YearPaper
2007 Colinge J, Bennett KL. Introduction to computational proteomics. PLoS Comput Biol 2007, 3:e114. 
Abstract: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933459/
2007 Colinge J. Peptide fragment intensity statistical modelling. Anal Chem 2007, 79, 7286–7290.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/17713966
2007 Pitzer E, Masselot A, Colinge J. Assessing peptide de novo sequencing algorithms performance on large and diverse data sets. Proteomics 2007, 7:3051–3054.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/17683051
2010 Burkard TR, Rix U, Breitwieser FP, Superti-Furga G, Colinge J. A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib. PLoS Comput Biol. 2010 Nov 18;6(11):e1001001.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/21124949
2010 Colinge J, Rix U, Superti-Furga G. Novel global network scores to analyze kinase inhibitor profiles. 2010 Sep 9, ORSC & APORC, 305-313. Lecture Notes;
Abstract:
2010 Ubaida Mohien C, Hartler J, Breitwieser F, Rix U, Remsing Rix L, Winter GE, Thallinger GG, Bennett KL, Superti-Furga G, Trajanoski Z, Colinge J. MASPECTRAS 2: An Integration and Analysis Platform for Proteomic Data. Proteomics. 2010 Jul;10(14):2719-22.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/20455215
2011 Breitwieser FP, Muller A, Dayon L, Kocher T, Hainard A, Pichler P, Schmidt- Erfurth U, Superti- Furga G, Sanchez JC, Mechtler K, Bennett KL, Colinge J. General statistical modeling of data from protein relative expression isobaric tags. J Proteome Res. 2011 Jun 3;10(6):2758-66.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/21526793
2011 Burkard TR, Planyavsky M, Kaupe I, Breitwieser FP, Burckstummer T, Bennett KL, Superti-Furga G, Colinge J. Initial characterization of the human central proteome. BMC Syst Biol. 2011;5:17.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/21269460
2012 Colinge J, Rix U, Bennett KL, Superti-Furga G. Systems biology analysis of protein-drug interactions. Proteomics Clin. Appl. 2012 Jan;6(1-2):102-16.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/22213655
2012 Stukalov A, Superti-Furga G, Colinge J. Deconvolution of targeted protein-protein interaction maps. J Proteome Res. 2012 Aug 3;11(8):4102-9. Epub 2012 Jul 10.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/22724552
2013 Breitwieser F, Colinge J. IsobarPTM: A software tool for the quantitative analysis of post-translationally modified proteins. J Proteomics. 2013 September 2; 90(100): 77–84.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23470796
2013 Colinge J. Systems Biology Analysis of Kinase Inhibitor Action in Leukemia Treatments. Biomed Tech (Berl). 2013 Sep 7.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/24042955
2013 Dürnberger G, Bürckstümmer T, Huber K, Giambruno R, Doerks T, Karayel E, Burkard TR, Kaupe I, Müller AC, Schönegger A, Ecker GF, Lohninger H, Bork P, Bennett KL, Superti-Furga G, Colinge J. Experimental characterization of the human non-sequence-specific nucleic acid interactome. Genome Biol. 2013 Jul 31;14(7):R81.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23902751
2013 Mellacheruvu D, Wright Z, Couzens AL, Lambert J-P, St-Denis N, Li T, Mitev YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, al-Hakim A, Bouchard A, Faubert D, Fermin D, Dunham WH, Goudreault M, Lin Z-Y, Gonzalez Badillo B, Pawson T, Durocher D, Coulombe B, Aebersold R, Superti-Furga S, Colinge J, Heck AJR, Choi H, Gstaiger M, Mohammed S, Cristea IM, Bennett KL, Washburn MP, Raught B, Ewing RM, Gingras A-C, Nesvizhskii A. The CRAPome: a Contaminant Repository for Affinity Purification Mass Spectrometry Data. Nature Methods May; 24(Suppl): S50–S51.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23921808
2014 Boucheron N, Tschismarov R, Goeschl L, Moser M, Lagger S, Sakaguchi S, Winter M, Lenz F, Vitko D, Breitwieser FP, Haust L, Hassan H, Bennett KL, Colinge J, Schreiner W, Egawa T, Taniuchi I, Matthias P, Seiser C, Ellmeier W. CD4 T cell lineage integrity is controlled by the histone deacetylases HDAC1 and HDAC2. Nat Immunol. 2014 May;15(5):439-48. doi: 10.1038/ni.2864. Epub 2014 Mar 30.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/24681565
2014 Kainulainen M, Habjan M, Hubel P, Busch L, Lau S, Colinge J, Superti-Furga G, Pichlmair A, Weber F. Virulence Factor NSs of Rift Valley Fever Virus Recruits the F-Box Protein FBXO3 To Degrade Subunit p62 of General Transcription Factor TFIIH. J Virol. 2014 Mar;88(6):3464-73. doi: 10.1128/JVI.02914-13. Epub 2014 Jan 8.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/24403578
2014 Boucheron N, Tschismarov R, Goeschl L, A Moser M, Lagger S, Sakaguchi S, Winter M, Lenz F, Vitko D, Breitwieser FP, Müller L, Hassan H, Bennett KL, Colinge J, Schreiner W, Egawa T, Taniuchi I, Matthias P, Seiser C, Ellmeier W. Corrigendum: CD4(+) T cell lineage integrity is controlled by the histone deacetylases HDAC1 and HDAC2. Nat Immunol. 2014 Aug 19;15(9):894.doi:10.1038/ni0914-894e.
