Publications
104. P.B. Jensen, L.J. Jensen and S. Brunak
“Mining electronic health records: towards better research applications and clinical care”
Nature Reviews Genetics, 2012.
[Abstract] [Full text]
103. J.W. Poulsen, C.T. Madsen, C. Young, C.D. Kelstrup, H.C. Grell, P. Henriksen, L.J. Jensen and M.L. Nielsen
“Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes”
to appear in Journal of Proteomics, 2012.
102. M. Frenkel-Morgenstern, T. Danon, T. Christian, T. Igarashi, L. Cohen, Y.-M. Hou and L.J. Jensen
“Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels”
Molecular Systems Biology, 8, 572, 2012.
[Abstract] [Full text]
101. R. Bergholdt, C. Brorsson, A. Palleja, L.A. Berchtold, T. Fløyel, C.H. Bang-Berthelsen, K.S. Frederiksen, L.J. Jensen, J. Størling and F. Pociot
“Identification of Novel Type 1 Diabetes Candidate Genes by Integrating Genome-Wide Association Data, Protein-Protein Interactions, and Human Pancreatic Islet Gene Expression”
Diabetes, 2012.
[Abstract] [Full text]
100. A. Romanel, L.J. Jensen, L. Cardelli and A. Csikász-Nagy
“Transcriptional regulation is a major controller of cell cycle transition dynamics”
PLoS One, 7, e29716, 2012
[Abstract] [Full text]
99. S. Powell, D. Szklarczyk, K. Trachana, A. Roth, M. Kuhn, J. Muller, R. Arnold, T. Rattei, I. Letunic, T. Doerks, L.J. Jensen, C. von Mering and P. Bork
“eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges”
Nucleic Acids Research, 40, D284-D289, 2012
[Abstract] [Full text] [WWW]
98. M. Kuhn, D. Szklarczyk, A. Franceschini, C. von Mering, L.J. Jensen and P. Bork
“STITCH 3: zooming in on protein-chemical interactions”
Nucleic Acids Research, 40, D876-D880, 2012
[Abstract] [Full text] [WWW]
97. A. Pallejà, H. Horn, S. Eliasson and L.J. Jensen
“DistiLD Database: diseases and traits in linkage disequilibrium blocks”
Nucleic Acids Research, 40, D1036-D1040, 2012
[Abstract] [Full text] [WWW]
96. P. Warrer, E.H. Hansen, L.J. Jensen and L. Aagaard
“Using text-mining techniques in electronic patient records to identify ADRs from medicine use”
to appear in British Journal of Clinical Pharmacology, 2011
[Abstract] [Full text]
95. E. Cappellini, L.J. Jensen, D. Szklarczyk, A. Ginolhac, R.A. da Fonseca, T.W. Stafford, S.R. Holen, M.J. Collins, L. Orlando, E. Willerslev, M.T. Gilbert and J.V. Olsen
“Proteomic analysis of a Pleistocene mammoth femur reveals more than one hundred ancient bone proteins”
Journal of Proteome Research, 11, 917-926, 2011
[Abstract] [Full text]
94. L.J. Jensen and A. Bateman
“The rise and fall of supervised machine learning techniques”
Bioinformatics, 27, 3331-3332, 2011
[Abstract] [Full text]
93. L.D. Parnell, P. Lindenbaum, K. Shameer, G.M. Dall’Olio, D.C. Swan, L.J. Jensen, S.J. Cockell, B.S. Pedersen, M.E. Mangan, C.A. Miller, I. Albert
“BioStar: An Online Question & Answer Resource for the Bioinformatics Community”
PLoS Computational Biology, 7, e1002216, 2011
[Abstract] [Full text] [WWW]
92. M.R. Waters, T.W. Stafford Jr., H.G. McDonald, C. Gustafson, M. Rasmussen, E. Cappellini, J.V. Olsen, D. Szklarczyk, L.J. Jensen, M.T.P. Gilbert, E. Willerslev
“Pre-Clovis Mastodon Hunting 13,800 Years Ago at the Manis Site, Washington”
Science, 334, 351-353, 2011
[Abstract] [Full text]
91. G.M. Dall’Olio, J. Marino, M. Schubert, K.L. Keys, M.I. Stefan, C.S. Gillespie, P. Poulain, K. Shameer, R. Sugar, B.M. Invergo, L.J. Jensen, J. Bertranpetit and H. Laayouni
“Ten Simple Rules for Getting Help from Online Scientific Communities”
PLoS Computational Biology, 7, e1002202, 2011
[Abstract] [Full text] [WWW]
90. F.S. Roque, P.B. Jensen, H. Schmock, M. Dalgaard, M. Andreatta, T. Hansen, K. Søeby, S. Bredkjær, A. Juul, T. Werge, L.J. Jensen, and Søren Brunak
“Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts”
PLoS Computational Biology, 7, e1002141, 2011
[Abstract] [Full text]
89. B.T. Weinert, S.A. Wagner, H. Horn, P. Henriksen, W.R. Liu, J.V. Olsen, L.J. Jensen and C. Choudhary
“Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation”
Science Signaling, 4, ra48, 2011
[Abstract] [Full text]
88. J. Raes, I. Letunic, T. Yamada, L.J. Jensen and P. Bork
“Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data”
Molecular Systems Biology, 7, 473, 2011
[Abstract] [Full text]
87. O. Fedorov, K. Huber, A. Eisenreich, P. Filippakopoulos, O. King, A.N. Bullock, D. Szklarczyk, L.J. Jensen, D. Fabbro, J. Trappe, U. Rauch, F. Bracher and S. Knapp
“Specific CLK inhibitors from a novel chemotype for regulation of alternative splicing”
Chemistry and Biology, 18, 67-76, 2011
[Abstract] [Full text]
86. J.M. Danielsen, K.B. Sylvestersen, S. Bekker-Jensen, D. Szklarczyk, J.W. Poulsen, H. Horn, L.J. Jensen, N. Mailand and M.L. Nielsen
“Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level”
Molecular and Cellular Proteomics, 10, 10.1074/mcp.M110.003590, 2011
[Abstract] [Full text]
85. H. Dinkel, C. Chica, A. Via, C. Gould, L.J. Jensen, T. Gibson and F. Diella
“Phospho.ELM: a database of phosphorylation sites – update 2011″
Nucleic Acids Research, 39, D261-267, 2011
[Abstract] [Full text]
84. D. Szklarczyk, A. Franceschini, M. Kuhn, M. Simonovic, A. Roth, P. Minguez, T. Doerks, M. Stark, J. Muller, P. Bork, L.J. Jensen and C. von Mering
“The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored”
Nucleic Acids Research, 39, D561-568, 2011
[Abstract] [Full text]
83. O. Gallego, M.J. Betts, J. Gvozdenovic-Jeremic, K. Maeda, C. Matetzki, C. Aguilar-Gurrieri, P. Beltran-Alvarez, S. Bonn, C. Fernández-Tornero, L.J. Jensen, M. Kuhn, J. Trott, V. Rybin, C.W. Müller, P. Bork, M. Kaksonen, R.B. Russell and A.-C. Gavin
“A systematic screen for protein–lipid interactions in Saccharomyces cerevisiae”
Molecular Systems Biology, 6, 430, 2010
[Abstract] [Full text]
82. M. Iskar, M. Campillos, M. Kuhn, L.J. Jensen, V. van Noort and P. Bork
“Drug-induced regulation of target expression”
PLoS Computational Biology, 6, e1000925, 2010
[Abstract] [Full text]
81. S.I. O’Donoghue, H. Horn, E. Pafilis, S. Haag, M. Kuhn, V.P. Satagopam, R. Schneider and L.J. Jensen
“Reflect: a practical approach to web semantics”
Journal of Web Semantics, 8, 182-189, 2010
80. L.J. Jensen and P. Bork
“Ontologies in quantitative biology: A basis for comparison, integration and discovery”
PLoS Biology, 8, e1000374, 2010
[Abstract] [Full text]
79. T. Blicher, R. Gupta, A. Wesolowska, L.J. Jensen and S. Brunak
“Protein Annotation in the Era of Personal Genomics”
Current Opinion in Structural Biology, 20, 335-341, 2010
[Abstract] [Full text]
78. M.W. Larsen, D.F. Zielinska, M. Martinelle, A. Hidalgo, L.J. Jensen, U.T. Bornscheuer and K. Hult
“Suppression of water as a nucleophile in Candida antarctica Lipase B catalysis”
ChemBioChem, 11, 796-801 , 2010
[Abstract] [Full text]
77. M.V. Granovskaia*, L.J. Jensen*, M.E. Ritchie*, J. Toedling, Y. Ning, P. Bork, W. Huber and L.M. Steinmetz
“High-resolution transcription atlas of the mitotic cell cycle in budding yeast”
Genome Biology, 11, R24, 2010
[Abstract] [Full text]
76. K. Trachana, L.J. Jensen and P. Bork
“Evolution and regulation of cellular periodic processes: a role for paralogues”
EMBO Reports, 11, 233-238, 2010
[Abstract] [Full text]
75. M. Kuhn, M. Campillos, I. Letunic, L.J. Jensen and P. Bork
“A side effect resource to capture phenotypic effects of drugs”
Molecular Systems Biology, 6, 343, 2010
[Abstract] [Full text] [WWW]
74. J.V. Olsen, M. Vermeulen, A. Santamaria, C. Kumar, M.L. Miller, L.J. Jensen, F. Gnad, J. Cox, T.S. Jensen, E.A. Nigg, S. Brunak and M. Mann
“A systems view of the cell cycle by quantitative phosphoproteomics reveals wide-spread stoichiometric phosphorylation events in mitosis”
Science Signaling, 3, ra3, 2010
[Abstract] [Full text]
73. J. Muller, D. Szklarczyk, P. Julien, I. Letunic, A. Roth, M. Kuhn, S. Powell, C. von Mering, T. Doerks, L.J. Jensen and P. Bork
“eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced Non-supervised Orthologous Groups, species and functional annotations”
Nucleic Acids Research, 38, D190-D195, 2010
[Abstract] [Full text] [WWW]
72. M. Kuhn, D. Szklarczyk, A. Franceschini, M. Campillos, C. von Mering, L.J. Jensen, A. Beyer and P. Bork
“STITCH 2: an interaction network database for small molecules and proteins”
Nucleic Acids Research, 38, D552-D566, 2010
[Abstract] [Full text] [WWW]
71. N. Gauthier, L.J. Jensen, R. Wernersson, S. Brunak and T.S. Jensen
“Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results”
Nucleic Acids Research, 38, D699-D702, 2010
[Abstract] [Full text] [WWW]
70. T. Soldatos, S.I. O’Donoghue, V. Satagopam, L.J. Jensen, N. Brown, A. Barbosa da Silva and R. Schneider
“Martini: using literature keywords to compare gene sets”
Nucleic Acids Research, 38, 26-38, 2010
[Abstract] [Full text] [WWW]
69. E. Pafilis, S.I. O’Donoghue, L.J. Jensen, H. Horn, M. Kuhn, N.P. Brown and R. Schneider
“Reflect: augmented browsing for the life scientist“
Nature Biotechnology, 27, 508-510, 2009
[Abstract] [Full text] [WWW]
68. A.S. Juncker, L.J. Jensen, A. Pierleoni, A. Bernsel, M.L. Tress, P. Bork, G. von Heijne, A. Valencia, C.A. Ouzounis, R. Casadio and S. Brunak
“Sequence-based feature prediction and annotation of proteins”
Genome Biology, 10, 206, 2009
[Abstract] [Full text]
67. T.A. Gianoulis, J. Raes, P.V. Patel, R. Bjornson, J.O. Korbel, I. Letunic, T. Yamada, A. Paccanaro, L.J. Jensen, M. Snyder, P. Bork and M.B. Gerstein
“Quantifying environmental adaptation of metabolic pathways in metagenomics”
Proceedings of the National Academy of Sciences, 106, 1374-1379, 2009
[Abstract] [Full text]
66. N. Saunders, P. Beltrão, L.J. Jensen, D. Jurczak, R. Krause, M. Kuhn and S. Wu
“Microblogging the ISMB: A New Approach to Conference Reporting”
PLoS Computational Biology, 5, e1000263, 2009
[Abstract] [Full text]
65. A. Csikász-Nagy, O. Kapuy, A. Tóth, C. Pál, L.J. Jensen, F. Uhlmann, J.J. Tyson and B. Novák
“Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation”
Molecular Systems Biology, 5, 236, 2009
[Abstract] [Full text]
64. L.J. Jensen*, M. Kuhn*, M. Stark, S. Chaffron, C. Creevey, J. Muller, T. Doerks, P. Julien, A. Roth, M. Simonovic, P. Bork and C. von Mering
“STRING 8 – a global view on proteins and their functional interactions in 630 model organisms”
Nucleic Acids Research, 37, D412-D416, 2009
[Abstract] [Full text] [WWW]
63. D. Frishman, M. Albert, H. Blankenburg, P. Bork, E.D. Harrington, H. Hermjakob, L.J. Jensen, D.A. Juan, T. Lengauer, P. Pagel, V. Schachter and A. Valencia
“Protein–protein interactions: analysis and prediction”
Modern Genome Annotation: The BioSapiens Network, Chapter 6.2, 353-410, 2009
62. A.L. Veuthey, B. Boeckmann, L.J. Jensen, A. Valencia A. Rausell and P. Bork
“Homologous and non-homologous sequence methods for assigning protein function”
Modern Genome Annotation: The BioSapiens Network, Chapter 4.4, 213-238, 2009
61. L.J. Jensen and P. Bork
“Not comparable, but complementary”
Science, 322, 56-57, 2008
[Abstract] [Full text]
60. R.B 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.C. Peitsch, D. Rebholz-Schuhmann, H. Shatkay and A. Valencia
“Text mining for biology – the way forward: opinions from leading scientists”
Genome Biology, 9, S7, 2008
[Abstract] [Full text]
59: M.L. Miller*, L.J. Jensen*, F. Diella, C. Jørgensen, M. Tinti, L. Li, M. Hsiung, S.A. Parker, J. Bordeaux, T. Sicheritz-Ponten, M. Olhovsky, A. Pasculescu, J. Alexander, S. Knapp, N. Blom, P. Bork, S. Li, G. Cesareni, T. Pawson, B.E. Turk, M.B. Yaffe, S. Brunak, R. Linding
“Linear motif atlas for phosphorylation-dependent signaling”
Science Signaling, 1, ra2, 2008
[Abstract] [Full text] [WWW]
58: M. Campillos*, M. Kuhn*, A.-C. Gavin, L.J. Jensen and P. Bork
“Drug target identification using side-effect similarity”
Science, 321, 263-266, 2008
[Abstract] [Full text]
