UniRef: comprehensive and non-redundant UniProt reference clusters

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

Li, W.-Z., & Godzik, A. (2006) · Bioinform. · doi:10.1093/bioinformatics/btl158 · Cited by 10,994 · see citing works

Database resources of the National Center for Biotechnology Information: update

Wheeler, D. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,691 · see citing works

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

Pruitt, K. D., Tatusova, T. A., & Maglott, D. R. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl842 · Cited by 4,441 · see citing works

The Universal Protein Resource (UniProt)

Bairoch, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki070 · Cited by 3,774 · see citing works

The Universal Protein Resource (UniProt): an expanding universe of protein information

Wu, C. H. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj161 · Cited by 1,116 · see citing works

Clustering of highly homologous sequences to reduce the size of large protein databases

Li, W.-Z., Jaroszewski, L., & Godzik, A. (2001) · Bioinform. · doi:10.1093/bioinformatics/17.3.282 · Cited by 1,021 · see citing works

Length-dependent prediction of protein intrinsic disorder

Peng, K., Predrag Radivojac, A., Vučetić, S., Dunker, A. K., & Zoran Obradovic, A. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-208 · Cited by 926 · see citing works

Selection of representative protein data sets

Hobohm, U., Scharf, M. E., Schneider, R., & Sander, C. (1992) · Protein Science · doi:10.1002/pro.5560010313 · Cited by 818 · see citing works

Database resources of the National Center for Biotechnology Information

Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Edgar, R., Federhen, S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl1031 · Cited by 734 · see citing works

Identification of multiple distinct Snf2 subfamilies with conserved structural motifs

Flaus, A. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl295 · Cited by 727 · see citing works

Ensembl 2007

Hubbard, T., Aken, B. L., Beal, K. M., Ballester, B., Cáccamo, M., Chen, Y., Clarke, L., Coates, G. M. P., Cunningham, F. M., Cutts, T., et al. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl996 · Cited by 636 · see citing works

The Universal Protein Resource (UniProt)

The UniProt Consortium (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl929 · Cited by 572 · see citing works

The RCSB PDB information portal for structural genomics

Kouranov, A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj120 · Cited by 523 · see citing works

A Conserved Supergene Locus Controls Colour Pattern Diversity in Heliconius Butterflies

Joron, M., Papa, R., Beltrán, M., Chamberlain, N. L., Mavárez, J., Baxter, S. W., Abanto, M., Bermingham, E., Humphray, S., Rogers, J., et al. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040303 · Cited by 296 · see citing works

Genome Organization of More Than 300 Defensin-Like Genes in Arabidopsis

Silverstein, K. A. T., Graham, M. A., Paape, T. D., & VandenBosch, K. A. (2005) · PLANT PHYSIOLOGY · doi:10.1104/pp.105.060079 · Cited by 265 · see citing works

The Abundance of Short Proteins in the Mammalian Proteome

Frith, M. C., Forrest, A. R. R., Nourbakhsh, E., Pang, K. C., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y., Bailey, T. L., & Grimmond, S. M. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020052 · Cited by 225 · see citing works

UniProt archive

Leinonen, R., Diez, F. G., Binns, D., Fleischmann, W., López, R., & Apweiler, R. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth191 · Cited by 217 · see citing works

Refinement and prediction of protein prenylation motifs

Maurer‐Stroh, S., & Eisenhaber, F. (2005) · Genome biology · doi:10.1186/gb-2005-6-6-r55 · Cited by 203 · see citing works

GeneRAGE: a robust algorithm for sequence clustering and domain detection

Enright, A. J., & Ouzounis, C. A. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.5.451 · Cited by 200 · see citing works

Proteomic and Bioinformatic Characterization of the Biogenesis and Function of Melanosomes

Chi, A., Valencia, J. C., Hu, Z.-Z., Watabe, H., Yamaguchi, H., Mangini, N. J., Huang, H., Canfield, V. A., Cheng, K. C., Yang, F., et al. (2006) · Journal of Proteome Research · doi:10.1021/pr060363j · Cited by 199 · see citing works

The TIGR Plant Transcript Assemblies database

Childs, K. L., Hamilton, J. P., Zhu, W., Ly, E., Cheung, F., Wu, H., Rabinowicz, P. D., Town, C. D., Buell, C. R., & Chan, A. P.-Y. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl785 · Cited by 188 · see citing works

AutoFACT: An Auto matic F unctional A nnotation and C lassification T ool

Koski, L. B., Gray, M. W., Lang, B. F., & Burger, G. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-151 · Cited by 188 · see citing works

Spectral clustering of protein sequences

Paccanaro, A. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj515 · Cited by 177 · see citing works

Comprehensive Structural Analysis of the Genome of Red Clover (Trifolium pratense L.)

