BLAST+: architecture and applications

Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302

<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool

Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480

Initial sequencing and comparative analysis of the mouse genome

Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187

A Greedy Algorithm for Aligning DNA Sequences

Zhang, Z., Schwartz, S., Wagner, L., & Miller, W. (2000) · Journal of Computational Biology · doi:10.1089/10665270050081478 · Cited by 5,459

NCBI BLAST: a better web interface

Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., & Madden, T. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn201 · Cited by 4,207

Database indexing for production MegaBLAST searches

Morgulis, A. O., Coulouris, G., Raytselis, Y., Madden, T., Agarwala, R., & Schäffer, A. A. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn322 · Cited by 1,395

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements

Schäffer, A. A. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.14.2994 · Cited by 1,375

[33] Analysis of compositionally biased regions in sequence databases

Wootton, J. C., & Federhen, S. (1996) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(96)66035-2 · Cited by 745

A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences

Morgulis, A. O., Gertz, E. M., Schäffer, A. A., & Agarwala, R. (2006) · Journal of Computational Biology · doi:10.1089/cmb.2006.13.1028 · Cited by 498

Rapid Evolution of Enormous, Multichromosomal Genomes in Flowering Plant Mitochondria with Exceptionally High Mutation Rates

Sloan, D. B., Alverson, A. J., Chuckalovcak, J. P., Wu, M., McCauley, D. E., Palmer, J. D., & TAYLOR, D. R. (2012) · PLoS Biology · doi:10.1371/journal.pbio.1001241 · Cited by 769

High speed BLASTN: an accelerated MegaBLAST search tool

Chen, Y., Ye, W., Zhang, Y., & Xu, Y. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv784 · Cited by 768

Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol

Elbrecht, V., & Leese, F. (2015) · PLOS ONE · doi:10.1371/journal.pone.0130324 · Cited by 765

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

Schmieder, R., & Edwards, R. A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017288 · Cited by 765

The genome sequence of segmental allotetraploid peanut Arachis hypogaea

Bertioli, D. J., Jenkins, J. W., Clevenger, J. P., Dudchenko, O., Gao, D., Seijo, G. R., Leal‐Bertioli, S. C. M., Ren, L., Farmer, A. D., Pandey, M. K., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0405-z · Cited by 758

Coronavirus Disease 2019 (COVID-19) Re-infection by a Phylogenetically Distinct Severe Acute Respiratory Syndrome Coronavirus 2 Strain Confirmed by Whole Genome Sequencing

To, K. K.-W., Hung, I. F.-N., Ip, J. D., Chu, A. W.-H., Chan, W.-M., Tam, A. R., Fong, C. H.-Y., Yuan, S., Tsoi, H.-W., Ng, A. C.-K., et al. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa1275 · Cited by 746

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

Gao, L., Gonda, I., Sun, H., Ma, Q., Bao, K., Tieman, D. M., Burzynski-Chang, E. A., Fish, T. L., Stromberg, K. A., Sacks, G. L., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0410-2 · Cited by 743

The genome of Chenopodium quinoa

Jarvis, D. E., Ho, Y. S., Lightfoot, D. J., Schmöckel, S. M., Li, B., Borm, T. J. A., Ohyanagi, H., Mineta, K., Michell, C., Saber, N., et al. (2017) · Nature · doi:10.1038/nature21370 · Cited by 737

WormBase ParaSite − a comprehensive resource for helminth genomics

Howe, K., Bolt, B. J., Shafie, M., Kersey, P. J., & Berriman, M. (2016) · Molecular and Biochemical Parasitology · doi:10.1016/j.molbiopara.2016.11.005 · Cited by 718

Whole-Genome Annotation with BRAKER

Hoff, K. J., Lomsadze, A., Borodovsky, M. Y., & Stanke, M. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9173-0_5 · Cited by 713

MetaQUAST: evaluation of metagenome assemblies

Mikheenko, A., Saveliev, V., & Gurevich, A. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btv697 · Cited by 711

Origin and evolution of the octoploid strawberry genome

Edger, P. P., Poorten, T. J., VanBuren, R., Hardigan, M. A., Colle, M., McKain, M. R., Smith, R. D., Teresi, S. J., Nelson, A. D. L., Wai, C. M., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0356-4 · Cited by 705

The global distribution and spread of the mobilized colistin resistance gene mcr-1

