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

Towards complete and error-free genome assemblies of all vertebrate species

Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03451-0 · Cited by 3,097

Towards complete and error-free genome assemblies of all vertebrate species

Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Gedman, G. L., et al. (2020) · doi:10.1101/2020.05.22.110833 · Cited by 3,097

YaHS: yet another Hi-C scaffolding tool

Zhou, C., McCarthy, S. A., & Durbin, R. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btac808 · Cited by 2,440

Cohesin Loss Eliminates All Loop Domains

Rao, S. S. P., Huang, S.-C., Glenn St Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.026 · Cited by 1,883

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

Abdennur, N., & Mirny, L. A. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btz540 · Cited by 1,759

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

Organization and function of the 3D genome

Bonev, B., & Cavalli, G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.112 · Cited by 1,174

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

Hsieh, T.-H. S., Cattoglio, C., Slobodyanyuk, E., Hansen, A. S., Rando, O. J., Tjian, R., & Darzacq, X. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.002 · Cited by 661

Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

Qin, P., Lu, H., Du, H., Wang, H., Chen, W., Chen, Z., He, Q., Ou, S., Zhang, H., Li, X., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.046 · Cited by 578

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

Su, J.-H., Zheng, P., Kinrot, S. S., Bintu, B., & Zhuang, X. (2020) · Cell · doi:10.1016/j.cell.2020.07.032 · Cited by 562

Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues

Bartosovic, M., Kabbe, M., & Castelo-Branco, G. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00869-9 · Cited by 483

Ancient gene linkages support ctenophores as sister to other animals

Schultz, D. T., Haddock, S. H. D., Bredeson, J. V., Green, R. E., Simakov, O., & Rokhsar, D. S. (2023) · Nature · doi:10.1038/s41586-023-05936-6 · Cited by 362

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

Redin, C., Brand, H., Collins, R. L., Kammin, T., Mitchell, E., Hodge, J. C., Hanscom, C., Pillalamarri, V., Seabra, C. M., Abbott, M.-A., et al. (2017) · Nature Genetics · doi:10.1038/ng.3720 · Cited by 334

High-resolution comparative analysis of great ape genomes

Kronenberg, Z. N., Fiddes, I. T., Gordon, D., Murali, S., Cantsilieris, S., Meyerson, O. S., Underwood, J. G., Nelson, B. J., Chaisson, M. J. P., Dougherty, M. L., et al. (2018) · Science · doi:10.1126/science.aar6343 · Cited by 350

Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity

Alexander, J. M., Guan, J., Li, B., Maliskova, L., Song, M., Shen, Y., Huang, B., Lomvardas, S., & Weiner, O. D. (2019) · eLife · doi:10.7554/elife.41769 · Cited by 346

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

Fang, R., Yu, M., Li, G., Chee, S., Liu, T., Schmitt, A. D., & Ren, B. (2016) · Cell Research · doi:10.1038/cr.2016.137 · Cited by 344

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

Kubo, N., Ishii, H., Xiong, X., Bianco, S., Meitinger, F., Hu, R., Hocker, J. D., Conte, M., Gorkin, D., Yu, M., et al. (2021) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-00539-5 · Cited by 289

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers

El Khattabi, L., Zhao, H., Kalchschmidt, J., Young, N., Jung, S., Van Blerkom, P., Kieffer-Kwon, P., Kieffer-Kwon, K.-R., Park, S., Wang, X., et al. (2019) · Cell · doi:10.1016/j.cell.2019.07.011 · Cited by 244

Semi-automated assembly of high-quality diploid human reference genomes

Jarvis, E. D., Formenti, G., Rhie, A., Guarracino, A., Yang, C., Wood, J., Tracey, A., Thibaud-Nissen, F., Vollger, M. R., Porubsky, D., et al. (2022) · Nature · doi:10.1038/s41586-022-05325-5 · Cited by 209