57: 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
[Abstract] [Full text] [WWW]
56: 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]
55: E. Harrington, L.J. Jensen and P. Bork
“Predicting biological networks from genomic data”
FEBS Letters, 582, 1251-1258, 2008
[Abstract] [Full text] [WWW]
54: 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] [WWW]
53: 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] [WWW]
52: 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] [WWW]
51: 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] [WWW]
50: 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]
49: 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]
48: 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]
47: 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] [WWW]
46: 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] [WWW]
45: 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]
44: 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]
43: 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] [WWW]
42: 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] [WWW]
41: 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] [WWW]
40: 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] [WWW]
39: 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] [WWW]
38: 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]
37: 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] [WWW]
36: 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] [WWW]
35: 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] [WWW]
34: 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]
33: 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]
32: 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]
31: 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]
30: 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]
29: L.J. Jensen and L.M. Steinmetz
“Re-analysis of data and its integration”
FEBS Letters, 579, 1802-1807, 2005
[Abstract] [Full text]
28: 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] [WWW]
27: 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] [WWW]
26: 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] [WWW]
25: 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]
24: 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]
23: 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
22: 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] [WWW]
21: 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] [WWW]
20: 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] [WWW]
19: 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]
18: 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
[WWW]
17: 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] [WWW]
16: 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] [WWW]
15: 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] [WWW]
14: 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] [WWW]
13: 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] [WWW]
12: 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] [WWW]
11: 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]
10: 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
[WWW]
9: 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] [WWW]
8: 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]
7: 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]
6: 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]
5: C. Friis, L.J. Jensen and D.W. Ussery
“Visualization of pathogenicity regions in bacteria”
Genetica, 108, 47-51, 2000
[Abstract] [WWW]
4: 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]
3: 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] [WWW]
2: L.J. Jensen, C. Friis and D.W Ussery
“Three views of microbial genomes”
Research in Microbiology, 150, 773-777, 1999
[Abstract] [WWW]
1: 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]
* These authors contributed equally.
