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

Cellular adhesiveness and cellulolytic capacity in Anaerolineae revealed by omics-based genome interpretation

Xia, Y., Wang, Y., Wang, Y., Chin, F. Y. L., & Zhang, T. (2016) · Biotechnology for Biofuels · doi:10.1186/s13068-016-0524-z · Cited by 297

Extrachromosomal circular DNA is common in yeast

Møller, H. D., Parsons, L. R., Jørgensen, T. S., Botstein, D., & Regenberg, B. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1508825112 · Cited by 296

CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes

Galardini, M., Biondi, E. G., Bazzicalupo, M., & Mengoni, A. (2011) · Source Code for Biology and Medicine · doi:10.1186/1751-0473-6-11 · Cited by 296

Linkage Mapping and Comparative Genomics Using Next-Generation RAD Sequencing of a Non-Model Organism

Baxter, S. W., Davey, J. W., Johnston, J. S., Shelton, A. M., Heckel, D. G., Jiggins, C. D., & Blaxter, M. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019315 · Cited by 295

Megaphylogeny resolves global patterns of mushroom evolution

Varga, T., Krizsán, K., Földi, C., Dima, B., Sánchez‐García, M., Ramirez, S. S., Szöllősi, G. J., Szarkándi, J. G., Papp, V., Albert, L., et al. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-0834-1 · Cited by 294

Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling

Reddy, S., Kimball, R. T., Pandey, A., Hosner, P. A., Braun, M. J., Hackett, S. J., Han, K.-L., Harshman, J. S., Huddleston, C. J., Kingston, S. E., et al. (2017) · Systematic Biology · doi:10.1093/sysbio/syx041 · Cited by 292

DEEPre: sequence-based enzyme EC number prediction by deep learning

Li, Y., Wang, S., Umarov, R. K., Xie, B., Fan, M., Li, L., & Gao, X. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx680 · Cited by 292

Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus

Hurgobin, B., Golicz, A. A., Bayer, P. E., Chan, C. K., Tirnaz, S., Dolatabadian, A., Schießl, S., Samans, B., Montenegro, J. D., Parkin, I. A. P., et al. (2017) · Plant Biotechnology Journal · doi:10.1111/pbi.12867 · Cited by 291

Two New Computational Methods for Universal DNA Barcoding: A Benchmark Using Barcode Sequences of Bacteria, Archaea, Animals, Fungi, and Land Plants

Tanabe, A. S., & Toju, H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0076910 · Cited by 289

Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2

Basu, A., Sarkar, A., & Maulik, U. (2020) · Scientific Reports · doi:10.1038/s41598-020-74715-4 · Cited by 289

A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event

Fan, Z., Tao, Y., Liu, P., Wang, L.-Y., Jin, J.-F., Zhang, F., & Zhang, Z. (2021) · GigaScience · doi:10.1093/gigascience/giab016 · Cited by 288

Expansion of the global RNA virome reveals diverse clades of bacteriophages

Neri, U., Wolf, Y. I., Roux, S., Camargo, A. P., Lee, B., Kazlauskas, D., Chen, I. M., Ivanova, N., Allen, L. Z., Páez-Espino, D., et al. (2022) · Cell · doi:10.1016/j.cell.2022.08.023 · Cited by 301

Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases

Franzén, O., Ermel, R., Cohain, A., Akers, N. K., Di Narzo, A., Talukdar, H. A., Foroughi-Asl, H., Giambartolomei, C., Fullard, J. F., Sukhavasi, K., et al. (2016) · Science · doi:10.1126/science.aad6970 · Cited by 288

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes

Roux, S., Krupovìč, M., Daly, R. A., Borges, A. L., Nayfach, S., Schulz, F., Sharrar, A. M., Carnevali, P. B. M., Cheng, J., Ivanova, N., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0510-x · Cited by 291

High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

Dugar, G., Herbig, A., Förstner, K. U., Heidrich, N., Reinhardt, R., Nieselt, K., & Sharma, C. M. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003495 · Cited by 286

Identifying lineage effects when controlling for population structure improves power in bacterial association studies

Earle, S. G., Wu, C., Charlesworth, J., Stoesser, N. E., Gordon, N. C., Walker, T. M., Spencer, C. C. A., Iqbal, Z., Clifton, D. A., Hopkins, K. L., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.41 · Cited by 287

The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits

Schartl, M., Walter, R. B., Shen, Y., Garcia, T., Catchen, J., Amores, A., Braasch, I., Chalopin, D., Volff, J., Lesch, K., et al. (2013) · Nature Genetics · doi:10.1038/ng.2604 · Cited by 284