Abstract: http://www.nature.com/ni/journal/v15/n9/full/ni0914-894e.html
2014 Colinge J, César-Razquin A, Huber K, Breitwieser FP, Májek P, Superti-Furga G. Building and exploring an integrated human kinase network: global organization and medical entry points. J Proteomics. 2014 Jul 31;107:113-27. doi: 10.1016/j.jprot.2014.03.028. Epub 2014 Apr 3.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/24704859
2014 Muellner MK, Duernberger G, Ganglberger F, Kerzendorfer C, Uras IZ, Schoenegger A, Bagienski K, Colinge J, Nijman SM. TOPS: a versatile software tool for statistical analysis and visualization of combinatorial gene-gene and gene-drug interaction screens. BMC Bioinformatics. 2014 Apr 8;15:98. doi: 10.1186/1471-2105-15-98.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/24712852
2015 Muellner MK, Mair B, Ibrahim Y, Kerzendorfer C, Lechtermann H, Trefzer C, Klepsch F, Müller AC, Leitner E, Macho-Maschler S, Superti-Furga G, Bennett KL, Baselga J, Rix U, Kubicek S, Colinge J, Serra V, Nijman SM. Targeting a cell state common to triple-negative breast cancers. Mol Syst Biol. 2015 Feb 19;11(1):789. doi: 10.15252/msb.20145664.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25699542
2015 Bhattacharya A, Hegazy AN, Deigendesch N, Kosack L, Cupovic J, Kandasamy RK, Hildebrandt A, Merkler D, Kühl AA, Vilagos B, Schliehe C, Panse I, Khamina K, Baazim H, Arnold I, Flatz L, Xu HC, Lang PA, Aderem A, Takaoka A, Superti-Furga G, Colinge J, Ludewig B, Löhning M, Bergthaler A. Superoxide Dismutase 1 Protects Hepatocytes from Type I Interferon-Driven Oxidative Damage. Immunity. 2015 Nov 17;43(5):974-86. doi: 10.1016/j.immuni.2015.10.013.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26588782
2015 Blomen VA, Májek P, Jae LT, Bigenzahn JW, Nieuwenhuis J, Staring J, Sacco R, van Diemen FR, Olk N, Stukalov A, Marceau C, Janssen H, Carette JE, Bennett KL, Colinge J, Superti-Furga G, Brummelkamp TR. Gene essentiality and synthetic lethality in haploid human cells. Science. 2015 Nov 27;350(6264):1092-6. doi: 10.1126/science.aac7557. Epub 2015 Oct 15.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26472760
2015 Harutyunyan AS, Giambruno R, Krendl C, Stukalov A, Klampfl T, Berg T, Chen D, Milosevic Feenstra JD, Jäger R, Gisslinger B, Gisslinger H, Rumi E, Passamonti F, Pietra D, Müller AC, Parapatics K, Breitwieser FP, Herrmann R, Colinge J, Bennett KL, Superti-Furga G, Cazzola M, Hammond E, Kralovics R. Germline RBBP6 mutations in familial myeloproliferative neoplasms. Blood. 2015 Nov 16. pii: blood-2015-09-668673.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26574608
2015 Hörmann K, Stukalov A, Müller AC, Heinz LX, Superti-Furga G, Colinge J, Bennett KL. A surface biotinylation strategy for reproducible plasma membrane protein purification and tracking of genetic and drug-induced alterations. J Proteome Res. 2015 Dec 24.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26699813
2015 Huber KV, Olek KM, Müller AC, Tan CS, Bennett KL, Colinge J, Superti-Furga G. Proteome-wide drug and metabolite interaction mapping by thermal-stability profiling. Nat Methods. 2015 Nov;12(11):1055-7. doi: 10.1038/nmeth.3590. Epub 2015 Sep 21.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/26389571
2015 Licciardello MP, Müllner MK, Dürnberger G, Kerzendorfer C, Boidol B, Trefzer C, Sdelci S, Berg T, Penz T, Schuster M, Bock C, Kralovics R, Superti-Furga G, Colinge J, Nijman SM, Kubicek S. NOTCH1 activation in breast cancer confers sensitivity to inhibition of SUMOylation. Oncogene. 2015 Jul;34(29):3780-90. doi: 10.1038/onc.2014.319. Epub 2014 Sep 29.
Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25263445
2017 Licciardello MP, Ringler A, Markt P, Klepsch F, Lardeau CH, Sdelci S, Schirghuber E, Müller AC, Caldera M, Wagner A, Herzog R, Penz T, Schuster M, Boidol B, Dürnberger G, Folkvaljon Y, Stattin P, Ivanov V, Colinge J, Bock C, Kratochwill K, Menche J, Bennett KL, Kubicek S. A combinatorial screen of the CLOUD uncovers a synergy targeting the androgen receptor. Nat Chem Biol. 2017 Jul;13(7):771-778. doi: 10.1038/nchembio.2382. Epub 2017 May 22.
Abstract: https://www.ncbi.nlm.nih.gov/pubmed/28530711