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 | PubMedLink |
|---|---|---|---|---|---|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Toward the simultaneous detection of multiple diseases with a highly cost-effective cell-free DNA methylome test. | Zeng W, Liu CC, Li S, Zhou Y, Stackpole ML, Xiao Y, Hu R, Tang C, Liu Q, Zeng W, Yeh A, Melehy A, Tran B, Noor Z, Yokomizo M, Amara D, Gumate S, Ahuja P, Li DY, Zhao J, Rose I, Walker C, Malik S, Zhu Y, Tseng HR, Garon EB, French SW, Magyar CE, Dry SM, Lajonchere CM, Geschwind D, Choi G, Saab S, Shetty A, Wong CR, King KG, Lu DS, Raman SS, Xiang X, Shetty K, Mishra L, Memarzadeh S, Liu Y, Alber F, Hsu W, Krysan K, Dubinett SM, Aberle DR, Agopian V, Han SB, Wong WH, Ni X, Li W, Zhou XJ | Proceedings of the National Academy of Sciences of the United States of America | 41941615 | Proc Natl Acad Sci U S A | 2026 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/41941615 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34985990 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34387327 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36598134 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33576390 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34734806 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/36945538 |
| 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 |
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| Single cell multiomics reveals drivers of metabolic dysfunction-associated steatohepatitis. | Elison W, Chang L, Xie Y, Miciano C, Yang Q, Mummey H, Lancione R, Corban S, Sakane S, Lucero J, Mamde S, Kim HY, Kim MJ, Melton R, Tucciarone L, Lie A, Loe T, Vashist T, Dang K, Elgamal R, Li D, Vu M, Farah EN, Seng C, Djulamsah J, Yang B, Buchanan J, Miller M, Tran M, Birrueta JO, Chi NC, Wang T, D'Antonio-Chronowska A, Wang A, Kisseleva T, Brenner D, Ren B, Gaulton KJ | medRxiv : the preprint server for health sciences | 40385416 | medRxiv | 2025 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/40385416 |
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| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35325048 |
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| Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina. | Yuan Y, Biswas P, Zemke NR, Dang K, Wu Y, D'Antonio M, Xie Y, Yang Q, Dong K, Lau PK, Li D, Seng C, Bartosik W, Buchanan J, Lin L, Lancione R, Wang K, Lee S, Gibbs Z, Ecker J, Frazer K, Wang T, Preissl S, Wang A, Ayyagari R, Ren B | bioRxiv : the preprint server for biology | 39764062 | bioRxiv | 2025 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/39764062 |
| Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues. | Yu M, Zemke NR, Chen Z, Juric I, Hu R, Raviram R, Abnousi A, Fang R, Zhang Y, Gorkin DU, Li YE, Zhao Y, Lee L, Mishra S, Schmitt AD, Qiu Y, Dickel DE, Visel A, Pennacchio LA, Hu M, Ren B | Nature structural & molecular biology | 39681766 | Nat Struct Mol Biol | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/39681766 |
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| A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons. | Szabó D, Franke V, Bianco S, Batiuk MY, Paul EJ, Kukalev A, Pfisterer UG, Irastorza-Azcarate I, Chiariello AM, Demharter S, Zea-Redondo L, Lopez-Atalaya JP, Nicodemi M, Akalin A, Khodosevich K, Ungless MA, Winick-Ng W, Pombo A | bioRxiv : the preprint server for biology | 38766140 | bioRxiv | 2024 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/38766140 |
| H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation. | Kubo N, Chen PB, Hu R, Ye Z, Sasaki H, Ren B | Molecular cell | 38513661 | Mol Cell | 2024 May 2 | https://www.ncbi.nlm.nih.gov/pubmed/38513661 |
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| Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm. | Schooley A, Venev SV, Aksenova V, Navarrete E, Dasso M, Dekker J | bioRxiv : the preprint server for biology | 39345587 | bioRxiv | 2024 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/39345587 |
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| DNA damage causes ATM-dependent heterochromatin loss leading to nuclear softening, blebbing, and rupture. | Eskndir N, Hossain M, Currey ML, Pho M, Berrada Y, Lin K, Manning G, Prince K, Stephens AD | Molecular biology of the cell | 39705376 | Mol Biol Cell | 2025 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/39705376 |
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| Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis. | Hildebrand EM, Polovnikov K, Dekker B, Liu Y, Lafontaine DL, Fox AN, Li Y, Venev SV, Mirny LA, Dekker J | Molecular cell | 38521067 | Mol Cell | 2024 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/38521067 |
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| DNA damage causes ATM-dependent heterochromatin loss leading to nuclear softening, blebbing, and rupture. | Eskndir N, Hossain M, Currey ML, Pho M, Berrada Y, Stephens AD | bioRxiv : the preprint server for biology | 38853925 | bioRxiv | 2024 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/38853925 |
