38713624 | Proc Natl Acad Sci U S A | 2024 May 14 |
| Mapping chromatin loops in single cells. | Yu M, Li Y, Hu M | Trends in genetics : TIG | 35400543 | Trends Genet | 2022 Jul |
| Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis. | Catta-Preta R, Lindtner S, Ypsilanti A, Price J, Abnousi A, Su-Feher L, Wang Y, Juric I, Jones IR, Akiyama JA, Hu M, Shen Y, Visel A, Pennacchio LA, Dickel D, Rubenstein JLR, Nord AS | bioRxiv : the preprint server for biology | 37425940 | bioRxiv | 2023 Jun 28 |
| High throughput PRIME editing screens identify functional DNA variants in the human genome. | Ren X, Yang H, Nierenberg JL, Sun Y, Chen J, Beaman C, Pham T, Nobuhara M, Takagi MA, Narayan V, Li Y, Ziv E, Shen Y | bioRxiv : the preprint server for biology | 37502948 | bioRxiv | 2023 Jul 12 |
| The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2. | Longhurst AD, Wang K, Suresh HG, Ketavarapu M, Ward HN, Jones IR, Narayan V, Hundley FV, Hassan AZ, Boone C, Myers CL, Shen Y, Ramani V, Andrews BJ, Toczyski DP | bioRxiv : the preprint server for biology | 38562687 | bioRxiv | 2024 Oct 16 |
| High-throughput PRIME-editing screens identify functional DNA variants in the human genome. | Ren X, Yang H, Nierenberg JL, Sun Y, Chen J, Beaman C, Pham T, Nobuhara M, Takagi MA, Narayan V, Li Y, Ziv E, Shen Y | Molecular cell | 38134886 | Mol Cell | 2023 Dec 21 |
| DeepGWAS: Enhance GWAS Signals for Neuropsychiatric Disorders via Deep Neural Network. | Li Y, Wen J, Li G, Chen J, Sun Q, Liu W, Guan W, Lai B, Szatkiewicz J, He X, Sullivan P | Research square | 36824788 | Res Sq | 2023 Feb 14 |
| THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data. | Rowland B, Huh R, Hou Z, Crowley C, Wen J, Shen Y, Hu M, Giusti-Rodríguez P, Sullivan PF, Li Y | PLoS genetics | 35259165 | PLoS Genet | 2022 Mar |
| Cell-type specific inference from bulk RNA-sequencing data by integrating single cell reference profiles via EPIC-unmix. | Tang C, Sun Q, Zeng X, Yang X, Liu F, Zhao J, Shen Y, Liu B, Wen J, Li Y | bioRxiv : the preprint server for biology | 38826297 | bioRxiv | 2024 May 24 |
| Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis. | Catta-Preta R, Lindtner S, Ypsilanti A, Seban N, Price JD, Abnousi A, Su-Feher L, Wang Y, Cichewicz K, Boerma SA, Juric I, Jones IR, Akiyama JA, Hu M, Shen Y, Visel A, Pennacchio LA, Dickel DE, Rubenstein JLR, Nord AS | Developmental cell | 39481376 | Dev Cell | 2025 Jan 20 |
| MUNIn: A statistical framework for identifying long-range chromatin interactions from multiple samples. | Liu W, Yang Y, Abnousi A, Zhang Q, Kubo N, Beem JSM, Li Y, Hu M | HGG advances | 34485947 | HGG Adv | 2021 Jul 8 |
| Genetic regulators of sputum mucin concentration and their associations with COPD phenotypes. | Van Buren E, Radicioni G, Lester S, O'Neal WK, Dang H, Kasela S, Garudadri S, Curtis JL, Han MK, Krishnan JA, Wan ES, Silverman EK, Hastie A, Ortega VE, Lappalainen T, Nawijn MC, Berge MVD, Christenson SA, Li Y, Cho MH, Kesimer M, Kelada SNP | PLoS genetics | 37352370 | PLoS Genet | 2023 Jun |
| From GWAS variant to function: A study of ∼148,000 variants for blood cell traits. | Sun Q, Crowley CA, Huang L, Wen J, Chen J, Bao EL, Auer PL, Lettre G, Reiner AP, Sankaran VG, Raffield LM, Li Y | HGG advances | 35047852 | HGG Adv | 2022 Jan 13 |
| A comprehensive comparison on cell-type composition inference for spatial transcriptomics data. | Chen J, Liu W, Luo T, Yu Z, Jiang M, Wen J, Gupta GP, Giusti P, Zhu H, Yang Y, Li Y | Briefings in bioinformatics | 35753702 | Brief Bioinform | 2022 Jul 18 |
| Innovative computational approaches shed light on genetic mechanisms underlying cognitive impairment among children born extremely preterm. | Liu W, Sun Q, Huang L, Bhattacharya A, Wang GW, Tan X, Kuban KCK, Joseph RM, O'Shea TM, Fry RC, Li Y, Santos HP Jr | Journal of neurodevelopmental disorders | 35240980 | J Neurodev Disord | 2022 Mar 3 |
| The PRC2.1 subcomplex opposes G1 progression through regulation of CCND1 and CCND2. | Longhurst AD, Wang K, Suresh HG, Ketavarapu M, Ward HN, Jones IR, Narayan V, Hundley FV, Hassan AZ, Boone C, Myers CL, Shen Y, Ramani V, Andrews BJ, Toczyski DP | eLife | 39903505 | Elife | 2025 Feb 4 |
| DMA-tudor interaction modules control the specificity of in vivo condensates. | Courchaine EM, Barentine AES, Straube K, Lee DR, Bewersdorf J, Neugebauer KM | Cell | 34115980 | Cell | 2021 Jul 8 |
| An integrated platform for high-throughput nanoscopy. | Barentine AES, Lin Y, Courvan EM, Kidd P, Liu M, Balduf L, Phan T, Rivera-Molina F, Grace MR, Marin Z, Lessard M, Rios Chen J, Wang S, Neugebauer KM, Bewersdorf J, Baddeley D | Nature biotechnology | 36914886 | Nat Biotechnol | 2023 Nov |
| Fluorogenic DNA-PAINT for faster, low-background super-resolution imaging. | Chung KKH, Zhang Z, Kidd P, Zhang Y, Williams ND, Rollins B, Yang Y, Lin C, Baddeley D, Bewersdorf J | Nature methods | 35501386 | Nat Methods | 2022 May |
| An automated Bayesian pipeline for rapid analysis of single-molecule binding data. | Smith CS, Jouravleva K, Huisman M, Jolly SM, Zamore PD, Grunwald D | Nature communications | 30655518 | Nat Commun | 2019 Jan 17 |
| REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. | Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, Hériché JK, Iudin A, Martins GG, Meehan T, Narayan K, Patwardhan A, Russell MRG, Saibil HR, Strambio-De-Castillia C, Swedlow JR, Tischer C, Uhlmann V, Verkade P, Barlow M, Bayraktar O, Birney E, Catavitello C, Cawthorne C, Wagner-Conrad S, Duke E, Paul-Gilloteaux P, Gustin E, Harkiolaki M, Kankaanpää P, Lemberger T, McEntyre J, Moore J, Nicholls AW, Onami S, Parkinson H, Parsons M, Romanchikova M, Sofroniew N, Swoger J, Utz N, Voortman LM, Wong F, Zhang P, Kleywegt GJ, Brazma A | Nature methods | 34021280 | Nat Methods | 2021 Dec |
| Interactions between ALS-linked FUS and nucleoporins are associated with defects in the nucleocytoplasmic transport pathway. | Lin YC, Kumar MS, Ramesh N, Anderson EN, Nguyen AT, Kim B, Cheung S, McDonough JA, Skarnes WC, Lopez-Gonzalez R, Landers JE, Fawzi NL, Mackenzie IRA, Lee EB, Nickerson JA, Grunwald D, Pandey UB, Bosco DA | Nature neuroscience | 34059832 | Nat Neurosci | 2021 Aug |
| Single-cell nuclear architecture across cell types in the mouse brain. | Takei Y, Zheng S, Yun J, Shah S, Pierson N, White J, Schindler S, Tischbirek CH, Yuan GC, Cai L | Science (New York, N.Y.) | 34591592 | Science | 2021 Oct 29 |
| ChromEMT: visualizing and reconstructing chromatin ultrastructure and 3D organization in situ. | Ou HD, Phan S, Deerinck TJ, Inagaki A, Ellisman MH, O'Shea CC | Nature protocols | 39613943 | Nat Protoc | 2025 Apr |
| Single mRNA Molecule Detection in Drosophila. | Little SC, Gregor T | Methods in molecular biology (Clifton, N.J.) | 29130194 | Methods Mol Biol | 2018 |
| Developmental enhancers and chromosome topology. | Furlong EEM, Levine M | Science (New York, N.Y.) | 30262496 | Science | 2018 Sep 28 |
| Transvection. | Fukaya T, Levine M | Current biology : CB | 29017034 | Curr Biol | 2017 Oct 9 |
| Bridging spatial and temporal scales of developmental gene regulation. | Cardona AH, Peixoto MM, Borjigin T, Gregor T | ArXiv | 39975433 | ArXiv | 2025 Jan 28 |
| Large distances separate coregulated genes in living Drosophila embryos. | Heist T, Fukaya T, Levine M | Proceedings of the National Academy of Sciences of the United States of America | 31285341 | Proc Natl Acad Sci U S A | 2019 Jul 23 |
| Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression. | Sato H, Das S, Singer RH, Vera M | Annual review of biochemistry | 32176523 | Annu Rev Biochem | 2020 Jun 20 |
| Dynamic Assembly and Disassembly of the Human DNA Polymerase δ Holoenzyme on the Genome In Vivo. | Drosopoulos WC, Vierra DA, Kenworthy CA, Coleman RA, Schildkraut CL | Cell reports | 32023453 | Cell Rep | 2020 Feb 4 |
| Imaging Organization of RNA Processing within the Nucleus. | Biswas J, Li W, Singer RH, Coleman RA | Cold Spring Harbor perspectives in biology | 34127450 | Cold Spring Harb Perspect Biol | 2021 Dec 1 |
| Selective Activation of Alternative MYC Core Promoters by Wnt-Responsive Enhancers. | Bardales JA, Wieser E, Kawaji H, Murakawa Y, Darzacq X | Genes | 29882899 | Genes (Basel) | 2018 May 23 |
| Evidence for an Integrated Gene Repression Mechanism Based on mRNA Isoform Toggling in Human Cells. | Hollerer I, Barker JC, Jorgensen V, Tresenrider A, Dugast-Darzacq C, Chan LY, Darzacq X, Tjian R, Ünal E, Brar GA | G3 (Bethesda, Md.) | 30723103 | G3 (Bethesda) | 2019 Apr 9 |
| Zipcode Binding Protein 1 (ZBP1; IGF2BP1): A Model for Sequence-Specific RNA Regulation. | Biswas J, Nunez L, Das S, Yoon YJ, Eliscovich C, Singer RH | Cold Spring Harbor symposia on quantitative biology | 32086331 | Cold Spring Harb Symp Quant Biol | 2019 |
