The Sequence Alignment/Map format and SAMtools

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849

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

Mapping short DNA sequencing reads and calling variants using mapping quality scores

Li, H., Ruan, J., & Durbin, R. (2008) · Genome Research · doi:10.1101/gr.078212.108 · Cited by 2,638

Next-Generation DNA Sequencing Methods

Mardis, E. R. (2008) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164359 · Cited by 2,469

Using the Velvet de novo Assembler for Short‐Read Sequencing Technologies

Zerbino, D. R. (2010) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1105s31 · Cited by 494

The Many Landscapes of Recombination in Drosophila melanogaster

Comeron, J. M., Ratnappan, R., & Bailin, S. S. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002905 · Cited by 510

A highly specific SpCas9 variant is identified by in vivo screening in yeast

Casini, A., Olivieri, M., Petris, G., Montagna, C., Reginato, G., Maule, G., Lorenzin, F., Prandi, D., Romanel, A., Demichelis, F., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4066 · Cited by 493

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

Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila

Bergland, A. O., Behrman, E. L., O’Brien, K. R., SCHMIDT, P. S., & Petrov, D. A. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004775 · Cited by 502

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

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

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

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

The functional landscape of the human phosphoproteome

Ochoa, D., Jarnuczak, A. F., Viéitez, C., Gehre, M., Soucheray, M., Mateus, A., Kleefeldt, A. A., Hill, A., Garcia-Alonso, L., Stein, F., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-019-0344-3 · Cited by 491

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

Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids

Beccari, L. L., Moris, N., Girgin, M., Turner, D. A., Baillie‐Johnson, P., Cossy, A.-C., Lütolf, M. P., Duboule, D., & Arias, A. M. (2018) · Nature · doi:10.1038/s41586-018-0578-0 · Cited by 507

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assemblyPreprint

Scheinin, I., Sie, D., Bengtsson, H. L., van de Wiel, M. A., Olshen, A. B., van Thuijl, H. F., Essen, H. F. H. V., Eijk, P. P., Rustenburg, F., Meijer, G. A., et al. (2014) · Genome Research · doi:10.1101/gr.175141.114 · Cited by 497

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

Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state

Verfaillie, A., Imrichova, H., Atak, Z. K., Dewaele, M., Rambow, F., Hulselmans, G., Christiaens, V., Svetlichnyy, D., Luciani, F., Van den Mooter, L., et al. (2015) · Nature Communications · doi:10.1038/ncomms7683 · Cited by 489

Recurrent AAV2-related insertional mutagenesis in human hepatocellular carcinomas

Nault, J.-C., Datta, S., Imbeaud, S., Franconi, A., Mallet, M., Couchy, G., Letouzé, E., Pilati, C., Verret, B., Blanc, J.-F., et al. (2015) · Nature Genetics · doi:10.1038/ng.3389 · Cited by 489

Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA

Sawyer, S., Krause, J., Guschanski, K., Savolainen, V., & Pääbo, S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034131 · Cited by 489

Emergence of Ceftazidime-Avibactam Resistance Due to Plasmid-Borne bla KPC-3 Mutations during Treatment of Carbapenem-Resistant Klebsiella pneumoniae Infections

Shields, R. K., Chen, L., Cheng, S., Chavda, K. D., Press, E. G., Snyder, A. C., Pandey, R., Doi, Y., Kreiswirth, B. N., Nguyen, M. H., et al. (2016) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.02097-16 · Cited by 489

Early farmers from across Europe directly descended from Neolithic Aegeans

Hofmanová, Z., Kreutzer, S., Hellenthal, G., Sell, C., Diekmann, Y., Díez-del-Molino, D., van Dorp, L., López, S., Kousathanas, A., Link, V., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1523951113 · Cited by 488

Molecular Profiling of the Residual Disease of Triple-Negative Breast Cancers after Neoadjuvant Chemotherapy Identifies Actionable Therapeutic Targets

