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 | PubMedLink |
|---|---|---|---|---|---|---|
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36624346 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37699958 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38370628 |
| scGHOST: Identifying single-cell 3D genome subcompartments. | Xiong K, Zhang R, Ma J | bioRxiv : the preprint server for biology | 37292994 | bioRxiv | 2023 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/37292994 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39122941 |
| map3C: a computational tool for processing multiomic single-cell Hi-C data. | Galasso J, Wang Y, Alber F, Ernst J, Luo C | bioRxiv : the preprint server for biology | 41287777 | bioRxiv | 2025 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/41287777 |
| TissueNarrator: Generative Modeling of Spatial Transcriptomics with Large Language Models. | Liu S, Tang J, Ma J, Liang S | bioRxiv : the preprint server for biology | 41394628 | bioRxiv | 2025 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/41394628 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34400556 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36175411 |
| UNADON: Transformer-based model to predict genome-wide chromosome spatial position. | Yang M, Ma J | ArXiv | 37163136 | ArXiv | 2023 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/37163136 |
| UNADON: transformer-based model to predict genome-wide chromosome spatial position. | Yang M, Ma J | Bioinformatics (Oxford, England) | 37387176 | Bioinformatics | 2023 Jun 30 | https://www.ncbi.nlm.nih.gov/pubmed/37387176 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33446254 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36865282 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38979140 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39829833 |
| MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures. | Zhan Y, Musella F, Alber F | PLoS computational biology | 40408515 | PLoS Comput Biol | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40408515 |
| Unified integration of spatial transcriptomics across platforms with LLOKI. | Haber E, Deshpande A, Ma J, Krieger S | Genome research | 41233159 | Genome Res | 2025 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/41233159 |
| 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 | Nature communications | 41253815 | Nat Commun | 2025 Nov 18 | https://www.ncbi.nlm.nih.gov/pubmed/41253815 |
| MIMYR: Generative modeling of missing tissue in spatial transcriptomics. | Deshpande A, Bei Z, Ma J, Krieger S | bioRxiv : the preprint server for biology | 41394599 | bioRxiv | 2025 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/41394599 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34400557 |
| Phase separation in genome organization across evolution. | Feric M, Misteli T | Trends in cell biology | 33771451 | Trends Cell Biol | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/33771451 |
| Integrative approaches in genome structure analysis. | Boninsegna L, Yildirim A, Zhan Y, Alber F | Structure (London, England : 1993) | 34963059 | Structure | 2022 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/34963059 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35864167 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36824908 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37546900 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37419111 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38744973 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37673975 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37845234 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39340981 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39091871 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39484446 |
| Unified integration of spatial transcriptomics across platforms. | Haber E, Deshpande A, Ma J, Krieger S | bioRxiv : the preprint server for biology | 40236180 | bioRxiv | 2025 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/40236180 |
| POPARI: Modeling multisample variation in spatial transcriptomics. | Alam S, Zhou T, Haber E, Chidester B, Liu S, Chen F, Ma J | bioRxiv : the preprint server for biology | 40462963 | bioRxiv | 2025 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/40462963 |
| Eykthyr reveals transcriptional regulators of spatial gene programs. | Krieger S, Haber E, Ma J | bioRxiv : the preprint server for biology | 40475415 | bioRxiv | 2025 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/40475415 |
| Senescence-Associated Chromatin Rewiring Promotes Inflammation and Transposable Element Activation. | Dalgarno A, Evans SA, Kelsey MMG, Nunez TA, Rocha A, Clark K, Sedivy JM, Neretti N | bioRxiv : the preprint server for biology | 40666907 | bioRxiv | 2025 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/40666907 |
| Multiscale and integrative single-cell Hi-C analysis with Higashi. | Zhang R, Zhou T, Ma J | Nature biotechnology | 34635838 | Nat Biotechnol | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/34635838 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35817938 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34465168 |
| Mapping Replication Timing in Single Mammalian Cells. | Bartlett DA, Dileep V, Baslan T, Gilbert DM | Current protocols | 34986273 | Curr Protoc | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34986273 |
| scGHOST: identifying single-cell 3D genome subcompartments. | Xiong K, Zhang R, Ma J | Nature methods | 38589516 | Nat Methods | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38589516 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36871158 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36265466 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37580627 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37873233 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39713364 |
| 3D genome organization shapes DNA damage susceptibility to platinum-based drugs. | Wang Y, Yildirim A, Boninsegna L, Christian V, Kang SL, Zhou XJ, Alber F | Nucleic acids research | 40433977 | Nucleic Acids Res | 2025 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/40433977 |
| Major nuclear locales define nuclear genome organization and function beyond A and B compartments. | Gholamalamdari O, van Schaik T, Wang Y, Kumar P, Zhang L, Zhang Y, Gonzalez GAH, Vouzas AE, Zhao PA, Gilbert DM, Ma J, van Steensel B, Belmont AS | eLife | 40279158 | Elife | 2025 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/40279158 |
