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Exploring the significance of PAK1 through chromosome conformation signatures in ibrutinib‐resistant chronic lymphocytic leukaemia

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HNF1B‐driven three‐dimensional chromatin structure for molecular classification in pancreatic cancers

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Unveiling Multi‐Scale Architectural Features in Single‐Cell Hi‐C Data Using scCAFE

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CTCF-RNA interactions orchestrate cell-specific chromatin loop organization

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Assessing Specific Networks of Chromatin Interactions with HiChIP

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DARIC, a Computational Framework for Identifying Quantitatively Differential Compartments from Hi-C Data

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dcHiC: differential compartment analysis of Hi-C datasetsPreprint

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Multi-omic analysis of hepatocellular carcinoma reveals aberrant cis-regulatory changes and dysregulated retrotransposons with prognostic potential

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3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibility

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Evaluation of the gene fusion landscape in early onset sporadic rectal cancer reveals association with chromatin architecture and genome stability

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Uncovering the regulatory landscape of early human B cell lymphopoiesis and its implications in the pathogenesis of B-ALL

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Delta.EPI: a probabilistic voting-based enhancer–promoter interaction prediction platform

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Computational methods for identifying enhancer‐promoter interactions

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Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains

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SnapHiC-G: identifying long-range enhancer–promoter interactions from single-cell Hi-C data via a global background model

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A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C dataPreprint

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Node features of chromosome structure networks and their connections to genome annotation

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Hierarchical Prediction and Perturbation of Chromatin Organization Reveal How Loop Domains Mediate Higher‐Order Architectures

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Pig Matrix: a matched multiomics 3D regulatory genomics database for evolutionary and comparative analyses in pigs

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Revisiting Assessment of Computational Methods for Hi-C Data Analysis

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Interchromosomal Colocalization with Parental Genes Is Linked to the Function and Evolution of Mammalian Retrocopies

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MUNIn: A statistical framework for identifying long-range chromatin interactions from multiple samples

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HiCEnterprise: identifying long range chromosomal contacts in Hi-C data

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The three-dimensional chromatin structure of the major human pancreatic cell types reveals lineage-specific regulatory architecture of T2D riskPreprint

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3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibilityPreprint

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Statistical modeling and significance estimation of multi-way chromatin contacts with HyperloopFinder

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Linking Iris Cis -Regulatory Variants to Primary Angle-Closure Glaucoma Via Clinical Imaging and Multiomics

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Spatial chromosome organization and adaptation of the radiation-resistant extremophile Deinococcus radiodurans

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HiCForecast: dynamic network optical flow estimation algorithm for spatiotemporal Hi-C data forecasting

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A Joint Analysis of RNA-DNA and DNA-DNA Interactomes Reveals Their Strong Association

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An integrative 3D-genome database for plants

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Single-molecule chromatin profiling reveals cell type-specific A/B compartment alteration and multi-enhancer transcriptional coordination

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Mapping of chromatin architecture and enhancer-promoter interactions in the cochlea

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A multi‐omics integrative gene network of pear ( Pyrus )

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An EGR1-dependent cascade modulates genome architecture at the CSF1R locus

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A reduced TBX5-dependent gene regulatory network links atrial fibrillation and heart failure

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EMF2 deficiency disrupts epigenetic and chromatin organization landscapes, blocking root regeneration competence in Arabidopsis

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CNVs, chromatin accessibility, and 3D chromatin structure in preadipocytes provide mechanistic insight into sheep fat-tailed formation

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A fourth subgenome of the Camelina genus reveals gene dominance is influenced by chromosomal proximity

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Topologically associating domains in the POLLED region are the same for Angus‐ and Brahman‐specific Hi‐C reads from F1 hybrid fetal tissue

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SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data

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Puzzle Hi-C: An accurate scaffolding software

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pC-SAC: A method for high-resolution 3D genome reconstruction from low-resolution Hi-C data

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Histo-LCM-Hi-C Reveals 3D Chromatin Conformations of Spatially Localized Rare Cells in Tissues at High Resolution

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Resources and challenges for integrative analysis of nuclear architecture data

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Chromatin architecture in addiction circuitry elucidates biological mechanisms underlying cigarette smoking and alcohol use traitsPreprint

Sey, N. Y. A., Hu, B., Iskhakova, M., Sun, H., Shokrian, N., Hutta, G. B., Marks, J. A., Quach, B. C., Johnson, E. O., Hancock, D. B., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.18.436046 · Cited by 1

Chromatin conformation dynamics during CD4+ T cell activation implicates autoimmune disease-associated genes and regulatory elementsPreprint

