BEDTools: a flexible suite of utilities for comparing genomic features

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

Improved tools for biological sequence comparison.

Pearson, W. R., & Lipman, D. J. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.8.2444 · Cited by 11,227

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

Galaxy: a platform for interactive large-scale genome analysis.Preprint

Giardine, B., Riemer, C., Hardison, R., Burhans, R. C., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., et al. (2005) · Genome Research · doi:10.1101/gr.4086505 · Cited by 2,217

Analysis of the human immunodeficiency virus-1 RNA packageome

Eckwahl, M. J., Arnion, H., Kharytonchyk, S., Zang, T., Bieniasz, P. D., Telesnitsky, A., & Wolin, S. L. (2016) · RNA · doi:10.1261/rna.057299.116 · Cited by 57

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

Earliest modern human genomes constrain timing of Neanderthal admixture

Sümer, A. P., Rougier, H., Villalba-Mouco, V., Huang, Y., Iasi, L. N. M., Essel, E., Bossoms Mesa, A., Furtwaengler, A., Peyrégne, S., de Filippo, C., et al. (2025) · Nature · doi:10.1038/s41586-024-08420-x · Cited by 58

Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9

Montefiori, L., Hernandez, L., Zhang, Z., Gilad, Y., Ober, C., Crawford, G., Nobrega, M., & Jo Sakabe, N. (2017) · Scientific Reports · doi:10.1038/s41598-017-02547-w · Cited by 54

The chromatin landscape of Th17 cells reveals mechanisms of diversification of regulatory and pro-inflammatory states

Thakore, P. I., Schnell, A., Zhao, M., Huang, L., Hou, Y., Christian, E., Zaghouani, S., Wang, C., Singh, V., Ma, S., et al. (2022) · doi:10.1101/2022.02.26.482041 · Cited by 57

Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens

Xu, Z., Sziraki, A., Lee, J., Zhou, W., & Cao, J. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-01948-9 · Cited by 52

Unicellular origin of the animal microRNA machinery

Bråte, J., Neumann, R. S., Fromm, B., Haraldsen, A. A. B., Tarver, J. E., Suga, H., Donoghue, P. C. J., Peterson, K. J., Ruiz-Trillo, I., Grini, P. E., et al. (2018) · Current Biology · doi:10.1016/j.cub.2018.08.018 · Cited by 53

SALL4 controls cell fate in response to DNA base composition

Pantier, R., Chhatbar, K., Quante, T., Skourti-Stathaki, K., Cholewa-Waclaw, J., Alston, G., Alexander-Howden, B., Lee, H. Y., Cook, A. G., Spruijt, C. G., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2020.11.046 · Cited by 45

Regulation of angiopoietin-like protein 4 production during and after exercise

Norheim, F., Hjorth, M., Langleite, T. M., Lee, S., Holen, T., Bindesbøll, C., Stadheim, H. K., Gulseth, H. L., Birkeland, K. I., Kielland, A., et al. (2014) · Physiological Reports · doi:10.14814/phy2.12109 · Cited by 53

Loss of Kat2a enhances transcriptional noise and depletes acute myeloid leukemia stem-like cells

Domingues, A. F., Kulkarni, R., Giotopoulos, G., Gupta, S., Vinnenberg, L., Arede, L., Foerner, E., Khalili, M., Adao, R. R., Johns, A., et al. (2020) · eLife · doi:10.7554/elife.51754 · Cited by 52

The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Rocafort, M., Bowen, J. K., Hassing, B., Cox, M. P., McGreal, B., de la Rosa, S., Plummer, K. M., Bradshaw, R. E., & Mesarich, C. H. (2022) · BMC Biology · doi:10.1186/s12915-022-01442-9 · Cited by 52

sc2GWAS: a comprehensive platform linking single cell and GWAS traits of human

Yin, M., Feng, C., Yu, Z., Zhang, Y., Li, Y., Wang, X., Song, C., Guo, M., & Li, C. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae1008 · Cited by 51

Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae

Qiu, C., Jin, H., Vvedenskaya, I., Llenas, J. A., Zhao, T., Malik, I., Visbisky, A. M., Schwartz, S. L., Cui, P., Čabart, P., et al. (2020) · Genome Biology · doi:10.1186/s13059-020-02040-0 · Cited by 43

Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation

Lin, L., DeMartino, J., Wang, D., van Son, G. J. F., van der Linden, R., Begthel, H., Korving, J., Andersson-Rolf, A., van den Brink, S., Lopez-Iglesias, C., et al. (2023) · Science · doi:10.1126/science.adi2246 · Cited by 50

Loss of protein phosphatase 2A regulatory subunit B56δ promotes spontaneous tumorigenesis in vivo

Lambrecht, C., Libbrecht, L., Sagaert, X., Pauwels, P., Hoorne, Y., Crowther, J., Louis, J. V., Sents, W., Sablina, A., & Janssens, V (2018) · Oncogene · doi:10.1038/onc.2017.350 · Cited by 50

Parasex Generates Phenotypic Diversity de Novo and Impacts Drug Resistance and Virulence in Candida albicans

Hirakawa, M. P., Chyou, D. E., Huang, D., Slan, A. R., & Bennett, R. J. (2017) · Genetics · doi:10.1534/genetics.117.300295 · Cited by 47

Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation

Ford, E., Grimmer, M. R., Stolzenburg, S., Bogdanovic, O., Mendoza, A. D., Farnham, P. J., Blancafort, P., & Lister, R. (2017) · doi:10.1101/170506 · Cited by 45

Chemical crosslinking enhances RNA immunoprecipitation for efficient identification of binding sites of proteins that photo-crosslink poorly with RNA

Patton, R. D., Sanjeev, M., Woodward, L. A., Mabin, J. W., Bundschuh, R., & Singh, G. (2020) · RNA · doi:10.1261/rna.074856.120 · Cited by 46

Gorillas have been infected with the HERV-K (HML-2) endogenous retrovirus much more recently than humans and chimpanzees

Holloway, J. R., Williams, Z. H., Freeman, M. M., Bulow, U., & Coffin, J. M. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1814203116 · Cited by 40

Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance

Kamrad, S., Grossbach, J., Rodríguez‐López, M., Mülleder, M., Townsend, S., Cappelletti, V., Stojanovski, G., Correia‐Melo, C., Picotti, P., Beyer, A., et al. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199270 · Cited by 40

Paleogenomic insights into the red complex bacteria Tannerella forsythia in Pre-Hispanic and Colonial individuals from Mexico

Bravo-Lopez, M., Villa-Islas, V., Rocha Arriaga, C., Villaseñor-Altamirano, A. B., Guzmán-Solís, A., Sandoval-Velasco, M., Wesp, J. K., Alcantara, K., López-Corral, A., Gómez-Valdés, J., et al. (2020) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2019.0580 · Cited by 40

An LTR retrotransposon‐derived lncRNA interacts with RNF169 to promote homologous recombination

Deng, B., Xu, W., Wang, Z., Liu, C., Lin, P., Li, B., Huang, Q., Yang, J., Zhou, H., & Qu, L. (2019) · The EMBO Reports · doi:10.15252/embr.201847650 · Cited by 40

STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer

Fleming, J. D., Giresi, P. G., Lindahl-Allen, M., Krall, E. B., Lieb, J. D., & Struhl, K. (2015) · Epigenetics & Chromatin · doi:10.1186/1756-8935-8-7 · Cited by 39

Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes

Nepal, C., & Andersen, J. B. (2023) · Nature Communications · doi:10.1038/s41467-023-38272-4 · Cited by 39

Protein quality control and regulated proteolysis in the genome‐reduced organism Mycoplasma pneumoniae

Burgos, R., Weber, M., Martinez, S., Lluch‐Senar, M., & Serrano, L. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209530 · Cited by 39

In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets

Niu, B., Coslo, D. M., Bataille, A. R., Albert, I., Pugh, B. F., & Omiecinski, C. J. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky692 · Cited by 37

Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles

Li, W., Calder, R. B., Mar, J. C., & Vijg, J. (2015) · Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis · doi:10.1016/j.mrfmmm.2015.01.002 · Cited by 34

A network of paralogous stress response transcription factors in the human pathogen Candida glabrata

Merhej, J., Thiebaut, A., Blugeon, C., Pouch, J., Ali Chaouche, M. E. A., Camadro, J.-M., Le Crom, S., Lelandais, G., & Devaux, F. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00645 · Cited by 36

