• Absalom N, Eghorn, LF, Villumsen IS, Karim N, Bay T, Olsen JV, Knudsen GM, Brauner-Osborne H, Frolund B, Clausen, RP, Chebib M, Wellendorph P. alpha 4 beta delta GABA(A) receptors are high affinity targets for gamma-hydroxybutyric acid (GHB). PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, AUG 14 2012, 109: 13404-13409

• Altmeyer, M. Addicted to PAR? A closer look at PARP inhibitor sensitivity. CELL CYCLE, NOV 1 2012, 11: 3916-3916

• Ambrus JI, Halliday JI, Kanizaj N, Absalom N, Harpsoe K, Balle T, Chebib M, McLeod MD. Covalent attachment of antagonists to the alpha 7 nicotinic acetylcholine receptor: synthesis and reactivity of substituted maleimides. CHEMICAL COMMUNICATIONS, 2012, 48: 6699-670

• Beck T, Gollapudi S, Brunak S, Graf N, Lemke HU, Dash D, Buchan I, Diaz C, Sanz F, Brookes A J. Knowledge Engineering for Health: A New Discipline Required to Bridge the ICT Gap Between Research and Healthcare. HUMAN MUTATION, MAY 2012, 33: 797-802

• Bekker-Jensen S, Mailand N. Ubiquitin and the DNA damage response: A new handle on histones. CELL CYCLE, SEP 1 2012, 11: 3153-3153

• Bekker-Jensen S, Mailand N. ICLS: A Chicken Without an Egg. NATURE REVIEWS MOLECULAR CELL BIOLOGY, JUN 2012, 13: 342-342

• Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C. Proteomic Investigations Reveal a Role for RNA Processing Factor THRAP3 in the DNA Damage Response. MOLECULAR CELL, APR 27 2012, 46: 212-225

• Benned-Jensen T, Norn C, Laurent S, Madsen CM, Larsen HM, Arfelt KN, Wolf RM, Frimurer, T, Sailer AW, Rosenkilde MM. Molecular Characterization of Oxysterol Binding to the Epstein-Barr Virus-induced Gene 2 (GPR183). JOURNAL OF BIOLOGICAL CHEMISTRY, OCT 12 2012, 287: 35470-35483

• Bergholdt R, Brorsson C, Palleja, A, Berchtold LA, Floyel T, Bang-Berthelsen CH, Frederiksen KS, Jensen L J, Storling J, Pociot F. Identification of Novel Type 1 Diabetes Candidate Genes by Integrating Genome-Wide Association Data, Protein-Protein Interactions, and Human Pancreatic Islet Gene Expression. DIABETES, APR 2012, 61: 954-962

• Bolanos-Garcia VM,Nilsson J, Blundell TL. The architecture of the BubR1 tetratricopeptide tandem repeat defines a protein motif underlying mitotic checkpoint-kinetochore communication. BIOARCHITECTURE 2(1), JAN 2012, 23-27, Review

• Cappellini E, Jensen L J, Szklarczyk D, Ginolhac A, da Fonseca RAR, Stafford TW Jr, Holen SR, Collins MJ, Orlando L, Willerslev E, Gilbert MTP, Olsen JV. Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins. JOURNAL OF PROTEOME RESEARCH, FEB 2012, 11: 917-926

• Croft L, Szklarczyk D, Jensen LJ, Gorodkin J. Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs. BMC SYSTEMS BIOLOGY, JUL 23 2012, 6: 90

• Damgaard RB, Nachbur U, Yabal M, Wong WWL, Fiil BK, Kastirr M, Rieser E, Rickard JA, Bankovacki A, Peschel C, Ruland J, Bekker-Jensen S, Mailand N, Kaufmann T, Strasser A, Walczak H, Silke J, Jost PJ, Gyrd-Hansen M. The Ubiquitin Ligase XIAP Recruits LUBAC for NOD2 Signaling in Inflammation and Innate Immunity. MOLECULAR CELL, JUN 29 2012, 46: 746-758

• Daniel JA, Nussenzweig A. Roles for histone H3K4 methyltransferase activities during immunoglobulin class-switch recombination, BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS, JUL 2012, 1819: 733-738

• Daniel JA, Pellegrini M, Lee BS, Guo Z, Filsuf D, Belkina NV, You Z, Paull TT, Sleckman BP, Feigenbaum L, Nussenzweig A. Loss of ATM kinase activity leads to embryonic lethality in mice. JOURNAL OF CELL BIOLOGY, AUG 6 2012, 198: 295-304

• Danielsen JR, Povlsen LK, Villumsen BH, Streicher W, Nilsson J, Wikstrom M, Bekker-Jensen S, Mailand N. DNA damage-inducible SUMOylation of HERC2 promotes RNF8 binding via a novel SUMO-binding Zinc finger. JOURNAL OF CELL BIOLOGY, APR 16 2012, 197: 179-187

• Dinant C, Bartek J, Bekker-Jensen S. Histone Displacement during Nucleotide Excision Repair. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, OCT 2012, 13: 13322-13337

• Do Vale, LHF, Gomez-Mendoza DP, Kim MS, Akhilesh P, Carlos AO, Ricart EXFF, Sousa MV. Secretome Analysis of the Fungus Trichoderma Harzianum Grown on Cellulose. PROTEOMICS, 2012,17: 2716-2728

• Egerod KL, Engelstoft MS, Grunddal KV, Nohr MK, Secher A, Sakata I, Pedersen J, Windelov JA, Fuchtbauer EM, Olsen J, Sundler F, Christensen JP, Wierup N, Olsen JV, Holst JJ, Zigman JM, Poulsen SS, Schwartz TW. A Major Lineage of Enteroendocrine Cells Coexpress CCK, Secretin, GIP, GLP-1, PYY, and Neurotensin but Not Somatostatin. ENDOCRINOLOGY, DEC 2012, 153: 5782-5795

• Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Jin J, Minguez P, Bork P, von Mering C, Jensen LJ. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. NUCLEIC ACIDS RESEARCH 41, (ePub NOV 2012), JAN 2013, 41(D1):D808-15

• Frenkel-Morgenstern M, Tamar D, Thomas C, Takao I, Cohen L, Hou YM, Juhl Jensen L. Genes Adopt Non-Optimal Codon Usage to Generate Cell Cycle-Dependent Oscillations in Protein Levels. MOLECULAR SYSTEMS BIOLOGY, FEB 2 2012, 8: 572

• Frogne T, Sylvestersen KB, Kubicek S, Nielsen ML, Hecksher-Sorensen J. Pdx1 Is Post-Translationally Modified In vivo and Serine 61 Is the Principal Site of Phosphorylation. PLOS ONE, APR 11 2012, 7: e35233

• Gudjonsson T, Altmeyer M, Savic V, Toledo L, Dinant C, Grofte M, Bartkova J, Poulsen M, Oka Y, Bekker-Jensen S, Mailand N, Neumann B, Heriche JK, Shearer R, Saunders D, Bartek J, Lukas J, Lukas C. TRIP12 and UBR5 Suppress Spreading of Chromatin Ubiquitylation at Damaged Chromosomes. CELL, AUG 17 2012, 150: 697-709

• Hogberg T, Frimurer TM, Sasmal PK. Melanin concentrating hormone receptor 1 (MCHR1) antagonists-Still a viable approach for obesity treatment? BIOORGANIC & MEDICINALCHEMISTRY LETTERS, OCT 1 2012, 22: 6039-6047

• Jensen P C, Thiele S, Steen A, Elder A, Kolbeck R, Ghosh S, Frimurer T M, Rosenkilde MM. Reversed binding of a small molecule ligand in homologous chemokine receptors – differential role of extracellular loop 2. BRITISH JOURNAL OF PHARMACOLOGY, MAY 2012, 166: 258-275

• Jensen P B, Jensen LJ, Brunak S. Mining electronic health records: towards better research applications and clinical care. NATURE REVIEWS GENETICS, JUN 2012, 13: 395-405

• Jorgensen 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. Cometin is a novel neurotrophic factor that promotes neurite outgrowth and neuroblast migration in vitro and supports survival of spiral ganglion neurons in vivo. EXPERIMENTAL NEUROLOGY, JAN 2012, 233: 172-181

• Jungmichel S, Clapperton JA, Lloyd J, Hari FJ, Spycher C, Pavic L, Li J, Haire, LF, Bonalli M, Larsen DH, Lukas C, Lukas J, MacMillan D, Nielsen ML, Stucki M, Smerdon SJ. The molecular basis of ATM-dependent dimerization of the Mdc1 DNA damage checkpoint mediator. NUCLEIC ACIDS RESEARCH. MAY 2012, 40: 3913-3928

• Junqueira M, Domont, G. Microbial Proteomics. JOURNAL OF PROTEOME RESEARCH, 2012, 11 (1): 1

• Junqueira M, Carvalho PC. Tools and Challenges for Diversity-Driven Proteomics in Brazil. PROTEOMICS, 2012, 12(17): 2601-2606

• Kazi JU, Sun J, Phung B, Zadjali F, Flores Morales A, Ronnstrand L. Suppressor of Cytokine Signaling 6 (SOCS6) Negatively Regulates Flt3 Signal Transduction through Direct Binding to Phosphorylated Tyrosines 591 and 919 of Flt3. JOURNAL OF BIOLOGICAL CHEMISTRY, OCT 19 2012, 287: 36509-36517

• Kelstrup C D, Young C, Lavallee R, Nielsen ML, Olsen JV. Optimized Fast and Sensitive Acquisition Methods for Shotgun Proteomics on a Quadrupole Orbitrap Mass Spectrometer. JOURNAL OF PROTEOME RESEARCH, JUN 2012, 11:3487-3497

• Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen L J, Bork P. STITCH 3: zooming in on protein-chemical interactions. NUCLEIC ACIDS RESEARCH, JAN 2012, 40: D876-D880

• Kruse T, Zhang G, Larsen MSY, Lischetti T, Streicher W, Nielsen TK, Bjørn SP, Nilsson J. Direct binding between BubR1 and B56-PP2A phosphatase complexes regulate mitotic progression. J. Cell. Science (JAN 2013), In press.

• Lage K, Greenway SC, Rosenfeld JA, Wakimoto H, Gorham JM, Segre AV, Roberts AE, Smoot LB, Pu WT, Pereira AC, Mesquita SM, Tommerup N, Brunak S, Ballif BC, Shaffer LG, Donahoe PK, Daly MJ, Seidman JG, Seidman CE, Larsen LA. Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, AUG 28 2012, 109: 14035-14040

• Lamond AI, Uhlen M, Horning S, Makarov A, Robinson CV, Serrano L, Hartl FU, Baumeister W, Werenskiold AK, Andersen JS, Vorm O, Linial M, Aebersold R, Mann M. Advancing Cell Biology Through Proteomics in Space and Time (PROSPECTS). MOLECULAR & CELLULAR PROTEOMICS, MAR 2012, 11

• Longoni M, Lage K, Russell MK, Loscertales M, Abdul-Rahman OA, Baynam G, Bleyl SB, Brady PD, Breckpot J, Chen CP, Devriendt K, Gillessen-Kaesbach G, Grix AW, Rope, AF, Shimokawa O, Strauss B, Wieczorek D, Zackai EH, Coletti CM, Maalouf FI, Noonan KM, Park JH, Tracy AA, Lee C, Donahoe PK, Pober, BR. Congenital diaphragmatic hernia interval on chromosome 8p23.1 characterized by genetics and protein interaction networks. AMERICAN JOURNAL OF MEDICAL GENETICS PART A, DEC 2012, 158A: 3148-3158