Sato, S., Isobe, S., Asamizu, E., Ohmido, N., Kataoka, R., Nakamura, Y., Kaneko, T., Sakurai, N., Okumura, K., Klimenko, I. A., et al. (2005) · DNA Research · doi:10.1093/dnares/dsi018 · Cited by 161 · see citing works

Sequencing and Analysis of Common Bean ESTs. Building a Foundation for Functional Genomics

Ramı́rez, M., Graham, M. A., Blanco-López, L., Silvente, S. T., Medrano-Soto, A., Blair, M. W., Hernández, G., Vance, C. P., & Lara, M. (2005) · PLANT PHYSIOLOGY · doi:10.1104/pp.104.054999 · Cited by 148 · see citing works

UniqueProt: creating representative protein sequence sets

Mika, S. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg620 · Cited by 121 · see citing works

The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties

Luscombe, N. M., Qian, J. X., Zhang, Z., Johnson, T., & Gerstein, M. (2002) · Genome biology · doi:10.1186/gb-2002-3-8-research0040 · Cited by 115 · see citing works

Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research

Stover, N. A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj054 · Cited by 107 · see citing works

Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters

Pavy, N., Paule, C., Parsons, L. S., Crow, J., Morency, M., Cooke, J. E. K., Johnson, J. E., Noumen, E., Guillet-Claude, C., Butterfield, Y. S. N., et al. (2005) · BMC Genomics · doi:10.1186/1471-2164-6-144 · Cited by 107 · see citing works

Genomic and Genetic Characterization of Rice Cen3 Reveals Extensive Transcription and Evolutionary Implications of a Complex Centromere

Yan, H., Ito, H., Nobuta, K., Ouyang, S., Jin, W., Tian, S., Lu, C., Venu, R. C., Wang, G., Green, P. J., et al. (2006) · The Plant Cell · doi:10.1105/tpc.106.043794 · Cited by 104 · see citing works

Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana

Mudge, J., Cannon, S. B., Kaló, P., Oldroyd, G. E. D., Roe, B. A., Town, C. D., & Young, N. D. (2005) · BMC Plant Biology · doi:10.1186/1471-2229-5-15 · Cited by 102 · see citing works

ProClust: improved clustering of protein sequences with an extended graph-based approach

Pipenbacher, P., Schliep, A., Schneckener, S., Schönhuth, A., Schomburg, D., & Schrader, R. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_2.s182 · Cited by 89 · see citing works

Incorporating background frequency improves entropy-based residue conservation measures

Wang, K., & Samudrala, R. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-385 · Cited by 86 · see citing works

Structure of human semicarbazide-sensitive amine oxidase/vascular adhesion protein-1

Jakobsson, E., Nilsson, J., Ogg, D., & Kleywegt, G. J. (2005) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444905028805 · Cited by 85 · see citing works

Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs

Pavy, N., Parsons, L. S., Paule, C., MacKay, J. J., & Bousquet, J. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-174 · Cited by 76 · see citing works

Databases and Information Integration for the Medicago truncatula Genome and Transcriptome

Cannon, S. B., Crow, J., Heuer, M., Wang, X., Cannon, E. K. S., Dwan, C., Lamblin, A.-F., Vasdewani, J., Mudge, J., Cook, A., et al. (2005) · PLANT PHYSIOLOGY · doi:10.1104/pp.104.059204 · Cited by 63 · see citing works

A normalised scale for structural genomics target ranking: The OB‐Score

Overton, I. M., & Barton, G. J. (2006) · FEBS Letters · doi:10.1016/j.febslet.2006.06.015 · Cited by 57 · see citing works

Comparative bioinformatics analyses and profiling of lysosome-related organelle proteomes

Hu, Z.-Z., Valencia, J. C., Huang, H., Chi, A., Shabanowitz, J., Hearing, V. J., Appella, E., & Wu, C. H. (2006) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2006.09.024 · Cited by 51 · see citing works

The predictive power of the CluSTr database

Petryszak, R., Kretschmann, E., Wieser, D., & Apweiler, R. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti542 · Cited by 50 · see citing works

pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer

Ng, A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj044 · Cited by 45 · see citing works

Saturating representation of loop conformational fragments in structure databanks.