Wang, R., van Dorp, L., Shaw, L. P., Bradley, P., Wang, Q., Wang, X., Jin, L., Zhang, Q., Liu, Y., Rieux, A., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03205-z · Cited by 703

ResFinder–an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes

Florensa, A. F., Kaas, R. S., Clausen, P. T. L. C., Aytan-Aktug, D., & Aarestrup, F. M. (2022) · Microbial Genomics · doi:10.1099/mgen.0.000748 · Cited by 695

Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins

Klemm, E. J., Shakoor, S., Page, A. J., Qamar, F. N., Judge, K., Saeed, D. K., Wong, V., Dallman, T. J., Nair, S., Baker, S. G., et al. (2018) · mBio · doi:10.1128/mbio.00105-18 · Cited by 676

Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival

Greening, C., Biswas, A., Carere, C. R., Jackson, C. J., Taylor, M. C., Stott, M. B., Cook, G. M., & Morales, S. E. (2015) · The ISME Journal · doi:10.1038/ismej.2015.153 · Cited by 671

VICTOR: genome-based phylogeny and classification of prokaryotic viruses

Meier‐Kolthoff, J. P., & Göker, M. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx440 · Cited by 674

A beginner’s guide to eukaryotic genome annotation

Yandell, M., & Ence, D. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3174 · Cited by 588

Improved metagenome binning and assembly using deep variational autoencoders

Nissen, J. N., Johansen, J., Allesøe, R. L., Sønderby, C. K., Armenteros, J. J. A., Grønbech, C. H., Jensen, L. J., Nielsen, H. B., Petersen, T. N., Winther, O., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-00777-4 · Cited by 663

Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods

Haas, B. J., Dobin, A., Li, B., Stransky, N., Pochet, N., & Regev, A. (2019) · Genome biology · doi:10.1186/s13059-019-1842-9 · Cited by 646

Isolation of an archaeon at the prokaryote–eukaryote interface

Imachi, H., Nobu, M. K., Nakahara, N., Morono, Y., Ogawara, M., Takaki, Y., Takano, Y., Uematsu, K., Ikuta, T., Ito, M., et al. (2020) · Nature · doi:10.1038/s41586-019-1916-6 · Cited by 624

The evolution and genomic basis of beetle diversity

McKenna, D. D., Shin, S., AHRENS, D. C., Balke, M., Beza-Beza, C., Clarke, D., Donath, A., Escalona, H. E., Friedrich, F., Letsch, H. O., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1909655116 · Cited by 625

PhyloSift: phylogenetic analysis of genomes and metagenomes

Darling, A. E., Jospin, G., Lowe, E., Matsen, F. A., IV, Bik, H. M., & Eisen, J. A. (2014) · PeerJ · doi:10.7717/peerj.243 · Cited by 625

Spatial organization of chromatin domains and compartments in single chromosomes

Wang, S., Su, J.-H., Beliveau, B. J., Bintu, B., Moffitt, J. R., Wu, C.-T., & Zhuang, X. (2016) · Science · doi:10.1126/science.aaf8084 · Cited by 617

The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies

Yoshida, C., Kruczkiewicz, P., Laing, C., Lingohr, E. J., Gannon, V. P. J., Nash, J. J., & Taboada, E. N. (2016) · PLoS ONE · doi:10.1371/journal.pone.0147101 · Cited by 617

Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades

Youngblut, N. D., Reischer, G. H., Walters, W. A., Schuster, N., Walzer, C., Stalder, G. L., Ley, R. E., & Farnleitner, A. H. (2019) · Nature Communications · doi:10.1038/s41467-019-10191-3 · Cited by 611

Untitled work

van der Ven (2019) · doi:10.12688/f1000research · Cited by 599

A review of methods and databases for metagenomic classification and assembly

Breitwieser, F. P., Lu, J., & Salzberg, S. L. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx120 · Cited by 595

Biosynthesis of Antinutritional Alkaloids in Solanaceous Crops Is Mediated by Clustered Genes

Itkin, M., Heinig, U., Tzfadia, O., Bhide, A. J., Shinde, B. A., Cárdenas, P. D., Bocobza, S. E., Unger, T., Malitsky, S., Finkers, R., et al. (2013) · Science · doi:10.1126/science.1240230 · Cited by 592