• Luijsterburg MS, Acs K, Ackermann L, Wiegant WW, Bekker-Jensen S, Larsen, DH, Khanna KK, van Attikum H, Mailand N, Dantuma NP. A new non-catalytic role for ubiquitin ligase RNF8 in unfolding higher-order chromatin structure. EMBO JOURNAL, MAY 30 2012, 31: 2511-2527

• Lundby A, Lage K, Weinert BT, Bekker-Jensen DB, Secher A, Skovgaard T, Kelstrup CD, Dmytriyev A, Choudhary C, Lundby C, Olsen JV. Proteomic Analysis of Lysine Acetylation Sites in Rat Tissues Reveals Organ Specificity and Subcellular Patterns. CELL REPORTS, AUG 2012, 2: 419-431

• Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV. Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues. NATURE COMMUNICATIONS, JUN 2012, 3: 876

• Lundh M, Christensen DP, Nielsen MD, Richardson SJ, Dahllof MS, Skovgaard T, Berthelsen J, Dinarello CA, Stevenazzi A, Mascagni P, Grunnet LG, Morgan NG, Mandrup-Poulsen T. Histone deacetylases 1 and 3 but not 2 mediate cytokine-induced beta cell apoptosis in INS-1 cells and dispersed primary islets from rats and are differentially regulated in the islets of type 1 diabetic children. DIABETOLOGIA, SEP 2012, 55: 2421-2431

• Mann M. Proteomics for biomedicine: a half-completed journey. EMBO MOLECULAR MEDICINE, FEB 2012, 4: 75-77

• Mantri M, Webby CJ, Loik ND, Hamed RB, Nielsen ML, McDonough MA, McCullagh JSO, Boettger A, Schofield CJ, Wolf A. Self-hydroxylation of the splicing factor lysyl hydroxylase. JMJD6. MEDCHEMCOMM, JAN 2012, 3: 80-85

• Mokrosinski J, Frimurer TM, Sivertsen B, Schwartz TW, Holst B. Modulation of Constitutive Activity and Signaling Bias of the Ghrelin Receptor by Conformational Constraint in the Second Extracellular Loop. JOURNAL OF BIOLOGICAL CHEMISTRY, SEP 28 2012, 287: 33488-33502

• Molck C, Harpsoe K, Gloriam DE, Clausen RP, Madsen U, Pedersen LO, Jimenez HN, Nielsen SM, Mathiesen JM, Brauner-Osborne H. Pharmacological Characterization and Modeling of the Binding Sites of Novel 1,3-Bis(pyridinylethynyl) benzenes as Metabotropic Glutamate Recptor 5-Selective Negative Allosteric Modulators. MOLECULAR PHARMACOLOGY, NOV 2012, 82: 929-937

• Mosbech A, Gibbs-Seymour I, Kagias K, Thorslund T, Beli P, Povlsen L, Nielsen SV, Smedegaard S, Sedgwick G, Lukas C, Hartmann-Petersen R, Lukas J, Choudhary C, Pocock R, Bekker-Jensen S, Mailand N. DVC1 (C1orf124) is a DNA damage-targeting p97 adaptor that promotes ubiquitin-dependent responses to replication blocks. NATURE STRUCTURAL & MOLECULAR BIOLOGY, NOV 2012, 19: 1084-1092

• Munch HK, Rasmussen, JE, Christensen JB, Jensen KJ. Site-Selective Three-Component Double Functionalization of Peptides and Proteins. JOURNAL OF PEPTIDE SCIENCE, SEP 2012, 18: S186-S186

• Ng TN, Schwartz DE, Lavery LL, Whiting GL, Russo B, Krusor B, Veres J, Broms P, Herlogsson L, Alam N, Hagel O, Nilsson J, Karlsson C. Scalable Printed Electronics: An Organic Decoder Addressing Ferroelectric Non-Volatile Memory. SCIENTIFIC REPORTS, 2012, 2: 585.

• Nilsson J. Looping in on Ndc80-How does a protein loop at the kinetochore control chromosome segregation? BIOESSAYS, DEC 2012, 34: 1070-1077

• Nilsson J, Ostergaard E, Nielsen TL, Nielsen M, Sterner O. 3-Alkyl- and 3-Amido-Isothiazoloquinolin-4-Ones as Ligands for the Benzodiazepine Site of Gaba(a) Receptors. BIOORGANIC CHEMISTRY, 2012, 40(1): 125-130

• Nilsson J, Gidlof R, Johansson M, Sterner O. Lactam Analogues of Galiellalactone. TETRAHEDRON, 2012, 68(16): 3336-3341

• Oestergaard VH, Pentzold C, Pedersen RT, Losif S, Alpi A, Bekker-Jensen S, Mailand N, Lisby M. RNF8 and RNF168 but not HERC2 are required for DNA damage-induced ubiquitylation in chicken DT40 cells. DNA REPAIR, NOV 1 2012, 11: 892-905

• Oplustilova L, Wolanin K, Mistrik M, Korinkova G, Simkova D, Bouchal J, Lenobel R, Bartkova J, Lau A, O’Connor MJ, Lukas J, Bartek J. Evaluation of candidate biomarkers to predict cancer cell sensitivity or resistance to PARP-1 inhibitor treatment. CELL CYCLE, OCT 15 2012, 11: 3837-3850

• Palleja A, Horn H, Eliasson S, Jensen LJ. DistiLD Database: diseases and traits in linkage disequilibrium blocks. NUCLEIC ACIDS RESEARCH, JAN 2012, 40: D1036-D1040

• Poulsen JW, Madsen CT, Young C, Poulsen FM, Nielsen ML. Using Guanidine-Hydrochloride for fast and efficient protein digestion and single-step affinity-purification mass spectrometry. JOURNAL OF PROTEOME RESEARCH, DEC 2012, ePub ahead of print