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

SOX9 reprograms endothelial cells by altering the chromatin landscape

Fuglerud, B. M., Drissler, S., Lotto, J., Stephan, T. L., Thakur, A., Cullum, R., & Hoodless, P. A. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac652 · Cited by 35

Mutations altering acetylated residues in the CTD of HIV-1 integrase cause defects in proviral transcription at early times after integration of viral DNA

Winans, S., & Goff, S. P. (2020) · PLOS Pathogens · doi:10.1371/journal.ppat.1009147 · Cited by 29

DNA-Diffusion: Leveraging Generative Models for Controlling Chromatin Accessibility and Gene Expression via Synthetic Regulatory Elements

DaSilva, L. F., Senan, S., Patel, Z. M., Reddy, A. J., Gabbita, S., Nussbaum, Z., Córdova, C. M. V., Wenteler, A., Weber, N., Tunjic, T. M., et al. (2024) · doi:10.1101/2024.02.01.578352 · Cited by 32

Atf3 links loss of epithelial polarity to defects in cell differentiation and cytoarchitecture

Donohoe, C. D., Csordás, G., Correia, A., Jindra, M., Klein, C., Habermann, B., & Uhlirova, M. (2018) · PLOS Genetics · doi:10.1371/journal.pgen.1007241 · Cited by 32

APOE from astrocytes restores Alzheimer’s Aβ-pathology and DAM-like responses in APOE deficient microglia

Preman, P., Moechars, D., Fertan, E., Wolfs, L., Serneels, L., Shah, D., Lamote, J., Poovathingal, S., Snellinx, A., Mancuso, R., et al. (2024) · EMBO Molecular Medicine · doi:10.1038/s44321-024-00162-7 · Cited by 32

Reconstruction of a Global Transcriptional Regulatory Network for Control of Lipid Metabolism in Yeast by Using Chromatin Immunoprecipitation with Lambda Exonuclease Digestion

Bergenholm, D., Liu, G., Holland, P., & Nielsen, J. (2018) · mSystems · doi:10.1128/msystems.00215-17 · Cited by 31

The vast majority of somatic mutations in plants are layer-specific

Goel, M., Campoy, J. A., Krause, K., Baus, L. C., Sahu, A., Sun, H., Walkemeier, B., Marek, M., Beaudry, R., Ruiz, D., et al. (2024) · Genome Biology · doi:10.1186/s13059-024-03337-0 · Cited by 31

Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA

Nagy, G., Czipa, E., Steiner, L., Nagy, T., Pongor, S., Nagy, L., & Barta, E. (2016) · BMC Genomics · doi:10.1186/s12864-016-2940-7 · Cited by 27

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

A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling

Sawyer, E. B., Phelan, J. E., Clark, T. G., & Cortes, T. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108695 · Cited by 25

Evolution of reduced co-activator dependence led to target expansion of a starvation response pathway

He, B. Z., Zhou, X., & O’Shea, E. K. (2017) · eLife · doi:10.7554/elife.25157 · Cited by 27

Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex

Sakai, A., Nakato, R., Ling, Y., Hou, X., Hara, N., Iijima, T., Yanagawa, Y., Kuwano, R., Okuda, S., Shirahige, K., et al. (2017) · Frontiers in Neuroscience · doi:10.3389/fnins.2017.00307 · Cited by 30

Synergy between regulatory elements can render cohesin dispensable for distal enhancer function

Hansen, K. L., Adachi, A. S., Braccioli, L., Kadvani, S., Boileau, R. M., Martinovic, M., Pokorny, B., Shah, R., Anderson, E. C., Zhang, K., et al. (2026) · Science · doi:10.1126/science.adt4221 · Cited by 29

Inherited determinants of early recurrent somatic mutations in prostate cancer

Romanel, A., Garritano, S., Stringa, B., Blattner, M., Dalfovo, D., Chakravarty, D., Soong, D., Cotter, K. A., Petris, G., Dhingra, P., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00046-0 · Cited by 29

An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum

Li, Y. E., Preissl, S., Hou, X., Zhang, Z., Zhang, K., Fang, R., Qiu, Y., Poirion, O., Li, B., Liu, H., et al. (2020) · doi:10.1101/2020.05.10.087585 · Cited by 187

Single cell chromatin accessibility reveals pancreatic islet cell type- and state-specific regulatory programs of diabetes risk

