BEDTools: a flexible suite of utilities for comparing genomic features

The Sequence Alignment/Map format and SAMtools

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Improved tools for biological sequence comparison.

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The Human Genome Browser at UCSC

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

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Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk pediatric cancer

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Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

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Elevated TREM2 Gene Dosage Reprograms Microglia Responsivity and Ameliorates Pathological Phenotypes in Alzheimer’s Disease Models

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The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity

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Metabolic control of TH17 and induced Treg cell balance by an epigenetic mechanism

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Reprogramming the Maternal Zebrafish Genome after Fertilization to Match the Paternal Methylation Pattern

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The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells

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Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription

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Widespread long-range cis-regulatory elements in the maize genome

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Different Neuronal Activity Patterns Induce Different Gene Expression Programs

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piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production

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Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)

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RNA promotes the formation of spatial compartments in the nucleus

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An atlas of dynamic chromatin landscapes in mouse fetal development

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Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

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Genome Organization Drives Chromosome Fragility

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Best practices for variant calling in clinical sequencing

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Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity

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Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG

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The prevalence, evolution and chromatin signatures of plant regulatory elements

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DNA methylation changes in plasticity genes accompany the formation and maintenance of memory

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Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genomePreprint

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Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

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Poretools: a toolkit for analyzing nanopore sequence data

Loman, N. J., & Quinlan, A. R. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu555 · Cited by 376

Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis

Shah, P. S., Link, N., Jang, G. Μ., Sharp, P. P., Zhu, T., Swaney, D. L., Johnson, J. R., Dollen, J. V., Ramage, H. R., Satkamp, L., et al. (2018) · Cell · doi:10.1016/j.cell.2018.11.028 · Cited by 382

Loss of BAP1 function leads to EZH2-dependent transformation

LaFave, L. M., Béguelin, W., Koche, R. P., Teater, M. R., Spitzer, B. G., Chramiec, A. G., Papalexi, E., Keller, M. D., Hricik, T., Konstantinoff, K., et al. (2015) · Nature Medicine · doi:10.1038/nm.3947 · Cited by 392

A cis-regulatory atlas in maize at single-cell resolution

Marand, A. P., Chen, Z., Gallavotti, A., & Schmitz, R. J. (2021) · Cell · doi:10.1016/j.cell.2021.04.014 · Cited by 387

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease

Nativio, R., Lan, Y., Donahue, G., Sidoli, S., Berson, A., Srinivasan, A. R., Shcherbakova, O., Amlie-Wolf, A., Nie, J., Cui, X., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0696-0 · Cited by 380

R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters

Chen, L., Chen, J., Zhang, X., Gu, Y., Xiao, R., Shao, C., Tang, P., Qian, H., Luo, D., Li, H., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.10.008 · Cited by 373

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

Zhang, Y., Li, T., Preißl, S., Amaral, M. L., Grinstein, J. D., Farah, E. N., Destici, E., Qiu, Y., Hu, R., Lee, A. Y., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0479-7 · Cited by 384

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

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Bottlenecks and Selective Sweeps during Domestication Have Increased Deleterious Genetic Variation in Dogs

Marsden, C. D., Ortega-Del Vecchyo, D., O’Brien, D. P., Taylor, J. F., Ramirez, O., Vilà, C., Marques-Bonet, T., Schnabel, R. D., Wayne, R. K., & Lohmueller, K. E. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1512501113 · Cited by 333

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis

Muhar, M., Ebert, A., Neumann, T., Umkehrer, C., Jude, J., Wieshofer, C., Rescheneder, P., Lipp, J., Herzog, V. A., Reichholf, B., et al. (2018) · Science · doi:10.1126/science.aao2793 · Cited by 371

A cross-disorder dosage sensitivity map of the human genome

Collins, R. L., Glessner, J., Porcu, E., Lepamets, M., Brandon, R. C., Lauricella, C., Han, L., Morley, T. J., Niestroj, L., Ulirsch, J. C., et al. (2022) · Cell · doi:10.1016/j.cell.2022.06.036 · Cited by 369

Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery

Greater Middle East Variome Consortium, Scott, E. M., Halees, A., Itan, Y., Spencer, E. G., He, Y., Azab, M. A., Gabriel, S. B., Belkadi, A., Boisson, B., et al. (2016) · Nature Genetics · doi:10.1038/ng.3592 · Cited by 376

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

Taylor, J. C., Martin, H. C., Lise, S., Broxholme, J., Cazier, J., Rimmer, A., Kanapin, A. A., Lunter, G. A., Fiddy, S., Allan, C., et al. (2015) · Nature Genetics · doi:10.1038/ng.3304 · Cited by 377

A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package

Meng, J., Lu, Z., Liu, H., Zhang, L., Zhang, S., Chen, Y., Rao, M. K., & Huang, Y. (2014) · Methods · doi:10.1016/j.ymeth.2014.06.008 · Cited by 375

METTL3 regulates heterochromatin in mouse embryonic stem cells

Xu, W., Li, J., He, C., Wen, J., Ma, H., Rong, B., 刁建波, Wang, L., Wang, J., Wu, F., et al. (2021) · Nature · doi:10.1038/s41586-021-03210-1 · Cited by 374

