BigWig and BigBed: enabling browsing of large distributed datasets

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041

The Human Genome Browser at UCSC

Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049

A genomic mutational constraint map using variation in 76,156 human genomes

Chen, S., Francioli, L. C., Goodrich, J. K., Collins, R. L., Kanai, M., Wang, Q., Alföldi, J., Watts, N. A., Vittal, C., Gauthier, L. D., et al. (2024) · Nature · doi:10.1038/s41586-023-06045-0 · Cited by 1,727

Ensembl 2015

Cunningham, F., Amode, M. R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fitzgerald, S., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1010 · Cited by 1,115

The UCSC genome browser and associated tools

Kuhn, R. M., Haussler, D., & Kent, W. J. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs038 · Cited by 883

Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells

Blaschke, K., Ebata, K. T., Karimi, M. M., Zepeda-Martínez, J. A., Goyal, P., Mahapatra, S., Tam, A., Laird, D. J., Hirst, M., Rao, A., et al. (2013) · Nature · doi:10.1038/nature12362 · Cited by 865

Brain cell type–specific enhancer–promoter interactome maps and disease - risk association

Nott, A., Holtman, I. R., Coufal, N. G., Schlachetzki, J. C. M., Yu, M., Hu, R., Han, C. Z., Pena, M., Xiao, J., Wu, Y., et al. (2019) · Science · doi:10.1126/science.aay0793 · Cited by 699

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science · doi:10.1126/science.abf7117 · Cited by 702

The UCSC Genome Browser database: 2014 update

Karolchik, D., Barber, G. P., Casper, J., Clawson, H., Cline, M. S., Diekhans, M., Dreszer, T. R., Fujita, P. A., Guruvadoo, L., Haeussler, M., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1168 · Cited by 670

A DNA methylation atlas of normal human cell types

Loyfer, N., Magenheim, J., Peretz, A., Cann, G., Bredno, J., Klochendler, A., Fox-Fisher, I., Shabi-Porat, S., Hecht, M., Pelet, T., et al. (2023) · Nature · doi:10.1038/s41586-022-05580-6 · Cited by 656

Loss of epigenetic information as a cause of mammalian aging

Yang, J.-H., Hayano, M., Griffin, P. T., Amorim, J. A., Bonkowski, M. S., Apostolides, J. K., Salfati, E. L., Blanchette, M., Munding, E. M., Bhakta, M., et al. (2023) · Cell · doi:10.1016/j.cell.2022.12.027 · Cited by 643

Base-resolution models of transcription-factor binding reveal soft motif syntax

Avsec, Ž., Weilert, M., Shrikumar, A., Krueger, S., Alexandari, A., Dalal, K., Fropf, R., McAnany, C., Gagneur, J., Kundaje, A., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00782-6 · Cited by 610

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

Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations

Merkle, F. T., Ghosh, S., Kamitaki, N., Mitchell, J., Avior, Y., Mello, C., Kashin, S., Mekhoubad, S., Ilic, D., Charlton, M., et al. (2017) · Nature · doi:10.1038/nature22312 · Cited by 506

Transcription factor trapping by RNA in gene regulatory elements

Sigova, A. A., Abraham, B. J., Ji, X., Molinie, B., Hannett, N. M., Guo, Y. E., Jangi, M., Giallourakis, C. C., Sharp, P. A., & Young, R. A. (2015) · Science · doi:10.1126/science.aad3346 · Cited by 492

Global characterization of macrophage polarization mechanisms and identification of M2-type polarization inhibitors

He, L., Jhong, J.-H., Chen, Q., Huang, K.-Y., Strittmatter, K., Kreuzer, J., DeRan, M., Wu, X., Lee, T.-Y., Slavov, N., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109955 · Cited by 354

Repression of Stress-Induced LINE-1 Expression Protects Cancer Cell Subpopulations from Lethal Drug Exposure