• Poulsen JW, Madsen CT, Young C, Kelstrup CD, Grell HC, Henriksen P, Juhl-Jensen L, Nielsen ML. Comprehensive profiling of proteome changes upon sequential deletion of deubiquitylating enzymes. JOURNAL OF PROTEOMICS, JUL 16 2012. 75: 3886-3897

• Poulsen M, Lukas C, Lukas J, Bekker-Jensen S, Mailand N. Human RNF169 is a negative regulator of the ubiquitin-dependent response to DNA double-strand breaks. JOURNAL OF CELL BIOLOGY, APR 16 20, 197: 189-199

• Povlsen, LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker- Jensen S, Mailand N, Choudhary C. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNAdamage bypass. NATURE CELL BIOLOGY, OCT 2012, 14: 1089-1098

• 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. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. NUCLEIC ACIDS RESEARCH, JAN 2012, 40: D284-D289

• Romanel A, Jensen LJ, Cardelli L & Csikász-Nagy A. Transcriptional regulation is a major controller of cell cycle transition dynamics. PLOS ONE 2012; 7(1): e29716

• Russell MK, Longoni M, Wells J, Maalouf FI, Tracy AA, Loscertales M, Ackerman KG, Pober BR, Lage L. Bult CR, Donahoe PK. Congenital diaphragmatic hernia candidate genes derived from embryonic transcriptomes. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, FEB 21 2012, 109: 2978-2983

• Santana-Farre R, Mirecki-Garrido M, Bocos C, Henriquez-Hernandez LA, Kahlon N, Herrera E, Norstedt G, Parini P, Flores Morales A, Fernandez-Perez L. Influence of Neonatal Hypothyroidism on Hepatic Gene Expression and Lipid Metabolism in Adulthood. PLOS ONE, MAY 16 2012, 7: e37386

• Sedgwick GG, Hayward DG, Di Fiore B, Pardo M, Yu L, Pines J, Nilsson J. Mechanisms controlling the temporal degradation of Nek2A and Kif18A by the APC/C-Cdc20 complex. EMBO Journal, January 2013, ePub ahead of print.

• Sedgwick GG, Townsend K, Martin A, Shimwell NJ, Grand RJA, Stewart GS, Nilsson J, Turnell, AS. Oncogene, Transcriptional intermediary factor 1γ binds to the anaphase-promoting complex/cyclosome and promotes mitosis. ONCOGENE, 2012 Nov 19. doi: 10.1038/onc.2012.501

• Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder CWG, Jacob J, Fernandes P, Nyroenen TH, De Las Rivas J, Blicher T, Jimenez RC, Loveland J, McDowall J, Jones P, Vaughan BW, Lopez R, Attwood K, Brooksbank C. Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers. BRIEFINGS IN BIOINFORMATICS, MAY 2012, 13: 383-389

• Skovgaard T, Uhlin U, Munch-Petersen B. Comparative active-site mutation study of human and Caenorhabditis elegans thymidine kinase 1. FEBS JOURNAL, MAY 2012, 279:1 777-1787

• Sylvestersen KB, Young C, Nielsen ML. Advances in characterizing ubiquitylation sites by mass spectrometry. CURRENT OPINION IN CHEMICAL BIOLOGY 2013, ePub Jan 2013, in press

• Talkowski ME, Rosenfeld JA, Blumenthal I, Pillalamarri V,, Chiang C, Heilbut A, Ernst C, Hanscom C, Rossin E, Lindgren M, Pereira S, Ruderfer D, Kirby A, Ripke S, Harris DJ Lee JH, Ha K, Kim HG, Solomon BD, Gropman AL, Lucente D, Sims K, Ohsumi TK, Borowsky ML, Loranger S, Quade B, Lage K, Miles J, Wu BL, Shen Y, Neale B, Shaffer LG, Daly MJ, Morton CC, Gusella JF. Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries. CELL, APR 27 2012, 149: 525

• Valentin-Hansen L, Groenen M, Nygaard R, Frimurer TM, Holliday ND, Schwartz TW. The Arginine of the DRY Motif in Transmembrane Segment III Functions as a Balancing Micro-switch in the Activation of the beta 2-Adrenergic Receptor. JOURNAL OF BIOLOGICAL CHEMISTRY, SEP 14 2012, 287: 31973-31982

• Wagner SA, Beli P, Weinert BT, Scholz C, Kelstrup CD, Young C, Nielsen ML, Olsen JV, Brakebusch C, Choudhary C. Proteomic Analyses Reveal Divergent Ubiquitylation Site Patterns in Murine tissues. MOLECULAR CELL PROTEOMICS, DEC 2012, 11(12): 1578–1585

• Warrer P, Hansen EH, Juhl-Jensen L, Aagaard L. Using text-mining techniques in electronic patient records to identify ADRs from medicine use. BRITISH JOURNAL OF CLINICAL PHARMACOLOGY, MAY 2012, 73: 674-684

• Wei W, Ba Z, Gao M, Wu Y, Ma Y, Amiard S, White CI; Danielsen JMR, Yang YG, Qi Y. A Role for Small RNAs in DNA Double-Strand Break Repair. CELL, MAR 30 2012, 149: 101-112

• Zadjali F, Santana-Farre R, Vesterlund M, Carow B, Mirecki-Garrido M, Hernandez-Hernandez I, Flodstrom-Tullberg M, Parini P, Rottenberg M, Norstedt G, Fernandez-Perez L, Flores Morales A. SOCS2 deletion protects against hepatic teatosis but worsens insulin resistance in high-fat-diet-fed mice. FASEB JOURNAL, AUG 2012, 26: 3282-3291

• Zhang G, Kelstrup CD, Hu XW, Hansen MJK, Singleton MR, Olsen JV, Nilsson J. The Ndc80 internal loop is required for recruitment of the Ska complex to establish end-on microtubule attachment to kinetochores. JOURNAL OF CELL SCIENCE, JUL 1 2012, 125: 3243-3253
  
  
  
• Zhang G, Beati H, Nilsson J, Wodarz A (2013) The Drosophila Microtubule-Associated Protein Mars Stabilizes Mitotic Spindles by Crosslinking Microtubules through Its N-Terminal Region. PLoS ONE, 8(4): e60596. doi:10.1371/journal.pone.0060596

• Bekker-Jensen S, Mailand N. The ubiquitin-and SUMO-dependent signaling response to DNA double-strand breaks. FEBS Lett. 2011 Sep 16;585(18):2914-9. Epub 2011 Jun 12.
  