Pahl, M. C., Sharma, P. K., Thomas, R. M., Thompson, Z., Mount, Z., Pippin, J. A., Morawski, P. A., Su, C., Campbell, D., Grant, S. F. A., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.05.535731 · Cited by 1

Dynamic chromatin architecture identifies new autoimmune-associated enhancers for IL2 and novel genes regulating CD4+ T cell activationPreprint

Pahl, M. C., Sharma, P. K., Thomas, R. M., Thompson, Z., Mount, Z., Pippin, J. A., Morawski, P. A., Sun, P., Su, C., Campbell, D., et al. (2024) · eLife · doi:10.7554/elife.96852.1 · Cited by 1

PDS5s control the Arabidopsis 3D genome by suppressing the formation of TAD-like domainsPreprint

Göbel, A.-M., Zhou, S., Wang, Z., Tzourtzou, S., Himmelbach, A., Zheng, S., Pradillo, M., Liu, C., & Jiang, H. L. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.31.606105 · Cited by 1

Dynamic chromatin architecture identifies new autoimmune-associated enhancers for IL2 and novel genes regulating CD4+ T cell activationPreprint

Pahl, M. C., Sharma, P. K., Thomas, R. M., Thompson, Z., Mount, Z., Pippin, J. A., Morawski, P. A., Sun, P., Su, C., Campbell, D., et al. (2024) · eLife · doi:10.7554/elife.96852.2 · Cited by 1

Epigenomic analysis of hepatocellular carcinoma reveals aberrant cis -regulatory changes and dysregulated retrotransposons with prognostic potentialsPreprint

Cheng, C.-C., Cheung, M. F., Lee, A. Y., Wu, Q., Chow, S. H.-C., Ang, J. Y. J., Medina, I. R., Lo, G., Wu, H., Yang, W., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.16.613254 · Cited by 1

Alterations in chromatin accessibility and conformation elucidate genetic mechanisms in ASDPreprint

Yin, J., Huang, J. I., Ou, J., Chen, G. T., Bicks, L. K., Wamsley, B., Cheng, Y., Chen, L., Haney, J. R., Wong, R., et al. (2025) · medRxiv · doi:10.1101/2025.04.02.25325129 · Cited by 1

Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human BrainPreprint

Xie, Y., Chang, L., Zhong, G., Rink, J. A., Baez-Becerra, T., Armand, E. J., Ding, W., Li, K., Bonne, É., Lie, A., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.02.703166 · Cited by 4

Variant-to-gene mapping in ocular cell types identifies candidate effector genes for primary open-angle glaucomaPreprint

Vrathasha, V., Pahl, M. C., Pippin, J. A., Nikonov, S. S., He, J., Halimitabrizi, M., Moksha, L., Salowe, R., Edziah, A.-A., Bradford, Y., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.20.707051 · Cited by 1

HiCORE: Hi-C analysis for identification of core chromatin loops with higher resolution and reliabilityPreprint

Lee, H., & Seo, P. J. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.01.322024

Exploring the Effects of Genetic Variation on Gene Regulation in Cancer in the Context of 3D Genome StructurePreprint

Osman, N. M., Shawky, A.-E.-M., & Bryliński, M. (2021) · Research Square · doi:10.21203/rs.3.rs-496328/v1

Retrieving high-resolution chromatin interactions and decoding enhancer regulatory potential in silicoPreprint

Gusmao, E. G., Mizi, A., Brant, L., & Papantonis, A. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.10.376533

Multiscale 3D Genome Reorganization during Skeletal Muscle Stem Cell Lineage Progression and Muscle AgingPreprint

Wang, H., Zhao, Y. F., Ding, Y., He, L., Li, Y., Chen, X., & Sun, H. (2021) · Research Square · doi:10.21203/rs.3.rs-1190496/v1

Multi-ancestry Genome-wide Association Study of Varicose Veins Reveals Polygenic Architecture, Genetic Overlap with Arterial and Venous Disease, and Novel Therapeutic OpportunitiesPreprint

Levin, M. G., Huffman, J. E., Verma, A., Sullivan, K. A., Rodriguez, A., Kainer, D., Garvin, M. R., Lane, M. J., Won, H., Li, B., et al. (2022) · medRxiv · doi:10.1101/2022.02.22.22271350

Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structurePreprint

Osman, N. M., Shawky, A.-E.-M., & Bryliński, M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.06.328567

Peer Review #2 of "HiCEnterprise: identifying long range chromosomal contacts in Hi-C data (v0.1)"

