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

Identification of common molecular subsequences

Smith, T. F., & Waterman, M. S. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90087-5 · Cited by 9,962

Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy AssessmentPreprint

Ewing, B., Hillier, L., Wendl, M. C., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.175 · Cited by 6,993

Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities

Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439

Accurate whole human genome sequencing using reversible terminator chemistry

Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684

SOAP: Short oligonucleotide alignment program

Li, R., Li, Y., Kristiansen, K., & Wang, J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn025 · Cited by 3,597

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

Marioni, J. C., Mason, C. E., Mane, S. M., Stephens, M., & Gilad, Y. (2008) · Genome Research · doi:10.1101/gr.079558.108 · Cited by 2,771

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

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., & Snyder, M. (2008) · Science · doi:10.1126/science.1158441 · Cited by 2,479

A Block-sorting Lossless Data Compression Algorithm

Burrows, M. T., & Wheeler, D. J. (1994) · Cited by 2,333

Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells

Guzzi, N., Cieśla, M., Ngoc, P. C. T., Lang, S., Arora, S., Dimitriou, M., Pimková, K., Sommarin, M. N. E., Munita, R., Lubas, M., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.008 · Cited by 533

Focused specificity of intestinal TH17 cells towards commensal bacterial antigens

Yang, Y., Torchinsky, M. B., Gobert, M., Xiong, H., Xu, M., Linehan, J. L., Alonzo, F., Ng, C., Chen, A., Lin, X., et al. (2014) · Nature · doi:10.1038/nature13279 · Cited by 520

Tau promotes neurodegeneration through global chromatin relaxation

Frost, B., Hemberg, M., Lewis, J., & Feany, M. B. (2014) · Nature Neuroscience · doi:10.1038/nn.3639 · Cited by 495

Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants

Pasquali, L., Gaulton, K. J., Rodríguez‐Seguí, S. A., Mularoni, L., Miguel-Escalada, I., Akerman, İ., Tena, J. J., Morán, I., Gómez-Marín, C., van de Bunt, M., et al. (2014) · Nature Genetics · doi:10.1038/ng.2870 · Cited by 521

Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma

Chen, L., Li, Y., Lin, C. H., Chan, T. H. M., Chow, R. K. K., Song, Y., Liu, M., Yuan, Y. F., Fu, L., Kong, K. L., et al. (2013) · Nature Medicine · doi:10.1038/nm.3043 · Cited by 519

Nutrient-sensing nuclear receptors coordinate autophagy

Lee, J. M., Wagner, M., Xiao, R., Kim, K. H., Feng, D., Lazar, M. A., & Moore, D. D. (2014) · Nature · doi:10.1038/nature13961 · Cited by 524

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

Changes in Transcript Abundance in Chlamydomonas reinhardtii following Nitrogen Deprivation Predict Diversion of Metabolism

Miller, R., Wu, G., Deshpande, R. R., Vieler, A., Gärtner, K., Li, X., Moellering, E. R., Zäuner, S., Cornish, A. J., Liu, B., et al. (2010) · PLANT PHYSIOLOGY · doi:10.1104/pp.110.165159 · Cited by 511

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

Hou, C., Li, L., Qin, Z. S., & Corces, V. G. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.08.031 · Cited by 525

High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9Preprint

Varshney, G. K., Pei, W., LaFave, M. C., Idol, J., Xu, L., Gallardo, V. E., Carrington, B., Bishop, K. S., Jones, M. S., Li, M., et al. (2015) · Genome Research · doi:10.1101/gr.186379.114 · Cited by 526

A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease

Mostafavi, S., Gaiteri, C., Sullivan, S. E., White, C. C., Tasaki, S., Xu, J., Taga, M., Klein, H.-U., Patrick, E., Komashko, V., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0154-9 · Cited by 509

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

KIAA1429 contributes to liver cancer progression through N6-methyladenosine-dependent post-transcriptional modification of GATA3

Lan, T., Li, H., Delin, Z., Xu, L., Liu, H., Hao, X., Yan, X., Liao, H., Chen, X., Xie, K., et al. (2019) · Molecular Cancer · doi:10.1186/s12943-019-1106-z · Cited by 509

Competition between DNA methylation and transcription factors determines binding of NRF1

Domcke, S., Bardet, A. F., Adrian Ginno, P., Hartl, D., Burger, L., & Schübeler, D. (2015) · Nature · doi:10.1038/nature16462 · Cited by 508

Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples

Adiconis, X., Borges-Rivera, D., Satija, R., DeLuca, D. S., Busby, M., Berlin, A. M., Sivachenko, A., Thompson, D. A., Wysoker, A., Fennell, T., et al. (2013) · Europe PMC (PubMed Central) · doi:10.1038/nmeth.2483 · Cited by 508

Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging

Gabriele, M., Brandão, H. B., Grosse-Holz, S., Jha, A., Dailey, G. M., Cattoglio, C., Hsieh, T.-H. S., Mirny, L., Zechner, C., & Hansen, A. S. (2022) · Science · doi:10.1126/science.abn6583 · Cited by 506

ShortStack: Comprehensive annotation and quantification of small RNA genes

Axtell, M. J. (2013) · RNA · doi:10.1261/rna.035279.112 · Cited by 514

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

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

Soldner, F., Stelzer, Y., Shivalila, C., Abraham, B. J., Latourelle, J. C., Barrasa, M. I., Goldmann, J. E., Myers, R. H., Young, R. A., & Jaenisch, R. (2016) · Nature · doi:10.1038/nature17939 · Cited by 508

Quantitative ChIP-Seq normalization reveals global modulation of the epigenome

Orlando, D. A., Chen, M. W., Brown, V. E., Solanki, S., Choi, Y. J., Olson, E. R., Fritz, C. C., Bradner, J. E., & Guenther, M. G. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.10.018 · Cited by 503

Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition

Lee, M. T., Bonneau, A. R., Takacs, C. M., Bazzini, A., Castellano, K. R., Fleming, E. S., & Giráldez, A. J. (2013) · Nature · doi:10.1038/nature12632 · Cited by 509

Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions

Han, K., Jeng, E. E., Hess, G. T., Morgens, D. W., Li, A., & Bassik, M. C. (2017) · Nature Biotechnology · doi:10.1038/nbt.3834 · Cited by 498

RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome

Treeck, B. V., Protter, D. S. W., Matheny, T., Khong, A., Link, C. D., & Parker, R. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1800038115 · Cited by 503

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

Degner, J. F., Marioni, J. C., Pai, A. A., Pickrell, J. K., Nkadori, E., Gilad, Y., & Pritchard, J. K. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp579 · Cited by 502

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

Bonn, S., Zinzen, R. P., Girardot, C., Gustafson, E. H., Perez-Gonzalez, A., Delhomme, N., Ghavi-Helm, Y., Wilczyński, B., Riddell, A., & Furlong, E. E. M. (2012) · Nature Genetics · doi:10.1038/ng.1064 · Cited by 502

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

Berka, R. M., Grigoriev, I. V., Otillar, R., Salamov, A. A., Grimwood, J., Reid, I. D., Ishmael, N., John, T., Darmond, C., Moisan, M.-C., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1976 · Cited by 508

Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza

Abbott, T. R., Dhamdhere, G. R., Liu, Y., Lin, X., Goudy, L., Zeng, L., Chemparathy, A., Chmura, S. A., Heaton, N. S., Debs, R. J., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.020 · Cited by 514

Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex

Hrvatin, S., Hochbaum, D. R., Nagy, M. A., Cicconet, M., Robertson, K., Cheadle, L., Zilionis, R., Ratner, A., Borges-Monroy, R., Klein, A. M., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-017-0029-5 · Cited by 497

Chapter 12: Human Microbiome Analysis

Morgan, X. C., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002808 · Cited by 496

MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function

Keegan, K. P., Glass, E. M., & Meyer, F. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3369-3_13 · Cited by 507

Epigenomic reprogramming during pancreatic cancer progression links anabolic glucose metabolism to distant metastasis

McDonald, O. G., Li, X., Saunders, T., Tryggvadottir, R., Mentch, S. J., Warmoes, M. O., Word, A. E., Carrer, A., Salz, T. H., Natsume, S., et al. (2017) · Nature Genetics · doi:10.1038/ng.3753 · 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

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

Zhao, Q.-Y., Wang, Y., Kong, Y.-M., Luo, D., Li, X., & Hao, P. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-s14-s2 · Cited by 479

Mettl1/Wdr4-Mediated m7G tRNA Methylome Is Required for Normal mRNA Translation and Embryonic Stem Cell Self-Renewal and Differentiation

