Publications
L.J. Jensen*, U. de Lichtenberg*, T.S. Jensen, S. Brunak and P. Bork
“Circular reasoning rather than cyclic expression”
Genome Biology, 9, 403, 2008
[Full text] [WWW]
M. Kuhn*, M. Campillos*, P. Gonzales*, L.J. Jensen* and P. Bork*
“Large-scale prediction of drug-target relationships”
FEBS Letters, 582, 1283-1290, 2008
[Abstract] [Full text] [WWW]
E. Harrington, L.J. Jensen and P. Bork
“Predicting biological networks from genomic data”
FEBS Letters, 582, 1251-1258, 2008
[Abstract] [Full text] [WWW]
M. Kuhn, C. von Mering, M. Campillos, L.J. Jensen and P. Bork
“STITCH: interaction networks of chemicals and proteins”
Nucleic Acids Research, 36, D684-D688, 2008
[Abstract] [Full text] [Citations] [WWW]
R. Linding, L.J. Jensen, A. Pasculescu, M. Olhovsky, K. Colwill, P. Bork, M.B. Yaffe and T. Pawson
“NetworKIN: a resource for exploring cellular phosphorylation networks”
Nucleic Acids Research, 36, D695-D699, 2008
[Abstract] [Full text] [Citations] [WWW]
S. Günther, M. Kuhn, M. Dunkel, M. Campillos, C. Senger, E. Petsalaki, J. Ahmed, E.G. Urdiales, A. Gewiess, L.J. Jensen, R. Schneider, R. Skoblo, R.B. Russell, P.E. Bourne, P. Bork and R. Preissner
“SuperTarget and Matador: resources for exploring drug-target relationships”
Nucleic Acids Research, 36, D919-D922, 2008
[Abstract] [Full text] [Citations] [WWW]
L.J. Jensen*, P. Julien*, M. Kuhn, C. von Mering, J. Muller, T. Doerks and P. Bork
“eggNOG: automated construction and annotation of orthologous groups of genes”
Nucleic Acids Research, 36, D250-D254, 2008
[Abstract] [Full text] [Citations] [WWW]
N.P. Gauthier, M.E. Larsen, R. Wernersson, U. de Lichtenberg, L.J. Jensen and S. Brunak
“Cyclebase.org - a comprehensive multi-organism online database of cell cycle experiments”
Nucleic Acids Research, 36, D854-D859, 2008
[Abstract] [Full text] [WWW]
P.K. Shah, L.P. Tripathi, L.J. Jensen, M. Gahnim, C. Mason, E.E. Furlong, V. Rodrigues, K.P. White, P. Bork and R. Sowdhamini
“Enhanced function annotations for Drosophila serine proteases: a case study for systematic annotation of multi-member gene families”
Gene, 407, 199-215, 2008
[Abstract] [Full text]
E.D. Harrington, A.H. Singh, T. Doerks, I. Letunic, C. von Mering, L.J. Jensen, J. Raes and P. Bork
“Quantitative assessment of protein function prediction from metagenomics shotgun sequences”
Proceedings of the National Academy of Sciences, 104, 13913-13918, 2007
[Abstract] [Full text] [Citations]
U. de Lichtenberg*, T.S. Jensen*, S. Brunak, P. Bork and L.J. Jensen
“Evolution of Cell Cycle Control - Same Molecular Machines, Different Regulation”
Cell Cycle, 6, 1819-1825, 2007
[Abstract] [Full text] [Citations] [WWW]
R. Linding*, L.J. Jensen*, G.J. Ostheimer*, M.A.T.M. van Vugt, C. Jørgensen, I.M. Miron, F. Diella, K. Colwill, L. Taylor, K. Elder, P. Metalnikov, V. Nguyen, A. Pasculescu, J. Jin, J.G. Park, L.D. Samson, J.R. Woodgett, R.B. Russell, P. Bork, M.B. Yaffe and T. Pawson
“Systematic discovery of in vivo phosphorylation networks”
Cell, 129, 1415-1426, 2007
[Abstract] [Full text] [Citations] [WWW]
C. von Mering, P. Hugenholtz, J. Raes, S.G. Tringe, T. Doerks, L.J. Jensen, N. Ward and P. Bork
“Quantitative phylogenetic assessment of microbial communities in diverse environments”
Science, 315, 1126-1130, 2007
[Abstract] [Full text] [Citations]
S.D. Hooper*, S. Boue*, R. Krause*, L.J. Jensen, C.E. Mason, M. Ghanim, K.P. White, E.E. Furlong and P. Bork
“Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis”
Molecular Systems Biology, 3, 72, 2007
[Abstract] [Full text] [Citations]
C. von Mering*, L.J. Jensen*, M. Kuhn, S. Chaffron, T. Doerks, B. Krüger, B. Snel and P. Bork
“STRING 7 - recent developments in the integration and prediction of protein interactions”
Nucleic Acids Research, 35, D358-D362, 2007
[Abstract] [Full text] [Citations] [WWW]
F. Perocchi, L.J. Jensen, J. Gagneur, U. Athing, C. von Mering, P. Bork, H. Prokisch and L.M. Steinmetz
“Assessing systems properties of yeast mitochondria through an interaction map of the organelle”
PLoS Genetics, 2, 1612-1624, 2006
[Abstract] [Full text] [Citations] [WWW]
L.J. Jensen*, T.S. Jensen*, U. de Lichtenberg*, S. Brunak and P. Bork
“Co-evolution of transcriptional and posttranslational cell cycle regulation”
Nature, 433, 594-597, 2006
[Abstract] [Full text] [Citations] [WWW]
T. Sandmann, L.J. Jensen, J.S. Jakobsen, M.M. Karzynski, M.P. Eichenlaub, P. Bork and E.E. Furlong
“A temporal map of transcription factor activity: Mef2 directly regulates target genes at all stages of muscle development”
Developmental Cell, 10, 797-807, 2006
[Abstract] [Full text] [Citations] [WWW]
S. Marguerat*, T.S. Jensen*, U. de Lichtenberg, B.T. Wilhelm, L.J. Jensen and J. Bähler
“The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast”
Yeast, 23, 261-277, 2006
[Abstract] [Full text] [Citations] [WWW]
M. Campillos, C. von Mering, L.J. Jensen and P. Bork
“Identification and analysis of evolutionarily cohesive functional modules in protein networks”
Genome Research, 16, 374-382, 2006
[Abstract] [Full text] [Citations]
A.-C. Gavin*, P. Aloy*, P. Grandi, R. Krause, M. Boesche, M. Marzioch, C. Rau, L.J. Jensen, S. Bastuck, B. Dümpelfeld, A. Edelmann, M.-A. Heurtier, V. Hoffman, C. Hoefert, K. Klein, M. Hudak, A.-M. Michon, M. Schelder, M. Schirle, M. Remor, T. Rudi, S. Hooper, A. Bauer, T. Bouwmeester, G. Casari, G. Drewes, G. Neubauer, J.M. Rick, B. Kuster, P. Bork, R.B. Russell and G. Superti-Furga
“Proteome survey reveals modularity of the yeast cell machinery”
Nature, 440, 631-636, 2006
[Abstract] [Full text] [Citations] [WWW]
L.J. Jensen, J. Saric and P. Bork
“Literature mining for the biologist: from information retrieval to biological discovery”
Nature Reviews Genetics, 7, 119-129, 2006
[Abstract] [Full text] [Citations] [WWW]
P. Worning*, L.J. Jensen*, P.F. Hallin, H.H. Stærfeldt and D.W. Ussery
“Origin of replication in circular prokaryotic chromosomes”
Environmental Microbiology, 8, 353-361, 2006
[Abstract] [Citations] [WWW]
J. Saric*, L.J. Jensen*, R. Ouzounova, R. Rojas and P. Bork
“Extraction of regulatory gene/protein networks from Medline”
Bioinformatics, 22, 645-650, 2006
[Abstract] [Full text] [Citations]
C. Taxis, Z. Kavagiou, P. Keller, L.J. Jensen, J. Colombelli, P. Bork, E.H.K. Stelzer and M. Knop
“Spore number control and breeding in Saccharomyces cerevisiae a key role for a self-organizing system”
Journal of Cell Biology, 171, 627-640, 2005
[Abstract] [Full text][Citations]
P.K. Shah, L.J. Jensen, S. Boue, and P. Bork
“Extraction of transcript diversity from scientific literature”
PLoS Computational Biology, 1, e10, 2005
[Abstract] [Full text] [Citations]
J.O. Korbel, T. Doerks, L.J. Jensen, C. Perez-Iratxeta, S. Kaczanowski, S.D. Hooper,M.A. Andrade, and P. Bork
