Rune Linding, PhD - Publications

European Molecular Biology Laboratory, Germany 
bioinformatics, disorder, signaling

44 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2014 Horn H, Schoof EM, Kim J, Robin X, Miller ML, Diella F, Palma A, Cesareni G, Jensen LJ, Linding R. KinomeXplorer: an integrated platform for kinome biology studies. Nature Methods. 11: 603-4. PMID 24874572 DOI: 10.1038/Nmeth.2968  0.32
2014 Pasculescu A, Schoof EM, Creixell P, Zheng Y, Olhovsky M, Tian R, So J, Vanderlaan RD, Pawson T, Linding R, Colwill K. CoreFlow: a computational platform for integration, analysis and modeling of complex biological data. Journal of Proteomics. 100: 167-73. PMID 24503186 DOI: 10.1016/J.Jprot.2014.01.023  1
2013 Robin X, Creixell P, Radetskaya O, Santini CC, Longden J, Linding R. Personalized network-based treatments in oncology. Clinical Pharmacology and Therapeutics. 94: 646-50. PMID 23995267 DOI: 10.1038/Clpt.2013.171  1
2013 Martin SF, Falkenberg H, Dyrlund TF, Khoudoli GA, Mageean CJ, Linding R. PROTEINCHALLENGE: crowd sourcing in proteomics analysis and software development. Journal of Proteomics. 88: 41-6. PMID 23220569 DOI: 10.1016/J.Jprot.2012.11.014  1
2012 Creixell P, Schoof EM, Erler JT, Linding R. Navigating cancer network attractors for tumor-specific therapy. Nature Biotechnology. 30: 842-8. PMID 22965061 DOI: 10.1038/Nbt.2345  1
2012 Creixell P, Schoof EM, Tan CS, Linding R. Mutational properties of amino acid residues: implications for evolvability of phosphorylatable residues. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 367: 2584-93. PMID 22889909 DOI: 10.1098/Rstb.2012.0076  1
2012 Creixell P, Linding R. Cells, shared memory and breaking the PTM code. Molecular Systems Biology. 8: 598. PMID 22866336 DOI: 10.1038/Msb.2012.33  1
2012 Erler JT, Linding R. Network medicine strikes a blow against breast cancer. Cell. 149: 731-3. PMID 22579276 DOI: 10.1016/J.Cell.2012.04.014  1
2011 Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, et al. Verification of systems biology research in the age of collaborative competition. Nature Biotechnology. 29: 811-5. PMID 21904331 DOI: 10.1038/Nbt.1968  1
2011 Olhovsky M, Williton K, Dai AY, Pasculescu A, Lee JP, Goudreault M, Wells CD, Park JG, Gingras AC, Linding R, Pawson T, Colwill K. OpenFreezer: a reagent information management software system. Nature Methods. 8: 612-3. PMID 21799493 DOI: 10.1038/Nmeth.1658  1
2011 Tan CSH, Schoof EM, Creixell P, Pasculescu A, Lim WA, Pawson T, Bader GD, Linding R. Response to comment on "positive selection of tyrosine loss in metazoan evolution" Science. 332: 917-b. DOI: 10.1126/Science.1188535  1
2010 Reinhardt HC, Hasskamp P, Schmedding I, Morandell S, van Vugt MA, Wang X, Linding R, Ong SE, Weaver D, Carr SA, Yaffe MB. DNA damage activates a spatially distinct late cytoplasmic cell-cycle checkpoint network controlled by MK2-mediated RNA stabilization. Molecular Cell. 40: 34-49. PMID 20932473 DOI: 10.1016/J.Molcel.2010.09.018  1
2010 Linding R. (R)evolution of complex regulatory systems. Science Signaling. 3: eg4. PMID 20571125 DOI: 10.1126/Scisignal.3127Eg4  1
2010 Linding R. Multivariate signal integration. Nature Reviews. Molecular Cell Biology. 11: 391. PMID 20445545 DOI: 10.1038/Nrm2906  1