| 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 | Cell systems | 40315848 | Cell Syst | 2025 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/40315848 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39271748 |
| Interpretable representation learning for 3D multi-piece intracellular structures using point clouds. | Vasan R, Ferrante AJ, Borensztejn A, Frick CL, Garrison P, Gaudreault N, Mogre SS, Mohammed FS, Morris B, Pires GG, Saelid D, Rafelski SM, Theriot JA, Viana MP | Nature methods | 40610730 | Nat Methods | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40610730 |
| 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 | Proceedings of the National Academy of Sciences of the United States of America | 40773232 | Proc Natl Acad Sci U S A | 2025 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/40773232 |
| HDCluster: High-Degree Graph Clustering for Robust Analysis of Single Molecule Localization Microscopy. | Khater IM, Nabi IR, Hamarneh G | bioRxiv : the preprint server for biology | 41279903 | bioRxiv | 2025 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/41279903 |
| Heimdall: A Modular Framework for Tokenization in Single-Cell Foundation Models. | Haber E, Alam S, Ho N, Liu R, Trop E, Liang S, Yang M, Krieger S, Ma J | bioRxiv : the preprint server for biology | 41292913 | bioRxiv | 2025 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/41292913 |
| An integrated view of the structure and function of the human 4D nucleome. | 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, Andréa W, 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 PJ, Alver BH, Schroeder AJ, Navelkar R, Bakker C, Ronchetti W, Ehmsen S, Veit AD, 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 | Nature | 41407856 | Nature | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/41407856 |
| Targeted DNase Hi-C. | Duan Z | Methods in molecular biology (Clifton, N.J.) | 32820399 | Methods Mol Biol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/32820399 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35288709 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35050714 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33954299 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36594573 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35871105 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37695017 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36261634 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38405970 |
| Molecular recording using DNA Typewriter. | Liao H, Choi J, Shendure J | Nature protocols | 38844553 | Nat Protoc | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38844553 |
| Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens. | Regalado SG, Qiu C, Lalanne JB, Martin BK, Duran M, Trapnell C, Keith A, Domcke S, Shendure J | bioRxiv : the preprint server for biology | 40475436 | bioRxiv | 2025 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/40475436 |
| Multicondition and multimodal temporal profile inference during mouse embryonic development. | Zhang R, Qiu C, Filippova GN, Li G, Shendure J, Vert JP, Deng X, Noble WS, Disteche CM | Genome research | 40813249 | Genome Res | 2025 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/40813249 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35794474 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36007540 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36251758 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37421399 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37205597 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37645782 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34579774 |
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| The 3D Genome as Moderator of Chromosomal Communication. | Dekker J, Mirny L | Cell | 26967279 | Cell | 2016 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/26967279 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28414321 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28057760 |
| FISH-ing for captured contacts: towards reconciling FISH and 3C. | Fudenberg G, Imakaev M | Nature methods | 28604723 | Nat Methods | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28604723 |
| Torque and buckling in stretched intertwined double-helix DNAs. | Brahmachari S, Marko JF | Physical review. E | 28618488 | Phys Rev E | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28618488 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28179124 |
| Physics and Biology (of Chromosomes). | Marko JF | Journal of molecular biology | 31866291 | J Mol Biol | 2020 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/31866291 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32603710 |
| Loop extrusion: theory meets single-molecule experiments. | Banigan EJ, Mirny LA | Current opinion in cell biology | 32534241 | Curr Opin Cell Biol | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32534241 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31980345 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31594803 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38402507 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28525758 |
| Phase separation drives heterochromatin domain formation. | Strom AR, Emelyanov AV, Mir M, Fyodorov DV, Darzacq X, Karpen GH | Nature | 28636597 | Nature | 2017 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/28636597 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29142071 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28905911 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29956254 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29743503 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29300163 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29979966 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30202056 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30143891 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30589412 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30799036 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31038454 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27145786 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26940867 |
| Compaction and segregation of sister chromatids via active loop extrusion. | Goloborodko A, Imakaev MV, Marko JF, Mirny L | eLife | 27192037 | Elife | 2016 May 18 | https://www.ncbi.nlm.nih.gov/pubmed/27192037 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27210764 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31792445 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31685986 |
