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BEDTools: a flexible suite of utilities for comparing genomic features
Open accessAbstract
MOTIVATION: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. RESULTS: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. AVAILABILITY AND IMPLEMENTATION: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools CONTACT: aaronquinlan@gmail.com; imh4y@virginia.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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“Peaks present in mock experiments were then subtracted with bedtools (Quinlan and Hall 2010), and the peak set was converted from BED to SAF format.”
From Mitochondrial retrograde control of transcription evolves with respiratory stress, metabolic adaptation, and virulence in budding yeasts (2026) · cites this paper as Quinlan and Hall 2010
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“Generation of consensus peak files from multiple biological replicates was performed using bedtools intersect”
From Super-enhancers include classical enhancers and facilitators to fully activate gene expression (2023) · cites this paper as [81]
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“Peaks in ENCODE blacklisted regions (95) were removed using the intersect function in bedtools2 (96) v2.30.0.”
From Synergy between regulatory elements can render cohesin dispensable for distal enhancer function (2026) · cites this paper as [96]
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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
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Iaco, A. D., Planet, E., Coluccio, A., Verp, S., Duc, J., & Trono, D. (2017) · Nature Genetics · doi:10.1038/ng.3858 · Cited by 608
Genome-wide inactivation of porcine endogenous retroviruses (PERVs)
Yang, L., Güell, M., Niu, D., George, H., Lesha, E., Grishin, D., Aach, J., Shrock, E. L., Xu, W., Poci, J., et al. (2015) · Science · doi:10.1126/science.aad1191 · Cited by 611
Disturbed mitochondrial dynamics in CD8+ TILs reinforce T cell exhaustion
Yu, Y.-R., Imrichova, H., Wang, H., Chao, T., Xiao, Z., Gao, M., Rincon-Restrepo, M., Franco, F., Genolet, R., Cheng, W.-C., et al. (2020) · Nature Immunology · doi:10.1038/s41590-020-0793-3 · Cited by 593
Targeted Disruption of HLA Genes via CRISPR-Cas9 Generates iPSCs with Enhanced Immune Compatibility
Xu, H., Wang, B., Ono, M., Kagita, A., Fujii, K., Sasakawa, N., Ueda, T., Gee, P., Nishikawa, M., Nomura, M., et al. (2019) · Cell stem cell · doi:10.1016/j.stem.2019.02.005 · Cited by 581
Genomic hallmarks of localized, non-indolent prostate cancer
Fraser, M. E., Sabelnykova, V. Y., Yamaguchi, T. N., Heisler, L. E., Livingstone, J. M., Huang, V., Shiah, Y.-J., Yousif, F., Lin, X., Masella, A. P., et al. (2017) · Nature · doi:10.1038/nature20788 · Cited by 602
Improved reference genome of Aedes aegypti informs arbovirus vector control
Matthews, B. J., Dudchenko, O., Kingan, S. B., Koren, S., Antoshechkin, I. A., Crawford, J. E., Glassford, W. J., Herre, M., Redmond, S. N., Rose, N. H., et al. (2018) · Nature · doi:10.1038/s41586-018-0692-z · Cited by 594
