Lars Juhl Jensen

Lars Juhl Jensen

professor, group leader


  1. 1998
  2. Scoring functions for computational algorithms applicable to the design of spiked oligonucleotides

    Jensen, Lars Juhl, Andersen, K. V., Svendsen, A. & Kretzschmar, T., 1998, In : Nucleic Acids Research. 26, 3, p. 697-702 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. 2000
  4. A DNA structural atlas for Escherichia coli

    Pedersen, A. G., Jensen, Lars Juhl, Brunak, S., Staerfeldt, H. H. & Ussery, D., 2000, In : Journal of Molecular Biology. 299, 4, p. 907-30 24 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation

    Jensen, Lars Juhl & Knudsen, S., 2000, In : Bioinformatics. 16, 4, p. 326-33 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima

    Worning, P., Jensen, Lars Juhl, Nelson, K. E., Brunak, S. & Ussery, D., 2000, In : Nucleic Acids Research. 28, 3, p. 706-9 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Visualization of pathogenicity regions in bacteria

    Jensen, Lars Juhl, Friis, C. & Ussery, D., 2000, In : Genetica. 108, 1, p. 47-51 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. 2001
  9. Published

    On the total number of genes and their length distribution in complete microbial genomes

    Skovgaard, M., Jensen, Lars Juhl, Brunak, Søren, Ussery, D. & Krogh, Anders, 2001, In : Trends in Genetics. 17, 8, p. 425-8 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. 2002
  11. A new non-linear normalization method for reducing variability in DNA microarray experiments

    Workman, C., Jensen, Lars Juhl, Jarmer, H. Ø., Berka, R., Gautier, L., Nielser, H. B., Saxild, H. H., Nielsen, C., Brunak, S. & Knudsen, S., 2002, In : Genome Biology (Online Edition). 3, 9, p. research0048

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Orphan protein function and its relation to glycosylation

    Gupta, R., Jensen, Lars Juhl & Brunak, S., 2002, In : Ernst Schering Foundation Symposium Proceedings. 38, p. 276-94 19 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Prediction of human protein function from post-translational modifications and localization features

    Jensen, Lars Juhl, Gupta, R., Blom, N., Devos, D., Tamames, J., Kesmir, C., Nielsen, H., Staerfeldt, H. H., Rapacki, K., Workman, C., Andersen, C. A. F., Knudsen, S., Krogh, A., Valencia, A. & Brunak, S., 2002, In : Journal of Molecular Biology. 319, 5, p. 1257-65 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. Prediction of novel archaeal enzymes from sequence-derived features

    Jensen, Lars Juhl, Skovgaard, M. & Brunak, S., 2002, In : Protein Science. 11, 12, p. 2894-8 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. The atlas visualisation of genome-wide information

    Skovgaard, M., Jensen, Lars Juhl, Friis, C., Stærfeldt, H. H., Worning, P., Brunak, S. & Ussery, D. W., 2002, Methods in Microbiology. Vol. 33. p. 49-63

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  16. 2003
  17. Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome

    Jensen, Lars Juhl, Skovgaard, M., Sicheritz-Pontén, T., Jørgensen, M. K., Lundegaard, C., Pedersen, C. C., Petersen, N. & Ussery, D., 2003, In : B M C Genomics. 4, 1, p. 12

    Research output: Contribution to journalJournal articleResearchpeer-review

  18. Functionality of system components: conservation of protein function in protein feature space

    Jensen, Lars Juhl, Ussery, D. & Brunak, S., 2003, In : Genome Research. 13, 11, p. 2444-9 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. Prediction of human protein function according to Gene Ontology categories

    Jensen, Lars Juhl, Gupta, R., Staerfeldt, H. & Brunak, S., 2003, In : Bioinformatics. 19, 5, p. 635-42 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. Protein disorder prediction: implications for structural proteomics

    Linding, R., Jensen, Lars Juhl, Diella, F., Bork, P., Gibson, T. J. & Russell, R. B., 2003, In : Structure. 11, 11, p. 1453-9 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. Protein feature based identification of cell cycle regulated proteins in yeast

    de Lichtenberg, U., Jensen, T. S., Jensen, Lars Juhl & Brunak, S., 2003, In : Journal of Molecular Biology. 329, 4, p. 663-74 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. 2004
  23. Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs

    Korbel, J. O., Jensen, Lars Juhl, von Mering, C. & Bork, P., 2004, In : Nature Biotechnology. 22, 7, p. 911-7 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  24. ArrayProspector: a web resource of functional associations inferred from microarray expression data

    Jensen, Lars Juhl, Lagarde, J., von Mering, C. & Bork, P., 2004, In : Nucleic Acids Research. 32, Web Server issue, p. W445-8

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. Comparative genomics of four Pseudomonas species

    Jensen, Lars Juhl, Skovgaard, M., Sicheritz-Ponten, T., Hansen, N. T., Johansen, H., Jørgensen, M. K., Kiil, K. & Ussery, D. W., 2004, The Phedomonads. p. 139-164

