Publications by authors named "Lars Juhl Jensen"

100Publications

Alcoholic liver disease: A registry view on comorbidities and disease prediction.

PLoS Comput Biol 2020 Sep 22;16(9):e1008244. Epub 2020 Sep 22.

Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.

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http://dx.doi.org/10.1371/journal.pcbi.1008244DOI Listing
September 2020

Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types.

NPJ Syst Biol Appl 2019 Aug 7;5(1):27. Epub 2019 Aug 7.

Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200, Copenhagen, Denmark.

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http://dx.doi.org/10.1038/s41540-019-0104-5DOI Listing
August 2019

Visualize omics data on networks with Omics Visualizer, a Cytoscape App.

F1000Res 2020 28;9:157. Epub 2020 Feb 28.

Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.12688/f1000research.22280.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7194485.2PMC
February 2020

SnapShot: S-Phase Entry and Exit.

Cell 2019 10;179(3):802-802.e1

NNF Center for Protein Research, University of Copenhagen, 2200 Copenhagen N., Denmark.

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http://dx.doi.org/10.1016/j.cell.2019.09.031DOI Listing
October 2019

Transcriptome analysis in patients with temporal lobe epilepsy.

Brain 2019 10;142(10):e55

Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1093/brain/awz265DOI Listing
October 2019

ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins.

PLoS Comput Biol 2019 08 22;15(8):e1007239. Epub 2019 Aug 22.

The Cancer Genomics and BioComputing of Complex Diseases lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.

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http://dx.doi.org/10.1371/journal.pcbi.1007239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6705771PMC
August 2019

Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types.

NPJ Syst Biol Appl 2019 7;5:27. Epub 2019 Aug 7.

1Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark.

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http://dx.doi.org/10.1038/s41540-019-0104-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6685999PMC
April 2020

CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision.

Bioinformatics 2020 01;36(1):264-271

Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen N 2200, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btz490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6956794PMC
January 2020

Design, implementation, and operation of a rapid, robust named entity recognition web service.

J Cheminform 2019 Mar 8;11(1):19. Epub 2019 Mar 8.

Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1186/s13321-019-0344-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6419787PMC
March 2019

A Guide to Dictionary-Based Text Mining.

Methods Mol Biol 2019 ;1939:73-89

Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1007/978-1-4939-9089-4_5DOI Listing
July 2019

An Integrative Approach to Virus-Host Protein-Protein Interactions.

Methods Mol Biol 2018 ;1819:175-196

Novo Nordisk Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.

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http://link.springer.com/10.1007/978-1-4939-8618-7_8
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http://dx.doi.org/10.1007/978-1-4939-8618-7_8DOI Listing
March 2019

WebCircRNA: Classifying the Circular RNA Potential of Coding and Noncoding RNA.

Genes (Basel) 2018 Nov 6;9(11). Epub 2018 Nov 6.

Center for Non-Coding RNA in Technology and Health, University of Copenhagen, 1870 Frederiksberg C, Denmark.

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http://www.mdpi.com/2073-4425/9/11/536
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http://dx.doi.org/10.3390/genes9110536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6266491PMC
November 2018

Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles.

Bioinformatics 2019 05;35(9):1494-1502

Department of Veterinary and Animal Sciences, Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg C, Denmark.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/bty859DOI Listing
May 2019

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

Viruses 2018 09 23;10(10). Epub 2018 Sep 23.

Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen N, Danmark.

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http://www.mdpi.com/1999-4915/10/10/519
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http://dx.doi.org/10.3390/v10100519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6213343PMC
September 2018

Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates.

PLoS One 2018 24;13(8):e0202369. Epub 2018 Aug 24.

Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0202369PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6108476PMC
February 2019

TISSUES 2.0: an integrative web resource on mammalian tissue expression.

Database (Oxford) 2018 01;2018

Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1093/database/bay003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808782PMC
January 2018

Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting.

Angew Chem Int Ed Engl 2018 06 26;57(25):7369-7374. Epub 2018 Apr 26.

Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.

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http://dx.doi.org/10.1002/anie.201713020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6032867PMC
June 2018

A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts.

PLoS Comput Biol 2018 02 15;14(2):e1005962. Epub 2018 Feb 15.

Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.

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http://dx.doi.org/10.1371/journal.pcbi.1005962DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5831415PMC
February 2018

LocText: relation extraction of protein localizations to assist database curation.

BMC Bioinformatics 2018 01 17;19(1):15. Epub 2018 Jan 17.

Bioinformatics & Computational Biology, Department of Informatics, Technical University of Munich (TUM), Boltzmannstr. 3, Garching, 85748, Germany.

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http://dx.doi.org/10.1186/s12859-018-2021-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5773052PMC
January 2018

Specifying RNA-Binding Regions in Proteins by Peptide Cross-Linking and Affinity Purification.

J Proteome Res 2017 08 7;16(8):2762-2772. Epub 2017 Jul 7.

Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences , DK-2200 Copenhagen, Denmark.

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http://dx.doi.org/10.1021/acs.jproteome.7b00042DOI Listing
August 2017

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper.

Mol Biol Evol 2017 08;34(8):2115-2122

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1093/molbev/msx148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850834PMC
August 2017

TIN-X: target importance and novelty explorer.

Bioinformatics 2017 Aug;33(16):2601-2603

Translational Informatics Division, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870731PMC
August 2017

Accurate Quantification of Site-specific Acetylation Stoichiometry Reveals the Impact of Sirtuin Deacetylase CobB on the Acetylome.

Mol Cell Proteomics 2017 05 2;16(5):759-769. Epub 2017 Mar 2.

From the ‡The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark

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http://dx.doi.org/10.1074/mcp.M117.067587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5417819PMC
May 2017

RAIN: RNA-protein Association and Interaction Networks.

Database (Oxford) 2017 10;2017. Epub 2017 Jan 10.

Center for Non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen,, Groennegaardsvej 3, DK-1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1093/database/baw167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5225963PMC
November 2017

Seqenv: linking sequences to environments through text mining.

PeerJ 2016 20;4:e2690. Epub 2016 Dec 20.

Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion Crete, Greece.

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http://dx.doi.org/10.7717/peerj.2690DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5178346PMC
December 2016

EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.

Database (Oxford) 2016 20;2016. Epub 2016 Feb 20.

Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark

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https://academic.oup.com/database/article-lookup/doi/10.1093
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http://dx.doi.org/10.1093/database/baw005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761108PMC
October 2016

Impact of microRNA-130a on the neutrophil proteome.

BMC Immunol 2015 Nov 25;16:70. Epub 2015 Nov 25.

The Granulocyte Research Laboratory, Department of Hematology, National University Hospital, University of Copenhagen, 9322, Blegdamsvej 9, DK-2100, Copenhagen Ø, Denmark.

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http://dx.doi.org/10.1186/s12865-015-0134-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4659159PMC
November 2015

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

Nucleic Acids Res 2016 Jan 20;44(D1):D380-4. Epub 2015 Nov 20.

Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden

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http://dx.doi.org/10.1093/nar/gkv1277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702904PMC
January 2016

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

Nucleic Acids Res 2016 Jan 17;44(D1):D286-93. Epub 2015 Nov 17.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg 69117, Germany Max Delbrück Centre for Molecular Medicine, Berlin 13125, Germany

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http://nar.oxfordjournals.org/content/early/2015/11/17/nar.g
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkv1248
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http://dx.doi.org/10.1093/nar/gkv1248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702882PMC
January 2016

Avoiding abundance bias in the functional annotation of post-translationally modified proteins.

Nat Methods 2015 Nov;12(11):1003-4

Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.

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http://www.nature.com/articles/nmeth.3621
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http://dx.doi.org/10.1038/nmeth.3621DOI Listing
November 2015

The SIDER database of drugs and side effects.

Nucleic Acids Res 2016 Jan 19;44(D1):D1075-9. Epub 2015 Oct 19.

European Molecular Biology Laboratory, Structural and Computational Biology Unit, Molecular Medicine Partnership Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Strasse 10, 13092 Berlin, Germany

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http://dx.doi.org/10.1093/nar/gkv1075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702794PMC
January 2016

Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow.

J Proteome Res 2015 Nov 28;14(11):4885-95. Epub 2015 Oct 28.

Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry , Am Klopferspitz 18, D-82152 Martinsried, Germany.

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http://dx.doi.org/10.1021/acs.jproteome.5b00720DOI Listing
November 2015

Comprehensive comparison of large-scale tissue expression datasets.

PeerJ 2015 30;3:e1054. Epub 2015 Jun 30.

Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.7717/peerj.1054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493645PMC
July 2015

Protein-protein interaction databases.

Methods Mol Biol 2015 ;1278:39-56

Faculty of Health Sciences, Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, København N, Denmark.

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http://dx.doi.org/10.1007/978-1-4939-2425-7_3DOI Listing
December 2015

ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life.

Bioinformatics 2015 Jun 24;31(11):1872-4. Epub 2015 Jan 24.

Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece, Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, Max Planck Institute for Marine Microbiology, Bremen, Germany, Jacobs University gGmbH, School of Engineering and Sciences, Bremen, Germany, Marine Biological Laboratory, Woods Hole, MA 02543, USA and National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443677PMC
June 2015

Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation.

Mol Cell Proteomics 2015 Mar 9;14(3):658-73. Epub 2015 Jan 9.

From the ‡Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany; §Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark

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http://dx.doi.org/10.1074/mcp.M114.042812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4349985PMC
March 2015

Discrepancies in listed adverse drug reactions in pharmaceutical product information supplied by the regulatory authorities in Denmark and the USA.

Pharmacol Res Perspect 2014 Jun 22;2(3):e00038. Epub 2014 Apr 22.

Danish Pharmacovigilance Research Project (DANPREP) Copenhagen, Denmark ; Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen Universitetsparken 2, DK-2100, Copenhagen, Denmark.

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http://dx.doi.org/10.1002/prp2.38DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4186409PMC
June 2014

DISEASES: text mining and data integration of disease-gene associations.

Methods 2015 Mar 5;74:83-9. Epub 2014 Dec 5.

Department of Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2014.11.020DOI Listing
March 2015

Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes.

Nucleic Acids Res 2015 Jan 5;43(Database issue):D1140-4. Epub 2014 Nov 5.

Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark

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http://dx.doi.org/10.1093/nar/gku1092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383920PMC
January 2015

Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients.

Nat Commun 2014 Jun 24;5:4022. Epub 2014 Jun 24.

1] Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Building 208, DK-2800 Kgs. Lyngby, Denmark [2] NNF Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.

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http://dx.doi.org/10.1038/ncomms5022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090719PMC
June 2014

A comparison of protein kinases inhibitor screening methods using both enzymatic activity and binding affinity determination.

PLoS One 2014 10;9(6):e98800. Epub 2014 Jun 10.

Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; Costerton Biofilm Center, Institute for International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0098800PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4051630PMC
October 2015

KinomeXplorer: an integrated platform for kinome biology studies.

Nat Methods 2014 Jun;11(6):603-4

Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark.

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http://dx.doi.org/10.1038/nmeth.2968DOI Listing
June 2014

DoReMi: context-based prioritization of linear motif matches.

PeerJ 2014 20;2:e315. Epub 2014 Mar 20.

NNF Center for Protein Research, University of Copenhagen , Denmark.

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http://dx.doi.org/10.7717/peerj.315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3970808PMC
April 2014

Dose-specific adverse drug reaction identification in electronic patient records: temporal data mining in an inpatient psychiatric population.

Drug Saf 2014 Apr;37(4):237-47

NNF Center for Protein Research, Department of Disease Systems Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.

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http://dx.doi.org/10.1007/s40264-014-0145-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975083PMC
April 2014

COMPARTMENTS: unification and visualization of protein subcellular localization evidence.

Database (Oxford) 2014 25;2014:bau012. Epub 2014 Feb 25.

Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany, Bioinformatics Core Facility, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg, Department of Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark, CSIRO Computational Informatics, Sydney, NSW 2113 Australia and Garvan Institute of Medical Research, Sydney, NSW 2100, Australia.

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http://dx.doi.org/10.1093/database/bau012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3935310PMC
August 2014

Protein-driven inference of miRNA-disease associations.

Bioinformatics 2014 Feb 21;30(3):392-7. Epub 2013 Nov 21.

Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, Department of Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research and The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btt677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3904518PMC
February 2014

Are graph databases ready for bioinformatics?

Bioinformatics 2013 Dec 17;29(24):3107-8. Epub 2013 Oct 17.

Department of Metabolic Genetics, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2100 Copenhagen Ø, Denmark and Department of Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2100 Copenhagen N, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btt549DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842757PMC
December 2013

The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text.

PLoS One 2013 18;8(6):e65390. Epub 2013 Jun 18.

Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065390PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3688812PMC
October 2017

Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text.

J Am Med Inform Assoc 2013 Sep-Oct;20(5):947-53. Epub 2013 May 23.

Department of Disease Systems Biology, Faculty of Health and Medical Sciences, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1136/amiajnl-2013-001708DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3756275PMC
December 2013

Systematic identification of proteins that elicit drug side effects.

Mol Syst Biol 2013 ;9:663

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1038/msb.2013.10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3693830PMC
September 2013

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

BMC Syst Biol 2012 Jul 23;6:90. Epub 2012 Jul 23.

Center for Non-coding RNA in Technology and Health, Division of Genetics and Bioinformatics, IBHV, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1186/1752-0509-6-90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3430561PMC
July 2012

Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes.

J Proteomics 2012 Jul 24;75(13):3886-97. Epub 2012 May 24.

Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health Sciences, DK-2200 Copenhagen, Denmark.

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http://dx.doi.org/10.1016/j.jprot.2012.04.055DOI Listing
July 2012

Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels.

Mol Syst Biol 2012 Feb 28;8:572. Epub 2012 Feb 28.

Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.1038/msb.2012.3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293633PMC
February 2012

Using text-mining techniques in electronic patient records to identify ADRs from medicine use.

Br J Clin Pharmacol 2012 May;73(5):674-84

Department of Pharmacology and Pharmacotherapy, Section for Social Pharmacy, Faculty of Pharmaceutical Sciences, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1111/j.1365-2125.2011.04153.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3403195PMC
May 2012

The rise and fall of supervised machine learning techniques.

Bioinformatics 2011 Dec 17;27(24):3331-2. Epub 2011 Nov 17.

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http://dx.doi.org/10.1093/bioinformatics/btr585DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232371PMC
December 2011

STITCH 3: zooming in on protein-chemical interactions.

Nucleic Acids Res 2012 Jan 9;40(Database issue):D876-80. Epub 2011 Nov 9.

Biotechnology Center, TU Dresden, 01062 Dresden, Germany.

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http://dx.doi.org/10.1093/nar/gkr1011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245073PMC
January 2012

DistiLD Database: diseases and traits in linkage disequilibrium blocks.

Nucleic Acids Res 2012 Jan 3;40(Database issue):D1036-40. Epub 2011 Nov 3.

Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.

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http://dx.doi.org/10.1093/nar/gkr899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245128PMC
January 2012

BioStar: an online question & answer resource for the bioinformatics community.

PLoS Comput Biol 2011 Oct 27;7(10):e1002216. Epub 2011 Oct 27.

Nutrition and Genomics Laboratory, Jean Mayer-United States Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203049PMC
October 2011

Pre-Clovis mastodon hunting 13,800 years ago at the Manis site, Washington.

Science 2011 Oct;334(6054):351-3

Center for the Study of the First Americans, Department of Anthropology, Texas A&M University, 4352 TAMU, College Station, TX 77843-4352, USA.

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http://dx.doi.org/10.1126/science.1207663DOI Listing
October 2011

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data.

Mol Syst Biol 2011 Mar;7:473

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1038/msb.2011.6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3094067PMC
March 2011

Drug-induced regulation of target expression.

PLoS Comput Biol 2010 Sep 9;6(9). Epub 2010 Sep 9.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1000925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936514PMC
September 2010

Protein annotation in the era of personal genomics.

Curr Opin Struct Biol 2010 Jun 18;20(3):335-41. Epub 2010 Apr 18.

NNF Center for Protein Research, Faculty of Health Sciences, Blegdamsvej 3b, DK-2200 Copenhagen N, Denmark.

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http://dx.doi.org/10.1016/j.sbi.2010.03.008DOI Listing
June 2010

Suppression of water as a nucleophile in Candida antarctica lipase B catalysis.