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| Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm. | Schooley A, Venev SV, Aksenova V, Lehman JW, Navarrete E, Pai AA, Dasso M, Dekker J | Nature cell biology | 41429936 | Nat Cell Biol | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/41429936 |
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| Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. | Gabriele M, Brandão HB, Grosse-Holz S, Jha A, Dailey GM, Cattoglio C, Hsieh TS, Mirny L, Zechner C, Hansen AS | Science (New York, N.Y.) | 35420890 | Science | 2022 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/35420890 |
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| Reeling it in: how DNA topology drives loop extrusion by condensin. | Narducci DN, Hansen AS | Nature structural & molecular biology | 35835869 | Nat Struct Mol Biol | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35835869 |
| Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics. | Belaghzal H, Borrman T, Stephens AD, Lafontaine DL, Venev SV, Weng Z, Marko JF, Dekker J | Nature genetics | 33574602 | Nat Genet | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33574602 |
| Single-molecule micromanipulation studies of methylated DNA. | Zaichuk T, Marko JF | Biophysical journal | 33838135 | Biophys J | 2021 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/33838135 |
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| Polyphony: an Interactive Transfer Learning Framework for Single-Cell Data Analysis. | Cheng F, Keller MS, Qu H, Gehlenborg N, Wang Q | IEEE transactions on visualization and computer graphics | 36155452 | IEEE Trans Vis Comput Graph | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36155452 |
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| Chromatin Dynamics are Highly Subdiffusive Across Seven Orders of Magnitude. | Mazzocca M, Narducci DN, Grosse-Holz S, Matthias J, Hansen AS | bioRxiv : the preprint server for biology | 40463058 | bioRxiv | 2025 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/40463058 |
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| Molecular crowding suppresses mechanical stress-driven DNA strand separation. | Desai PR, Marko JF | Biophysical journal | 40312912 | Biophys J | 2025 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/40312912 |
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| Independence of centromeric and pericentromeric chromatin stability on CCAN components. | Biggs RJ, Sun M, Sundararajan K, Hendrix E, Straight AF, Marko JF | Molecular biology of the cell | 39937678 | Mol Biol Cell | 2025 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/39937678 |
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| Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions. | Smith RG, Fu Y, Schiela KL, Dautle M, Williams R, Wilson HM, Azadegan C, Whetstine JR, Dekker J, Liu Y | bioRxiv : the preprint server for biology | 40766525 | bioRxiv | 2025 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/40766525 |
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| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30655336 |
| Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF. | Hansen AS, Hsieh TS, Cattoglio C, Pustova I, Saldaña-Meyer R, Reinberg D, Darzacq X, Tjian R | Molecular cell | 31522987 | Mol Cell | 2019 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/31522987 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31168090 |
| 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 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29217590 |
| 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 |
| 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 |
| 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 |
| Supercoiling DNA Locates Mismatches. | Dittmore A, Brahmachari S, Takagi Y, Marko JF, Neuman KC | Physical review letters | 29053317 | Phys Rev Lett | 2017 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/29053317 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30999490 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/28435001 |
| 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 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/34312537 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35932276 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27182590 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/27021249 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29728444 |
| 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 |
| 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 |
| 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 |
| 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 |
| Chromosome Compaction by Active Loop Extrusion. | Goloborodko A, Marko JF, Mirny LA | Biophysical journal | 27224481 | Biophys J | 2016 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/27224481 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29079757 |
| 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 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/33154377 |
| Dense Bicoid hubs accentuate binding along the morphogen gradient. | Mir M, Reimer A, Haines JE, Li XY, Stadler M, Garcia H, Eisen MB, Darzacq X | Genes & development | 28982761 | Genes Dev | 2017 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/28982761 |