    Research output: Chapter in Book/Report/Conference proceedingBook chapterCommunication

  26. Feature-based prediction of non-classical and leaderless protein secretion

    Bendtsen, J. D., Jensen, Lars Juhl, Blom, N., Von Heijne, G. & Brunak, S., 2004, In : Protein Engineering Design and Selection (Print). 17, 4, p. 349-56 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  27. Protein interaction networks from yeast to human

    Bork, P., Jensen, Lars Juhl, von Mering, C., Ramani, A. K., Lee, I. & Marcotte, E. M., 2004, In : Current Opinion in Structural Biology. 14, 3, p. 292-9 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  28. 2005
  29. Comparison of computational methods for the identification of cell cycle-regulated genes

    de Lichtenberg, U., Jensen, Lars Juhl, Fausbøll, A., Jensen, T. S., Bork, P. & Brunak, S., 2005, In : Bioinformatics. 21, 7, p. 1164-71 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Crystal ball. Systems biology: in the broadest sense of the word

    Ussery, D., de Lichtenberg, U. & Jensen, Lars Juhl, 2005, In : Environmental Microbiology. 7, 4, p. 482-3 2 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  31. Dynamic complex formation during the yeast cell cycle

    de Lichtenberg, U., Jensen, Lars Juhl, Brunak, S. & Bork, P., 2005, In : Science (New York, N.Y.). 307, 5710, p. 724-7 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. Extraction of transcript diversity from scientific literature

    Shah, P. K., Jensen, Lars Juhl, Boué, S. & Bork, P., 2005, In : P L o S Computational Biology. 1, 1, p. e10

    Research output: Contribution to journalJournal articleResearchpeer-review

  33. Large-scale extraction of gene regulation for model organisms in an ontological context

    Saric, J., Jensen, Lars Juhl & Rojas, I., 2005, In : In Silico Biology. 5, 1, p. 21-32 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Re-analysis of data and its integration

    Jensen, Lars Juhl & Steinmetz, L. M., 2005, In : F E B S Letters. 579, 8, p. 1802-7 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. STRING: known and predicted protein-protein associations, integrated and transferred across organisms

    von Mering, C., Jensen, Lars Juhl, Snel, B., Hooper, S. D., Krupp, M., Foglierini, M., Jouffre, N., Huynen, M. A. & Bork, P., 2005, In : Nucleic Acids Research. 33, Database issue, p. D433-7

    Research output: Contribution to journalJournal articleResearchpeer-review

  36. Spore number control and breeding in saccharomyces cerevisiae a key role for a self-organixzing system

    Taxis, C., Kavagiou, Z., Keller, P., Jensen, Lars Juhl, Colombelli, J., Bork, P., Stelzer, E. H. K. & Knop, M., 2005, In : Journal of Cell Biology. 171, p. 627-640

    Research output: Contribution to journalJournal articleResearchpeer-review

  37. Systematic association of genes to phenotypes by genome and literature mining

    Korbel, J. O., Doerks, T., Jensen, Lars Juhl, Perez-Iratxeta, C., Kaczanowski, S., Hooper, S. D., Andrade, M. A. & Bork, P., 2005, In : P L o S Biology (Online). 3, 5, p. e134

    Research output: Contribution to journalJournal articleResearchpeer-review

  38. 2006
  39. Assessing systems properties of yeast mitochondria through an interaction map of the organelle

    Perocchi, F., Jensen, Lars Juhl, Gagneur, J., Ahting, U., von Mering, C., Bork, P., Prokisch, H. & Steinmetz, L. M., 2006, In : P L o S Genetics (Online). 2, 10, p. e170

    Research output: Contribution to journalJournal articleResearchpeer-review

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

    Jensen, Lars Juhl, Jensen, T. S., de Lichtenberg, U., Brunak, S. & Bork, P., 2006, In : Nature Study. 443, 7111, p. 594-7 4 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  41. Extraction of regulatory gene/protein networks from Medline

    Saric, J., Jensen, Lars Juhl, Ouzounova, R., Rojas, I. & Bork, P., 2006, In : Bioinformatics. 22, 6, p. 645-50 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

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

    Campillos, M., von Mering, C., Jensen, Lars Juhl & Bork, P., 2006, In : Genome Research. 16, 3, p. 374-82 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  43. Literature mining for the biologist: from information retrieval to biological discovery

    Jensen, Lars Juhl, Saric, J. & Bork, P., 2006, In : Nature Reviews. Genetics. 7, 2, p. 119-29 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  44. Origin of replication in circular prokaryotic chromosomes

    Worning, P., Jensen, Lars Juhl, Hallin, P. F., Staerfeldt, H. & Ussery, D., 2006, In : Environmental Microbiology. 8, 2, p. 353-61 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  45. Proteome survey reveals modularity of the yeast cell machinery

