Publications of D. Szklarczyk

Publications of D. Szklarczyk

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2023 3 publication(s).
22.
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.
Fullam A, Letunic I, Schmidt TSB, Ducarmon QR, Karcher N, Khedkar S, Kuhn M, Larralde M, Maistrenko OM, Malfertheiner L, Milanese A, Rodrigues JFM, Sanchis-López C, Schudoma C, Szklarczyk D, Sunagawa S, Zeller G, Huerta-Cepas J, von Mering C, Bork P, Mende DR
2023 Jan 6; 51: D760-D766. PubMed: 36408900.
Abstract + PDF
21.
eggNOG 6.0: enabling comparative genomics across 12 535 organisms.
Hernández-Plaza A, Szklarczyk D, Botas J, Cantalapiedra CP, Giner-Lamia J, Mende DR, Kirsch R, Rattei T, Letunic I, Jensen LJ, Bork P, von Mering C, Huerta-Cepas J
2023 Jan 6; 51: D389-D394. PubMed: 36399505.
Abstract + PDF
20.
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest.
Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, Gable AL, Fang T, Doncheva NT, Pyysalo S, Bork P, Jensen LJ, von Mering C
2023 Jan 6; 51: D638-D646. PubMed: 36370105.
Abstract + PDF
2021 3 publication(s).
19.
GUNC: detection of chimerism and contamination in prokaryotic genomes.
2021 Jun 13; 22(1): 178. PubMed: 34120611.
Abstract + PDF
18.
Correction to 'The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets'.
Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C
2021 Oct 11; 49(18): 10800. PubMed: 34530444.
PDF
17.
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.
Szklarczyk D, Gable AL, Nastou KC, Lyon D, Kirsch R, Pyysalo S, Doncheva NT, Legeay M, Fang T, Bork P, Jensen LJ, von Mering C
2021 Jan 8; 49(D1): D605-D612. PubMed: 33237311.
Abstract + PDF
2019 2 publication(s).
16.
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P
2019 Jan 8; 47: D309-D314. PubMed: 30418610.
Abstract + PDF
15.
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, von Mering C
2019 Jan 8; 47: D607-D613. PubMed: 30476243.
Abstract + PDF
2017 2 publication(s).
14.
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
2017 Aug 1; 34(8): 2115-2122. PubMed: 28460117.
Abstract + PDF
13.
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.
Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C
2017 Jan 4; 45(D1): D362-D368. PubMed: 27924014.
Abstract + PDF
2016 3 publication(s).
12.
Standardized benchmarking in the quest for orthologs.
Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M
2016 May 4; 13(5): 425-30. Epub 2016 Apr 4; PubMed: 27043882.
Abstract + PDF
11.
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P
2016 Jan 4; 44: D286-93. Epub 2015 Nov 17; PubMed: 26582926.
Abstract + PDF
10.
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M
2016 Jan 4; 44: D380-4. Epub 2015 Nov 20; PubMed: 26590256.
Abstract + PDF
2015 1 publication(s).
9.
STRING v10: protein-protein interaction networks, integrated over the tree of life.
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C
2015 Jan 28; 43: D447-52. Epub 2014 Oct 28; PubMed: 25352553.
Abstract + PDF
2014 2 publication(s).
8.
STITCH 4: integration of protein-chemical interactions with user data.
Kuhn M, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P
2014 Jan 1; 42(Database issue): D401-7. Epub 2013 Nov 28; PubMed: 24293645.
Abstract + PDF
7.
eggNOG v4.0: nested orthology inference across 3686 organisms.
Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey CJ, Kuhn M, Jensen LJ, von Mering C, Bork P
2014 Jan 1; 42(Database issue): D231-9. Epub 2013 Dec 1; PubMed: 24297252.
Abstract + PDF
2013 1 publication(s).
6.
STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ
2013 Jan 1; 41: D808-15. Epub 2012 Nov 29; PubMed: 23203871.
Abstract + PDF
2012 2 publication(s).
5.
STITCH 3: zooming in on protein-chemical interactions.
Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P
2012 Jan 1; 40: D876-80. Epub 2011 Nov 9; PubMed: 22075997.
Abstract + PDF
4.
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P
2012 Jan 1; 40: D284-9. Epub 2011 Nov 16; PubMed: 22096231.
Abstract + PDF
2011 1 publication(s).
3.
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C
2011 Jan 2; 39: D561-8. Epub 2010 Nov 2; PubMed: 21045058.
Abstract + PDF
2010 2 publication(s).
2.
STITCH 2: an interaction network database for small molecules and proteins.
Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P
2010 Jan 6; 38: D552-6. Epub 2009 Nov 6; PubMed: 19897548.
Abstract + PDF
1.
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
2010 Jan 9; 38: D190-5. Epub 2009 Nov 9; PubMed: 19900971.
Abstract + PDF