(2021) · PeerJ · doi:10.7287/peerj.10558v0.1/reviews/2

Peer Review #1 of "HiCEnterprise: identifying long range chromosomal contacts in Hi-C data (v0.1)"

(2021) · PeerJ · doi:10.7287/peerj.10558v0.1/reviews/1

Peer Review #3 of "HiCEnterprise: identifying long range chromosomal contacts in Hi-C data (v0.1)"

(2021) · PeerJ · doi:10.7287/peerj.10558v0.1/reviews/3

DARIC, a Computational Framework for Identifying Quantitatively Differential Compartments from Hi-C DataPreprint

Yan, K., Liu, N., Orkin, S. H., & Yuan, G. (2022) · SSRN Electronic Journal · doi:10.2139/ssrn.4168307

Calculating the spatial density of regulatory chromatin interactions using multi-modal datasets from the same cell line

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Chromatin conformation dynamics during CD4+ T cell activation implicates autoimmune disease-associated genes and regulatory elementsPreprint

Wells, A. D., Pahl, M. C., Sharma, P. K., Thomas, R. M., Thompson, Z., Mount, Z., Pippin, J. A., Morawski, P. A., Campbell, D., Grant, S. F. A., et al. (2023) · Research Square · doi:10.21203/rs.3.rs-2855977/v1

Machine learning of enhancer-promoter specificity based on enhancer perturbation studies reveals a distinct class of enhancersPreprint

Barth, D., Cardwell, J., & Han, M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.30.547290

Uncovering the regulatory landscape of early human B-cell lymphopoiesis and its implications in the pathogenesis of B-cell acute lymphoblastic leukemiaPreprint

Planell, N., Martinez‐de‐Morentin, X., Mouzo, D., Lara‐Astiaso, D., Vilas‐Zornoza, A., Martín‐Úriz, P. S., Alignani, D., Paiva, B., Maillo, A., Kurowska, A. K., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.01.547234

Spatial chromosome organization and adaptation of the radiation-resistant extremophile Deinococcus radioduransPreprint

Qiu, Q.-T., Zhang, C., Gao, Z., & Ma, B. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.19.567671

Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity and tumor-specific looping-mediated biological pathwaysPreprint

Choppavarapu, L., Fang, K., Liu, T., & Jin, V. X. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.13.584872

Supervised learning of enhancer–promoter specificity based on genome-wide perturbation studies highlights areas for improvement in learning

Barth, D., Van, R., Cardwell, J., & Han, M. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae367

Shared and unique chromatin accessibility and 3D functional interactions of substance use disorder loci implicate cell types beyond the brainPreprint

Trang, B. K., Chesi, A., Toikumo, S., Pippin, J. A., Pahl, M. C., O’Brien, J. M., Amundadottir, L. T., Brown, K. M., Yang, W., Welles, J. E., et al. (2024) · medRxiv · doi:10.1101/2024.07.18.24310649

Reviewer #3 (Public Review): Dynamic chromatin architecture identifies new autoimmune-associated enhancers for IL2 and novel genes regulating CD4+ T cell activation

(2024) · eLife · doi:10.7554/elife.96852.2.sa1

Reviewer #1 (Public Review): Dynamic chromatin architecture identifies new autoimmune-associated enhancers for IL2 and novel genes regulating CD4+ T cell activation

(2024) · eLife · doi:10.7554/elife.96852.2.sa3

Author response: Dynamic chromatin architecture identifies new autoimmune-associated enhancers for IL2 and novel genes regulating CD4+ T cell activation

Pahl, M. C., Sharma, P. K., Thomas, R. M., Thompson, Z., Mount, Z., Pippin, J. A., Morawski, P. A., Sun, P., Su, C., Campbell, D., et al. (2024) · eLife · doi:10.7554/elife.96852.2.sa0

Reviewer #2 (Public Review): Dynamic chromatin architecture identifies new autoimmune-associated enhancers for IL2 and novel genes regulating CD4+ T cell activation

(2024) · eLife · doi:10.7554/elife.96852.2.sa2

eLife Assessment: Dynamic chromatin architecture identifies new autoimmune-associated enhancers for IL2 and novel genes regulating CD4+ T cell activation

Banovich, N. E. (2024) · eLife · doi:10.7554/elife.96852.2.sa4

Overcoming Artificial Structures in Resolution‐Enhanced Hi‐C Data by Signal Decomposition and Multi‐Scale Attention

Li, Q., Li, K. Y., Nicoletti, C., Tsui, S. K., Puri, P., Cao, Q., & Yip, K. Y.-L. (2026) · Advanced Science · doi:10.1002/advs.202524180