Fernández‐Fuentes, N., & Fiser, A. (2006) · BMC Structural Biology · doi:10.1186/1472-6807-6-15 · Cited by 43 · see citing works

Proteome profiling of human epithelial ovarian cancer cell line TOV-112D

Gagné, J., Gagné, P., Hunter, J. M., Bonicalzi, M.-È., Lemay, J., Kelly, I., Page, C. L., Provencher, D. M., Mes‐Masson, A., Droit, A., et al. (2005) · Molecular and Cellular Biochemistry · doi:10.1007/s11010-005-7556-1 · Cited by 42 · see citing works

CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks

Kinjo, A. R., & Nishikawa, K. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-401 · Cited by 41 · see citing works

RSDB: representative protein sequence databases have high information content

Bhak, J., Holm, L., Heger, A., & Chothia, C. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.5.458 · Cited by 40 · see citing works

Death inducer obliterator protein 1 in the context of DNA regulation

Rojas, A. M., Sánchez‐Pulido, L., Fütterer, A., van Wely, K. H. M., Martínez‐A, C., & Valencia, A. (2005) · FEBS Journal · doi:10.1111/j.1742-4658.2005.04759.x · Cited by 40 · see citing works

Association of nucleotide patterns with gene function classes: application to human 3′ untranslated sequences

Conklin, D., Jonassen, I., Aasland, R., & Taylor, W. R. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.1.182 · Cited by 31 · see citing works

Challenges and Solutions in Proteomics

Huang, H., Shukla, H. D., Wu, C. H., & Saxena, S. P. (2007) · Current Genomics · doi:10.2174/138920207780076910 · Cited by 26 · see citing works

High throughput profile-profile based fold recognition for the entire human proteome

McGuffin, L. J., Smith, R. T., Bryson, K., Sørensen, S.-A., & Jones, D. T. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-288 · Cited by 23 · see citing works

On single and multiple models of protein families for the detection of remote sequence relationships

Casbon, J. A., & Saqi, M. A. S. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-48 · Cited by 12 · see citing works

Specific Modification of a Na + Binding Site in NADH:Quinone Oxidoreductase from Klebsiella pneumoniae with Dicyclohexylcarbodiimide

Vgenopoulou, I., Gemperli, A. C., & Steuber, J. (2006) · Journal of Bacteriology · doi:10.1128/jb.188.9.3264-3272.2006 · Cited by 10 · see citing works

DOUTfinder--identification of distant domain outliers using subsignificant sequence similarity

Novatchkova, M., Schneider, G., Fritz, R., Eisenhaber, F., & Schleiffer, A. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl332 · Cited by 9 · see citing works

Cd-hit: Accelerated for clustering the next-generation sequencing data

Fu, L., Niu, B., Zhu, Z., Wu, S., & Li, W. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts565 · Cited by 11,175 · see citing works

Sensitive protein alignments at tree-of-life scale using DIAMOND

Buchfink, B., Reuter, K., & Drost, H.-G. (2021) · Nature Methods · doi:10.1038/s41592-021-01101-x · Cited by 5,097 · see citing works

UniProt: a hub for protein information

The UniProt Consortium (2015) · Nucleic Acids Research · doi:10.1093/nar/gku989 · Cited by 5,106 · see citing works

UniProt: the universal protein knowledgebase

The UniProt Consortium (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1099 · Cited by 4,436 · see citing works

The Pfam protein families database

Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1065 · Cited by 3,719 · see citing works

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

Rives, A., Meier, J., Sercu, T., Goyal, S., Lin, Z., Liu, J., Guo, D., Ott, M., Zitnick, C. L., Ma, J., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2016239118 · Cited by 3,286 · see citing works

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

Lloyd-Price, J., Arze, C., Ananthakrishnan, A. N., Schirmer, M., Avila-Pacheco, J., Poon, T. W., Andrews, E., Ajami, N. J., Bonham, K. S., Brislawn, C. J., et al. (2019) · Nature · doi:10.1038/s41586-019-1237-9 · Cited by 3,143 · see citing works

CD-HIT Suite: a web server for clustering and comparing biological sequences

Huang, Y., Niu, B., Gao, Y., Fu, L., & Li, W. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq003 · Cited by 2,618 · see citing works

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303 · see citing works

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B., Wu, C. H., & the UniProt Consortium (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu739 · Cited by 1,928 · see citing works

