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Publications

2011  

  • Cdc20 control of cell fate during prolonged mitotic arrest.
    Jakob Nilsson.
    Bioessays. 2011 Dec;33(12):903-9. doi: 10.1002/bies.201100094. Epub 2011 Nov 2.

  • Proteomic analysis of a Pleistocene mammoth femur reveals more than one hundred ancient bone proteins.
    Cappellini E, Jensen LJ, Szklarczyk D, Ginolhac A, da Fonseca RA, Stafford TW, Holen SR, Collins MJ, Orlando L, Willerslev E, Gilbert MT, Olsen JV.J.
    Proteome Res. 2011 Nov 21. [Epub ahead of print]

  • A Systematic Study of Site-specific GalNAc-type O-Glycosylation Modulating Proprotein Convertase Processing.
    Gram Schjoldager KT, Vester-Christensen MB, Goth CK, Petersen TN, Brunak S, Bennett EP, Levery SB, Clausen H.J.
    Biol Chem. 2011 Nov 18;286(46):40122-32. Epub 2011 Sep 20.

  • EggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
    Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P.
    Nucleic Acids Res. 2011 Nov 16. [Epub ahead of print]

  • STITCH 3: zooming in on protein-chemical interactions.
    Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P.
    Nucleic Acids Res. 2011 Nov 9. [Epub ahead of print].

  • Structure of a Blinkin-BUBR1 complex reveals an interaction essential for kinetochore-mitotic checkpoint regulation underlying an unanticipated binding site.
    Victor M. Bolanos-Garcia*, Tiziana Lischetti, Dijana Matak-Vinković, Ernesto Cota, Pete J. Simpson, Dimitri Y. Chirgadze, David R. Spring, Carol V. Robinson, Jakob Nilsson, and Tom L. Blundell*
    Structure. 2011 Nov 9;19(11):1691-700. Epub 2011 Oct 13.

  • BK(Ca) and K(V) channels limit conducted vasomotor responses in rat mesenteric terminal arterioles.
    Hald BO, Jacobsen JC, Braunstein TH, Inoue R, Ito Y, Sørensen PG, Holstein-Rathlou NH, Jensen LJ.
    Pflugers Arch. 2011 Nov 4. [Epub ahead of print]

  • DistiLD Database: diseases and traits in linkage disequilibrium blocks.
    Pallejà A, Horn H, Eliasson S, Jensen LJ.
    Nucleic Acids Res. 2011 Nov 3. [Epub ahead of print].

  • The ubiquitin-selective segregase VCP/p97 orchestrates the response to DNA double-strand breaks.
    Meerang M, Ritz D, Paliwal S, Garajova Z, Bosshard M, Mailand N, Janscak P, Hübscher U, Meyer H, and Ramadan K. (2011).
    Nature Cell Biology. 2011 Oct 23;13(11):1376-82. doi: 10.1038/ncb2367.

  • Pre-Clovis mastodon hunting 13,800 years ago at the Manis site, Washington.
    Waters MR, Stafford TW Jr, McDonald HG, Gustafson C, Rasmussen M, Cappellini E, Olsen JV, Szklarczyk D, Jensen LJ, Gilbert MT, Willerslev E.
    Science. 2011 Oct 21;334(6054):351-3.

  • Global phosphoproteome profiling reveals unanticipated networks responsive to cisplatin treatment of embryonic stem cells.
    Pines A, Kelstrup CD, Vrouwe MG, Puigvert JC, Typas D, Misovic B, de Groot A, von Stechow L, van de Water B, Danen EH, Vrieling H, Mullenders LH, Olsen JV.
    Mol Cell Biol. 2011 Oct 17. [Epub ahead of print].

  • A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
    Sebastian A. Wagner, Petra Beli, Brian T. Weinert, Michael L. Nielsen, Jürgen Cox, Matthias Mann, Chunaram Choudhary
    Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. Epub 2011 Sep 1.

  • An Aboriginal Australian genome reveals separate human dispersals into Asia.
    Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgreen S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega FM, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MC, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MT, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijff P, Migliano AB, Gallego Romero I, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sicheritz-Pontén T, Villems R, Nielsen R, Wang J, Willerslev E.
    Science. 2011 Oct 7;334(6052):94-8. Epub 2011 Sep 22.

