english

Liste des publications

Progiciels

Isobar: a R Bioconductor package for the analysis of quantitative proteomic data, both at the global protein level but also at the PTM level (Breitwieser et al, 2011; Breitwieser & Colinge, 2013).

 

BI-MAP: a C++/R package for the analysis of affinity purification-mass spectrometry data (protein-protein interactions) aimed at inferring robust protein complexes (Stukalov et al, 2012).

 

Phenyx: a commercial mass spectrometry data search engine derived from the OLAV scoring system (Colinge et al., 2003; Colinge et al., 2004; Colinge et al., 2007) we developed at GenProt Inc.

 

InSilicoSpectro: a Perl CPAN library to analyze and process mass spectrometry data (Colinge et al., 2006).

 

Liste des Publications

Boulos RE, Tremblay N, Arneodo A, Borgnat P, Audit B. Multi-scale structural community organisation of the human genome. BMC Bioinformatics. 2017 Apr 11;18(1): 209. doi: 10.1186/s12859-017 - 1616-x.

 

Sobecki M, Mrouj K, Colinge J, Gerbe F, Jay P, Krasinska L, Dulic V, Fisher D. Cell cycle regulation accounts for variability in Ki-67 expression levels. Cancer Res. 2017 Mar 10. pii: canres.0707.2016. doi: 10.1158/0008-5472.CAN-16-0707. [Epub ahead of print]

 

Martins R, Maier J, Gorki AD, Huber KV, Sharif O, Starkl P, Saluzzo S, Quattrone F, Gawish R, Lakovits K, Aichinger MC, Radic-Sarikas B, Lardeau CH, Hladik A, Korosec A, Brown M, Vaahtomeri K, Duggan M, Kerjaschki D, Esterbauer H, Colinge J, Eisenbarth SC, Decker T, Bennett KL, Kubicek S, Sixt M, Superti-Furga G, Knapp S. Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions. Nat Immunol. 2016 Dec;17(12):1361-1372. doi: 10.1038/ni.3590.

 

Hart RJ, Cornillot E, Abraham A, Molina E, Nation CS, Ben Mamoun C, Aly AS. Genetic Characterization of Plasmodium Putative Pantothenate Kinase Genes Reveals Their Essential Role in Malaria Parasite Transmission to the Mosquito. Sci Rep. 2016 Sep 20;6:33518. doi: 10.1038/ srep 33518.

 

Dwivedi A, Khim N, Reynes C, Ravel P, Ma L, Tichit M, Bourchier C, Kim S, Dourng D, Khean C, Chim P, Siv S, Frutos R, Lek D, Mercereau-Puijalon O, Ariey F, Menard D, Cornillot E. Plasmodium falciparum parasite population structure and gene flow associated to anti-malarial drugs resistance in Cambodia. Malar J. 2016 Jun 14;15:319.

 

Cornillot E, Dassouli A, Pachikara N, Lawres L, Renard I, Francois C, Randazzo S, Brès V, Garg A, Brancato J, Pazzi JE, Pablo J, Hung C, Teng A, Shandling AD, Huynh VT, Krause PJ, Lepore T, Delbecq S, Hermanson G, Liang X, Williams S, Molina DM, Ben Mamoun C. A targeted immunomic approach identifies diagnostic antigens in the human pathogen Babesia microti. Transfusion. 2016 May 17. [Epub ahead of print]

 

Beziaud L, Mansi L, Ravel P, Lauret Marie-Joseph E, Laheurte C, Rangan L, Bonnefoy F, Pallandre JR, Boullerot L, Gamonet C, Vrecko S, Queiroz L, Maurina T, Mouillet G, Nguyen Tan Hon T, Curtit E, Royer B, Gaugler B, Bayry J, Tartour E, Thierry-Vuillemin A, Pivot X, Borg C, Godet Y, Adotévi O. Rapalogs efficacy relies on the modulation of antitumor T cell immunity. Cancer Res. 2016 May 17.[Epub ahead of print]

 

Mazouzi A, Stukalov A, Müller AC, Chen D, Wiedner M, Prochazkova J, Chiang SC, Schuster M, Breitwieser FP, Pichlmair A, El-Khamisy SF, Bock C, Kralovics R, Colinge J, Bennett KL, Loizou JI. A Comprehensive Analysis of the Dynamic Response to Aphidicolin-Mediated Replication Stress Uncovers Targets for ATM and ATMIN. Cell Rep. 2016 Apr 14. [Epub ahead of print]

 

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. [Epub ahead of print]

 

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- 986. doi: 10.1016/j.immuni. 2015. 10.013.