| Cooler: scalable storage for Hi-C data and other genomically labeled arrays. | Abdennur N, Mirny LA | Bioinformatics (Oxford, England) | 31290943 | Bioinformatics | 2020 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/31290943 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32647330 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32213324 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27367781 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34286910 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33045724 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33301731 |
| Fast and efficient DNA replication with purified human proteins. | Baris Y, Taylor MRG, Aria V, Yeeles JTP | Nature | 35585232 | Nature | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35585232 |
| Estimating Cellular Abundances of Halo-tagged Proteins in Live Mammalian Cells by Flow Cytometry. | Cattoglio C, Darzacq X, Tjian R, Hansen AS | Bio-protocol | 33654751 | Bio Protoc | 2020 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/33654751 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27152443 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29930090 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29967174 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30143029 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30192578 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28467304 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28364020 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28355183 |
| Causes and consequences of nuclear gene positioning. | Shachar S, Misteli T | Journal of cell science | 28404786 | J Cell Sci | 2017 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/28404786 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31582744 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31582763 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31586479 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31427067 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31488662 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30890172 |
| Two major mechanisms of chromosome organization. | Mirny LA, Imakaev M, Abdennur N | Current opinion in cell biology | 31228682 | Curr Opin Cell Biol | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31228682 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29077530 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29348367 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29548184 |
| Mechanics and Buckling of Biopolymeric Shells and Cell Nuclei. | Banigan EJ, Stephens AD, Marko JF | Biophysical journal | 29045860 | Biophys J | 2017 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/29045860 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28825700 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27437574 |
| TAD disruption as oncogenic driver. | Valton AL, Dekker J | Current opinion in genetics & development | 27111891 | Curr Opin Genet Dev | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27111891 |
| The interplay between asymmetric and symmetric DNA loop extrusion. | Banigan EJ, Mirny LA | eLife | 33295869 | Elife | 2020 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/33295869 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32929283 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32213323 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28228067 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28157505 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31757850 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32999386 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35585235 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33654750 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38370777 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38747464 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28537556 |
| Software tools for visualizing Hi-C data. | Yardımcı GG, Noble WS | Genome biology | 28159004 | Genome Biol | 2017 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/28159004 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29990539 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30127060 |
| Understanding Spatial Genome Organization: Methods and Insights. | Ramani V, Shendure J, Duan Z | Genomics, proteomics & bioinformatics | 26876719 | Genomics Proteomics Bioinformatics | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26876719 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28818938 |
| Human Pluripotent Stem Cell-Derived Engineered Tissues: Clinical Considerations. | Stevens KR, Murry CE | Cell stem cell | 29499147 | Cell Stem Cell | 2018 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/29499147 |
| Supervised classification enables rapid annotation of cell atlases. | Pliner HA, Shendure J, Trapnell C | Nature methods | 31501545 | Nat Methods | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31501545 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31395619 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30923229 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30853548 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31431802 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31740366 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36298508 |
| ChromMovie: A Molecular Dynamics Approach for Simultaneous Modeling of Chromatin Conformation Changes from Multiple Single-Cell Hi-C Maps. | Banecki KH, Chai H, Ruan Y, Plewczynski D | bioRxiv : the preprint server for biology | 40475498 | bioRxiv | 2025 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/40475498 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30096365 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29706548 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31362752 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33281862 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32832596 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32175768 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28358394 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29078395 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30778195 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32094912 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36078056 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35595799 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27789526 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28128213 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28803781 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37066361 |