| 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 |
| Adapting dCas9-APEX2 for subnuclear proteomic profiling. | Gao XD, Rodríguez TC, Sontheimer EJ | Methods in enzymology | 30691651 | Methods Enzymol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30691651 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30625026 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/31205001 |
| Higher-Order Organization Principles of Pre-translational mRNPs. | Metkar M, Ozadam H, Lajoie BR, Imakaev M, Mirny LA, Dekker J, Moore MJ | Molecular cell | 30415953 | Mol Cell | 2018 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/30415953 |
| 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 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/35483357 |
| 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 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/29735996 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/30238154 |
| Receptor-Ligand Rebinding Kinetics in Confinement. | Erbaş A, Olvera de la Cruz M, Marko JF | Biophysical journal | 31029377 | Biophys J | 2019 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/31029377 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | https://www.ncbi.nlm.nih.gov/pubmed/32250245 |
| 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 |
| 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 |
| 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 |
| OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries. | An L, Yang T, Yang J, Nuebler J, Xiang G, Hardison RC, Li Q, Zhang Y | Genome biology | 31847870 | Genome Biol | 2019 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/31847870 |
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| Quantitative 3-D morphometric analysis of individual dendritic spines. | Basu S, Saha PK, Roszkowska M, Magnowska M, Baczynska E, Das N, Plewczynski D, Wlodarczyk J | Scientific reports | 29476060 | Sci Rep | 2018 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/29476060 |
| 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 |
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| 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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| 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 |
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| 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 |
| 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 |
| 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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| PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies. | Bokota G, Sroka J, Basu S, Das N, Trzaskoma P, Yushkevich Y, Grabowska A, Magalska A, Plewczynski D | BMC bioinformatics | 33596823 | BMC Bioinformatics | 2021 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/33596823 |
| Cohesin Loss Eliminates All Loop Domains. | Rao SSP, Huang SC, Glenn St Hilaire B, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, Huang X, Shamim MS, Shin J, Turner D, Ye Z, Omer AD, Robinson JT, Schlick T, Bernstein BE, Casellas R, Lander ES, Aiden EL | Cell | 28985562 | Cell | 2017 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/28985562 |
| The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations. | Menghi F, Barthel FP, Yadav V, Tang M, Ji B, Tang Z, Carter GW, Ruan Y, Scully R, Verhaak RGW, Jonkers J, Liu ET | Cancer cell | 30017478 | Cancer Cell | 2018 Aug 13 | https://www.ncbi.nlm.nih.gov/pubmed/30017478 |
| 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 |
| ASXL1 interacts with the cohesin complex to maintain chromatid separation and gene expression for normal hematopoiesis. | Li Z, Zhang P, Yan A, Guo Z, Ban Y, Li J, Chen S, Yang H, He Y, Li J, Guo Y, Zhang W, Hajiramezanali E, An H, Fajardo D, Harbour JW, Ruan Y, Nimer SD, Yu P, Chen X, Xu M, Yang FC | Science advances | 28116354 | Sci Adv | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28116354 |
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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 |
| 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 |
| 3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome. | Wlasnowolski M, Sadowski M, Czarnota T, Jodkowska K, Szalaj P, Tang Z, Ruan Y, Plewczynski D | Nucleic acids research | 32442297 | Nucleic Acids Res | 2020 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/32442297 |
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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 |
| 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 |
| ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs. | Chai H, Tjong H, Li P, Liao W, Wang P, Wong CH, Ngan CY, Leonard WJ, Wei CL, Ruan Y | Nature communications | 36639381 | Nat Commun | 2023 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/36639381 |
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| enhancer3D: 3D chromatin structures and enhancer-promoter distance profiles for archaic and modern human genomes. | Wlasnowolski M, Kozlov N, Wojcik M, Jacobs GS, Plewczynski D | Nucleic acids research | 41296557 | Nucleic Acids Res | 2026 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/41296557 |
| Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie. | Banecki KH, Chai H, Ruan Y, Plewczynski D | Genome research | 41951435 | Genome Res | 2026 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/41951435 |
| Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions. | Chiliński M, Lipiński J, Agarwal A, Ruan Y, Plewczynski D | Scientific reports | 37474564 | Sci Rep | 2023 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/37474564 |
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| ShapeGTB: the role of local DNA shape in prioritization of functional variants in human promoters with machine learning. | Malkowska M, Zubek J, Plewczynski D, Wyrwicz LS | PeerJ | 30519505 | PeerJ | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30519505 |
| Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia. | Wang P, Tang Z, Lee B, Zhu JJ, Cai L, Szalaj P, Tian SZ, Zheng M, Plewczynski D, Ruan X, Liu ET, Wei CL, Ruan Y | Genome biology | 32393309 | Genome Biol | 2020 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/32393309 |
| 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 |
| 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 |
| 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 |
| 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 |
| Spring Model - Chromatin Modeling Tool Based on OpenMM. | Kadlof M, Rozycka J, Plewczynski D | Methods (San Diego, Calif.) | 31790732 | Methods | 2020 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/31790732 |
| Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. | Zhu Y, Gujar AD, Wong CH, Tjong H, Ngan CY, Gong L, Chen YA, Kim H, Liu J, Li M, Mil-Homens A, Maurya R, Kuhlberg C, Sun F, Yi E, deCarvalho AC, Ruan Y, Verhaak RGW, Wei CL | Cancer cell | 33836152 | Cancer Cell | 2021 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/33836152 |
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| 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 |
| 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 |
| 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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| 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 |
| 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 |
| RNA structure interactions and ribonucleoprotein processes of the influenza A virus. | Dawson WK, Lazniewski M, Plewczynski D | Briefings in functional genomics | 29040388 | Brief Funct Genomics | 2018 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/29040388 |
| The structural variability of the influenza A hemagglutinin receptor-binding site. | Lazniewski M, Dawson WK, Szczepinska T, Plewczynski D | Briefings in functional genomics | 29253080 | Brief Funct Genomics | 2018 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/29253080 |
| Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction. | Al Bkhetan Z, Plewczynski D | Scientific reports | 29581440 | Sci Rep | 2018 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/29581440 |
| Three-dimensional organization and dynamics of the genome. | Szalaj P, Plewczynski D | Cell biology and toxicology | 29568981 | Cell Biol Toxicol | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/29568981 |
| 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 |
| 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 |
| 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 |
| HiCDiffusion - diffusion-enhanced, transformer-based prediction of chromatin interactions from DNA sequences. | Chiliński M, Plewczynski D | BMC genomics | 39407104 | BMC Genomics | 2024 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/39407104 |
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| CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci. | Tasan I, Sustackova G, Zhang L, Kim J, Sivaguru M, HamediRad M, Wang Y, Genova J, Ma J, Belmont AS, Zhao H | Nucleic acids research | 29912475 | Nucleic Acids Res | 2018 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/29912475 |
| Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. | Chen Y, Zhang Y, Wang Y, Zhang L, Brinkman EK, Adam SA, Goldman R, van Steensel B, Ma J, Belmont AS | The Journal of cell biology | 30154186 | J Cell Biol | 2018 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/30154186 |
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| p53 mediates target gene association with nuclear speckles for amplified RNA expression. | Alexander KA, Coté A, Nguyen SC, Zhang L, Gholamalamdari O, Agudelo-Garcia P, Lin-Shiao E, Tanim KMA, Lim J, Biddle N, Dunagin MC, Good CR, Mendoza MR, Little SC, Belmont A, Joyce EF, Raj A, Berger SL | Molecular cell | 33823140 | Mol Cell | 2021 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/33823140 |
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| Incorporation of noncanonical base Z yields modified mRNA with minimal immunogenicity and improved translational capacity in mammalian cells. | Zhang M, Singh N, Ehmann ME, Zheng L, Zhao H | iScience | 37720088 | iScience | 2023 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/37720088 |
| MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning. | Zhang R, Ma J | Cell systems | 32550271 | Cell Syst | 2020 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/32550271 |