Lin, S., Liu, Q., Lelyveld, V. S., Choe, J., Szostak, J. W., & Gregory, R. I. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.001 · Cited by 494

Pathogen Webs in Collapsing Honey Bee Colonies

Cornman, R. S., Tarpy, D. R., Chen, Y., Jeffreys, L., Lopez, D., Pettis, J. S., vanEngelsdorp, D., & Evans, J. D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043562 · Cited by 489

Efficient ablation of genes in human hematopoietic stem and effector cells using CRISPR/Cas9

Mandal, P. K., Ferreira, L. M. R., Collins, R., Meissner, T. B., Boutwell, C. L., Friesen, M., Vrbanac, V., Garrison, B. S., Stortchevoi, A., Bryder, D., et al. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.10.004 · Cited by 475

Integration of omic networks in a developmental atlas of maize

Walley, J. W., Sartor, R. C., Shen, Z., Schmitz, R. J., Wu, K. J., Urich, M. A., Nery, J. R., Smith, L. G., Schnable, J. C., Ecker, J. R., et al. (2016) · Science · doi:10.1126/science.aag1125 · Cited by 488

Retrovirus-like Gag Protein Arc1 Binds RNA and Traffics across Synaptic Boutons

Ashley, J., Cordy, B., Lucia, D., Fradkin, L. G., Budnik, V., & Thomson, T. (2018) · Cell · doi:10.1016/j.cell.2017.12.022 · Cited by 488

CRISPR/Cas9: a molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae

Mans, R., van Rossum, H. M., Wijsman, M., Backx, A. H., Kuijpers, N. G. A., van den Broek, M. A., Daran-Lapujade, P. A. S., Pronk, J. T., van Maris, A. J. A., & Daran, J.-M. G. (2015) · FEMS Yeast Research · doi:10.1093/femsyr/fov004 · Cited by 486

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

Searching for SNPs with cloud computing

Langmead, B., Schatz, M. C., Lin, J., Pop, M., & Salzberg, S. L. (2009) · Genome biology · doi:10.1186/gb-2009-10-11-r134 · Cited by 490

Sox4 Is a Master Regulator of Epithelial-Mesenchymal Transition by Controlling Ezh2 Expression and Epigenetic Reprogramming

Tiwari, N., Tiwari, V. K., Waldmeier, L., Balwierz, P. J., Arnold, P., Pachkov, M. V., Meyer‐Schaller, N., Schübeler, D., van Nimwegen, E., & Christofori, G. (2013) · Cancer Cell · doi:10.1016/j.ccr.2013.04.020 · Cited by 494

Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism

Fadista, J., Vikman, P. J., Ottosson-Laakso, E., Mollet, I. G., Esguerra, J. L. S., Taneera, J., Storm, P., Osmark, P., Ladenvall, C., Prasad, R. B., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1402665111 · Cited by 480

Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry

Xu, L., Zhu, L., Tu, L., Liu, L., Yuan, D., Jin, L., Long, L., & Zhang, X. (2011) · Journal of Experimental Botany · doi:10.1093/jxb/err245 · Cited by 485

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

Jan, C. H., Friedman, R. C., Ruby, J. G., & Bartel, D. P. (2010) · Nature · doi:10.1038/nature09616 · Cited by 485

PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression.

Liu, W., Tanasa, B., Tyurina, O. V., Zhou, T. Y., Gassmann, R., Liu, W. T., Ohgi, K. A., Benner, C., Garcia-Bassets, I., Aggarwal, A. K., et al. (2010) · Nature · doi:10.1038/nature09272 · Cited by 441

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonizationPreprint

Sharon, I., Morowitz, M. J., Thomas, B. C., Costello, E. K., Relman, D. A., & Banfield, J. F. (2012) · Genome Research · doi:10.1101/gr.142315.112 · Cited by 481

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

eIF5A Functions Globally in Translation Elongation and Termination

Schuller, A. P., Wu, C. C., Dever, T. E., Buskirk, A. R., & Green, R. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.03.003 · Cited by 489

Comprehensive serological profiling of human populations using a synthetic human virome

Xu, G. J., Kula, T., Xu, Q., Li, M. Z., Vernon, S. D., Ndung’u, T., Ruxrungtham, K., Sánchez, J., Brander, C., Chung, R. T., et al. (2015) · Science · doi:10.1126/science.aaa0698 · Cited by 487