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

Ashkenazy, H., Erez, E., Martz, E., Pupko, T., & Ben‐Tal, N. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq399 · Cited by 1,822 · see citing works

JPred4: a protein secondary structure prediction server

Drozdetskiy, A., Cole, C., Procter, J. B., & Barton, G. J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv332 · Cited by 1,714 · see citing works

Activities at the Universal Protein Resource (UniProt)

The UniProt Consortium (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1140 · Cited by 1,736 · see citing works

SIFT missense predictions for genomes

Vaser, R., Adusumalli, S., Leng, S. N., Sikic, M., & Ng, P. C. (2016) · Nature Protocols · doi:10.1038/nprot.2015.123 · Cited by 1,510 · see citing works

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2017) · doi:10.1038/s41564-018-0171-1 · Cited by 1,742 · see citing works

The Jpred 3 secondary structure prediction server

Cole, C., Barber, J. D., & Barton, G. J. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn238 · Cited by 1,432 · see citing works

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

Shihab, H. A., Gough, J., Cooper, D. N., Stenson, P. D., Barker, G., Edwards, K. J., Day, I. N. M., & Gaunt, T. R. (2012) · Human Mutation · doi:10.1002/humu.22225 · Cited by 1,319 · see citing works

Strains, functions and dynamics in the expanded Human Microbiome Project

Lloyd-Price, J., Mahurkar, A., Rahnavard, G., Crabtree, J., Orvis, J., Hall, A. B., Brady, A., Creasy, H. H., McCracken, C., Giglio, M. G., et al. (2017) · Nature · doi:10.1038/nature23889 · Cited by 1,267 · see citing works

Reorganizing the protein space at the Universal Protein Resource (UniProt)

The UniProt Consortium (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr981 · Cited by 1,223 · see citing works

Unusual biology across a group comprising more than 15% of domain Bacteria

Brown, C. T., Hug, L. A., Thomas, B. C., Sharon, I., Castelle, C. J., Singh, A., Wilkins, M. J., Wrighton, K. C., Williams, K. H., & Banfield, J. F. (2015) · Nature · doi:10.1038/nature14486 · Cited by 1,216 · see citing works

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

Anantharaman, K., Brown, C., Hug, L., Sharon, I., Castelle, C., Probst, A., Thomas, B., Singh, A., Wilkins, M., Karaoz, U., et al. (2016) · Nature Communications · doi:10.1038/ncomms13219 · Cited by 1,040 · see citing works

ProteinBERT: a universal deep-learning model of protein sequence and function

Brandes, N., Ofer, D., Peleg, Y., Rappoport, N., & Linial, M. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac020 · Cited by 1,009 · see citing works

A transposase strategy for creating libraries of circularly permuted proteins

Mehta, M., Liu, S., & Silberg, J. J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks060 · Cited by 1,042 · see citing works

A large-scale evaluation of computational protein function prediction

Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M., Wittkop, T., Sokolov, A., Graim, K., Funk, C., Verspoor, K., Ben-Hur, A., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2340 · Cited by 1,028 · see citing works

Improved prediction of protein-protein interactions using AlphaFold2

Bryant, P., Pozzati, G., & Elofsson, A. (2021) · doi:10.1101/2021.09.15.460468 · Cited by 1,025 · see citing works

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

Tsirigos, K. D., Peters, C., Shu, N., Käll, L., & Elofsson, A. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv485 · Cited by 917 · see citing works

The Universal Protein Resource (UniProt) in 2010

The UniProt Consortium (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp846 · Cited by 1,412 · see citing works

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

Contreras‐Moreira, B., & Vinuesa, P. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.02411-13 · Cited by 886 · see citing works

Pi-Pi contacts are an overlooked protein feature relevant to phase separation

Vernon, R. M., Chong, P. A., Tsang, B., Kim, T. H., Bah, A., Farber, P. J., Lin, H., & Forman-Kay, J. D. (2018) · eLife · doi:10.7554/elife.31486 · Cited by 905 · see citing works

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

Jones, D. T., & Cozzetto, D. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu744 · Cited by 861 · see citing works

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

Asnicar, F., Thomas, A. M., Beghini, F., Mengoni, C., Manara, S., Manghi, P., Zhu, Q., Bolzan, M., Cumbo, F., May, U., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16366-7 · Cited by 869 · see citing works

The Universal Protein Resource (UniProt)

The UniProt Consortium (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm895 · Cited by 824 · see citing works