The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems

Chylinski, K., Le Rhun, A., & Charpentier, E. (2013) · RNA Biology · doi:10.4161/rna.24321 · Cited by 353

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

Tuttle, E. M., Bergland, A. O., Korody, M. L., Brewer, M. S., Newhouse, D., Minx, P. J., Stager, M., Betuel, A. M., Cheviron, Z. A., Warren, W. C., et al. (2016) · Current Biology · doi:10.1016/j.cub.2015.11.069 · Cited by 370

Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil

Voloch, C. M., da Silva Francisco, R., de Almeida, L. G. P., Cardoso, C. C., Brustolini, O. J., Gerber, A. L., Guimarães, A. P. D. C., Mariani, D., da Costa, R. M., Ferreira, O. C., et al. (2021) · Journal of Virology · doi:10.1128/jvi.00119-21 · Cited by 372

Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation

Gibson, B. A., Zhang, Y., Jiang, H., Hussey, K. M., Shrimp, J. H., Lin, H., Schwede, F., Yu, Y., & Kraus, W. L. (2016) · Science · doi:10.1126/science.aaf7865 · Cited by 381

phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes

Gruber‐Vodicka, H. R., Seah, B. K. B., & Pruesse, E. (2020) · mSystems · doi:10.1128/msystems.00920-20 · Cited by 382

Genome evolution and diversity of wild and cultivated potatoes

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Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells

Bulut-Karslioglu, A., De La Rosa-Velázquez, I. A., Ramirez, F., Barenboim, M., Onishi-Seebacher, M., Arand, J., Galán, C., Winter, G. E., Engist, B., Gerle, B., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.05.029 · Cited by 368

Mapping and characterization of structural variation in 17,795 human genomes

Genomics, N. C. F. C. D., Abel, H. J., Larson, D. E., Regier, A. A., Chiang, C., Das, I., Kanchi, K. L., Layer, R. M., Neale, B. M., Salerno, W. J., et al. (2020) · Nature · doi:10.1038/s41586-020-2371-0 · Cited by 310

The genetic basis and cell of origin of mixed phenotype acute leukaemia

Alexander, T., Gu, Z., Iacobucci, I., Dickerson, K. M., Choi, J. K., Xu, B., Payne-Turner, D., Yoshihara, H., Loh, M. L., Horan, J., et al. (2018) · Nature · doi:10.1038/s41586-018-0436-0 · Cited by 369

LTR-Retrotransposon Control by tRNA-Derived Small RNAs

Schorn, A. J., Gutbrod, M. J., LeBlanc, C., & Martienssen, R. (2017) · Cell · doi:10.1016/j.cell.2017.06.013 · Cited by 366

Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease

Nativio, R., Donahue, G., Berson, A., Lan, Y., Amlie-Wolf, A., Tuzer, F., Toledo, J. B., Gosai, S. J., Gregory, B. D., Torres, C., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0101-9 · Cited by 363

Assembly of a pan-genome from deep sequencing of 910 humans of African descent

Sherman, R. M., Forman, J., Antonescu, V., Puiu, D., Daya, M., Rafaels, N., Boorgula, M. P., Chavan, S., Vergara, C., Ortega, V. E., et al. (2019) · Nature Genetics · doi:10.1038/s41588-018-0273-y · Cited by 355

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

Stadhouders, R., Vidal, E., Serra, F., Stefano, B. D., Dily, F. L., Quilez, J., Gómez, A., Collombet, S., Berenguer, C., Cuartero, Y., et al. (2018) · Nature Genetics · doi:10.1038/s41588-017-0030-7 · Cited by 362

Modulation of circRNA Metabolism by m6A Modification

Timoteo, G. D., Dattilo, D., Centrón-Broco, A., Colantoni, A., Guarnacci, M., Rossi, F., Incarnato, D., Oliviero, S., Fatica, A., Morlando, M., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107641 · Cited by 366

Local and systemic responses to SARS-CoV-2 infection in children and adults

Yoshida, M., Worlock, K. B., Huang, N., Lindeboom, R. G. H., Butler, C. R., Kumasaka, N., Dominguez Conde, C., Mamanova, L., Bolt, L., Richardson, L., et al. (2022) · Nature · doi:10.1038/s41586-021-04345-x · Cited by 365

The cis-regulatory dynamics of embryonic development at single-cell resolution

Cusanovich, D. A., Reddington, J. P., Garfield, D. A., Daza, R. M., Aghamirzaie, D., Marco-Ferreres, R., Pliner, H. A., Christiansen, L., Qiu, X., Steemers, F. J., et al. (2018) · Nature · doi:10.1038/nature25981 · Cited by 363

HIF1A Employs CDK8-Mediator to Stimulate RNAPII Elongation in Response to Hypoxia

Galbraith, M. D., Allen, M. A., Bensard, C., Wang, X., Schwinn, M. K., Qin, B., Long, H. W., Daniels, D. L., Hahn, W. C., Dowell, R. D., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.048 · Cited by 379