Deeply conserved synteny and the evolution of metazoan chromosomes

Simakov, O., Bredeson, J., Berkoff, K., Marletaz, F., Mitros, T., Schultz, D. T., O’Connell, B. L., Dear, P., Martinez, D. E., Steele, R. E., et al. (2022) · Science Advances · doi:10.1126/sciadv.abi5884 · Cited by 197

Neuronal enhancers are hotspots for DNA single-strand break repair

Wu, W., Kargbo-Hill, S. E., Nathan, W. J., Paiano, J., Callen, E., Wang, D., Shinoda, K., van Wietmarschen, N., Colón-Mercado, J. M., Zong, D., et al. (2021) · Nature · doi:10.1038/s41586-021-03468-5 · Cited by 223

Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk

Rajarajan, P., Borrman, T., Liao, W., Schrode, N., Flaherty, E., Casiño, C., Powell, S., Yashaswini, C., LaMarca, E. A., Kassim, B., et al. (2018) · Science · doi:10.1126/science.aat4311 · Cited by 219

Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function

Link, V. M., Duttke, S. H., Chun, H. B., Holtman, I. R., Westin, E., Hoeksema, M. A., Abe, Y., Skola, D., Romanoski, C. E., Tao, J., et al. (2018) · Cell · doi:10.1016/j.cell.2018.04.018 · Cited by 182

Subtype-specific 3D genome alteration in acute myeloid leukaemia

Xu, J., Song, F., Lyu, H., Kobayashi, M., Zhang, B., Zhao, Z., Hou, Y., Wang, X., Luan, Y., Jia, B., et al. (2022) · Nature · doi:10.1038/s41586-022-05365-x · Cited by 208

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

Huang, H., Zhu, Q., Jussila, A., Han, Y., Bintu, B., Kern, C., Conte, M., Zhang, Y., Bianco, S., Chiariello, A. M., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00863-6 · Cited by 187

Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale

Zhou, J. (2022) · Nature Genetics · doi:10.1038/s41588-022-01065-4 · Cited by 177

CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions

Gasperini, M., Findlay, G. M., McKenna, A., Milbank, J. H., Lee, C., Zhang, M. D., Cusanovich, D. A., & Shendure, J. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.06.010 · Cited by 143

How subtle changes in 3D structure can create large changes in transcription

Xiao, J. Y., Hafner, A., & Boettiger, A. N. (2021) · eLife · doi:10.7554/elife.64320 · Cited by 162

Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development

Ngan, C. Y., Wong, C. H., Tjong, H., Wang, W., Goldfeder, R. L., Choi, C., He, H., Gong, L., Lin, J., Urban, B., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0581-x · Cited by 140

Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element

Huang, P., Keller, C. A., Giardine, B., Grevet, J. D., Davies, J. O. J., Hughes, J. R., Kurita, R., Nakamura, Y., Hardison, R. C., & Blobel, G. A. (2017) · Genes & Development · doi:10.1101/gad.303461.117 · Cited by 127

Incorporation of a nucleoside analog maps genome repair sites in postmitotic human neurons

Reid, D. A., Reed, P. J., Schlachetzki, J. C. M., Nitulescu, I. I., Chou, G., Tsui, E. C., Jones, J. R., Chandran, S., Lu, A. T., McClain, C. A., et al. (2021) · Science · doi:10.1126/science.abb9032 · Cited by 121

Epigenetic maintenance of topological domains in the highly rearranged gibbon genome

Lazar, N. H., Nevonen, K. A., O'Connell, B., McCann, C., O'Neill, R. J., Green, R. E., Meyer, T. J., Okhovat, M., & Carbone, L. (2018) · Genome Research · doi:10.1101/gr.233874.117 · Cited by 107

Topological structures and syntenic conservation in sea anemone genomes

Zimmermann, B., Montenegro, J. D., Robb, S. M. C., Fropf, W. J., Weilguny, L., He, S., Chen, S., Lovegrove-Walsh, J., Hill, E. M., Chen, C.-Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-44080-7 · Cited by 106

A Mutation in the Transcription Factor Foxp3 Drives T Helper 2 Effector Function in Regulatory T Cells