Ongoing and future developments at the Universal Protein Resource

The UniProt Consortium (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1020 · Cited by 730 · see citing works

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

Franzosa, E. A., Hsu, T. Y., Sirota‐Madi, A., Shafquat, A., Abu-Ali, G., Morgan, X. C., & Huttenhower, C. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3451 · Cited by 725 · see citing works

Language models enable zero-shot prediction of the effects of mutations on protein function

Meier, J., Rao, R., Verkuil, R., Liu, J., Sercu, T., & Rives, A. (2021) · doi:10.1101/2021.07.09.450648 · Cited by 635 · see citing works

Update on activities at the Universal Protein Resource (UniProt) in 2013

The UniProt Consortium (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1068 · Cited by 674 · see citing works

Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

Wrighton, K. C., Thomas, B. C., Sharon, I., Miller, C. S., Castelle, C. J., VerBerkmoes, N. C., Wilkins, M. J., Hettich, R. L., Lipton, M. S. W., Williams, K. H., et al. (2012) · Science · doi:10.1126/science.1224041 · Cited by 643 · see citing works

Native Chemical Ligation and Extended Methods: Mechanisms, Catalysis, Scope, and Limitations

Agouridas, V., Mahdi, O. E., Diemer, V., Cargoët, M., Monbaliu, J. M., & Melnyk, O. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00712 · Cited by 653 · see citing works

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

Hug, L. A., Castelle, C. J., Wrighton, K. C., Thomas, B. C., Sharon, I., Frischkorn, K. R., Williams, K. H., Tringe, S. G., & Banfield, J. F. (2013) · Microbiome · doi:10.1186/2049-2618-1-22 · Cited by 643 · see citing works

Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction

Shen, Y., Maupetit, J., Derreumaux, P., & Tufféry, P. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct500592m · Cited by 634 · see citing works

Human gut bacteria produce ΤΗ17-modulating bile acid metabolites

Paik, D., Yao, L., Zhang, Y., Bae, S., D’Agostino, G. D., Zhang, M., Kim, E., Franzosa, E. A., Avila-Pacheco, J., Bisanz, J. E., et al. (2022) · Nature · doi:10.1038/s41586-022-04480-z · Cited by 594 · see citing works

Insights into the Maize Pan-Genome and Pan-Transcriptome

Hirsch, C. N., Foerster, J. M., Johnson, J. M., Sekhon, R. S., Muttoni, G., Vaillancourt, B., Peñagaricano, F., Lindquist, E., Pedraza, M. A., Barry, K., et al. (2014) · The Plant Cell · doi:10.1105/tpc.113.119982 · Cited by 562 · see citing works

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

Schirmer, M., Franzosa, E. A., Lloyd‐Price, J., McIver, L. J., Schwager, R., Poon, T. W., Ananthakrishnan, A. N., Andrews, E., Barron, G., Lake, K., et al. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0089-z · Cited by 570 · see citing works

ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function

Celniker, G., Nimrod, G., Ashkenazy, H., Glaser, F., Martz, E., Mayrose, I., Pupko, T., & Ben‐Tal, N. (2013) · Israel Journal of Chemistry · doi:10.1002/ijch.201200096 · Cited by 551 · see citing works

The Universal Protein Resource (UniProt) 2009

The UniProt Consortium (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn664 · Cited by 546 · see citing works

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

Castelle, C. J., Wrighton, K. C., Thomas, B. C., Hug, L. A., Brown, C. T., Wilkins, M. J., Frischkorn, K. R., Tringe, S. G., Singh, A., Markillie, L. M., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.01.014 · Cited by 536 · see citing works

Ultrafast clustering algorithms for metagenomic sequence analysis

Li, W., Fu, L., Niu, B., Wu, S., & Wooley, J. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbs035 · Cited by 498 · see citing works

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 · see citing works

Learning the protein language: Evolution, structure, and function

Bepler, T., & Berger, B. (2021) · Cell Systems · doi:10.1016/j.cels.2021.05.017 · Cited by 483 · see citing works

Efficient evolution of human antibodies from general protein language models

Hie, B. L., Shanker, V. R., Xu, D., Bruun, T. U. J., Weidenbacher, P., Tang, S.-G., Wu, W., Pak, J., & Kim, P. S. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01763-2 · Cited by 452 · see citing works

Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery

Parchman, T. L., Geist, K. S., Grahnen, J. A., Benkman, C. W., & Buerkle, C. A. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-180 · Cited by 446 · see citing works

