For the vast majority of the publications that are registered in PubMed a link is provided to the abstract [PubMed]. For journals with electronic access a link is provided to the publishers site [Publisher]. The paper is provided as a PDF file when allowed by the publisher [PDF]. Furthermore, links are provided to related web resources such as prediction servers [WWW]. Please note that in some cases a PDF file can be obtained for free from the publisher although redistribution is not allowed; in these cases there will be a [Publisher] link but no [PDF] link. Otherwise, reprints can usually be obtained by sending me an email.
"Prediction of protein function from sequence derived protein features"
Technical University of Denmark, Lyngby, Denmark, 2002
[PDF]
[WWW]
(Last change: 25 October 2004)
R. Altman, C.M. Bergman, J. Blake, C. Blaschke, A. Cohen, F. Gannon, L. Grivell, U. Hahn, W. Hersh, L. Hirschman, L.J. Jensen, M. Krallinger, B. Mons, S.I. O'Donoghue, M. Peitsch, D. Rebholz-Schumann, H. Shatkay, A. Valencia
"Text mining for biology: the way forward"
to appear in Genome Biology, 2008
L.J. Jensen*, U. de Lichtenberg, T.S. Jensen, S. Brunak and P. Bork
"Circular reasoning rather than cyclic expression"
to appear in Genome Biology, 2008
[WWW]
E. Harrington, L.J. Jensen and P. Bork
"Predicting biological networks from genomic data"
FEBS Letters, 582, 1251-1268, 2008
[PubMed]
[Publisher]
[PDF]
[WWW]
M. Kuhn*, M. Campillos*, P. Gonzales*, L.J. Jensen* and P. Bork*
"Large-scale prediction of drug-target relationships"
to appear in FEBS Letters, 2008
[PubMed]
[Publisher]
[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
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
[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, D854-D859, 2008
[PubMed]
[Publisher]
[PDF]
[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, 199-215, 2008
[PubMed]
[Publisher]
[PDF]
[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, 2007
[PubMed]
[Publisher]
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
[PubMed]
[Publisher]
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
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[Publisher]
[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
[PubMed]
[Publisher]
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
[PubMed]
[Publisher]
[PDF]
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
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
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
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[PDF]
[Cover]
[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
[PubMed]
[Publisher]
[PDF]
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
[PubMed]
[Publisher]
[PDF]
P.K. Shah, L.J. Jensen, S. Boue and P. Bork
"Extraction of transcript diversity from scientific literature"
PLoS Computational Biology, 1, e10, 2005
[PubMed]
[Publisher]
[PDF]
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
[PubMed]
[Publisher]
[PDF]
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
[PubMed]
[Publisher]
[PDF]
L.J. Jensen and L.M. Steinmetz
"Re-analysis of data and its integration"
FEBS Letters, 579, 1802-1807, 2005
[PubMed]
[Publisher]
[PDF]
U. de Lichtenberg*, L.J. Jensen*, S. Brunak and P. Bork
"Dynamic complex formation during the yeast cell cycle"
Science, 307, 724-727, 2005
[PubMed]
[Publisher]
[PDF]
[Supplement]
[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
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
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
[PubMed]
[Publisher]
[PDF]
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
[PDF]
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
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
[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
[PDF]
[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
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
[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
This is included as Paper IV in my Ph.D. thesis
[PubMed]
[Publisher]
[PDF]
[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
An earlier version is included as Paper V in my Ph.D. thesis
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
[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
This is included as Paper VII in my Ph.D. thesis
[PubMed]
[Publisher]
[PDF]
[WWW]
L.J. Jensen, M. Skovgaard, and S. Brunak
"Prediction of novel archaeal enzymes from sequence-derived features"
Protein Science, 11, 2894-2898, 2002
This is included as Paper VI in my Ph.D. thesis
[PubMed]
[Publisher]
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
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
This is included as Paper VIII in my Ph.D. thesis
[Cover]
[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
This is included as Paper II in my Ph.D. thesis
[PubMed]
[Publisher]
[PDF]
[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
This is included as Paper III in my Ph.D. thesis
[PubMed]
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
This is included as Paper I in my Ph.D. thesis
[PubMed]
[Publisher]
[PDF]
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
[PubMed]
[Publisher]
[PDF]
C. Friis, L.J. Jensen and D.W. Ussery
"Visualization of pathogenicity regions in bacteria"
Genetica, 108, 47-51, 2000
[PubMed]
[PDF]
[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
[PubMed]
[Publisher]
[PDF]
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
[PubMed]
[Publisher]
[PDF]
[Cover]
[WWW]
L.J. Jensen, C. Friis and D.W Ussery
"Three views of microbial genomes"
Research in Microbiology, 150, 773-777, 1999
[PubMed]
[PDF]
[Cover]
[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
[PubMed]
[Publisher]
[PDF]
* These authors contributed equally.