CHARMER: detecting and harmonizing high-confidence chromatin interactions across tissues and Hi-C protocolsPreprint

Cole, S., Kuksa, P. P., Cifello, J., Valladares, O., Leung, Y. Y., & Wang, L. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.25.625258

DeCGR: an interactive toolkit for deciphering complex genomic rearrangements from Hi-C data

Li, J., Sun, M., Ye, Y., & Gao, L. (2024) · BMC Genomics · doi:10.1186/s12864-024-11085-5

Gene mobility elements mediate cell type specific genome organization and radial gene movement in vivoPreprint

Lucas, T., Wang, L.-I., Glass-Klaiber, J., Quiroz, E., Patra, S., Molotkova, N., & Kohwi, M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.30.626181

Identifying associations between short tandem repeat sequences and gene expression in yeast reveals specific repeated motifs encoding transcriptional regulatory proteins

Yu, Z., Liang, Y., Xiang, M., Xu, K., Xu, X., Ran, D., Luo, Y., Chen, B., Bo, X., & Chen, H. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.02.003

Altered chromatin accessibility mediated by somatic cohesin mutations amplifies FLI1-Menin output to promote leukemogenesisPreprint

Xu, J. J., Scoca, V., Chen, Y., Zhan, Y. A., Fisher, A., Udoh, E.-O., Fernando, S., Alija, B., Pantazi, J., Sudunagunta, V. S., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.01.646632

Nuc3DMap delineates finer nucleosome-based three-dimensional chromatin architecturePreprint

Fang, K., Choppavarapu, L., Liu, T., Knight, P. A., & Jin, V. X. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.03.647017

Protocol for investigating chromatin architecture in adult skeletal muscle stem cells using high-throughput chromosome conformation capture

Kang, J., Zeng, Y., Li, N., He, L., Wang, H., Sun, K., & Zhao, Y. F. (2025) · STAR Protocols · doi:10.1016/j.xpro.2025.103962

Loopsim: enrichment analysis of chromosome conformation capture with fast empirical distribution simulation

Shaked, G., Zhang, H., Zhang, Z., Zhou, J., Gudjonsson, J. E., Elder, J. T., Patrick, M. T., & Tsoi, L. C. (2025) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaf098

Towards universal modeling of transcript isoform expression levelsPreprint

Chow, S. H.-C., Shi, C. H., Deshpande, A. J., Cao, Q., & Yip, K. Y.-L. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.21.665977

A new subgenome of the Camelina genus reveals genome dominance is controlled by chromosomal proximityPreprint

Chaudhary, R., Koh, K. C., Gao, P., Perumal, S., Higgins, E. E., Horner, K. N., Robinson, S. J., Wang, Z., Eynck, C., Bandi, V., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.18.670935

STRIDE: A Sequencing Depth Robust Metric for Sparse Chromosome Conformation Capture Data Comparison

Xu, B., Gao, X., Tao, W., Zhang, Z., & Li, F. (2026) · Advanced Science · doi:10.1101/2025.10.08.681271

Hi-C informed kernel association test: integrating 3-dimensional genome structure into variant-set association for whole-genome sequencing dataPreprint

Huang, Y., Basu, R., Lu, W., Holloway, S. T., Li, Y., & Tzeng, J. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.28.684891

DiffHiChIP: Identifying differential chromatin contacts from HiChIP data

Bhattacharyya, S., Figueroa, D. S., Georgopoulos, K., & Ay, F. (2025) · Cell Reports Methods · doi:10.1016/j.crmeth.2025.101214

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contactsPreprint

Ay, F., Bailey, T. L., & Noble, W. S. (2014) · Genome Research · doi:10.1101/gr.160374.113 · Cited by 479

Identification of significant chromatin contacts from HiChIP data by FitHiChIP

Bhattacharyya, S., Chandra, V., Vijayanand, P., & Ay, F. (2019) · Nature Communications · doi:10.1038/s41467-019-11950-y · Cited by 238

Fine mapping chromatin contacts in capture Hi-C data

Eijsbouts, C. Q., Burren, O. S., Newcombe, P. J., & Wallace, C. (2019) · BMC Genomics · doi:10.1186/s12864-018-5314-5 · Cited by 19

ChromContact: A web tool for analyzing spatial contact of chromosomes from Hi-C data

Sato, T., & Suyama, M. (2015) · BMC Genomics · doi:10.1186/s12864-015-2282-x · Cited by 7

SOFTWARE Open Access ChromContact: A web tool for analyzing

(2016)