The genome of Aiptasia , a sea anemone model for coral symbiosis

Baumgarten, S., Simakov, O., Esherick, L. Y., Liew, Y. J., Lehnert, E. M., Michell, C., Li, Y., Hambleton, E. A., Guse, A., Oates, M. E., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1513318112 · Cited by 438 · see citing works

Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease

Bowerman, K. L., Rehman, S. F., Vaughan, A., Lachner, N., Budden, K. F., Kim, R., Wood, D., Gellatly, S. L., Shukla, S. D., Wood, L. G., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19701-0 · Cited by 432 · see citing works

Drug repurposing for cancer therapy

Xia, Y., Sun, M., Huang, H., & Jin, W.-L. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01808-1 · Cited by 443 · see citing works

A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction

Cai, C., Leu, A. O., Xie, G.-J., Guo, J., Feng, Y., Zhao, J., Tyson, G. W., Yuan, Z., & Hu, S. (2018) · The ISME Journal · doi:10.1038/s41396-018-0109-x · Cited by 411 · see citing works

Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance

Suez, J., Cohen, Y., Valdés‐Mas, R., Mor, U., Dori-Bachash, M., Federici, S., Zmora, N., Leshem, A., Heinemann, M., Linevsky, R., et al. (2022) · Cell · doi:10.1016/j.cell.2022.07.016 · Cited by 431 · see citing works

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

Rives, A., Meier, J., Sercu, T., Goyal, S., Lin, Z., Liu, J., Guo, D., Ott, M., Zitnick, C. L., Ma, J., et al. (2019) · doi:10.1101/622803 · Cited by 3,280 · see citing works

PEP-FOLD: an online resource for de novo peptide structure prediction

Maupetit, J., Derreumaux, P., & Tufféry, P. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp323 · Cited by 404 · see citing works

The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk

Wang, D. D., Nguyen, L. H., Li, Y., Yan, Y., Ma, W., Rinott, E., Ivey, K. L., Shai, I., Willett, W. C., Hu, F. B., et al. (2021) · Nature Medicine · doi:10.1038/s41591-020-01223-3 · Cited by 386 · see citing works

A global metagenomic map of urban microbiomes and antimicrobial resistance

Danko, D., Bezdan, D., Afshin, E. E., Ahsanuddin, S., Bhattacharya, C., Butler, D., Chng, K. R., Donnellan, D., Hecht, J., Jackson, K., et al. (2021) · Cell · doi:10.1016/j.cell.2021.05.002 · Cited by 396 · see citing works

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

Magnan, C. N., & Baldi, P. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu352 · Cited by 363 · see citing works

NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases

Costa, M., Manton, J. D., Ostrovsky, A. D., Prohaska, S., & Jefferis, G. S. X. E. (2016) · Neuron · doi:10.1016/j.neuron.2016.06.012 · Cited by 294 · see citing works

Improving Protein Expression, Stability, and Function with ProteinMPNN

(2024) · doi:10.1021/jacs.3c10941 · Cited by 344 · see citing works

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir

Walsh, A. M., Crispie, F., Kilcawley, K. N., O’Sullivan, Ó., O’Sullivan, M. G., Claesson, M. J., & Cotter, P. D. (2016) · mSystems · doi:10.1128/msystems.00052-16 · Cited by 352 · see citing works

Collective judgment predicts disease-associated single nucleotide variants

Capriotti, E., Altman, R. B., & Bromberg, Y. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-s3-s2 · Cited by 341 · see citing works

Transformer protein language models are unsupervised structure learners

Rao, R., Meier, J., Sercu, T., Ovchinnikov, S., & Rives, A. (2020) · doi:10.1101/2020.12.15.422761 · Cited by 341 · see citing works

Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae

Leu, A. O., Cai, C., McIlroy, S. J., Southam, G., Orphan, V. J., Yuan, Z., Hu, S., & Tyson, G. W. (2020) · The ISME Journal · doi:10.1038/s41396-020-0590-x · Cited by 334 · see citing works

Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

Kantor, R. S., Wrighton, K. C., Handley, K. M., Sharon, I., Hug, L. A., Castelle, C. J., Thomas, B. C., & Banfield, J. F. (2013) · mBio · doi:10.1128/mbio.00708-13 · Cited by 307 · see citing works

pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination

Lobley, A., Sadowski, M. I., & Jones, D. T. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp302 · Cited by 302 · see citing works

The Draft Genome Sequence of European Pear (Pyrus communis L. ‘Bartlett’)