"Computational approaches to cell cycle analysis"
PhD Program in Computational Biology
Instituto Gulbenkian de Ciencia, Oeiras, Portugal, April 29-May 2, 2008
[PPT]
[PPT]
[PPT]
[WWW]
"Integration of biomedical literature and databases"
Nordic Conference for Scolarly Communication 2008
Scandic Star Hotel, Lund, Sweden, April 21-23, 2008
[PPT]
[WWW]
"Network integration of heterogeneous data"
8th Course in Bioinformatics & Systems Biology for Molecular Biologists
Bertinoro di Romagna, Bertinoro, Italy, March 16-20, 2008
[PPT]
[WWW]
[WWW]
[WWW]
"Literature mining and large-scale data integration"
Computational and Systems Biology Course
Centre for Computational and Systems Biology (CoSBi), Trento, Italy, March 10-14, 2008
[PPT]
[WWW]
[WWW]
[WWW]
[WWW]
"Functional association networks - The STRING and STITCH web resources"
European Molecular Biology Laboratory, Heidelberg, Germany, February 1, 2008
[PPT]
[WWW]
[WWW]
"Systematic discovery of phosphorylation networks - Combining linear motifs and protein interactions"
Munich, Germany, November 7, 2007
[PPT]
[WWW]
"Systematic discovery of phosphorylation networks - Combining linear motifs and protein interactions"
Novel approaches to study kinase and GTPase signaling
Plate-forme Génomique fonctionnelle Bordeaux Aquitaine, Bordeaux, France, September 26-28, 2007
[PPT]
[WWW]
"Bioinformatics of cellular processes"
EMBO Practical Course on Methods in Cell Biology: Exploring the Dynamics of Cellular Organization
European Molecular Biology Laboratory, Heidelberg, Germany, August 23-31, 2007
[PPT]
[WWW]
"Analysis of metagenomes"
Max Planck Institute for Marine Microbiology, Bremen, Germany, August 24-25, 2007
[PPT]
[AVI]
"Just-in-time assembly - Co-evolution of transcriptional and post-translational cell-cycle regulation of protein complexes"
15th International Conference on Intelligent Systems for Molecular Biology
Austria Center Vienna, Vienna, Austria, July 22-25, 2007
[PPT]
[WWW]
"Prediction of protein networks through data integration"
MIPS Retreat
Kloster Frauenchiemsee, Chiemsee, Germany, July 9-10, 2007
[PPT]
[WWW]
[WWW]
"Just-in-time assembly - Co-evolution of transcriptional and post-translational cell-cycle regulation of protein complexes"
MIPS Retreat
Kloster Frauenchiemsee, Chiemsee, Germany, July 9-10, 2007
[PPT]
[WWW]
"Integration of biomedical data and electronic publications"
10th International Symposium on Electronic Theses and Dissertations
Uppsala University, Uppsala, Sweden, June 13-16, 2007
[PPT]
"Biomedical literature mining (and why we really need open access"
The 28th IATUL annual conference: Global Access to Science - Scientific Publishing for the Future
Royal Institute of Technology (KTH), Stockholm, Sweden, June 11-14, 2007
[PPT]
"Literature Mining and Systems Biology"
Bioinformatics & Gene Discovery
Technical University of Denmark, Lyngby, Denmark, June 8, 2007
[PPT]
"Just-in-time assembly - Co-evolution of transcriptional and post-translational cell-cycle regulation of protein complexes"
European Bioinformatics Institute, Hinxton, England, May 21, 2007
[PPT]
[WWW]
"The STRING database - Quality scores for heterogeneous interaction data"
Lyon, France, April 23-25, 2007
