Peer Bork

Research summary

The STRING database integrates direct (physical) and indirect (functional) protein-protein associations from automated literature text mining, interaction-experiment databases, curated pathway sources, and computational predictions based on co-expression and conserved genomic context. Version 10 expanded coverage to more than 2,000 organisms with scalable algorithms for cross-species transfer of interaction evidence [4]; v11 introduced increased coverage and tooling explicitly designed to support functional enrichment in genome-wide experimental datasets [1]; the 2021 release added customizable networks and functional characterization for user-uploaded gene/measurement sets [5]; and the 2023 release extended enrichment analysis to arbitrary sequenced genomes of interest [6]. The 2017 release prioritized quality control and broader accessibility through a redesigned web interface [7]. A parallel strand quantifies the genetic potential of the human gut microbiome. Illumina-based metagenomic sequencing of faecal samples from 124 European individuals produced 576.7 Gb of sequence and a non-redundant catalogue of 3.3 million microbial genes — roughly 150 times the size of the human gene complement — with the observation that most of these genes are shared across the cohort and that more than 99% are bacterial [2]. A third strand supports phylogenetic visualization. The Interactive Tree Of Life (iTOL) v5 rewrites the tree display engine, adds a MEME-motif dataset type, extends annotation options to non-numerical categorical values and multiple values per node, and provides direct manual drawing and labeling tools on rendered trees [3]. Across all of these resources, the engineering choices prioritize web accessibility, scalable integration of heterogeneous evidence types, and direct linkage between sequence-level data and higher-order biological context.

Recent publications

1. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets2018 · Nucleic Acids Research · 18989 citationsDOI
2. A method and server for predicting damaging missense mutations2010 · Nature Methods · 13510 citationsDOI
3. A human gut microbial gene catalogue established by metagenomic sequencing2010 · Nature · 11567 citationsDOI
4. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation2021 · Nucleic Acids Research · 11457 citationsDOI
5. STRING v10: protein–protein interaction networks, integrated over the tree of life2014 · Nucleic Acids Research · 11038 citationsDOI
6. The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets2020 · Nucleic Acids Research · 8440 citationsDOI
7. The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest2022 · Nucleic Acids Research · 8318 citationsDOI
8. Enterotypes of the human gut microbiome2011 · Nature · 7574 citationsDOI
9. The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible2016 · Nucleic Acids Research · 7416 citationsDOI
10. Initial sequencing and comparative analysis of the mouse genome2002 · Nature · 7230 citationsDOI

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External profiles

• ORCID: https://orcid.org/0000-0002-2627-833X
• OpenAlex: openalex.org

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