RNA-Mediated Feedback Control of Transcriptional Condensates
Henninger, J. E., Oksuz, O., Shrinivas, K., Sagi, I., LeRoy, G., Zheng, M., Andrews, J. O., Zamudio, A. V., Lazaris, C., Hannett, N. M., et al. (2020) · Cell · doi:10.1016/j.cell.2020.11.030 · Cited by 571
Chromatin accessibility profiling by ATAC-seq
Grandi, F. C., Modi, H., Kampman, L., & Corces, M. R. (2022) · Nature Protocols · doi:10.1038/s41596-022-00692-9 · Cited by 557
Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis
Fiddes, I. T., Lodewijk, G. A., Mooring, M., Bosworth, C. M., Ewing, A. D., Mantalas, G. L., Novak, A. M., van den Bout, A., Bishara, A., Rosenkrantz, J. L., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.051 · Cited by 595
The genetic landscape of mutations in Burkitt lymphoma
Love, C., Sun, Z., Jima, D. D., Li, G., Zhang, J., Miles, R. R., Richards, K. L., Dunphy, C. H., Choi, W. W. L., Srivastava, G., et al. (2012) · Nature Genetics · doi:10.1038/ng.2468 · Cited by 609
Byrd, A. L., Deming, C., Cassidy, S. K. B., Harrison, O. J., Ng, W.-I., Conlan, S., Program, N. C. S., Belkaid, Y., Segre, J. A., & Kong, H. H. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aal4651 · Cited by 607
Characterizing the Major Structural Variant Alleles of the Human Genome
Audano, P. A., Sulovari, A., Graves-Lindsay, T. A., Cantsilieris, S., Sorensen, M., Welch, A. E., Dougherty, M. L., Nelson, B. J., Shah, A., Dutcher, S. K., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.019 · Cited by 492
Common genetic variation drives molecular heterogeneity in human iPSCs
Kilpinen, H., Goncalves, A., Leha, A., Afzal, V., Alasoo, K., Ashford, S., Bala, S., Bensaddek, D., Casale, F. P., Culley, O. J., et al. (2017) · Nature · doi:10.1038/nature22403 · Cited by 586
Sexual-dimorphism in human immune system aging
Márquez, E. J., Chung, C.-H., Marches, R., Rossi, R. J., Nehar-Belaid, D., Eroglu, A., Mellert, D. J., Kuchel, G. A., Banchereau, J., & Ucar, D. (2020) · Nature Communications · doi:10.1038/s41467-020-14396-9 · Cited by 584
m6A modulates haematopoietic stem and progenitor cell specification
Zhang, C., Chen, Y., Sun, B., Wang, L., Yang, Y., Ma, D., Lv, J., Heng, J., Ding, Y., Xue, Y., et al. (2017) · Nature · doi:10.1038/nature23883 · Cited by 584
Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow
Malinsky, M., Svardal, H., Tyers, A. M., Miska, E. A., Genner, M. J., Turner, G. F., & Durbin, R. M. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0717-x · Cited by 568
Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease
Gjoneska, E., Pfenning, A. R., Mathys, H., Quon, G., Kundaje, A., Tsai, L.-H., & Kellis, M. (2015) · Nature · doi:10.1038/nature14252 · Cited by 576
Assessing the performance of the Oxford Nanopore Technologies MinION
Laver, T. W., Harrison, J., O’Neill, P. A., Moore, K., Farbos, A., Paszkiewicz, K. H., & Studholme, D. J. (2015) · Biomolecular Detection and Quantification · doi:10.1016/j.bdq.2015.02.001 · Cited by 563
Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly
Zhu, T., Wang, L., Rimbert, H., Rodriguez, J., Deal, K. R., Oliveira, R. D., Choulet, F., Keeble‐Gagnère, G., Tibbits, J. F. G., Rogers, J., et al. (2021) · The Plant Journal · doi:10.1111/tpj.15289 · Cited by 602