[PPT]
[WWW]
"Just-in-time assembly - the evolution of transcriptional and post-translational cell-cycle regulation of protein complexes"
University of Natural Resources and Applied Life Sciences, Vienna, Austria, February 15, 2007
[PPT]
[WWW]
"The STRING database"
Introduction to Bioinformatics
Heidelberg University, Heidelberg, Germany, November 29, 2006
[PPT]
[WWW]
"Cross-species data integration"
Centre for Molecular Biology and Neuroscience, Rikshospitalet-Radiumhospitalet, Oslo, Norway, October 25, 2006
[PPT]
[WWW]
"Mining large-scale data sets on the eukaryotic cell cycle"
Data and Text Mining for Integrative Biology
Humboldt University, Berlin, Germany, September 18-22, 2006
[PPT]
[WWW]
"Prediction of protein function"
BioSys course
Technical University of Denmark, Lyngby, Denmark, September 11-12, 2006
[PPT]
"Open access - making the most of biomedical literature mining"
Open Access indenfor naturvidenskaberne
Copenhagen University Library, Copenhagen, Denmark, September 8, 2006
[PPT]
"Protein function prediction"
Fifth European School in Bioinformatics
Budapest, September 4-8, 2006
[PPT]
"The STRING database"
14th International Conference on Intelligent Systems for Molecular Biology, Software demo
Fortaleza Conference Center, Fortaleza, Brazil, August 6-10, 2006
[PPT]
[WWW]
"Biological literature mining - from information retrieval to biological discovery"
14th International Conference on Intelligent Systems for Molecular Biology, Tutorial
Fortaleza Conference Center, Fortaleza, Brazil, August 6-10, 2006
[PPT]
"Protein networks as a scaffold for structuring other data"
SEMM
IFOM, Milan, Italy, June 15-16, 2006
[PPT]
"Introduction to STRING"
SEMM
IFOM, Milan, Italy, June 15-16, 2006
[PPT]
[WWW]
"Evolutionary self-organization in molecular networks"
EMBO Workshop on Principles of Self-Organization in Living Matter
European Molecular Biology Laboratory, Heidelberg, Germany, June 2-4, 2006
[PPT]
"Open access - making the most of biomedical literature mining"
Berlin 4 Open Access - From Promise to Practice
Max-Planck-Institute for Gravitational Physics, Potsdam-Golm, Germany, March 29-31, 2006
[PPT]
"STRING - Modeling of biological systems through cross-species data integration"
Journée Thematique Biologie des Systèmes
INRA, Jouy-en-Josas, France, February 2, 2006
[PPT]
[WWW]
"Text mining for protein and small molecule relations"
BCB-Seminar
Charite, Berlin, Germany, Januar 19, 2006
[PPT]
"Biomedical literature mining"
Bioinformatics & Gene Discovery
Technical University of Denmark, Lyngby, Denmark, January 2, 2006
[PPT]
"STRING - Cross-species integration of known and predicted protein-protein interactions"
University of Southern California, Los Angeles, California, December 15, 2005
[PPT]
[WWW]
"Integration of diverse large-scale datasets"
IPAM Proteomics Reunion Conference
UCLA, Lake Arrowhead, California, December 11-16, 2005
[PPT]
"Protein interaction networks from yeast to human"
Danish Proteomics Society and Danish Society for Biochemistry and Molecular Biology Symposium
University of Southern Denmark, Odense, Denmark, December 8, 2005
[PPT]
"Biomedical literature mining"
BioSys course