Guler, G. D., Tindell, C. A., Pitti, R., Wilson, C., Nichols, K., KaiWai Cheung, T., Kim, H.-J., Wongchenko, M., Yan, Y., Haley, B., et al. (2017) · Cancer Cell · doi:10.1016/j.ccell.2017.07.002 · Cited by 277

The UCSC Genome Browser database: 2022 update

Lee, B. T., Barber, G. P., Benet-Pagès, A., Casper, J., Clawson, H., Diekhans, M., Fischer, C., Gonzalez, J. N., Hinrichs, A. S., Lee, C. M., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab959 · Cited by 273

Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation

Song, Y., Botvinnik, O. B., Lovci, M. T., Kakaradov, B., Liu, P., Xu, J. L., & Yeo, G. W. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.06.003 · Cited by 204

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

FactorNet: A deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data

Quang, D., & Xie, X. (2019) · Methods · doi:10.1016/j.ymeth.2019.03.020 · Cited by 204

SCAF4 and SCAF8, mRNA Anti-Terminator Proteins

Gregersen, L. H., Mitter, R., Ugalde, A. P., Nojima, T., Proudfoot, N. J., Agami, R., Stewart, A., & Svejstrup, J. Q. (2019) · Cell · doi:10.1016/j.cell.2019.04.038 · Cited by 140

Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1

Minderjahn, J., Schmidt, A., Fuchs, A., Schill, R., Raithel, J., Babina, M., Schmidl, C., Gebhard, C., Schmidhofer, S., Mendes, K., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-13960-2 · Cited by 136

Widespread activation of developmental gene expression characterized by PRC1-dependent chromatin looping

Loubiere, V., Papadopoulos, G. L., Szabo, Q., Martinez, A.-M., & Cavalli, G. (2020) · Science Advances · doi:10.1126/sciadv.aax4001 · Cited by 126

Somatic and Germline Mutation Periodicity Follow the Orientation of the DNA Minor Groove around Nucleosomes

Pich, O., Muiños, F., Sabarinathan, R., Reyes-Salazar, I., Gonzalez-Perez, A., & Lopez-Bigas, N. (2018) · Cell · doi:10.1016/j.cell.2018.10.004 · Cited by 123

Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome Stability

Zatreanu, D., Han, Z., Mitter, R., Tumini, E., Williams, H., Gregersen, L., Dirac-Svejstrup, A. B., Roma, S., Stewart, A., Aguilera, A., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.037 · Cited by 124

DNA punch cards for storing data on native DNA sequences via enzymatic nicking

Tabatabaei, S. K., Wang, B., Athreya, N. B. M., Enghiad, B., Hernandez, A. G., Fields, C. J., Leburton, J.-P., Soloveichik, D., Zhao, H., & Milenkovic, O. (2020) · Nature Communications · doi:10.1038/s41467-020-15588-z · Cited by 120

Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness

Pachano, T., Sánchez-Gaya, V., Ealo, T., Mariner-Faulí, M., Bleckwehl, T., Asenjo, H. G., Respuela, P., Cruz-Molina, S., Muñoz-San Martín, M., Haro, E., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00888-x · Cited by 116

Active DNA demethylation promotes cell fate specification and the DNA damage response

Wang, D., Wu, W., Callen, E., Pavani, R., Zolnerowich, N., Kodali, S., Zong, D., Wong, N., Noriega, S., Nathan, W. J., et al. (2022) · Science · doi:10.1126/science.add9838 · Cited by 113

Adeno-associated Virus Genome Population Sequencing Achieves Full Vector Genome Resolution and Reveals Human-Vector Chimeras

Tai, P. W. L., Xie, J., Fong, K., Seetin, M., Heiner, C., Su, Q., Weiand, M., Wilmot, D., Zapp, M. L., & Gao, G. (2018) · Molecular Therapy - Methods & Clinical Development · doi:10.1016/j.omtm.2018.02.002 · Cited by 102

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Baranasic, D., Hörtenhuber, M., Balwierz, P. J., Zehnder, T., Mukarram, A. K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01089-w · Cited by 101

Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs

Janssens, D. H., Wu, S. J., Sarthy, J. F., Meers, M. P., Myers, C. H., Olson, J. M., Ahmad, K., & Henikoff, S. (2018) · Epigenetics & Chromatin · doi:10.1186/s13072-018-0243-8 · Cited by 73

Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2

Malik, V., Glaser, L. V., Zimmer, D., Velychko, S., Weng, M., Holzner, M., Arend, M., Chen, Y., Srivastava, Y., Veerapandian, V., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11054-7 · Cited by 72

DOT1L modulates the senescence-associated secretory phenotype through epigenetic regulation of IL1A

Leon, K. E., Buj, R., Lesko, E., Dahl, E. S., Chen, C.-W., Tangudu, N. K., Imamura-Kawasawa, Y., Kossenkov, A. V., Hobbs, R. P., & Aird, K. M. (2021) · Journal of Cell Biology · doi:10.1083/jcb.202008101 · Cited by 70

Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs

Cates, K., McCoy, M. J., Kwon, J.-S., Liu, Y., Abernathy, D. G., Zhang, B., Liu, S., Gontarz, P., Kim, W. K., Chen, S., et al. (2021) · Cell Stem Cell · doi:10.1016/j.stem.2020.08.015 · Cited by 67

Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus

Chen, L.-F., Long, H. K., Park, M., Swigut, T., Boettiger, A. N., & Wysocka, J. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.03.009 · Cited by 66

The glucose-sensing transcription factor MLX promotes myogenesis via myokine signaling

Hunt, L. C., Xu, B., Finkelstein, D., Fan, Y., Carroll, P. A., Cheng, P.-F., Eisenman, R. N., & Demontis, F. (2015) · Genes & Development · doi:10.1101/gad.267419.115 · Cited by 64

Order and stochasticity in the folding of individual Drosophila genomes

Ulianov, S. V., Zakharova, V. V., Galitsyna, A. A., Kos, P. I., Polovnikov, K. E., Flyamer, I. M., Mikhaleva, E. A., Khrameeva, E. E., Germini, D., Logacheva, M. D., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20292-z · Cited by 64

Adipocytes fail to maintain cellular identity during obesity due to reduced PPARγ activity and elevated TGFβ-SMAD signaling

Roh, H. C., Kumari, M., Taleb, S., Tenen, D., Jacobs, C., Lyubetskaya, A., Tsai, L. T.-Y., & Rosen, E. D. (2020) · Molecular Metabolism · doi:10.1016/j.molmet.2020.101086 · Cited by 62

Zinc finger protein SALL4 functions through an AT-rich motif to regulate gene expression

Kong, N. R., Bassal, M. A., Tan, H. K., Kurland, J. V., Yong, K. J., Young, J. J., Yang, Y., Li, F., Lee, J. D., Liu, Y., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2020.108574 · Cited by 56

TAF5L and TAF6L Maintain Self-Renewal of Embryonic Stem Cells via the MYC Regulatory Network

Seruggia, D., Oti, M., Tripathi, P., Canver, M. C., LeBlanc, L., Di Giammartino, D. C., Bullen, M. J., Nefzger, C. M., Sun, Y. B. Y., Farouni, R., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.03.025 · Cited by 51

High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts

Chia, M., Li, C., Marques, S., Pelechano, V., Luscombe, N. M., & van Werven, F. J. (2021) · Genome Biology · doi:10.1186/s13059-020-02245-3 · Cited by 47

The gene regulatory basis of bystander activation in CD8 + T cells

Watson, N. B., Patel, R. K., Kean, C., Veazey, J., Oyesola, O. O., Laniewski, N., Grenier, J. K., Wang, J., Tabilas, C., Yee Mon, K. J., et al. (2024) · Science Immunology · doi:10.1126/sciimmunol.adf8776 · Cited by 46

A c-Myb mutant causes deregulated differentiation due to impaired histone binding and abrogated pioneer factor function