| Efficient and Reproducible Multigene Expression after Single-Step Transfection Using Improved BAC Transgenesis and Engineering Toolkit. | Zhao B, Chaturvedi P, Zimmerman DL, Belmont AS | ACS synthetic biology | 32216371 | ACS Synth Biol | 2020 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/32216371 |
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| Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions. | Xiong K, Ma J | Nature communications | 31699985 | Nat Commun | 2019 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/31699985 |
| CTCF and cohesin promote focal detachment of DNA from the nuclear lamina. | van Schaik T, Liu NQ, Manzo SG, Peric-Hupkes D, de Wit E, van Steensel B | Genome biology | 36050765 | Genome Biol | 2022 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/36050765 |
| TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes. | Zhang L, Zhang Y, Chen Y, Gholamalamdari O, Wang Y, Ma J, Belmont AS | Genome research | 33355299 | Genome Res | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33355299 |
| Perturbations in 3D genome organization can promote acquired drug resistance. | Manjón AG, Manzo SG, Prekovic S, Potgeter L, van Schaik T, Liu NQ, Flach K, Peric-Hupkes D, Joosten S, Teunissen H, Friskes A, Ilic M, Hintzen D, Franceschini-Santos VH, Zwart W, de Wit E, van Steensel B, Medema RH | Cell reports | 37733591 | Cell Rep | 2023 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/37733591 |
| Exploiting sequence-based features for predicting enhancer-promoter interactions. | Yang Y, Zhang R, Singh S, Ma J | Bioinformatics (Oxford, England) | 28881991 | Bioinformatics | 2017 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/28881991 |
| Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression. | van Steensel B, Belmont AS | Cell | 28525751 | Cell | 2017 May 18 | https://www.ncbi.nlm.nih.gov/pubmed/28525751 |
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| High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells. | Zhao PA, Sasaki T, Gilbert DM | Genome biology | 32209126 | Genome Biol | 2020 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/32209126 |
| An efficient gene knock-in strategy using 5'-modified double-stranded DNA donors with short homology arms. | Yu Y, Guo Y, Tian Q, Lan Y, Yeh H, Zhang M, Tasan I, Jain S, Zhao H | Nature chemical biology | 31873222 | Nat Chem Biol | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/31873222 |
| Two-Color Imaging of Nonrepetitive Endogenous Loci in Human Cells. | Tasan I, Su CJ, Enghiad B, Zhang M, Mishra S, Zhao H | ACS synthetic biology | 32822529 | ACS Synth Biol | 2020 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/32822529 |
| Expanding the Potential of Mammalian Genome Engineering via Targeted DNA Integration. | Zhang M, Yang C, Tasan I, Zhao H | ACS synthetic biology | 33596056 | ACS Synth Biol | 2021 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/33596056 |
| TALEN outperforms Cas9 in editing heterochromatin target sites. | Jain S, Shukla S, Yang C, Zhang M, Fatma Z, Lingamaneni M, Abesteh S, Lane ST, Xiong X, Wang Y, Schroeder CM, Selvin PR, Zhao H | Nature communications | 33504770 | Nat Commun | 2021 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/33504770 |
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| Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. | Mowery CT, Freimer JW, Chen Z, Casaní-Galdón S, Umhoefer JM, Arce MM, Gjoni K, Daniel B, Sandor K, Gowen BG, Nguyen V, Simeonov DR, Garrido CM, Curie GL, Schmidt R, Steinhart Z, Satpathy AT, Pollard KS, Corn JE, Bernstein BE, Ye CJ, Marson A | Nature genetics | 38811842 | Nat Genet | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38811842 |
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| An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. | Shah PP, Keough KC, Gjoni K, Santini GT, Abdill RJ, Wickramasinghe NM, Dundes CE, Karnay A, Chen A, Salomon REA, Walsh PJ, Nguyen SC, Whalen S, Joyce EF, Loh KM, Dubois N, Pollard KS, Jain R | Genome biology | 36691074 | Genome Biol | 2023 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/36691074 |
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| De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes. | Gjoni K, Ren X, Everitt A, Shen Y, Pollard KS | bioRxiv : the preprint server for biology | 39574698 | bioRxiv | 2024 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/39574698 |
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| ChromaFold predicts the 3D contact map from single-cell chromatin accessibility. | Gao VR, Yang R, Das A, Luo R, Luo H, McNally DR, Karagiannidis I, Rivas MA, Wang ZM, Barisic D, Karbalayghareh A, Wong W, Zhan YA, Chin CR, Noble W, Bilmes JA, Apostolou E, Kharas MG, Béguelin W, Viny AD, Huangfu D, Rudensky AY, Melnick AM, Leslie CS | bioRxiv : the preprint server for biology | 37546906 | bioRxiv | 2023 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/37546906 |
| Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions. | Luo R, Yan J, Oh JW, Xi W, Shigaki D, Wong W, Cho HS, Murphy D, Cutler R, Rosen BP, Pulecio J, Yang D, Glenn RA, Chen T, Li QV, Vierbuchen T, Sidoli S, Apostolou E, Huangfu D, Beer MA | Nature genetics | 37488417 | Nat Genet | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37488417 |
| CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant. | Kaplan SJ, Wong W, Yan J, Pulecio J, Cho HS, Li Q, Zhao J, Leslie-Iyer J, Kazakov J, Murphy D, Luo R, Dey KK, Apostolou E, Leslie CS, Huangfu D | Cell reports | 39163202 | Cell Rep | 2024 Aug 27 | https://www.ncbi.nlm.nih.gov/pubmed/39163202 |
| Chromatin interaction-aware gene regulatory modeling with graph attention networks. | Karbalayghareh A, Sahin M, Leslie CS | Genome research | 35396274 | Genome Res | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35396274 |
| HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. | Sahin M, Wong W, Zhan Y, Van Deynze K, Koche R, Leslie CS | Nature communications | 34099725 | Nat Commun | 2021 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/34099725 |
| 3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles. | Uyehara CM, Apostolou E | Cell reports | 37059094 | Cell Rep | 2023 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/37059094 |
| Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression. | Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E | bioRxiv : the preprint server for biology | 37577543 | bioRxiv | 2023 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/37577543 |
| Three-dimensional regulatory hubs support oncogenic programs in glioblastoma. | Breves SL, Di Giammartino DC, Nicholson J, Cirigliano S, Mahmood SR, Lee UJ, Martinez-Fundichely A, Jungverdorben J, Singhania R, Rajkumar S, Kirou R, Studer L, Khurana E, Polyzos A, Fine HA, Apostolou E | Molecular cell | 40147440 | Mol Cell | 2025 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/40147440 |
| Functional chromatin signatures premark future lineage-specific enhancers. | Pulecio J, Tayyebi Z, Liu D, Wong W, Luo R, Damodaran JR, Kaplan SJ, Hu N, Cho HS, Yan J, Murphy D, Rickert RW, Shukla A, Zhong A, Torre D, Li Q, González F, Yang D, Li W, Zhou T, Apostolou E, Leslie CS, Huangfu D | Cell genomics | 41856116 | Cell Genom | 2026 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/41856116 |
| Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies. | Scourzic L, Salataj E, Apostolou E | Frontiers in immunology | 34054841 | Front Immunol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34054841 |
| Cohesin drives chromatin scanning during the RAD51-mediated homology search. | Marin-Gonzalez A, Rybczynski AT, Nilavar NM, Nguyen D, Karwacki-Neisius V, Li AG, Zou RS, Avilés-Vázquez FJ, Kanemaki MT, Scully R, Ha T | bioRxiv : the preprint server for biology | 39990468 | bioRxiv | 2025 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/39990468 |
| 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 |
| GAGA zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion. | Feng XA, Yamadi M, Fu Y, Ness KM, Liu C, Ahmed I, Bowman GD, Johnson ME, Ha T, Wu C | Nature structural & molecular biology | 40764461 | Nat Struct Mol Biol | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/40764461 |
| 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 |
| 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 |
| 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 |
| Cohesin drives chromatin scanning during the RAD51-mediated homology search. | Marin-Gonzalez A, Rybczynski AT, Nilavar NM, Nguyen D, Li AG, Karwacki-Neisius V, Zou RS, Avilés-Vázquez FJ, Kanemaki MT, Scully R, Ha T | Science (New York, N.Y.) | 41343630 | Science | 2025 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/41343630 |
| Light activation and deactivation of Cas9 for DNA repair studies. | Zou RS, Ha T | Methods in enzymology | 34776214 | Methods Enzymol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34776214 |
| Kinetic principles underlying pioneer function of GAGA transcription factor in live cells. | Tang X, Li T, Liu S, Wisniewski J, Zheng Q, Rong Y, Lavis LD, Wu C | Nature structural & molecular biology | 35835866 | Nat Struct Mol Biol | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35835866 |
| 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 |
| Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization. | Sang M, Au G, Johnson ME | PNAS nexus | 41815936 | PNAS Nexus | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41815936 |
| 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 |
| Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice. | Deshpande RA, Marin-Gonzalez A, Barnes HK, Woolley PR, Ha T, Paull TT | Nature communications | 37717054 | Nat Commun | 2023 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/37717054 |
| GAGA-associated factor fosters loop formation in the Drosophila genome. | Li X, Tang X, Bing X, Catalano C, Li T, Dolsten G, Wu C, Levine M | Molecular cell | 37003261 | Mol Cell | 2023 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/37003261 |
| Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization. | Sang M, Au G, Johnson ME | bioRxiv : the preprint server for biology | 40027831 | bioRxiv | 2025 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/40027831 |
| 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 |
| 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 |
| Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulation. | Singh AP, Wu P, Ryabichko S, Raimundo J, Swan M, Wieschaus E, Gregor T, Toettcher JE | Cell reports | 35320726 | Cell Rep | 2022 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/35320726 |
| Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies. | Voortman L, Anderson C, Urban E, Yuan L, Tran S, Neuhaus-Follini A, Derrick J, Gregor T, Johnston RJ Jr | Developmental cell | 35835116 | Dev Cell | 2022 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/35835116 |
| Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. | Brückner DB, Chen H, Barinov L, Zoller B, Gregor T | bioRxiv : the preprint server for biology | 36711618 | bioRxiv | 2023 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/36711618 |
| Efficient Genome Editing with Chimeric Oligonucleotide-Directed Editing. | Nguyen LT, Rakestraw NR, Pizzano BLM, Young CB, Huang Y, Beerensson KT, Fang A, Antal SG, Anamisis KV, Peggs CMD, Yan J, Jing Y, Burdine RD, Adamson B, Toettcher JE, Myhrvold C, Jain PK | bioRxiv : the preprint server for biology | 39026836 | bioRxiv | 2024 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/39026836 |
| Chromosome structure in Drosophila is determined by boundary pairing not loop extrusion. | Bing X, Ke W, Fujioka M, Kurbidaeva A, Levitt S, Levine M, Schedl P, Jaynes JB | eLife | 39110499 | Elife | 2024 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/39110499 |
| Recording morphogen signals reveals mechanisms underlying gastruloid symmetry breaking. | McNamara HM, Solley SC, Adamson B, Chan MM, Toettcher JE | Nature cell biology | 39358450 | Nat Cell Biol | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39358450 |
| Efficient prime editing in two-cell mouse embryos using PEmbryo. | Kim-Yip RP, McNulty R, Joyce B, Mollica A, Chen PJ, Ravisankar P, Law BK, Liu DR, Toettcher JE, Ivakine EA, Posfai E, Adamson B | Nature biotechnology | 38321114 | Nat Biotechnol | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/38321114 |
| Latent space of a small genetic network: Geometry of dynamics and information. | Seyboldt R, Lavoie J, Henry A, Vanaret J, Petkova MD, Gregor T, François P | Proceedings of the National Academy of Sciences of the United States of America | 35737842 | Proc Natl Acad Sci U S A | 2022 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/35737842 |
| Light-switchable transcription factors obtained by direct screening in mammalian cells. | Zhu L, McNamara HM, Toettcher JE | Nature communications | 37268649 | Nat Commun | 2023 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/37268649 |
| Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo. | Ho EK, Oatman HR, McFann SE, Yang L, Johnson HE, Shvartsman SY, Toettcher JE | Development (Cambridge, England) | 37602510 | Development | 2023 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/37602510 |
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| Recording morphogen signals reveals origins of gastruloid symmetry breaking. | McNamara HM, Solley SC, Adamson B, Chan MM, Toettcher JE | bioRxiv : the preprint server for biology | 37333235 | bioRxiv | 2023 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/37333235 |
| A conserved coupling of transcriptional ON and OFF periods underlies bursting dynamics. | Chen PT, Levo M, Zoller B, Gregor T | Nature structural & molecular biology | 40664961 | Nat Struct Mol Biol | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40664961 |
| Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag. | Brumbaugh-Reed EH, Aoki K, Toettcher JE | bioRxiv : the preprint server for biology | 38293146 | bioRxiv | 2024 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/38293146 |
| Efficient genome editing with chimeric oligonucleotide-directed editing. | Nguyen LT, Rakestraw NR, Pizzano BLM, Iyyappan R, Young CB, Huang Y, Beerensson KT, Fang A, Antal SG, Anamisis KV, Peggs CMD, Yan J, Jing Y, Lewis JG, Burdine RD, Adamson B, Jiang Z, Toettcher JE, Myhrvold C, Jain PK | Nature communications | 41968146 | Nat Commun | 2026 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/41968146 |
| Chromosome-level organization of the regulatory genome in the Drosophila nervous system. | Mohana G, Dorier J, Li X, Mouginot M, Smith RC, Malek H, Leleu M, Rodriguez D, Khadka J, Rosa P, Cousin P, Iseli C, Restrepo S, Guex N, McCabe BD, Jankowski A, Levine MS, Gambetta MC | Cell | 37536338 | Cell | 2023 Aug 31 | https://www.ncbi.nlm.nih.gov/pubmed/37536338 |
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| Synthetic developmental biology: New tools to deconstruct and rebuild developmental systems. | McNamara HM, Ramm B, Toettcher JE | Seminars in cell & developmental biology | 35484026 | Semin Cell Dev Biol | 2023 May 30 | https://www.ncbi.nlm.nih.gov/pubmed/35484026 |
| Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag. | Brumbaugh-Reed EH, Gao Y, Aoki K, Toettcher JE | Nature communications | 39112465 | Nat Commun | 2024 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/39112465 |
| A live-cell biosensor of in vivo receptor tyrosine kinase activity reveals feedback regulation of a developmental gradient. | Ho EK, Kim-Yip RP, Simpkins AG, Farahani PE, Oatman HR, Posfai E, Shvartsman SY, Toettcher JE | Cell reports | 40581929 | Cell Rep | 2025 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/40581929 |