Chagné, D., Crowhurst, R. N., Pindo, M., Thrimawithana, A. H., Deng, C. H., Ireland, H. S., Fiers, M. W. E. J., Dzierzon, H., Cestaro, A., Fontana, P., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0092644 · Cited by 298 · see citing works

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 291 · see citing works

Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients

Peters, B. A., Wilson, M., Moran, U., Pavlick, A., Izsak, A., Wechter, T., Weber, J. S., Osman, I., & Ahn, J. (2019) · Genome Medicine · doi:10.1186/s13073-019-0672-4 · Cited by 263 · see citing works

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

Angiuoli, S. V., Matalka, M. N., Gussman, A., Galens, K., Vangala, M., Riley, D. R. J., Arze, C., White, J. R., White, O. R., & Fricke, W. F. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-356 · Cited by 282 · see citing works

Molecular Principles of the Interactions of Disordered Proteins

Mészáros, B., Tompa, P., Simon, I., & Dosztányi, Z. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.07.004 · Cited by 277 · see citing works

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

Probst, A., Ladd, B., Jarett, J., Geller-McGrath, D., Sieber, C., Emerson, J., Anantharaman, K., Thomas, B., Malmstrom, R., Stieglmeier, M., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-017-0098-y · Cited by 260 · see citing works

MMseqs software suite for fast and deep clustering and searching of large protein sequence sets

Hauser, M., Steinegger, M., & Söding, J. (2016) · Bioinform. · doi:10.1093/bioinformatics/btw006 · Cited by 265 · see citing works

ConSurf‐DB: An accessible repository for the evolutionary conservation patterns of the majority of PDB proteins

Chorin, A. B., Masrati, G., Kessel, A., Narunsky, A., Sprinzak, J., Lahav, S., Ashkenazy, H., & Ben‐Tal, N. (2019) · Protein Science · doi:10.1002/pro.3779 · Cited by 268 · see citing works

Genome-reconstruction for eukaryotes from complex natural microbial communitiesPreprint

West, P. T., Probst, A. J., Grigoriev, I. V., Thomas, B. C., & Banfield, J. F. (2018) · Genome Research · doi:10.1101/gr.228429.117 · Cited by 268 · see citing works

The MiST2 database: a comprehensive genomics resource on microbial signal transduction

Ulrich, L. E., & Zhulin, I. B. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp940 · Cited by 262 · see citing works

Removal of lycopene substrate inhibition enables high carotenoid productivity in Yarrowia lipolytica

Ma, Y., Liu, N., Greisen, P. J., Li, J., Qiao, K., Huang, S., & Stephanopoulos, G. N. (2022) · Nature Communications · doi:10.1038/s41467-022-28277-w · Cited by 249 · see citing works

Single nucleotide polymorphism discovery in elite north american potato germplasm

Hamilton, J. P., Hansey, C. N., Whitty, B. R., Stoffel, K. M., Massa, A. N., Deynze, A. V., Jong, W. S. D., Douches, D. S., & Buell, C. R. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-302 · Cited by 247 · see citing works

Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems

Burstein, D. E., Sun, C. L., Brown, C. T., Sharon, I., Anantharaman, K., Probst, A. J., Thomas, B. C., & Banfield, J. F. (2016) · Nature Communications · doi:10.1038/ncomms10613 · Cited by 235 · see citing works

PROMALS3D: Multiple Protein Sequence Alignment Enhanced with Evolutionary and Three-Dimensional Structural Information

Pei, J., & Grishin, N. V. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-646-7_17 · Cited by 241 · see citing works

Bilingual language model for protein sequence and structure

Heinzinger, M., Weissenow, K., Sanchez, J. G., Henkel, A., Mirdita, M., Steinegger, M., & Rost, B. (2024) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqae150 · Cited by 311 · see citing works

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Hingamp, P., Grimsley, N. H., Acinas, S. G., Clérissi, C., Subirana, L., Poulain, J., Ferrera, I., Sarmento, H., Villar, É., Lima‐Mendez, G., et al. (2013) · The ISME Journal · doi:10.1038/ismej.2013.59 · Cited by 237 · see citing works

Structure Analysis Uncovers a Highly Diverse but Structurally Conserved Effector Family in Phytopathogenic Fungi

de Guillen, K. M., Ortiz, D., Gracy, J., Fournier, E., Kroj, T., & Padilla, A. (2015) · PLoS Pathogens · doi:10.1371/journal.ppat.1005228 · Cited by 237 · see citing works