Fuglerud, B. M., Lemma, R. B., Wanichawan, P., Sundaram, A. Y. M., Eskeland, R., & Gabrielsen, O. S. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx364 · Cited by 36

Uniform dynamics of cohesin-mediated loop extrusion in living human cells

Sabaté, T., Lelandais, B., Robert, M.-C., Szalay, M., Tinevez, J.-Y., Bertrand, E., & Zimmer, C. (2025) · Nature Genetics · doi:10.1038/s41588-025-02406-9 · Cited by 32

Erosion of the Epigenetic Landscape and Loss of Cellular Identity as a Cause of Aging in Mammals

Yang, J.-H., Griffin, P. T., Vera, D. L., Apostolides, J. K., Hayano, M., Meer, M. V., Salfati, E. L., Su, Q., Munding, E. M., Blanchette, M., et al. (2019) · doi:10.1101/808642 · Cited by 38

Inositol Polyphosphate Multikinase Physically Binds to the SWI/SNF Complex and Modulates BRG1 Occupancy in Mouse Embryonic Stem Cells

Beon, J., Han, S., Yang, H., Park, S. E., Hyun, K., Lee, S.-Y., Rhee, H.-W., Seo, J. K., Kim, J., Kim, S., et al. (2022) · eLife · doi:10.7554/elife.73523 · Cited by 15

Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging

Sabaté, T., Lelandais, B., Bertrand, E., & Zimmer, C. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad034 · Cited by 13

Cardiac differentiation roadmap for analysis of plasticity and balanced lineage commitment

Snabel, R. R., Cofiño-Fabrés, C., Baltissen, M., Schwach, V., Passier, R., & Veenstra, G. J. C. (2025) · Stem Cell Reports · doi:10.1016/j.stemcr.2025.102422 · Cited by 10

Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

(2025) · doi:10.1186/s13059-025-03475-z · Cited by 10

Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

Almeida, M. V., Blumer, M., Yuan, C. U., Sierra, P., Price, J. L., Quah, F. X., Friman, A., Dallaire, A., Vernaz, G., Putman, A. L. K., et al. (2024) · doi:10.1101/2024.04.01.587621 · Cited by 5

CBP-IDRs regulate acetylation and gene expression

Gelder, K. L., Carruthers, N. A., Gilbert, G., Harrison, L. J., Evans, B. V., Evans, T. I., Ball, S. S., Dunning, M., Craggs, T. D., Twelvetrees, A. E., et al. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.117109 · Cited by 5

Heritable Tissue‐Specific Gene Expression Associates With Chronic Wound Microbial Species

Omeir, K., Ancira, J., Gabrilska, R., Tipton, C., Miller, C., Noe, A., Subasinghe, K., Rowe, M., Phillips, N., Wolcott, J., et al. (2025) · Wound Repair and Regeneration · doi:10.1111/wrr.70055 · Cited by 3

Leukemia mutated proteins PHF6 and PHIP form a chromatin complex that represses acute myeloid leukemia stemness

Pawar, A. S., Somers, P., Alex, A., Grana, J., Feist, V. K., George, S. S., Jalnapurkar, S. S., Antony, C., Verner, R., White-Brown, S. K., et al. (2025) · Genes & Development · doi:10.1101/gad.352602.125 · Cited by 3

Post-mitotic transcriptional activation and 3D regulatory interactions show locus- and differentiation-specific sensitivity to cohesin depletion

Lee, U., Laguillo-Diego, A., Wong, W., Ni, Z., Cheng, L., Li, J., Pelham-Webb, B., Pertsinidis, A., Leslie, C., & Apostolou, E. (2025) · doi:10.1101/2025.02.13.638153 · Cited by 3

Population-scale single-nucleus multi-omic profiling of skeletal muscle reveals extensive context-specific genetic regulation

Varshney, A., Manickam, N., Orchard, P., Tovar, A., Ventresca, C., Zhang, Z., Feng, F., Mears, J., Erdos, M. R., Narisu, N., et al. (2026) · Nature Genetics · doi:10.1038/s41588-026-02786-6