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

Zheng, W., Zhao, S., Yin, Y., Zhang, H., Needham, D. M., Evans, E. D., Dai, C. L., Lu, P. J., Alm, E. J., & Weitz, D. A. (2022) · Science · doi:10.1126/science.abm1483 · Cited by 283

High-throughput microbial culturomics using automation and machine learning

Huang, Y., Sheth, R. U., Zhao, S., Cohen, L. A., Dabaghi, K., Moody, T., Sun, Y., Ricaurte, D., Richardson, M., Velez-Cortes, F., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01674-2 · Cited by 283

NCBI BLAST+ integrated into Galaxy

Cock, P., Chilton, J. M., Grüning, B. A., Johnson, J. E., & Soranzo, N. (2015) · GigaScience · doi:10.1186/s13742-015-0080-7 · Cited by 283

cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters

Gilchrist, C. L. M., Booth, T., van Wersch, B., van Grieken, L., Medema, M. H., & Chooi, Y. (2021) · Bioinformatics Advances · doi:10.1093/bioadv/vbab016 · Cited by 283

The Single-Nucleotide Resolution Transcriptome of Pseudomonas aeruginosa Grown in Body Temperature

Wurtzel, O., Yoder-Himes, D. R., Han, K., Dandekar, A. A., Edelheit, S., Greenberg, E. P., Sorek, R., & Lory, S. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1002945 · Cited by 282

Metabarcoding Is Powerful yet Still Blind: A Comparative Analysis of Morphological and Molecular Surveys of Seagrass Communities

Cowart, D. A., Pinheiro, M. M., Mouchel, O., Maguer, M., Grall, J., Miné, J., & Arnaud‐Haond, S. (2015) · PLoS ONE · doi:10.1371/journal.pone.0117562 · Cited by 281

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin

Wu, G., Zhao, H., Li, C., Rajapakse, M. P., Wong, W. C., Xu, J., Saunders, C. W., Reeder, N. L., Reilman, R., Scheynius, A., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005614 · Cited by 278

HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly

Sim, S. B., Corpuz, R. L., Simmonds, T. J., & Geib, S. M. (2022) · BMC Genomics · doi:10.1186/s12864-022-08375-1 · Cited by 278

Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis

Wesolowska-Andersen, A., Bahl, M. I., Carvalho, V., Kristiansen, K., Sicheritz-Pontén, T., Gupta, R., & Licht, T. R. (2014) · Microbiome · doi:10.1186/2049-2618-2-19 · Cited by 277

Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae

Zhang, R., Wang, Y., Jin, J., Stull, G. W., Bruneau, A., Cardoso, D., de Queiroz, L. P., Moore, M. J., Zhang, S., Chen, S., et al. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa013 · Cited by 277

AnnoTree: visualization and exploration of a functionally annotated microbial tree of life

Mendler, K., Chen, H., Parks, D. H., Lobb, B., Hug, L. A., & Doxey, A. C. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz246 · Cited by 276

Incongruence in the phylogenomics era

Steenwyk, J. L., Li, Y., Zhou, X., Shen, X., & Rokas, A. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00620-x · Cited by 292

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

Bacharach, E., Mishra, N., Briese, T., Zody, M. C., Kembou-Ringert, J. E., Zamostiano, R., Berkowitz, A., Ng, J., Nitido, A. D., Corvelo, A., et al. (2016) · mBio · doi:10.1128/mbio.00431-16 · Cited by 273

Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond

Mascher, M., Richmond, T., Gerhardt, D. J., Himmelbach, A., Clissold, L., Sampath, D., Ayling, S., Steuernagel, B., Pfeifer, M., D'Ascenzo, M. D., et al. (2013) · The Plant Journal · doi:10.1111/tpj.12294 · Cited by 272

A chickpea genetic variation map based on the sequencing of 3,366 genomes

Varshney, R. K., Roorkiwal, M., Sun, S., Bajaj, P., Chitikineni, A., Thudi, M., Singh, N. P., Du, X., Upadhyaya, H. D., Khan, A. W., et al. (2021) · Nature · doi:10.1038/s41586-021-04066-1 · Cited by 270

Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry

Colle, M., Leisner, C. P., Wai, C. M., Ou, S., Bird, K. A., Wang, J., Wisecaver, J. H., Yocca, A. E., Alger, E. I., Tang, H., et al. (2019) · GigaScience · doi:10.1093/gigascience/giz012 · Cited by 269

Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes

Crisp, A., Boschetti, C., Perry, M., Tunnacliffe, A., & Micklem, G. (2015) · Genome Biology · doi:10.1186/s13059-015-0607-3 · Cited by 268

MetaDome: Pathogenicity analysis of genetic variants through aggregation of homologous human protein domains

Wiel, L., Baakman, C. A. B., Gilissen, D., Veltman, J. A., Vriend, G., & Gilissen, C. (2019) · Human Mutation · doi:10.1002/humu.23798 · Cited by 268

Ultra‐barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA

Kane, N. C., Sveinsson, S., Dempewolf, H., Yang, J., Zhang, D., Engels, J. M. M., & Cronk, Q. (2012) · American Journal of Botany · doi:10.3732/ajb.1100570 · Cited by 267

The Analysis of Eight Transcriptomes from All Poriferan Classes Reveals Surprising Genetic Complexity in Sponges

Riesgo, A., Farrar, N., Windsor, P. J., Giribet, G., & Leys, S. P. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu057 · Cited by 266

A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

Schoville, S. D., Chen, Y. H., Andersson, M. N., Benoit, J. B., Bhandari, A., Bowsher, J. H., Brevik, K. A., Cappelle, K., Chen, M.-J. M., Childers, A. K., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-20154-1 · Cited by 266

Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM

Acman, M., Wang, R., van Dorp, L., Shaw, L. P., Wang, Q., Luhmann, N., Yin, Y., Sun, S., Chen, H., Wang, H., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28819-2 · Cited by 270

The Penium margaritaceum Genome: Hallmarks of the Origins of Land Plants

Jiao, C., Sørensen, I., Sun, X., Sun, H., Behar, H., Alseekh, S., Philippe, G., Palacio‐López, K., Sun, L., Reed, R., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.019 · Cited by 265

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

Bayliss, S., Thorpe, H. A., Coyle, N. M., Sheppard, S. K., & Feil, E. J. (2019) · GigaScience · doi:10.1093/gigascience/giz119 · Cited by 263

A reference-grade wild soybean genome

Xie, M., Chung, C., Li, M., Wong, F., Wang, X., Liu, A., Wang, Z., Leung, A. K.-Y., Wong, T.-H., Tong, S.-W., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09142-9 · Cited by 262

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

Deng, X., Gu, W., Federman, S., du Plessis, L., Pybus, O. G., Faria, N. R., Wang, C., Yu, G., Bushnell, B., Pan, C., et al. (2020) · Science · doi:10.1126/science.abb9263 · Cited by 262

TreeViewer : Flexible, modular software to visualise and manipulate phylogenetic trees

Bianchini, G., & Sánchez‐Baracaldo, P. (2024) · Ecology and Evolution · doi:10.1002/ece3.10873 · Cited by 262

Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma

Au, L., Hatipoglu, E., de Massy, M. R., Litchfield, K., Beattie, G., Rowan, A., Schnidrig, D., Thompson, R. H., Byrne, F., Horswell, S. D., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.10.001 · Cited by 262

PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database

Davis, J. J., Gerdes, S., Olsen, G. J., Olson, R., Pusch, G. D., Shukla, M. P., Vonstein, V., Wattam, A. R., & Yoo, H. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00118 · Cited by 261

Generalist species drive microbial dispersion and evolution

Sriswasdi, S., Yang, C.-C., & Iwasaki, W. (2017) · Nature Communications · doi:10.1038/s41467-017-01265-1 · Cited by 260

Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia

Zazhytska, M., Kodra, A. L., Hoagland, D. A., Frere, J. J., Fullard, J. F., Shayya, H. J., McArthur, N. G., Møller, R., Uhl, S. A., Omer, A. D., et al. (2022) · Cell · doi:10.1016/j.cell.2022.01.024 · Cited by 260

Exploring the repeat protein universe through computational protein design

Brunette, T., Parmeggiani, F., Huang, P., Bhabha, G., Ekiert, D. C., Tsutakawa, S. E., Hura, G. L., Tainer, J. A., & Baker, D. A. (2015) · Nature · doi:10.1038/nature16162 · Cited by 258

An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages

Radhakrishnan, G. V., Keller, J., Rich, M. K., Vernié, T., Mbadinga, D. L. M., Vigneron, N., Cottret, L., Clemente, H. S., Libourel, C., Cheema, J., et al. (2020) · Nature Plants · doi:10.1038/s41477-020-0613-7 · Cited by 258

eDNA metabarcoding as a biomonitoring tool for marine protected areas

Gold, Z. J., Sprague, J. L., Kushner, D. J., Marin, E. Z., & Barber, P. H. (2021) · PLoS ONE · doi:10.1371/journal.pone.0238557 · Cited by 258

Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis

Hsu, P. Y., Calviello, L., Wu, H.-Y. L., Li, F., Rothfels, C. J., Ohler, U., & Benfey, P. N. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1614788113 · Cited by 257

Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing

Ushio, M., Murakami, H., Masuda, R., Sado, T., Miya, M. U., Sakurai, S., Yamanaka, H., Minamoto, T., & Kondoh, M. (2018) · Metabarcoding and Metagenomics · doi:10.3897/mbmg.2.23297 · Cited by 257

Adaptation and conservation insights from the koala genome

Johnson, R. N., O’Meally, D., Chen, Z., Etherington, G., Ho, S. Y. W., Nash, W. J., Grueber, C. E., Cheng, Y., Whittington, C. M., Dennison, S., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0153-5 · Cited by 260

Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline

Baril, T., Galbraith, J. D., & Hayward, A. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae068 · Cited by 257

Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding

Allan, E. A., Starks, H. A., Chávez, F. P., Sassoubre, L. M., Block, B. A., & Boehm, A. B. B. (2017) · PLoS ONE · doi:10.1371/journal.pone.0176343 · Cited by 256

Temperature and pH define the realised niche space of arbuscular mycorrhizal fungi

Davison, J., Moora, M., Semchenko, M., Adenan, S., Ahmed, T. A.-F., Ахметжанова, А. А., Alatalo, J. M., Al‐Quraishy, S., Andrianova, E. A., Anslan, S., et al. (2021) · New Phytologist · doi:10.1111/nph.17240 · Cited by 256

Computational methods for Gene Orthology inference

Kristensen, D. M., Wolf, Y. I., Mushegian, A. R., & Koonin, E. V. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbr030 · Cited by 255

The Genome of the Anaerobic Fungus Orpinomyces sp. Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader

Youssef, N. H., Couger, M. B., Struchtemeyer, C. G., Liggenstoffer, A. S., Prade, R. A., Najar, F. Z., Atiyeh, H. K., Wilkins, M. R., & Elshahed, M. S. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.00821-13 · Cited by 255

The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization

Du, K., Stöck, M., Kneitz, S., Klopp, C., Woltering, J. M., Adolfi, M. C., Feron, R., Prokopov, D., Makunin, A., Kichigin, I. G., et al. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-1166-x · Cited by 255

Gegenees: Fragmented Alignment of Multiple Genomes for Determining Phylogenomic Distances and Genetic Signatures Unique for Specified Target Groups

Ågren, J., Sundström, A., Håfström, T., & Segerman, B. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039107 · Cited by 254

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

Daily, J. A. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-0930-z · Cited by 254

High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq

Behrens, A., Rodschinka, G., & Nedialkova, D. D. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.01.028 · Cited by 254

A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection

Goodacre, N., Aljanahi, A., Nandakumar, S., Mikailov, M., & Khan, A. S. (2018) · mSphere · doi:10.1128/mspheredirect.00069-18 · Cited by 253

A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds

Wållberg, A., Bunikis, I., Pettersson, O. V., Mosbech, M., Childers, A. K., Evans, J. D., Mikheyev, A. S., Robertson, H. M., Robinson, G. E., & Webster, M. T. (2019) · BMC Genomics · doi:10.1186/s12864-019-5642-0 · Cited by 253

PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL

Janson, G., Zhang, C., Prado, M. G., & Paiardini, A. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw638 · Cited by 251

PLSDB: advancing a comprehensive database of bacterial plasmids

Schmartz, G. P., Hartung, A., Hirsch, P., Kern, F., Fehlmann, T., Müller, R., & Keller, A. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab1111 · Cited by 251

Genomic characterization of Nontuberculous Mycobacteria

Fedrizzi, T., Meehan, C. J., Grottola, A., Giacobazzi, E., Serpini, G. F., Tagliazucchi, S., Fabio, A., Bettua, C., Bertorelli, R., Sanctis, V. D., et al. (2017) · Scientific Reports · doi:10.1038/srep45258 · Cited by 250

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

Mukherjee, S., Seshadri, R., Varghese, N. J., Eloe-Fadrosh, E. A., Meier-Kolthoff, J. P., Göker, M., Coates, R. C., Hadjithomas, M., Pavlopoulos, G. A., Paez-Espino, D., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3886 · Cited by 267