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

Brewer, T. E., Handley, K. M., Carini, P., Gilbert, J. A., & Fierer, N. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.198 · Cited by 234 · see citing works

Metatranscriptome of human faecal microbial communities in a cohort of adult men

Abu-Ali, G., Mehta, R. S., Lloyd‐Price, J., Mallick, H., Branck, T. A., Ivey, K. L., Drew, D. A., DuLong, C. R., Rimm, E. B., Izard, J., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-017-0084-4 · Cited by 230 · see citing works

Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search

(2022) · doi:10.1038/s41467-022-33729-4 · Cited by 226 · see citing works

Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India

Gupta, A., Dhakan, D. B., Maji, A., Saxena, R., K., V., Mahajan, S., Pulikkan, J., Kurian, J., Gomez, A. M., Scaria, J., et al. (2019) · mSystems · doi:10.1128/msystems.00438-19 · Cited by 229 · see citing works

Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome

Brooks, B., Olm, M. R., Firek, B. A., Baker, R., Thomas, B. C., Morowitz, M. J., & Banfield, J. F. (2017) · Nature Communications · doi:10.1038/s41467-017-02018-w · Cited by 226 · see citing works

Protein Bioinformatics Databases and Resources

Chen, C., Huang, H., & Wu, C. H. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-6783-4_1 · Cited by 224 · see citing works

Megaphages infect Prevotella and variants are widespread in gut microbiomes

Devoto, A. E., Santini, J. M., Olm, M. R., Anantharaman, K., Munk, P., Tung, J., Archie, E. A., Turnbaugh, P. J., Seed, K. D., Blekhman, R., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-018-0338-9 · Cited by 210 · see citing works

Large-scale determination of previously unsolved protein structures using evolutionary information

Ovchinnikov, S., Kinch, L., Park, H., Liao, Y., Pei, J., Kim, D. E., Kamisetty, H., Grishin, N. V., & Baker, D. (2015) · eLife · doi:10.7554/elife.09248 · Cited by 222 · see citing works

Challenges and perspectives of metaproteomic data analysis

Heyer, R., Schallert, K., Zoun, R., Becher, B., Saake, G., & Benndorf, D. (2017) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2017.06.1201 · Cited by 219 · see citing works

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

Castelle, C., Hug, L., Wrighton, K., Thomas, B., Williams, K., Wu, D., Tringe, S., Singer, S., Eisen, J., & Banfield, J. (2013) · Nature Communications · doi:10.1038/ncomms3120 · Cited by 224 · see citing works

The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches

Dhakan, D. B., Maji, A., Sharma, A. K., Saxena, R., Pulikkan, J., Grace, T., Gomez, A. M., Scaria, J., Amato, K. R., & Sharma, V. K. (2019) · GigaScience · doi:10.1093/gigascience/giz004 · Cited by 217 · see citing works

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 230 · see citing works

Learning from prepandemic data to forecast viral escape

Thadani, N. N., Gurev, S. F., Notin, P., Youssef, N., Rollins, N. J., Ritter, D., Sander, C., Gal, Y., & Marks, D. S. (2023) · Nature · doi:10.1038/s41586-023-06617-0 · Cited by 212 · see citing works

Fermented-food metagenomics reveals substrate-associated differences in taxonomy and health-associated and antibiotic resistance determinants

Leech, J., Cabrera-Rubio, R., Walsh, A. M., Macori, G., Walsh, C. J., Barton, W., Finnegan, L., Crispie, F., O’Sullivan, O., Claesson, M. J., et al. (2020) · mSystems · doi:10.1128/msystems.00522-20 · Cited by 200 · see citing works

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm098 Databases and ontologies UniRef: comprehensive and non-redundant UniProt reference

Suzek, B. E., Huang, H., Mcgarvey, P., Mazumder, R., & Wu, C. H. (2008)

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B., Wu, C. H., & the UniProt Consortium (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu739 · Cited by 1,928 · see citing works

The Universal Protein Resource (UniProt): an expanding universe of protein information

Wu, C. H. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj161 · Cited by 1,116 · see citing works

doi:10.1093/nar/gkj161 The Universal Protein Resource (UniProt): an expanding universe of protein information

Wu, C. H., Apweiler, R., Bairoch, A., Natale, D. A., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., López, R., et al. (2005)

Removing near-neighbour redundancy from large protein sequence collections.

Holm, L., & Sander, C. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.5.423 · Cited by 297 · see citing works