Subsistence strategies in traditional societies distinguish gut microbiomes

Obregon-Tito, A. J., Tito, R. Y., Metcalf, J., Sankaranarayanan, K., Clemente, J. C., Ursell, L. K., Zech Xu, Z., Van Treuren, W., Knight, R., Gaffney, P. M., et al. (2015) · Nature Communications · doi:10.1038/ncomms7505 · Cited by 587

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., Novak, A. M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., et al. (2020) · Nature · doi:10.1038/s41586-020-2871-y · Cited by 586

Design of a synthetic yeast genome

Richardson, S. M., MITCHELL, L. A., Stracquadanio, G., Yang, K., Dymond, J. S., DiCarlo, J. E., Lee, D., Huang, C. L. V., Chandrasegaran, S., Cai, Y., et al. (2017) · Science · doi:10.1126/science.aaf4557 · Cited by 589

New CRISPR–Cas systems from uncultivated microbes

Burstein, D. E., Harrington, L. B., Strutt, S. C., Probst, A. J., Anantharaman, K., Thomas, B. C., Doudna, J. A., & Banfield, J. F. (2016) · Nature · doi:10.1038/nature21059 · Cited by 583

Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome

Nayfach, S., Páez-Espino, D., Call, L., Low, S. J., Sberro, H., Ivanova, N. N., Proal, A. D., Fischbach, M. A., Bhatt, A. S., Hugenholtz, P., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00928-6 · Cited by 580

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

Chun, J., & Rainey, F. A. (2014) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.054171-0 · Cited by 580

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

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

Database resources of the National Center for Biotechnology Information

Sayers, E. W., Agarwala, R., Bolton, E., Brister, J. R., Canese, K., Clark, K., Connor, R. P., Fiorini, N., Funk, K., Hefferon, T. W., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1069 · Cited by 576

Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28

Smargon, A. A., Cox, D. B. T., Pyzocha, N. K., Zheng, K., Slaymaker, I. M., Gootenberg, J. S., Abudayyeh, O. A., Essletzbichler, P., Shmakov, S., Makarova, K. S., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2016.12.023 · Cited by 575

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

Moffitt, J. R., Hao, J., Wang, G., Chen, K. H., Babcock, H. P., & Zhuang, X. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1612826113 · Cited by 568

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

Su, J.-H., Zheng, P., Kinrot, S. S., Bintu, B., & Zhuang, X. (2020) · Cell · doi:10.1016/j.cell.2020.07.032 · Cited by 562

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

Stewart, R. D., Auffret, M. D., Warr, A., Wiser, A. H., Press, M. O., Langford, K. W., Liachko, I., Snelling, T. J., Dewhurst, R. J., Walker, A. W., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03317-6 · Cited by 559

The pangenome of an agronomically important crop plant Brassica oleracea

Golicz, A. A., Bayer, P. E., Barker, G. C., Edger, P. P., Kim, H. R., Martinez, P. A., Chan, C. K., Severn‐Ellis, A. A., McCombie, W. R., Parkin, I. A. P., et al. (2016) · Nature Communications · doi:10.1038/ncomms13390 · Cited by 553

The Gut Microbiota in Prediabetes and Diabetes: A Population-Based Cross-Sectional Study

Wu, H., Tremaroli, V., Schmidt, C., Lundqvist, A., Olsson, L. M., Kramer, M. M., Gummesson, A., Perkins, R., Bergström, G. M. L., & Bäckhed, F. (2020) · Cell Metabolism · doi:10.1016/j.cmet.2020.06.011 · Cited by 545

amoA ‐based consensus phylogeny of ammonia‐oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions

Pester, M., Rattei, T., Flechl, S., Gröngröft, A., Richter, A. A., Overmann, J., Reinhold‐Hurek, B., Loy, A., & Wagner, M. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02666.x · Cited by 542

GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins

Brůna, T., Lomsadze, A., & Borodovsky, M. Y. (2020) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaa026 · Cited by 557

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

Lücking, R., Aime, M. C., Robbertse, B., Miller, A. N., Ariyawansa, H. A., Aoki, T., Cardinali, G., Crous, P. W., Druzhinina, I. S., Geiser, D. M., et al. (2020) · IMA Fungus · doi:10.1186/s43008-020-00033-z · Cited by 541

Preventing mussel adhesion using lubricant-infused materials

Amini, S., Kolle, S., Petrone, L., Ahanotu, O., Sunny, S., Sutanto, C. N., Hoon, S. S., Cohen, L. A., Weaver, J. C., Aizenberg, J., et al. (2017) · Science · doi:10.1126/science.aai8977 · Cited by 539