| Single-molecule imaging of transcription dynamics in somatic stem cells. | Wheat JC, Sella Y, Willcockson M, Skoultchi AI, Bergman A, Singer RH, Steidl U | Nature | 32581360 | Nature | 2020 Jul |
| A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes. | Teves SS, An L, Bhargava-Shah A, Xie L, Darzacq X, Tjian R | eLife | 29939130 | Elife | 2018 Jun 25 |
| Bromodomains regulate dynamic targeting of the PBAF chromatin-remodeling complex to chromatin hubs. | Kenworthy CA, Haque N, Liou SH, Chandris P, Wong V, Dziuba P, Lavis LD, Liu WL, Singer RH, Coleman RA | Biophysical journal | 35364106 | Biophys J | 2022 May 3 |
| MS2-TRIBE Evaluates Both Protein-RNA Interactions and Nuclear Organization of Transcription by RNA Editing. | Biswas J, Rahman R, Gupta V, Rosbash M, Singer RH | iScience | 32674054 | iScience | 2020 Jul 24 |
| Retargeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains. | Sato H, Wu B, Delahaye F, Singer RH, Greally JM | The Journal of cell biology | 31110057 | J Cell Biol | 2019 Jun 3 |
| dCas9-targeted locus-specific protein isolation method identifies histone gene regulators. | Tsui C, Inouye C, Levy M, Lu A, Florens L, Washburn MP, Tjian R | Proceedings of the National Academy of Sciences of the United States of America | 29507191 | Proc Natl Acad Sci U S A | 2018 Mar 20 |
| Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II. | Lu H, Yu D, Hansen AS, Ganguly S, Liu R, Heckert A, Darzacq X, Zhou Q | Nature | 29849146 | Nature | 2018 Jun |
| Quantitative imaging of loop extruders rebuilding interphase genome architecture after mitosis. | Brunner A, Morero NR, Zhang W, Hossain MJ, Lampe M, Pflaumer H, Halavatyi A, Peters JM, Beckwith KS, Ellenberg J | The Journal of cell biology | 39786339 | J Cell Biol | 2025 Mar 3 |
| Identification of new transmembrane proteins concentrated at the nuclear envelope using organellar proteomics of mesenchymal cells. | Cheng LC, Baboo S, Lindsay C, Brusman L, Martinez-Bartolomé S, Tapia O, Zhang X, Yates JR 3rd, Gerace L | Nucleus (Austin, Tex.) | 31142202 | Nucleus | 2019 Dec |
| Shared and Distinctive Neighborhoods of Emerin and Lamin B Receptor Revealed by Proximity Labeling and Quantitative Proteomics. | Cheng LC, Zhang X, Abhinav K, Nguyen JA, Baboo S, Martinez-Bartolomé S, Branon TC, Ting AY, Loose E, Yates JR 3rd, Gerace L | Journal of proteome research | 35972904 | J Proteome Res | 2022 Sep 2 |
| Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope. | Cheng LC, Zhang X, Baboo S, Nguyen JA, Martinez-Bartolomé S, Loose E, Diedrich J, Yates JR 3rd, Gerace L | Life science alliance | 37433644 | Life Sci Alliance | 2023 Sep |
| Understanding molecular mechanisms of disease through spatial proteomics. | Pankow S, Martínez-Bartolomé S, Bamberger C, Yates JR | Current opinion in chemical biology | 30308467 | Curr Opin Chem Biol | 2019 Feb |
| Messages from the voices within: regulation of signaling by proteins of the nuclear lamina. | Gerace L, Tapia O | Current opinion in cell biology | 29306725 | Curr Opin Cell Biol | 2018 Jun |
| Differential contribution of steady-state RNA and active transcription in chromatin organization. | Barutcu AR, Blencowe BJ, Rinn JL | EMBO reports | 31448565 | EMBO Rep | 2019 Oct 4 |
| Long Noncoding RNAs: Molecular Modalities to Organismal Functions. | Rinn JL, Chang HY | Annual review of biochemistry | 32569523 | Annu Rev Biochem | 2020 Jun 20 |
| Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. | Maass PG, Barutcu AR, Weiner CL, Rinn JL | Molecular cell | 29625035 | Mol Cell | 2018 Apr 5 |
| High-throughput identification of RNA nuclear enrichment sequences. | Shukla CJ, McCorkindale AL, Gerhardinger C, Korthauer KD, Cabili MN, Shechner DM, Irizarry RA, Maass PG, Rinn JL | The EMBO journal | 29335281 | EMBO J | 2018 Mar 15 |
| Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking. | Kaewsapsak P, Shechner DM, Mallard W, Rinn JL, Ting AY | eLife | 29239719 | Elife | 2017 Dec 14 |
| Interchromosomal interactions: A genomic love story of kissing chromosomes. | Maass PG, Barutcu AR, Rinn JL | The Journal of cell biology | 30181316 | J Cell Biol | 2019 Jan 7 |
| A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus. | Barutcu AR, Maass PG, Lewandowski JP, Weiner CL, Rinn JL | Nature communications | 29654311 | Nat Commun | 2018 Apr 13 |
| Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C. | Maass PG, Barutcu AR, Weiner CL, Rinn JL | Molecular cell | 29526697 | Mol Cell | 2018 Mar 15 |
| Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING). | Maass PG, Barutcu AR, Shechner DM, Weiner CL, Melé M, Rinn JL | Nature structural & molecular biology | 29343869 | Nat Struct Mol Biol | 2018 Feb |
| Liquid phase condensation in cell physiology and disease. | Shin Y, Brangwynne CP | Science (New York, N.Y.) | 28935776 | Science | 2017 Sep 22 |
| Compartmentalization of telomeres through DNA-scaffolded phase separation. | Jack A, Kim Y, Strom AR, Lee DSW, Williams B, Schaub JM, Kellogg EH, Finkelstein IJ, Ferro LS, Yildiz A, Brangwynne CP | Developmental cell | 35077681 | Dev Cell | 2022 Jan 24 |
| The nucleolus as a multiphase liquid condensate. | Lafontaine DLJ, Riback JA, Bascetin R, Brangwynne CP | Nature reviews. Molecular cell biology | 32873929 | Nat Rev Mol Cell Biol | 2021 Mar |
| The liquid nucleome - phase transitions in the nucleus at a glance. | Strom AR, Brangwynne CP | Journal of cell science | 31754043 | J Cell Sci | 2019 Nov 21 |
| Probing and engineering liquid-phase organelles. | Bracha D, Walls MT, Brangwynne CP | Nature biotechnology | 31792412 | Nat Biotechnol | 2019 Dec |
| Protein Phase Separation Provides Long-Term Memory of Transient Spatial Stimuli. | Dine E, Gil AA, Uribe G, Brangwynne CP, Toettcher JE | Cell systems | 29859829 | Cell Syst | 2018 Jun 27 |
| Controlling the material properties and rRNA processing function of the nucleolus using light. | Zhu L, Richardson TM, Wacheul L, Wei MT, Feric M, Whitney G, Lafontaine DLJ, Brangwynne CP | Proceedings of the National Academy of Sciences of the United States of America | 31399547 | Proc Natl Acad Sci U S A | 2019 Aug 27 |
| Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds. | Bracha D, Walls MT, Wei MT, Zhu L, Kurian M, Avalos JL, Toettcher JE, Brangwynne CP | Cell | 30500534 | Cell | 2018 Nov 29 |
| Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome. | Shin Y, Chang YC, Lee DSW, Berry J, Sanders DW, Ronceray P, Wingreen NS, Haataja M, Brangwynne CP | Cell | 30500535 | Cell | 2018 Nov 29 |
| Competing Protein-RNA Interaction Networks Control Multiphase Intracellular Organization. | Sanders DW, Kedersha N, Lee DSW, Strom AR, Drake V, Riback JA, Bracha D, Eeftens JM, Iwanicki A, Wang A, Wei MT, Whitney G, Lyons SM, Anderson P, Jacobs WM, Ivanov P, Brangwynne CP | Cell | 32302570 | Cell | 2020 Apr 16 |
| Nucleated transcriptional condensates amplify gene expression. | Wei MT, Chang YC, Shimobayashi SF, Shin Y, Strom AR, Brangwynne CP | Nature cell biology | 32929202 | Nat Cell Biol | 2020 Oct |
| Properties of repression condensates in living Ciona embryos. | Treen N, Shimobayashi SF, Eeftens J, Brangwynne CP, Levine M | Nature communications | 33692345 | Nat Commun | 2021 Mar 10 |
| Polycomb condensates can promote epigenetic marks but are not required for sustained chromatin compaction. | Eeftens JM, Kapoor M, Michieletto D, Brangwynne CP | Nature communications | 34620850 | Nat Commun | 2021 Oct 7 |
| Mechanical Frustration of Phase Separation in the Cell Nucleus by Chromatin. | Zhang Y, Lee DSW, Meir Y, Brangwynne CP, Wingreen NS | Physical review letters | 34241518 | Phys Rev Lett | 2021 Jun 25 |
| Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets. | Shin Y, Berry J, Pannucci N, Haataja MP, Toettcher JE, Brangwynne CP | Cell | 28041848 | Cell | 2017 Jan 12 |
| Composition-dependent thermodynamics of intracellular phase separation. | Riback JA, Zhu L, Ferrolino MC, Tolbert M, Mitrea DM, Sanders DW, Wei MT, Kriwacki RW, Brangwynne CP | Nature | 32405004 | Nature | 2020 May |
| Peripherical Blood hsa-miR-335-5p Quantification as a Prognostic, but Not Diagnostic, Marker of Gastric Cancer. | Ramírez-Vidal L, Becerril-Rico J, Monroy-Mora A, Tinajero-Rodríguez JM, Centeno-Cruz F, Oñate-Ocaña LF, Ortiz-Sánchez E | Diagnostics (Basel, Switzerland) | 39125490 | Diagnostics (Basel) | 2024 Jul 26 |
| STRIDE-a fluorescence method for direct, specific in situ detection of individual single- or double-strand DNA breaks in fixed cells. | Kordon MM, Zarębski M, Solarczyk K, Ma H, Pederson T, Dobrucki JW | Nucleic acids research | 31832687 | Nucleic Acids Res | 2020 Feb 20 |
| Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription. | Feng Y, Wang Y, Wang X, He X, Yang C, Naseri A, Pederson T, Zheng J, Zhang S, Xiao X, Xie W, Ma H | Genome biology | 33292531 | Genome Biol | 2020 Dec 8 |