Chembiochem 2010 Apr;11(6):796-801

Department of Biochemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, 10691 Stockholm, Sweden.

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http://doi.wiley.com/10.1002/cbic.200900743
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http://dx.doi.org/10.1002/cbic.200900743DOI Listing
April 2010

Evolution and regulation of cellular periodic processes: a role for paralogues.

EMBO Rep 2010 Mar 19;11(3):233-8. Epub 2010 Feb 19.

European Molecular Biology Laboratory Heidelberg, Heidelberg, Germany.

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http://dx.doi.org/10.1038/embor.2010.9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2838706PMC
March 2010

A side effect resource to capture phenotypic effects of drugs.

Mol Syst Biol 2010 19;6:343. Epub 2010 Jan 19.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1038/msb.2009.98DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824526PMC
February 2010

Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results.

Nucleic Acids Res 2010 Jan 24;38(Database issue):D699-702. Epub 2009 Nov 24.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.

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http://dx.doi.org/10.1093/nar/gkp1044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808877PMC
January 2010

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

Nucleic Acids Res 2010 Jan 6;38(Database issue):D552-6. Epub 2009 Nov 6.

Biotechnology Center, TU Dresden, 01062 Dresden, Germany.

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http://dx.doi.org/10.1093/nar/gkp937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808890PMC
January 2010

Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation.

Mol Syst Biol 2009 20;5:236. Epub 2009 Jan 20.

The Microsoft Research, University of Trento Centre for Computational and Systems Biology, Povo, Trento, Italy.

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http://dx.doi.org/10.1038/msb.2008.73DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2644172PMC
March 2009

Biochemistry. Not comparable, but complementary.

Science 2008 Oct;322(5898):56-7

European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.

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http://dx.doi.org/10.1126/science.1164801DOI Listing
October 2008

Drug target identification using side-effect similarity.

Science 2008 Jul;321(5886):263-6

European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1126/science.1158140DOI Listing
July 2008

Large-scale prediction of drug-target relationships.

FEBS Lett 2008 Apr 20;582(8):1283-90. Epub 2008 Feb 20.

European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.febslet.2008.02.024DOI Listing
April 2008

STITCH: interaction networks of chemicals and proteins.

Nucleic Acids Res 2008 Jan 15;36(Database issue):D684-8. Epub 2007 Dec 15.

European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1093/nar/gkm795DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238848PMC
January 2008

NetworKIN: a resource for exploring cellular phosphorylation networks.

Nucleic Acids Res 2008 Jan 2;36(Database issue):D695-9. Epub 2007 Nov 2.

Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkm902DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238868PMC
January 2008

SuperTarget and Matador: resources for exploring drug-target relationships.

Nucleic Acids Res 2008 Jan 16;36(Database issue):D919-22. Epub 2007 Oct 16.

Structural Bioinformatics Group, Institute of Molecular Biology and Bioinformatics, Charité-University Medicine Berlin, Arnimallee 22, 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gkm862DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238858PMC
January 2008

eggNOG: automated construction and annotation of orthologous groups of genes.

Nucleic Acids Res 2008 Jan 16;36(Database issue):D250-4. Epub 2007 Oct 16.

European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1093/nar/gkm796DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238944PMC
January 2008

Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments.

Nucleic Acids Res 2008 Jan 16;36(Database issue):D854-9. Epub 2007 Oct 16.

Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark.

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http://dx.doi.org/10.1093/nar/gkm729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238932PMC
January 2008

Evolution of cell cycle control: same molecular machines, different regulation.

Cell Cycle 2007 Aug 4;6(15):1819-25. Epub 2007 Jun 4.

Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark.

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http://dx.doi.org/10.4161/cc.6.15.4537DOI Listing
August 2007

Co-evolution of transcriptional and post-translational cell-cycle regulation.

Nature 2006 Oct 27;443(7111):594-7. Epub 2006 Sep 27.

European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature05186DOI Listing
October 2006

Identification and analysis of evolutionarily cohesive functional modules in protein networks.

Genome Res 2006 Mar 31;16(3):374-82. Epub 2006 Jan 31.

The European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1101/gr.4336406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1415216PMC
March 2006