“Systematic association of genes to phenotypes by genome and literature mining”
PLoS Biology, 5, e134, 2005
[Abstract] [Full text] [Citations]
D.W. Ussery, U. de Lichtenberg, and L.J. Jensen
“Systems biology: in the broadest sense of the word”
Environmental Microbiology, 7, 482-483, 2005
[Abstract] [Full text] [Citations]
L.J. Jensen and L.M. Steinmetz
“Re-analysis of data and its integration”
FEBS Letters, 579, 1802-1807, 2005
[Abstract] [Full text] [Citations]
U. de Lichtenberg*, L.J. Jensen*, S. Brunak and P. Bork
“Dynamic complex formation during the yeast cell cycle”
Science, 307, 724-727, 2005
[Abstract] [Full text] [Citations] [WWW]
U. de Lichtenberg*, L.J. Jensen*, A. Fausbøll, T.S. Jensen, P. Bork and S. Brunak
“Comparison of computational methods for the identification of cell cycle regulated genes”
Bioinformatics, 21, 1164-1171, 2005
[Abstract] [Full text] [Citations] [WWW]
C. von Mering, L.J. Jensen, B. Snel, S.D. Hooper, M. Krupp, M. Foglierini, N. Jouffre, M.A. Huynen and P. Bork
“STRING: Known and predicted protein-protein associations, integrated and transferred across organisms”
Nucleic Acids Research, 33, D433-D437, 2005
[Abstracts] [Full text] [Citations] [WWW]
J. Saric, L.J. Jensen, and I. Rojas
“Large-scale extraction of gene regulation for model organisms in an ontological context”
In Silico Biology, 5, 0004, 2004
[Abstract] [Full text] [Citations]
J.O. Korbel, L.J. Jensen, C. von Mering and P. Bork
“Analysis of genomic context: Prediction of functional associations from bidirectionally transcribed gene pairs”
Nature Biotechnology, 22, 911-917, 2004
[Abstract] [Full text] [Citations]
J. Saric, L.J. Jensen, R. Ouzounova, I. Rojas and P. Bork
“Extracting Regulatory Gene Expression Networks from PubMed”
Proceedings of the 42nd Annual Meeting of the Association for Computational Linguistics, 192-199, 2004
[Citations]
L.J. Jensen, J. Lagarde, C. von Mering and P. Bork
“ArrayProspector: A web resource of functional associations inferred from microarray expression data”
Nucleic Acids Research, 32, W445-W448, 2004
[Abstract] [Full text] [Citations] [WWW]
P. Bork*, L.J. Jensen*, C. von Mering*, A.K. Ramani*, I. Lee* and E.M. Marcotte*
“Protein interaction networks from yeast to human”
Current Opinions in Structural Biology, 14, 292-299, 2004
[Abstract] [Full text] [Citations] [WWW]
J.D. Bendtsen, L.J. Jensen, N. Blom, G. von Heijne and S. Brunak
“Feature based prediction of non-classical and leaderless protein secretion”
Protein Engineering Design and Selection, 17, 349-356, 2004
[Abstract] [Full text] [Citations] [WWW]
L.J. Jensen and P. Bork
“Quality analysis and integration of large-scale molecular data sets”
Drug Discovery Today: TARGETS, 3, 51-56, 2004
[WWW]
L.J. Jensen, M. Skovgaard, T. Sicheritz-Pontén, N.T. Hansen, H. Johanson, M.K. Jørgensen, K. Kiil and D.W. Ussery
“Comparative genomics of four Pseudomonas species”
The Pseudomonads, Vol 1, Chapter 5, 139-164, 2004
[Citations] [WWW]
R. Linding*, L.J. Jensen*, F. Diella, P. Bork, T.J. Gibson and R.B. Russell
“Protein disorder prediction: implications for structural proteomics”
Structure, 11, 1453-1459, 2003
[Abstract] [Full text] [Citations] [WWW]
L.J. Jensen, D.W. Ussery, and S. Brunak
“Functionality of system components: Conservation of protein function in protein feature space”
Genome Research, 13, 2444-2449, 2003