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice

Olsson, A., Venkatasubramanian, M., Chaudhri, V. K., Aronow, B. J., Salomonis, N., Singh, H., & Grimes, H. L. (2016) · Nature · doi:10.1038/nature19348 · Cited by 476

A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics

Rapicavoli, N. A., Qu, K., Zhang, J., Mikhail, M. E., Laberge, R.-M., & Chang, H. Y. (2013) · eLife · doi:10.7554/elife.00762 · Cited by 482

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

Vonk, F. J., Casewell, N. R., Henkel, C. V., Heimberg, A. M., Jansen, H. J., McCleary, R. J. R., Kerkkamp, H. M. I., Vos, R. A., Guerreiro, I. M., Calvete, J. J., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1314702110 · Cited by 487

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

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

Fabbro, C. D., Scalabrin, S., Morgante, M., & Giorgi, F. M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0085024 · Cited by 478

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

Hughes, J. R., Roberts, N., McGowan, S., Hay, D., Giannoulatou, E., Lynch, M., De Gobbi, M., Taylor, S., Gibbons, R., & Higgs, D. R. (2014) · Nature Genetics · doi:10.1038/ng.2871 · Cited by 461

Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver

Rey, G., Cesbron, F., Rougemont, J., Reinke, H., Brunner, M., & Naef, F. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000595 · Cited by 490

Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons

Wetmore, K. M., Price, M. N., Waters, R. J., Lamson, J. S., He, J., Hoover, C. A., Blow, M. J., Bristow, J. D., Butland, G. P., Arkin, A. P., et al. (2015) · mBio · doi:10.1128/mbio.00306-15 · Cited by 480

KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands

Farcas, A. M., Blackledge, N. P., Sudbery, I. M., Long, H. K., McGouran, J. F., Rose, N. R., Lee, S., Sims, D., Cerase, A., Sheahan, T. W., et al. (2012) · eLife · doi:10.7554/elife.00205 · Cited by 502

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

Zabidi, M. A., Arnold, C. D., Schernhuber, K., Pagani, M., Rath, M., Frank, O., & Stark, A. (2015) · Nature · doi:10.1038/nature13994 · Cited by 471

The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis

Pomerantz, M. M., Li, F., Takeda, D. Y., Lenci, R., Chonkar, A., Chabot, M., Cejas, P., Vazquez, F., Cook, J., Shivdasani, R. A., et al. (2015) · Nature Genetics · doi:10.1038/ng.3419 · Cited by 470

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

Hon, G. C., Rajagopal, N., Shen, Y., McCleary, D. F., Yue, F., Dang, M. D., & Ren, B. (2013) · Nature Genetics · doi:10.1038/ng.2746 · Cited by 477

Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease

Dubinkina, V. B., Tyakht, A., Odintsova, V. Y., Yarygin, K. S., Kovarsky, B. A., Pavlenko, A. V., Ischenko, D. S., Popenko, A., Alexeev, D. G., Taraskina, A. Y., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0359-2 · Cited by 472

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

Marinov, G. K., Williams, B. A., McCue, K., Schroth, G. P., Gertz, J., Myers, R. M., & Wold, B. J. (2014) · Genome Research · doi:10.1101/gr.161034.113 · Cited by 468

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

Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs

Zhang, Y., Zhang, X., Shi, J., Tuorto, F., Li, X., Liu, Y., Liebers, R., Zhang, L., Qu, Y., Qian, J., et al. (2018) · Nature Cell Biology · doi:10.1038/s41556-018-0087-2 · Cited by 468

High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer

Grosselin, K., Durand, A., Marsolier, J., Poitou, A., Marangoni, E., Nemati, F., Dahmani, A., Lameiras, S., Reyal, F., Frenoy, O., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0424-9 · Cited by 466

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

Zarnack, K., König, J., Tajnik, M., Martincorena, I., Eustermann, S., Stévant, I., Reyes, A., Anders, S., Luscombe, N. M., & Ule, J. (2013) · Cell · doi:10.1016/j.cell.2012.12.023 · Cited by 477

BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment

Winter, G. E., Mayer, A., Buckley, D. L., Erb, M. A., Roderick, J. E., Vittori, S., Reyes, J. M., di Iulio, J., Souza, A., Ott, C. J., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.06.004 · Cited by 465

Annotating non-coding regions of the genome.