Technical University of Denmark, Lyngby, Denmark, October 24, 2005
[PPT]
"STRING - Modeling of biological systems through cross-species data integration"
12th European Congress on Biotechnology
Technical University of Denmark, Lyngby, Denmark, August 21-24, 2005
[PPT]
[WWW]
"Modeling the dynamic assembly of cell cycle complexes from high-throughput data"
EMBO Young Investigators Programme, 3rd Symposium
European Molecular Biology Laboratory, Heidelberg, Germany, June 24-26, 2005
[PPT]
[WWW]
"STRING - Cross-species integration of known and predicted protein-protein interactions"
Samuel Lunenfeld Research Institute, Mt. Sinai Hospital, Toronto, Canada, April 28, 2005
[PPT]
[WWW]
"Dynamic complex formation during the yeast cell cycle"
Samuel Lunenfeld Research Institute, Mt. Sinai Hospital, Toronto, Canada, April 28, 2005
[PPT]
[WWW]
"STRING - Modeling of pathways through cross-species integration of large-scale data"
Sienabiotech, Siena, April 21, 2005
[PPT]
[WWW]
"Dynamic complex formation during the yeast cell cycle"
EMBL white seminar
European Molecular Biology Laboratory, Heidelberg, Germany, February 4, 2005
[PPT]
[WWW]
"Proteomics - Analysis and integration of large-scale data sets"
Second European School on Bioinformatics
CMBI, Nijmegen, Netherlands, January 22-25, 2005
[PPT]
[WWW]
"STRING - Prediction of functional relations, modules, and networks from heterogeneous genome-scale data"
Netherlands Conference on Bioinformatics 2004
Hanzehogeschool, Groningen, Netherlands, October 7-8, 2004
[PPT]
[WWW]
"STRING - Prediction of functionally associated proteins from heterogeneous genome scale data sets"
EBI Industry Workshop
European Bioinformatics Institute, Hinxton, England, September 27-29, 2004
[PPT]
[WWW]
"STRING - Prediction of protein networks through integration of diverse large-scale data sets"
Genomes to Systems
Manchester International Convension Center, Manchester, England, September 1-3, 2004
[PPT]
[WWW]
"DisEMBL - Artificial neural network prediction of protein disorder"
12th International Conference on Intelligent Systems for Molecular Biology, Software demo
Scottish Exhibition & Conference Center, Glasgow, Scotland, July 29-August 4, 2004
[PPT]
[WWW]
"STRING - Prediction of protein networks through integration of diverse large-scale data sets"
12th International Conference on Intelligent Systems for Molecular Biology, Genome Annotation SIG
Scottish Exhibition & Conference Center, Glasgow, Scotland, July 29-August 4, 2004
[PPT]
[WWW]
"STRING - Predicting novel metabolic pathways through the integration of diverse genome-scale data"
12th International Conference on Intelligent Systems for Molecular Biology, BioPathways SIG
Scottish Exhibition & Conference Center, Glasgow, Scotland, July 29-August 4, 2004
[PPT]
[WWW]
"Interaction prediction with STRING - Principles and examples"
EMBL Lab Day
European Molecular Biology Laboratory, Heidelberg, Germany, June 15, 2004
[PPT]
[WWW]
"STRING: Prediction of protein networks through integration of diverse large-scale data sets"
EMBL white seminar
European Molecular Biology Laboratory, Heidelberg, Germany, April 2, 2004
[PPT]
[WWW]
"From ELMs to function: interaction networks and feature spaces"
7th ELM meeting