Stein, J. C., Yu, Y., Copetti, D., Zwickl, D. J., Zhang, L., Zhang, C., Chougule, K. M., Gao, D., Iwata‐Otsubo, A., Goicoechea, J. L., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0040-0 · Cited by 585
Partial uracil–DNA–glycosylase treatment for screening of ancient DNA
Rohland, N., Harney, E., Mallick, S., Nordenfelt, S., & Reich, D. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2013.0624 · Cited by 572
Widespread natural variation of DNA methylation within angiosperms
Niederhuth, C. E., Bewick, A. J., Ji, L., Alabady, M., Kim, K. D., Li, Q., Rohr, N. A., Rambani, A., Burke, J. M., Udall, J. A., et al. (2016) · Genome biology · doi:10.1186/s13059-016-1059-0 · Cited by 557
Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain
Evrony, G. D., Cai, X., Lee, E., Hills, L. B., Elhosary, P. C., Lehmann, H. S., Parker, J. J., Atabay, K. D., Gilmore, E. C., Poduri, A., et al. (2012) · Cell · doi:10.1016/j.cell.2012.09.035 · Cited by 548
Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago
Rasmussen, S., Allentoft, M. E., Nielsen, K. R., Orlando, L., Sikora, M., Sjögren, K.-G., Pedersen, A. G., Schubert, M., Dam, A. V., Kapel, C. M. O., et al. (2015) · Cell · doi:10.1016/j.cell.2015.10.009 · Cited by 589
SpeedSeq: ultra-fast personal genome analysis and interpretation
Chiang, C., Layer, R. M., Faust, G. G., Lindberg, M. R., Rose, D. B., Garrison, E. P., Marth, G., Quinlan, A. R., & Hall, I. M. (2015) · Nature Methods · doi:10.1038/nmeth.3505 · Cited by 555
Self-citationChromatin modifications as determinants of muscle stem cell quiescence and chronological aging
Liu, L., Cheung, T. H., Charville, G. W., Hurgo, B. M. C., Leavitt, T., Shih, J., Brunet, A., & Rando, T. A. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.05.043 · Cited by 544
Transposable elements reveal a stem cell-specific class of long noncoding RNAs
Kelley, D., & Rinn, J. (2012) · Genome Biology · doi:10.1186/gb-2012-13-11-r107 · Cited by 531
Parental influence on human germline de novo mutations in 1,548 trios from Iceland
Jónsson, H., Sulem, P., Kehr, B., Kristmundsdottir, S., Zink, F., Hjartarson, E., Hardarson, M. T., Hjorleifsson, K. E., Eggertsson, H. P., Gudjonsson, S. A., et al. (2017) · Nature · doi:10.1038/nature24018 · Cited by 561
Tavares, L., Dimitrova, E., Oxley, D., Webster, J. A., Poot, R. A., Demmers, J., Bezstarosti, K., Taylor, S., Ura, H., Koide, H., et al. (2012) · Cell · doi:10.1016/j.cell.2011.12.029 · Cited by 583
Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling
Meers, M. P., Tenenbaum, D., & Henikoff, S. (2019) · Epigenetics & Chromatin · doi:10.1186/s13072-019-0287-4 · Cited by 556
The genomic landscape underlying phenotypic integrity in the face of gene flow in crows
Poelstra, J. W., Vijay, N., Bossu, C. M., Lantz, H., Ryll, B., Müller, I., Baglione, V., Unneberg, P., Wikelski, M. C., Grabherr, M. G., et al. (2014) · Science · doi:10.1126/science.1253226 · Cited by 551
NONCODEV5: a comprehensive annotation database for long non-coding RNAs