PANNZER2: a rapid functional annotation web server

Törönen, P., Medlar, A. J., & Holm, L. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky350 · Cited by 539

Identification of Klebsiella capsule synthesis loci from whole genome data

Wyres, K. L., Wick, R. R., Gorrie, C. L., Jenney, A. W. J., Follador, R., Thomson, N. R., & Holt, K. E. (2016) · Microbial Genomics · doi:10.1099/mgen.0.000102 · Cited by 536

Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution

Cheng, S., Xian, W., Fu, Y., Marin, B., Keller, J., Wu, T., Sun, W., Li, X., Xu, Y., Zhang, Y., et al. (2019) · Cell · doi:10.1016/j.cell.2019.10.019 · Cited by 528

Computational approaches to natural product discovery

Medema, M. H., & Fischbach, M. A. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1884 · Cited by 519

Genomic Diversity of Severe Acute Respiratory Syndrome–Coronavirus 2 in Patients With Coronavirus Disease 2019

Shen, Z., Xiao, Y., Kang, L., Ma, W., Shi, L., Zhang, L., Zhou, Z., Yang, J., Zhong, J., Yang, D., et al. (2020) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa203 · Cited by 513

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

Lagkouvardos, I., Pukall, R., Abt, B., Foesel, B. U., Meier‐Kolthoff, J. P., Kumar, N., Bresciani, A., Martínez, I., Just, S., Ziegler, C., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.131 · Cited by 510

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

Hördt, A., López, M. G., Meier‐Kolthoff, J. P., Schleuning, M., Weinhold, L.-M., Tindall, B. J., Gronow, S., Kyrpides, N. C., Woyke, T., & Göker, M. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00468 · Cited by 510

Identification of Novel Mobilized Colistin Resistance Gene mcr-9 in a Multidrug-Resistant, Colistin-Susceptible Salmonella enterica Serotype Typhimurium Isolate

Carroll, L. M., Gaballa, A., Guldimann, C., Sullivan, G., Henderson, L. O., & Wiedmann, M. (2019) · mBio · doi:10.1128/mbio.00853-19 · Cited by 506

Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome

Song, Z., Cai, Y., Lao, X., Wang, X., Lin, X., Cui, Y., Kalavagunta, P. K., Liao, J., Jin, L., Shang, J., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0628-3 · Cited by 505

Rapid and sensitive detection of genome contamination at scale with FCS-GX

Astashyn, A., Tvedte, E. S., Sweeney, D., Sapojnikov, V., Bouk, N., Joukov, V., Mozes, E., Strope, P. K., Sylla, P. M., Wagner, L., et al. (2024) · Genome biology · doi:10.1186/s13059-024-03198-7 · Cited by 502

Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes

Skippington, E., Barkman, T. J., Rice, D. W., & Palmer, J. D. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1504491112 · Cited by 499

Chapter 12: Human Microbiome Analysis

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

RefSeq microbial genomes database: new representation and annotation strategy

Tatusova, T. A., Ciufo, S. A., Fedorov, B., O’Neill, K. E., & Tolstoy, I. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1274 · Cited by 495

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

A microbial supply chain for production of the anti-cancer drug vinblastine

Zhang, J., Hansen, L. G., Gudich, O., Viehrig, K., Lassen, L. M. M., Schrübbers, L. C., Adhikari, K. B., Rubaszka, P., Carrasquer-Alvarez, E., Chen, L., et al. (2022) · Nature · doi:10.1038/s41586-022-05157-3 · Cited by 491

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

Sun, P., Jiao, B., Yang, Y. P., Shan, L., Li, T., Li, X., Xi, Z., Wang, X., & Liu, J. (2022) · Molecular Plant · doi:10.1016/j.molp.2022.10.018 · Cited by 490

Metabolism of Oligosaccharides and Starch in Lactobacilli: A Review

Gänzle, M. G., & Follador, R. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00340 · Cited by 492

The natural history of cutaneous propionibacteria, and reclassification of selected species within the genus Propionibacterium to the proposed novel genera Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov.