| What are tethering elements? | Li X, Levine M | Current opinion in genetics & development | 38237456 | Curr Opin Genet Dev | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38237456 |
| Functional analysis of the Drosophila eve locus in response to non-canonical combinations of gap gene expression levels. | Haroush N, Levo M, Wieschaus EF, Gregor T | Developmental cell | 37890488 | Dev Cell | 2023 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/37890488 |
| Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. | Brückner DB, Chen H, Barinov L, Zoller B, Gregor T | Science (New York, N.Y.) | 37384691 | Science | 2023 Jun 30 | https://www.ncbi.nlm.nih.gov/pubmed/37384691 |
| 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 |
| Control of gastruloid patterning and morphogenesis by the Erk and Akt signaling pathways. | Underhill EJ, Toettcher JE | Development (Cambridge, England) | 37590131 | Development | 2023 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/37590131 |
| In vivo measurements of receptor tyrosine kinase activity reveal feedback regulation of a developmental gradient. | Ho EK, Kim-Yip RP, Simpkins AG, Farahani PE, Oatman HR, Posfai E, Shvartsman SY, Toettcher JE | bioRxiv : the preprint server for biology | 39829924 | bioRxiv | 2025 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/39829924 |
| Transcription factor clusters as information transfer agents. | Munshi R, Ling J, Ryabichko S, Wieschaus EF, Gregor T | Science advances | 39742495 | Sci Adv | 2025 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/39742495 |
| Deriving a genetic regulatory network from an optimization principle. | Sokolowski TR, Gregor T, Bialek W, Tkačik G | Proceedings of the National Academy of Sciences of the United States of America | 39752518 | Proc Natl Acad Sci U S A | 2025 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/39752518 |
| Transcription factor clusters as information transfer agents. | Munshi R, Ling J, Ryabichko S, Wieschaus E, Gregor T | ArXiv | 38495568 | ArXiv | 2024 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/38495568 |
| 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 |
| 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 |
| 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 |
| Utilizing flow cytometry sorting signal width to enrich for cells positive to endogenous gene integration of fluorescent proteins. | Faber GP, Hauschner H, Atrash MK, Bilinsky L, Shav-Tal Y | Cytometry. Part A : the journal of the International Society for Analytical Cytology | 37158244 | Cytometry A | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37158244 |
| 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 |
| 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 |
| 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 |
| Deep learning enables fast, gentle STED microscopy. | Ebrahimi V, Stephan T, Kim J, Carravilla P, Eggeling C, Jakobs S, Han KY | bioRxiv : the preprint server for biology | 36747618 | bioRxiv | 2023 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/36747618 |
| 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 |
| 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 |
| Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers. | Yang MG, Richter HJ, Wang S, McNally CP, Harris N, Dhillon S, Maresca M, de Wit E, Willenbring H, Maher J, Goodarzi H, Ramani V | bioRxiv : the preprint server for biology | 39896524 | bioRxiv | 2025 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/39896524 |
| 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 |
| 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 |
| Emerging roles of transcriptional condensates as temporal signal integrators. | Meyer K, Huang B, Weiner OD | Nature reviews. Genetics | 40240649 | Nat Rev Genet | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40240649 |
| 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 |
| YAP charge patterning mediates signal integration through transcriptional co-condensates. | Meyer K, Yserentant K, Cheloor-Kovilakam R, Ruff KM, Chung CI, Shu X, Huang B, Weiner OD | Nature communications | 40796733 | Nat Commun | 2025 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/40796733 |
| 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 |
| 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 |
| 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 |
| YAP charge patterning mediates signal integration through transcriptional co-condensates. | Meyer K, Yserentant K, Cheloor-Kovilakam R, Ruff KM, Chung CI, Shu X, Huang B, Weiner OD | bioRxiv : the preprint server for biology | 39149273 | bioRxiv | 2024 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/39149273 |
| 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 |
| 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 |
| Understanding Regulatory Mechanisms of Brain Function and Disease through 3D Genome Organization. | Liu W, Zhong W, Chen J, Huang B, Hu M, Li Y | Genes | 35456393 | Genes (Basel) | 2022 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/35456393 |
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