Fang, S., Zhang, L., Guo, J., Niu, Y., Wu, Y., Li, H., Zhao, L., Li, X., Teng, X., Sun, X., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1107 · Cited by 561
m6A RNA Methylation Is Regulated by MicroRNAs and Promotes Reprogramming to Pluripotency
Chen, T., Hao, Y., Zhang, Y., Li, M., Wang, M., Han, W., Yong-sheng, W., Lv, Y., Hao, J., Wang, L., et al. (2015) · Cell stem cell · doi:10.1016/j.stem.2015.01.016 · Cited by 552
Mosaic Copy Number Variation in Human Neurons
McConnell, M. J., Lindberg, M. R., Brennand, K. J., Piper, J. C., Voet, T., Cowing-Zitron, C., Shumilina, S., Lasken, R. S., Vermeesch, J. R., Hall, I. M., et al. (2013) · Science · doi:10.1126/science.1243472 · Cited by 551
Self-citationGupta, S., Ellis, S. E., Ashar, F. N., Moes, A., Bader, J. S., Zhan, J., West, A. B., & Arking, D. E. (2014) · Nature Communications · doi:10.1038/ncomms6748 · Cited by 504
Démenais, F., Margaritte‐Jeannin, P., Barnes, K. C., Cookson, W., Altmüller, J., Ang, W., Barr, R. G., Beaty, T. H., Becker, A. B., Beilby, J. P., et al. (2017) · Nature Genetics · doi:10.1038/s41588-017-0014-7 · Cited by 547
Long non-coding RNAs as a source of new peptides
Ruiz‐Orera, J., Messeguer, X., Subirana, J. A., & Albà, M. M. (2014) · eLife · doi:10.7554/elife.03523 · Cited by 560
Uncovering hidden variation in polyploid wheat
Krasileva, K. V., Vasquez-Gross, H. A., Howell, T. A., Bailey, P. C. E., Paraiso, F., Clissold, L., Simmonds, J., Ramirez-Gonzalez, R. H., Wang, X., Borrill, P., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1619268114 · Cited by 552
FUS affects circular RNA expression in murine embryonic stem cell-derived motor neurons
Errichelli, L., Modigliani, S. D., Laneve, P., Colantoni, A., Legnini, I., Capauto, D., Rosa, A., Santis, R. D., Scarfò, R., Peruzzi, G., et al. (2017) · Nature Communications · doi:10.1038/ncomms14741 · Cited by 548
Genomic evidence for the Pleistocene and recent population history of Native Americans
Raghavan, M., Steinrücken, M., Harris, K., Schiffels, S., Rasmussen, S., DeGiorgio, M., Albrechtsen, A., Valdiosera, C., Ávila-Arcos, M. C., Malaspinas, A.-S., et al. (2015) · Science · doi:10.1126/science.aab3884 · Cited by 540
Schubert, M., Ermini, L., Sarkissian, C. D., Jónsson, H., Ginolhac, A., Schaefer, R., Martin, M. D., Fernández, R., Kircher, M., McCue, M., et al. (2014) · Nature Protocols · doi:10.1038/nprot.2014.063 · Cited by 562
ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors
Schmidl, C., Rendeiro, A. F., Sheffield, N. C., & Bock, C. (2015) · Nature Methods · doi:10.1038/nmeth.3542 · Cited by 509
H3K4me3 breadth is linked to cell identity and transcriptional consistency
Benayoun, B. A., Pollina, E. A., Ucar, D., Mahmoudi, S., Karra, K., Wong, E. D., Devarajan, K., Daugherty, A. C., Kundaje, A. B., Mancini, E., et al. (2014) · Cell · doi:10.1016/j.cell.2014.06.027 · Cited by 536
TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A
Brown, A., Wilkins, O. G., Keuss, M. J., Kargbo-Hill, S. E., Zanovello, M., Lee, W. C., Bampton, A., Lee, F. C. Y., Masino, L., Qi, Y. A., et al. (2022) · Nature · doi:10.1038/s41586-022-04436-3 · Cited by 545
RNA-seq differential expression studies: more sequence or more replication?