 

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. [Epub ahead of print]

 

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 Oct 15. pii: aac7557. [Epub ahead of print]

 

Dia N, Lavie L, Faye N, Méténier G, Yeramian E, Duroure C, Toguebaye BS, Frutos R, Niang MN, Vivarès CP, Ben Mamoun C, Cornillot E. Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signatures. BMC Genomics, 2015, sous presse.

 

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.

 

Heinz LX, Baumann CL, Köberlin MS, Snijder B, Gawish R, Shui G, Sharif O, Aspalter IM, Müller AC, Kandasamy RK, Breitwieser FP, Pichlmair A, Bruckner M, Rebsamen M, Blüml S, Karonitsch T, Fauster A, Colinge J, Bennett KL, Knapp S, Wenk MR, Superti-Furga G. The Lipid-Modifying Enzyme SMPDL3B Negatively Regulates Innate Immunity. Cell Rep. 2015 Jun 16. pii: S2211-1247(15)00504-5. doi: 10.1016/j.celrep.2015.05.006. [Epub ahead of print]

 

Fauster A, Rebsamen M, Huber KV, Bigenzahn JW, Stukalov A, Lardeau CH, Scorzoni S, Bruckner M, Gridling M, Parapatics K, Colinge J, Bennett KL, Kubicek S, Krautwald S, Linkermann A, Superti-Furga G.
A cellular screen identifies ponatinib and pazopanib as inhibitors of necroptosis. Cell Death Dis. 2015 May 21;6:e1767. doi: 10.1038/cddis. 2015.130.

 

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(2):789. doi: 10.15252/msb.20145664.

 

Herdy B, Karonitsch T, Vladimer GI, Tan CS, Stukalov A, Trefzer C, Bigenzahn JW, Theil T, Holinka J, Kiener HP, Colinge J, Bennett KL, Superti-Furga G. The RNA-binding protein HuR/ELAVL1 regulates IFN-β mRNA abundance and the type I IFN response. Eur J Immunol. 2015 Feb 12. doi: 10.1002/eji .201444979

 

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. 2014 Sep 29. doi: 10.1038/onc.2014.319. [Epub ahead of print]

 

Gridling M, Ficarro S, Breitwieser FP, Song L, Parapatics K, Colinge J, Haura EB, Marto J, Superti-Furga G, Bennett KL, Rix U. Identification of kinase inhibitor targets in the lung cancer microenvironment by chemical and phosphoproteomics. Mol Cancer Ther, 2014, pii: molcanther.0152.2014.


Sharif O, Gawish R, Warszawska JM, Martins R, Lakovits K, Hladik A, Doninger B, Brunner J, Korosec A, Schwarzenbacher RE, Berg T, Kralovics R, Colinge J, Mesteri I, Gilfillan S, Salmaggi A, Verschoor A, Colonna M, Knapp S. The triggering receptor expressed on myeloid cells 2 inhibits complement component 1q effector mechanisms and exerts detrimental effects during pneumococcal pneumonia. PLoS Pathog, 2014, 10(6):e1004167.


Maurer M, Müller AC, Parapatics K, Pickl WF, Wagner C, Rudashevskaya EL, Breitwieser FP, Colinge J, Garg K, Griss J, Bennett KL, Wagner SN. Comprehensive Comparative and Semiquantitative Proteome of a Very Low Number of Native and Matched Epstein-Barr-Virus-Transformed B Lymphocytes Infiltrating Human Melanoma. J Proteome Res, 2014, 13(6):2830-2845.


