Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

Durand, N. C., Robinson, J., Shamim, M. S., Machol, I., Mesirov, J. P., Lander, E. S., & Aiden, E. L. (2016) · Cell Systems · doi:10.1016/j.cels.2015.07.012 · Cited by 2,421

An oestrogen-receptor-α-bound human chromatin interactome

Fullwood, M. J., Liu, M. H., Pan, Y. F., Liu, J., Han, X., Mohamed, Y. B., Orlov, Y. L., Velkov, S., Ho, A., Poh, H. M., et al. (2009) · Nature · doi:10.1038/nature08497 · Cited by 1,752

A map of the cis-regulatory sequences in the mouse genome

Shen, Y., Yue, F., McCleary, D. F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V. V., et al. (2012) · Nature · doi:10.1038/nature11243 · Cited by 1,361

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

Mumbach, M. R., Rubin, A. J., Flynn, R. A., Dai, C., Khavari, P. A., Greenleaf, W. J., & Chang, H. Y. (2016) · Nature Methods · doi:10.1038/nmeth.3999 · Cited by 1,139

Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data

Dekker, J., Marti-Renom, M. A., & Mirny, L. A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3454 · Cited by 1,068

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

Mifsud, B., Tavares-Cadete, F., Young, A. N., Sugar, R., Schoenfelder, S., Ferreira, L., Wingett, S. W., Andrews, S., Grey, W., Ewels, P. A., et al. (2015) · Nature Genetics · doi:10.1038/ng.3286 · Cited by 990

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

Tang, Z., Luo, O. J., Li, X., Zheng, M., Zhu, J. J., Szalaj, P., Trzaskoma, P., Magalska, A., Wlodarczyk, J., Ruszczycki, B., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.024 · Cited by 982

Topology of mammalian developmental enhancers and their regulatory landscapes

de Laat, W., & Duboule, D. (2013) · Nature · doi:10.1038/nature12753 · Cited by 521

Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies

Tang, L., Hill, M., Ellinor, P., & Li, M. (2022) · Genome Biology · doi:10.1186/s13059-021-02597-4 · Cited by 8

Genetic variants drive altered epigenetic regulation of endotoxin response in BTBR macrophages

Ciernia, A. V., Link, V. M., Careaga, M., LaSalle, J. M., & Ashwood, P. (2020) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2020.05.058 · Cited by 8

High-throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases

Jones, I. R., Ren, X., & Shen, Y. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac193 · Cited by 8

3D genome organization and its study in livestock breeding

Cheng, J., Cao, X., Wang, S., Zhang, J., Yue, B., Zhang, X., Huang, Y., Lan, X., Ren, G., & Chen, H. (2023) · Journal of Integrative Agriculture · doi:10.1016/j.jia.2023.04.007 · Cited by 9

Integration with systems biology approaches and -omics data to characterize risk variation

Young, H. E., Cote, A. C., & Huckins, L. M. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-819602-1.00017-6 · Cited by 9

Ultrafine mapping of chromosome conformation at hundred basepair resolution reveals regulatory genome architecture

Zhu, Y., Rosenfeld, M. G., & Suh, Y. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2313285120 · Cited by 8

A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model

Golov, A. K., Gavrilov, A. A., Kaplan, N., & Razin, S. V. (2024) · eLife · doi:10.7554/elife.91596.3 · Cited by 10

Cell type-specific enhancer-promoter connectivity maps in the human brain and disease risk associationPreprint

Nott, A., Holtman, I., Coufal, N., Schlachetzki, J., Yu, M., Hu, R., Han, C. Z., Pena, M., Xiao, J., Wu, Y., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/778183 · Cited by 11

Characterization of altered molecular mechanisms in Parkinson’s disease through cell type-resolved multi-omics analysesPreprint

Lee, A., Kim, C., Park, S.-W., Jun, K., Eom, J., Lee, S., Chung, S. J., Rissman, R. A., Chung, J., Masliah, E., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.13.479386 · Cited by 8

