Publications of LJ. Jensen in the journal "Nucleic Acids Res".

Publications of LJ. Jensen in the journal "Nucleic Acids Res".

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2023 2 publication(s).
28.
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
Nucleic Acids Res.
2023 Jan 6; 51: D389-D394. PubMed: 36399505.
Abstract + PDF
27.
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
Nucleic Acids Res.
2023 Jan 6; 51: D638-D646. PubMed: 36370105.
Abstract + PDF
2021 2 publication(s).
26.
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
Nucleic Acids Res.
2021 Oct 11; 49(18): 10800. PubMed: 34530444.
PDF
25.
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
Nucleic Acids Res.
2021 Jan 8; 49(D1): D605-D612. PubMed: 33237311.
Abstract + PDF
2019 2 publication(s).
24.
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
Nucleic Acids Res.
2019 Jan 8; 47: D309-D314. PubMed: 30418610.
Abstract + PDF
23.
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
Nucleic Acids Res.
2019 Jan 8; 47: D607-D613. PubMed: 30476243.
Abstract + PDF
2017 1 publication(s).
22.
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
Nucleic Acids Res.
2017 Jan 4; 45(D1): D362-D368. PubMed: 27924014.
Abstract + PDF
2016 3 publication(s).
21.
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
Nucleic Acids Res.
2016 Jan 4; 44: D286-93. Epub 2015 Nov 17; PubMed: 26582926.
Abstract + PDF
20.
The SIDER database of drugs and side effects.
Kuhn M, Letunic I, Jensen LJ, Bork P
Nucleic Acids Res.
2016 Jan 4; 44: D1075-9. Epub 2015 Oct 19; PubMed: 26481350.
Abstract + PDF
19.
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
Nucleic Acids Res.
2016 Jan 4; 44: D380-4. Epub 2015 Nov 20; PubMed: 26590256.
Abstract + PDF
2015 1 publication(s).
18.
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
Nucleic Acids Res.
2015 Jan 28; 43: D447-52. Epub 2014 Oct 28; PubMed: 25352553.
Abstract + PDF
2014 2 publication(s).
17.
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
Nucleic Acids Res.
2014 Jan 1; 42(Database issue): D401-7. Epub 2013 Nov 28; PubMed: 24293645.
Abstract + PDF
16.
eggNOG v4.0: nested orthology inference across 3686 organisms.
Nucleic Acids Res.
2014 Jan 1; 42(Database issue): D231-9. Epub 2013 Dec 1; PubMed: 24297252.
Abstract + PDF
2013 1 publication(s).
15.
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
Nucleic Acids Res.
2013 Jan 1; 41: D808-15. Epub 2012 Nov 29; PubMed: 23203871.
Abstract + PDF
2012 2 publication(s).
14.
STITCH 3: zooming in on protein-chemical interactions.
Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P
Nucleic Acids Res.
2012 Jan 1; 40: D876-80. Epub 2011 Nov 9; PubMed: 22075997.
Abstract + PDF
13.
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
Nucleic Acids Res.
2012 Jan 1; 40: D284-9. Epub 2011 Nov 16; PubMed: 22096231.
Abstract + PDF
2011 1 publication(s).
12.
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
Nucleic Acids Res.
2011 Jan 2; 39: D561-8. Epub 2010 Nov 2; PubMed: 21045058.
Abstract + PDF
2010 2 publication(s).
11.
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
Nucleic Acids Res.
2010 Jan 6; 38: D552-6. Epub 2009 Nov 6; PubMed: 19897548.
Abstract + PDF
10.
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
Nucleic Acids Res.
2010 Jan 9; 38: D190-5. Epub 2009 Nov 9; PubMed: 19900971.
Abstract + PDF
2009 1 publication(s).
9.
STRING 8--a global view on proteins and their functional interactions in 630 organisms.
Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey CJ, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C
Nucleic Acids Res.
2009 Jan 21; 37: D412-6. Epub 2008 Oct 21; PubMed: 18940858.
Abstract + PDF
2008 4 publication(s).
8.
SuperTarget and Matador: resources for exploring drug-target relationships.
Günther S, Kuhn M, Dunkel M, Campillos M, Senger C, Petsalaki E, Ahmed J, Urdiales EG, Gewiess A, Jensen LJ, Schneider R, Skoblo R, Russell RB, Bourne PE, Bork P, Preissner R
Nucleic Acids Res.
2008 Jan 16; 36: D919-22. Epub 2007 Oct 16; PubMed: 17942422.
Abstract + PDF
7.
eggNOG: automated construction and annotation of orthologous groups of genes.
Nucleic Acids Res.
2008 Jan 16; 36: D250-4. Epub 2007 Oct 16; PubMed: 17942413.
Abstract + PDF
6.
STITCH: interaction networks of chemicals and proteins.
Nucleic Acids Res.
2008 Jan 15; 36: D684-8. Epub 2007 Dec 15; PubMed: 18084021.
Abstract + PDF
5.
NetworKIN: a resource for exploring cellular phosphorylation networks.
Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T
Nucleic Acids Res.
2008 Jan 2; 36: D695-9. Epub 2007 Nov 2; PubMed: 17981841.
Abstract + PDF
2007 2 publication(s).
4.
Cyclebase.org a comprehensive multi-organism online database of cell-cycle experiments.
Gauthier NP, Larsen ME, Wernersson R, Lichtenberg UD, Jensen LJ, Brunak S, Jensen TS
Nucleic Acids Res.
2007 Oct 16; 36: D854-9. PubMed: 17940094.
Abstract + PDF
3.
STRING 7--recent developments in the integration and prediction of protein interactions.
von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P
Nucleic Acids Res.
2007 Jan 10; 35: D358-62. Epub 2006 Nov 10; PubMed: 17098935.
Abstract + PDF
2005 1 publication(s).
2.
STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
Nucleic Acids Res.
2005 Jan 1; 33(Database issue): D433-7. PubMed: 15608232.
Abstract + PDF
2004 1 publication(s).
1.
ArrayProspector: a web resource of functional associations inferred from microarray expression data.
Nucleic Acids Res.
2004 Jul 1; 32(Web Server issue): W445-8. PubMed: 15215427.
Abstract + PDF