Peer Bork

Research interests

Publications

• InterPro: the protein sequence classification resource in 2025

  Nucleic Acids Research · 2024 · 10.1093/nar/gkae1082

• Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool

  Nucleic Acids Research · 2024 · 10.1093/nar/gkae268

• The STRING database in 2025: protein networks with directionality of regulation

  Nucleic Acids Research · 2024 · 10.1093/nar/gkae1113

• InterPro in 2022

  Nucleic Acids Research · 2022 · https://doi.org/10.1093/nar/gkac993

• The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest

  Nucleic Acids Research · 2022 · https://doi.org/10.1093/nar/gkac1000

• Swarm Learning for decentralized and confidential clinical machine learning

  Nature · 2021 · https://doi.org/10.1038/s41586-021-03583-3

• Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

  Nucleic Acids Research · 2021 · https://doi.org/10.1093/nar/gkab301

• eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

  Molecular Biology and Evolution · 2021 · https://doi.org/10.1093/molbev/msab293

• The InterPro protein families and domains database: 20 years on

  Nucleic Acids Research · 2020 · 10.1093/nar/gkaa977

• SMART: recent updates, new developments and status in 2020

  Nucleic Acids Research · 2020 · 10.1093/nar/gkaa937

• Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment

  Cell · 2020 · 10.1016/j.cell.2020.08.001

• The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets

  Nucleic Acids Research · 2020 · 10.1093/nar/gkaa1074

• Interactive Tree Of Life (iTOL) v4: recent updates and new developments

  Nucleic Acids Research · 2019 · 10.1093/nar/gkz239

• Marine DNA Viral Macro- and Microdiversity from Pole to Pole

  Cell · 2019 · 10.1016/j.cell.2019.03.040

• STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

  Nucleic Acids Research · 2018 · https://doi.org/10.1093/nar/gky1131

• Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

  Cell Host & Microbe · 2018 · 10.1016/j.chom.2018.06.005

• eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

  Nucleic Acids Research · 2018 · 10.1093/nar/gky1085

• InterPro in 2019: improving coverage, classification and access to protein sequence annotations

  Nucleic Acids Research · 2018 · 10.1093/nar/gky1100

• The Human Gut Microbiome: From Association to Modulation

  Cell · 2018 · 10.1016/j.cell.2018.02.044

• Recovery of gut microbiota of healthy adults following antibiotic exposure

  Nature Microbiology · 2018 · 10.1038/s41564-018-0257-9

• 20 years of the SMART protein domain annotation resource

  Nucleic Acids Research · 2017 · 10.1093/nar/gkx922

• Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

  Molecular Biology and Evolution · 2017 · 10.1093/molbev/msx148

• Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

  Nature Biotechnology · 2017 · 10.1038/nbt.3893

• Enterotypes in the landscape of gut microbial community composition

  Nature Microbiology · 2017 · 10.1038/s41564-017-0072-8

• Human gut microbes impact host serum metabolome and insulin sensitivity

  Nature · 2016 · 10.1038/nature18646

• Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

  Nature · 2016 · 10.1038/nature19366

• The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

  Nucleic Acids Research · 2016 · 10.1093/nar/gkw937

• Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

  Nucleic Acids Research · 2016 · 10.1093/nar/gkw290

• Plankton networks driving carbon export in the oligotrophic ocean

  Nature · 2016 · 10.1038/nature16942

• InterPro in 2017—beyond protein family and domain annotations

  Nucleic Acids Research · 2016 · 10.1093/nar/gkw1107

• eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

  Nucleic Acids Research · 2015 · 10.1093/nar/gkv1248

• Determinants of community structure in the global plankton interactome

  Science · 2015 · 10.1126/science.1262073

• Eukaryotic plankton diversity in the sunlit ocean

  Science · 2015 · 10.1126/science.1261605

• The SIDER database of drugs and side effects

  Nucleic Acids Research · 2015 · 10.1093/nar/gkv1075

• Structure and function of the global ocean microbiome

  Science · 2015 · 10.1126/science.1261359

• Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

  Nature · 2015 · 10.1038/nature15766

• STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

  Nucleic Acids Research · 2015 · 10.1093/nar/gkv1277

• An integrated catalog of reference genes in the human gut microbiome

  Nature Biotechnology · 2014 · 10.1038/nbt.2942

• STRING v10: protein–protein interaction networks, integrated over the tree of life

