UniRef: comprehensive and non-redundant UniProt reference clusters

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

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Database resources of the National Center for Biotechnology Information: update

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

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The Universal Protein Resource (UniProt)

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

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

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Length-dependent prediction of protein intrinsic disorder

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Selection of representative protein data sets

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Identification of multiple distinct Snf2 subfamilies with conserved structural motifs

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Database resources of the National Center for Biotechnology Information

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

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UniProt: a hub for protein information

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UniProt: the universal protein knowledgebase

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The Pfam protein families database

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

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

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

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

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

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JPred4: a protein secondary structure prediction server

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Activities at the Universal Protein Resource (UniProt)

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SIFT missense predictions for genomes

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

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The Jpred 3 secondary structure prediction server

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

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Strains, functions and dynamics in the expanded Human Microbiome Project

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

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

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

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

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A transposase strategy for creating libraries of circularly permuted proteins

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A large-scale evaluation of computational protein function prediction

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Improved prediction of protein-protein interactions using AlphaFold2

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

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The Universal Protein Resource (UniProt) in 2010

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

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

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

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

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

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The Universal Protein Resource (UniProt)

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Ongoing and future developments at the Universal Protein Resource

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

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

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

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

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

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

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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

Human gut bacteria produce ΤΗ17-modulating bile acid metabolites

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Insights into the Maize Pan-Genome and Pan-Transcriptome

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Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

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

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The Universal Protein Resource (UniProt) 2009

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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

Ultrafast clustering algorithms for metagenomic sequence analysis

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Targeted RNA sequencing reveals the deep complexity of the human transcriptome

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Learning the protein language: Evolution, structure, and function

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Efficient evolution of human antibodies from general protein language models

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

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

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

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Drug repurposing for cancer therapy

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

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

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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

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

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

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A global metagenomic map of urban microbiomes and antimicrobial resistance

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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 365

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

Improving Protein Expression, Stability, and Function with ProteinMPNN

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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 360

Collective judgment predicts disease-associated single nucleotide variants

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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

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

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

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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

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 302

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

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

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

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Molecular Principles of the Interactions of Disordered Proteins

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

Probst, A. J., Ladd, B., Jarett, J. K., Geller‐McGrath, D., Sieber, C. M. K., Emerson, J., Anantharaman, K., Thomas, B. C., Malmstrom, R. R., Stieglmeier, M., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-017-0098-y · Cited by 267

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

Hauser, M., Steinegger, M., & Söding, J. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw006 · Cited by 263

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 279

Genome-reconstruction for eukaryotes from complex natural microbial communitiesPreprint

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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

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

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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

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 247

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

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

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

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 240

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

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