Balko, J. M., Giltnane, J. M., Wang, K., Schwarz, L. J., Young, C. D., Cook, R. S., Owens, P., Sanders, M. E., Kuba, M. G., Sanchez, V. M., et al. (2013) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0286 · Cited by 489

Integrated allelic, transcriptional, and phenomic dissection of the cardiac effects of titin truncations in health and disease

Roberts, A. M., Ware, J. S., Herman, D. S., Schäfer, S., Baksi, J. A., Bick, A. G., Buchan, R. J., Walsh, R., John, S., Wilkinson, S., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.3010134 · Cited by 502

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Li, F., Brouwer, P., Carretero‐Paulet, L., Cheng, S., de Vries, J., Delaux, P., Eily, A. N., Koppers, N., Kuo, L., Li, Z., et al. (2018) · Nature Plants · doi:10.1038/s41477-018-0188-8 · Cited by 492

Optimal ancient DNA yields from the inner ear part of the human petrous bone

Pinhasi, R., Fernandes, D., Sirak, K., Novak, M., Connell, S., Alpaslan-Roodenberg, S., Gerritsen, F., Moiseyev, V., Gromov, A., Raczky, P., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0129102 · Cited by 487

Artifactual variation in randomly amplified polymorphic DNA banding patterns.

Ellsworth, D. L., Rittenhouse, K. D., & Honeycutt, R. L. (1993) · PubMed · Cited by 487

Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data

Vital, M., Karch, A., & Pieper, D. H. (2017) · mSystems · doi:10.1128/msystems.00130-17 · Cited by 502

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

Mapping the genomic landscape of CRISPR-Cas9 cleavage

Cameron, P., Fuller, C. K., Donohoue, P. D., Jones, B. N., Thompson, M. S., Carter, M. M., Gradia, S., Vidal, B., Garner, E., Slorach, E. M., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4284 · Cited by 443

Identification of direct targets and modified bases of RNA cytosine methyltransferases

Khoddami, V., & Cairns, B. R. (2013) · Nature Biotechnology · doi:10.1038/nbt.2566 · Cited by 484

Loss of p53 drives neuron reprogramming in head and neck cancer

Amit, M., Takahashi, H., Dragomir, M. P., Lindemann, A., Gleber-Netto, F. O., Pickering, C. R., Anfossi, S., Osman, A. A., Cai, Y., Wang, R., et al. (2020) · Nature · doi:10.1038/s41586-020-1996-3 · Cited by 483

Lactobacillus plantarum-derived indole-3-lactic acid ameliorates colorectal tumorigenesis via epigenetic regulation of CD8+ T cell immunity

Zhang, Q., Zhao, Q., Li, T., Lu, L., Wang, F., Zhang, H., Liu, Z., Ma, H., Zhu, Q., Wang, J., et al. (2023) · Cell Metabolism · doi:10.1016/j.cmet.2023.04.015 · Cited by 488

Base-Resolution Mapping Reveals Distinct m1A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts

Li, X., Xiong, X., Zhang, M., Wang, K., Chen, Y., Zhou, J. L., Mao, Y., Lv, J., Yi, D., Chen, X., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.10.019 · Cited by 482

A route to de novo domestication of wild allotetraploid rice

Yu, H. J., Lin, T., Meng, X., Du, H., Zhang, J., Liu, G., Chen, M., Jing, Y., Kou, L., Li, X., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.013 · Cited by 485

NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads

Hu, J., Wang, Z., Sun, Z., Hu, B., Ayoola, A. O., Liang, F., Li, J., Sandoval, J. R., Cooper, D. N., Ye, K., et al. (2024) · Genome Biology · doi:10.1186/s13059-024-03252-4 · Cited by 431

Recessive mutations in DGKE cause atypical hemolytic-uremic syndrome

Lemaire, M. J., Frémeaux‐Bacchi, V., Schaefer, F. S., Choi, M., Tang, W. H., Quintrec, M. L., Fakhouri, F., Taque, S., Nobili, F., Martinez, F., et al. (2013) · Nature Genetics · doi:10.1038/ng.2590 · Cited by 490