Chiou, J., Zeng, C., Cheng, Z., Han, J. Y., Schlichting, M., Huang, S., Wang, J., Sui, Y., Deogaygay, A., Okino, M.-L., et al. (2019) · doi:10.1101/693671 · Cited by 189

The progeroid gene BubR1 regulates axon myelination and motor function

Choi, C.-I., Yoo, K. H., Hussaini, S. M. Q., Jeon, B. T., Welby, J., Gan, H., Scarisbrick, I. A., Zhang, Z., Baker, D. J., van Deursen, J. M., et al. (2016) · Aging · doi:10.18632/aging.101032 · Cited by 26

Locus-specific induction of gene expression from heterochromatin loci during cellular senescence

Tomimatsu, K., Bihary, D., Olan, I., Parry, A. J., Schoenfelder, S., Chan, A. S. L., Slater, G. S. C., Ito, Y., Rugg-Gunn, P. J., Kirschner, K., et al. (2021) · Nature Aging · doi:10.1038/s43587-021-00147-y · Cited by 25

Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function

Narducci, D. N., & Hansen, A. S. (2025) · Molecular Cell · doi:10.1016/j.molcel.2024.11.032 · Cited by 25

RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit

Milligan, L., Sayou, C., Tuck, A., Auchynnikava, T., Reid, J. E., Alexander, R., Alves, F. D. L., Allshire, R., Spanos, C., Rappsilber, J., et al. (2017) · eLife · doi:10.7554/elife.27082 · Cited by 23

DNA Repair Inhibition Leads to Active Export of Repetitive Sequences to the Cytoplasm Triggering an Inflammatory Response

Song, X., Aw, J. T. M., Ma, F., Cheung, M. F., Leung, D., & Herrup, K. (2021) · The Journal of Neuroscience · doi:10.1523/jneurosci.0845-21.2021 · Cited by 23

Enrichment of schizophrenia heritability in both neuronal and glia cell regulatory elements

Tansey, K. E., & Hill, M. J. (2018) · Translational Psychiatry · doi:10.1038/s41398-017-0053-y · Cited by 21

Evaluation of genetic demultiplexing of single-cell sequencing data from model species

Cardiello, J. F., Joven Araus, A., Giatrellis, S., Helsens, C., Simon, A., & Leigh, N. D. (2023) · Life Science Alliance · doi:10.26508/lsa.202301979 · Cited by 21

Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage

Taskent, O., Lin, Y. L., Patramanis, I., Pavlidis, P., & Gokcumen, O. (2020) · Genetics · doi:10.1534/genetics.120.303167 · Cited by 20

Intravitreal Administration of Retinal Organoids-Derived Exosomes Alleviates Photoreceptor Degeneration in Royal College of Surgeons Rats by Targeting the Mitogen-Activated Protein Kinase Pathway

Han, J., Chang, H., Yang, J., Choi, H., Park, H., Jun, H., Choi, J., Paik, S.-S., Chung, K., Shin, H., et al. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241512068 · Cited by 20

Repression of interrupted and intact rDNA by the SUMO pathway in drosophila melanogaster

Luo, Y., Fefelova, E., Ninova, M., Chen, Y.-C. A., & Aravin, A. A. (2020) · eLife · doi:10.7554/elife.52416 · Cited by 19

RNA polymerase drives ribonucleotide excision DNA repair in E. coli

Hao, Z., Gowder, M., Proshkin, S., Bharati, B. K., Epshtein, V., Svetlov, V., Shamovsky, I., & Nudler, E. (2023) · Cell · doi:10.1016/j.cell.2023.04.029 · Cited by 19

Positive and negative feedback regulation of the TGF-β1 explains two equilibrium states in skin aging

Haga, M., Iida, K., & Okada, M. (2024) · iScience · doi:10.1016/j.isci.2024.109708 · Cited by 19

Intracellular IL-1 Receptor Antagonist Isoform 1 Released from Keratinocytes upon Cell Death Acts as an Inhibitor for the Alarmin IL-1α

Martin, P., Palmer, G., Rodriguez, E., Palomo, J., Lemeille, S., Goldstein, J., & Gabay, C. (2020) · The Journal of Immunology · doi:10.4049/jimmunol.1901074 · Cited by 19

Microbiota assessments for the identification and confirmation of slit defect-causing bacteria in milk and cheddar cheese

