Publications of LJ. Jensen

Publications of LJ. Jensen

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2023 2 publication(s).
77.
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
76.
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.
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2021 2 publication(s).
75.
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.
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74.
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.
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2019 2 publication(s).
73.
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.
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72.
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.
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2017 2 publication(s).
71.
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
2017 Aug 1; 34(8): 2115-2122. PubMed: 28460117.
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70.
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.
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2016 4 publication(s).
69.
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.
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68.
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.
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67.
The SIDER database of drugs and side effects.
Kuhn M, Letunic I, Jensen LJ, Bork P
2016 Jan 4; 44: D1075-9. Epub 2015 Oct 19; PubMed: 26481350.
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66.
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.
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2015 1 publication(s).
65.
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).
64.
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.
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63.
eggNOG v4.0: nested orthology inference across 3686 organisms.
2014 Jan 1; 42(Database issue): D231-9. Epub 2013 Dec 1; PubMed: 24297252.
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2013 2 publication(s).
62.
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.
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61.
Systematic identification of proteins that elicit drug side effects.
Kuhn M, Al Banchaabouchi M, Campillos M, Jensen LJ, Gross C, Gavin AC, Bork P
2013 Apr 30; 9: 663. PubMed: 23632385.
Abstract + PDF
2012 2 publication(s).
60.
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.
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59.
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.
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2011 2 publication(s).
58.
Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data.
2011 Mar 15; 7: 473. PubMed: 21407210.
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57.
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.
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2010 8 publication(s).
56.
A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae.
Gallego O, Betts MJ, Gvozdenovic-Jeremic J, Maeda K, Matetzki C, Aguilar-Gurrieri C, Beltran-Alvarez P, Bonn S, Fernández-Tornero C, Jensen LJ, Kuhn M, Trott J, Rybin V, Müller CW, Bork P, Kaksonen M, Russell RB, Gavin AC
2010 Nov 30; 6: 430. PubMed: 21119626.
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55.
High-resolution transcription atlas of the mitotic cell cycle in budding yeast.
Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM
2010 Mar 1; 11(3): R24. Epub 2010 Mar 1; PubMed: 20193063.
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54.
Drug-Induced Regulation of Target Expression.
2010 Sep 9; 6(9): . PubMed: 20838579.
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53.
Ontologies in quantitative biology: a basis for comparison, integration, and discovery.
Jensen LJ, Bork P
2010 May 25; 8(5): e1000374. PubMed: 20520843.
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52.
A side effect resource to capture phenotypic effects of drugs.
2010; 6: 343. PubMed: 20087340.
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51.
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.
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50.
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.
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49.
Evolution and regulation of cellular periodic processes: a role for paralogues.
Trachana K, Jensen LJ, Bork P
2010 Mar 19; 11(3): 233-8. Epub 2010 Feb 19; PubMed: 20168326.
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2009 5 publication(s).
48.
Quantifying environmental adaptation of metabolic pathways in metagenomics.
Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB
2009 Feb 3; 106(5): 1374-9. Epub 2009 Jan 22; PubMed: 19164758.
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47.
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
2009 Jan 21; 37: D412-6. Epub 2008 Oct 21; PubMed: 18940858.
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46.
Sequence-based feature prediction and annotation of proteins.
Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S
2009 Feb 2; 10(2): 206. Epub 2009 Feb 2; PubMed: 19226438.
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45.
Reflect: augmented browsing for the life scientist.
Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R
2009 Jun; 27(6): 508-10. PubMed: 19513049.
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44.
Microblogging the ISMB: a new approach to conference reporting.
Saunders N, Beltrão P, Jensen LJ, Jurczak D, Krause R, Kuhn M, Wu S
2009 Jan; 5(1): e1000263. PubMed: 19180175.
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2008 12 publication(s).
43.
Drug target identification using side-effect similarity.
Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P
2008 Jul 11; 321(5886): 263-6. PubMed: 18621671. Media echos.
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42.
Protein-protein interactions: analysis and prediction.
Frishman D, Albrecht M, Blankenburg H, Bork P, Harrington ED, Hermjakob H, Jensen LJ, Juan DA, Lengauer T, Pagel P, Schächter V, Valencia A
In: Frishman D and Valencia A (Editors): Modern genome annotation pp.353–412. BID: 20.