Alexander, R. P., Fang, G., Rozowsky, J., Snyder, M., & Gerstein, M. B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2814 · Cited by 464

Noninvasive Prenatal Testing and Incidental Detection of Occult Maternal Malignancies

Bianchi, D. W., Chudova, D. I., Sehnert, A. J., Bhatt, S., Murray, K. A., Prosen, T. L., Garber, J. E., Wilkins-Haug, L. E., Vora, N. L., Warsof, S., et al. (2015) · JAMA · doi:10.1001/jama.2015.7120 · Cited by 463

Widespread RNA and DNA Sequence Differences in the Human Transcriptome

Li, M., Wang, I. X., Li, Y., Bruzel, A., Richards, A. L., Toung, J. M., & Cheung, V. G. (2011) · Science · doi:10.1126/science.1207018 · Cited by 462

BATF–JUN is critical for IRF4-mediated transcription in T cells

Li, P., Spolski, R. J., Liao, W., Wang, L., Murphy, T. L., MURPHY, K. M. M., & Leonard, W. J. (2012) · Nature · doi:10.1038/nature11530 · Cited by 467

High-density lipoprotein mediates anti-inflammatory reprogramming of macrophages via the transcriptional regulator ATF3

Nardo, D. D., Labzin, L. I., Kono, H., Seki, R., Schmidt, S. V., Beyer, M., Xu, D., Zimmer, S., Lahrmann, C., Schildberg, F. A., et al. (2013) · Nature Immunology · doi:10.1038/ni.2784 · Cited by 477

15 years of GDR: New data and functionality in the Genome Database for Rosaceae

Jung, S., Lee, T., Cheng, C.-H., Buble, K., Zheng, P., Yu, J., Humann, J. L., Ficklin, S. P., Gašić, K., Scott, K. A., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1000 · Cited by 469

Polyploidy can drive rapid adaptation in yeast

Selmecki, A. M., Maruvka, Y. E., Richmond, P. A., Guillet, M., Shoresh, N., Sorenson, A. L., De, S., Kishony, R., Michor, F., Dowell, R. D., et al. (2015) · Nature · doi:10.1038/nature14187 · Cited by 456

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

Makarevitch, I., Waters, A. J., West, P. T., Stitzer, M. C., Hirsch, C. N., Ross‐Ibarra, J., & Springer, N. M. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1004915 · Cited by 474

Massively parallel Cas13 screens reveal principles for guide RNA design

Wessels, H.-H., Méndez-Mancilla, A., Guo, X., Legut, M., Daniloski, Z., & Sanjana, N. E. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0456-9 · Cited by 418

Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements

De Cecco, M., Criscione, S. W., Peckham, E. J., Hillenmeyer, S., Hamm, E. A., Manivannan, J., Peterson, A. L., Kreiling, J. A., Neretti, N., & Sedivy, J. M. (2013) · Aging Cell · doi:10.1111/acel.12047 · Cited by 459

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

The genetic and epigenetic landscape of the Arabidopsis centromeres

Naish, M., Alonge, M., Włodzimierz, P., Tock, A. J., Abramson, B. W., Schmücker, A., Mandáková, T. M., Jamge, B., Lambing, C., Kuo, P. C., et al. (2021) · Science · doi:10.1126/science.abi7489 · Cited by 444

Genome sequence of the progenitor of wheat A subgenome Triticum urartu

Ling, H., Ma, B., Shi, X., Liu, H., Dong, L., Sun, H., Cao, Y., Gao, Q., Zheng, S., Li, Y., et al. (2018) · Nature · doi:10.1038/s41586-018-0108-0 · Cited by 455

Latest Developed Strategies to Minimize the Off-Target Effects in CRISPR-Cas-Mediated Genome Editing

Naeem, M., Majeed, S., Hoque, M. Z., & Ahmad, I. (2020) · Cells · doi:10.3390/cells9071608 · Cited by 457

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

Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

Luo, C., Tsementzi, D., Kyrpides, N., Read, T., & Konstantinidis, K. T. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030087 · Cited by 337

Akt-mTORC1 signaling regulates Acly to integrate metabolic input to control of macrophage activation

Covarrubias, A. J., Aksoylar, H., Yu, J., Snyder, N. W., Worth, A. J., Iyer, S. S., Wang, J., Ben‐Sahra, I., Byles, V., Polynne-Stapornkul, T., et al. (2016) · eLife · doi:10.7554/elife.11612 · Cited by 469

Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells

Guenther, M. G., Frampton, G. M., Soldner, F., Hockemeyer, D., Mitalipova, M., Jaenisch, R., & Young, R. A. (2010) · Cell Stem Cell · doi:10.1016/j.stem.2010.06.015 · Cited by 456

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

Klambauer, G., Schwarzbauer, K., Mayr, A., Clevert, D.-A., Mitterecker, A., Bodenhofer, U., & Hochreiter, S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks003 · Cited by 454

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

Chromosome and gene copy number variation allow major structural change between species and strains of LeishmaniaPreprint

Rogers, M. B., Hilley, J. D., Dickens, N. J., Wilkes, J., Bates, P. A., Depledge, D. P., Harris, D., Her, Y., Herzyk, P., Imamura, H., et al. (2011) · Genome Research · doi:10.1101/gr.122945.111 · Cited by 448

Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq

Treutlein, B., Lee, Q. Y., Camp, J. G., Mall, M., Koh, W. L. C., Shariati, S. A., Sim, S., Neff, N. F., Skotheim, J. M., Wernig, M., et al. (2016) · Nature · doi:10.1038/nature18323 · Cited by 442

An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome

Ng, B., White, C. C., Klein, H.-U., Sieberts, S. K., McCabe, C., Patrick, E., Xu, J., Yu, L., Gaiteri, C., Bennett, D. A., et al. (2017) · Nature Neuroscience · doi:10.1038/nn.4632 · Cited by 452

Impact of delivery mode-associated gut microbiota dynamics on health in the first year of life

Reyman, M., van Houten, M. A., van Baarle, D., Bosch, A. A. T. M., Man, W. H., Chu, M. L. J. N., Arp, K., Watson, R. L., Sanders, E. A. M., Fuentes, S., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13014-7 · Cited by 477

NOX4 inhibition potentiates immunotherapy by overcoming cancer-associated fibroblast-mediated CD8 T-cell exclusion from tumors

Ford, K., Hanley, C. J., Mellone, M., Szyndralewiez, C., Heitz, F., Wiesel, P., Wood, O., Machado, M., Lopez, M.-A., Ganesan, A.-P., et al. (2020) · Cancer Research · doi:10.1158/0008-5472.can-19-3158 · Cited by 411

Deep RNA Sequencing Reveals Dynamic Regulation of Myocardial Noncoding RNAs in Failing Human Heart and Remodeling With Mechanical Circulatory Support

Yang, K., Yamada, K. A., Patel, A., Topkara, V. K., George, I., Cheema, F. H., Ewald, G. A., Mann, D. L., & Nerbonne, J. M. (2014) · Circulation · doi:10.1161/circulationaha.113.003863 · Cited by 453

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

Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing

Hovestadt, V., Jones, D., Picelli, S., Wang, W., Kool, M., Northcott, P. A., Sultan, M., Stachurski, K., Ryzhova, M. V., Warnatz, H.-J., et al. (2014) · Nature · doi:10.1038/nature13268 · Cited by 452

Regulation of m6A Transcripts by the 3ʹ→5ʹ RNA Helicase YTHDC2 Is Essential for a Successful Meiotic Program in the Mammalian Germline

Wojtas, M. N., Pandey, R. R., Mendel, M., Homolka, D., Sachidanandam, R., & Pillai, R. S. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.09.021 · Cited by 459

PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants

Chow, C.-N., Lee, T.-Y., Hung, Y.-C., Li, G.-Z., Tseng, K.-C., Liu, Y.-H., Kuo, P.-L., Zheng, H.-Q., & Chang, W. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1081 · Cited by 439

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce

Reyes-Chin-Wo, S., Wang, Z., Yang, X., Kozik, A., Arikit, S., Song, C., Xia, L., Froenicke, L., Lavelle, D. O., Truco, M. J., et al. (2017) · Nature Communications · doi:10.1038/ncomms14953 · Cited by 450

Transformation of a text T,

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2015)

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400

SOAP2: an improved ultrafast tool for short read alignment

Li, R., Yu, C., Li, Y., Lam, T., Yiu, S., Kristiansen, K., & Wang, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp336 · Cited by 3,763

Fast and memory efficient approach for mapping NGS reads to a reference genome

Kumar, S., Agarwal, S., & Ranvijay (2019) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720019500082 · Cited by 27

Fast and accurate long-read alignment with Burrows-Wheeler transform.

Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063