Xue, Z., Brooks, J. T., Quart, Z., Stevens, E. T., Kable, M. E., Heidenreich, J., McLeod, J., & Marco, M. L. (2021) · mSystems · doi:10.1128/msystems.01114-20 · Cited by 17

Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding

Paldi, F., Szalay, M.-F., Dufau, S., Di Stefano, M., Reboul, H., Jost, D., Bantignies, F., & Cavalli, G. (2026) · Nature Genetics · doi:10.1038/s41588-025-02489-4 · Cited by 18

Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

Viner, C., Ishak, C. A., Johnson, J., Walker, N. J., Shi, H., Sjöberg-Herrera, M. K., Shen, S. Y., Lardo, S. M., Adams, D. J., Ferguson-Smith, A. C., et al. (2016) · doi:10.1101/043794 · Cited by 18

Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis

Lim, B., Kamal, A., Gomez Ramos, B., Adrian Segarra, J. M., Ibarra, I. L., Dignas, L., Kindinger, T., Volz, K., Rahbari, M., Rahbari, N., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02081-w · Cited by 17

Sequential verification of transcription by Integrator and Restrictor

Estell, C., Łazowski, K., Eaton, J. D., & West, S. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.09.025 · Cited by 16

Integrative characterization of the near‐minimal bacterium Mesoplasma florum

Matteau, D., Lachance, J., Grenier, F., Gauthier, S., Daubenspeck, J. M., Dybvig, K., Garneau, D., Knight, T. F., Jacques, P., & Rodrigue, S. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209844 · Cited by 16

Somatic cancer variants enriched in Alzheimer’s disease microglia-like cells drive inflammatory and proliferative states

Huang, A. Y., Zhou, Z., Talukdar, M., Enyenihi, L., Miller, M. B., Chhouk, B., Rosen, I., Zheng, M., Zhou, M., Yang, A., et al. (2026) · Cell · doi:10.1016/j.cell.2026.03.040 · Cited by 15

Whole-genome sequencing of copy number variation analysis in Ethiopian cattle reveals adaptations to diverse environments

Ayalew, W., Xiaoyun, W., Tarekegn, G. M., Tessema, T. S., Chu, M., Liang, C., Naboulsi, R., Van Damme, R., Bongcam-Rudloff, E., & Ping, Y. (2024) · BMC Genomics · doi:10.1186/s12864-024-10936-5 · Cited by 15

Allosteric Integrase Inhibitor Influences on HIV-1 Integration and Roles of LEDGF/p75 and HDGFL2 Host Factors

Singh, P., Li, W., Bedwell, G., Fadel, H., Poeschla, E., & Engelman, A. (2022) · Viruses · doi:10.3390/v14091883 · Cited by 13

Molecular and cellular processes disrupted in the early postnatal Down syndrome prefrontal cortex

Risgaard, R. D., Hanthanan Arachchilage, K., Knaack, S. A., Hosseini, M., Chen, R. J., Kumarage, P., Schmidt, D. K., Huang, X., Sheng, J., Wang, C. J., et al. (2026) · Science · doi:10.1126/science.aea1549 · Cited by 12

Microevolutionary dynamics of eccDNA in Chinese hamster ovary cells grown in fed-batch cultures under control and lactate-stressed conditions

Chitwood, D. G., Wang, Q., Klaubert, S. R., Green, K., Wu, C. H., Harcum, S. W., & Saski, C. A. (2023) · Scientific Reports · doi:10.1038/s41598-023-27962-0 · Cited by 12

Trait-associated noncoding variant regions affect TBX3 regulation and cardiac conduction

van Weerd, J. H., Mohan, R. A., van Duijvenboden, K., Hooijkaas, I. B., Wakker, V., Boukens, B. J., Barnett, P., & Christoffels, V. M. (2020) · eLife · doi:10.7554/elife.56697 · Cited by 12

Putative contributions of the sex chromosome proteins SOX3 and SRY to neurodevelopmental disorders

Tahira, A. C., Barbosa, A. R., Feltrin, A. S., Gastaldi, V. D., de Toledo, V. H. C., de Carvalho Pereira, J. G., Lisboa, B. C. G., de Souza Reis, V. N., dos Santos, A. C. F., Maschietto, M., et al. (2019) · American Journal of Medical Genetics Part B: Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32704 · Cited by 11