| A conundrum in 3-D genome organization and expression? | Pederson T | Molecular biology of the cell | 36399617 | Mol Biol Cell | 2022 Dec 1 |
| PML-like subnuclear bodies, containing XRCC1, juxtaposed to DNA replication-based single-strand breaks. | Kordon MM, Szczurek A, Berniak K, Szelest O, Solarczyk K, Tworzydło M, Wachsmann-Hogiu S, Vaahtokari A, Cremer C, Pederson T, Dobrucki JW | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 30260704 | FASEB J | 2019 Feb |
| Nucleolar structure connects with global nuclear organization. | Wang C, Ma H, Baserga SJ, Pederson T, Huang S | Molecular biology of the cell | 37610836 | Mol Biol Cell | 2023 Nov 1 |
| Nucleolar structure connects with global nuclear organization. | Wang C, Ma H, Baserga SJ, Pederson T, Huang S | bioRxiv : the preprint server for biology | 37034708 | bioRxiv | 2023 Mar 31 |
| SARS-CoV-2 infection in pregnancy is associated with robust inflammatory response at the maternal-fetal interface. | Lu-Culligan A, Chavan AR, Vijayakumar P, Irshaid L, Courchaine EM, Milano KM, Tang Z, Pope SD, Song E, Vogels CBF, Lu-Culligan WJ, Campbell KH, Casanovas-Massana A, Bermejo S, Toothaker JM, Lee HJ, Liu F, Schulz W, Fournier J, Muenker MC, Moore AJ, Yale IMPACT Team, Konnikova L, Neugebauer KM, Ring A, Grubaugh ND, Ko AI, Morotti R, Guller S, Kliman HJ, Iwasaki A, Farhadian SF | medRxiv : the preprint server for health sciences | 33532791 | medRxiv | 2021 Jan 26 |
| Maternal respiratory SARS-CoV-2 infection in pregnancy is associated with a robust inflammatory response at the maternal-fetal interface. | Lu-Culligan A, Chavan AR, Vijayakumar P, Irshaid L, Courchaine EM, Milano KM, Tang Z, Pope SD, Song E, Vogels CBF, Lu-Culligan WJ, Campbell KH, Casanovas-Massana A, Bermejo S, Toothaker JM, Lee HJ, Liu F, Schulz W, Fournier J, Muenker MC, Moore AJ, Yale IMPACT Team, Konnikova L, Neugebauer KM, Ring A, Grubaugh ND, Ko AI, Morotti R, Guller S, Kliman HJ, Iwasaki A, Farhadian SF | Med (New York, N.Y.) | 33969332 | Med | 2021 May 14 |
| Distinct features of nucleolus-associated domains in mouse embryonic stem cells. | Bizhanova A, Yan A, Yu J, Zhu LJ, Kaufman PD | Chromosoma | 32219510 | Chromosoma | 2020 Jun |
| The p150N domain of chromatin assembly factor-1 regulates Ki-67 accumulation on the mitotic perichromosomal layer. | Matheson TD, Kaufman PD | Molecular biology of the cell | 27807046 | Mol Biol Cell | 2017 Jan 1 |
| Ki-67 Contributes to Normal Cell Cycle Progression and Inactive X Heterochromatin in p21 Checkpoint-Proficient Human Cells. | Sun X, Bizhanova A, Matheson TD, Yu J, Zhu LJ, Kaufman PD | Molecular and cellular biology | 28630280 | Mol Cell Biol | 2017 Sep 1 |
| Ki-67: more than a proliferation marker. | Sun X, Kaufman PD | Chromosoma | 29322240 | Chromosoma | 2018 Jun |
| Genome architecture and expression 2019-2020: the transition phase. | Pederson T | Current opinion in genetics & development | 33279815 | Curr Opin Genet Dev | 2021 Apr |
| Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries. | Bizhanova A, Kaufman PD | Biochimica et biophysica acta. Gene regulatory mechanisms | 33307247 | Biochim Biophys Acta Gene Regul Mech | 2021 Jan |
| Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin. | Vertii A, Ou J, Yu J, Yan A, Pagès H, Liu H, Zhu LJ, Kaufman PD | Genome research | 31201210 | Genome Res | 2019 Aug |
| The UVSSA protein is part of a genome integrity homeostasis network with links to transcription-coupled DNA repair and ATM signaling. | Kordon MM, Arron S, Cleaver JE, Bezrookove V, Karentz D, Lu B, Perr E, Chang D, Pederson T | Proceedings of the National Academy of Sciences of the United States of America | 35254895 | Proc Natl Acad Sci U S A | 2022 Mar 15 |
| The redundancy of the mammalian heterochromatic compartment. | Politz JCR, Scalzo D, Groudine M | Current opinion in genetics & development | 26706451 | Curr Opin Genet Dev | 2016 Apr |
| Prelamin A processing, accumulation and distribution in normal cells and laminopathy disorders. | Casasola A, Scalzo D, Nandakumar V, Halow J, Recillas-Targa F, Groudine M, Rincón-Arano H | Nucleus (Austin, Tex.) | 26900797 | Nucleus | 2016 |
| Olfactory receptor genes make the case for inter-chromosomal interactions. | Bashkirova E, Lomvardas S | Current opinion in genetics & development | 31491591 | Curr Opin Genet Dev | 2019 Apr |
| A mixed-scale dense convolutional neural network for image analysis. | Pelt DM, Sethian JA | Proceedings of the National Academy of Sciences of the United States of America | 29279403 | Proc Natl Acad Sci U S A | 2018 Jan 9 |
| LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice. | Monahan K, Horta A, Lomvardas S | Nature | 30626972 | Nature | 2019 Jan |
| Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons. | Monahan K, Schieren I, Cheung J, Mumbey-Wafula A, Monuki ES, Lomvardas S | eLife | 28933695 | Elife | 2017 Sep 21 |
| Soft X-ray tomography: virtual sculptures from cell cultures. | Guo J, Larabell CA | Current opinion in structural biology | 31495562 | Curr Opin Struct Biol | 2019 Oct |
| Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties. | Boeynaems S, Holehouse AS, Weinhardt V, Kovacs D, Van Lindt J, Larabell C, Van Den Bosch L, Das R, Tompa PS, Pappu RV, Gitler AD | Proceedings of the National Academy of Sciences of the United States of America | 30926670 | Proc Natl Acad Sci U S A | 2019 Apr 16 |
| A Guide to Packing Your DNA. | Dekker J, Guttman M, Lomvardas S | Cell | 27058655 | Cell | 2016 Apr 7 |
| Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo. | Le Gros MA, Clowney EJ, Magklara A, Yen A, Markenscoff-Papadimitriou E, Colquitt B, Myllys M, Kellis M, Lomvardas S, Larabell CA | Cell reports | 27851973 | Cell Rep | 2016 Nov 15 |
| Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice. | Bashkirova EV, Klimpert N, Monahan K, Campbell CE, Osinski JM, Tan L, Schieren I, Pourmorady A, Stecky B, Barnea G, Xie XS, Abdus-Saboor I, Shykind B, Jones-Marlin B, Gronostajski RM, Fleischmann A, Lomvardas S | bioRxiv : the preprint server for biology | 36993168 | bioRxiv | 2023 Sep 19 |
| Multivalent Small-Molecule Pan-RAS Inhibitors. | Welsch ME, Kaplan A, Chambers JM, Stokes ME, Bos PH, Zask A, Zhang Y, Sanchez-Martin M, Badgley MA, Huang CS, Tran TH, Akkiraju H, Brown LM, Nandakumar R, Cremers S, Yang WS, Tong L, Olive KP, Ferrando A, Stockwell BR | Cell | 28235199 | Cell | 2017 Feb 23 |
| Editorial: Neural epigenetics. | Greenberg ME, Lomvardas S | Current opinion in neurobiology | 31787169 | Curr Opin Neurobiol | 2019 Dec |
| Switchable resolution in soft x-ray tomography of single cells. | Weinhardt V, Chen JH, Ekman AA, Guo J, Remesh SG, Hammel M, McDermott G, Chao W, Oh S, Le Gros MA, Larabell CA | PloS one | 31978064 | PLoS One | 2020 |
| Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus. | Ma J, Do M, Le Gros MA, Peskin CS, Larabell CA, Mori Y, Isaacson SA | PLoS computational biology | 33196636 | PLoS Comput Biol | 2020 Nov |
| Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence. | Belk JA, Yao W, Ly N, Freitas KA, Chen YT, Shi Q, Valencia AM, Shifrut E, Kale N, Yost KE, Duffy CV, Daniel B, Hwee MA, Miao Z, Ashworth A, Mackall CL, Marson A, Carnevale J, Vardhana SA, Satpathy AT | Cancer cell | 35750052 | Cancer Cell | 2022 Jul 11 |
| Spatiotemporal co-dependency between macrophages and exhausted CD8(+) T cells in cancer. | Kersten K, Hu KH, Combes AJ, Samad B, Harwin T, Ray A, Rao AA, Cai E, Marchuk K, Artichoker J, Courau T, Shi Q, Belk J, Satpathy AT, Krummel MF | Cancer cell | 35623342 | Cancer Cell | 2022 Jun 13 |
| Lymph node colonization induces tumor-immune tolerance to promote distant metastasis. | Reticker-Flynn NE, Zhang W, Belk JA, Basto PA, Escalante NK, Pilarowski GOW, Bejnood A, Martins MM, Kenkel JA, Linde IL, Bagchi S, Yuan R, Chang S, Spitzer MH, Carmi Y, Cheng J, Tolentino LL, Choi O, Wu N, Kong CS, Gentles AJ, Sunwoo JB, Satpathy AT, Plevritis SK, Engleman EG | Cell | 35525247 | Cell | 2022 May 26 |
| Differential usage of transcriptional repressor Zeb2 enhancers distinguishes adult and embryonic hematopoiesis. | Huang X, Ferris ST, Kim S, Choudhary MNK, Belk JA, Fan C, Qi Y, Sudan R, Xia Y, Desai P, Chen J, Ly N, Shi Q, Bagadia P, Liu T, Guilliams M, Egawa T, Colonna M, Diamond MS, Murphy TL, Satpathy AT, Wang T, Murphy KM | Immunity | 34004142 | Immunity | 2021 Jul 13 |
| Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility. | Lareau CA, Liu V, Muus C, Praktiknjo SD, Nitsch L, Kautz P, Sandor K, Yin Y, Gutierrez JC, Pelka K, Satpathy AT, Regev A, Sankaran VG, Ludwig LS | Nature protocols | 36792778 | Nat Protoc | 2023 May |
| Macrophage inflammatory and regenerative response periodicity is programmed by cell cycle and chromatin state. | Daniel B, Belk JA, Meier SL, Chen AY, Sandor K, Czimmerer Z, Varga Z, Bene K, Buquicchio FA, Qi Y, Kitano H, Wheeler JR, Foster DS, Januszyk M, Longaker MT, Chang HY, Satpathy AT | Molecular cell | 36521490 | Mol Cell | 2023 Jan 5 |
| Lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade. | Pai JA, Hellmann MD, Sauter JL, Mattar M, Rizvi H, Woo HJ, Shah N, Nguyen EM, Uddin FZ, Quintanal-Villalonga A, Chan JM, Manoj P, Allaj V, Baine MK, Bhanot UK, Jain M, Linkov I, Meng F, Brown D, Chaft JE, Plodkowski AJ, Gigoux M, Won HH, Sen T, Wells DK, Donoghue MTA, de Stanchina E, Wolchok JD, Loomis B, Merghoub T, Rudin CM, Chow A, Satpathy AT | Cancer cell | 37001526 | Cancer Cell | 2023 Apr 10 |
| FOXO1 is a master regulator of CAR T memory programming. | Doan A, Mueller KP, Chen A, Rouin GT, Daniel B, Lattin J, Chen Y, Mozarsky B, Markovska M, Arias-Umana J, Hapke R, Jung I, Xu P, Klysz D, Bashti M, Quinn PJ, Sandor K, Zhang W, Hall J, Lareau C, Grupp SA, Fraietta JA, Sotillo E, Satpathy AT, Mackall CL, Weber EW | Research square | 37986944 | Res Sq | 2023 Nov 7 |
| The temporal progression of lung immune remodeling during breast cancer metastasis. | McGinnis CS, Miao Z, Superville D, Yao W, Goga A, Reticker-Flynn NE, Winkler J, Satpathy AT | Cancer cell | 38821060 | Cancer Cell | 2024 Jun 10 |
| Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade. | Raposo CJ, Yan PK, Chen AY, Majidi S, Hiam-Galvez KJ, Satpathy AT | bioRxiv : the preprint server for biology | 39990338 | bioRxiv | 2025 Feb 15 |
| Divergent clonal differentiation trajectories of T cell exhaustion. | Daniel B, Yost KE, Hsiung S, Sandor K, Xia Y, Qi Y, Hiam-Galvez KJ, Black M, J Raposo C, Shi Q, Meier SL, Belk JA, Giles JR, Wherry EJ, Chang HY, Egawa T, Satpathy AT | Nature immunology | 36289450 | Nat Immunol | 2022 Nov |
| Runx3 drives a CD8(+) T cell tissue residency program that is absent in CD4(+) T cells. | Fonseca R, Burn TN, Gandolfo LC, Devi S, Park SL, Obers A, Evrard M, Christo SN, Buquicchio FA, Lareau CA, McDonald KM, Sandford SK, Zamudio NM, Zanluqui NG, Zaid A, Speed TP, Satpathy AT, Mueller SN, Carbone FR, Mackay LK | Nature immunology | 35882933 | Nat Immunol | 2022 Aug |
| Regulation of immune signal integration and memory by inflammation-induced chromosome conformation. | Daniel B, Chen AY, Sandor K, Zhang W, Miao Z, Lareau CA, Yost KE, Chang HY, Satpathy AT | bioRxiv : the preprint server for biology | 38496446 | bioRxiv | 2024 Mar 4 |
| FOXO1 is a master regulator of memory programming in CAR T cells. | Doan AE, Mueller KP, Chen AY, Rouin GT, Chen Y, Daniel B, Lattin J, Markovska M, Mozarsky B, Arias-Umana J, Hapke R, Jung IY, Wang A, Xu P, Klysz D, Zuern G, Bashti M, Quinn PJ, Miao Z, Sandor K, Zhang W, Chen GM, Ryu F, Logun M, Hall J, Tan K, Grupp SA, McClory SE, Lareau CA, Fraietta JA, Sotillo E, Satpathy AT, Mackall CL, Weber EW | Nature | 38600391 | Nature | 2024 May |
| Skin basal cell carcinomas assemble a pro-tumorigenic spatially organized and self-propagating Trem2+ myeloid niche. | Haensel D, Daniel B, Gaddam S, Pan C, Fabo T, Bjelajac J, Jussila AR, Gonzalez F, Li NY, Chen Y, Hou J, Patel T, Aasi S, Satpathy AT, Oro AE | Nature communications | 37164949 | Nat Commun | 2023 May 10 |
| Interrogating immune cells and cancer with CRISPR-Cas9. | Buquicchio FA, Satpathy AT | Trends in immunology | 33812776 | Trends Immunol | 2021 May |
| BCL6-dependent TCF-1(+) progenitor cells maintain effector and helper CD4(+) T cell responses to persistent antigen. | Xia Y, Sandor K, Pai JA, Daniel B, Raju S, Wu R, Hsiung S, Qi Y, Yangdon T, Okamoto M, Chou C, Hiam-Galvez KJ, Schreiber RD, Murphy KM, Satpathy AT, Egawa T | Immunity | 35637103 | Immunity | 2022 Jul 12 |
| Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium. | Wang J, Lareau CA, Bautista JL, Gupta AR, Sandor K, Germino J, Yin Y, Arvedson MP, Reeder GC, Cramer NT, Xie F, Ntranos V, Satpathy AT, Anderson MS, Gardner JM | Science immunology | 34767455 | Sci Immunol | 2021 Nov 12 |
| Enhanced T cell effector activity by targeting the Mediator kinase module. | Freitas KA, Belk JA, Sotillo E, Quinn PJ, Ramello MC, Malipatlolla M, Daniel B, Sandor K, Klysz D, Bjelajac J, Xu P, Burdsall KA, Tieu V, Duong VT, Donovan MG, Weber EW, Chang HY, Majzner RG, Espinosa JM, Satpathy AT, Mackall CL | Science (New York, N.Y.) | 36356142 | Science | 2022 Nov 11 |
| Enhanced safety and efficacy of protease-regulated CAR-T cell receptors. | Labanieh L, Majzner RG, Klysz D, Sotillo E, Fisher CJ, Vilches-Moure JG, Pacheco KZB, Malipatlolla M, Xu P, Hui JH, Murty T, Theruvath J, Mehta N, Yamada-Hunter SA, Weber EW, Heitzeneder S, Parker KR, Satpathy AT, Chang HY, Lin MZ, Cochran JR, Mackall CL | Cell | 35483375 | Cell | 2022 May 12 |
| Central control of dynamic gene circuits governs T cell rest and activation. | Arce MM, Umhoefer JM, Arang N, Kasinathan S, Freimer JW, Steinhart Z, Shen H, Pham MTN, Ota M, Wadhera A, Dajani R, Dorovskyi D, Chen YY, Liu Q, Zhou Y, Swaney DL, Obernier K, Shy BR, Carnevale J, Satpathy AT, Krogan NJ, Pritchard JK, Marson A | Nature | 39663454 | Nature | 2025 Jan |
| Epigenetic regulation of T cell exhaustion. | Belk JA, Daniel B, Satpathy AT | Nature immunology | 35624210 | Nat Immunol | 2022 Jun |
| Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations. | Miller TE, Lareau CA, Verga JA, DePasquale EAK, Liu V, Ssozi D, Sandor K, Yin Y, Ludwig LS, El Farran CA, Morgan DM, Satpathy AT, Griffin GK, Lane AA, Love JC, Bernstein BE, Sankaran VG, van Galen P | Nature biotechnology | 35210612 | Nat Biotechnol | 2022 Jul |
| Distinct epigenomic landscapes underlie tissue-specific memory T cell differentiation. | Buquicchio FA, Fonseca R, Yan PK, Wang F, Evrard M, Obers A, Gutierrez JC, Raposo CJ, Belk JA, Daniel B, Zareie P, Yost KE, Qi Y, Yin Y, Nico KF, Tierney FM, Howitt MR, Lareau CA, Satpathy AT, Mackay LK | Immunity | 39043184 | Immunity | 2024 Sep 10 |
| TERRA-LSD1 phase separation promotes R-loop formation for telomere maintenance in ALT cancer cells. | Xu M, Senanayaka D, Zhao R, Chigumira T, Tripathi A, Tones J, Lackner RM, Wondisford AR, Moneysmith LN, Hirschi A, Craig S, Alishiri S, O'Sullivan RJ, Chenoweth DM, Reiter NJ, Zhang H | Nature communications | 38461301 | Nat Commun | 2024 Mar 9 |
| SUMO promotes DNA repair protein collaboration to support alternative telomere lengthening in the absence of PML. | Zhao R, Xu M, Yu X, Wondisford AR, Lackner RM, Salsman J, Dellaire G, Chenoweth DM, O'Sullivan RJ, Zhao X, Zhang H | Genes & development | 39038850 | Genes Dev | 2024 Aug 20 |
| Telomeric SUMO level influences the choices of APB formation pathways and ALT efficiency. | Zhao R, Wivagg A, Lackner RM, Salsman J, Dellaire G, Matunis MJ, Chenoweth DM, Zhao X, Zhang H | bioRxiv : the preprint server for biology | 39896638 | bioRxiv | 2025 Jan 20 |
| SUMO Promotes DNA Repair Protein Collaboration to Support Alterative Telomere Lengthening in the Absence of PML. | Zhao R, Xu M, Wondisford AR, Lackner RM, Salsman J, Dellaire G, Chenoweth DM, O'Sullivan RJ, Zhao X, Zhang H | bioRxiv : the preprint server for biology | 38463993 | bioRxiv | 2024 Feb 29 |
| RAD51AP1 regulates ALT-HDR through chromatin-directed homeostasis of TERRA. | Kaminski N, Wondisford AR, Kwon Y, Lynskey ML, Bhargava R, Barroso-González J, García-Expósito L, He B, Xu M, Mellacheruvu D, Watkins SC, Modesti M, Miller KM, Nesvizhskii AI, Zhang H, Sung P, O'Sullivan RJ | Molecular cell | 36265488 | Mol Cell | 2022 Nov 3 |
| CRISPR Cas13-Based Tools to Track and Manipulate Endogenous Telomeric Repeat-Containing RNAs in Live Cells. | Xu M, Chigumira T, Chen Z, Tones J, Zhao R, Dahl KN, Chenoweth DM, Zhang H | Frontiers in molecular biosciences | 35174207 | Front Mol Biosci | 2021 |
| Frontiers in biomolecular condensate research. | Mayr C, Mittag T, Tang TD, Wen W, Zhang H, Zhang H | Nature cell biology | 36973422 | Nat Cell Biol | 2023 Apr |
| Phase Separation in Biology and Disease; Current Perspectives and Open Questions. | Boeynaems S, Chong S, Gsponer J, Holt L, Milovanovic D, Mitrea DM, Mueller-Cajar O, Portz B, Reilly JF, Reinkemeier CD, Sabari BR, Sanulli S, Shorter J, Sontag E, Strader L, Stachowiak J, Weber SC, White M, Zhang H, Zweckstetter M, Elbaum-Garfinkle S, Kriwacki R | Journal of molecular biology | 36690068 | J Mol Biol | 2023 Mar 1 |
| Cotranslational molecular condensation of cochaperones and assembly factors facilitates axonemal dynein biogenesis. | Li Y, Xu W, Cheng Y, Djenoune L, Zhuang C, Cox AL, Britto CJ, Yuan S, Wang S, Sun Z | Proceedings of the National Academy of Sciences of the United States of America | 39541357 | Proc Natl Acad Sci U S A | 2024 Nov 19 |
| Mechanism of EHMT2-mediated genomic imprinting associated with Prader-Willi syndrome. | Wang SE, Cheng Y, Lim J, Jang MA, Forrest EN, Kim Y, Donahue M, Qiao SN, Xiong Y, Jin J, Wang S, Jiang YH | Research square | 39011107 | Res Sq | 2024 Jul 3 |
| ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization. | Hu M, Yang B, Cheng Y, Radda JSD, Chen Y, Liu M, Wang S | Scientific reports | 33328483 | Sci Rep | 2020 Dec 16 |
| Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue. | Liu M, Yang B, Hu M, Radda JSD, Chen Y, Jin S, Cheng Y, Wang S | Nature protocols | 33903756 | Nat Protoc | 2021 May |
| Tracing the evolution of single-cell cancer 3D genomes: an atlas for cancer gene discovery. | Liu M, Jin S, Agabiti SS, Jensen TB, Yang T, Radda JSD, Ruiz CF, Baldissera G, Rajaei M, Townsend JP, Muzumdar MD, Wang S | bioRxiv : the preprint server for biology | 37546882 | bioRxiv | 2024 Sep 9 |
| Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations. | Patterson B, Yang B, Tanaka Y, Kim KY, Cakir B, Xiang Y, Kim J, Wang S, Park IH | Science advances | 37540754 | Sci Adv | 2023 Aug 4 |
| Foxp3 Orchestrates Reorganization of Chromatin Architecture to Establish Regulatory T Cell Identity. | Liu Z, Lee DS, Liang Y, Zheng Y, Dixon JR | bioRxiv : the preprint server for biology | 36865315 | bioRxiv | 2023 Mar 21 |
| Foxp3 orchestrates reorganization of chromatin architecture to establish regulatory T cell identity. | Liu Z, Lee DS, Liang Y, Zheng Y, Dixon JR | Nature communications | 37932264 | Nat Commun | 2023 Nov 6 |
| Coming full circle: On the origin and evolution of the looping model for enhancer-promoter communication. | Popay TM, Dixon JR | The Journal of biological chemistry | 35691341 | J Biol Chem | 2022 Aug |
| Stress as a Chromatin Landscape Architect. | Vertii A | Frontiers in cell and developmental biology | 34970548 | Front Cell Dev Biol | 2021 |
| Monoallelically expressed noncoding RNAs form nucleolar territories on NOR-containing chromosomes and regulate rRNA expression. | Hao Q, Liu M, Daulatabad SV, Gaffari S, Song YJ, Srivastava R, Bhaskar S, Moitra A, Mangan H, Tseng E, Gilmore RB, Frier SM, Chen X, Wang C, Huang S, Chamberlain S, Jin H, Korlach J, McStay B, Sinha S, Janga SC, Prasanth SG, Prasanth KV | eLife | 38240312 | Elife | 2024 Jan 19 |
| Nucleoli and the nucleoli-centromere association are dynamic during normal development and in cancer. | Rodrigues A, MacQuarrie KL, Freeman E, Lin A, Willis AB, Xu Z, Alvarez AA, Ma Y, White BEP, Foltz DR, Huang S | Molecular biology of the cell | 36753381 | Mol Biol Cell | 2023 Apr 1 |
| Contribution of CENP-F to FOXM1-Mediated Discordant Centromere and Kinetochore Transcriptional Regulation. | Khurana S, Varma D, Foltz DR | Molecular and cellular biology | 38779933 | Mol Cell Biol | 2024 |
| Reduce, Retain, Recycle: Mechanisms for Promoting Histone Protein Degradation versus Stability and Retention. | Hogan AK, Foltz DR | Molecular and cellular biology | 33753462 | Mol Cell Biol | 2021 May 21 |
| Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin in different cell types. | Kumar P, Gholamalamdari O, Zhang Y, Zhang L, Vertii A, van Schaik T, Peric-Hupkes D, Sasaki T, Gilbert DM, van Steensel B, Ma J, Kaufman PD, Belmont AS | bioRxiv : the preprint server for biology | 37961445 | bioRxiv | 2023 Nov 1 |
| The histone H3/H4 chaperone CHAF1B prevents the mislocalization of CENP-A for chromosomal stability. | Shrestha RL, Balachandra V, Kim JH, Rossi A, Vadlamani P, Sethi SC, Ozbun L, Lin S, Cheng KC, Chari R, Karpova TS, Pegoraro G, Foltz DR, Caplen NJ, Basrai MA | Journal of cell science | 37129573 | J Cell Sci | 2023 May 15 |
| PAF49: An RNA Polymerase I subunit essential for rDNA transcription and stabilization of PAF53. | McNamar R, Freeman E, Baylor KN, Fakhouri AM, Huang S, Knutson BA, Rothblum LI | The Journal of biological chemistry | 37356716 | J Biol Chem | 2023 Aug |
| Dynamic chromosome association with nuclear organelles in living cells. | Phan LMU, Yeo WH, Zhang HF, Huang S | Histochemistry and cell biology | 38811432 | Histochem Cell Biol | 2024 Jul |
| Contribution of CENP-F to FOXM1-mediated discordant centromere and kinetochore transcriptional regulation. | Khurana S, Foltz DR | bioRxiv : the preprint server for biology | 38234763 | bioRxiv | 2023 Dec 27 |
| The perinucleolar compartment: structure, function, and utility in anti-cancer drug development. | Makeyev EV, Huang S | Nucleus (Austin, Tex.) | 38281066 | Nucleus | 2024 Dec |
| Attractor Ranked Radial Basis Function Network: A Nonparametric Forecasting Approach for Chaotic Dynamic Systems. | Masnadi-Shirazi M, Subramaniam S | Scientific reports | 32123218 | Sci Rep | 2020 Mar 2 |
| STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts. | Zimmer JT, Rosa-Mercado NA, Canzio D, Steitz JA, Simon MD | Molecular cell | 34520723 | Mol Cell | 2021 Nov 4 |
| Stress-induced RNA-chromatin interactions promote endothelial dysfunction. | Calandrelli R, Xu L, Luo Y, Wu W, Fan X, Nguyen T, Chen CJ, Sriram K, Tang X, Burns AB, Natarajan R, Chen ZB, Zhong S | Nature communications | 33060583 | Nat Commun | 2020 Oct 15 |
| From structure to function, how bioinformatics help to reveal functions of our genomes. | Zheng X, Zhong S | Genome biology | 28950915 | Genome Biol | 2017 Sep 26 |
| Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. | Biancon G, Joshi P, Zimmer JT, Hunck T, Gao Y, Lessard MD, Courchaine E, Barentine AES, Machyna M, Botti V, Qin A, Gbyli R, Patel A, Song Y, Kiefer L, Viero G, Neuenkirchen N, Lin H, Bewersdorf J, Simon MD, Neugebauer KM, Tebaldi T, Halene S | Molecular cell | 35303483 | Mol Cell | 2022 Mar 17 |
| The three-dimensional organization of the genome in cellular senescence and age-associated diseases. | Evans SA, Horrell J, Neretti N | Seminars in cell & developmental biology | 30031215 | Semin Cell Dev Biol | 2019 Jun |
| RNAs as Proximity-Labeling Media for Identifying Nuclear Speckle Positions Relative to the Genome. | Chen W, Yan Z, Li S, Huang N, Huang X, Zhang J, Zhong S | iScience | 30240742 | iScience | 2018 Jun 29 |
| Bayesian Estimation of Three-Dimensional Chromosomal Structure from Single-Cell Hi-C Data. | Rosenthal M, Bryner D, Huffer F, Evans S, Srivastava A, Neretti N | Journal of computational biology : a journal of computational molecular cell biology | 31211598 | J Comput Biol | 2019 Nov |
| Co-expression Network Approach Reveals Functional Similarities among Diseases Affecting Human Skeletal Muscle. | Mukund K, Subramaniam S | Frontiers in physiology | 29249983 | Front Physiol | 2017 |
| GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data. | Calandrelli R, Wu Q, Guan J, Zhong S | Genomics, proteomics & bioinformatics | 30553884 | Genomics Proteomics Bioinformatics | 2018 Oct |
| Skeletal muscle: A review of molecular structure and function, in health and disease. | Mukund K, Subramaniam S | Wiley interdisciplinary reviews. Systems biology and medicine | 31407867 | Wiley Interdiscip Rev Syst Biol Med | 2020 Jan |
| A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome. | Lu J, Cao X, Zhong S | PLoS computational biology | 30586383 | PLoS Comput Biol | 2018 Dec |
| Mapping RNA-chromatin interactions by sequencing with iMARGI. | Wu W, Yan Z, Nguyen TC, Bouman Chen Z, Chien S, Zhong S | Nature protocols | 31619811 | Nat Protoc | 2019 Nov |
| EpiAlignment: alignment with both DNA sequence and epigenomic data. | Lu J, Cao X, Zhong S | Nucleic acids research | 31114924 | Nucleic Acids Res | 2019 Jul 2 |
| Evaluating Enhancer Function and Transcription. | Field A, Adelman K | Annual review of biochemistry | 32197056 | Annu Rev Biochem | 2020 Jun 20 |
| Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression. | Rosa-Mercado NA, Zimmer JT, Apostolidi M, Rinehart J, Simon MD, Steitz JA | Molecular cell | 33400923 | Mol Cell | 2021 Feb 4 |
| The maternal blood lipidome is indicative of the pathogenesis of severe preeclampsia. | He B, Liu Y, Maurya MR, Benny P, Lassiter C, Li H, Subramaniam S, Garmire LX | Journal of lipid research | 34547287 | J Lipid Res | 2021 |
| Modular and mechanistic changes across stages of colorectal cancer. | Rahiminejad S, Maurya MR, Mukund K, Subramaniam S | BMC cancer | 35448980 | BMC Cancer | 2022 Apr 21 |
| The coilin N-terminus mediates multivalent interactions between coilin and Nopp140 to form and maintain Cajal bodies. | Courchaine E, Gelles-Watnick S, Machyna M, Straube K, Sauyet S, Enright J, Neugebauer KM | Nature communications | 36224177 | Nat Commun | 2022 Oct 12 |
| Long noncoding RNA LEENE promotes angiogenesis and ischemic recovery in diabetes models. | Tang X, Luo Y, Yuan D, Calandrelli R, Malhi NK, Sriram K, Miao Y, Lou CH, Tsark W, Tapia A, Chen AT, Zhang G, Roeth D, Kalkum M, Wang ZV, Chien S, Natarajan R, Cooke JP, Zhong S, Chen ZB | The Journal of clinical investigation | 36512424 | J Clin Invest | 2023 Feb 1 |
| Topological and functional comparison of community detection algorithms in biological networks. | Rahiminejad S, Maurya MR, Subramaniam S | BMC bioinformatics | 31029085 | BMC Bioinformatics | 2019 Apr 27 |