Quantitative evidence for early metastatic seeding in colorectal cancer

Hu, Z., Ding, J., Ma, Z., Sun, R., Seoane, J. A., Shaffer, J. S., Suarez, C. J., Berghoff, A. S., Cremolini, C., Falcone, A., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0423-x · Cited by 480

Diverse alterations associated with resistance to KRAS(G12C) inhibition

Zhao, Y., Murciano-Goroff, Y. R., Xue, J. Y., Ang, A., Lucas, J., Mai, T. T., Da Cruz Paula, A. F., Saiki, A. Y., Mohn, D., Achanta, P., et al. (2021) · Nature · doi:10.1038/s41586-021-04065-2 · Cited by 479

Mutations in TUBG1, DYNC1H1, KIF5C and KIF2A cause malformations of cortical development and microcephaly

Poirier, K., Lebrun, N., Broix, L., Tian, G., Saillour, Y., Boscheron, C., Parrini, E., Valence, S., Saintpierre, B., Oger, M., et al. (2013) · Nature Genetics · doi:10.1038/ng.2613 · Cited by 479

The 3,000 rice genomes project

The 3, 0. R. G. P. (2014) · GigaScience · doi:10.1186/2047-217x-3-7 · Cited by 479

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

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

DNA-guided DNA interference by a prokaryotic Argonaute

Swarts, D. C., Jore, M. M., Westra, E. R., Zhu, Y., Janssen, J. H., Snijders, A. P., Wang, Y., Patel, D. J., Berenguer, J., Brouns, S. J. J., et al. (2014) · Nature · doi:10.1038/nature12971 · Cited by 479

Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer

Murtaza, M., Dawson, S., McNamara, K. L., Rueda, O. M., Provenzano, E., Grant, J. W., Chin, S., Tsui, D. W. Y., Marass, F., Gale, D. G., et al. (2015) · Nature Communications · doi:10.1038/ncomms9760 · Cited by 486

Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing

Sereika, M., Kirkegaard, R. H., Karst, S. M., Michaelsen, T. Y., Sørensen, E. A., Wollenberg, R. D., & Albertsen, M. (2022) · Nature Methods · doi:10.1038/s41592-022-01539-7 · Cited by 514

Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction

Wang, X., Xu, Y., Zhang, S., Cao, L., Huang, Y., Cheng, J.-F., Wu, G., Tian, S., Chen, C., Liu, Y., et al. (2017) · Nature Genetics · doi:10.1038/ng.3839 · Cited by 486

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

Ali, O. A., O’Rourke, S. M., Amish, S. J., Meek, M. H., Luikart, G., Jeffres, C. A., & Miller, M. R. (2015) · Genetics · doi:10.1534/genetics.115.183665 · Cited by 496

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Tett, A., Huang, K. D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.08.018 · Cited by 476

Fast Computation and Applications of Genome Mappability

Derrien, T., Estellé, J., Marco‐Sola, S., Knowles, D. G., Raineri, E., Guigó, R., & Ribeca, P. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030377 · Cited by 493

Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instabilityPreprint

Akagi, K., Li, J., Broutian, T. R., Padilla‐Nash, H. M., Xiao, W., Jiang, B., Rocco, J. W., Teknos, T. N., Kumar, B., Wangsa, D., et al. (2013) · Genome Research · doi:10.1101/gr.164806.113 · Cited by 492

Life-threatening influenza and impaired interferon amplification in human IRF7 deficiency

Ciancanelli, M. J., Huang, S. X. L., Luthra, P., Garner, H., Itan, Y., Volpi, S., Lafaille, F. G., Trouillet, C., Schmolke, M., Albrecht, R. A., et al. (2015) · Science · doi:10.1126/science.aaa1578 · Cited by 475

COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence

Naveca, F. G., do Nascimento, V. A., de Souza, V. C., Corado, A. D. L. G., Nascimento, F., Silva, G., Costa, Á., Duarte, D., Pessoa, K., Mejía, M., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01378-7 · Cited by 496

Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing

Jiang, Y.-H., Yuen, R. K. C., Jin, X., Wang, M., Chen, N., Wu, X., Ju, J., Mei, J., Shi, Y., He, M., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.06.012 · Cited by 474

Petabase-scale sequence alignment catalyses viral discovery

Edgar, R. C., Taylor, B., Lin, V., Altman, T., Barbera, P., Meleshko, D., Lohr, D., Novakovsky, G., Buchfink, B., Al-Shayeb, B., et al. (2022) · Nature · doi:10.1038/s41586-021-04332-2 · Cited by 495

Improved transcriptome assembly using a hybrid of long and short reads with StringTie

Shumate, A., Wong, B. Y., Pertea, G. M., & Pertea, M. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009730 · Cited by 488

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

Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

Karthikeyan, S., Levy, J. I., Hoff, P. L. D., Humphrey, G. C., Birmingham, A., Jepsen, K., Farmer, S., Tubb, H. M., Valles, T., Tribelhorn, C., et al. (2022) · Nature · doi:10.1038/s41586-022-05049-6 · Cited by 472

Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients

Bost, P., Giladi, A., Liu, Y., Bendjelal, Y., Xu, G., David, E., Blecher-Gonen, R., Cohen, M., Medaglia, C., Li, H., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.006 · Cited by 471

A Draft Genome Sequence of Nicotiana benthamiana to Enhance Molecular Plant-Microbe Biology Research

Bombarely, A., Rosli, H. G., Vrebalov, J., Moffett, P., Mueller, L. A., & Martin, G. B. (2012) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-06-12-0148-ta · Cited by 478

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

Nayfach, S., Rodriguez-Mueller, B., Garud, N., & Pollard, K. S. (2016) · Genome Research · doi:10.1101/gr.201863.115 · Cited by 470

Immunodeficiency, autoinflammation and amylopectinosis in humans with inherited HOIL-1 and LUBAC deficiency

Boisson, B., Laplantine, E., Prando, C., Giliani, S., Israelsson, E., Xu, Z., Abhyankar, A., Israël, L., Trevejo-Nuñez, G., Bogunovic, D., et al. (2012) · Nature Immunology · doi:10.1038/ni.2457 · Cited by 489

Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells

Hess, G. T., Frésard, L., Han, K., Lee, C. H., Li, A., Cimprich, K. A., Montgomery, S. B., & Bassik, M. C. (2016) · Nature Methods · doi:10.1038/nmeth.4038 · Cited by 474

Scientific Guidance for the submission of dossiers on Food Enzymes

EFSA Panel on Food Contact Materials, E. A. P. A. (. C. P., Lambré, C., Baviera, J. M. B., Bolognesi, C., Cocconcelli, P. S., Crebelli, R., Gott, D. M., Grob, K., Lampi, E., Mengelers, M. J. B., et al. (2021) · EFSA Journal · doi:10.2903/j.efsa.2021.6851 · Cited by 468

A recent bottleneck of Y chromosome diversity coincides with a global change in culturePreprint

Karmin, M., Saag, L., Vicente, M., Sayres, M. A. W., Järve, M., Talas, U. G., Rootsi, S., Ilumäe, A.-M., Mägi, R., Mitt, M., et al. (2015) · Genome Research · doi:10.1101/gr.186684.114 · Cited by 480

Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation

Petersen, J. M., Kemper, A., Gruber‐Vodicka, H. R., Cardini, U., van der Geest, M., Kleiner, M., Bulgheresi, S., Mußmann, M., Herbold, C. W., Seah, B. K. B., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.195 · Cited by 475

Maternal H3K27me3 controls DNA methylation-independent imprinting

Inoue, A., Jiang, L., Lu, F., Suzuki, T., & Zhang, Y. (2017) · Nature · doi:10.1038/nature23262 · Cited by 483