Salzer E, Kansu A, Sic H, Májek P, Ikincio?ullari A, Dogu FE, Prengemann NK, Santos-Valente E, Pickl WF, Bilic I, Ban SA, Kulo?lu Z, Demir AM, Ensari A, Colinge J, Rizzi M, Eibel H, Boztug K. Early-onset inflammatory bowel disease and common variable immunodeficiency-like disease caused by IL-21 deficiency. J Allergy Clin Immunol, 2014, pii: S0091-6749(14)00299-1.


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, pii: S1874-3919(14)00150-X. *corresponding authors

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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, 15:98.


Huber KV, Salah E, Radic B, Gridling M, Elkins JM, Stukalov A, Jemth AS, Göktürk C, Sanjiv K, Strömberg K, Pham T, Berglund UW, Colinge J, Bennett KL, Loizou JI, Helleday T, Knapp S, Superti-Furga G. Stereospecific targeting of MTH1 by (S)-crizotinib as an anticancer strategy. Nature, 2014, 508:222-227.


Boucheron N, Tschismarov R, Goeschl L, Moser MA, 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. CD4+ T cell lineage integrity is controlled by the histone deacetylases HDAC1 and HDAC2. Nat Immunol, 2014, 15:439-448.


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, 88:3464-3473.


Fritzsche R, Karra D, Bennett KL, Ang FY, Heraud-Farlow JE, Tolino M, Doyle M, Bauer KE, Thomas S, Planyavsky M, Arn E, Bakosova A, Jungwirth K, Hörmann A, Palfi Z, Sandholzer J, Schwarz M, Macchi P, Colinge J, Superti-Furga G, Kiebler MA: Interactome of Two Diverse RNA Granules Links mRNA Localization to Translational Repression in Neurons. Cell Rep, 2013, S2211-1247(13)00690-6.

 

Li J, Bennett K, Stukalov A, Fang B, Zhang G, Yoshida T, Okamoto I, Kim JY, Song L, Bai Y, Qian X, Rawal B, Schell M, Grebien F, Winter G, Rix U, Eschrich S, Colinge J, Koomen J, Superti-Furga G, Haura EB: Perturbation of the mutated EGFR interactome identifies vulnerabilities and resistance mechanisms. Mol Syst Biol, 2013, 9:705.


Bürckstümmer T, Banning C, Hainzl P, Schobesberger R, Kerzendorfer C, Pauler FM, Chen D, Them N, Schischlik F, Rebsamen M, Smida M, de la Cruz FF, Lapao A, Liszt M, Eizinger B, Guenzl PM, Blomen VA, Konopka T, Gapp B, Parapatics K, Maier B, Stöckl J, Fischl W, Salic S, Taba Casari MR, Knapp S, Bennett KL, Bock C, Colinge J, Kralovics R, Ammerer G, Casari G, Brummelkamp TR, Superti-Furga G, Nijman SM: A reversible gene trap collection empowers haploid genetics in human cells, Nat Methods, 2013, 10:965-971.


Rix1 U*, Colinge J*, Blatt K, Gridling M, Remsing Rix LL, Parapatics K, Cerny-Reiterer S, Burkard TR,  Jäger U, Melo JV, Bennett KL, Valent P, Superti-Furga G: A target-disease network model of second-generation BCR-ABL inhibitor action in Ph+ ALL, PLoS ONE, 2013, 8:e77155. *Equal contribution.


Giambruno R, Grebien F, Stukalov A, Knoll C, Planyavsky M, Rudashevskaya EL, Colinge J, Superti-Furga G, Bennett KL: Affinity Purification Strategies for Proteomic Analysis of Transcription Factor Complexes, J Proteome Res, 2013, 12:4018-4027.


Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis NA, Li T, Miteva 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 ZY, Badillo BG, Pawson T, Durocher D, Coulombe B, Aebersold R, Superti-Furga G, Colinge J, Heck AJ, Choi H, Gstaiger M, Mohammed S, Cristea IM, Bennett KL, Washburn MP, Raught B, Ewing RM, Gingras AC, Nesvizhskii AI: The CRAPome: a contaminant repository for affinity purification-mass spectrometry data, Nat Methods, 2013, 10:730-736.