2010 Tan CS, Jørgensen C, Linding R. Roles of “junk phosphorylation” in modulating biomolecular association of phosphorylated proteins? Cell Cycle (Georgetown, Tex.). 9: 1276-80. PMID 20234177 DOI: 10.4161/Cc.9.7.11066  1
2010 van Vugt MA, Gardino AK, Linding R, Ostheimer GJ, Reinhardt HC, Ong SE, Tan CS, Miao H, Keezer SM, Li J, Pawson T, Lewis TA, Carr SA, Smerdon SJ, Brummelkamp TR, et al. A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint. Plos Biology. 8: e1000287. PMID 20126263 DOI: 10.1371/Journal.Pbio.1000287  1
2010 Jørgensen C, Linding R. Simplistic pathways or complex networks? Current Opinion in Genetics & Development. 20: 15-22. PMID 20096559 DOI: 10.1016/J.Gde.2009.12.003  1
2010 Erler JT, Linding R. Network-based drugs and biomarkers. The Journal of Pathology. 220: 290-6. PMID 19921715 DOI: 10.1002/Path.2646  1
2010 Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, ... ... Linding R, et al. ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Research. 38: D167-80. PMID 19920119 DOI: 10.1093/Nar/Gkp1016  1
2009 Jørgensen C, Sherman A, Chen GI, Pasculescu A, Poliakov A, Hsiung M, Larsen B, Wilkinson DG, Linding R, Pawson T. Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells. Science (New York, N.Y.). 326: 1502-9. PMID 20007894 DOI: 10.1126/Science.1176615  1
2009 Jin J, Xie X, Chen C, Park JG, Stark C, James DA, Olhovsky M, Linding R, Mao Y, Pawson T. Eukaryotic protein domains as functional units of cellular evolution. Science Signaling. 2: ra76. PMID 19934434 DOI: 10.1126/Scisignal.2000546  1
2009 Tan CS, Linding R. Experimental and computational tools useful for (re)construction of dynamic kinase-substrate networks. Proteomics. 9: 5233-42. PMID 19834900 DOI: 10.1002/Pmic.200900266  1
2009 Van Hoof D, Muñoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J. Phosphorylation dynamics during early differentiation of human embryonic stem cells. Cell Stem Cell. 5: 214-26. PMID 19664995 DOI: 10.1016/J.Stem.2009.05.021  1
2009 Tan CS, Bodenmiller B, Pasculescu A, Jovanovic M, Hengartner MO, Jørgensen C, Bader GD, Aebersold R, Pawson T, Linding R. Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Science Signaling. 2: ra39. PMID 19638616 DOI: 10.1126/Scisignal.2000316  1
2009 Tan CS, Pasculescu A, Lim WA, Pawson T, Bader GD, Linding R. Positive selection of tyrosine loss in metazoan evolution. Science (New York, N.Y.). 325: 1686-8. PMID 19589966 DOI: 10.1126/Science.1174301  1
2009 Wang K, Alvarez MJ, Bisikirska BC, Linding R, Basso K, Dalla Favera R, Califano A. Dissecting the interface between signaling and transcriptional regulation in human B cells. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 264-75. PMID 19209707  1
2009 Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, Faria D, Bull S, Pawson T, Morris Q, Wrana JL. Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nature Biotechnology. 27: 199-204. PMID 19182785 DOI: 10.1038/Nbt.1522  1
2008 Bakal C, Linding R, Llense F, Heffern E, Martin-Blanco E, Pawson T, Perrimon N. Phosphorylation networks regulating JNK activity in diverse genetic backgrounds. Science (New York, N.Y.). 322: 453-6. PMID 18927396 DOI: 10.1126/Science.1158739  1
2008 Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, ... ... Linding R, et al. Linear motif atlas for phosphorylation-dependent signaling. Science Signaling. 1: ra2. PMID 18765831 DOI: 10.1126/Scisignal.1159433  1