Gene exchange drives the ecological success of a multi-host bacterial pathogen

Richardson, E. J., Bacigalupe, R., Harrison, E. M., Weinert, L. A., Lycett, S., Vrieling, M., Robb, K., Hoskisson, P. A., Holden, M. T. G., Feil, E. J., et al. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0617-0 · Cited by 249

Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes

Petit, R. A., & Read, T. D. (2020) · mSystems · doi:10.1128/msystems.00190-20 · Cited by 251

Massive horizontal transfer of transposable elements in insects

Peccoud, J., Loiseau, V., Cordaux, R., & Gilbert, C. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1621178114 · Cited by 248

Escherichia coli ST131- H 22 as a Foodborne Uropathogen

Liu, C. M., Stegger, M., Aziz, M., Johnson, T. J., Waits, K., Nordstrom, L., Gauld, L., Weaver, B., Rolland, D., Statham, S., et al. (2018) · mBio · doi:10.1128/mbio.00470-18 · Cited by 248

Antimicrobial Resistance Prediction in PATRIC and RAST

Davis, J. J., Boisvert, S., Brettin, T. S., Kenyon, R. W., Mao, C., Olson, R., Overbeek, R., Santerre, J., Shukla, M. P., Wattam, A. R., et al. (2016) · Scientific Reports · doi:10.1038/srep27930 · Cited by 247

Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank

Steinegger, M., & Salzberg, S. L. (2020) · Genome Biology · doi:10.1186/s13059-020-02023-1 · Cited by 246

Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex

Garrido‐Sanz, D., Meier‐Kolthoff, J. P., Göker, M., Martín, M., Rivilla, R., & Redondo‐Nieto, M. (2016) · PLoS ONE · doi:10.1371/journal.pone.0150183 · Cited by 246

Genome-Based Taxonomic Classification of Bacteroidetes

Hahnke, R. L., Meier‐Kolthoff, J. P., García-López, M., Mukherjee, S., Huntemann, M., Ivanova, N., Woyke, T., Kyrpides, N. C., Klenk, H., & Göker, M. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.02003 · Cited by 246

The small unicellular diazotrophic symbiont, UCYN-A, is a key player in the marine nitrogen cycle

Martínez‐Pérez, C., Mohr, W., Löscher, C. R., Dekaezemacker, J., Littmann, S., Yilmaz, P., Lehnen, N., Fuchs, B. M., Lavik, G., Schmitz, R. A., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.163 · Cited by 245

Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes

Cannon, S. B., McKain, M. R., Harkess, A., Nelson, M. N., Dash, S., Deyholos, M. K., Peng, Y., Joyce, B. L., Stewart, C. N., Rolf, M., et al. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu296 · Cited by 244

Prevotella copri increases fat accumulation in pigs fed with formula diets

Chen, C., Fang, S., Hong Kui, W. E. I., He, M., Fu, H., Xiong, X., Zhou, Y., Wu, J., Gao, J., Yang, H., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01110-0 · Cited by 250

PhaTYP: predicting the lifestyle for bacteriophages using BERT

Shang, J., Tang, X., & Sun, Y. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac487 · Cited by 242

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

Eme, L., Tamarit, D., Caceres, E., Stairs, C. W., Anda, V. D., Schön, M. E., Seitz, K. W., Dombrowski, N., Lewis, W. H., Homa, F., et al. (2023) · Nature · doi:10.1038/s41586-023-06186-2 · Cited by 247

Comparing and evaluating metagenome assembly tools from a microbiologist's perspective - not only size matters!

Vollmers, J., Wiegand, S., & Kaster, A.-K. (2017) · PLoS ONE · doi:10.1371/journal.pone.0169662 · Cited by 240

sRNAtoolbox: an integrated collection of small RNA research tools

Rueda, A., Barturen, G., Lebrón, R., Gómez‐Martín, C., Martín-Alganza, A., Oliver, J. L. T., & Hackenberg, M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv555 · Cited by 241

A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions

Conte, M. A., Gammerdinger, W., Bartie, K. L., Penman, D. J., & Kocher, T. D. (2017) · BMC Genomics · doi:10.1186/s12864-017-3723-5 · Cited by 240

RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants

Li, P., Quan, X., Jia, G., Xiao, J., Cloutier, S., & You, F. M. (2016) · BMC Genomics · doi:10.1186/s12864-016-3197-x · Cited by 239