Scholz, C. F. P., & Kilian, M. (2016) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.001367 · Cited by 489

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

ICEberg 2.0: an updated database of bacterial integrative and conjugative elements

Liu, M., Li, X., Xie, Y., Bi, D., Sun, J., Li, J., Tai, C., Deng, Z., & Ou, H. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1123 · Cited by 483

Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea

Yamamoto, S., Masuda, R., Sato, Y., Sado, T., Araki, H., Kondoh, M., Minamoto, T., & Miya, M. U. (2017) · Scientific Reports · doi:10.1038/srep40368 · Cited by 484

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

iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria

Roux, S., Camargo, A. P., Coutinho, F. H., Dabdoub, S. M., Dutilh, B. E., Nayfach, S., & Tritt, A. (2023) · PLoS Biology · doi:10.1371/journal.pbio.3002083 · Cited by 493

PLSDB: a resource of complete bacterial plasmids

Galata, V., Fehlmann, T., Backes, C., & Keller, A. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1050 · Cited by 469

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

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

Chen, Z. J., Sreedasyam, A., Ando, A., Song, Q., Santiago, L. M. D., Hulse‐Kemp, A. M., Ding, M., Ye, W., Kirkbride, R. C., Jenkins, J. W., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0614-5 · Cited by 471

Computational approaches to predict bacteriophage–host relationships

Edwards, R. A., McNair, K., Faust, K., Raes, J., & Dutilh, B. E. (2015) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuv048 · Cited by 466

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

Cas13d Is a Compact RNA-Targeting Type VI CRISPR Effector Positively Modulated by a WYL-Domain-Containing Accessory Protein

Yan, W. X., Chong, S., Zhang, H., Makarova, K. S., Koonin, E. V., Cheng, D. R., & Scott, D. A. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.02.028 · Cited by 463

Microplastic bacterial communities in the Bay of Brest: Influence of polymer type and size

Frère, L., Maignien, L., Chalopin, M., Huvet, A., Rinnert, E., Morrison, H. G., Kerninon, S., Cassone, A.-L., Christophe Lambert, B., Réveillaud, J., et al. (2018) · Environmental Pollution · doi:10.1016/j.envpol.2018.07.023 · Cited by 463

Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

Port, J. A., O’Donnell, J. L., Romero‐Maraccini, O. C., Leary, P. R., Litvin, S. Y., Nickols, K. J., Yamahara, K. M., & Kelly, R. P. (2015) · Molecular Ecology · doi:10.1111/mec.13481 · Cited by 462

Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome

Mars, R. A. T., Yang, Y., Ward, T., Houtti, M., Priya, S., Lekatz, H. R., Tang, X., Sun, Z., Kalari, K. R., Korem, T., et al. (2020) · Cell · doi:10.1016/j.cell.2020.08.007 · Cited by 456

SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations

Hooper, C. M., Castleden, I. R., Tanz, S. K., Aryamanesh, N., & Millar, A. H. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1041 · Cited by 452

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

Schwager, E. E., Sharma, P. P., Clarke, T. H., Leite, D. J., Wierschin, T., Pechmann, M., Akiyama‐Oda, Y., Esposito, L. A., Bechsgaard, J., Bilde, T., et al. (2017) · BMC Biology · doi:10.1186/s12915-017-0399-x · Cited by 451

Identification of protein secretion systems in bacterial genomes

Abby, S. S., Cury, J., Guglielmini, J., Néron, B., Touchon, M., & Rocha, E. P. C. (2016) · Scientific Reports · doi:10.1038/srep23080 · Cited by 451

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Salazar, G., Paoli, L., Alberti, A., Huerta‐Cepas, J., Ruscheweyh, H., Miguelangel Cuenca, V., Field, C. M., Coelho, L. P., Cruaud, C., Engelen, S., et al. (2019) · Cell · doi:10.1016/j.cell.2019.10.014 · Cited by 448

Discovery of antimicrobial peptides in the global microbiome with machine learning

Júnior, C. D. S., Torres, M. D. T., Duan, Y., del Río, Á. R., Schmidt, T., Chong, H., Fullam, A., Kuhn, M., Zhu, C., Houseman, A., et al. (2024) · Cell · doi:10.1016/j.cell.2024.05.013 · Cited by 460

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

Chen, L., Qiu, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Bibi, F., Yang, Y., Wang, J., Nie, W., et al. (2019) · Science · doi:10.1126/science.aav6202 · Cited by 441

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Yates, A. D., Allen, J., Amode, R., Azov, A. G., Barba, M., Becerra, A., Bhai, J. N. N. T., Campbell, L. I., Martinez, M. C., Chakiachvili, M., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1007 · Cited by 440

