List of works - Damian Szklarczyk

"Orphan" retrogenes in the human genome

scientific article published on 12 October 2012

Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling.

scientific article published on 14 May 2019

Analysis of the human kinome and phosphatome reveals diseased signaling networks induced by overexpression

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

scientific article published on 29 April 2017

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

article

GUNC: detection of chimerism and contamination in prokaryotic genomes

scientific article published on 13 June 2021

Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs

scientific article (publication date: 23 July 2012)

Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network

scientific article published on 02 September 2020

Pre-Clovis Mastodon Hunting 13,800 Years Ago at the Manis Site, Washington

scientific article (publication date: 20 October 2011)

Protein-Protein Interaction Databases

scientific article (publication date: 2015)

Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins

scientific article (publication date: 3 February 2012)

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

scientific article

STITCH 2: an interaction network database for small molecules and proteins

scientific article (publication date: 2010)

STITCH 4: integration of protein-chemical interactions with user data

scientific article

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

scientific article (publication date: 20 November 2015)

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

scientific article (publication date: 2015)

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

scientific article published on 22 November 2018

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

scientific article (publication date: 2013)

Specific CLK Inhibitors from a Novel Chemotype for Regulation of Alternative Splicing

scientific article

Standardized benchmarking in the quest for orthologs

scientific article (publication date: 4 April 2016)

Ten Years of Collaborative Progress in the Quest for Orthologs

scientific article published on 2 April 2021

The Quest for Orthologs benchmark service and consensus calls in 2020

scientific article published on 06 May 2020

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

scientific article

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

scientific article published on 18 October 2016

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

scientific article published on 25 November 2020

Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies

scientific article published on 06 May 2019

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines.

scientific article published on 5 February 2015

Viruses.STRING: A Virus-Host Protein-Protein Interaction Database

scholarly article by Helen Victoria Cook published in September 2018

WeGET: predicting new genes for molecular systems by weighted co-expression.

scientific article

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

scientific article (publication date: 17 November 2015)

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

scientific article published on 01 January 2019

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

scientific article

eggNOG v4.0: nested orthology inference across 3686 organisms

scientific article (publication date: December 2013)

List of works by Damian Szklarczyk

"Orphan" retrogenes in the human genome

Analysis of the Human Kinome and Phosphatome by Mass Cytometry Reveals Overexpression-Induced Effects on Cancer-Related Signaling.

Analysis of the human kinome and phosphatome reveals diseased signaling networks induced by overexpression

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

GUNC: detection of chimerism and contamination in prokaryotic genomes

Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs

Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network

Pre-Clovis Mastodon Hunting 13,800 Years Ago at the Manis Site, Washington

Protein-Protein Interaction Databases

Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

STITCH 2: an interaction network database for small molecules and proteins

STITCH 4: integration of protein-chemical interactions with user data

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

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

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

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

Specific CLK Inhibitors from a Novel Chemotype for Regulation of Alternative Splicing

Standardized benchmarking in the quest for orthologs

Ten Years of Collaborative Progress in the Quest for Orthologs

The Quest for Orthologs benchmark service and consensus calls in 2020

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

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

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

Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines.

Viruses.STRING: A Virus-Host Protein-Protein Interaction Database

WeGET: predicting new genes for molecular systems by weighted co-expression.

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

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

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

eggNOG v4.0: nested orthology inference across 3686 organisms