| Integrative analysis of vascular endothelial cell genomic features identifies AIDA as a coronary artery disease candidate gene. | Lalonde S, Codina-Fauteux VA, de Bellefon SM, Leblanc F, Beaudoin M, Simon MM, Dali R, Kwan T, Lo KS, Pastinen T, Lettre G | Genome biology | 31287004 | Genome Biol | 2019 Jul 8 |
| Toward a Three-Dimensional Chromosome Shape Alphabet. | Soto C, Bryner D, Neretti N, Srivastava A | Journal of computational biology : a journal of computational molecular cell biology | 33720766 | J Comput Biol | 2021 Jun |
| Alu transposable elements rewire enhancer-promoter network through RNA pairing. | Wen X, Zhong S | Molecular cell | 37738962 | Mol Cell | 2023 Sep 21 |
| Single-cell multiplex chromatin and RNA interactions in aging human brain. | Wen X, Luo Z, Zhao W, Calandrelli R, Nguyen TC, Wan X, Richard JLC, Zhong S | bioRxiv : the preprint server for biology | 37425846 | bioRxiv | 2024 Mar 4 |
| Single-cell multiplex chromatin and RNA interactions in ageing human brain. | Wen X, Luo Z, Zhao W, Calandrelli R, Nguyen TC, Wan X, Charles Richard JL, Zhong S | Nature | 38538789 | Nature | 2024 Apr |
| Atheroprotective Flow Upregulates ITPR3 (Inositol 1,4,5-Trisphosphate Receptor 3) in Vascular Endothelium via KLF4 (Krüppel-Like Factor 4)-Mediated Histone Modifications. | He M, Huang TS, Li S, Hong HC, Chen Z, Martin M, Zhou X, Huang HY, Su SH, Zhang J, Wang WT, Kang J, Huang HD, Zhang J, Chien S, Shyy JY | Arteriosclerosis, thrombosis, and vascular biology | 30917677 | Arterioscler Thromb Vasc Biol | 2019 May |
| Emerging Roles of Non-Coding RNA Transcription. | Kaikkonen MU, Adelman K | Trends in biochemical sciences | 30145998 | Trends Biochem Sci | 2018 Sep |
| RNA, Action through Interactions. | Nguyen TC, Zaleta-Rivera K, Huang X, Dai X, Zhong S | Trends in genetics : TIG | 30177410 | Trends Genet | 2018 Nov |
| Genome-wide colocalization of RNA-DNA interactions and fusion RNA pairs. | Yan Z, Huang N, Wu W, Chen W, Jiang Y, Chen J, Huang X, Wen X, Xu J, Jin Q, Zhang K, Chen Z, Chien S, Zhong S | Proceedings of the National Academy of Sciences of the United States of America | 30718424 | Proc Natl Acad Sci U S A | 2019 Feb 19 |
| Histone Signatures Predict Therapeutic Efficacy in Breast Cancer. | Mollah SA, Subramaniam S | IEEE open journal of engineering in medicine and biology | 32412527 | IEEE Open J Eng Med Biol | 2020 |
| GIVE: portable genome browsers for personal websites. | Cao X, Yan Z, Wu Q, Zheng A, Zhong S | Genome biology | 30016975 | Genome Biol | 2018 Jul 18 |
| Enhancer hubs and loop collisions identified from single-allele topologies. | Allahyar A, Vermeulen C, Bouwman BAM, Krijger PHL, Verstegen MJAM, Geeven G, van Kranenburg M, Pieterse M, Straver R, Haarhuis JHI, Jalink K, Teunissen H, Renkens IJ, Kloosterman WP, Rowland BD, de Wit E, de Ridder J, de Laat W | Nature genetics | 29988121 | Nat Genet | 2018 Aug |
| Coordinated histone modifications and chromatin reorganization in a single cell revealed by FRET biosensors. | Peng Q, Lu S, Shi Y, Pan Y, Limsakul P, Chernov AV, Qiu J, Chai X, Shi Y, Wang P, Ji Y, Li YJ, Strongin AY, Verkhusha VV, Izpisua Belmonte JC, Ren B, Wang Y, Chien S, Wang Y | Proceedings of the National Academy of Sciences of the United States of America | 30478057 | Proc Natl Acad Sci U S A | 2018 Dec 11 |
| Time varying causal network reconstruction of a mouse cell cycle. | Masnadi-Shirazi M, Maurya MR, Pao G, Ke E, Verma IM, Subramaniam S | BMC bioinformatics | 31142274 | BMC Bioinformatics | 2019 May 29 |
| DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats. | Brocks D, Schmidt CR, Daskalakis M, Jang HS, Shah NM, Li D, Li J, Zhang B, Hou Y, Laudato S, Lipka DB, Schott J, Bierhoff H, Assenov Y, Helf M, Ressnerova A, Islam MS, Lindroth AM, Haas S, Essers M, Imbusch CD, Brors B, Oehme I, Witt O, Lübbert M, Mallm JP, Rippe K, Will R, Weichenhan D, Stoecklin G, Gerhäuser C, Oakes CC, Wang T, Plass C | Nature genetics | 28604729 | Nat Genet | 2017 Jul |
| EpiCompare: an online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features. | He Y, Wang T | Bioinformatics (Oxford, England) | 28605501 | Bioinformatics | 2017 Oct 15 |
| An Evolutionary Insertion in the Mxra8 Receptor-Binding Site Confers Resistance to Alphavirus Infection and Pathogenesis. | Kim AS, Zimmerman O, Fox JM, Nelson CA, Basore K, Zhang R, Durnell L, Desai C, Bullock C, Deem SL, Oppenheimer J, Shapiro B, Wang T, Cherry S, Coyne CB, Handley SA, Landis MJ, Fremont DH, Diamond MS | Cell host & microbe | 32075743 | Cell Host Microbe | 2020 Mar 11 |
| Perinatal deiodinase 2 expression in hepatocytes defines epigenetic susceptibility to liver steatosis and obesity. | Fonseca TL, Fernandes GW, McAninch EA, Bocco BM, Abdalla SM, Ribeiro MO, Mohácsik P, Fekete C, Li D, Xing X, Wang T, Gereben B, Bianco AC | Proceedings of the National Academy of Sciences of the United States of America | 26508642 | Proc Natl Acad Sci U S A | 2015 Nov 10 |
| Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. | Sundaram V, Choudhary MN, Pehrsson E, Xing X, Fiore C, Pandey M, Maricque B, Udawatta M, Ngo D, Chen Y, Paguntalan A, Ray T, Hughes A, Cohen BA, Wang T | Nature communications | 28348391 | Nat Commun | 2017 Mar 28 |
| Mammalian genome innovation through transposon domestication. | Modzelewski AJ, Gan Chong J, Wang T, He L | Nature cell biology | 36008480 | Nat Cell Biol | 2022 Sep |
| Soluble inflammatory mediators induce transcriptional re-organization that is independent of dna methylation changes in cultured human chorionic villous trophoblasts. | Jiang K, Wong L, Chen Y, Xing X, Li D, Wang T, Jarvis JN | Journal of reproductive immunology | 29800761 | J Reprod Immunol | 2018 Aug |
| Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq. | Xing X, Zhang B, Li D, Wang T | Methods in molecular biology (Clifton, N.J.) | 29224147 | Methods Mol Biol | 2018 |
| A non-randomized procedure for large-scale heterogeneous multiple discrete testing based on randomized tests. | Dai X, Lin N, Li D, Wang T | Biometrics | 30387496 | Biometrics | 2019 Jun |
| Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer's disease pathology and cognitive symptoms. | Li P, Marshall L, Oh G, Jakubowski JL, Groot D, He Y, Wang T, Petronis A, Labrie V | Nature communications | 31113950 | Nat Commun | 2019 May 21 |
| A high-fat diet alters genome-wide DNA methylation and gene expression in SM/J mice. | Keleher MR, Zaidi R, Hicks L, Shah S, Xing X, Li D, Wang T, Cheverud JM | BMC genomics | 30526554 | BMC Genomics | 2018 Dec 7 |
| Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity. | Pan Y, Daito T, Sasaki Y, Chung YH, Xing X, Pondugula S, Swamidass SJ, Wang T, Kim AH, Yano H | Scientific reports | 27516062 | Sci Rep | 2016 Aug 12 |
| Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. | Gu J, Stevens M, Xing X, Li D, Zhang B, Payton JE, Oltz EM, Jarvis JN, Jiang K, Cicero T, Costello JF, Wang T | G3 (Bethesda, Md.) | 26888867 | G3 (Bethesda) | 2016 Apr 7 |
| Parent-of-Origin Effects of the APOB Gene on Adiposity in Young Adults. | Hochner H, Allard C, Granot-Hershkovitz E, Chen J, Sitlani CM, Sazdovska S, Lumley T, McKnight B, Rice K, Enquobahrie DA, Meigs JB, Kwok P, Hivert MF, Borecki IB, Gomez F, Wang T, van Duijn C, Amin N, Rotter JI, Stamatoyannopoulos J, Meiner V, Manor O, Dupuis J, Friedlander Y, Siscovick DS | PLoS genetics | 26451733 | PLoS Genet | 2015 Oct |
| Co-opted transposons help perpetuate conserved higher-order chromosomal structures. | Choudhary MN, Friedman RZ, Wang JT, Jang HS, Zhuo X, Wang T | Genome biology | 31973766 | Genome Biol | 2020 Jan 24 |
| Characterization of a Mouse Model of Börjeson-Forssman-Lehmann Syndrome. | Cheng C, Deng PY, Ikeuchi Y, Yuede C, Li D, Rensing N, Huang J, Baldridge D, Maloney SE, Dougherty JD, Constantino J, Jahani-Asl A, Wong M, Wozniak DF, Wang T, Klyachko VA, Bonni A | Cell reports | 30403997 | Cell Rep | 2018 Nov 6 |
| Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human. | Liu S, Yu Y, Zhang S, Cole JB, Tenesa A, Wang T, McDaneld TG, Ma L, Liu GE, Fang L | BMC biology | 32620158 | BMC Biol | 2020 Jul 3 |
| The qBED track: a novel genome browser visualization for point processes. | Moudgil A, Li D, Hsu S, Purushotham D, Wang T, Mitra RD | Bioinformatics (Oxford, England) | 32941613 | Bioinformatics | 2021 May 23 |
| Cellular diversity of the regenerating caudal fin. | Hou Y, Lee HJ, Chen Y, Ge J, Osman FOI, McAdow AR, Mokalled MH, Johnson SL, Zhao G, Wang T | Science advances | 32851162 | Sci Adv | 2020 Aug |
| Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors. | Wu J, Krchma K, Lee HJ, Prabhakar S, Wang X, Zhao H, Xing X, Seong RH, Fremont DH, Artyomov MN, Wang T, Choi K | Cell reports | 33207205 | Cell Rep | 2020 Nov 17 |
