Damian Szklarczyk

The share of this author’s assessed papers carrying a ⚑ flag. A concentration is a prompt for expert review — never, on its own, a determination about the person.

Collaborators, sized by shared output and coloured by their own reproducibility (green = high, red = low). Click a node to open their card. A pattern is a prompt for review, never a determination.

How this author’s assessed papers reproduced — the outcome of reproduction attempts, not a judgement of the person. Coverage is partial and grows over time.

Assessed papers (1)

• Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.
  2022 L1 94/100

1 assessed by us (1 reproduced) · 71 not yet assessed — every PubMed paper on record, linked below.

• PaxDb v6.0: reprocessed, LLM-selected, curated protein abundance data across organisms ↗

  Nucleic Acids Research · 2025 · PMID 41182819
  not yet assessed
• eggNOG v7: phylogeny-based orthology predictions and functional annotations ↗

  Nucleic Acids Research · 2025 · PMID 41359032
  not yet assessed
• SPACE: STRING proteins as complementary embeddings ↗

  Bioinformatics · 2025 · PMID 40924541
  not yet assessed
• eggNOG v7: phylogeny-based orthology predictions and functional annotations ↗

  2025
  not yet assessed
• The STRING database in 2025: protein networks with directionality of regulation ↗

  Nucleic Acids Research · 2024 · PMID 39558183
  not yet assessed
• Enhancing coevolutionary signals in protein–protein interaction prediction through clade-wise alignment integration ↗

  Scientific Reports · 2024 · PMID 38472223
  not yet assessed
• SPACE: STRING proteins as complementary embeddings ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024
  not yet assessed
• PaxDb 5.0: Curated Protein Quantification Data Suggests Adaptive Proteome Changes in Yeasts ↗

  Molecular & Cellular Proteomics · 2023 · PMID 37659604
  not yet assessed
• The SIB Swiss Institute of Bioinformatics Semantic Web of data ↗

  Nucleic Acids Research · 2023 · PMID 37878411
  not yet assessed
• CanIsoNet: a database to study the functional impact of isoform switching events in diseases ↗

  Bioinformatics Advances · 2023 · PMID 37123454
  not yet assessed
• PaxDB 5.0: curated protein quantification data suggests adaptive proteome changes ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2023
  not yet assessed
• Clade-wise alignment integration improves co-evolutionary signals for protein-protein interaction prediction ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2023
  not yet assessed
• The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest

  Open MIND · 2023
  not yet assessed
• The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest ↗

  Nucleic Acids Research · 2022 · PMID 36370105
  not yet assessed
• eggNOG 6.0: enabling comparative genomics across 12 535 organisms ↗

  Nucleic Acids Research · 2022 · PMID 36399505
  not yet assessed
• Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks ↗

  Journal of Proteome Research · 2022 · PMID 36512705
  not yet assessed
• proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes ↗

  Nucleic Acids Research · 2022 · PMID 36408900
  not yet assessed
• Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments

  Briefings in Bioinformatics · 2022 · PMID 36088548
  L1 94/100
• Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2022
  not yet assessed
• Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2022
  not yet assessed
• Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments ↗

  Zenodo (CERN European Organization for Nuclear Research) · 2022
  not yet assessed
• Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments

  Open MIND · 2022
  not yet assessed
• GUNC: detection of chimerism and contamination in prokaryotic genomes ↗

  Genome biology · 2021 · PMID 34120611
  not yet assessed
• Ten Years of Collaborative Progress in the Quest for Orthologs ↗

  Molecular Biology and Evolution · 2021 · PMID 33822172
  not yet assessed
• Correction to ‘The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets’ ↗

  Nucleic Acids Research · 2021
  not yet assessed
• CanIsoNet: A Database to Study the Functional Impact of Isoform Switching Events in Diseases ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• Additional file 2 of GUNC: detection of chimerism and contamination in prokaryotic genomes ↗

  Open MIND · 2021
  not yet assessed
• The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets ↗

  Nucleic Acids Research · 2020 · PMID 33237311
  not yet assessed
• The Quest for Orthologs benchmark service and consensus calls in 2020 ↗

  Nucleic Acids Research · 2020 · PMID 32374845
  not yet assessed
• Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network ↗

  Scientific Reports · 2020 · PMID 32879328
  not yet assessed
• GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2020
  not yet assessed
• Interpreting copy number variation pattern in cancer with STRING protein interaction network ↗

  Faculty of 1000 Research Ltd · 2020
  not yet assessed
• Referee report. For: Cancer Publication Portal: an online tool for summarizing and searching human cancer-genomic publications [version 1; peer review: 2 approved with reservations] ↗

  Faculty of 1000 Research Ltd · 2020
  not yet assessed
• Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling ↗

