| 1 | GENCODE 2025: reference gene annotation for human and mouse | 15.5 | 346 | Citations (PDF) |
| 2 | EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2024 | 15.5 | 11 | Citations (PDF) |
| 3 | Ensembl 2025 | 15.5 | 599 | Citations (PDF) |
| 4 | HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production | 2.7 | 5 | Citations (PDF) |
| 5 | mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies | 4.7 | 3 | Citations (PDF) |
| 6 | CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome | 3.2 | 1 | Citations (PDF) |
| 7 | A bacterial and viral genome catalogue from Atlantic salmon highlights diverse gut microbiome compositions at pre- and post-smolt life stages | 4.0 | 2 | Citations (PDF) |
| 8 | SPIRE: a Searchable, Planetary-scale mIcrobiome REsource | 15.5 | 89 | Citations (PDF) |
| 9 | Ensembl 2024 | 15.5 | 742 | Citations (PDF) |
| 10 | Establishing the ELIXIR Microbiome Community | 0.5 | 1 | Citations (PDF) |
| 11 | Fungtion: A Server for Predicting and Visualizing Fungal Effector Proteins | 4.1 | 8 | Citations (PDF) |
| 12 | The growing repertoire of phage anti-defence systems | 8.1 | 93 | Citations (PDF) |
| 13 | Diversity and specificity of molecular functions in cyanobacterial symbionts | 3.4 | 8 | Citations (PDF) |
| 14 | CELEBRIMBOR: core and accessory genes from metagenomes | 4.7 | 2 | Citations (PDF) |
| 15 | Microbial occurrence and symbiont detection in a global sample of lichen metagenomes | 5.0 | 27 | Citations (PDF) |
| 16 | Ensembl 2023 | 15.5 | 1,049 | Citations (PDF) |
| 17 | MGnify: the microbiome sequence data analysis resource in 2023 | 15.5 | 429 | Citations (PDF) |
| 18 | Staphylococcal diversity in atopic dermatitis from an individual to a global scale | 15.1 | 63 | Citations (PDF) |
| 19 | VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models | 3.1 | 27 | Citations (PDF) |
| 20 | The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data | 15.5 | 10 | Citations (PDF) |
| 21 | Metagenomics approach for Polymyxa betae genome assembly enables comparative analysis towards deciphering the intracellular parasitic lifestyle of the plasmodiophorids | 2.8 | 11 | Citations (PDF) |
| 22 | Ensembl Genomes 2022: an expanding genome resource for non-vertebrates | 15.5 | 412 | Citations (PDF) |
| 23 | A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae | 11.5 | 27 | Citations (PDF) |
| 24 | A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications | 3.2 | 12 | Citations (PDF) |
| 25 | Screening of global microbiomes implies ecological boundaries impacting the distribution and dissemination of clinically relevant antimicrobial resistance genes | 4.4 | 19 | Citations (PDF) |
| 26 | metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data | 3.2 | 4 | Citations (PDF) |
| 27 | Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research | 6.6 | 132 | Citations (PDF) |
| 28 | The InterPro protein families and domains database: 20 years on | 15.5 | 2,186 | Citations (PDF) |
| 29 | Rfam 14: expanded coverage of metagenomic, viral and microRNA families | 15.5 | 1,017 | Citations (PDF) |
| 30 | Pfam: The protein families database in 2021 | 15.5 | 6,285 | Citations (PDF) |
| 31 | Massive expansion of human gut bacteriophage diversityCell, 2021, 184, 1098-1109.e9 | 33.6 | 591 | Citations (PDF) |
| 32 | Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes | 2.4 | 37 | Citations (PDF) |
| 33 | Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data | 14.4 | 68 | Citations (PDF) |
| 34 | An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities | 3.4 | 39 | Citations (PDF) |
| 35 | R2DT is a framework for predicting and visualising RNA secondary structure using templates | 13.7 | 139 | Citations (PDF) |
| 36 | Reporting guidelines for human microbiome research: the STORMS checklist | 33.0 | 436 | Citations (PDF) |
| 37 | A catalogue of 1,167 genomes from the human gut archaeome | 16.0 | 162 | Citations (PDF) |
| 38 | Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions | 16.0 | 154 | Citations (PDF) |
| 39 | MGnify: the microbiome analysis resource in 2020 | 15.5 | 384 | Citations (PDF) |
| 40 | Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation | 15.5 | 14 | Citations (PDF) |
| 41 | Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli | 3.3 | 111 | Citations (PDF) |
| 42 | The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences | 4.7 | 68 | Citations (PDF) |
| 43 | Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics | 3.0 | 111 | Citations (PDF) |
| 44 | Microbiota Characterization of Agricultural Green Waste-Based Suppressive Composts Using Omics and Classic Approaches | 3.1 | 37 | Citations (PDF) |
| 45 | A unified catalog of 204,938 reference genomes from the human gut microbiome | 29.8 | 1,298 | Citations (PDF) |
| 46 | 3DPatch: fast 3D structure visualization with residue conservation | 4.7 | 3 | Citations (PDF) |