Ancient Genomes Illuminate the Origins and Dynamic History of East Asian Cattle

Cai, D., Kim, D., Zhang, N., Wang, X., Li, T., Li, J., Li, C., Lian, S., Shao, X., Hu, S., et al. (2025) · Science · doi:10.1126/science.adu9904 · Cited by 11

A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease

Nim, H. T., Dang, L., Thiyagarajah, H., Bakopoulos, D., See, M., Charitakis, N., Sibbritt, T., Eichenlaub, M. P., Archer, S. K., Fossat, N., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02539-0 · Cited by 11

A SWI/SNF-specific Ig-like domain, SWIFT, is a transcription factor binding platform

Jain, S. U., Williamson, K. E., Ying, A. W., Turner, A. M., Jiang, R. J., Raval, S., So, K., Allison, M. J., Sankar, A., Sáme Guerra, D. D., et al. (2026) · Science · doi:10.1126/science.aeb3627 · Cited by 11

Genome-scale CRISPR screens identify PTGES3 as a direct modulator of androgen receptor function in advanced prostate cancer

Li, H., Melnyk, J. E., Fu, B. X. H., Shrestha, R., Zhang, M., Sjöström, M., Feng, S., Anderson, J. A., Han, W., Chesner, L. N., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02388-8 · Cited by 10

Genomes of critically endangered saola are shaped by population structure and purging

Garcia-Erill, G., Liu, S., Le, M. D., Hurley, M. M., Nguyen, H. D., Nguyen, D. Q., Nguyen, D. H., Santander, C. G., Sánchez Barreiro, F., Gomes Martins, N. F., et al. (2025) · Cell · doi:10.1016/j.cell.2025.03.040 · Cited by 10

Predicting gene expression from histone marks using chromatin deep learning models depends on histone mark function, regulatory distance and cellular states

Murphy, A. E., Askarova, A., Lenhard, B., Skene, N. G., & Marzi, S. J. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae1212 · Cited by 10

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

Combined genome-wide association study of 136 quantitative ear morphology traits in multiple populations reveal 8 novel loci

Li, Y., Xiong, Z., Zhang, M., Hysi, P. G., Qian, Y., Adhikari, K., Weng, J., Wu, S., Du, S., Gonzalez-Jose, R., et al. (2023) · PLOS Genetics · doi:10.1371/journal.pgen.1010786 · Cited by 9

A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome

Liang, S.-A., Ren, T., Zhang, J., He, J., Wang, X., Jiang, X., He, Y., McCoy, R. C., Fu, Q., Akey, J. M., et al. (2025) · Genome Biology · doi:10.1186/s13059-025-03502-z · Cited by 8

RnhP is a plasmid‐borne RNase HI that contributes to genome maintenance in the ancestral strain Bacillus subtilis NCIB 3610

Nye, T. M., McLean, E. K., Burrage, A. M., Dennison, D. D., Kearns, D. B., & Simmons, L. A. (2021) · Molecular Microbiology · doi:10.1111/mmi.14601 · Cited by 7

An extended transcription factor regulatory network controls hepatocyte identity

Dubois‐Chevalier, J., Gheeraert, C., Berthier, A., Boulet, C., Dubois, V., Guille, L., Fourcot, M., Marot, G., Gauthier, K., Dubuquoy, L., et al. (2023) · EMBO Reports · doi:10.15252/embr.202357020 · Cited by 6

Defining the roles of the Integrator, NEXT, and nuclear exosome complexes in Drosophila oogenesis

Lee, Y., Biasini, A., Tipping, C., Hong, S. H., & Zamore, P. D. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116329 · Cited by 6

Advancing the Indian Cattle Pangenome: Characterizing Non-Reference Sequences in Bos indicus

Azam, S., Sahu, A., Pandey, N. K., Neupane, M., Van Tassell, C. P., Rosen, B. D., Gandham, R. K., Rath, S. N., & Majumdar, S. S. (2025) · Journal of Animal Science and Biotechnology · doi:10.1186/s40104-024-01133-1 · Cited by 5

Accurate, comprehensive gene annotation and ortholog identification across thousands of vertebrate genomes with TOGA2