Duernberger G, Burckstummer T, Huber K, Giambruno R, Doerks T, Karayel E, Burkard TR, Kaupe I, Muller AC, Schonegger 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, 14:R81 [Editor's Picks, highly accessed].


Chamrád I, Rix U, Stukalov A, Gridling M, Parapatics K, Müller AC, Altiok S, Colinge J, Superti-Furga G, Haura EB, Bennett KL: A Miniaturized Chemical Proteomic Approach for Target Profiling of Clinical Kinase Inhibitors in Tumor Biopsies, J Proteome Res, 2013, 12:4005-4017.


Borgdorff V, Rix U, Winter GE, Gridling M, Müller AC, Breitwieser FP, Wagner C, Colinge J, Bennett KL, Superti-Furga G, Wagner SN: A chemical biology approach identifies AMPK as a modulator of melanoma oncogene MITF, Oncogene, 2014.


Breitwieser FP, Colinge J: isobarPTM: A Software Tool for the Quantitative Analysis of Post-translationally Modified Proteins, J Proteomics, 2013, 90:77-84.


Varjosalo M, Sacco R, Stukalov A, van Drogen A, Planyavsky M, Hauri S, Aebersold R, Bennett KL, Colinge J, Gstaiger M, Superti-Furga G: Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS, Nat Methods, 2013, 10:307-314.


Rudashevskaya EL, Breitwieser FP, Huber ML, Colinge J, M?ller AC, Bennett KL: Multiple and sequential data acquisition method: an improved method for fragmentation and detection of cross-linked peptides on a hybrid linear trap quadrupole Orbitrap Velos mass spectrometer, Anal Chem, 2013, 85:1454-1461.


Pollreisz A, Funk M, Breitwieser FP, Parapatics K, Sacu S, Georgopoulos M, Dunavoelgyi R, Zlabinger GJ, Colinge J, Bennett KL, Schmidt-Erfurth U: Quantitative proteomics of aqueous and vitreous fluid from patients with idiopathic epiretinal membranes, Exp Eye Res. 2013, 108:48-58.

Winter GE, Rix U, Carlson SM, Gleixner KV, Grebien F, Gridling M, Müller AC, Breitwieser FP, Bilban M, Colinge J, Valent P, Bennett KL, White FM, Superti-Furga G: Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML. Nat Chem Biol, 2012, 8:905-12.


Pichlmair A, Kandasamy K, Alvisi G, Mulhern O, Sacco R, Habjan M, Binder M, Stefanovic A, Eberle CA, Goncalves A, Bürckstümmer T, Müller A, Fauster A, Holze C, Lindsten K, Goodbourn S, Kochs G, Weber F, Bartenschlager R, Bowie AG, Bennett KL,  Colinge J, Superti-Furga G: Viral immune modulators perturb the human molecular network by common and unique strategies, Nature, 2012, 487:486-90.


Milosevic JD, Puda A, Malcovati L, Berg T, Hofbauer M, Stukalov A, Klampfl T, Harutyunyan AS, Gisslinger H, Gisslinger B, Burjanivova T, Rumi E, Pietra D, Elena C, Vannucchi AM, Doubek M, Dvorakova D, Robesova B, Wieser R, Koller E, Suvajdzic N, Tomin D, Tosic N, Colinge J, Racil Z, Steurer M, Pavlovic S, Cazzola M, Kralovics R: Clinical significance of genetic aberrations in secondary acute myeloid leukemia, Am J Hematol, Epub.

 

Stukalov A, Superti-Furga G, Colinge J: Deconvolution of targeted protein-protein interaction maps. J Proteome Res, 2012, 11:4102-9.


Müller AC, Breitwieser FP, Fischer H, Schuster C, Brandt O, Colinge J, Superti-Furga G, Stingl G, Elbe-Bürger A, Bennett KL: A Comparative Proteomic Study of Human Skin Suction Blister Fluid from Healthy Individuals Using Immunodepletion and iTRAQ-Labelling. J Proteome Res, 2012, 11:3715-3727.