Liu, Y., Zhou, J., & White, K. P. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt688 · Cited by 497
Schwartzentruber, J., Cooper, S., Liu, J. Z., Barrio-Hernandez, I., Bello, E., Kumasaka, N., Young, A. M. H., Franklin, R. J. M., Johnson, T., Estrada, K., et al. (2021) · Nature Genetics · doi:10.1038/s41588-020-00776-w · Cited by 532
The Rosa genome provides new insights into the domestication of modern roses
Raymond, O., Gouzy, J., Just, J., Badouin, H., Verdenaud, M., Lemainque, A., Vergne, P., Moja, S., Choisne, N., Pont, C., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0110-3 · Cited by 463
Somatic mutation landscapes at single-molecule resolution
Abascal, F., Harvey, L. M. R., Mitchell, E., Lawson, A. R. J., Lensing, S. V., Ellis, P., Russell, A. J. C., Alcantara, R. E., Baez-Ortega, A., Wang, Y., et al. (2021) · Nature · doi:10.1038/s41586-021-03477-4 · Cited by 546
for UK Primary Sjögren's Syndrome Registry, Lessard, C. J., Li, H., Adrianto, I., Ice, J. A., Rasmussen, A., Grundahl, K. M., Kelly, J. A., Dozmorov, M. G., Miceli‐Richard, C., et al. (2013) · Nature Genetics · doi:10.1038/ng.2792 · Cited by 542
Gazal, S., Finucane, H. K., Furlotte, N. A., Loh, P.-R., Palamara, P. F., Liu, X., Schoech, A., Bulik-Sullivan, B., Neale, B. M., Gusev, A., et al. (2017) · Nature Genetics · doi:10.1038/ng.3954 · Cited by 525
N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas
Fu, Y., Luo, G., Chen, K., Deng, X., Yu, M., Han, D., Hao, Z., Liu, J., Lu, X., Doré, L. C., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.010 · Cited by 533
Genome-wide analysis of noncoding regulatory mutations in cancer
Weinhold, N., Jacobsen, A., Schultz, N., Sander, C., & Lee, W. (2014) · Nature Genetics · doi:10.1038/ng.3101 · Cited by 484
Ke, Y., Xu, Y., Chen, X., Feng, S., Liu, Z., Sun, Y., Yao, X., Li, F., Zhu, W. Z., Gao, L., et al. (2017) · Cell · doi:10.1016/j.cell.2017.06.029 · Cited by 531
Punctuated copy number evolution and clonal stasis in triple-negative breast cancer
Gao, R., Davis, A., McDonald, T. O., Sei, E., Shi, X., Wang, Y., Tsai, P. C., Casasent, T. D., Waters, J., Zhang, H., et al. (2016) · Nature Genetics · doi:10.1038/ng.3641 · Cited by 533
The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape
Weinberg, D. N., Papillon-Cavanagh, S., Chen, H., Yue, Y., Chen, X., Rajagopalan, K. N., Horth, C., McGuire, J. T., Xu, X., Nikbakht, H., et al. (2019) · Nature · doi:10.1038/s41586-019-1534-3 · Cited by 524
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 493
Self-citationThe structural basis for cohesin–CTCF-anchored loops
Li, Y., Haarhuis, J. H. I., Sedeño Cacciatore, Á., Oldenkamp, R., van Ruiten, M. S., Willems, L., Teunissen, H., Muir, K. W., de Wit, E., Rowland, B. D., et al. (2020) · Nature · doi:10.1038/s41586-019-1910-z · Cited by 459
Annala, M., Vandekerkhove, G. R., Khalaf, D. J., Taavitsainen, S., Beja, K., Warner, E. W., Sunderland, K., Kollmannsberger, C., Eigl, B. J., Finch, D. L., et al. (2018) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-0937 · Cited by 523
Systemic Human ILC Precursors Provide a Substrate for Tissue ILC Differentiation
Lim, A. I., Li, Y., Lopez‐Lastra, S., Stadhouders, R., Paul, F., Casrouge, A., Serafini, N., Puel, A., Bustamante, J. C., Surace, L., et al. (2017) · Cell · doi:10.1016/j.cell.2017.02.021 · Cited by 515
A pathway coordinated by DELE1 relays mitochondrial stress to the cytosol