From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis

Yan, F., Powell, D., Curtis, D. J., & Wong, N. C. (2020) · Genome biology · doi:10.1186/s13059-020-1929-3 · Cited by 487

Altered proliferation and networks in neural cells derived from idiopathic autistic individuals

Marchetto, M. C., Belinson, H., Tian, Y., Freitas, B. C., Fu, C., Vadodaria, K. C., Beltrao-Braga, P. C., Trujillo, C. A., Mendes, A. P. D., Padmanabhan, K., et al. (2017) · Molecular Psychiatry · doi:10.1038/mp.2016.95 · Cited by 466

RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity

Pefanis, E., Wang, J., Rothschild, G., Lim, J., Kazadi, D., Sun, J., Federation, A., Chao, J., Elliott, O., Liu, Z.-P., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.034 · Cited by 464

Recurrent somatic mutations in ACVR1 in pediatric midline high-grade astrocytoma

Fontebasso, A. M., Papillon-Cavanagh, S., Schwartzentruber, J., Nikbakht, H., Gerges, N., Fiset, P.-O., Bechet, D., Faury, D., De Jay, N., Ramkissoon, L. A., et al. (2014) · Nature Genetics · doi:10.1038/ng.2950 · Cited by 465

Evolution and transmission of drug-resistant tuberculosis in a Russian population

Casali, N., Nikolayevskyy, V., Balabanova, Y., Harris, S. R., Ignatyeva, O. A., Kontsevaya, I., Corander, J., Bryant, J. M., Parkhill, J., Nejentsev, S., et al. (2014) · Nature Genetics · doi:10.1038/ng.2878 · Cited by 465

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

Wong, V., Baker, S. G., Pickard, D., Parkhill, J., Page, A. J., Feasey, N., Kingsley, R. A., Thomson, N. R., Keane, J. A., Weill, F., et al. (2015) · Nature Genetics · doi:10.1038/ng.3281 · Cited by 473

Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits

Fang, L., Wang, Q., Hu, Y., Jia, Y., Chen, J., Liu, B., Zhang, Z., Guan, X., Chen, S., Zhou, B., et al. (2017) · Nature Genetics · doi:10.1038/ng.3887 · Cited by 465

Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis

Quainoo, S., Coolen, J. P. M., van Hijum, S. A. F. T., Huynen, M. A., Melchers, W. J. G., van Schaik, W., & Wertheim, H. F. L. (2017) · Clinical Microbiology Reviews · doi:10.1128/cmr.00016-17 · Cited by 488

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

Parker, M. T., Knop, K., Sherwood, A. V., Schurch, N., Mackinnon, K., Gould, P. D., Hall, A. J. W., Barton, G. J., & Simpson, G. G. (2020) · eLife · doi:10.7554/elife.49658 · Cited by 474

Disruption of KMT2D perturbs germinal center B cell development and promotes lymphomagenesis

Zhang, J., Dominguez-Sola, D., Hussein, S., Lee, J., Holmes, A. B., Bansal, M., Vlasevska, S., Mo, T., Tang, H., Basso, K., et al. (2015) · Nature Medicine · doi:10.1038/nm.3940 · Cited by 493

Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer’s disease

Cruchaga, C., Karch, C. M., Jin, S. C., Benitez, B. A., Cai, Y., Guerreiro, R., Harari, O., Norton, J., Budde, J., Bertelsen, S., et al. (2014) · Nature · doi:10.1038/nature12825 · Cited by 461

Premature Termination of Reprogramming In Vivo Leads to Cancer Development through Altered Epigenetic Regulation

Ohnishi, K., Semi, K., Yamamoto, T., Shimizu, M., Tanaka, A., Mitsunaga, K., Okita, K., Osafune, K., Arioka, Y., Maeda, T., et al. (2014) · Cell · doi:10.1016/j.cell.2014.01.005 · Cited by 460