Colinge J,* Rix U, Bennett KL, Superti-Furga G: Systems biology analysis of protein-drug interactions. Proteomics Clin Appl 2012, 6(1-2):102-116.


Muellner MK, Uras IZ, Gapp BV, Kerzendorfer C, Smida M, Lechtermann H, Craig-Mueller N, Colinge J, Duernberger G, Nijman SM: A chemical-genetic screen reveals a mechanism of resistance to PI3K inhibitors in cancer. Nat Chem Biol 2011, 7(11):787-93.

 

Goncalves A, Bürckstümmer T, Dixit E, Scheicher R, Górna MW, Karayel E, Sugar C, Stukalov A, Berg T, Kralovics R, Planyavsky M, Bennett KL, Colinge J, Superti-Furga G: Functional dissection of the TBK1 molecular network. PLoS One 2011;6(9):e23971.

 

Winter GE, Rix U, Lissat A, Stukalov A, Müllner MK, Bennett KL, Colinge J, Nijman SM, Kubicek S, Kovar H, Kontny U, Superti-Furga G: An integrated chemical biology approach identifies specific vulnerability of Ewing's sarcoma to combined inhibition of Aurora kinases A and B. Mol Cancer Ther 2011, 10(10):1846-56.

 

Bennett KL, Funk M, Tschernutter M, Breitwieser FP, Planyavsky M, Ubaida Mohien C, Muller A, Trajanoski Z, Colinge J, Superti-Furga G, Schmidt-Erfurth U: Proteomic analysis of human cataract aqueous humour: Comparison of one-dimensional gel LCMS with two-dimensional LCMS of unlabelled and iTRAQ(R)-labelled specimens. J Proteomics 2011, 74(2):151-166.


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, 10(6):2758-2766.


Bennett KL, Funk M, Tschernutter M, Breitwieser FP, Planyavsky M, Mohien CU, Muller A, Trajanoski Z, Colinge J, Superti-Furga G, Schmidt-Erfurth U: Proteomic analysis of human cataract aqueous humour: Comparison of one-dimensional gel LCMS with two-dimensional LCMS of unlabelled and iTRAQ(R)-labelled specimens. J Proteomics 2011, 74(2):151-166.


Burkard TR, Planyavsky M, Kaupe I, Breitwieser FP, Buerckstuemmer T, Bennett KL, Superti-Furga G, Colinge J: Initial characterization of the human central proteome. BMC Syst Biol 2011, 5(1):17.

 

Haura EB, Muller A, Breitwieser FP, Li J, Grebien F, Colinge J, Bennett KL: Using iTRAQ combined with tandem affinity purification to enhance low-abundance proteins associated with somatically mutated EGFR core complexes in lung cancer. J Proteome Res 2011, 10(1):182-190.


Zivkovic A, Sharif O, Stich K, Doninger B, Biaggio M, Colinge J, Bilban M, Mesteri I, Hazemi P, Lemmens-Gruber R, Knapp S: TLR 2 and CD14 mediate innate immunity and lung inflammation to staphylococcal Panton-Valentine leukocidin in vivo. J Immunol 2011, 186(3):1608-1617.


Baumann CL, Aspalter IM, Sharif O, Pichlmair A, Bluml S, Grebien F, Bruckner M, Pasierbek P, Aumayr K, Planyavsky M, Bennett KL, Colinge J, Knapp S, Superti-Furga G: CD14 is a coreceptor of Toll-like receptors 7 and 9. J Exp Med 2010, 207(12):2689-2701.


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, 6(11):e1001001.


Colinge J, Rix U, Superti-Furga G: Novel global network scores to analyze kinase inhibitor profiles. In: 4th International conference on computational systems biology. Edited by Chen L, Zhang X, Shen B, Wu L, Wang Y, vol. 13. Suzhou, China: World Publishing Company; 2010: 305-313.


Li J, Rix U, Fang B, Bai Y, Edwards A, Colinge J, Bennett KL, Gao J, Song L, Eschrich S, Superti-Furga G, Koomen J, Haura EB: A chemical and phosphoproteomic characterization of dasatinib action in lung cancer. Nat Chem Biol 2010, 6(4):291-299.