Identifying genetic variants associated with chromatin looping and genome function

Bhattacharyya, S., & Ay, F. (2024) · Nature Communications · doi:10.1038/s41467-024-52296-4 · Cited by 8

3C methods in cancer research: recent advances and future prospects

Yoon, I., Kim, U., Jung, K. O., Song, Y., Park, T., & Lee, D.-S. (2024) · Experimental & Molecular Medicine · doi:10.1038/s12276-024-01236-9 · Cited by 7

Unraveling the 3D genome of human malaria parasites

Batugedara, G., & Roch, K. G. L. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.07.015 · Cited by 7

Heart Enhancers: Development and Disease Control at a Distance

Yuan, X., Scott, I. C., & Wilson, M. D. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.642975 · Cited by 7

Elucidating the structure and function of the nucleus—The NIH Common Fund 4D Nucleome program

Roy, A. L., Conroy, R., Taylor, V. G., Mietz, J. A., Fingerman, I. M., Pazin, M. J., Smith, P., Hutter, C. M., Singer, D. S., & Wilder, E. L. (2023) · Molecular Cell · doi:10.1016/j.molcel.2022.12.025 · Cited by 9

HiChIP and Hi-C Protocol Optimized for Primary Murine T Cells

Ζελένκα, Τ., & Spilianakis, C. G. (2021) · Methods and Protocols · doi:10.3390/mps4030049 · Cited by 6

Human endothelial colony forming cells (ECFCs) require endothelial protein C receptor (EPCR) for cell cycle progression and angiogenic activity

Chambers, S. E. J., Guduric‐Fuchs, J., Pedrini, E., Bertelli, P. M., Charoensuk, C., Peixoto, E., Pathak, V., Alhamdan, H. I., Xie, R., Krasnodembskaya, A. D., et al. (2025) · Angiogenesis · doi:10.1007/s10456-025-09982-8 · Cited by 6

Genetic and Epigenetic Dysregulation of Transcriptional Enhancers in Cancer

Botten, G. A., & Xu, J. (2024) · Annual Review of Cancer Biology · doi:10.1146/annurev-cancerbio-060324-114306 · Cited by 7

Population-based structure modeling reveals key roles of nuclear microenviroment in gene functionsPreprint

Yıldırım, A., Hua, N., Boninsegna, L., Polles, G., Gong, K. Q., Hao, S., Li, W., Zhou, X. J., & Alber, F. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.11.451976 · Cited by 6

A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping modelPreprint

Golov, A. K., Gavrilov, A. A., Kaplan, N., & Razin, S. V. (2023) · eLife · doi:10.7554/elife.91596 · Cited by 5

Computational Approaches for Understanding Sequence Variation Effects on the 3D Genome Architecture

Avdeyev, P., & Zhou, J. (2022) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-102521-012018 · Cited by 5

Hooked Up from a Distance: Charting Genome-Wide Long-Range Interaction Maps in Neural Cells Chromatin to Identify Novel Candidate Genes for Neurodevelopmental Disorders

Mercurio, S., Pozzolini, G., Baldi, R., Barilà, S. E., Pitasi, M., Catona, O., D’Aurizio, R., & Nicolis, S. K. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24021164 · Cited by 5

Free energy-based model of CTCF-mediated chromatin looping in the human genome

Dawson, W., Łaźniewski, M., & Plewczyński, D. (2020) · Methods · doi:10.1016/j.ymeth.2020.05.025 · Cited by 5

Why Single-Cell Sequencing Has Promise in MDS

Zhang, X., & Grimes, H. L. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.769753 · Cited by 5

A systematic evaluation of Hi-C data enhancement methods for enhancing PLAC-seq and HiChIP data

Huang, L., Yang, Y., Li, G., Jiang, M.-Z., Wen, J., Abnousi, A., Rosen, J. D., Hu, M., & Li, Y. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac145 · Cited by 5

