4D Nucleome (4DN)
4D Nucleome (4DN)
Program Publications
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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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Integrative approaches in genome structure analysis. | Boninsegna L, Yildirim A, Zhan Y, Alber F | Structure (London, England : 1993) | 34963059 | Structure | 2022 Jan 6 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| scGHOST: Identifying single-cell 3D genome subcompartments. | Xiong K, Zhang R, Ma J | bioRxiv : the preprint server for biology | 37292994 | bioRxiv | 2023 May 25 |
| 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 |
| 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 |
| UNADON: Transformer-based model to predict genome-wide chromosome spatial position. | Yang M, Ma J | ArXiv | 37163136 | ArXiv | 2023 Jul 1 |
| UNADON: transformer-based model to predict genome-wide chromosome spatial position. | Yang M, Ma J | Bioinformatics (Oxford, England) | 37387176 | Bioinformatics | 2023 Jun 30 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Multiscale and integrative single-cell Hi-C analysis with Higashi. | Zhang R, Zhou T, Ma J | Nature biotechnology | 34635838 | Nat Biotechnol | 2022 Feb |
| 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 |
| 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 |
| Mapping Replication Timing in Single Mammalian Cells. | Bartlett DA, Dileep V, Baslan T, Gilbert DM | Current protocols | 34986273 | Curr Protoc | 2022 Jan |
| scGHOST: identifying single-cell 3D genome subcompartments. | Xiong K, Zhang R, Ma J | Nature methods | 38589516 | Nat Methods | 2024 May |
| 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 |
| 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 |
| 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 |
| 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 |
| Targeted DNase Hi-C. | Duan Z | Methods in molecular biology (Clifton, N.J.) | 32820399 | Methods Mol Biol | 2021 |
| X-chromosome regulation and sex differences in brain anatomy. | Raznahan A, Disteche CM | Neuroscience and biobehavioral reviews | 33171144 | Neurosci Biobehav Rev | 2021 Jan |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Characterizing cis-regulatory elements using single-cell epigenomics. | Preissl S, Gaulton KJ, Ren B | Nature reviews. Genetics | 35840754 | Nat Rev Genet | 2023 Jan |
| 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 |
| 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 |
| Epigenetic regulatory layers in the 3D nucleus. | Willemin A, Szabó D, Pombo A | Molecular cell | 38242127 | Mol Cell | 2024 Feb 1 |
| 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 |
| 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 |
| Spatially resolved epigenomic profiling of single cells in complex tissues. | Lu T, Ang CE, Zhuang X | Cell | 36272405 | Cell | 2022 Nov 10 |
| Spatially resolved epigenomic profiling of single cells in complex tissues. | Lu T, Ang CE, Zhuang X | Cell | 37172568 | Cell | 2023 May 11 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
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| Chromosome Compaction by Active Loop Extrusion. | Goloborodko A, Marko JF, Mirny LA | Biophysical journal | 27224481 | Biophys J | 2016 May 24 |
| 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 |
| Physics and Biology (of Chromosomes). | Marko JF | Journal of molecular biology | 31866291 | J Mol Biol | 2020 Jan 17 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Adapting dCas9-APEX2 for subnuclear proteomic profiling. | Gao XD, Rodríguez TC, Sontheimer EJ | Methods in enzymology | 30691651 | Methods Enzymol | 2019 |
| Cooler: scalable storage for Hi-C data and other genomically labeled arrays. | Abdennur N, Mirny LA | Bioinformatics (Oxford, England) | 31290943 | Bioinformatics | 2020 Jan 1 |
| 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 |
| 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 |
| The interplay between asymmetric and symmetric DNA loop extrusion. | Banigan EJ, Mirny LA | eLife | 33295869 | Elife | 2020 Dec 9 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
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| 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 |
| Mechanics and Buckling of Biopolymeric Shells and Cell Nuclei. | Banigan EJ, Stephens AD, Marko JF | Biophysical journal | 29045860 | Biophys J | 2017 Oct 17 |
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| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Phase separation drives heterochromatin domain formation. | Strom AR, Emelyanov AV, Mir M, Fyodorov DV, Darzacq X, Karpen GH | Nature | 28636597 | Nature | 2017 Jul 13 |
| Receptor-Ligand Rebinding Kinetics in Confinement. | Erbaş A, Olvera de la Cruz M, Marko JF | Biophysical journal | 31029377 | Biophys J | 2019 May 7 |
| Two major mechanisms of chromosome organization. | Mirny LA, Imakaev M, Abdennur N | Current opinion in cell biology | 31228682 | Curr Opin Cell Biol | 2019 Jun |
| Compaction and segregation of sister chromatids via active loop extrusion. | Goloborodko A, Imakaev MV, Marko JF, Mirny L | eLife | 27192037 | Elife | 2016 May 18 |
| Causes and consequences of nuclear gene positioning. | Shachar S, Misteli T | Journal of cell science | 28404786 | J Cell Sci | 2017 May 1 |
| 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 |
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| 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 |
| 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 |
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| 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 |
| 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 |
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| 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 |
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