[Abstract] [Full text] [Citations] [WWW]
U. de Lichtenberg, T.S. Jensen, L.J. Jensen, and S. Brunak
“Protein feature based identification of cell cycle regulated proteins in yeast”
Journal of Molecular Biology, 329, 663-674, 2003
[Abstract] [Full text] [Citations] [WWW]
L.J. Jensen, M. Skovgaard, T. Sicheritz-Pontén, M.K. Jørgensen, C. Lundegaard, C.C. Pedersen, N. Petersen and D.W. Ussery
“Analysis of two large functionally uncharacterized regions in the Methanopyrus kandleri AV19 genome”
BMC Genomics, 4, art. 12, 2003
[Abstract] [Full text] [Citations [WWW]
L.J. Jensen, R. Gupta, H.H. Stærfeldt and S. Brunak
“Prediction of human protein function according to Gene Ontology categories”
Bioinformatics, 19, 635-642, 2003
[Abstract] [Full text] [Citations] [WWW]
L.J. Jensen, M. Skovgaard, and S. Brunak
“Prediction of novel archaeal enzymes from sequence-derived features”
Protein Science, 11, 2894-2898, 2002
[Abstract] [Full text] [Citations] [WWW]
C. Workman, L.J. Jensen, H. Jarmer, R. Berka, L. Gautier, H.H. Saxild, C. Nielsen, S. Brunak, and S. Knudsen
“A new non-linear normalization method to reduce variability in DNA microarray experiments”
Genome Biology, 3, 0048.1-0048.16, 2002
[Abstract] [Full text] [Citations]
M. Skovgaard, L.J. Jensen, C. Friis, H.H. Stærfeldt, P. Worning, S. Brunak and D.W. Ussery
“The atlas visualisation of genome-wide information”
Methods in Microbiology, 33, Chapter 3, 49-63, 2002
[Citations] [WWW]
L.J. Jensen*, R. Gupta*, N. Blom, D. Devos, J. Tamames, C. Kesmir, H. Nielsen, H.H. Stærfeldt, K. Rapacki, C. Workman, C.A.F. Andersen, S. Knudsen, A. Krogh, A. Valencia and S. Brunak
“Prediction of human protein function from post-translational modifications and localization features”
Journal of Molecular Biology, 319, 1257-1265, 2002
[Abstract] [Full text] [Citations] [WWW]
R. Gupta, L.J. Jensen and S. Brunak
“Orphan protein function and its relation to glycosylation”
Ernst Schering Research Foundation Proceedings, 38, Chapter 13, 275-294, 2002
[Abstract] [Citations]
M. Skovgaard, L.J. Jensen, S. Brunak, D. Ussery and A. Krogh
“On the total number of genes and their length distribution in complete microbial genomes”
Trends in Genetics, 17, 425-428, 2001
[Abstract] [Full text] [Citations]
P. Worning, L.J. Jensen, K.E. Nelson, S. Brunak and D.W. Ussery
“Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima“
Nucleic Acids Research, 28, 706-709, 2000
[Abstract] [Full text] [Citations]
C. Friis, L.J. Jensen and D.W. Ussery
“Visualization of pathogenicity regions in bacteria”
Genetica, 108, 47-51, 2000
[Abstract] [Citations] [WWW]
L.J. Jensen and S. Knudsen
“Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation”
Bioinformatics, 16, 326-333, 2000
[Abstract] [Full text] [Citations]
A.G. Pedersen*, L.J. Jensen*, H.H. Stærfeldt, S. Brunak and D.W. Ussery
“A DNA structural atlas of E. coli“
Journal of Molecular Biology, 299, 907-930, 2000
[Abstract] [Full text] [Citations] [WWW]
L.J. Jensen, C. Friis and D.W Ussery
“Three views of microbial genomes”
Research in Microbiology, 150, 773-777, 1999
[Abstract] [Citations] [WWW]
L.J. Jensen, K.V. Andersen, A. Svendsen and T. Kretzschmar
“Scoring functions for computational algorithms applicable to the design of spiked oligonucleotides”
Nucleic Acids Research, 26, 697-702, 1998
[Abstract] [Full text] [Citations]
* These authors contributed equally.