  
• Bentin T and Nielsen ML. RNA-DNA sequence differences (RDD) spell genetic code ambiguities? Artificial DNA, 2011. Volume 2, Issue 3 July/August/September 2011.
  
  
• 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. Huntingtin-interacting protein 14 is a type 1 diabetes candidate protein regulating insulin secretion and beta-cell apoptosis. Proc Natl Acad Sci USA. 2011 Sep 13;108(37):E681-8. Epub 2011 Jun 24.
  
  
• Blasius M, Forment JV, Thakkar N, Wagner SA, Choudhary C, Jackson SP. A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1. Genome Biol. 2011 Aug 18;12(8):R78. [Epub ahead of print].
  
  
• 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. Proteomic analysis of a Pleistocene mammoth femur reveals more than one hundred ancient bone proteins. Proteome Res. 2011 Nov 21. [Epub ahead of print]
  
  
• Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F. Phospho.ELM: a database of phosphorylation sites--update 2011. Nucleic Acids Res. 2011 Jan; 39 (Database issue): D261-7. Epub ahead of print: 2010 Nov 9.
  
  
• Vernet E, Sauer J, Andersen A, Jensen KJ, Voldborg B. Predictive mutagenesis of ligation-independent cloning (LIC) vectors for protein expression and site-specific chemical conjugation. Analytical Biochemistry. 2011 Jul 15;414(2):312-4.
  
  
• Roque FS, Jensen PB, Schmock H, Dalgaard M, Andreatta MA, Hansen T, Søeby K, Bredkjær S, Juul A, Werge T, Jensen LJ, Brunak S. Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts. PLoS Comput Biol. 2011 Aug;7(8):e1002141. Epub 2011 Aug 25.
  
  
• Zadjali F, Santana-Farre R, Ellis E, Norstedt G, Fernandez-Perez L, Flores-Morales A. A Liver X Receptor agonist down-regulates Growth Hormone signaling in the liver. Hormone Molecular Biology and Clinical Investigation. Oct 2011. In press.
  
  
• 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. Specific CLK Inhibitors from a Novel Chemotype for Regulation of Alternative Splicing. Chem Biol. 2011 Jan 28;18(1):67-76.
  
  
• Dall'Olio GM, Marino J, Schubert M, Keys KL, Stefan MI, Gillespie CS, Poulain P, Shameer K, Sugar R, Invergo BM, Jensen LJ, Bertranpetit J, Laayouni H. Ten Simple Rules for Getting Help from Online Scientific Communities. PLoS Comput Biol. 2011 Sep;7(9):e1002202. Epub 2011 Sep 29.
  
  
• Gram Schjoldager KT, Vester-Christensen MB, Goth CK, Petersen TN, Brunak S, Bennett EP, Levery SB, Clausen H.J. A Systematic Study of Site-specific GalNAc-type O-Glycosylation Modulating Proprotein Convertase Processing. Biol Chem. 2011 Nov 18;286(46):40122-32. Epub 2011 Sep 20.
  
  
• Hald BO, Jacobsen JC, Braunstein TH, Inoue R, Ito Y, Sørensen PG, Holstein-Rathlou NH, Jensen LJ. BK(Ca) and K(V) channels limit conducted vasomotor responses in rat mesenteric terminal arterioles. Pflugers Arch. 2011 Nov 4. [Epub ahead of print]
  
  
• Raes J, Letunic I, Yamada T, Jensen LJ, Bork P. Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Molecular Systems Biology. 2011 Mar 15;7:473
  
  
• Jensen MK, Pers TH, Dworzynski P, Girman CJ, Brunak S, Rimm EB. Protein Interaction-Based Genome-Wide Analysis of Incident Coronary Heart Disease. Circ Cardiovasc Genet. 2011 Oct 1;4(5):549-556. Epub 2011 Aug 31.
  
  
• 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. Cometin is a novel neurotrophic factor that promotes neurite outgrowth and neuroblast migration in vitro and supports survival of spiral ganglion neurons in vivo. Exp Neurol. 2011 Oct 2. [Epub ahead of print].
  
  
• Jurgen Cox , Nadin Neuhauser , Annette Michalski , Richard A Scheltema , Jesper V Olsen , and Matthias Mann. Andromeda - a peptide search engine integrated into the MaxQuant environment. J. Proteome Res., Epub 2011 Jan 21.
  
  
  
• Kelstrup CD, Hekmat O, Francavilla C, Olsen JV. Pinpointing Phosphorylation Sites: Quantitative Filtering and a Novel Site-specific x-Ion Fragment. J Proteome Res. 2011 Jul 1;10(7):2937-48. Epub 2011 Apr 28.
• Kotzsch A, Vernet E, Hammarström M, Berthelsen J, Weigelt J, Gräslund S, Sundström M. A secretory system for bacterial production of high-profile protein targets. Protein Science. 2011 Jan 24. doi: 10.1002/pro.593. Epub ahead of print.
  
  
• Rigbolt KTG, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B. System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation. Science Signaling. 2011 Mar 15;4(164):rs3.
  
