CPR > Publications
Publications
2010
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A versatile selection system for folding competent proteins using genetic complementation in a eukaryotic host
Christina Lyngsø, Søren Kjærulff, Sven Müller, Tomas Bratt, Uffe Mortensen, Florence Dal Degan
Protein Science, 2010
Accepted Article Online: Jan 15 2010 11:32AM
DOI: 10.1002/pro.337
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A side effect resource to capture phenotypic effects of drugs
M. Kuhn, M. Campillos, I. Letunic, L.J. Jensen and P. Bork
Molecular Systems Biology, accepted (publication date not yet known)
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A systems view of the cell cycle by quantitative phosphoproteomics reveals wide-spread stoichiometric phosphorylation events in mitosis
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
Science Signaling, accepted (publication date not yet known)
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eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced Non-supervised Orthologous Groups, species and functional annotations
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
Nucleic Acids Research, advance online publication (official publication date January 2010)
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HERC2 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes
Bekker-Jensen S, Danielsen JR, Fugger K, Gromova I, Nerstedt A, Bartek J, Lukas J, Mailand N. (2009).
Nature Cell Biol., in press
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STITCH 2: an interaction network database for small molecules and proteins
M. Kuhn, D. Szklarczyk, A. Franceschini, M. Campillos, C. von Mering, L.J. Jensen, A. Beyer and P. Bork
Nucleic Acids Research, advance online publication (official publication date January 2010
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Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results
N. Gauthier, L.J. Jensen, R. Wernersson, S. Brunak and T.S. Jensen
Nucleic Acids Research, advance online publication (official publication date January 2010)
2009
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Ezrin mediates c-Myc actions in prostate cancer cell invasion
Y-C Chuan, D Iglesias-Gato, L Fernandez-Perez, A Cedazo-Minguez, S-T Pang, G Norstedt, Å Pousette and A Flores-Morales
Oncogene, advance online publication, December 14, 2009; doi:10.1038/ onc.2009.442
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Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics
Pan C, Olsen JV, Daub H, Mann M.
Mol Cell Proteomics. 2009 Dec; 8(12):2796-808.
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A dual pressure linear ion trap - Orbitrap instrument with very high sequencing speed
Olsen JV, Schwartz JC, Griep-Raming J, Nielsen ML, Damoc E, Denisov E, Lange O, Remes P, Taylor D, Splendore M, Wouters ER, Senko M, Makarov A, Mann M, Horning S.
Mol Cell Proteomics. 2009 Dec; 8(12):2759-69.
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MSQuant, an Open Source Platform for Mass Spectrometry-Based Quantitative Proteomics
Mortensen P, Gouw JW, Olsen JV, Ong SE, Rigbolt KT, Bunkenborg J, Cox J, Foster LJ, Heck AJ, Blagoev B, Andersen JS, Mann M.
J Proteome Res. 2009 Nov 18.
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Global analysis of the yeast osmotic stress response by quantitative proteomics
Soufi B, Kelstrup CD, Stoehr G, Fröhlich F, Walther TC, Olsen JV.
Mol. BioSyst. 2009 Nov; 5(11):1337-46.
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Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes
Choudhary C, Olsen JV, Brandts C, Cox J, Böhmer FD, Gerke V, Schmidt-Arras D, Berdel WE, Müller-Tidow C, Mann M, Serve H.
Mol Cell. 2009 Oct 23; 36(2):326-39.
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General proteomics strategy for quantitative interactome profiling in cell extracts
Sharma K, Weber C, Bairlein M, Greff Z, Kéri G, Cox J, Olsen JV & Daub H.
Nat Methods. 2009 Oct; 6(10):741-4.
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High accuracy identification and bioinformatic analysis of in-vivo protein phosphorylation sites in yeast
Gnad F, de Godoy LMF, Cox J, Neuhauser N, Ren S, Olsen JV, Mann M.
Proteomics. 2009 Sep 30;9(20):4642-4652.
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Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions
Chunaram Choudhary, Chanchal Kumar, Florian Gnad, Michael L. Nielsen, Michael Rehman, Tobias Walther, Jesper V. Olsen, Matthias Mann
Science, July 2009 (Manuscript Number: 1175371)
Download abstract - please click here.
Download reprint - please click here.