| Whole-Genome DNA Methylation Profiling Identifies Epigenetic Signatures of Uterine Carcinosarcoma. | Li J, Xing X, Li D, Zhang B, Mutch DG, Hagemann IS, Wang T | Neoplasia (New York, N.Y.) | 28088687 | Neoplasia | 2017 Feb |
| Comparison of differential accessibility analysis strategies for ATAC-seq data. | Gontarz P, Fu S, Xing X, Liu S, Miao B, Bazylianska V, Sharma A, Madden P, Cates K, Yoo A, Moszczynska A, Wang T, Zhang B | Scientific reports | 32576878 | Sci Rep | 2020 Jun 23 |
| FeatSNP: An Interactive Database for Brain-Specific Epigenetic Annotation of Human SNPs. | Ma CY, Madden P, Gontarz P, Wang T, Zhang B | Frontiers in genetics | 31001319 | Front Genet | 2019 |
| Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation. | Zhou J, Sears RL, Xing X, Zhang B, Li D, Rockweiler NB, Jang HS, Choudhary MNK, Lee HJ, Lowdon RF, Arand J, Tabers B, Gu CC, Cicero TJ, Wang T | BMC genomics | 28899353 | BMC Genomics | 2017 Sep 12 |
| MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts. | Abernathy DG, Kim WK, McCoy MJ, Lake AM, Ouwenga R, Lee SW, Xing X, Li D, Lee HJ, Heuckeroth RO, Dougherty JD, Wang T, Yoo AS | Cell stem cell | 28886366 | Cell Stem Cell | 2017 Sep 7 |
| Noncoding genetic variation in GATA3 increases acute lymphoblastic leukemia risk through local and global changes in chromatin conformation. | Yang H, Zhang H, Luan Y, Liu T, Yang W, Roberts KG, Qian MX, Zhang B, Yang W, Perez-Andreu V, Xu J, Iyyanki S, Kuang D, Stasiak LA, Reshmi SC, Gastier-Foster J, Smith C, Pui CH, Evans WE, Hunger SP, Platanias LC, Relling MV, Mullighan CG, Loh ML, Yue F, Yang JJ | Nature genetics | 35115686 | Nat Genet | 2022 Feb |
| AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis. | Liu S, Li D, Lyu C, Gontarz PM, Miao B, Madden PAF, Wang T, Zhang B | Genomics, proteomics & bioinformatics | 34273560 | Genomics Proteomics Bioinformatics | 2021 Aug |
| Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer. | Iyyanki T, Zhang B, Wang Q, Hou Y, Jin Q, Xu J, Yang H, Liu T, Wang X, Song F, Luan Y, Yamashita H, Chien R, Lyu H, Zhang L, Wang L, Warrick J, Raman JD, Meeks JJ, DeGraff DJ, Yue F | Genome biology | 33858483 | Genome Biol | 2021 Apr 15 |
| Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease. | Zhang B, Kim MY, Elliot G, Zhou Y, Zhao G, Li D, Lowdon RF, Gormley M, Kapidzic M, Robinson JF, McMaster MT, Hong C, Mazor T, Hamilton E, Sears RL, Pehrsson EC, Marra MA, Jones SJM, Bilenky M, Hirst M, Wang T, Costello JF, Fisher SJ | Developmental cell | 33891899 | Dev Cell | 2021 May 3 |
| Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis. | Karlow JA, Miao B, Xing X, Wang T, Zhang B | Communications biology | 34021236 | Commun Biol | 2021 May 21 |
| Spatial transcriptomics reveals a cnidarian segment polarity program in Nematostella vectensis. | He S, Shao W, Chen SC, Wang T, Gibson MC | Current biology : CB | 37315559 | Curr Biol | 2023 Jul 10 |
| WashU Epigenome Browser update 2019. | Li D, Hsu S, Purushotham D, Sears RL, Wang T | Nucleic acids research | 31165883 | Nucleic Acids Res | 2019 Jul 2 |
| Genome-wide DNA methylation profiling of primary colorectal laterally spreading tumors identifies disease-specific epimutations on common pathways. | Zhu L, Yan F, Wang Z, Dong H, Bian C, Wang T, Yu E, Li J | International journal of cancer | 30183087 | Int J Cancer | 2018 Nov 15 |
| Jointly characterizing epigenetic dynamics across multiple human cell types. | Zhang Y, An L, Yue F, Hardison RC | Nucleic acids research | 27095202 | Nucleic Acids Res | 2016 Aug 19 |
| Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility. | Lee HJ, Hou Y, Chen Y, Dailey ZZ, Riddihough A, Jang HS, Wang T, Johnson SL | Genome biology | 32106888 | Genome Biol | 2020 Feb 27 |
| DNA methyltransferase 3b regulates articular cartilage homeostasis by altering metabolism. | Shen J, Wang C, Li D, Xu T, Myers J, Ashton JM, Wang T, Zuscik MJ, McAlinden A, O'Keefe RJ | JCI insight | 28614801 | JCI Insight | 2017 Jun 15 |
| Epigenomic differences in the human and chimpanzee genomes are associated with structural variation. | Zhuo X, Du AY, Pehrsson EC, Li D, Wang T | Genome research | 33303495 | Genome Res | 2021 Feb |
| DeepH&M: Estimating single-CpG hydroxymethylation and methylation levels from enrichment and restriction enzyme sequencing methods. | He Y, Jang HS, Xing X, Li D, Vasek MJ, Dougherty JD, Wang T | Science advances | 32937429 | Sci Adv | 2020 Jul |
| An integrative ENCODE resource for cancer genomics. | Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, Ung M, Ma L, Yu S, Cao Q, Harmanci A, Yan KK, Sethi A, Gürsoy G, Schoenberg MR, Rozowsky J, Warrell J, Emani P, Yang YT, Galeev T, Kong X, Liu S, Li X, Krishnan J, Feng Y, Rivera-Mulia JC, Adrian J, Broach JR, Bolt M, Moran J, Fitzgerald D, Dileep V, Liu T, Mei S, Sasaki T, Trevilla-Garcia C, Wang S, Wang Y, Zang C, Wang D, Klein RJ, Snyder M, Gilbert DM, Yip K, Cheng C, Yue F, Liu XS, White KP, Gerstein M | Nature communications | 32728046 | Nat Commun | 2020 Jul 29 |
| ETV2/ER71 regulates hematopoietic regeneration by promoting hematopoietic stem cell proliferation. | Xu CX, Lee TJ, Sakurai N, Krchma K, Liu F, Li D, Wang T, Choi K | The Journal of experimental medicine | 28461595 | J Exp Med | 2017 Jun 5 |
| Genome-wide association study identifies a novel locus for cannabis dependence. | Agrawal A, Chou YL, Carey CE, Baranger DAA, Zhang B, Sherva R, Wetherill L, Kapoor M, Wang JC, Bertelsen S, Anokhin AP, Hesselbrock V, Kramer J, Lynskey MT, Meyers JL, Nurnberger JI, Rice JP, Tischfield J, Bierut LJ, Degenhardt L, Farrer LA, Gelernter J, Hariri AR, Heath AC, Kranzler HR, Madden PAF, Martin NG, Montgomery GW, Porjesz B, Wang T, Whitfield JB, Edenberg HJ, Foroud T, Goate AM, Bogdan R, Nelson EC | Molecular psychiatry | 29112194 | Mol Psychiatry | 2018 May |
| Robust principal component analysis for accurate outlier sample detection in RNA-Seq data. | Chen X, Zhang B, Wang T, Bonni A, Zhao G | BMC bioinformatics | 32600248 | BMC Bioinformatics | 2020 Jun 29 |
| A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development. | Modzelewski AJ, Shao W, Chen J, Lee A, Qi X, Noon M, Tjokro K, Sales G, Biton A, Anand A, Speed TP, Xuan Z, Wang T, Risso D, He L | Cell | 34644528 | Cell | 2021 Oct 28 |
| Evolution of Epigenetic Regulation in Vertebrate Genomes. | Lowdon RF, Jang HS, Wang T | Trends in genetics : TIG | 27080453 | Trends Genet | 2016 May |
| Cell-type-specific 3D epigenomes in the developing human cortex. | Song M, Pebworth MP, Yang X, Abnousi A, Fan C, Wen J, Rosen JD, Choudhary MNK, Cui X, Jones IR, Bergenholtz S, Eze UC, Juric I, Li B, Maliskova L, Lee J, Liu W, Pollen AA, Li Y, Wang T, Hu M, Kriegstein AR, Shen Y | Nature | 33057195 | Nature | 2020 Nov |
| The epigenomic landscape of transposable elements across normal human development and anatomy. | Pehrsson EC, Choudhary MNK, Sundaram V, Wang T | Nature communications | 31822674 | Nat Commun | 2019 Dec 10 |
| Analysis of Hi-C Data for Discovery of Structural Variations in Cancer. | Song F, Xu J, Dixon J, Yue F | Methods in molecular biology (Clifton, N.J.) | 34415534 | Methods Mol Biol | 2022 |
| HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. | Yang T, Zhang F, Yardımcı GG, Song F, Hardison RC, Noble WS, Yue F, Li Q | Genome research | 28855260 | Genome Res | 2017 Nov |
| Transposable elements drive widespread expression of oncogenes in human cancers. | Jang HS, Shah NM, Du AY, Dailey ZZ, Pehrsson EC, Godoy PM, Zhang D, Li D, Xing X, Kim S, O'Donnell D, Gordon JI, Wang T | Nature genetics | 30926969 | Nat Genet | 2019 Apr |
| Long-Term In Vitro Expansion of Epithelial Stem Cells Enabled by Pharmacological Inhibition of PAK1-ROCK-Myosin II and TGF-β Signaling. | Zhang C, Lee HJ, Shrivastava A, Wang R, McQuiston TJ, Challberg SS, Pollok BA, Wang T | Cell reports | 30332641 | Cell Rep | 2018 Oct 16 |
| Derivation of trophoblast stem cells from naïve human pluripotent stem cells. | Dong C, Beltcheva M, Gontarz P, Zhang B, Popli P, Fischer LA, Khan SA, Park KM, Yoon EJ, Xing X, Kommagani R, Wang T, Solnica-Krezel L, Theunissen TW | eLife | 32048992 | Elife | 2020 Feb 12 |
| Non-small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Never-smokers. | Karlow JA, Pehrsson EC, Xing X, Watson M, Devarakonda S, Govindan R, Wang T | Genomics, proteomics & bioinformatics | 37742993 | Genomics Proteomics Bioinformatics | 2023 Oct |
| Spatial transcriptomics reveals a conserved segment polarity program that governs muscle patterning in Nematostella vectensis. | He S, Shao W, Chen SC, Wang T, Gibson MC | bioRxiv : the preprint server for biology | 36711919 | bioRxiv | 2023 Jan 10 |
| Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the "Gene-Battery" Model. | Sundaram V, Wang T | BioEssays : news and reviews in molecular, cellular and developmental biology | 29206283 | Bioessays | 2018 Jan |