De novo assembly of the goldfish ( Carassius auratus ) genome and the evolution of genes after whole-genome duplication

Chen, Z., Omori, Y., Koren, S., Shirokiya, T., Kuroda, T., Miyamoto, A., Wada, H., Fujiyama, A., Toyoda, A., Zhang, S., et al. (2019) · Science Advances · doi:10.1126/sciadv.aav0547 · Cited by 239

Genomic and Transcriptomic Characterization of Natural Killer T Cell Lymphoma

Xiong, J., Cui, B., Wang, N., Dai, Y.-T., Zhang, H., Wang, C., Zhong, H., Cheng, S., Ouyang, B., Hu, Y., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.02.005 · Cited by 239

BOLD v4: A Centralized Bioinformatics Platform for DNA-Based Biodiversity Data

Ratnasingham, S., Wei, C., Chan, D. S. W., Agda, J. R. A., Agda, J., Ballesteros‐Mejia, L., Boutou, H. A., Bastami, Z. M. E., Ma, E., Manjunath, R., et al. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-3581-0_26 · Cited by 238

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes

Sberro, H., Fremin, B. J., Zlitni, S., Edfors, F., Greenfield, N., Snyder, M. P., Pavlopoulos, G. A., Kyrpides, N. C., & Bhatt, A. S. (2019) · Cell · doi:10.1016/j.cell.2019.07.016 · Cited by 237

Escherichia coli Sequence Type 410 Is Causing New International High-Risk Clones

Roer, L., Overballe‐Petersen, S., Hansen, F., Schønning, K., Wang, M., Røder, B. L., Hansen, D. S., Justesen, U. S., Andersen, L. P., Fuglsang-Damgaard, D., et al. (2018) · mSphere · doi:10.1128/msphere.00337-18 · Cited by 237

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

Brown, S. P., Grillo, M. A., Podowski, J. C., & Heath, K. D. (2020) · Microbiome · doi:10.1186/s40168-020-00915-9 · Cited by 238

AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens

Li, C., Sutherland, D., Hammond, S. A., Yang, C., Taho, F., Bergman, L. C., Houston, S., Warren, R. L., Wong, T., Hoang, L., et al. (2022) · BMC Genomics · doi:10.1186/s12864-022-08310-4 · Cited by 245

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts

Testa, A. C., Hane, J. K., Ellwood, S. R., & Oliver, R. P. (2015) · BMC Genomics · doi:10.1186/s12864-015-1344-4 · Cited by 234

A distinct abundant group of microbial rhodopsins discovered using functional metagenomics

Pushkarev, A., Inoue, K., Larom, S., Flores‐Uribe, J., Singh, M. P., Konno, M., Tomida, S., Ito, S., Nakamura, R., Tsunoda, S. P., et al. (2018) · Nature · doi:10.1038/s41586-018-0225-9 · Cited by 234

Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data

Page, A. J., Silva, N. H. D., Hunt, M., Quail, M. A., Parkhill, J., Harris, S. R., Otto, T. D., & Keane, J. A. (2016) · Microbial Genomics · doi:10.1099/mgen.0.000083 · Cited by 234

High-Throughput CRISPR/Cas9 Mutagenesis Streamlines Trait Gene Identification in Maize

Liu, H., Jian, L., Xu, J., Zhang, Q., Zhang, M., Jin, M., Peng, Y., Yan, J., Han, B., Liu, J., et al. (2020) · The Plant Cell · doi:10.1105/tpc.19.00934 · Cited by 234

Olfactory receptor and circuit evolution promote host specialization

Auer, T. O., Khallaf, M. A., Silbering, A. F., Zappia, G., Ellis, K. E., Álvarez-Ocaña, R., Arguello, J. R., Hansson, B. S., Jefferis, G. S. X. E., Caron, S. J. C., et al. (2020) · Nature · doi:10.1038/s41586-020-2073-7 · Cited by 234

Host identity is a dominant driver of mycorrhizal fungal community composition during ecosystem development

Martínez‐García, L. B., Richardson, S. J., Tylianakis, J. M., Peltzer, D. A., & Dickie, I. A. (2014) · New Phytologist · doi:10.1111/nph.13226 · Cited by 233

Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes

Carter, M. M., Olm, M. R., Merrill, B. D., Dahan, D., Tripathi, S. M., Spencer, S. P., Yu, F. B., Jain, S., Neff, N. F., Jha, A. R., et al. (2023) · Cell · doi:10.1016/j.cell.2023.05.046 · Cited by 233

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