  Molecular Cell · 2019 · PMID 31101498
  not yet assessed
• Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies ↗

  BMC Bioinformatics · 2019 · PMID 31060495
  not yet assessed
• Pathogenic impact of transcript isoform switching in 1209 cancer samples covering 27 cancer types using an isoform-specific interaction network ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2019
  not yet assessed
• Additional file 6 of Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies ↗

  Figshare · 2019
  not yet assessed
• STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets ↗

  Nucleic Acids Research · 2018 · PMID 30476243
  not yet assessed
• eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses ↗

  Nucleic Acids Research · 2018 · PMID 30418610
  not yet assessed
• Viruses.STRING: A Virus-Host Protein-Protein Interaction Database ↗

  Viruses · 2018 · PMID 30249048
  not yet assessed
• Viruses.STRING: A virus–host protein–protein interaction database ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Analysis of the human kinome and phosphatome reveals diseased signaling networks induced by overexpression ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Analysis of the Human Kinome and Phosphatome Reveals Diseased Signaling Networks Induced by Overexpression ↗

  SSRN Electronic Journal · 2018
  not yet assessed
• Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper ↗

  Molecular Biology and Evolution · 2017 · PMID 28460117
  not yet assessed
• Gearing up to handle the mosaic nature of life in the quest for orthologs ↗

  Bioinformatics · 2017 · PMID 28968857
  not yet assessed
• The STRING database in 2017

  2017
  not yet assessed
• The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible ↗

  Nucleic Acids Research · 2016 · PMID 27924014
  not yet assessed
• Standardized benchmarking in the quest for orthologs ↗

  Nature Methods · 2016 · PMID 27043882
  not yet assessed
• Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2016
  not yet assessed
• NOVEL GENES INVOLVED IN NEUROPATHIC PAIN IN PATIENTS ↗

  Data Archiving and Networked Services (DANS) · 2016
  not yet assessed
• eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences ↗

  Nucleic Acids Research · 2015 · PMID 26582926
  not yet assessed
• STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data ↗

  Nucleic Acids Research · 2015 · PMID 26590256
  not yet assessed
• Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell‐lines ↗

  PROTEOMICS · 2015 · PMID 25656970
  not yet assessed
• Protein-Protein Interaction Databases ↗

  Methods in molecular biology · 2015 · PMID 25859942
  not yet assessed
• WeGET: predicting new genes for molecular systems by weighted co-expression ↗

  Nucleic Acids Research · 2015 · PMID 26582928
  not yet assessed
• STRING v10: protein–protein interaction networks, integrated over the tree of life ↗

  Nucleic Acids Research · 2014 · PMID 25352553
  not yet assessed
• Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse ↗

  Nature · 2013 · PMID 23803765
  not yet assessed
• eggNOG v4.0: nested orthology inference across 3686 organisms ↗

  Nucleic Acids Research · 2013 · PMID 24297252
  not yet assessed
• STITCH 4: integration of protein–chemical interactions with user data ↗

  Nucleic Acids Research · 2013 · PMID 24293645
  not yet assessed
• STRING v9.1: protein-protein interaction networks, with increased coverage and integration ↗

  Nucleic Acids Research · 2012 · PMID 23203871
  not yet assessed
• "Orphan" Retrogenes in the Human Genome ↗

  Molecular Biology and Evolution · 2012 · PMID 23066043
  not yet assessed
• Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs ↗

  BMC Systems Biology · 2012 · PMID 22824421
  not yet assessed
• eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges ↗

  Nucleic Acids Research · 2011 · PMID 22096231
  not yet assessed
• STITCH 3: zooming in on protein-chemical interactions ↗

  Nucleic Acids Research · 2011 · PMID 22075997
  not yet assessed
• Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins ↗

  Journal of Proteome Research · 2011 · PMID 22103443
  not yet assessed
• Specific CLK Inhibitors from a Novel Chemotype for Regulation of Alternative Splicing ↗

  Chemistry & Biology · 2011 · PMID 21276940
  not yet assessed
• Pre-Clovis Mastodon Hunting 13,800 Years Ago at the Manis Site, Washington ↗

  Science · 2011 · PMID 22021854
  not yet assessed
• The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored ↗

  Nucleic Acids Research · 2010 · PMID 21045058
  not yet assessed
• Mass Spectrometric Analysis of Lysine Ubiquitylation Reveals Promiscuity at Site Level ↗

  Molecular & Cellular Proteomics · 2010 · PMID 21139048
  not yet assessed
• STITCH 2: an interaction network database for small molecules and proteins ↗

  Nucleic Acids Research · 2009 · PMID 19897548
  not yet assessed
• eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations ↗

  Nucleic Acids Research · 2009 · PMID 19900971
  not yet assessed