  • BioStar: An Online Question & Answer Resource for the Bioinformatics Community.
    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.
    PLoS Comput Biol. 2011 Oct;7(10):e1002216. Epub 2011 Oct 27.

  • Cometin is a novel neurotrophic factor that promotes neurite outgrowth and neuroblast migration in vitro and supports survival of spiral ganglion neurons in vivo.
    Jørgensen JR, Fransson A, Fjord-Larsen L, Thompson LH, Houchins JP, Andrade N, Torp M, Kalkkinen N, Andersson E, Lindvall O, Ulfendahl M, Brunak S, Johansen TE, Wahlberg LU.
    Exp Neurol. 2011 Oct 2. [Epub ahead of print].

  • Protein Interaction-Based Genome-Wide Analysis of Incident Coronary Heart Disease.
    Jensen MK, Pers TH, Dworzynski P, Girman CJ, Brunak S, Rimm EB.
    Circ Cardiovasc Genet. 2011 Oct 1;4(5):549-556. Epub 2011 Aug 31.

  • A Liver X Receptor agonist down-regulates Growth Hormone signaling in the liver.
    Fahad Zadjali, Ruyman Santana-Farre, Ewa Ellis, Gunnar Norstedt, Leandro Fernandez-Perez and Amilcar Flores-Morales.
    Hormone Molecular Biology and Clinical Investigation. Oct 2011. In press.

  • SignalP 4.0: discriminating signal peptides from transmembrane regions.
    Petersen TN, Brunak S, von Heijne G, Nielsen H.
    Nat Methods. 2011 Sep 29;8(10):785-6. doi: 10.1038/nmeth.1701. No abstract available.

  • The ubiquitin- and SUMO-dependent signaling response to DNA double-strand breaks.
    Bekker-Jensen S, Mailand N.
    FEBS Lett. 2011 Sep 16;585(18):2914-9. Epub 2011 Jun 12.

  • Huntingtin-interacting protein 14 is a type 1 diabetes candidate protein regulating insulin secretion and beta-cell apoptosis.
    Berchtold LA, Størling ZM, Ortis F, Lage K, Bang-Berthelsen C, Bergholdt R, Hald J, Brorsson CA, Eizirik DL, Pociot F, Brunak S, Størling J.
    Proc Natl Acad Sci USA. 2011 Sep 13;108(37):E681-8. Epub 2011 Jun 24.

  • Ten Simple Rules for Getting Help from Online Scientific Communities.
    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.
    PLoS Comput Biol. 2011 Sep;7(9):e1002202. Epub 2011 Sep 29.


  • A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1.
    Blasius M, Forment JV, Thakkar N, Wagner SA, Choudhary C, Jackson SP.
    Genome Biol. 2011 Aug 18;12(8):R78. [Epub ahead of print].

  • Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts.
    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.
    PLoS Comput Biol. 2011 Aug;7(8):e1002141. Epub 2011 Aug 25.

  • Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation.
    Weinert BT, Wagner SA, Horn H, Henriksen P, Liu WR, Olsen JV, Jensen LJ, Choudhary C.
    Sci Signal. 2011 Jul 26;4(183):ra48.

  • Predictive mutagenesis of ligation-independent cloning (LIC) vectors for protein expression and site-specific chemical conjugation.
    Erik Vernet, Jørgen Sauer, Andreas Andersen, Knud J Jensen, Bjørn Voldborg
    Analytical Biochemistry. 2011 Jul 15;414(2):312-4.

  • Phosphorylation of the Autophagy Receptor Optineurin Restricts Salmonella Growth.
    Wild P, Farhan H, McEwan DG, Wagner S, Rogov VV, Brady NR, Richter B, Korac J, Waidmann O, Choudhary C, Dötsch V, Bumann D, Dikic I.
    Science. 2011 Jul 8;333(6039):228-33. Epub 2011 May 26.

  • Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes.
    Pers TH, Hansen NT, Lage K, Koefoed P, Dworzynski P, Miller ML, Flint TJ, Mellerup E, Dam H, Andreassen OA, Djurovic S, Melle I, Børglum AD, Werge T, Purcell S, Ferreira MA, Kouskoumvekaki I, Workman CT, Hansen T, Mors O, Brunak S.
    Genet Epidemiol. 2011 Jul;35(5):318-32. doi: 10.1002/gepi.20580. Epub 2011 Apr 11.