Fessler, E., Eckl, E.-M., Schmitt, S., Mancilla, I. A., Meyer-Bender, M., Hanf, M., Philippou‐Massier, J., Krebs, S., Zischka, H., & Jae, L. T. (2020) · Nature · doi:10.1038/s41586-020-2076-4 · Cited by 515
Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals
Vernot, B., Tucci, S., Kelso, J., Schraiber, J. G., Wolf, A. B., Gittelman, R. M., Dannemann, M., Grote, S., McCoy, R. C., Norton, H., et al. (2016) · Science · doi:10.1126/science.aad9416 · Cited by 459
DNMT1-interacting RNAs block gene-specific DNA methylation
Ruscio, A. D., Ebralidze, A. K., Benoukraf, T., Amabile, G., Goff, L. A., Terragni, J., Figueroa, M. E., de Figueiredo‐Pontes, L. L., Alberich-Jordà, M., Zhang, P., et al. (2013) · Nature · doi:10.1038/nature12598 · Cited by 529
Merino, D. M., McShane, L. M., Fabrizio, D. A., Funari, V. A., Chen, S., White, J. R., Wenz, P., Baden, J. F., Barrett, J. C., Chaudhary, R., et al. (2020) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2019-000147 · Cited by 528
Jühling, F., Kretzmer, H., Bernhart, S. H., Otto, C., Stadler, P. F., & Hoffmann, S. (2015) · Genome Research · doi:10.1101/gr.196394.115 · Cited by 509
Mahat, D. B., Kwak, H., Booth, G. T., Jonkers, I. H., Danko, C. G., Patel, R. K., Waters, C. T., Munson, K. M., Core, L. J., & Lis, J. T. (2016) · Nature Protocols · doi:10.1038/nprot.2016.086 · Cited by 517
Paris, J., Morgan, M., Campos, J., Spencer, G. J., Shmakova, A., Ivanova, I., Mapperley, C., Lawson, H., Wotherspoon, D., Sepúlveda, C., et al. (2019) · Cell stem cell · doi:10.1016/j.stem.2019.03.021 · Cited by 509
The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans
Tully, B., Graham, E. D., & Heidelberg, J. F. (2018) · Scientific Data · doi:10.1038/sdata.2017.203 · Cited by 516
An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
Jacobs, F. M. J., Greenberg, D., Nguyen, N., Haeussler, M., Ewing, A. D., Katzman, S., Paten, B., Salama, S. R., & Haussler, D. (2014) · Nature · doi:10.1038/nature13760 · Cited by 506
Inherited and de novo genetic risk for autism impacts shared networks
Ruzzo, E. K., Pérez-Cano, L., Jung, J.-Y., Wang, L.-K., Kashef-Haghighi, D., Hartl, C., Singh, C., Xu, J., Hoekstra, J. N., Leventhal, O., et al. (2019) · Cell · doi:10.1016/j.cell.2019.07.015 · Cited by 457
annotatr: genomic regions in context
Cavalcante, R. G., & Sartor, M. A. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx183 · Cited by 506
Transcriptional plasticity promotes primary and acquired resistance to BET inhibition
Rathert, P., Roth, M., Neumann, T., Muerdter, F., Roe, J., Muhar, M., Deswal, S., Cerny‐Reiterer, S., Peter, B., Jude, J., et al. (2015) · Nature · doi:10.1038/nature14898 · Cited by 514
SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline
Tamames, J., & Puente‐Sánchez, F. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.03349 · Cited by 511
Glioma progression is shaped by genetic evolution and microenvironment interactions
Varn, F. S., Johnson, K. C., Martinek, J., Huse, J. T., Nasrallah, M. P., Wesseling, P., Cooper, L., Malta, T. M., Wade, T. E., Sabedot, T. S., et al. (2022) · Cell · doi:10.1016/j.cell.2022.04.038 · Cited by 516
Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles
Walz, S., Lorenzin, F., Morton, J. P., Wiese, K. E., von Eyß, B., Herold, S., Rycak, L., Dumay‐Odelot, H., Karim, S. A., Bartkuhn, M., et al. (2014) · Nature · doi:10.1038/nature13473 · Cited by 502
Huang, Q., Wu, X., Wang, Z., Chen, X., Wang, L., Lu, Y., Xiong, D., Liu, Q., Tian, Y., Lin, H., et al. (2022) · Cell · doi:10.1016/j.cell.2022.09.020 · Cited by 486