Mohien CU, Hartler J, Breitwieser F, Rix U, Rix LR, 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, 10(14):2719-2722.


Brehme M, Hantschel O, Colinge J, Kaupe I, Planyavsky M, Kocher T, Mechtler K, Bennett KL, Superti-Furga G: Charting the molecular network of the drug target Bcr-Abl. Proc Natl Acad Sci U S A 2009, 106(18):7414-7419.


Burckstummer T, Baumann C, Bluml S, Dixit E, Durnberger G, Jahn H, Planyavsky M, Bilban M, Colinge J, Bennett KL, Superti-Furga G: An orthogonal proteomic-genomic screen identifies AIM2 as a cytoplasmic DNA sensor for the inflammasome. Nat Immunol 2009, 10(3):266-272.


Fernbach NV, Planyavsky M, Muller A, Breitwieser FP, Colinge J, Rix U, Bennett KL: Acid elution and one-dimensional shotgun analysis on an Orbitrap mass spectrometer: an application to drug affinity chromatography. J Proteome Res 2009, 8(10):4753-4765.


Remsing Rix LL, Rix U, Colinge J, Hantschel O, Bennett KL, Stranzl T, Muller A, Baumgartner C, Valent P, Augustin M, Till JH, Superti-Furga G: Global target profile of the kinase inhibitor bosutinib in primary chronic myeloid leukemia cells. Leukemia 2009, 23(3):477-485.


Rix U, Remsing Rix LL, Terker AS, Fernbach NV, Hantschel O, Planyavsky M, Breitwieser FP, Herrmann H, Colinge J, Bennett KL, Augustin M, Till JH, Heinrich MC, Valent P, Superti-Furga G: A comprehensive target selectivity survey of the BCR-ABL kinase inhibitor INNO-406 by kinase profiling and chemical proteomics in chronic myeloid leukemia cells. Leukemia 2009, 24(1):44-50.


Hantschel O, Gstoettenbauer A, Colinge J, Kaupe I, Bilban M, Burkard TR, Valent P, Superti-Furga G: The chemokine interleukin-8 and the surface activation protein CD69 are markers for Bcr-Abl activity in chronic myeloid leukemia. Mol Oncol 2008, 2(3):272-281.


Colinge J: Peptide fragment intensity statistical modeling. Anal Chem 2007, 79(19):7286-7290.


Colinge J, Bennett KL: Introduction to computational proteomics. PLoS Comput Biol 2007, 3(7):e114.


Hantschel O, Rix U, Schmidt U, Burckstummer T, Kneidinger M, Schutze G, Colinge J, Bennett KL, Ellmeier W, Valent P, Superti-Furga G: The Btk tyrosine kinase is a major target of the Bcr-Abl inhibitor dasatinib. Proc Natl Acad Sci U S A 2007, 104(33):13283-13288.


Pitzer E, Masselot A, Colinge J: Assessing peptide de novo sequencing algorithms performance on large and diverse data sets. Proteomics 2007, 7(17):3051-3054.


Rix U, Hantschel O, Durnberger G, Remsing Rix LL, Planyavsky M, Fernbach NV, Kaupe I, Bennett KL, Valent P, Colinge J, Kocher T, Superti-Furga G: Chemical proteomic profiles of the BCR-ABL inhibitors imatinib, nilotinib, and dasatinib reveal novel kinase and nonkinase targets. Blood 2007, 110(12):4055-4063.


Colinge J, Masselot A, Carbonell P, Appel RD: InSilicoSpectro: an open-source proteomics library. J Proteome Res 2006, 5(3):619-624.

 

Colinge J, Chiappe D, Lagache S, Moniatte M, Bougueleret L: Differential proteomics via probabilistic peptide identification scores. Anal Chem 2005, 77(2):596-606.


Colinge J, Cusin I, Reffas S, Mahe E, Niknejad A, Rey PA, Mattou H, Moniatte M, Bougueleret L: Experiments in searching small proteins in unannotated large eukaryotic genomes. J Proteome Res 2005, 4(1):167-174.