| 47 | The EMBL-EBI search and sequence analysis tools APIs in 2019 | 15.5 | 4,234 | Citations (PDF) |
| 48 | Microbial community drivers of PK/NRP gene diversity in selected global soils | 11.5 | 42 | Citations (PDF) |
| 49 | Microbial abundance, activity and population genomic profiling with mOTUs2 | 13.7 | 425 | Citations (PDF) |
| 50 | A new genomic blueprint of the human gut microbiota | 37.9 | 1,237 | Citations (PDF) |
| 51 | RNAcentral: a hub of information for non-coding RNA sequences | 15.5 | 75 | Citations (PDF) |
| 52 | RNAcentral: a hub of information for non-coding RNA sequences | 15.5 | 268 | Citations (PDF) |
| 53 | The Pfam protein families database in 2019 | 15.5 | 4,609 | Citations (PDF) |
| 54 | Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes | 15.5 | 37 | Citations (PDF) |
| 55 | InterPro in 2019: improving coverage, classification and access to protein sequence annotations | 15.5 | 1,474 | Citations (PDF) |
| 56 | TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations | 4.7 | 66 | Citations (PDF) |
| 57 | A human gut bacterial genome and culture collection for improved metagenomic analyses | 29.8 | 569 | Citations (PDF) |
| 58 | Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species | 15.5 | 519 | Citations (PDF) |
| 59 | Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families | 15.5 | 975 | Citations (PDF) |
| 60 | EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies | 15.5 | 201 | Citations (PDF) |
| 61 | The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database | 15.5 | 1,688 | Citations (PDF) |
| 62 | Eleven quick tips to build a usable REST API for life sciences | 3.1 | 20 | Citations (PDF) |
| 63 | Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments | 3.2 | 129 | Citations (PDF) |
| 64 | Non‐Coding RNA Analysis Using the Rfam Database | 3.3 | 479 | Citations (PDF) |
| 65 | HMMER web server: 2018 update | 15.5 | 2,452 | Citations (PDF) |
| 66 | InterPro in 2017—beyond protein family and domain annotations | 15.5 | 1,524 | Citations (PDF) |
| 67 | The HMMER Web Server for Protein Sequence Similarity Search | 3.3 | 195 | Citations (PDF) |
| 68 | The metagenomic data life-cycle: standards and best practices | 3.2 | 61 | Citations (PDF) |
| 69 | RNAcentral: a comprehensive database of non-coding RNA
sequences | 15.5 | 242 | Citations (PDF) |
| 70 | ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services | 0.5 | 11 | Citations (PDF) |
| 71 | EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data | 15.5 | 101 | Citations (PDF) |
| 72 | GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations | 2.7 | 22 | Citations (PDF) |
| 73 | The Dfam database of repetitive DNA families | 15.5 | 768 | Citations (PDF) |
| 74 | Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors | 15.5 | 714 | Citations (PDF) |
| 75 | The European Bioinformatics Institute in 2016: Data growth and integration | 15.5 | 122 | Citations (PDF) |
| 76 | The Pfam protein families database: towards a more sustainable future | 15.5 | 6,106 | Citations (PDF) |
| 77 | HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes | 15.5 | 65 | Citations (PDF) |
| 78 | Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes | 3.1 | 190 | Citations (PDF) |
| 79 | Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat: Figure 1. | 2.7 | 8 | Citations (PDF) |
| 80 | HMMER web server: 2015 update | 15.5 | 988 | Citations (PDF) |
| 81 | The InterPro protein families database: the classification resource after 15 years | 15.5 | 1,325 | Citations (PDF) |
| 82 | The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam | 6.6 | 6 | Citations (PDF) |
| 83 | RNAcentral: an international database of ncRNA sequences | 15.5 | 121 | Citations (PDF) |
| 84 | Rfam 12.0: updates to the RNA families database | 15.5 | 1,134 | Citations (PDF) |
| 85 | iPfam: a database of protein family and domain interactions found in the Protein Data Bank | 15.5 | 170 | Citations (PDF) |
| 86 | Pfam: the protein families database | 15.5 | 6,174 | Citations (PDF) |
| 87 | Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis | 3.0 | 1 | Citations (PDF) |
| 88 | Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila | 3.0 | 3 | Citations (PDF) |
| 89 | The challenge of increasing Pfam coverage of the human proteome | 2.7 | 5 | Citations (PDF) |
| 90 | The challenge of increasing Pfam coverage of the human proteome | 2.7 | 24 | Citations (PDF) |
| 91 | Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions | 15.5 | 1,623 | Citations (PDF) |
| 92 | The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold | 0.5 | 2 | Citations (PDF) |
| 93 | The Pfam protein families database | 15.5 | 3,496 | Citations (PDF) |
| 94 | Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference | 2.7 | 10 | Citations (PDF) |
| 95 | Making your database available through Wikipedia: the pros and cons | 15.5 | 31 | Citations (PDF) |