ISG Hotel, Heidelberg, Germany, February 28, 2004
[PPT]
"Transcriptomics and lexico-syntactic analysis"
Erasmus MC, Rotterdam, Netherlands, November 18, 2003
[PPT]
"There and Back Again - Constructing and interpreting networks of functional associations"
Technical University of Denmark, Lyngby, Denmark, October 2, 2003
[PPT]
[WWW]
"Utilizing literature for biological discovery"
E-BioSci/ORIEL Annual Workshop
Villa Monastero, Varenna, Italy, September 2-5, 2003
[PDF]
[PPT]
"Prediction of human protein function from post-translational modifications and localization features"
31st Annual Meeting of Danish Society for Biochemsitry and Molecular Biology
Gl. Avernæs, Ebberup, Denmark, October 28-30, 2002
[WWW]
"Prediction of protein function from sequence derived protein features"
Ph.D. Lecture
Technical University of Denmark, Lyngby, October 23, 2002
[PPT]
[WWW]
"From bioinformatics to systems biology"
Danish Biotechnology Conference VIII
Munkebjerg, Vejle, Denmark, May 23-24, 2002
[WWW]
"Ab initio prediction of human orphan protein function"
1st Baltic Biotech Forum
Schloss Teschow, Teschow, Germany, November 8-9, 2001
[WWW]
"Ab initio prediction of human orphan protein function"
Medicon Valley BioConference 2001
DGI-Byen, Copenhagen, Denmark, September 19-20, 2001
[WWW]
"A bioinformatics approach to orphan function prediction"
Drug Design and Discovery
The Royal Danish School of Pharmacy, Copenhagen, Denmark, March 5-9, 2001
[WWW]
"Prediction of orphan protein functions"
Computational Molecular Biology
Technical University of Eindhoven, Eindhoven, The Netherlands, January 15-17, 2001
[WWW]
"Ab initio prediction of human orphan protein function"
Workshop on Microbial Diversity and Molecular Ecology
Stiftsgården Akersberg, Höör, Sweden, November 24-26, 2000
[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"
15th International Conference on Intelligent Systems for Molecular Biology, 2007
[PDF]
[WWW]
L.J. Jensen*, T.S. Jensen*, U. de Lichtenberg*, S. Brunak and P. Bork
"Just-in-time assembly of cell-cycle protein complexes"
15th International Conference on Intelligent Systems for Molecular Biology, 2007
[PDF]
[WWW]
L.J. Jensen, C. von Mering and P. Bork
"STRING: Predicting protein networks from genomic context and external data"
12th International Conference on Intelligent Systems for Molecular Biology, 2004
[PDF]
[WWW]
J.D. Bendtsen, L.J. Jensen, N. Blom and S. Brunak
"Feature based prediction of non-classical protein secretion"
Bioinformatics 2003, 2003
[WWW]
L.J. Jensen, C. von Mering and P. Bork
"PROPHECIES: Inferring functional links through cross-species analysis of expression data"
Bioinformatics 2003, 2003
[PPT]
[WWW]
K. Julenius, R. Gupta, K. Rapacki, L.J. Jensen, and S. Brunak
"NetOGlyc 3.0: Prediction of mucin type O-glycosylaion sites form sequence and sequence-derived features"
Bioinformatics 2003, 2003
[WWW]
U. de Lichtenberg, T.S. Jensen, L.J. Jensen and S. Brunak
"Protein feature based identification of cell cycle regulated proteins in yeast"
Bioinformatics 2003, 2003
[WWW]
M. Skovgaard, L.J. Jensen, T. Sicheritz-Pontén and D.W. Ussery
"Functionally uncharacterized genes in prokarytic genomes - junk or treasure?"