Malovichko, Y. V., Bein, B., Gonzales-Irribarren, A., Leushkin, E., Hilgers, L., Stephen, A., Yi, X., Albertini, M., Stadager, T., Zumpt, M., et al. (2026) · doi:10.64898/2026.06.30.735536 · Cited by 5

A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation

Ge, A. Y., Arab, A., Dai, R., Navickas, A., Fish, L., Garcia, K., Asgharian, H., Goudreau, J., Lee, S., Keenan, K., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-77314-9 · Cited by 4

Distinct Cellular Phenotypes of Language and Executive Decline in Amyotrophic Lateral Sclerosis

Petrescu, J., Gouveia Roque, C., Jackson, C. A., Daly, A. C., Butti, Z., Kang, K., Casel, O., Leung, M., Reilly, L., Eschbach, J., et al. (2026) · Cell · doi:10.1016/j.cell.2026.07.008 · Cited by 4

Study of blood linear RNA nominates CD55 and DLD as early-stage biomarkers for Parkinson's disease

Beric, A., Sahin, S., Sanchez, S., Yang, Z., Kumar, R., Alfradique-Dunham, I., Sanford, J., Western, D., Phillips, B., Budde, J. P., et al. (2026) · Brain · doi:10.1093/brain/awag014 · Cited by 2

CDK8 fine-tunes IL-6 transcriptional activities by limiting STAT3 resident time at the gene loci

Martinez-Fabregas, J., Wang, L., Pohler, E., Cozzani, A., Kazemian, M., Mitra, S., & Moraga, I. (2020) · doi:10.1101/2020.03.19.998351 · Cited by 2

Neural crest induction requires SALL4-mediated BAF recruitment to lineage specific enhancers

Demurtas, M., Barnada, S. M., van Domselaar, E., Mitchell, Z. H., Deelen, L., & Trizzino, M. (2025) · Development · doi:10.1242/dev.205248 · Cited by 2

The impact of identity-by-descent on fitness and disease in natural and domesticated Canid populations

Mooney, J. A., Yohannes, A., & Lohmueller, K. E. (2020) · doi:10.1101/2020.11.16.385443 · Cited by 1

Mitochondrial retrograde control of transcription evolves with respiratory stress, metabolic adaptation, and virulence in budding yeasts

Łabędzka-Dmoch, K., Bui, T. H. D., Piątkowski, J., Dilling, M., Jagiełło, P., Kabza, W., & Golik, P. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag005 · Cited by 1

TBX3 advances the developmental chromatin landscape toward the hepatic fate

Stephan, T. L., Cullum, R., Drissler, S., Thomas, A., Fuglerud, B. M., Clement-Ranney, M., Lotto, J., Krentz, N. A. J., Duncan, S. A., & Hoodless, P. A. (2025) · Developmental Cell · doi:10.1016/j.devcel.2025.05.014 · Cited by 1

Augmented prediction of multi-species protein–RNA interactions using evolutionary conservation of RNA-binding proteins

He, J., Zhou, T., Hu, L.-F., Jiao, Y., Wang, J., Yan, S., Jia, S., Chen, Q., Zhu, W., Zhang, J., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-72351-6

A phenome-wide structural variant map from 467,152 UK Biobank genomes

Atanur, S. S., Hu, F., Lou, H., Li, X., Zou, X. Z., O’Dell, S., Deevi, S. V. V., Sawczuk, P., Megy, K., Fairhurst-Hunter, Z., et al. (2026) · Cell · doi:10.1016/j.cell.2026.09.035

BEDTools: The Swiss‐Army Tool for Genome Feature Analysis

Quinlan, A. R. (2014) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1112s47 · Cited by 2,286

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

Dale, R., Pedersen, B. S., & Quinlan, A. R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr539 · Cited by 507

BEDOPS: high-performance genomic feature operations

Neph, S. J., Kuehn, M. S., Reynolds, A. P., Haugen, E., Thurman, R. E., Johnson, A., Rynes, E., Maurano, M. T., Vierstra, J. D., Thomas, S., et al. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts277 · Cited by 971

bedtools: interval arithmetic for genomes

Quinlan, A. (2020) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.3834603

Bedtoolsr: An R package for genomic data analysis and manipulation.

Phanstiel, D. H., Patwardhan, M. N., Davis, E. S., & Wenger, C. D. (2024) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/sbzm-zc31