Allet N, Barrillat N, Baussant T, Boiteau C, Botti P, Bougueleret L, Budin N, Canet D, Carraud S, Chiappe D, Christmann N, Colinge J, Cusin I, Dafflon N, Depresle B, Fasso I, Frauchiger P, Gaertner H, Gleizes A, Gonzalez-Couto E, Jeandenans C, Karmime A, Kowall T, Lagache S, Mahé E, Masselot A, Mattou H, Moniatte M, Niknejad A, Paolini M, Perret F, Pinaud N, Ranno F, Raimondi S, Reffas S, Regamey PO, Rey PA, Rodriguez-Tomé P, Rose K, Rossellat G, Saudrais C, Schmidt C, Villain M, Zwahlen C: In vitro and in silico processes to identify differentially expressed proteins. Proteomics 2004, 4(8):2333-2351.


Colinge J, Masselot A, Cusin I, Mahe E, Niknejad A, Argoud-Puy G, Reffas S, Bederr N, Gleizes A, Rey PA, Bougueleret L: High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics. Proteomics 2004, 4(7):1977-1984.


Magnin J, Masselot A, Menzel C, Colinge J: OLAV-PMF: a novel scoring scheme for high-throughput peptide mass fingerprinting. J Proteome Res 2004, 3(1):55-60.


Rose K, Bougueleret L, Baussant T, Bohm G, Botti P, Colinge J, Cusin I, Gaertner H, Gleizes A, Heller M, Jimenez S, Johnson A, Kussmann M, Menin L, Menzel C, Ranno F, Rodriguez-Tome P, Rogers J, Saudrais C, Villain M, Wetmore D, Bairoch A, Hochstrasser D: Industrial-scale proteomics: from liters of plasma to chemically synthesized proteins. Proteomics 2004, 4(7):2125-2150.


Colinge J, Magnin J, Dessingy T, Giron M, Masselot A: Improved peptide charge state assignment. Proteomics 2003, 3(8):1434-1440.


Colinge J, Masselot A, Giron M, Dessingy T, Magnin J: OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics 2003, 3(8):1454-1463.


Ghersa P, Gelati M, Colinge J, Feger G, Power C, Papoian R, Salmaggi A: MIG--differential gene expression in mouse brain endothelial cells. Neuroreport 2002, 13(1):9-14.


Colinge J, Feger G: Detecting the impact of sequencing errors on SAGE data. Bioinformatics 2001, 17(9):840-842.


Walchli S, Colinge J, Hooft van Huijsduijnen R: MetaBlasts: tracing protein tyrosine phosphatase gene family roots from Man to Drosophila melanogaster and Caenorhabditis elegans genomes. Gene 2000, 253(2):137-143.


Colinge J, Rappaz J: A strongly nonlinear problem arising in glaciology. Mathem Modelling Numer Analysis 1999, 33:395-406.

 

Blatter H, Clarke GKC, Colinge J: Stress and velocity fields in glaciers : Part II. Sliding and basal stress distribution. J Glaciol 1998, 44:457-466.


Colinge J, Blatter H: Stress and velocity fields in glaciers : Part I. Finite differences schemes for higher order glacier models. J Glaciol 1998, 44:448-456.

 

Brevets

System and method for scoring peptide matches. Colinge J, Masselot A. US 7409296 (2008), priority 2003.

 

Use of SARP-1 for the treatment and/or Prevention of Scleroderma. Plater-Zyberk, C., Power, C., Colinge, J., EP 1411970 (2004), US 2005113291 (2005), priority 2000.

Discrete substructural analysis . Church, D., Colinge, J., EP 1366440 (2003), US 2004083060 (2004), and other countries, priority 2000.

 

A method for the identification of gene transcripts with improved efficiency in the treatment of errors. Colinge, J., Feger, G., EP 1113382 (2001), US 2003138794 (2003), priority 1999.

 

Automated method for identifying related biomolecular sequences. Hooft van Huijsduijnen, R., Colinge, J., EP 1232282B1 (2005), priority 1999.

 

© Institut de Recherche en Cancérologie de Montpellier - 2011 - Tous droits réservés - Mentions légales - Conception : ID Alizés