Super interactive promoters provide insight into cell type-specific regulatory networks in blood lineage cell types

Wen, J., Lagler, T. M., Sun, Q., Yang, Y., Chen, J., Harigaya, Y., Sankaran, V. G., Hu, M., Reiner, A. P., Raffield, L. M., et al. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1009984 · Cited by 5

Metabolic resilience is encoded in genome plasticityPreprint

Agudelo, L. Z., Tuyéras, R., Llinares, C., Morcuende, Á., Park, Y., Sun, N., Linna-Kuosmanen, S., Atabaki‐Pasdar, N., Ho, L., Galani, K., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-716965/v1 · Cited by 5

Boosting the detection of enhancer-promoter loops via normalization methods for chromatin interaction data

Wang, X., Shi, D., Xue, F., Liu, Y., Yang, H., & Jiang, L.-H. (2026) · Nature Communications · doi:10.1038/s41467-026-69082-z · Cited by 4

SCN1A: bioinformatically informed revised boundaries for promoter and enhancer regions

Pagni, S., Custodio, H. M., Frankish, A., Mudge, J. M., Mills, J. D., & Sisodiya, S. M. (2023) · Human Molecular Genetics · doi:10.1093/hmg/ddad015 · Cited by 4

Long-range chromatin interactions in pathogenic gene expression control

Kong, N., & Jung, I. (2020) · Transcription · doi:10.1080/21541264.2020.1843958 · Cited by 4

Assessing Specific Networks of Chromatin Interactions with HiChIP

Giammartino, D. C. D., Polyzos, A., & Apostolou, E. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2497-5_7 · Cited by 4

Targeted DNase Hi-C

Duan, Z. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0664-3_5 · Cited by 4

Simultaneous profiling of DNA methylation and chromatin architecture in mixed populations and in single cellsPreprint

Li, G., Liu, Y., Zhang, Y., Fang, R., Kellis, M., & Ren, B. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/470963 · Cited by 4

dcHiC: differential compartment analysis of Hi-C datasetsPreprint

Chakraborty, A., Wang, J., & Ay, F. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.02.429297 · Cited by 4

A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model

Golov, A. K., Gavrilov, A. A., Kaplan, N., & Razin, S. V. (2023) · doi:10.7554/elife.91596.1 · Cited by 4

Conservation and variability of long-range interactions in structurally diverse maize genomes

Liu, H., Ma, X., Jiang, S., Li, Z., Dai, W., Liang, Z., Springer, N. M., & Zhang, M. (2025) · Nature Communications · doi:10.1038/s41467-025-65065-8 · Cited by 3

EmbedTAD Using Graph Embedding and Unsupervised Learning to Identify TADs from High-Resolution Hi-C Data

Chowdhury, H. M. A. M., & Oluwadare, O. (2025) · Communications Biology · doi:10.1038/s42003-025-09224-z · Cited by 3

Activity-Dependent Chromatin Mechanisms in Cerebellar Motor Learning

Valnegri, P., Yamada, T., & Yang, Y. (2022) · Neuromethods · doi:10.1007/978-1-0716-2026-7_7 · Cited by 3

HiCAR: Analysis of Open Chromatin Associated Long‐range Chromatin Interaction Using Low‐Input Materials

Wei, X., Tran, D., & Diao, Y. (2023) · Current Protocols · doi:10.1002/cpz1.899 · Cited by 3

Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles

Wang, Y., & Wang, Y. (2024) · npj Systems Biology and Applications · doi:10.1038/s41540-024-00388-8 · Cited by 3

Beyond the Chromosome: Recent Developments in Decoding the Significance of Extrachromosomal Circular DNA (eccDNA) in Human Malignancies

Tsiakanikas, P., Athanasopoulou, K., Darioti, I. A., Agiassoti, V. T., Theocharis, S., Scorilas, A., & Adamopoulos, P. (2024) · Life · doi:10.3390/life14080922 · Cited by 5

Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes

Buka, K., Parteka-Tojek, Z., Agarwal, A., Denkiewicz, M., Korsak, S., Chiliński, M., Banecki, K. H., & Plewczyński, D. (2025) · Communications Biology · doi:10.1038/s42003-025-07847-w · Cited by 4

Methods of massive parallel reporter assays for investigation of enhancers

Romanov, S. E., Kalashnikova, D. A., & Laktionov, P. P. (2021) · Vavilov Journal of Genetics and Breeding · doi:10.18699/vj21.038 · Cited by 3

Integrating extrusion complex-associated pattern to predict cell type-specific long-range chromatin loops

Deng, Y., Tang, L., Zhou, X., Wang, W., & Li, M. (2022) · iScience · doi:10.1016/j.isci.2022.105687 · Cited by 3

Computational methods for identifying enhancer‐promoter interactions

Gong, H., Chen, Z., Tang, Y., Li, M., Zhang, S., Zhang, X., & Chen, Y. (2023) · Quantitative Biology · doi:10.15302/j-qb-022-0322 · Cited by 3

Recent advances in chromosome capture techniques unraveling 3D genome architecture in germ cells, health, and disease

Pandupuspitasari, N. S., Khan, F. A., Huang, C., Ali, A., Yousaf, M. R., Shakeel, F., Putri, E. M., Negara, W., Muktiani, A., Prasetiyono, B. W. H. E., et al. (2023) · Functional & Integrative Genomics · doi:10.1007/s10142-023-01146-5 · Cited by 3

MMCT-Loop: a mix model-based pipeline for calling targeted 3D chromatin loops

Tang, L., Liao, J., Hill, M., Hu, J., Zhao, Y.-C., Ellinor, P., & Li, M. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae029 · Cited by 3

3D genome sequencing technology in its mid-teens: past, present, and future

Chai, H., & Ruan, Y. (2025) · Trends in Genetics · doi:10.1016/j.tig.2025.07.010 · Cited by 4

A Comprehensive Toolbox to Analyze Enhancer–Promoter Functions

Giaimo, B. D., Friedrich, T., & Borggrefe, T. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1597-3_1 · Cited by 3

Capture Hi-C: Characterization of chromatin contacts

Davis, R. R., Campbell, M., Izumiya, Y., & Tepper, C. G. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-819414-0.00021-5 · Cited by 3

Robust Hi-C chromatin loop maps in human neurogenesis and brain tissues at high-resolutionPreprint

Lu, L., Liu, X., Huang, W., Giusti‐Rodríguez, P., Cui, J., Zhang, S., Xu, W., Wen, Z., Ma, S., Rosen, J. D., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/744540 · Cited by 3

MLL3/MLL4 Histone Methyltranferase Activity Dependent Chromatin Organization at Enhancers during Embryonic Stem Cell DifferentiationPreprint

Kubo, N., Hu, R., Ye, Z., & Ren, B. (2021) · bioRxiv · doi:10.1101/2021.03.17.435905 · Cited by 2

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

Chen, S., Wang, J., Jung, I., Qiu, Z., Gao, X., & Li, Y. (2024) · Genome Research · doi:10.1101/gr.279274.124 · Cited by 3

Variant-to-function mapping of late-onset Alzheimer’s disease GWAS signals in human microglial cell models implicates RTFDC1 at the CASS4 locus

Burton, E. A., Argenziano, M., Cook, K., Ridler, M., Lu, S., Su, C., Manduchi, E., Littleton, S. H., Leonard, M. E., Hodge, K. M., et al. (2024) · doi:10.1101/2024.08.22.609230 · Cited by 3

Supervised Chromatin Loop Detection Using Peakachu Version 2

Wang, X. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-4136-1_11 · Cited by 2

Mapping 3D genome organization at nucleosome-scale with Micro-C and Region Capture Micro-C (RCMC)