  • Pinpointing Phosphorylation Sites: Quantitative Filtering and a Novel Site-specific x-Ion Fragment.
    Kelstrup CD, Hekmat O, Francavilla C, Olsen JV.
    J Proteome Res. 2011 Jul 1;10(7):2937-48. Epub 2011 Apr 28.

  • RNA-DNA sequence differences (RDD) spell genetic code ambiguities?
    Bentin T and Nielsen ML
    Artificial DNA, 2011. Volume 2, Issue 3 July/August/September 2011.

  • Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia.
    Wesolowska A, Dalgaard MD, Borst L, Gautier L, Bak M, Weinhold N, Nielsen BF, Helt LR, Audouze K, Nersting J, Tommerup N, Brunak S, Sicheritz-Ponten T, Leffers H, Schmiegelow K, Gupta R.
    Leukemia. 2011 Jun;25(6):1001-6. doi: 10.1038/leu.2011.32. Epub 2011 Mar 18.

  • Separation of the gluconeogenic and mitochondrial functions of PGC-1(alpha) through S6 kinase.
    Lustig Y, Ruas JL, Estall JL, Lo JC, Devarakonda S, Laznik D, Choi JH, Ono H, Olsen JV, Spiegelman BM.
    Genes Dev. 2011 Jun 15;25(12):1232-44. doi: 10.1101/gad.2054711. Epub 2011 Jun 6.

  • The SOCS2 ubiquitin ligase complex regulates GH receptor level.
    Vesterlund M, Fahad Al-Zadjali, Persson T, Kessler BM, Nielsen ML, Norstedt G and Flores-Morales A
    PLOS One. 2011;6(9):e25358. Epub 2011 Sep 29.

  • Phosphorylation of the yeast γ-tubulin Tub4 regulates microtubule function.
    Lin TC, Gombos L, Neuner A, Sebastian D, Olsen JV, Hrle A, Benda C, Schiebel E.
    PLoS One. 2011 May 5;6(5):e19700.

  • Screening of genetic parameters for soluble protein expression in Escherichia coli.
    Vernet E, Kotzsch A, Voldborg B, Sundström M
    Prot Expr Purif, 2011 May;77(1):104-11. Epub 2010 Dec 2.

  • Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data.
    J. Raes, I. Letunic, T. Yamada, L.J. Jensen, P. Bork
    Molecular Systems Biology. 2011 Mar 15;7:473.

  • System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation.
    Kristoffer T. G. Rigbolt, Tatyana A. Prokhorova, Vyacheslav Akimov, Jeanette Henningsen, Pia T. Johansen, Irina Kratchmarova, Moustapha Kassem, Matthias Mann, Jesper V. Olsen, and Blagoy Blagoev
    Science Signaling. 2011 Mar 15;4(164):rs3. 

  • 53BP1 nuclear bodies form around DNA lesions generated by mitotic transmission of chromosomes under replication stress.
    Lukas C, Savic V, Bekker-Jensen S, Doil C, Neumann B, Pedersen RS, Grøfte M, Chan KL, Hickson ID, Bartek J, Lukas J.
    Nat Cell Biol. 2011 Mar;13(3):243-53.

  • Effective representation and storage of mass spectrometry-based proteomics data sets for the scientific community.
    Olsen JV, Mann M.
    Science Signaling. 2011 Feb 15;4(160):pe7.  

  • Specific CLK Inhibitors from a Novel Chemotype for Regulation of Alternative Splicing.
    Fedorov O, Huber K, Eisenreich A, Filippakopoulos P, King O, Bullock AN, Szklarczyk D, Jensen LJ, Fabbro D, Trappe J, Rauch U, Bracher F, Knapp S.
    Chem Biol. 2011 Jan 28;18(1):67-76.

  • A secretory system for bacterial production of high-profile protein targets. A Kotzsch, E Vernet, M Hammarström, J Berthelsen, J Weigelt, S Gräslund and M Sundström.
    Protein Science.     2011 Jan 24. doi: 10.1002/pro.593. Epub ahead of print.

  • Andromeda - a peptide search engine integrated into the MaxQuant environment.
    Jurgen Cox , Nadin Neuhauser , Annette Michalski , Richard A Scheltema , Jesper V Olsen , and Matthias Mann
    J. Proteome Res., Epub 2011 Jan 21. 