Epigenetic regulation of brain region-specific microglia clearance activity

Ayata, P., Badimon, A., Strasburger, H. J., Duff, M. K., Montgomery, S. E., Loh, Y.-H. E., Ebert, A., Pimenova, A. A., Ramirez, B. R., Chan, A. T., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0192-3 · Cited by 460

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

A clinically applicable integrative molecular classification of meningiomas

Nassiri, F., Liu, J., Patil, V. S., Mamatjan, Y., Wang, J. Z., Hugh-White, R., Macklin, A. M., Khan, S., Singh, O., Karimi, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03850-3 · Cited by 474

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element

Cho, S. W., Xu, J., Sun, R., Mumbach, M. R., Carter, A. C., Chen, Y. G., Yost, K. E., Kim, J., He, J., Nevins, S. A., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.068 · Cited by 459

A compendium of uniformly processed human gene expression and splicing quantitative trait loci

Kerimov, N., Hayhurst, J. D., Peikova, K., Manning, J. R., Walter, P., Kolberg, L., Samoviča, M., Sakthivel, M. P., Kuzmin, I., Trevanion, S. J., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00924-w · Cited by 440

Mistargeted mitochondrial proteins activate a proteostatic response in the cytosol

Wróbel, L., Topf, U., Brągoszewski, P., Wiese, S., Sztolsztener, M. E., Oeljeklaus, S., Varabyova, A., Lirski, M., Chrościcki, P., Mroczek, S., et al. (2015) · Nature · doi:10.1038/nature14951 · Cited by 471

Assuring the quality of next-generation sequencing in clinical laboratory practice

Gargis, A. S., Kalman, L. V., Berry, M. W., Bick, D. P., Dimmock, D., Hambuch, T. M., Lu, F., Lyon, E., Voelkerding, K. V., Zehnbauer, B. A., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2403 · Cited by 460

Enhancer Reprogramming Promotes Pancreatic Cancer Metastasis

Roe, J., Hwang, C., Somerville, T. D. D., Milazzo, J. P., Lee, E. J., Silva, B. D., Maiorino, L., Tiriac, H., Young, C. M., Miyabayashi, K., et al. (2017) · Cell · doi:10.1016/j.cell.2017.07.007 · Cited by 465

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

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

Iverson, V., Morris, R. M., Frazar, C. D., Berthiaume, C. T., Morales, R. L., & Armbrust, E. V. (2012) · Science · doi:10.1126/science.1212665 · Cited by 475

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

Wang, M., Tu, L., Lin, M., Lin, Z., Wang, P., Yang, Q., Ye, Z., Shen, C., Li, J., Zhang, L., et al. (2017) · Nature Genetics · doi:10.1038/ng.3807 · Cited by 461

The 1000 Genomes Project: Data Management and Community Access

Clarke, L., Zheng-Bradley, X., Smith, R. I., Kulesha, E., Xiao, C., Toneva, I., Vaughan, B. W., Preuss, D., Leinonen, R., Shumway, M., et al. (2012) · Nature Methods · doi:10.1038/nmeth.1974 · Cited by 447

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life

Yassour, M., Jason, E., Hogstrom, L. J., Arthur, T. D., Tripathi, S., Siljander, H., Selvenius, J., Oikarinen, S., Hyöty, H., Virtanen, S. M., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.06.007 · Cited by 455

A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour

Zhang, L.-Y., Hu, J. Y., Han, X., Li, J., Gao, Y., Richards, C. M., Zhang, C., Tian, Y., Liu, G., Gul, H., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09518-x · Cited by 472

AP-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

Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients

Ni, X., Zhuo, M., Su, Z., Duan, J., Gao, Y., Wang, Z., Zong, C., Bai, H., Chapman, A. R., Zhao, J., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1320659110 · Cited by 454

pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

Hundal, J., Carreno, B. M., Petti, A. A., Linette, G. P., Griffith, O. L., Mardis, E. R., & Griffith, M. (2016) · Genome Medicine · doi:10.1186/s13073-016-0264-5 · Cited by 454