H3K27M induces defective chromatin spread of PRC2-mediated repressive H3K27me2/me3 and is essential for glioma tumorigenesis

Harutyunyan, A. S., Krug, B., Chen, H., Papillon‐Cavanagh, S., Zeinieh, M. P., Jay, N. D., Deshmukh, S., Chen, C. C. L., Belle, J. I., Mikael, L. G., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09140-x · Cited by 367

CONTRA: copy number analysis for targeted resequencing

Li, J., Lupat, R., Amarasinghe, K. C., Thompson, E. R., Doyle, M., Ryland, G. L., Tothill, R. W., Halgamuge, S. K., Campbell, I., & Gorringe, K. L. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts146 · Cited by 360

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Green, R. E., Braun, E. L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., Vandewege, M. W., St. John, J. A., Capella-Gutiérrez, S., Castoe, T. A., et al. (2014) · Science · doi:10.1126/science.1254449 · Cited by 359

High-depth African genomes inform human migration and health

Choudhury, A., Aron, S., Botigué, L. R., Sengupta, D., Botha, G., Bensellak, T., Wells, G., Kumuthini, J., Shriner, D., Fakim, Y. J., et al. (2020) · Nature · doi:10.1038/s41586-020-2859-7 · Cited by 373

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

Jacques, P., Jeyakani, J., & Bourque, G. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003504 · Cited by 360

Influenza-induced monocyte-derived alveolar macrophages confer prolonged antibacterial protection

Aegerter, H., Kulikauskaite, J., Crotta, S., Patel, H., Kelly, G. P., Hessel, E. M., Mack, M., Beinke, S., & Wack, A. (2020) · Nature Immunology · doi:10.1038/s41590-019-0568-x · Cited by 367

hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing

Pintacuda, G., Wei, G., Roustan, C., Kirmizitas, B. A., Solcan, N., Cerase, A., Castelló, A., Mohammed, S., Moindrot, B., Nesterova, T. B., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.11.013 · Cited by 356

TransmiR v2.0: an updated transcription factor-microRNA regulation database

Tong, Z., Cui, Q., Wang, J., & Zhou, Y. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1023 · Cited by 356

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

Corces, M. R., Shcherbina, A., Kundu, S., Gloudemans, M. J., Frésard, L., Granja, J. M., Louie, B. H., Eulalio, T., Shams, S., Bagdatli, S. T., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-00721-x · Cited by 358

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder

Werling, D. M., Brand, H., An, J.-Y., Stone, M. R., Zhu, L., Glessner, J. T., Collins, R. L., Dong, S., Layer, R. M., Markenscoff-Papadimitriou, E., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0107-y · Cited by 293

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

Profiling of Discrete Gynecological Cancers Reveals Novel Transcriptional Modules and Common Features Shared by Other Cancer Types and Embryonic Stem Cells

Pappa, K. I., Polyzos, A., Jacob‐Hirsch, J., Amariglio, N., Vlachos, G. D., Loutradis, D., & Anagnou, N. P. (2015) · PLoS ONE · doi:10.1371/journal.pone.0142229 · Cited by 355

Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior

Doan, R. N., Bae, B.-I., Cubelos, B., Chang, C. Y., Hossain, A. A., Al-Saad, S., Mukaddes, N. M., Öner, Ö., Al‐Saffar, M., Balkhy, S., et al. (2016) · Cell · doi:10.1016/j.cell.2016.08.071 · Cited by 357

A novel m6A reader Prrc2a controls oligodendroglial specification and myelination

Wu, R., Li, A., Sun, B., Sun, J.-G., Zhang, J., Zhang, T., Chen, Y., Xiao, Y., Gao, Y., Zhang, Q., et al. (2019) · Cell Research · doi:10.1038/s41422-018-0113-8 · Cited by 366

BATF and IRF4 cooperate to counter exhaustion in tumor-infiltrating CAR T cells

Seo, H., González‐Avalos, E., Zhang, W., Ramchandani, P., Yang, C., Lio, C. J., Rao, A., & Hogan, P. G. (2021) · Nature Immunology · doi:10.1038/s41590-021-00964-8 · Cited by 354

GC skew at the 5′ and 3′ ends of human genes links R-loop formation to epigenetic regulation and transcription terminationPreprint

Ginno, P. A., Lim, Y. W., Lott, P. C., Korf, I. F., & Chedin, F. L. (2013) · Genome Research · doi:10.1101/gr.158436.113 · Cited by 360

Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum

López-Barragán, M. J., Lemieux, J., Quiñones, M., Williamson, K., Molina-Cruz, A., Cui, K.-R., Barillas-Mury, C., Zhao, K.-J., & Su, X.-Z. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-587 · Cited by 373

Epigenetic Silencing of CDR1as Drives IGF2BP3-Mediated Melanoma Invasion and Metastasis

Hanniford, D., Ulloa-Morales, A. J., Karz, A., Berzoti-Coelho, M. G., Moubarak, R. S., Sánchez‐Sendra, B., Kloetgen, A., Dávalos, V., Imig, J., Wu, P., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2019.12.007 · Cited by 348

The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment

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