  
• Kuhn M, Szklarczyk D, Franceschini A, von Mering C, Jensen LJ, Bork P. STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Res. 2011 Nov 9. [Epub ahead of print].

• Parnell LD, Lindenbaum P, Shameer K, Dall'Olio GM, Swan DC, Jensen LJ, Cockell SJ, Pedersen BS, Mangan ME, Miller CA, Albert I. BioStar: An Online Question & Answer Resource for the Bioinformatics Community. PLoS Comput Biol. 2011 Oct;7(10):e1002216. Epub 2011 Oct 27.
  
  
• Lin TC, Gombos L, Neuner A, Sebastian D, Olsen JV, Hrle A, Benda C, Schiebel E. Phosphorylation of the yeast γ-tubulin Tub4 regulates microtubule function. PLoS One. 2011 May 5;6(5):e19700.
  
  
• Lukas C, Savic V, Bekker-Jensen S, Doil C, Neumann B, Pedersen RS, Grøfte M, Chan KL, Hickson ID, Bartek J, Lukas J. 53BP1 nuclear bodies form around DNA lesions generated by mitotic transmission of chromosomes under replication stress. Nat Cell Biol. 2011 Mar;13(3):243-53.
  
  
• Lundby A, Olsen JV. GeLCMS for In-Depth Protein Characterization and Advanced Analysis of Proteomes. Methods Mol Biol. 2011;753:143-55.
  
  
• Lustig Y, Ruas JL, Estall JL, Lo JC, Devarakonda S, Laznik D, Choi JH, Ono H, Olsen JV, Spiegelman BM. Separation of the gluconeogenic and mitochondrial functions of PGC-1(alpha) through S6 kinase.Genes Dev. 2011 Jun 15;25(12):1232-44. doi: 10.1101/gad.2054711. Epub 2011 Jun 6.
  
  
• Meerang M, Ritz D, Paliwal S, Garajova Z, Bosshard M, Mailand N, Janscak P, Hübscher U, Meyer H, and Ramadan K. (2011). The ubiquitin-selective segregase VCP/p97 orchestrates the response to DNA double-strand breaks. Nature Cell Biology. 2011 Oct 23;13(11):1376-82. doi: 10.1038/ncb2367.
  
  
• Nilsson J, Cdc20 control of cell fate during prolonged mitotic arrest. Bioessays. 2011 Dec; 33(12):903-9. doi: 10.1002/bies.201100094. Epub 2011 Nov 2.
  
  
• Olsen JV, Mann M. Effective representation and storage of mass spectrometry-based proteomics data sets for the scientific community. Science Signaling. 2011 Feb 15;4(160):pe7.
  
  
• Pallejà A, Horn H, Eliasson S, Jensen LJ. DistiLD Database: diseases and traits in linkage disequilibrium blocks. Nucleic Acids Res. 2011 Nov 3. [Epub ahead of print].
  
  
• 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. Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes. Genet Epidemiol. 2011 Jul;35(5):318-32. doi: 10.1002/gepi.20580. Epub 2011 Apr 11.
  
  
• Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011 Sep 29;8(10):785-6. doi: 10.1038/nmeth.1701. No abstract available.
  
  
• 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. Global phosphoproteome profiling reveals unanticipated networks responsive to cisplatin treatment of embryonic stem cells. Mol Cell Biol. 2011 Oct 17. [Epub ahead of print].
  
  
• 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. EggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res. 2011 Nov 16. [Epub ahead of print]
  
  
• 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. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science. 2011 Oct 7;334(6052):94-8. Epub 2011 Sep 22.
  
  
• Sebastian A. Wagner, Petra Beli, Brian T. Weinert, Michael L. Nielsen, Jürgen Cox, Matthias Mann, Chunaram Choudhary. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. Epub 2011 Sep 1.
  
  
• Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, Mering CV. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011 Jan; 39 (Database issue): D561-8. Epub ahead of print: 2010 Nov 2.
  
  
• Vernet E, Kotzsch A, Voldborg B, Sundström M. Screening of genetic parameters for soluble protein expression in Escherichia coli. Prot Expr Purif, 2011 May;77(1):104-11. Epub 2010 Dec 2.
  
  
• Vesterlund M, Fahad Al-Zadjali, Persson T, Kessler BM, Nielsen ML, Norstedt G and Flores-Morales A. The SOCS2 ubiquitin ligase complex regulates GH receptor level. PLOS One. 2011;6(9):e25358. Epub 2011 Sep 29.
  
  
• 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 of a Blinkin-BUBR1 complex reveals an interaction essential for kinetochore-mitotic checkpoint regulation underlying an unanticipated binding site. Structure. 2011 Nov 9;19(11):1691-700. Epub 2011 Oct 13.
  
  
• Waters MR, Stafford TW Jr, McDonald HG, Gustafson C, Rasmussen M, Cappellini E, Olsen JV, Szklarczyk D, Jensen LJ, Gilbert MT, Willerslev E. Pre-Clovis mastodon hunting 13,800 years ago at the Manis site, Washington. Science. 2011 Oct 21;334(6054):351-3.
  
  
• Weinert BT, Wagner SA, Horn H, Henriksen P, Liu WR, Olsen JV, Jensen LJ, Choudhary C. Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation. Sci Signal. 2011 Jul 26;4(183):ra48.
  
  
• 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. Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia. Leukemia. 2011 Jun;25(6):1001-6. doi: 10.1038/leu.2011.32. Epub 2011 Mar 18.
  
  
• 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. Phosphorylation of the Autophagy Receptor Optineurin Restricts Salmonella Growth. Science. 2011 Jul 8;333(6039):228-33. Epub 2011 May 26.
  