Van Gool, F., Nguyen, M. L. T., Mumbach, M. R., Satpathy, A. T., Rosenthal, W. L., Giacometti, S., Le, D. T., Liu, W., Brusko, T. M., Anderson, M. S., et al. (2019) · Immunity · doi:10.1016/j.immuni.2018.12.016 · Cited by 102

Genome structures resolve the early diversification of teleost fishes

Parey, E., Louis, A., Montfort, J., Bouchez, O., Roques, C., Iampietro, C., Lluch, J., Castinel, A., Donnadieu, C., Desvignes, T., et al. (2023) · Science · doi:10.1126/science.abq4257 · Cited by 87

Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops

Oh, H. J., Aguilar, R., Kesner, B., Lee, H.-G., Kriz, A. J., Chu, H.-P., & Lee, J. T. (2021) · Cell · doi:10.1016/j.cell.2021.11.012 · Cited by 84

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency

Pękowska, A., Klaus, B., Xiang, W., Severino, J., Daigle, N., Klein, F. A., Oleś, M., Casellas, R., Ellenberg, J., Steinmetz, L. M., et al. (2018) · Cell Systems · doi:10.1016/j.cels.2018.09.003 · Cited by 74

Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet

Hu, R., Li, X., Hu, Y., Zhang, R., Lv, Q., Zhang, M., Sheng, X., Zhao, F., Chen, Z., Ding, Y., et al. (2023) · Cell · doi:10.1016/j.cell.2023.07.003 · Cited by 55

TLR8 escapes X chromosome inactivation in human monocytes and CD4+ T cells

Youness, A., Cenac, C., Faz-López, B., Grunenwald, S., Barrat, F. J., Chaumeil, J., Mejía, J. E., & Guéry, J.-C. (2023) · Biology of Sex Differences · doi:10.1186/s13293-023-00544-5 · Cited by 58

Structural Variation and Introgression from Wild Populations in East Asian Cattle Genomes Confer Adaptation to Local Environment

Xia, X., Zhang, F., Li, S., Luo, X., Peng, L., Dong, Z., Pausch, H., Leonard, A. S., Crysnanto, D., Wang, S., et al. (2023) · Genome biology · doi:10.1186/s13059-023-03052-2 · Cited by 53

The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle

Furlan-Magaril, M., Ando-Kuri, M., Arzate-Mejía, R. G., Morf, J., Cairns, J., Román-Figueroa, A., Tenorio-Hernández, L., Poot-Hernández, A. C., Andrews, S., Várnai, C., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02374-3 · Cited by 39

A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797)

Destanović, D., Schultz, D. T., Styfhals, R., Cruz, F., Gómez-Garrido, J., Gut, M., Gut, I., Fiorito, G., Simakov, O., Alioto, T. S., et al. (2023) · G3: Genes, Genomes, Genetics · doi:10.1093/g3journal/jkad220 · Cited by 36

Measurement of differential chromatin interactions with absolute quantification of architecture (AQuA-HiChIP)

Gryder, B. E., Khan, J., & Stanton, B. Z. (2020) · Nature Protocols · doi:10.1038/s41596-019-0285-9 · Cited by 35

‘Generating chromosome geometries in a minimal cell from cryo-electron tomograms and chromosome conformation capture maps’

Gilbert, B. R., Thornburg, Z. R., Lam, V., Rashid, F.-Z. M., Glass, J. I., Villa, E., Dame, R. T., & Luthey-Schulten, Z. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.644133 · Cited by 30

Chromatin Looping Links Target Genes with Genetic Risk Loci for Dermatological Traits

Shi, C., Ray-Jones, H., Ding, J., Duffus, K., Fu, Y., Gaddi, V. P., Gough, O., Hankinson, J., Martin, P., McGovern, A., et al. (2021) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2021.01.015 · Cited by 32

Karyotypic stasis and swarming influenced the evolution of viral tolerance in a species-rich bat radiation