Zerbino, D. R., Wilder, S. P., Johnson, N., Juettemann, T., & Flicek, P. R. (2015) · Genome Biology · doi:10.1186/s13059-015-0621-5 · Cited by 429
The impact of structural variation on human gene expression
GTEx Consortium, Chiang, C., Scott, A. J., Davis, J. R., Tsang, E. K., Li, X., Kim, Y., Hadzic, T., Damani, F. N., Ganel, L., et al. (2017) · Nature Genetics · doi:10.1038/ng.3834 · Cited by 495
Self-citationAP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection
Vierbuchen, T., Ling, E., Cowley, C. J., Couch, C. H., Wang, X., Harmin, D. A., Roberts, C. W. M., & Greenberg, M. E. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.11.026 · Cited by 455
Widespread contribution of transposable elements to the innovation of gene regulatory networksPreprint
Sundaram, V., Cheng, Y., Ma, Z., Li, D., Xing, X., Edge, P., Snyder, M. P., & Wang, T. (2014) · Genome Research · doi:10.1101/gr.168872.113 · Cited by 499
Targeted RNA sequencing reveals the deep complexity of the human transcriptome
Mercer, T. R., Gerhardt, D. J., Dinger, M. E., Crawford, J., Trapnell, C., Jeddeloh, J. A., Mattick, J. S., & Rinn, J. L. (2011) · Nature Biotechnology · doi:10.1038/nbt.2024 · Cited by 490
dDocent : a RADseq, variant-calling pipeline designed for population genomics of non-model organisms
Puritz, J. B., Hollenbeck, C. M., & Gold, J. R. (2014) · PeerJ · doi:10.7717/peerj.431 · Cited by 514
Natural selection interacts with recombination to shape the evolution of hybrid genomes
Schumer, M., Xu, C., Powell, D. L., Durvasula, A., Skov, L., Holland, C., Blazier, J. C., Sankararaman, S., Andolfatto, P., Rosenthal, G. G., et al. (2018) · Science · doi:10.1126/science.aar3684 · Cited by 412
Gremme, G., Steinbiss, S., & Kurtz, S. (2013) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2013.68 · Cited by 494
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
DART-seq: an antibody-free method for global m6A detection
Meyer, K. D. (2019) · Nature Methods · doi:10.1038/s41592-019-0570-0 · Cited by 490
In vivo base editing rescues Hutchinson–Gilford progeria syndrome in mice
Koblan, L. W., Erdos, M. R., Wilson, C., Cabral, W. A., Levy, J. M., Xiong, Z., Tavarez, U. L., Davison, L. M., Gete, Y. G., Mao, X., et al. (2021) · Nature · doi:10.1038/s41586-020-03086-7 · Cited by 489
The birth of the Epitranscriptome: deciphering the function of RNA modifications
Saletore, Y., Meyer, K. D., Korlach, J., Vilfan, I. D., Jaffrey, S. R., & Mason, C. E. (2012) · Genome biology · doi:10.1186/gb-2012-13-10-175 · Cited by 500
Deciphering the “m6A Code” via Antibody-Independent Quantitative Profiling
García-Campos, M. A., Edelheit, S., Toth, U., Safra, M., Shachar, R., Viukov, S. V., Winkler, R., Nir, R., Lasman, L., Brandis, A. S., et al. (2019) · Cell · doi:10.1016/j.cell.2019.06.013 · Cited by 479
Passive and active DNA methylation and the interplay with genetic variation in gene regulation
Gutierrez-Arcelus, M., Lappalainen, T., Montgomery, S. B., Buil, A., Ongen, H., Yurovsky, A., Bryois, J., Giger, T., Romano, L., Planchon, A., et al. (2013) · eLife · doi:10.7554/elife.00523 · Cited by 440
Somatic mutation rates scale with lifespan across mammals
Cagan, A., Baez-Ortega, A., Brzozowska, N., Abascal, F., Coorens, T. H. H., Sanders, M. A., Lawson, A. R. J., Harvey, L. M. R., Bhosle, S., Jones, D., et al. (2022) · Nature · doi:10.1038/s41586-022-04618-z · Cited by 481
Effector CD8 T cells dedifferentiate into long-lived memory cells