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Reflect: augmented browsing for the life scientist
E. Pafilis, S.I. O'Donoghue, L.J. Jensen, H. Horn, M. Kuhn, N.P. Brown and R. Schneider
Nature Biotechnology, 27, 508-510, Jun. 2009
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Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs
Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS.
Nat Biotechnol, May 24 2009. [Epub ahead of print]
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Quantifying environmental adaptation of metabolic pathways in metagenomics
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
Proceedings of the National Academy of Sciences, 106, 1374-1379, Feb. 2009
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NetPhosBac: Prediction of protein phosphorylation sites in bacteria
Martin L. Miller*, Boumediene Soufi*, Carsten Jers, Nikolaj Blom, Ivan Mijakovic.
Proteomics. 2009 Jan; 9 (1):116-25. Epub ahead of print: 2008 Dec 3.
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Microblogging the ISMB: A New Approach to Conference Reporting
N. Saunders, P. Beltrão, L.J. Jensen, D. Jurczak, R. Krause, M. Kuhn and S. Wu
PLoS Computational Biology, 5, e1000263, Jan. 2009
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Cell cycle regulation by feed-forward loops coupling transcription
and phosphorylation
A. Csikász-Nagy, O. Kapuy, A. Tóth, C. Pál, L.J. Jensen, F. Uhlmann, J.J. Tyson and B. Novák
Molecular Systems Biology, Jan. 2009
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STRING 8 - a global view on proteins and their functional interactions in 630 organisms
Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, Mering CV.
Nucleic Acids Res. Jan. 2009
2008
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NetPhosBac: Prediction of protein phosphorylation sites in bacteria
Martin L. Miller*, Boumediene Soufi*, Carsten Jers, Nikolaj Blom, Ivan Mijakovic. Proteomics. 2008, Dec 3. [Epub ahead of print]
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A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes
K. Lage, N.T. Hansen, E.O. Karlberg, A.C.Eklund, F.S. Roque, P.K. Donahoe, Z. Szallasi, T.S. Jensen, S. Brunak.
Proc Natl Acad Sci U S A. 105:20870-5, 2008.
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Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast
Lyris M. F. de Godoy, Jesper V. Olsen, Jürgen Cox1, Michael L. Nielsen, Nina C. Hubner, Florian Fröhlich, Tobias C. Walther & Matthias Mann
Nature. 28 Sept. 2008
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Linear Motif Atlas for Phosphorylation-Dependent Signaling
Martin L. Miller*, Lars J. Jensen*, Francesca Diella, Claus Jørgensen, Michele Tinti, Lei Li, Marilyn Hsiung, Sirlester A. Parker, Jennifer Bordeaux, Thomas Sicheritz-Ponten, Marina Olhovsky, Jes Alexander, Stefan Knapp, Nikolaj Blom, Peer Bork, Shawn Li, Gianni Cesareni, Tony Pawson, Benjamin E. Turk, Michael B. Yaffe, Søren Brunak, Rune Linding.
Science Signaling. 2008 Sep 2;1(35):ra2. -
Text mining for biology - the way forward: opinions from leading scientists
Altman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, Krallinger M, Mons B, O'Donoghue SI, Peitsch MC, Rebholz-Schuhmann D, Shatkay H, Valencia A.
Genome Biol. 2008;9 Suppl 2:S7. Epub 2008 Sep 1. -
Drug target identification using side-effect similarity
M. Campillos*, M. Kuhn*, A.-C. Gavin, L.J. Jensen and P. Bork
Science, 2008 Jul 11;321(5886):263-6.
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Circular reasoning rather than cyclic expression
L.J. Jensen*, U. de Lichtenberg*, T.S. Jensen, S. Brunak and P. Bork
Genome Biology, 2008;9(6):403. Epub 2008 Jun 23.
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Predicting biological networks from genomic data
E. Harrington, L.J. Jensen and P. Bork
FEBS Letters, 2008 Apr 9;582(8):1251-8. Epub 2008 Feb 21. Review. -
Large-scale prediction of drug-target relationships
M. Kuhn*, M. Campillos*, P. Gonzales*, L.J. Jensen* and P. Bork*
FEBS Letters, 2008 Apr 9;582(8):1283-90. Epub 2008 Feb 20. Review.
* = contributed equally