ISBN: 978-3-211-75122-0 Publisher: Springer
41.
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
2008 Jan 16; 36: D919-22. Epub 2007 Oct 16; PubMed: 17942422.
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40.
Predicting biological networks from genomic data.
Harrington ED, Jensen LJ, Bork P
2008 Apr 9; 582(8): 1251-8. Epub 2008 Feb 21; PubMed: 18294967.
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39.
Biochemistry. Not comparable, but complementary.
Jensen LJ, Bork P
2008 Oct 3; 322(5898): 56-7. PubMed: 18832636.
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38.
Circular reasoning rather than cyclic expression.
Jensen LJ, de Lichtenberg U, Jensen TS, Brunak S, Bork P
2008 Jun 23; 9(6): 403. Epub 2008 Jun 23; PubMed: 18598377.
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37.
eggNOG: automated construction and annotation of orthologous groups of genes.
2008 Jan 16; 36: D250-4. Epub 2007 Oct 16; PubMed: 17942413.
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36.
Large-scale prediction of drug-target relationships.
Kuhn M, Campillos M, González P, Jensen LJ, Bork P
2008 Apr 9; 582(8): 1283-90. Epub 2008 Feb 20; PubMed: 18291108.
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35.
STITCH: interaction networks of chemicals and proteins.
2008 Jan 15; 36: D684-8. Epub 2007 Dec 15; PubMed: 18084021.
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34.
NetworKIN: a resource for exploring cellular phosphorylation networks.
Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T
2008 Jan 2; 36: D695-9. Epub 2007 Nov 2; PubMed: 17981841.
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33.
Linear motif atlas for phosphorylation-dependent signaling.
Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R
2008 Sep 2; 1(35): ra2. PubMed: 18765831.
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32.
Enhanced function annotations for Drosophila serine proteases: A case study for systematic annotation of multi-member gene families.
Shah PK, Tripathi LP, Jensen LJ, Gahnim M, Mason C, Furlong EE, Rodrigues V, White KP, Bork P, Sowdhamini R
2008 Jan 15; 407(1-2): 199-215. Epub 2007 Oct 15; PubMed: 17996400.
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2007 7 publication(s).
31.
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
2007 Oct 16; 36: D854-9. PubMed: 17940094.
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30.
Quantitative assessment of protein function prediction from metagenomics shotgun sequences.
2007 Aug 28; 104(35): 13913-8. Epub 2007 Aug 23; PubMed: 17717083.
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29.
Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis.
Hooper SD, Boue S, Krause R, Jensen LJ, Mason CE, Ghanim M, White KP, Furlong EE, Bork P
2007; 3: 72. PubMed: 17224916.
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28.
Evolution of Cell Cycle Control: Same Molecular Machines, Different Regulation.
Lichtenberg UD, Jensen TS, Brunak S, Bork P, Jensen LJ
2007 Aug 1; 6(15): 1819-25. Epub 2007 Jun 4; PubMed: 17671420.
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27.
Systematic Discovery of In Vivo Phosphorylation Networks.
Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jørgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JG, Samson LD, Woodgett JR, Russell RB, Bork P, Yaffe MB, Pawson T
2007 Jun 29; 129(7): 1415-26. Epub 2007 Jun 14; PubMed: 17570479. Media echos.
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26.
Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments.
von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P
2007 Feb 23; 315(5815): 1126-30. Epub 2007 Feb 1; PubMed: 17272687. Media echos.
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25.
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
2007 Jan 10; 35: D358-62. Epub 2006 Nov 10; PubMed: 17098935.
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2006 9 publication(s).
24.
Identification and analysis of evolutionarily cohesive functional modules in protein networks.
2006 Mar; 16(3): 374-82. Epub 2006 Jan 31; PubMed: 16449501.
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23.
Proteome survey reveals modularity of the yeast cell machinery.
Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dümpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper SD, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G
2006 Mar 30; 440(7084): 631-6. Epub 2006 Jan 22; PubMed: 16429126. Media echos.
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22.
Co-evolution of transcriptional and post-translational cell-cycle regulation.
Jensen LJ, Jensen TS, de Lichtenberg U, Brunak S, Bork P
2006 Oct 5; 443(7111): 594-7. Epub 2006 Sep 27; PubMed: 17006448. Media echos.
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21.