  Nucleic Acids Research · 2014 · https://doi.org/10.1093/nar/gku1003

• Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

  Nature Biotechnology · 2014 · 10.1038/nbt.2939

• The InterPro protein families database: the classification resource after 15 years

  Nucleic Acids Research · 2014 · 10.1093/nar/gku1243

• SMART: recent updates, new developments and status in 2015

  Nucleic Acids Research · 2014 · 10.1093/nar/gku949

• Richness of human gut microbiome correlates with metabolic markers

  Nature · 2013 · 10.1038/nature12506

• eggNOG v4.0: nested orthology inference across 3686 organisms

  Nucleic Acids Research · 2013 · 10.1093/nar/gkt1253

• STRING v9.1: protein-protein interaction networks, with increased coverage and integration

  Nucleic Acids Research · 2012 · 10.1093/nar/gks1094

• Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

  Nature Biotechnology · 2011 · 10.1038/nbt.1823

• SMART 7: recent updates to the protein domain annotation resource

  Nucleic Acids Research · 2011 · 10.1093/nar/gkr931

• InterPro in 2011: new developments in the family and domain prediction database

  Nucleic Acids Research · 2011 · 10.1093/nar/gkr948

• Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

  Nucleic Acids Research · 2011 · 10.1093/nar/gkr201

• Enterotypes of the human gut microbiome

  Nature · 2011 · 10.1038/nature09944

• The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

  Nucleic Acids Research · 2010 · 10.1093/nar/gkq973

• A side effect resource to capture phenotypic effects of drugs

  Molecular Systems Biology · 2010 · 10.1038/msb.2009.98

• A method and server for predicting damaging missense mutations

  Nature Methods · 2010 · https://doi.org/10.1038/nmeth0410-248

• A human gut microbial gene catalogue established by metagenomic sequencing

  Nature · 2010 · https://doi.org/10.1038/nature08821

• STRING 8--a global view on proteins and their functional interactions in 630 organisms

  Nucleic Acids Research · 2008 · 10.1093/nar/gkn760

• InterPro: the integrative protein signature database

  Nucleic Acids Research · 2008 · 10.1093/nar/gkn785

• Drug Target Identification Using Side-Effect Similarity

  Science · 2008 · 10.1126/science.1158140

• SMART 6: recent updates and new developments

  Nucleic Acids Research · 2008 · 10.1093/nar/gkn808

• The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

  Nature · 2008 · 10.1038/nature06617

• STITCH: interaction networks of chemicals and proteins

  Nucleic Acids Research · 2007 · 10.1093/nar/gkm795

• SuperTarget and Matador: resources for exploring drug-target relationships

  Nucleic Acids Research · 2007 · 10.1093/nar/gkm862

• Systematic Discovery of In Vivo Phosphorylation Networks

  Cell · 2007 · 10.1016/j.cell.2007.05.052

• Proteome survey reveals modularity of the yeast cell machinery

  Nature · 2006 · 10.1038/nature04532

• STRING 7--recent developments in the integration and prediction of protein interactions

  Nucleic Acids Research · 2006 · 10.1093/nar/gkl825

• Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

  Bioinformatics · 2006 · 10.1093/bioinformatics/btl529

• Insights into social insects from the genome of the honeybee Apis mellifera

  Nature · 2006 · 10.1038/nature05260

• Toward Automatic Reconstruction of a Highly Resolved Tree of Life

  Science · 2006 · 10.1126/science.1123061

• PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

  Nucleic Acids Research · 2006 · 10.1093/nar/gkl315

• Literature mining for the biologist: from information retrieval to biological discovery

  Nature Reviews Genetics · 2006 · 10.1038/nrg1768

• Comparative Metagenomics of Microbial Communities

  Science · 2005 · 10.1126/science.1107851

• Protein Disorder Prediction

  Structure · 2003 · 10.1016/j.str.2003.10.002

• Comparative assessment of large-scale data sets of protein–protein interactions

  Nature · 2002 · 10.1038/nature750

• Immunity-Related Genes and Gene Families in Anopheles gambiae

  Science · 2002 · 10.1126/science.1077136

• Functional organization of the yeast proteome by systematic analysis of protein complexes

  Nature · 2002 · 10.1038/415141a

• SMART, a simple modular architecture research tool: Identification of signaling domains

  Proceedings of the National Academy of Sciences · 1998 · 10.1073/pnas.95.11.5857

Current projects

No projects listed.