    Gavin, A., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, Lars Juhl, Bastuck, S., Dümpelfeld, B., Edelmann, A., Heurtier, M., Hoffman, V., Hoefert, C., Klein, K., Hudak, M., Michon, A., Schelder, M., Schirle, M., Remor, M., Rudi, T., Hooper, S., Bauer, A., Bouwmeester, T., Casari, G., Drewes, G., Neubauer, G., Rick, J. M., Kuster, B., Bork, P., Russell, R. B. & Superti-Furga, G., 2006, In : Nature Study. 440, 7084, p. 631-6 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  46. The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast

    Marguerat, S., Jensen, T. S., de Lichtenberg, U., Wilhelm, B. T., Jensen, Lars Juhl & Bähler, J., 2006, In : Yeast (Chichester, England). 23, 4, p. 261-77 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  47. 2007
  48. Evolution of cell cycle control: same molecular machines, different regulation

    de Lichtenberg, U., Jensen, T. S., Brunak, S., Bork, P. & Jensen, Lars Juhl, 2007, In : Cell Cycle. 6, 15, p. 1819-25 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  49. Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis

    Hooper, S. D., Boué, S., Krause, R., Jensen, Lars Juhl, Mason, C. E., Ghanim, M., White, K. P., Furlong, E. E. M. & Bork, P., 2007, In : Molecular Systems Biology. 3, p. 72

    Research output: Contribution to journalJournal articleResearchpeer-review

  50. Quantitative assessment of protein function prediction from metagenomics shotgun sequences

    Harrington, E. D., Singh, A., Doerks, T., Letunic, I., von Mering, C., Jensen, Lars Juhl, Raes, J. & Bork, P., 2007, In : Proceedings of the National Academy of Sciences of the United States of America. 104, 35, p. 13913-8 6 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  51. Quantitative phylogenetic assessment of microbial communities in diverse environments

    von Mering, C., Hugenholtz, P., Raes, J., Tringe, S. G., Doerks, T., Jensen, Lars Juhl, Ward, N. & Bork, P., 2007, In : Science (New York, N.Y.). 315, 5815, p. 1126-30 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  52. STRING 7--recent developments in the integration and prediction of protein interactions

    von Mering, C., Jensen, Lars Juhl, Kuhn, M., Chaffron, S., Doerks, T., Krüger, B., Snel, B. & Bork, P., 2007, In : Nucleic Acids Research. 35, Database issue, p. D358-62

    Research output: Contribution to journalJournal articleResearchpeer-review

  53. Systematic discovery of in vivo phosphorylation networks

    Linding, R., Jensen, Lars Juhl, Ostheimer, G. J., van Vugt, M. A. T. M., Jørgensen, C., Miron, I. M., Diella, F., Colwill, K., Taylor, L., Elder, K., Metalnikov, P., Nguyen, V., Pasculescu, A., Jin, J., Park, J. G., Samson, L. D., Woodgett, J. R., Russell, R. B., Bork, P., Yaffe, M. B. & Pawson, T., 2007, In : Cell. 129, 7, p. 1415-26 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  54. 2008
  55. Published

    Circular reasoning rather than cyclic expression

    Jensen, Lars Juhl, de Lichtenberg, U., Jensen, T. S., Brunak, Søren & Bork, P., 2008, In : Genome Biology. 9, 6, p. 403

    Research output: Contribution to journalJournal articleResearchpeer-review

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

    Gauthier, N. P., Larsen, M. E., Wernersson, R., de Lichtenberg, U., Jensen, Lars Juhl, Brunak, S. & Jensen, T. S., 2008, In : Nucleic Acids Research. 36, Database issue, p. D854-9

    Research output: Contribution to journalJournal articleResearchpeer-review

  57. Published

    Drug target identification using side-effect similarity

    Campillos, M., Kuhn, M., Gavin, A., Jensen, Lars Juhl & Bork, P., 2008, In : Science. 321, 5886, p. 263-6 3 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  58. Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families

    Shah, P. K., Tripathi, L. P., Jensen, Lars Juhl, Gahnim, M., Mason, C., Furlong, E. E., Rodrigues, V., White, K. P., Bork, P. & Sowdhamini, R., 2008, In : Gene. 407, 1-2, p. 199-215 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  59. Published

    Large-scale prediction of drug-target relationships

    Kuhn, M., Campillos, M., González, P., Jensen, Lars Juhl & Bork, P., 2008, In : F E B S Letters. 582, 8, p. 1283-90 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  60. Published

    Linear motif atlas for phosphorylation-dependent signaling

    Miller, M. L., Jensen, Lars Juhl, Diella, F., Jørgensen, Claus Bøttcher, Tinti, M., Li, L., Hsiung, M., Parker, S. A., Bordeaux, J., Sicheritz-Ponten, T., Olhovsky, M., Pasculescu, A., Alexander, J., Knapp, S., Blom, N., Bork, P., Li, S., Cesareni, G., Pawson, T., Turk, B. E., Yaffe, M. B., Brunak, Søren & Linding, R., 2008, In : Science signaling. 1, 35, p. ra2

    Research output: Contribution to journalJournal articleResearchpeer-review

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