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| Unveiling Epigenetic Regulatory Elements Associated with Breast Cancer Development. | Jardanowska-Kotuniak M, Dramiński M, Wlasnowolski M, Łapiński M, Sengupta K, Agarwal A, Filip A, Ghosh N, Pancaldi V, Grynberg M, Saha I, Plewczynski D, Dąbrowski MJ | International journal of molecular sciences | 40724805 | Int J Mol Sci | 2025 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/40724805 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30810368 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30849367 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/26686651 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39605637 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27259209 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28916711 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33740473 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33398196 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30173918 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38106048 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37947442 |
| Native nucleosomes intrinsically encode genome organization principles. | Park S, Merino-Urteaga R, Karwacki-Neisius V, Carrizo GE, Athreya A, Marin-Gonzalez A, Benning NA, Park J, Mitchener MM, Bhanu NV, Garcia BA, Zhang B, Muir TW, Pearce EL, Ha T | Nature | 40335690 | Nature | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40335690 |
| Chromatin boundary permeability is controlled by CTCF conformational ensembles. | Rudnizky S, Murray PJ, Sørensen EW, Koenig TJR, Pangeni S, Merino-Urteaga R, Chhabra H, Caccianini L, Davidson IF, Osorio-Valeriano M, Hook PW, Meneses P, Hao J, Zarb JS, Hatzakis NS, Timp W, Farnung L, Vos SM, Peters J, Aksimentiev A, Ha T | bioRxiv : the preprint server for biology | 41394605 | bioRxiv | 2026 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/41394605 |
| Cas9 deactivation with photocleavable guide RNAs. | Zou RS, Liu Y, Wu B, Ha T | Molecular cell | 33662274 | Mol Cell | 2021 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/33662274 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33657402 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37024653 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36967246 |
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| Imaging the time course of DNA damage response at a nonrepetitive endogenous locus. | Rybczynski AT, Cottle WT, Chen PT, Kwon J, Shang T, Wang Y, Meneses P, Pangeni S, Park Y, Gavrilov M, Ha T | Cell reports methods | 41187749 | Cell Rep Methods | 2025 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/41187749 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36945584 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38895373 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39573578 |
| Nonrandom interchromatin trafficking through dynamic multiphase speckle connections. | Kim J, Gonzalez GAH, Venkata NC, Han KY, Belmont AS | bioRxiv : the preprint server for biology | 40475533 | bioRxiv | 2025 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/40475533 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35741072 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37369761 |
| HLH-30/TFEB Rewires the Chaperone Network to Promote Proteostasis Upon Perturbations to the Coenzyme A and Iron-Sulfur Cluster Biosynthesis Pathways. | Shalash R, Solomon DM, Levi-Ferber M, von Chrzanowski H, Atrash MK, Nakar B, Avivi MY, Hauschner H, Swisa A, Meléndez A, Shav-Tal Y, Henis-Korenblit S | Aging cell | 40304211 | Aging Cell | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40304211 |
| Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space. | Venkata NC, Kim J, Faber G, Misra S, Bektash A, Chaturvedi P, Hernanadez G, Dopie J, Kanemaki MT, Han KY, Shav Tal Y, Belmont AS | bioRxiv : the preprint server for biology | 40909587 | bioRxiv | 2025 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/40909587 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35788677 |
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| Multiplane 2.5D microscopy for high-throughput high-resolution tissue imaging. | Wang LM, Pandey D, Zhang W, Han KY | Journal of biomedical optics | 41111487 | J Biomed Opt | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/41111487 |
| HybriSeq: Probe-based Device-free Single-cell RNA Profiling. | Foyt D, Brown D, Zhou S, Moser B, Zhu Q, Gartner ZJ, Huang B | bioRxiv : the preprint server for biology | 37808850 | bioRxiv | 2025 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/37808850 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39229246 |
| Understanding how genetically encoded tags and crowding agents affect phase separation by heterochromatin protein HP1α. | Zhou ZK, Hong K, Huang B, Narlikar GJ | Cell reports methods | 40262618 | Cell Rep Methods | 2025 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/40262618 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38315854 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37521779 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37696956 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39314305 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38811792 |
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| HMGB1 deforms nucleosomal DNA to generate a dynamic chromatin environment counteracting the effects of linker histone. | Saunders HS, Chio US, Moore CM, Ramani V, Cheng Y, Narlikar GJ | Science advances | 40815652 | Sci Adv | 2025 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/40815652 |
| HybriSeq: probe-based device-free single-cell RNA profiling. | Foyt D, Brown D, Zhou S, Moser B, Zhu Q, Gartner ZJ, Huang B | Communications biology | 40830572 | Commun Biol | 2025 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/40830572 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33734687 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/38720076 |
| SPIDR enables multiplexed mapping of RNA-protein interactions and uncovers a mechanism for selective translational suppression upon cell stress. | Wolin E, Guo JK, Blanco MR, Goronzy IN, Gorhe D, Dong W, Perez AA, Keskin A, Valenzuela E, Abdou AA, Urbinati CR, Kaufhold R, Rube HT, Brito Querido J, Guttman M, Jovanovic M | Cell | 40701149 | Cell | 2025 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/40701149 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37214923 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/37333139 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/39587360 |
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