Foley, N. M., Harris, A. J., Bredemeyer, K. R., Ruedi, M., Puechmaille, S. J., Teeling, E. C., Criscitiello, M. F., & Murphy, W. J. (2024) · Cell Genomics · doi:10.1016/j.xgen.2023.100482 · Cited by 31

Exogenous artificial DNA forms chromatin structure with active transcription in yeast

Zhou, J., Zhang, C., Wei, R., Han, M., Wang, S., Yang, K., Zhang, L., Chen, W., Wen, M., Li, C., et al. (2022) · Science China Life Sciences · doi:10.1007/s11427-021-2044-x · Cited by 24

HiC-GNN: A Generalizable Model for 3D Chromosome Reconstruction Using Graph Convolutional Neural Networks

Hovenga, V., Oluwadare, O., & Kalita, J. (2021) · doi:10.1101/2021.11.29.470405 · Cited by 21

Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle

Xia, X., Wang, F., Luo, X., Li, S., Lyu, Y., Zheng, Y., Ma, Z., Qu, K., Song, R., Liu, J., et al. (2025) · Advanced Science · doi:10.1002/advs.202503258 · Cited by 14

Rapid Macrosatellite Evolution Promotes X-Linked Hybrid Male Sterility in a Feline Interspecies Cross

Bredemeyer, K. R., Seabury, C. M., Stickney, M. J., McCarrey, J. R., vonHoldt, B. M., & Murphy, W. J. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab274 · Cited by 13

Notch1 Phase Separation Coupled Percolation facilitates target gene expression and enhancer looping

Foran, G., Hallam, R. D., Megaly, M., Turgambayeva, A., Antfolk, D., Li, Y., Luca, V. C., & Necakov, A. (2024) · Scientific Reports · doi:10.1038/s41598-024-71634-6 · Cited by 11

From FISH to Hi-C: The Chromatin Architecture of the Chromosomal Region 7q36.3, Frequently Rearranged in Leukemic Cells, Is Evolutionary Conserved

Gulino, G. M., Bruno, F., Sturiale, V., Brancato, D., Ragusa, D., Tosi, S., Saccone, S., & Federico, C. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22052338 · Cited by 10

A chromosome-level reference genome assembly of the Reeve’s moray eel (Gymnothorax reevesii)

Zhang, K., Huang, Y., Zhang, Y., Liang, R., Li, Q., Li, R., Zhao, X., Bian, C., Chen, Y., Wu, J., et al. (2023) · Scientific Data · doi:10.1038/s41597-023-02394-7 · Cited by 8

Chromatin structures from integrated AI and polymer physics model

Schultz, E. R., Kyhl, S., Willett, R., & de Pablo, J. J. (2025) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1012912 · Cited by 6

A telomere-to-telomere chromosome-scale genome assembly of glass catfish (Kryptopterus vitreolus)

Bian, C., Li, D., Wang, Y., He, Z., Chen, W.-T., Chong, C.-M., Zhou, H., & Shi, Q. (2025) · Scientific Data · doi:10.1038/s41597-025-04841-z · Cited by 2

A complete telomere-to-telomere chromosome-level genome assembly of X-ray tetra (Pristella maxillaris)

Bian, C., Hu, C., He, Z., Li, Z., & Shi, Q. (2025) · Scientific Data · doi:10.1038/s41597-025-04824-0 · Cited by 2

Reference genomes of four miniature and non-miniature cypriniform fishes inhabiting acidic peat-swamp forest blackwaters of Southeast Asia

Sudasinghe, H., Liu, Z., Triginer-Llabrés, L., Hui Tan, H., Britz, R., Salzburger, W., Peichel, C. L., & Rüber, L. (2026) · doi:10.64898/2026.03.21.713365 · Cited by 2

INSIG1 parallel substitution drives lipid/sterol metabolic plasticity mediating desert adaptation in ungulates

Li, X., He, Z., Liu, A., Meng, F., Zhang, X., Li, N., Liu, H., Lu, Y., Wu, Z., Fan, H., et al. (2026) · Communications Biology · doi:10.1038/s42003-026-09523-z · Cited by 1