  • Structural basis for c-KIT inhibition by the suppressor of cytokine signaling 6 (SOCS6) ubiquitin ligase.
    Zadjali F, Pike AC, Vesterlund M, Sun J, Wu C, Li SS, Rönnstrand L, Knapp S, Bullock AN, Flores-Morales A.
    J Biol Chem. 2011 Jan 7; 286 (1): 480-90. Epub ahead of print: 2010 Oct 28.

  • Phospho.ELM: a database of phosphorylation sites--update 2011.
    Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F.
    Nucleic Acids Res. 2011 Jan; 39 (Database issue): D261-7. Epub ahead of print: 2010 Nov 9. 

  • The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
    Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, Mering CV.
    Nucleic Acids Res. 2011 Jan; 39 (Database issue): D561-8. Epub ahead of print: 2010 Nov 2. 

  • GeLCMS for In-Depth Protein Characterization and Advanced Analysis of Proteomes.
    Lundby A, Olsen JV.
    Methods Mol Biol. 2011;753:143-55. 

2010 

  • Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.
    JM Danielsen, KB Sylvestersen, S Bekker-Jensen, D Szklarczyk, JW Poulsen, H Horn, LJ Jensen, N Mailand and ML Nielsen.
    Mol. Cell. Proteomics.     Epud 2010 Dec 7. 

  • Assembly and function of DNA double-strand break repair foci in mammalian cells.
    Bekker-Jensen S, Mailand N.
    DNA Repair, 2010 Dec 10; 9 (12): 1219-28.

  • Feasibility of large scale phosphoproteomics with higher energy collisional dissociation fragmentation.
    Nagaraj N, D'Souza RCJ, Cox J, Olsen JV and Mann M.
    J Proteome Res., 2010 Dec 3; 9 (12):6786-94. 

  • Phospho.ELM: a database of phosphorylation sites--update 2011.
    Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F.
    Nucleic Acids Res. Epub ahead of print: 2010 Nov 9.

  • The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
    Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, Mering CV.
    Nucleic Acids Res. Epub ahead of print: 2010 Nov 2. 

  • Structural basis for c-KIT inhibition by the suppressor of cytokine signaling 6 (SOCS6) ubiquitin ligase.
    Zadjali F, Pike AC, Vesterlund M, Sun J, Wu C, Li SS, Rönnstrand L, Knapp S, Bullock AN, Flores-Morales A.
    J Biol Chem. Epub ahed of print: 2010 Oct 28.
     

  • Drug-induced regulation of target expression.
    Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V, Bork P.
    PLoS Comput Biol. 2010 Sep 9;6(9).

  • Human SIRT6 promotes DNA end resection through CtIP deacetylation.
    Kaidi A, Weinert BT, Choudhary C, Jackson SP.
    Science. 2010 Sep 10; 329 (5997):1348-53.

  • Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers.
    Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, Lee KK, Olsen JV, Hyman AA, Stunnenberg HG, Mann M.
    Cell. 2010 Sep 17; 142 (6):967-80. 
     

  • Yeast expression proteomics by high-resolution mass spectrometry.
    Walther TC, Olsen JV, Mann M.
    Methods Enzymol. 2010; 470:259-80.
     

  • High resolution transcription atlas of the mitotic cell cycle in budding yeast
    Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM.
    Genome Biol. 2010;11(3):R24.
     

  • 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. 2010;6:343.
     

  • Reflect: a practical approach to web semantics
    S.I. O'Donoghue, H. Horn, E. Pafilisa, S. Haag, M. Kuhn, V.P. Satagopam, R. Schneider and L.J. Jensen
    Web Semantics: Science, Services and Agents on the World Wide Web 2010;8(2-3):182-189.

  • Predicting posttranslational lysine acetylation using support vector machines
    Gnad F, Ren S, Choudhary C, Cox J, Mann M
    Bioinformatics. 2010 Jul 1;26(13):1666-8.  

  • Quantitative phosphoproteomics dissection of seven-transmembrane receptor signaling using full and biased agonists
    Christensen GL, Kelstrup CD, Lyngsø C, Sarwar U, Bøgebo R, Shiekh SP, Gammeltoft S, Olsen JV, Hansen JL
    Mol Cell Proteomics. 2010 Jul;9(7):1540-53.