Huseyin, M. K., Hong, C. K. Y., Nagano, M., Drayton, J. A., Jusuf, J. M., Yang, J., Ramanathan, V., Goel, V. Y., Kim, S. Y., & Hansen, A. S. (2026) · Nature Protocols · doi:10.1038/s41596-026-01393-3 · Cited by 3

The cardiac 4D nucleome: nuclear and chromatin dynamics across development, disease and ageing

Wang, Y., & Dobreva, G. D. (2026) · Nature Reviews Cardiology · doi:10.1038/s41569-026-01322-7 · Cited by 2

Characterization of Gene Regulatory Elements in Human Fetal Cortical Development: Enhancing Our Understanding of Neurodevelopmental Disorders and Evolution

Guo, Q., Wu, S. J., & Geschwind, D. H. (2023) · Developmental Neuroscience · doi:10.1159/000530929 · Cited by 2

HPTAD: A computational method to identify topologically associating domains from HiChIP and PLAC-seq datasets

Rosen, J. D., Lee, L., Abnousi, A., Chen, J.-W., Wen, J., Hu, M., & Li, Y. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.01.003 · Cited by 2

Assessment of 3D Interactions Between Promoters and Distal Regulatory Elements with Promoter Capture Hi-C (PCHi-C)

Karasu, N., & Sexton, T. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1597-3_13 · Cited by 2

Discovery and Functional Characterization of Pro-growth Enhancers in Human Cancer CellsPreprint

Chen, P.-S. B., Fiaux, P. C., Li, B., Zhang, K., Kubo, N., Jiang, S., Hu, R., Wu, S.-H., Wang, M.-C., Wang, W., et al. (2021) · bioRxiv · doi:10.1101/2021.02.04.429675 · Cited by 3

Super interactive promoters provide insight into cell type-specific regulatory networks in blood lineage cell typesPreprint

Lagler, T. M., Yang, Y., Harigaya, Y., Sankaran, V. G., Hu, M., Reiner, A. P., Raffield, L. M., Wen, J., & Li, Y. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.15.435494 · Cited by 2

HiC-LDNet: A general and robust deep learning framework for accurate chromatin loop detection in genome-wide contact mapsPreprint

Chen, S., Wang, J., Gao, X., & Li, Y. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.30.478367 · Cited by 2

Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactionsPreprint

Xu, J., Kumar, S., Hua, N., Kou, Y., Lei, X., Rout, M. P., Aitchison, J. D., Alber, F., & Chen, L. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.03.478915 · Cited by 2

Fusion Neural Network (FusNet) for predicting protein-mediated loopsPreprint

Tang, L., Huang, W., Hill, M. C., Ellinor, P. T., & Li, M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.24.546360 · Cited by 2

Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancerPreprint

Song, Y., Li, F., Wang, S., Wang, Y., Lai, C., Chen, L., Jiang, N., Li, J., Chen, X., Bailey, S. D., et al. (2024) · Genome Research · doi:10.1101/gr.278418.123 · Cited by 2

Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications

Arshadi, A., Tolomeo, D., Venuto, S., & Storlazzi, C. T. (2023) · Genes · doi:10.3390/genes14061304 · Cited by 1

An integrative 3D-genome database for plants

Yang, Q., Wu, T., Liu, M., Zhang, X., Sun, X., Feng, D., Lu, Y. Y., Chen, X., Hong, Y., Ma, W., et al. (2025) · Plant Communications · doi:10.1016/j.xplc.2025.101346 · Cited by 1

Human Accelerated Regions: Functional Studies and Methodological Approaches (A Review)

Knyazeva, A. S., & Шнайдер, Т. А. (2026) · Cell and Tissue Biology · doi:10.1134/s1990519x25600784 · Cited by 1

Accurate prediction of cohesin and RNA Polymerase II-associated chromatin interactions using convolutional neural networks

Abbas, A. A., Chandratre, K. R., Liu, C., Zhang, M. Q., & Mani, R. S. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag258 · Cited by 1

Three-dimensional chromatin architecture in crustaceans: Emerging evidence, structural principles, and future directions: A review