| A map of cis-regulatory elements and 3D genome structures in zebrafish. | Yang H, Luan Y, Liu T, Lee HJ, Fang L, Wang Y, Wang X, Zhang B, Jin Q, Ang KC, Xing X, Wang J, Xu J, Song F, Sriranga I, Khunsriraksakul C, Salameh T, Li D, Choudhary MNK, Topczewski J, Wang K, Gerhard GS, Hardison RC, Wang T, Cheng KC, Yue F | Nature | 33239788 | Nature | 2020 Dec |
| Tissue-specific usage of transposable element-derived promoters in mouse development. | Miao B, Fu S, Lyu C, Gontarz P, Wang T, Zhang B | Genome biology | 32988383 | Genome Biol | 2020 Sep 28 |
| Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish. | Lee HJ, Hou Y, Maeng JH, Shah NM, Chen Y, Lawson HA, Yang H, Yue F, Wang T | Genome research | 35649578 | Genome Res | 2022 Jul |
| Uncovering the transcriptomic and epigenomic landscape of nicotinic receptor genes in non-neuronal tissues. | Zhang B, Madden P, Gu J, Xing X, Sankar S, Flynn J, Kroll K, Wang T | BMC genomics | 28583088 | BMC Genomics | 2017 Jun 5 |
| Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer. | Lowdon RF, Wang T | PloS one | 28333948 | PLoS One | 2017 |
| The Hologram in My Hand: How Effective is Interactive Exploration of 3D Visualizations in Immersive Tangible Augmented Reality? | Bach B, Sicat R, Beyer J, Cordeil M, Pfister H | IEEE transactions on visualization and computer graphics | 28866590 | IEEE Trans Vis Comput Graph | 2018 Jan |
| HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples. | Lekschas F, Bach B, Kerpedjiev P, Gehlenborg N, Pfister H | IEEE transactions on visualization and computer graphics | 28866592 | IEEE Trans Vis Comput Graph | 2018 Jan |
| Chromoscope: interactive multiscale visualization for structural variation in human genomes. | L'Yi S, Maziec D, Stevens V, Manz T, Veit A, Berselli M, Park PJ, Głodzik D, Gehlenborg N | Nature methods | 37914857 | Nat Methods | 2023 Dec |
| Toward a common standard for data and specimen provenance in life sciences. | Wittner R, Holub P, Mascia C, Frexia F, Müller H, Plass M, Allocca C, Betsou F, Burdett T, Cancio I, Chapman A, Chapman M, Courtot M, Curcin V, Eder J, Elliot M, Exter K, Goble C, Golebiewski M, Kisler B, Kremer A, Leo S, Lin-Gibson S, Marsano A, Mattavelli M, Moore J, Nakae H, Perseil I, Salman A, Sluka J, Soiland-Reyes S, Strambio-De-Castillia C, Sussman M, Swedlow JR, Zatloukal K, Geiger J | Learning health systems | 38249839 | Learn Health Syst | 2024 Jan |
| Visual Pattern-Driven Exploration of Big Data. | Behrisch M, Schreck T, Krüger R, Gehlenborg N, Lekschas F, Pfister H | 2018 International Symposium on Big Data Visual and Immersive Analytics (BDVA) : Konstanz, Germany, October 17 -19, 2018. IEEE International Symposium on Big Data Visual and Immersive Analytics (4th : 2018 : Konstanz, Germany) | 31396383 | 2018 Int Symp Big Data Vis Immers Analyt (BDVA) (2018) | 2018 Oct |
| HiNT: a computational method for detecting copy number variations and translocations from Hi-C data. | Wang S, Lee S, Chu C, Jain D, Kerpedjiev P, Nelson GM, Walsh JM, Alver BH, Park PJ | Genome biology | 32293513 | Genome Biol | 2020 Mar 23 |
| DXR: A Toolkit for Building Immersive Data Visualizations. | Sicat R, Li J, Choi J, Cordeil M, Jeong WK, Bach B, Pfister H | IEEE transactions on visualization and computer graphics | 30136991 | IEEE Trans Vis Comput Graph | 2019 Jan |
| Resources and challenges for integrative analysis of nuclear architecture data. | Jung YL, Kirli K, Alver BH, Park PJ | Current opinion in genetics & development | 33450522 | Curr Opin Genet Dev | 2021 Apr |
| Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs. | Lee S, Bakker CR, Vitzthum C, Alver BH, Park PJ | Bioinformatics (Oxford, England) | 34978573 | Bioinformatics | 2022 Mar 4 |
| Determination of complete chromosomal haplotypes by bulk DNA sequencing. | Tourdot RW, Brunette GJ, Pinto RA, Zhang CZ | Genome biology | 33957932 | Genome Biol | 2021 May 6 |
| Genome-wide enhancer maps link risk variants to disease genes. | Nasser J, Bergman DT, Fulco CP, Guckelberger P, Doughty BR, Patwardhan TA, Jones TR, Nguyen TH, Ulirsch JC, Lekschas F, Mualim K, Natri HM, Weeks EM, Munson G, Kane M, Kang HY, Cui A, Ray JP, Eisenhaure TM, Collins RL, Dey K, Pfister H, Price AL, Epstein CB, Kundaje A, Xavier RJ, Daly MJ, Huang H, Finucane HK, Hacohen N, Lander ES, Engreitz JM | Nature | 33828297 | Nature | 2021 May |
| QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy. | Boehm U, Nelson G, Brown CM, Bagley S, Bajcsy P, Bischof J, Dauphin A, Dobbie IM, Eriksson JE, Faklaris O, Fernandez-Rodriguez J, Ferrand A, Gelman L, Gheisari A, Hartmann H, Kukat C, Laude A, Mitkovski M, Munck S, North AJ, Rasse TM, Resch-Genger U, Schuetz LC, Seitz A, Strambio-De-Castillia C, Swedlow JR, Nitschke R | Nature methods | 34021279 | Nat Methods | 2021 Dec |
| Community-developed checklists for publishing images and image analyses. | Schmied C, Nelson MS, Avilov S, Bakker GJ, Bertocchi C, Bischof J, Boehm U, Brocher J, Carvalho M, Chiritescu C, Christopher J, Cimini BA, Conde-Sousa E, Ebner M, Ecker R, Eliceiri K, Fernandez-Rodriguez J, Gaudreault N, Gelman L, Grunwald D, Gu T, Halidi N, Hammer M, Hartley M, Held M, Jug F, Kapoor V, Koksoy AA, Lacoste J, Dévédec SL, Guyader SL, Liu P, Martins GG, Mathur A, Miura K, Montero Llopis P, Nitschke R, North A, Parslow AC, Payne-Dwyer A, Plantard L, Ali R, Schroth-Diez B, Schütz L, Scott RT, Seitz A, Selchow O, Sharma VP, Spitaler M, Srinivasan S, Strambio-De-Castillia C, Taatjes D, Tischer C, Jambor HK | ArXiv | 36824427 | ArXiv | 2023 Sep 14 |
| Community-developed checklists for publishing images and image analyses. | Schmied C, Nelson MS, Avilov S, Bakker GJ, Bertocchi C, Bischof J, Boehm U, Brocher J, Carvalho MT, Chiritescu C, Christopher J, Cimini BA, Conde-Sousa E, Ebner M, Ecker R, Eliceiri K, Fernandez-Rodriguez J, Gaudreault N, Gelman L, Grunwald D, Gu T, Halidi N, Hammer M, Hartley M, Held M, Jug F, Kapoor V, Koksoy AA, Lacoste J, Le Dévédec S, Le Guyader S, Liu P, Martins GG, Mathur A, Miura K, Montero Llopis P, Nitschke R, North A, Parslow AC, Payne-Dwyer A, Plantard L, Ali R, Schroth-Diez B, Schütz L, Scott RT, Seitz A, Selchow O, Sharma VP, Spitaler M, Srinivasan S, Strambio-De-Castillia C, Taatjes D, Tischer C, Jambor HK | Nature methods | 37710020 | Nat Methods | 2024 Feb |
| HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data. | Jain D, Chu C, Alver BH, Lee S, Lee EA, Park PJ | Bioinformatics (Oxford, England) | 33136153 | Bioinformatics | 2021 May 23 |
| Tasks, Techniques, and Tools for Genomic Data Visualization. | Nusrat S, Harbig T, Gehlenborg N | Computer graphics forum : journal of the European Association for Computer Graphics | 31768085 | Comput Graph Forum | 2019 Jun |
| Hormonal Imbalances in Prader-Willi and Schaaf-Yang Syndromes Imply the Evolution of Specific Regulation of Hypothalamic Neuroendocrine Function in Mammals. | Hoyos Sanchez MC, Bayat T, Gee RRF, Fon Tacer K | International journal of molecular sciences | 37685915 | Int J Mol Sci | 2023 Aug 23 |
| The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data. | Reiff SB, Schroeder AJ, Kırlı K, Cosolo A, Bakker C, Mercado L, Lee S, Veit AD, Balashov AK, Vitzthum C, Ronchetti W, Pitman KM, Johnson J, Ehmsen SR, Kerpedjiev P, Abdennur N, Imakaev M, Öztürk SU, Çamoğlu U, Mirny LA, Gehlenborg N, Alver BH, Park PJ | Nature communications | 35501320 | Nat Commun | 2022 May 2 |
| Peax: Interactive Visual Pattern Search in Sequential Data Using Unsupervised Deep Representation Learning. | Lekschas F, Peterson B, Haehn D, Ma E, Gehlenborg N, Pfister H | Computer graphics forum : journal of the European Association for Computer Graphics | 34334852 | Comput Graph Forum | 2020 Jun |
| MDEmic: a metadata annotation tool to facilitate management of FAIR image data in the bioimaging community. | Kunis S, Hänsch S, Schmidt C, Wong F, Strambio-De-Castillia C, Weidtkamp-Peters S | Nature methods | 34635849 | Nat Methods | 2021 Dec |
| Pattern-Driven Navigation in 2D Multiscale Visualizations with Scalable Insets. | Lekschas F, Behrisch M, Bach B, Kerpedjiev P, Gehlenborg N, Pfister H | IEEE transactions on visualization and computer graphics | 31442989 | IEEE Trans Vis Comput Graph | 2020 Jan |
| Tibanna: software for scalable execution of portable pipelines on the cloud. | Lee S, Johnson J, Vitzthum C, Kırlı K, Alver BH, Park PJ | Bioinformatics (Oxford, England) | 31077294 | Bioinformatics | 2019 Nov 1 |
| A Generic Framework and Library for Exploration of Small Multiples through Interactive Piling. | Lekschas F, Zhou X, Chen W, Gehlenborg N, Bach B, Pfister H | IEEE transactions on visualization and computer graphics | 33026994 | IEEE Trans Vis Comput Graph | 2021 Feb |
| GiniQC: a measure for quantifying noise in single-cell Hi-C data. | Horton CA, Alver BH, Park PJ | Bioinformatics (Oxford, England) | 32003786 | Bioinformatics | 2020 May 1 |