Cell type transcriptome atlas for the planarian Schmidtea mediterranea

Fincher, C. T., Wurtzel, O., de Hoog, T., Kravarik, K. M., & Reddien, P. W. (2018) · Science · doi:10.1126/science.aaq1736 · Cited by 436

Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data

Zhang, S., Yin, Y., Jones, M. B., Zhang, Z., Kaiser, B. L. D., Dinsmore, B. A., Fitzgerald, C., Fields, P. I., & Deng, X. (2015) · Journal of Clinical Microbiology · doi:10.1128/jcm.00323-15 · Cited by 432

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)

Lamichhaney, S., Fan, G., Widemo, F., Gunnarsson, U., Schwochow, D., Hoeppner, M. P., Kerje, S., Gustafson, U., Shi, C., Zhang, H., et al. (2015) · Nature Genetics · doi:10.1038/ng.3430 · Cited by 431

ECOD: an evolutionary classification of protein domains

Cheng, H., Schaeffer, R. D., Liao, Y., Kinch, L. N., Pei, J., Shi, S., Kim, B.-H., & Grishin, N. V. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003926 · Cited by 426

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

Wang, Z., Pascual‐Anaya, J., Zadissa, A., Li, W., Niimura, Y., Huang, Z., Li, C., White, S., Xiong, Z., Fang, D., et al. (2013) · Nature Genetics · doi:10.1038/ng.2615 · Cited by 425

Comprehensive description of blood microbiome from healthy donors assessed by 16 S targeted metagenomic sequencing

Païssé, S., Valle, C., Servant, F., Courtney, M., Burcelin, R., Amar, J., & Lelouvier, B. (2016) · Transfusion · doi:10.1111/trf.13477 · Cited by 431

Database resources of the National Center for Biotechnology Information

Sayers, E. W., Beck, J. D., Brister, J. R., Bolton, E., Canese, K., Comeau, D. C., Funk, K., Ketter, A., Kim, S., Kimchi, A., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz899 · Cited by 420

Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation

Soria‐Carrasco, V., Gompert, Z., Comeault, A. A., Farkas, T. E., Parchman, T. L., Johnston, J. S., Buerkle, C. A., Feder, J. L., Bast, J., Schwander, T., et al. (2014) · Science · doi:10.1126/science.1252136 · Cited by 423

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor

Nobu, M. K., Narihiro, T., Rinke, C., Kamagata, Y., Tringe, S. G., Woyke, T., & Liu, W. (2015) · The ISME Journal · doi:10.1038/ismej.2014.256 · Cited by 410

The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases

Altae-Tran, H., Kannan, S., Demircioglu, F. E., Oshiro, R., Nety, S. P., McKay, L. J., Dlakić, M., Inskeep, W. P., Makarova, K. S., Macrae, R. K., et al. (2021) · Science · doi:10.1126/science.abj6856 · Cited by 407

The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier

Cao, Z., Pan, X., Yang, Y., Huang, Y., & Shen, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty085 · Cited by 407

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

Abby, S. S., Néron, B., Ménager, H., Touchon, M., & Rocha, E. P. C. (2014) · PLoS ONE · doi:10.1371/journal.pone.0110726 · Cited by 404

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

Sun, S., Zhou, Y., Chen, J., Shi, J., Zhao, H., Zhao, H., Song, W., Zhang, M., Cui, Y., Dong, X., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0182-0 · Cited by 405

Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets

Filippis, F. D., Pasolli, E., Tett, A., Tarallo, S., Naccarati, A., Angelis, M. D., Neviani, E., Cocolin, L., Gobbetti, M., Segata, N., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.01.004 · Cited by 403

BLAST: improvements for better sequence analysis

Ye, J., McGinnis, S., & Madden, T. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl164 · Cited by 774

NCBI BLAST: a better web interface

Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., & Madden, T. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn201 · Cited by 4,207

High speed BLASTN: an accelerated MegaBLAST search tool

Chen, Y., Ye, W., Zhang, Y., & Xu, Y. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv784 · Cited by 768

BLAST++: a tool for BLASTing queries in batches

Wang, H., Ong, T.-H., Ooi, B. C., & Tan, K. (2003) · Asia-Pacific Bioinformatics Conference · Cited by 9

Improved BLAST searches using longer words for protein seeding

Shiryev, S. A., Papadopoulos, J. S., Schäffer, A. A., & Agarwala, R. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm479 · Cited by 113