  
• Zadjali F, Pike AC, Vesterlund M, Sun J, Wu C, Li SS, Rönnstrand L, Knapp S, Bullock AN, Flores-Morales A. Structural basis for c-KIT inhibition by the suppressor of cytokine signaling 6 (SOCS6) ubiquitin ligase. J Biol Chem. 2011 Jan 7; 286 (1): 480-90. Epub ahead of print: 2010 Oct 28.

• Bekker-Jensen S, Danielsen JR, Fugger K, Gromova I, Nerstedt A, Bartek J, Lukas J, Mailand N. (2009). HERC2 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. Nature Cell Biol. 2010 Jan;12(1):80-6. Sup pp 1-12. Epub ahead of print: 2009 Dec 20.
  
  
• Bekker-Jensen S, Mailand N. Assembly and function of DNA double-strand break repair foci in mammalian cells. DNA Repair, 2010 Dec 10; 9 (12): 1219-28
  
  
• Blicher T, Gupta RA, Wesolowska LJ. Jensen and S. Brunak. Protein annotation in the era of personal genomics. Current Opinion in Structural Biology. 2010 Jun;20(3):335-41.
  
  
• Choudhary C, Mann M. Decoding signaling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol. 2010 Jun;11(6):427-39. Review.
  
  
• Christensen GL, Kelstrup CD, Lyngsø C, Sarwar U, Bøgebo R, Shiekh SP, Gammeltoft S, Olsen JV, Hansen JL.  Quantitative phosphoproteomics dissection of seven-transmembrane receptor signaling using full and biased agonists. Mol Cell Proteomics. 2010 Jul;9(7):1540-53.
  
  
• Chuan YC, Iglesias-Gato D, Fernandez-Perez L, Cedazo-Minguez A, Pang ST, Norstedt G, Pousette Å, Flores-Morales A. Ezrin mediates c-Myc actions in prostate cancer cell invasion. Oncogene. 2010 Mar 11;29(10):1531-42. Epub ahead of print: 2009 Dec 14.
  
  
• Danielsen JM, KB Sylvestersen, S Bekker-Jensen, D Szklarczyk, JW Poulsen, H Horn, LJ Jensen, N Mailand and ML Nielsen. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Mol. Cell. Proteomics. Epud 2010 Dec 7.
  
  
• Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ, Diella F. Phospho.ELM: a database of phosphorylation sites--update 2011. Nucleic Acids Res. Epub ahead of print: 2010 Nov 9.
  
  
• Gnad F, Ren S, Choudhary C, Cox J, Mann M. Predicting posttranslational lysine acetylation using support vector machines. Bioinformatics. 2010 Jul 1;26(13):1666-8.
  
  
• Granovskaia MV, Jensen LJ, Ritchie ME, Toedling J, Ning Y, Bork P, Huber W, Steinmetz LM. High resolution transcription atlas of the mitotic cell cycle in budding yeast. Genome Biol. 2010;11(3):R24.
  
  
• Iskar M, Campillos M, Kuhn M, Jensen LJ, van Noort V, Bork P. Drug-induced regulation of target expression. PLoS Comput Biol. 2010 Sep 9;6(9).
  
  
• Jensen LJ and Bork P. Ontologies in quantitative biology: A basis for comparison, integration and discovery. PLoS Biology. 2010 May 25;8(5):e1000374.
  
  
• Kaidi A, Weinert BT, Choudhary C, Jackson SP. Human SIRT6 promotes DNA end resection through CtIP deacetylation.  Science. 2010 Sep 10; 329 (5997):1348-53.
  
  
• Kuhn M, Campillos M, Letunic I, Jensen LJ and Bork P. A side effect resource to capture phenotypic effects of drugs. Molecular Systems Biology. 2010;6:343.
  
  
• Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P. STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Research. 2010 Jan;38(Database issue):D552-6. Epub ahead of print: 2009 Nov 6.
  
  
• 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. Dissecting spatio-temporal protein networks driving human heart development and related disorders. Mol Syst Biol. 2010 Jun 22;6:381.
  
  
• Larsen MW, Zielinska DF, Martinelle M, Hidalgo A, Jensen LJ, Bornscheuer UT, Hult K. Suppression of water as a nucleophile in Candida antarctica lipase B catalysis. Chembiochem. 2010 Apr 12;11(6):796-801.
  
  
• Lundby A, Tseng GN, Schmitt N. Structural basis for K(V)7.1-KCNE(x) interactions in the I(Ks) channel complex. Heart Rhythm. 2010 May; 7(5):708-13.
  
  
• Lyngsø C, Kjærulff S, Müller S, Bratt T, Mortensen U, Dal Degan F. A versatile selection system for folding competent proteins using genetic complementation in a eukaryotic host. Protein Science. 2010 Mar;19(3):579-92.
  
  
• Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced Non-supervised Orthologous Groups, species and functional annotations. Nucleic Acids Research. 2010 Jan;38(Database issue):D190-5. Epub ahead of print: 2009 Nov 9.
  
  
• Nagaraj N, D'Souza RCJ, Cox J, Olsen JV and Mann M. Feasibility of large scale phosphoproteomics with higher energy collisional dissociation fragmentation. J Proteome Res., 2010 Dec 3; 9 (12):6786-94.
  
  
• O'Donoghue SI, Horn H, Pafilisa E, Haag S, Kuhn H, Satagopam VP, Schneider R and Jensen LJ.  Reflect: a practical approach to web semantics. Web Semantics: Science, Services and Agents on the World Wide Web 2010;8(2-3):182-189.
  
  
• Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Science Signaling. 2010 Jan 12;3(104):ra3.
  
  
• 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. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature. 2010 Feb 11;463:757-762.
  
  
• Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, Mering CV. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. Epub ahead of print: 2010 Nov 2.
  
  
• Trachana K, Jensen LJ, Bork P. Evolution and regulation of cellular periodic processes: a role for paralogues. EMBO Reports. 2010 Mar;11(3):233-8.
  