Wikumpriya, G. C. (2026) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2026.152499 · Cited by 1

Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts in mouse embryonic stem cells

Fortin, H. J., Struba, A. Z., Bustan, A., & Baker, C. L. (2026) · Genome biology · doi:10.1186/s13059-026-04155-2

Capturing Chromosome Conformation Across Length Scales

Yang, L., Oksuz, B. A., Dekker, J., & Gibcus, J. H. (2023) · Journal of Visualized Experiments · doi:10.3791/64001 · Cited by 1

Capturing Chromosome Conformation Across Length Scales

Yang, L., Oksuz, B. A., Dekker, J., & Gibcus, J. H. (2023) · Journal of Visualized Experiments · doi:10.3791/64001-v · Cited by 1

ccLoopER: Deep Prediction of CTCF and cohesin Mediated Chromatin looping Using DNA Transformer Model

Halder, A. K., Agarwal, A., Korsak, S., Jodkowska, K., & Plewczyński, D. (2023) · Lecture notes in computer science · doi:10.1007/978-3-031-45170-6_91 · Cited by 1

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

Cayford, J., de la Mata, S. H., Schmiedel, B. J., Chandra, V. K., Vijayanad, P., & Seumois, G. (2020) · Journal of Visualized Experiments · doi:10.3791/61617 · Cited by 1

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

Cayford, J., de la Mata, S. H., Schmiedel, B. J., Chandra, V., Vijayanad, P., & Seumois, G. (2020) · Journal of Visualized Experiments · doi:10.3791/61617-v · Cited by 1

Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-κB bindingPreprint

Wang, L., Taylor, T., Rathnakumar, K., Khyzha, N., Liang, M., Alizada, A., Campitelli, L., Pour, S. E., Patel, Z. M., Antounians, L., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.25.513724 · Cited by 2

A multi-enhancer hub at the Ets1 locus controls T cell differentiation and allergic inflammation through 3D genome topologyPreprint

Chandra, A., Yoon, S., Michieletto, M. F., Goldman, N., Ferrari, E. K., Fasolino, M., Joannas, L. D., Kee, B. L., Henao‐Mejia, J., & Vahedi, G. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.28.514213 · Cited by 1

Large-scale manipulation of radial positioning does not affect most aspects of genome organizationPreprint

Guetta, M., Kariti, H., Sherman, L., Israitel, L., Tel-Paz, M., Avidan, N., Shemer, R., & Kaplan, N. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.22.609170 · Cited by 1

Characterizing trajectory-like chromatin architectures with Fun2Preprint

Zhangding, Z., Liu, X., & Hu, J. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.25.640072 · Cited by 1

Commentary: Nuclear dynamics of the Set1C subunit Spp1 prepares meiotic recombination sites for break formation

Fillér, C., Hornyák, L., & Roszik, J. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00496

Organizing Principles for the Spatial Folding of Chromosomes

Josipović, N., & Papantonis, A. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-814879-2.00005-4

Epigenomic, Transcriptome and Image-Based Biomarkers of Aging

Yan, Y., Mu, Y., Chen, W., & Han, J. J. (2019) · Healthy ageing and longevity · doi:10.1007/978-3-030-24970-0_5

Investigation of ChIP-Seq Technology

Song, T. Y. (2020) · International Journal of Software & Hardware Research in Engineering · doi:10.26821/ijshre.8.9.2020.8901

Using Open Chromatin Enrichment and Network Hi-C (OCEAN-C) to Identify Open Chromatin Interactions

Jia, L., Li, C., & Li, T. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1597-3_12

New Techniques for Mechanical Measurements in the Superconducting Magnet Models

Guinchard, M., Artoos, K., Gerardin, A., & Kuzmin, A. (2010) · JACOW · doi:10.18429/jacow-ipac2010-mopeb043 · Cited by 1

Structural Consistency Support in an Integral Design System

Després, B., Lipp, M., Piloty, R., & Schellin, U. (1992)

Faculty Opinions recommendation of Cell-type-specific 3D epigenomes in the developing human cortex.