A Menin-MLL Inhibitor Induces Specific Chromatin Changes and Eradicates Disease in Models of MLL-Rearranged Leukemia

Krivtsov, A. V., Evans, K., Gadrey, J. Y., Eschle, B. K., Hatton, C., Uckelmann, H. J., Ross, K. N., Perner, F., Olsen, S. N., Pritchard, T., et al. (2019) · Cancer Cell · doi:10.1016/j.ccell.2019.11.001 · Cited by 460

Gut microbiome function predicts response to anti-integrin biologic therapy in Inflammatory Bowel diseases

Ananthakrishnan, A. N., Luo, C., Yajnik, V., Khalili, H., Garber, J. J., Stevens, B. W., Cleland, T., & Xavier, R. J. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.04.010 · Cited by 451

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Rodriguez-Martin, B., Alvarez, E. G., Baez-Ortega, A., Zamora, J., Supek, F., Demeulemeester, J., Santamarina, M., Ju, Y. S., Temes, J., Garcia-Souto, D., et al. (2020) · Nature Genetics · doi:10.1038/s41588-019-0562-0 · Cited by 451

Neandertal and Denisovan DNA from Pleistocene sediments

Slon, V., Hopfe, C., Weiß, C. L., Mafessoni, F., de la Rasilla, M., Lalueza-Fox, C., Rosas, A., Soressi, M., Knul, M. V., Miller, R., et al. (2017) · Science · doi:10.1126/science.aam9695 · Cited by 465

The EDS1–PAD4–ADR1 node mediates Arabidopsis pattern-triggered immunity

Pruitt, R. N., Locci, F., Wanke, F., Zhang, L., Saile, S. C., Joe, A., Karelina, D., Hua, C., Fröhlich, K., Wan, W.-L., et al. (2021) · Nature · doi:10.1038/s41586-021-03829-0 · Cited by 462

The landscape and therapeutic relevance of cancer-associated transcript fusions

Yoshihara, K., Wang, Q., Torres-Garcia, W., Zheng, S., Vegesna, R., Kim, H., & Verhaak, R. G. W. (2015) · Oncogene · doi:10.1038/onc.2014.406 · Cited by 450

Targeted Next-generation Sequencing of Advanced Prostate Cancer Identifies Potential Therapeutic Targets and Disease Heterogeneity

Beltran, H., Yelensky, R., Frampton, G. M., Park, K., Downing, S. R., MacDonald, T. Y., Jarosz, M. V., Lipson, D., Tagawa, S. T., Nanus, D. M., et al. (2012) · European Urology · doi:10.1016/j.eururo.2012.08.053 · Cited by 450

The pangenome of hexaploid bread wheat

Montenegro, J. D., Golicz, A. A., Bayer, P. E., Hurgobin, B., Lee, H., Chan, C. K., Visendi, P., Lai, K., Doležel, J., Batley, J., et al. (2017) · The Plant Journal · doi:10.1111/tpj.13515 · Cited by 465

Sequence Alignment/Map format: a comprehensive review of approaches and applications

Liu, Y., Shen, X., Gong, Y., Liu, Y., Song, B., & Zeng, X. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad320 · Cited by 49

SAM/BAM format v1.5 extensions for de novo assembliesPreprint

Cock, P., Bonfield, J., Chevreux, B., & Li, H. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/020024 · Cited by 20

SAM/BAM Format

Robinson, P. M., & Hansen, P. (2017) · Chapman & Hall/CRC eBooks · doi:10.1201/9781315154770-9 · Cited by 1

Sambamba: fast processing of NGS alignment formats

Tarasov, A., Vilella, A. J., Cuppen, E. P. J. G., Nijman, I. J., & Prins, P. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv098 · Cited by 2,426

BAMnostic: an OS-agnostic toolkit for genomic sequence analysis

Sherman, M. D., & Mills, R. E. (2018) · The Journal of Open Source Software · doi:10.21105/joss.00826 · Cited by 3