Youngblood, B., Hale, J. S., Kissick, H. T., Ahn, E., Xu, X., Wieland, A., Araki, K., West, E. E., Ghoneim, H. E., Fan, Y., et al. (2017) · Nature · doi:10.1038/nature25144 · Cited by 481
RNA-seq: impact of RNA degradation on transcript quantification
Romero, I. G., Pai, A. A., Tung, J., & Gilad, Y. (2014) · BMC Biology · doi:10.1186/1741-7007-12-42 · Cited by 497
BRCA1 Recruitment to Transcriptional Pause Sites Is Required for R-Loop-Driven DNA Damage Repair
Hatchi, E., Skourti-Stathaki, K., Ventz, S., Pinello, L., Yen, A., Kamieniarz-Gdula, K., Dimitrov, S. D., Pathania, S., McKinney, K. M., Eaton, M. L., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.01.011 · Cited by 473
Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution
Liu, Y., Siejka-Zielińska, P., Velikova, G., Bi, Y., Yuan, F., Tomková, M., Bai, C., Chen, L., Schuster‐Böckler, B., & Song, C. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0041-2 · Cited by 480
Spatial genomic heterogeneity within localized, multifocal prostate cancer
Boutros, P. C., Fraser, M. E., Harding, N. J., de Borja, R., Trudel, D., Lalonde, E., Meng, A. X., Hennings-Yeomans, P. H., McPherson, A., Sabelnykova, V. Y., et al. (2015) · Nature Genetics · doi:10.1038/ng.3315 · Cited by 472
Unique features of the m6A methylome in Arabidopsis thaliana
Luo, G., MacQueen, A., Zheng, G., Duan, H., Doré, L. C., Lu, Z., Liu, J., Chen, K., Jia, G., Bergelson, J. M., et al. (2014) · Nature Communications · doi:10.1038/ncomms6630 · Cited by 477
Detection and characterization of lung cancer using cell-free DNA fragmentomes
Mathios, D., Johansen, J. S., Cristiano, S., Medina, J. E., Phallen, J. A., Larsen, K. R., Bruhm, D. C., Niknafs, N., Ferreira, L., Adleff, V., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24994-w · Cited by 476
The complete sequence of a human Y chromosome
Rhie, A., Nurk, S., Cechova, M., Hoyt, S. J., Taylor, D. J., Altemose, N., Hook, P. W., Koren, S., Rautiainen, M., Alexandrov, I. A., et al. (2023) · Nature · doi:10.1038/s41586-023-06457-y · Cited by 471
Enhancer transcripts mark active estrogen receptor binding sitesPreprint
Hah, N., Murakami, S., Nagari, A., Danko, C. G., & Kraus, W. L. (2013) · Genome Research · doi:10.1101/gr.152306.112 · Cited by 491
Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl
Busslinger, G. A., Stocsits, R. R., van der Lelij, P., Axelsson, E., Tedeschi, A., Galjart, N., & Peters, J.-M. (2017) · Nature · doi:10.1038/nature22063 · Cited by 468
Metadata
- Authors
- Quinlan, A. R., & Hall, I. M.
- Affiliations
- University of Virginia (US)
- Corresponding author
- Quinlan, Aaron R.
- Hall, Ira M.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-01-28
- Volume
- 26
- Issue
- 6
- Pages
- 841-842
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC2832824
- OpenAlex
- W2102619694
- Cited by
- 27,437
- References
- 4
- Citations by year
- 2026: 2474 · 2025: 3385 · 2024: 3380 · 2023: 2862 · 2022: 2676 · 2021: 2957 · 2020: 2267 · 2019: 1731 · 2018: 1533 · 2017: 1185 · 2016: 932 · 2015: 743 · 2014: 616 · 2013: 387 · 2012: 212
- FWCI
- 88.15
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust
- National Institutes of Health (1dp2od006493-01)
- National Human Genome Research Institute (F32HG005197)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- bedtools, BAM alignment file, genome annotation, feature overlap, next-generation sequencing data
- MeSH terms
- Software, Genome, Internet, Genomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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