Bioinformatics 2003, 2003
L.J. Jensen, R. Gupta, D.W. Ussery and S. Brunak
"Functionality of system components: Conservation of protein function in protein feature space"
3rd International Conference on Systems Biology, 2002
[PPT]
[WWW]
L.J. Jensen, R. Gupta, D.W. Ussery and S. Brunak
"Functionality of system components: Conservation of protein function in protein feature space"
31st Annual Meeting of Danish Society for Biochemsitry and Molecular Biology, 2002
[PPT]
[WWW]
L.J. Jensen, R. Gupta and S. Brunak
"Ab initio prediction of Gene Ontology classes for orphan proteins"
Bioinformatics 2002, 2002
[PPT]
[WWW]
L.J. Jensen, R. Gupta, D. Devos, J. Tamames, H. Nielsen, N. Blom, C. Kesmir, C. Workman, H.H. Stærfeldt, K. Rapacki, S. Knudsen, C.A.F. Andersen, A. Krogh, A. Valencia and S. Brunak
"Ab initio prediction of human orphan protein function"
9th International Conference on Intelligent Systems for Molecular Biology, 2001
[PPT]
[WWW]
M. Skovgaard, L.J. Jensen, S. Brunak and D.W. Ussery
"An estimate of the total number of genes in microbial genomes based on length distributions"
9th International Conference on Intelligent Systems for Molecular Biology, 2001
P. Worning, L.J. Jensen, H.H. Stærfeldt and D.W. Ussery
"Origin of replication in circular bacterial genomes and plasmids"
9th International Conference on Intelligent Systems for Molecular Biology, 2001
P. Worning, L.J. Jensen, H.H. Stærfeldt and D.W. Ussery
"Origin of replication in circular bacterial genomes and plasmids"
Bioinformatics 2001, 2001
A.G. Pedersen, L.J. Jensen, H.H. Stærfeldt, S. Brunak and D.W. Ussery
"DNA structural atlases for complete genomes"
EMBO Workshop on Cell Cycle and Nucleoid Organisation in Bacteria, 2000
[WWW]
A.G. Pedersen, L.J. Jensen, S. Brunak, H.H. Stærfeldt and D.W. Ussery
"A DNA structural atlas for Escherichia coli"
8'th International Conference on Intelligent Systems for Molecular Biology, 2000
[WWW]
D.W. Ussery, L.J. Jensen, R.R. Sinden and P. Worning
"Analysis of DNA repeats in complete genomes"
18th International Congress of Biochemistry and Molecular Biology, 2000
C. Friis, L.J. Jensen and D.W. Ussery
"Localisation of DNA repeats in complete chromosomes"
Bioinformatics 2000, 2000
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"
Bioinformatics 2000, 2000
D.W. Ussery, A.G. Pedersen, L.J. Jensen, C. Friis, H.H. Stærfeldt and S. Brunak
"A DNA structural atlas for E. coli"
Third Annual Conference On Computational Genomics, 1999
[WWW]
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"
Third Annual Conference On Computational Genomics, 1999
C. Friis, L.J. Jensen and D.W. Ussery
"Three Views of microbial genomes"
7th Annual Conference on Small Genomes, 1999
[WWW]
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"
7th Annual Conference on Small Genomes, 1999
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"
Annual meeting of the Danish Society for Biochemistry and Molecular Biology, 1999
D.W. Ussery, A.G. Pedersen, L.J. Jensen, H.H. Stærfeldt and P. Worning
"A DNA structural atlas for E. coli"
Bioinformatics '99, 1999
[WWW]
L.J. Jensen, A.G. Pedersen, H.H. Stærfeldt, S. Brunak and D.W. Ussery
"A DNA structural atlas of promoters in microbial genomes"
Microbial Genomes III: Sequenceing, Functional Characterization and Comparative Genomics, 1999
[WWW]
D.W. Ussery, A.G. Pedersen, L.J. Jensen, H.H. Stærfeldt and S. Brunak
"A DNA structural atlas of Escherichia coli"
2nd Annual Conference on Computational Genomics, 1998
[WWW]