| 96 | InterPro in 2011: new developments in the family and domain prediction database | 15.5 | 959 | Citations (PDF) |
| 97 | Dfam: a database of repetitive DNA based on profile hidden Markov models | 15.5 | 318 | Citations (PDF) |
| 98 | HMMER web server: interactive sequence similarity searching | 15.5 | 5,806 | Citations (PDF) |
| 99 | Rfam: Wikipedia, clans and the "decimal" release | 15.5 | 362 | Citations (PDF) |
| 100 | Representative Proteomes: A Stable, Scalable and Unbiased Proteome Set for Sequence Analysis and Functional Annotation | 2.3 | 100 | Citations (PDF) |
| 101 | Clustered Coding Variants in the Glutamate Receptor Complexes of Individuals with Schizophrenia and Bipolar Disorder | 2.3 | 56 | Citations (PDF) |
| 102 | The structure of BVU2987 fromBacteroides vulgatusreveals a superfamily of bacterial periplasmic proteins with possible inhibitory function | 0.7 | 8 | Citations (PDF) |
| 103 | DUFs: families in search of function | 0.7 | 242 | Citations (PDF) |
| 104 | The crystal structure of a bacterial Sufu‐like protein defines a novel group of bacterial proteins that are similar to the N‐terminal domain of human Sufu | 5.9 | 12 | Citations (PDF) |
| 105 | Bacterial Pleckstrin Homology Domains: A Prokaryotic Origin for the PH Domain | 4.1 | 36 | Citations (PDF) |
| 106 | The Pfam protein families database | 15.5 | 2,767 | Citations (PDF) |
| 107 | DASMI: exchanging, annotating and assessing molecular interaction data | 4.7 | 15 | Citations (PDF) |
| 108 | Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors | 4.7 | 72 | Citations (PDF) |
| 109 | InterPro: the integrative protein signature database | 15.5 | 1,948 | Citations (PDF) |
| 110 | Rfam: updates to the RNA families database | 15.5 | 885 | Citations (PDF) |
| 111 | The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes | 1.8 | 6 | Citations (PDF) |
| 112 | Modifier Effects between Regulatory and Protein-Coding Variation | 3.2 | 37 | Citations (PDF) |
| 113 | Experience using web services for biological sequence analysis | 6.6 | 24 | Citations (PDF) |
| 114 | Pfam 10 years on: 10 000 families and still growing | 6.6 | 117 | Citations (PDF) |
| 115 | Identifying Protein Domains with the Pfam Database | 3.3 | 66 | Citations (PDF) |
| 116 | New developments in the InterPro database | 15.5 | 450 | Citations (PDF) |
| 117 | ProServer: a simple, extensible Perl DAS server | 4.7 | 34 | Citations (PDF) |
| 118 | SCOOP: a simple method for identification of novel protein superfamily relationships | 4.7 | 50 | Citations (PDF) |
| 119 | The Pfam protein families database | 15.5 | 6,637 | Citations (PDF) |
| 120 | Predicting active site residue annotations in the Pfam database | 3.0 | 321 | Citations (PDF) |
| 121 | Integrating sequence and structural biology with DAS | 3.0 | 73 | Citations (PDF) |
| 122 | Pfam: clans, web tools and services | 15.5 | 2,142 | Citations (PDF) |
| 123 | iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions | 4.7 | 296 | Citations (PDF) |
| 124 | Conformational Changes of Escherichia coli σ54-RNA-Polymerase upon Closed–Promoter Complex Formation | 4.1 | 4 | Citations (PDF) |
| 125 | The Second Paradigm for Activation of Transcription | 4.3 | 37 | Citations (PDF) |
| 126 | The Pfam protein families database | 15.5 | 3,317 | Citations (PDF) |
| 127 | Identifying Protein Domains with the Pfam Database | 3.3 | 29 | Citations (PDF) |
| 128 | The PASTA domain: a β-lactam-binding domain | 6.7 | 221 | Citations (PDF) |
| 129 | Escherichia coli RNA polymerase core and holoenzyme structures | 7.3 | 40 | Citations (PDF) |
| 130 | Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins | 15.5 | 541 | Citations (PDF) |
| 131 | The C-Terminal 12 Amino Acids of ςN Are Required for Structure and Function | 2.8 | 3 | Citations (PDF) |
| 132 | Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies | 0.0 | 39 | Citations (PDF) |
| 133 | Unifying the known and unknown microbial coding sequence space | 0.7 | 117 | Citations (PDF) |
| 134 | plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets | 0.9 | 1 | Citations (PDF) |
| 135 | plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets | 0.9 | 0 | Citations (PDF) |
| 136 | An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources | 3.1 | 6 | Citations (PDF) |
| 137 | HoloFoodR: a statistical programming framework for holo-omics data integration workflows | 4.7 | 0 | Citations (PDF) |
| 138 | Ensembl 2026 | 15.5 | 17 | Citations (PDF) |
| 139 | nf-core/proteinfamilies: a scalable pipeline for the generation of protein families | 3.2 | 0 | Citations (PDF) |
| 140 | Gut microbiome community structure correlates with different behavioral phenotypes in the Belyaev Farm-Fox Experiment | 4.4 | 0 | Citations (PDF) |
| 141 | HMMER web server: 2026 update | 15.5 | 0 | Citations (PDF) |