Sharrocks, A. D. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.738832662.793581292

Faculty Opinions recommendation of Circular ecDNA promotes accessible chromatin and high oncogene expression.

Lu, Y. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.736936388.793568931

Faculty Opinions recommendation of Circular ecDNA promotes accessible chromatin and high oncogene expression.

Abounader, R., & Mulcahy, E. Q. X. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.736936388.793568918

Faculty Opinions recommendation of Circular ecDNA promotes accessible chromatin and high oncogene expression.

Dalal, Y., & Arunkumar, G. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.736936388.793567812

Inferring Single-Molecule Chromatin Interactions via Online Convex Network Dictionary LearningPreprint

Peng, J., Pan, C., Lyu, H., Kim, M., Cheng, A. W., & Milenković, O. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.28.501904

DeDoc2 identifies and characterizes the hierarchy and dynamics of chromatin TAD-like domains in the single cellsPreprint

Zhang, Z., Li, A., Zeng, G., Wang, H., & Li, X. (2022) · Research Square · doi:10.21203/rs.3.rs-1863314/v1

A 3D genome atlas of genetic variants and their pathological effectsPreprint

Tang, L., Hill, M., He, M.-X., Chen, J.-H., Ellinor, P., & Li, M. (2022) · bioRxiv · doi:10.1101/2022.11.27.518071

Exploring the roles of RNAPII in genome organization

Zhang, S. (2022) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-9632

Practical application of massively parallel reporter assay in biotechnology and medicine

Romanov, S. E., & Laktionov, P. P. (2023) · Journal of clinical practice · doi:10.17816/clinpract115063

Data from Chromatin Looping Shapes KLF5-Dependent Transcriptional Programs in Human Epithelial Cancers

Liu, Y., Guo, B., Aguilera-Jimenez, E., Chu, V. S., Zhou, J., Wu, Z., Francis, J. M., Yang, X., Choi, P. S., Bailey, S. D., et al. (2023) · doi:10.1158/0008-5472.c.6512668.v1

Reviewer #2 (Public Review): A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model

Golov, A. K., Gavrilov, A. A., Kaplan, N., et al. (2023) · eLife · doi:10.7554/elife.91596.1.sa1

eLife Assessment: A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model

Xu, J. (2023) · eLife · doi:10.7554/elife.91596.1.sa3

An in silico procedure for generating protein-mediated chromatin interaction data and comparison of significant interaction calling methods

Lou, S., & Lin, S.-L. (2024) · PLoS ONE · doi:10.1371/journal.pone.0287521

Hi-Tag: a simple and efficient method for identifying protein-mediated long-range chromatin interactions with low cell numbers

Qi, X., Zhang, L., Zhao, Q., Zhou, P., Zhang, S., Li, J., Zheng, Z., Xiang, Y., Dai, X., Jin, Z., et al. (2024) · Science China Life Sciences · doi:10.1007/s11427-023-2441-0 · Cited by 3

ChromE-seq: Chromatin and Expression Co-assay with Sequencing v1Preprint

Liao, Z., & Ma, S. (2025) · doi:10.17504/protocols.io.e6nvwbq4wvmk/v1

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

Juric, I., Yu, M., Abnousi, A., Raviram, R., Fang, R., Zhao, Y., Zhang, Y., Qiu, Y., Yang, Y., Li, Y., et al. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006982 · Cited by 121

Deciphering the effects of proximity ligation in chromatin contact maps to understand single molecule interactions data

Kim, M., Zheng, M., Tian, S. Z., Lee, B., Capurso, D., Chuang, J. H., & Ruan, Y. (2018) · Research in Computational Molecular Biology

ChIP‐based methods for the identification of long‐range chromatin interactions

Fullwood, M. J., & Ruan, Y. (2009) · Journal of Cellular Biochemistry · doi:10.1002/jcb.22116 · Cited by 251