  • Decoding signaling networks by mass spectrometry-based proteomics
    Choudhary C, Mann M
    Nat Rev Mol Cell Biol. 2010 Jun;11(6):427-39. Review.

  • Dissecting spatio-temporal protein networks driving human heart development and related disorders
    Lage K, Møllgård K, Greenway S, Wakimoto H, Gorham JM, Workman CT, Bendsen E, Hansen NT, Rigina O, Roque FS, Wiese C, Christoffels VM, Roberts AE, Smoot LB, Pu WT, Donahoe PK, Tommerup N, Brunak S, Seidman CE, Seidman JG, Larsen LA.
    Mol Syst Biol. 2010 Jun 22;6:381.

  • The phosphoproteome of toll-like receptor-activated macrophages
    Weintz G*, Olsen JV*, Frühauf K, Niedzielska M, Amit I, Jantsch J, Mages J, Frech C, Dölken L, Mann M, Lang R
    Mol Syst Biol. 2010 Jun 8;6:371.

     
  • Protein annotation in the era of personal genomics
    T. Blicher, R. Gupta, A. Wesolowska, L.J. Jensen and S. Brunak
    Current Opinion in Structural Biology. 2010 Jun;20(3):335-41.

     
  • Ontologies in quantitative biology: A basis for comparison, integration and discovery
    L.J. Jensen and P. Bork
    PLoS Biology. 2010 May 25;8(5):e1000374.

  • Structural basis for K(V)7.1-KCNE(x) interactions in the I(Ks) channel complex.
    Lundby A, Tseng GN, Schmitt N.
    Heart Rhythm. 2010 May;7(5):708-13.

  • Suppression of water as a nucleophile in Candida antarctica lipase B catalysis
    Larsen MW, Zielinska DF, Martinelle M, Hidalgo A, Jensen LJ, Bornscheuer UT, Hult K.
    Chembiochem. 2010 Apr 12;11(6):796-801.

  • 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 Mar;19(3):579-92.

  • 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. 2010 Mar 11;29(10):1531-42. Epub ahead of print: 2009 Dec 14.

  • Evolution and regulation of cellular periodic processes: a role for paralogues
    Trachana K, Jensen LJ, Bork P.
    EMBO Reports. 2010 Mar;11(3):233-8.

  • Ancient human genome sequence of an extinct Palaeo-Eskimo
    Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MT, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Grønnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TF, Ramsey CB, Hansen TV, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Pontén T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E.
    Nature. 2010 Feb 11;463:757-762.

     
  • Understanding the proteome - the missing link for successful drug discovery
    Wikström, M., Sundström, M.  
    BIOforum Europe. 2010;1-2:12-13. 

  • Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during 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. 2010 Jan 12;3(104):ra3.

  • 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. 2010 Jan;38(Database issue):D190-5. Epub ahead of print: 2009 Nov 9.

  • 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. 2010 Jan;12(1):80-6. Sup pp 1-12. Epub ahead of print: 2009 Dec 20.

  • 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. 2010 Jan;38(Database issue):D552-6. Epub ahead of print: 2009 Nov 6.

  • 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. 2010 Jan;38(Database issue):D699-702. Epub ahead of print: 2009 Nov 24. 

     

2009

  • 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.

  • 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.

  • 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.

  • 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.

  • Proteomics strategy for quantitative protein interaction 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.

  • 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.

  • 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. 2009 Aug 14;325(5942):834-40.

  • 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. 2009 Jun;27(6):508-10.

  • 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. 2009 Jun;27(6):549-55.

  • 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
    Proc Natl Acad Sci U S A. 2009 Feb 3;106(5):1374-9.

  • 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. 

     
  • 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. 2009 Jan;5(1):e1000263.

  • 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. 2009;5:236.

  • 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. 2009 Jan;37(Database issue):D412-6. Epub ahead of print: 2008 Oct 21. 

2008
 

  • 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. 2008 Dec 30;105(52):20870-5.

     
  • Not comparable, but complementary
    L.J. Jensen, P. Bork
    Science. 2008 Oct 3;322(5898):56-7.

  • 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. 2008 Oct 30;455(7217):1251-4.

  • 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. 

  • 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.

  • 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. 

  • Predicting biological networks from genomic data
    E. Harrington, L.J. Jensen and P. Bork
    FEBS Letters. 2008 Apr 9;582(8):1251-8. 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. Review.

* = contributed equally