Lars Juhl Jensen

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. pmc STITCH: interaction networks of chemicals and proteins
    Michael Kuhn
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 36:D684-8. 2008
  2. ncbi request reprint Literature mining for the biologist: from information retrieval to biological discovery
    Lars Juhl Jensen
    European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Nat Rev Genet 7:119-29. 2006
  3. pmc A side effect resource to capture phenotypic effects of drugs
    Michael Kuhn
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 6:343. 2010
  4. doi request reprint Drug target identification using side-effect similarity
    Monica Campillos
    European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Science 321:263-6. 2008
  5. pmc eggNOG: automated construction and annotation of orthologous groups of genes
    Lars Juhl Jensen
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nucleic Acids Res 36:D250-4. 2008
  6. pmc Systematic identification of proteins that elicit drug side effects
    Michael Kuhn
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 9:663. 2013
  7. doi request reprint Biochemistry. Not comparable, but complementary
    Lars Juhl Jensen
    European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Science 322:56-7. 2008
  8. pmc ArrayProspector: a web resource of functional associations inferred from microarray expression data
    Lars Juhl Jensen
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Nucleic Acids Res 32:W445-8. 2004
  9. pmc Identification and analysis of evolutionarily cohesive functional modules in protein networks
    Monica Campillos
    The European Molecular Biology Laboratory EMBL, 69117 Heidelberg, Germany
    Genome Res 16:374-82. 2006
  10. ncbi request reprint Proteome survey reveals modularity of the yeast cell machinery
    Anne Claude Gavin
    Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 440:631-6. 2006

Collaborators

Detail Information

Publications28

  1. pmc STITCH: interaction networks of chemicals and proteins
    Michael 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/...
  2. ncbi request reprint Literature mining for the biologist: from information retrieval to biological discovery
    Lars 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...
  3. pmc A side effect resource to capture phenotypic effects of drugs
    Michael 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...
  4. doi request reprint Drug target identification using side-effect similarity
    Monica 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...
  5. pmc eggNOG: automated construction and annotation of orthologous groups of genes
    Lars 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...
  6. pmc Systematic identification of proteins that elicit drug side effects
    Michael Kuhn
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 9:663. 2013
    ..Taken together, we show that a large fraction of complex drug side effects are mediated by individual proteins and create a reference for such relations...
  7. doi request reprint Biochemistry. Not comparable, but complementary
    Lars Juhl Jensen
    European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Science 322:56-7. 2008
  8. pmc ArrayProspector: a web resource of functional associations inferred from microarray expression data
    Lars 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...
  9. pmc Identification and analysis of evolutionarily cohesive functional modules in protein networks
    Monica Campillos
    The European Molecular Biology Laboratory EMBL, 69117 Heidelberg, Germany
    Genome Res 16:374-82. 2006
    ....
  10. ncbi request reprint Proteome survey reveals modularity of the yeast cell machinery
    Anne 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...
  11. doi request reprint Large-scale prediction of drug-target relationships
    Michael 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...
  12. pmc Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data
    Jeroen 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...
  13. pmc Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system
    Christof Taxis
    The European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    J Cell Biol 171:627-40. 2005
    ..This is beneficial for the immediate fitness of the population of postmeiotic cells...
  14. pmc A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae
    Oriol Gallego
    Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Heidelberg, Germany
    Mol Syst Biol 6:430. 2010
    ....
  15. ncbi request reprint Re-analysis of data and its integration
    Lars 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...
  16. ncbi request reprint Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families
    Parantu 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...
  17. ncbi request reprint Co-evolution of transcriptional and post-translational cell-cycle regulation
    Lars Juhl Jensen
    European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Nature 443:594-7. 2006
    ....
  18. ncbi request reprint Protein disorder prediction: implications for structural proteomics
    Rune 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...
  19. pmc Systematic discovery of in vivo phosphorylation networks
    Rune 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...
  20. pmc Prediction of novel archaeal enzymes from sequence-derived features
    Lars 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...
  21. pmc Functionality of system components: conservation of protein function in protein feature space
    Lars 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...
  22. ncbi request reprint Feature-based prediction of non-classical and leaderless protein secretion
    Jannick 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...
  23. doi request reprint Linear motif atlas for phosphorylation-dependent signaling
    Martin 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)...
  24. ncbi request reprint Comparison of computational methods for the identification of cell cycle-regulated genes
    Ulrik 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...
  25. ncbi request reprint Crystal ball. Systems biology: in the broadest sense of the word
    David W Ussery
    Ulrik de Lichtenberg, Center for Biological Sequence Analysis, Technical University of Denmark
    Environ Microbiol 7:482-3. 2005
  26. ncbi request reprint Extraction of regulatory gene/protein networks from Medline
    Jasmin 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...
  27. pmc SuperTarget and Matador: resources for exploring drug-target relationships
    Stefan 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...
  28. pmc A new non-linear normalization method for reducing variability in DNA microarray experiments
    Christopher 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...