Research Topics
| Lars Juhl JensenSummaryAffiliation: European Molecular Biology Laboratory Country: Germany Publications
| Collaborators
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Detail Information
Publications
Literature mining for the biologist: from information retrieval to biological discoveryLars Juhl Jensen
European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
Nat Rev Genet 7:119-29. 2006..However, the latter will require the integration of literature and high-throughput data, which should encourage close collaborations between biologists and computational linguists...
A side effect resource to capture phenotypic effects of drugsMichael Kuhn
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Mol Syst Biol 6:343. 2010..We illustrate the potential of SIDER with a number of analyses. The resource is freely available for academic research at http://sideeffects.embl.de...- Large-scale prediction of drug-target relationshipsMichael Kuhn
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
FEBS Lett 582:1283-90. 2008..We finally discuss how phenotypic data could help to expand our understanding of the complex mechanisms of drug action... - Protein disorder prediction: implications for structural proteomicsRune Linding
EMBL, Biocomputing Unit, Meyerhofstr 1, D 69117 Heidelberg, Germany
Structure 11:1453-9. 2003..The tool is freely available via a web interface (http://dis.embl.de) and can be downloaded for use in large-scale studies... 
Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic dataJeroen Raes
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Mol Syst Biol 7:473. 2011..Together, our results show that the functional community composition derived from metagenomes is an important quantitative readout for molecular trait-based biogeography and ecology...- Biochemistry. Not comparable, but complementaryLars Juhl Jensen
European Molecular Biology Laboratory, D-69117 Heidelberg, Germany
Science 322:56-7. 2008 - A systematic screen for protein-lipid interactions in Saccharomyces cerevisiaeOriol Gallego
Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Heidelberg, Germany
Mol Syst Biol 6:430. 2010.... - Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene familiesParantu K Shah
European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany
Gene 407:199-215. 2008..Utilization of such multi-fold approaches results in 10-fold increase of function annotation for Drosophila serine proteases and demonstrates value in increasing annotations in multiple genomes... - STITCH: interaction networks of chemicals and proteinsMichael Kuhn
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nucleic Acids Res 36:D684-8. 2008..5 million genes across 373 genomes and their interactions contained in the STRING database. STITCH is available at http://stitch.embl.de/... - Re-analysis of data and its integrationLars Juhl Jensen
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
FEBS Lett 579:1802-7. 2005..Here, we demonstrate the power of data re-analysis and integration by applying it in a case study to data from deletion phenotype screens and mRNA expression profiling... - ArrayProspector: a web resource of functional associations inferred from microarray expression dataLars Juhl Jensen
European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
Nucleic Acids Res 32:W445-8. 2004..The resource allows every association to be inspected visually and can be accessed at http://www.bork.embl.de/ArrayProspector... - eggNOG: automated construction and annotation of orthologous groups of genesLars Juhl Jensen
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nucleic Acids Res 36:D250-4. 2008..Users can query the resource for individual genes via a web interface or download the complete set of orthologous groups at http://eggnog.embl.de... - Drug target identification using side-effect similarityMonica Campillos
European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Science 321:263-6. 2008..Nine of these were tested and confirmed in cell assays, documenting the feasibility of using phenotypic information to infer molecular interactions and hinting at new uses of marketed drugs... - Linear motif atlas for phosphorylation-dependent signalingMartin Lee Miller
Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
Sci Signal 1:ra2. 2008..The atlas is available as a community resource (http://netphorest.info)... - SuperTarget and Matador: resources for exploring drug-target relationshipsStefan Günther
Structural Bioinformatics Group, Institute of Molecular Biology and Bioinformatics, Charite University Medicine Berlin, Arnimallee 22, 14195 Berlin, Germany
Nucleic Acids Res 36:D919-22. 2008..SuperTarget and Matador are available at http://insilico.charite.de/supertarget and http://matador.embl.de... - Systematic discovery of in vivo phosphorylation networksRune Linding
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
Cell 129:1415-26. 2007..Applying this approach to DNA damage signaling, we show that 53BP1 and Rad50 are phosphorylated by CDK1 and ATM, respectively. We describe a scalable strategy to evaluate predictions, which suggests that BCLAF1 is a GSK-3 substrate... - Prediction of novel archaeal enzymes from sequence-derived featuresLars Juhl Jensen
Center for Biological Sequence Analysis, BioCentrum-DTU, The Technical University of Denmark, DK-2800 Lyngby, Denmark
Protein Sci 11:2894-8. 2002..The method does not make use of sequence similarity; rather, it relies on predicted protein features like cotranslational and posttranslational modifications, secondary structure, and simple physical/chemical properties... - Functionality of system components: conservation of protein function in protein feature spaceLars Juhl Jensen
Center for Biological Sequence Analysis, BioCentrum-DTU, The Technical University of Denmark, DK-2800 Lyngby, Denmark
Genome Res 13:2444-9. 2003..From this analysis, we conclude that for the posttranslational modifications studied, both the cellular use and the sequence motifs are conserved within Eukarya... - Feature-based prediction of non-classical and leaderless protein secretionJannick Dyrløv Bendtsen
Center for Biological Sequence Analysis BioCentrum DTU, Building 208, Technical University of Denmark, DK 2800 Lyngby, Denmark
Protein Eng Des Sel 17:349-56. 2004..By scanning the entire human proteome we identified new proteins potentially undergoing non-classical secretion. Predictions can be made at http://www.cbs.dtu.dk/services/SecretomeP... - Comparison of computational methods for the identification of cell cycle-regulated genesUlrik de Lichtenberg
Center for Biological Sequence Analysis, Technical University of Denmark DK-2800 Lyngby, Denmark
Bioinformatics 21:1164-71. 2005..We present a simple permutation-based method that performs better than most existing methods... - Crystal ball. Systems biology: in the broadest sense of the wordDavid W Ussery
Ulrik de Lichtenberg, Center for Biological Sequence Analysis, Technical University of Denmark
Environ Microbiol 7:482-3. 2005 - Extraction of regulatory gene/protein networks from MedlineJasmin Saric
EML Research gGmbH D 69118 Heidelberg, Germany
Bioinformatics 22:645-50. 2006..The biomedical literature, however, contains information on several other equally important regulatory mechanisms, in particular phosphorylation, which we now expanded for our rule-based system also to extract... - Proteome survey reveals modularity of the yeast cell machineryAnne-Claude Gavin
Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nature 440:631-6. 2006..This study provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling... - Identification and analysis of evolutionarily cohesive functional modules in protein networksMonica Campillos
The European Molecular Biology Laboratory EMBL, 69117 Heidelberg, Germany
Genome Res 16:374-82. 2006.... - A new non-linear normalization method for reducing variability in DNA microarray experimentsChristopher Workman
Genedata AG, Basel, Switzerland
Genome Biol 3:research0048. 2002..Current normalization techniques are most often linear and therefore not capable of fully correcting for these effects...