Databases, tools, and other resources

STRING: Analysis of known and predicted protein-protein interactions

In collaboration with Christian von Mering, Lars Juhl Jensen

• The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest (2023)
• The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets (2021)
• STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets (2019)
• The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible (2017)
• STRING 7--recent developments in the integration and prediction of protein interactions (2006)
• STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene (2000)

SMART: Analysis of protein domains

In collaboration with Ivica Letunic

• SMART: recent updates, new developments and status in 2020 (2021)
• 20 years of the SMART protein domain annotation resource (2018)
• SMART 5: domains in the context of genomes and networks (2006)
• SMART, a simple modular architecture research tool: Identification of signaling domains (1998)

proGenomes: A resource for consistent functional and taxonomic annotations of prokaryotic genomes

In collaboration with Daniel Mende

• proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes (2023)
• proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes (2020)
• proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes (2017)

eggNOG: A database of orthologous groups of genes

In collaboration with Jaime Huerta-Cepas, Christian von Mering, Lars Juhl Jensen

• eggNOG 6.0: enabling comparative genomics across 12535 organisms (2023)
• eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2019)
• eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences (2016)
• eggNOG v4.0: nested orthology inference across 3686 organisms (2014)
• eggNOG: automated construction and annotation of orthologous groups of genes (2008)

GMGC: An integrated, consistently-processed, gene catalog of the microbial world, combining metagenomics and high-quality sequenced isolates

In collaboration with Luis Pedro Coelho

• Towards the biogeography of prokaryotic genes (2022)

SPIRE: A Searchable Planetary-scale mIcrobiome REsource that integrates various consistently processed metagenome-derived microbial data modalities across habitats, geography and phylogeny

• SPIRE: a Searchable, Planetary-scale mIcrobiome REsource (2024)

proMGE: A resource for the retrieval of Mobile Genetic Elements from genomes

• Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes (2022)

Enterotypes: Reference-based Enterotype Classification Tool

• Refined Enterotyping Reveals Dysbiosis in Global Fecal Metagenomes (2024)
• Enterotypes of the human gut microbiome (2015)

Microbial Load Predictor: A computational tool designed to predict the fecal microbial load (microbial cells per gram or cell density) of adult fecal samples directly from the taxonomic profile of the gut microbiome

• Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations (2024)

mOTUs: A tool for microbial abundance profiling using marker genes

In collaboration with Georg Zeller, Shinichi Sunagawa

• Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments (2022)
• Microbial abundance, activity and population genomic profiling with mOTUs2 (2019)
• Metagenomic species profiling using universal phylogenetic marker genes (2013)

NGLess: A domain-specific language for NGS (next-generation sequencing data) processing

In collaboration with Luis Pedro Coelho

• NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language (2019)

metaSNV: A tool for metagenomic strain level analysis

In collaboration with Shinichi Sunagawa

• metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes (2021)
• metaSNV: A tool for metagenomic strain level analysis (2017)

iTOL: An online tool for the display and manipulation of phylogenetic trees

In collaboration with Ivica Letunic

• Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool (2024)
• Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation (2021)
• Interactive Tree Of Life (iTOL) v4: recent updates and new developments (2019)
• Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees (2016)
• Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation (2007)

ETE 3: A Python framework for the analysis and visualization of trees.

In collaboration with Jaime Huerta-Cepas

• ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data (2016)

iPath: Interactive exploration of biochemical pathways and networks

In collaboration with Takuji Yamada, Ivica Letunic

• iPath3.0: interactive pathways explorer v3 (2018)
• iPath2.0: interactive pathway explorer (2011)
• iPath: interactive exploration of biochemical pathways and networks (2008)

SIDER: A database of drugs and side effects

• The SIDER database of drugs and side effects (2016)

STITCH: Database of known and predicted interactions of chemicals and proteins

• STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data (2016)
• STITCH: interaction networks of chemicals and proteins (2008)

PTMcode: A resource for functional associations of post-translational modifications within and between proteins

• PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins (2015)
• PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins (2013)

Companion website for TARA Oceans paper

• Structure and function of the global ocean microbiome (2015)

Chaetomium thermophilum genome resource: The first complete genome of a true thermophilic eukaryote

• Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile (2011)

AQUA: An automatic quality improvment for multiple sequence alignment

• AQUA: Automated quality improvement for multiple sequence alignments (2010)

PAL2NAL: Conversion of protein sequence alignments into the codon alignments + Ka/Ks-Calculations

• Robust conversion of protein sequence alignments into the corresponding codon alignments (2006)

PolyPhen: Prediction of functional effect of human nsSNPs

• Human non-synonymous SNPs: server and survey (2002)

BLAST2GENE: Gene analysis in genomic regions

• conversion of BLAST output into independent genes and gene fragments (2004)