2008 Pawson T, Linding R. Network medicine. Febs Letters. 582: 1266-70. PMID 18282479 DOI: 10.1016/j.febslet.2008.02.011  1
2008 Jørgensen C, Linding R. Directional and quantitative phosphorylation networks. Briefings in Functional Genomics & Proteomics. 7: 17-26. PMID 18270216 DOI: 10.1093/Bfgp/Eln001  1
2008 Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T. NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Research. 36: D695-9. PMID 17981841 DOI: 10.1093/Nar/Gkm902  1
2008 Linding R, VanHook AM. Science signaling podcast: 28 October 2008 Science Signaling. 1. DOI: 10.1126/Scisignal.143Pc10  1
2007 Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jørgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JG, et al. Systematic discovery of in vivo phosphorylation networks. Cell. 129: 1415-26. PMID 17570479 DOI: 10.1016/J.Cell.2007.05.052  1
2005 Neduva V, Linding R, Su-Angrand I, Stark A, de Masi F, Gibson TJ, Lewis J, Serrano L, Russell RB. Systematic discovery of new recognition peptides mediating protein interaction networks. Plos Biology. 3: e405. PMID 16279839 DOI: 10.1371/Journal.Pbio.0030405  1
2005 Ingham RJ, Colwill K, Howard C, Dettwiler S, Lim CS, Yu J, Hersi K, Raaijmakers J, Gish G, Mbamalu G, Taylor L, Yeung B, Vassilovski G, Amin M, Chen F, ... ... Linding R, et al. WW domains provide a platform for the assembly of multiprotein networks. Molecular and Cellular Biology. 25: 7092-106. PMID 16055720 DOI: 10.1128/Mcb.25.16.7092-7106.2005  1
2005 Pawson T, Linding R. Synthetic modular systems--reverse engineering of signal transduction. Febs Letters. 579: 1808-14. PMID 15763556 DOI: 10.1016/j.febslet.2005.02.013  1
2004 Linding R, Schymkowitz J, Rousseau F, Diella F, Serrano L. A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins. Journal of Molecular Biology. 342: 345-53. PMID 15313629 DOI: 10.1016/J.Jmb.2004.06.088  1
2004 Diella F, Cameron S, Gemünd C, Linding R, Via A, Kuster B, Sicheritz-Pontén T, Blom N, Gibson TJ. Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. Bmc Bioinformatics. 5: 79. PMID 15212693 DOI: 10.1186/1471-2105-5-79  1
2003 Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB. Protein disorder prediction: implications for structural proteomics. Structure (London, England : 1993). 11: 1453-9. PMID 14604535 DOI: 10.1016/J.Str.2003.10.002  1
2003 Bimpikis K, Budd A, Linding R, Gibson TJ. BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases. Nucleic Acids Research. 31: 3792-4. PMID 12824420 DOI: 10.1093/Nar/Gkg535  1
2003 Linding R, Russell RB, Neduva V, Gibson TJ. GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Research. 31: 3701-8. PMID 12824398 DOI: 10.1093/Nar/Gkg519  1
2003 Puntervoll P, Linding R, Gemünd C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferrè F, Maselli V, Via A, Cesareni G, Diella F, et al. ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Research. 31: 3625-30. PMID 12824381 DOI: 10.1093/Nar/Gkg545  1
2002 Aasland R, Abrams C, Ampe C, Ball LJ, Bedford MT, Cesareni G, Gimona M, Hurley JH, Jarchau T, Lehto VP, Lemmon MA, Linding R, Mayer BJ, Nagai M, Sudol M, et al. Normalization of nomenclature for peptide motifs as ligands of modular protein domains. Febs Letters. 513: 141-4. PMID 11911894 DOI: 10.1016/S0014-5793(01)03295-1  1
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