  
• Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, Lee KK, Olsen JV, Hyman AA, Stunnenberg HG, Mann M. Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell. 2010 Sep 17; 142 (6):967-80.
  
  
• Walther TC, Olsen JV, Mann M. Yeast expression proteomics by high-resolution mass spectrometry. Methods Enzymol. 2010; 470:259-80.
  
  
• Weintz G*, Olsen JV*, Frühauf K, Niedzielska M, Amit I, Jantsch J, Mages J, Frech C, Dölken L, Mann M, Lang R.  The phosphoproteome of toll-like receptor-activated macrophages. Mol Syst Biol. 2010 Jun 8;6:371.
  
  
• Wikström, M., Sundström, M. Understanding the proteome - the missing link for successful drug discovery. BIOforum Europe. 2010;1-2:12-13.
• Zadjali F, Pike AC, Vesterlund M, Sun J, Wu C, Li SS, Rönnstrand L, Knapp S, Bullock AN, Flores-Morales A. Structural basis for c-KIT inhibition by the suppressor of cytokine signaling 6 (SOCS6) ubiquitin ligase. J Biol Chem. Epub ahed of print: 2010 Oct 28.

• Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther T, Olsen JV, Mann M. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science. 2009 Aug 14;325(5942):834-40.
  
  
• Choudhary C, Olsen JV, Brandts C, Cox J, Böhmer FD, Gerke V, Schmidt-Arras D, Berdel WE, Müller-Tidow C, Mann M, Serve H. Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes. Mol Cell. 2009 Oct 23;36(2):326-39.
  
  
• Csikász-Nagy A, Kapuy O, Tóth A, Pál C, Jensen LJ, Uhlmann F, Tyson JJ, Novák B. Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation. Molecular Systems Biology. 2009; 5:236.
  
  
• Gauthier N, Jensen LJ, Wernersson R, Brunak S, Jensen TS. Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. Nucleic Acids Research. 2010 Jan;38(Database issue):D699-702. Epub ahead of print: 2009 Nov 24.
  
  
• Gnad F, de Godoy LMF, Cox J, Neuhauser N, Ren S, Olsen JV, Mann M. High accuracy identification and bioinformatic analysis of in-vivo protein phosphorylation sites in yeast. Proteomics. 2009 Sep 30;9(20):4642-4652.
  
  
• Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, Mering CV. STRING 8 - a global view on proteins and their functional interactions in 630 organisms.
  Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6. Epub ahead of print: 2008 Oct 21.
  
  
• Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol. 2009 Jun;27(6):549-55.
  
  
• Martin L. Miller*, Boumediene Soufi*, Carsten Jers, Nikolaj Blom, Ivan Mijakovic. NetPhosBac: Prediction of protein phosphorylation sites in bacteria. Proteomics. 2009 Jan;9(1):116-25. Epub ahead of print: 2008 Dec 3.
  
  
• 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. A dual pressure linear ion trap - Orbitrap instrument with very high sequencing speed. Mol Cell Proteomics. 2009 Dec;8(12):2759-69.
  
  
• Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R. Reflect: augmented browsing for the life scientist. Nature Biotechnology. 2009 Jun;27(6):508-10.
  
  
• Pan C, Olsen JV, Daub H, Mann M. Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics. Mol Cell Proteomics. 2009 Dec;8(12):2796-808.
  
  
• Saunders N, Beltrão P, L.J. Jensen, D. Jurczak, R. Krause, M. Kuhn and S. Wu. Microblogging the ISMB: A New Approach to Conference Reporting. PLoS Computational Biology. 2009 Jan;5(1):e1000263.
  
  
• Sharma K, Weber C, Bairlein M, Greff Z, Kéri G, Cox J, Olsen JV & Daub H. Proteomics strategy for quantitative protein interaction profiling in cell extracts. Nat Methods. 2009 Oct;6(10):741-4.
  
  
• Soufi B, Kelstrup CD, Stoehr G, Fröhlich F, Walther TC, Olsen JV. Global analysis of the yeast osmotic stress response by quantitative proteomics. Mol. BioSyst. 2009 Nov;5(11):1337-46.
  
  
• 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. Proc Natl Acad Sci U S A. 2009 Feb 3;106(5):1374-9.

• 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. Text mining for biology - the way forward: opinions from leading scientists. Genome Biol. 2008; 9 Suppl 2:S7.
  
  
• Campillos M*, Kuhn M*, Gavin AC, Jensen LJ, Bork P. Drug target identification using side-effect similarity. Science. 2008 Jul 11; 321(5886):263-6.
  
  
• Harrington E, Jensen LJ, Bork P. Predicting biological networks from genomic data. FEBS Letters. 2008 Apr 9; 582(8):1251-8. Review.
  
  
• Jensen LJ*, de Lichtenberg U*, Jensen TS, Brunak S, Bork P. Circular reasoning rather than cyclic expression. Genome Biology. 2008; 9(6):403.
  
  
• Jensen LJ, Bork J. Not comparable, but complementary. Science. 2008 Oct 3;322(5898):56-7.
  
  
• Kuhn M*, Campillos M*, Gonzales P*, Jensen LJ*, Bork P*. Large-scale prediction of drug-target relationships. FEBS Letters. 2008 Apr 9; 582(8):1283-90. Review.
  
  
• Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque FS, Donahoe PK, Szallasi Z, Jensen TS, Brunak S. A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20870-5.
  
  
• Lyris M. de Godoy F, Olsen JV, Cox J, Nielsen ML, Hubner NC, Fröhlich F, Walther TC, Mann M. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature. 2008 Oct 30;455(7217):1251-4.
  
  
• Miller ML*, Jensen LJ*, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R. Linear motif atlas for phosphorylation-dependent signaling. Science Signaling. 2008 Sep 2;1(35):ra2.

*= contributed equally