Literature mining for the biologist: from information retrieval to biological discovery.
Jensen LJ, Saric J, Bork P
2006 Feb; 7(2): 119-29. PubMed: 16418747.
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20.
The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast.
Marguerat S, Jensen TS, de Lichtenberg U, Wilhelm BT, Jensen LJ, Bähler J
2006 Mar; 23(4): 261-77. PubMed: 16544289.
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19.
Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle.
Perocchi F, Jensen LJ, Gagneur J, Ahting U, von Mering C, Bork P, Prokisch H, Steinmetz LM
2006 Oct 20; 2(10): e170. PubMed: 17054397.
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18.
A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development.
Sandmann T, Jensen LJ, Jakobsen JS, Karzynski MM, Eichenlaub MP, Bork P, Furlong EE
2006 Jun; 10(6): 797-807. PubMed: 16740481.
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17.
Extraction of regulatory gene/protein networks from Medline.
Saric J, Jensen LJ, Ouzounova R, Rojas I, Bork P
2006 Mar 15; 22(6): 645-50. Epub 2005 Jul 26; PubMed: 16046493.
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16.
Origin of replication in circular prokaryotic chromosomes.
Worning P, Jensen LJ, Hallin PF, Stærfeldt HH, Ussery DW
2006 Feb; 8(2): 353-361. PubMed: 16423021.
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2005 9 publication(s).
15.
Dynamic complex formation during the yeast cell cycle.
de Lichtenberg U, Jensen LJ, Brunak S, Bork P
2005 Feb 4; 307(5710): 724-7. PubMed: 15692050. Media echos.
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14.
Comparison of computational methods for the identification of cell cycle-regulated genes.
de Lichtenberg U, Jensen LJ, Fausbøll A, Jensen TS, Bork P, Brunak S
2005 Apr 1; 21(7): 1164-71. Epub 2004 Oct 28; PubMed: 15513999.
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13.
Re-analysis of data and its integration.
Jensen LJ, Steinmetz LM
2005 Mar 21; 579(8): 1802-7. PubMed: 15763555.
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12.
Systematic association of genes to phenotypes by genome and literature mining.
2005 May; 3(5): e134. Epub 2005 Apr 5; PubMed: 15799710. Media echos.
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11.
Large-scale extraction of gene regulation for model organisms in an ontological context.
Saric J, Jensen LJ, Rojas I
2005; 5(1): 21-32. PubMed: 15972005.
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10.
Extraction of transcript diversity from scientific literature.
Shah PK, Jensen LJ, Boue S, Bork P
2005 Jun; 1(1): e10. Epub 2005 Jun 24; PubMed: 16103899.
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9.
Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system.
Taxis C, Keller P, Kavagiou Z, Jensen LJ, Colombelli J, Bork P, Stelzer EH, Knop M
2005 Nov 21; 171(4): 627-40. Epub 2005 Nov 14; PubMed: 16286509.
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8.
Crystal ball. Systems biology: in the broadest sense of the word.
Ussery DW, de Lichtenberg U, Jensen LJ
2005 Apr; 7(4): 482-3. PubMed: 15816924.
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7.
STRING: known and predicted protein-protein associations, integrated and transferred across organisms.
2005 Jan 1; 33(Database issue): D433-7. PubMed: 15608232.
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2004 5 publication(s).
6.
Protein interaction networks from yeast to human.
Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, Marcotte EM
2004 Jun; 14(3): 292-9. PubMed: 15193308.
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5.
Quality analysis and integration of large scale molecular data sets.
Jensen LJ, Bork P
2004 Apr; 3(2): 51-56. PID: 308.
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4.
ArrayProspector: a web resource of functional associations inferred from microarray expression data.
2004 Jul 1; 32(Web Server issue): W445-8. PubMed: 15215427.
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3.
Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs.
2004 Jul; 22(7): 911-7. PubMed: 15229555.
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2.
Extracting regulatory gene expression networks from Pubmed.
Saric J, Jensen LJ, Ouzounova R, Rojas I, Bork P
2004; : 192-199. PID: 395.
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2003 1 publication(s).
1.
Protein disorder prediction: implications for structural proteomics.
Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB
2003 Nov; 11(11): 1453-9. PubMed: 14604535.
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