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Articles 2016

(2016) The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic Acids Res 44:D27-37 [PMID:26615188]

Bady P, Delorenzi M, Hegi ME (2016) Sensitivity Analysis of the MGMT-STP27 Model and Impact of Genetic and Epigenetic Context to Predict the MGMT Methylation Status in Gliomas and Other Tumors. J Mol Diagn 18:350-361 [PMID:26927331]

Barras D, Missiaglia E, Wirapati P, Sieber OM, Jorissen RN, Love C, Molloy PL, Jones IT, McLaughlin S, Gibbs P, Guinney J, Simon IM, Roth A, Bosman FT, Tejpar S, Delorenzi M (2016) BRAF V600E mutant colorectal cancer subtypes based on gene expression. Clin Cancer Res : [PMID:27354468]

Buhl IK, Gerster S, Delorenzi M, Jensen T, Jensen PB, Bosman F, Tejpar S, Roth A, Brunner N, Hansen A, Knudsen S (2016) Cell Line Derived 5-FU and Irinotecan Drug-Sensitivity Profiles Evaluated in Adjuvant Colon Cancer Trial Data. PLoS One 11:e0155123 [PMID:27171152]

Cardoso F, van't Veer LJ, Bogaerts J, Slaets L, Viale G, Delaloge S, Pierga JY, Brain E, Causeret S, DeLorenzi M, Glas AM, Golfinopoulos V, Goulioti T, Knox S, Matos E, Meulemans B, Neijenhuis PA, Nitz U, Passalacqua R, Ravdin P, Rubio IT, Saghatchian M, Smilde TJ, Sotiriou C, Stork L, Straehle C, Thomas G, Thompson AM, van der Hoeven JM, Vuylsteke P, Bernards R, Tryfonidis K, Rutgers E, Piccart M (2016) 70-Gene Signature as an Aid to Treatment Decisions in Early-Stage Breast Cancer. N Engl J Med 375:717-729 [PMID:27557300]

Mathias A, Perriard G, Canales M, Soneson C, Delorenzi M, Schluep M, Du Pasquier RA (2016) Increased ex vivo antigen presentation profile of B cells in multiple sclerosis. Mult Scler : [PMID:27503907]

Neubert NJ, Soneson C, Barras D, Baumgaertner P, Rimoldi D, Delorenzi M, Fuertes Marraco SA, Speiser DE (2016) A Well-Controlled Experimental System to Study Interactions of Cytotoxic T Lymphocytes with Tumor Cells. Front Immunol 7:326 [PMID:27625650]

Nygard SB, Vainer B, Nielsen SL, Bosman F, Tejpar S, Roth A, Delorenzi M, Brunner N, Budinska E (2016) DNA Topoisomerase I Gene Copy Number and mRNA Expression Assessed as Predictive Biomarkers for Adjuvant Irinotecan in Stage II/III Colon Cancer. Clin Cancer Res 22:1621-1631 [PMID:26542057]

Schell MJ, Yang M, Missiaglia E, Delorenzi M, Soneson C, Yue B, Nebozhyn MV, Loboda A, Bloom G, Yeatman TJ (2016) A Composite Gene Expression Signature Optimizes Prediction of Colorectal Cancer Metastasis and Outcome. Clin Cancer Res 22:734-745 [PMID:26446941]

Scholz G, Jandus C, Zhang L, Grandclement C, Lopez-Mejia IC, Soneson C, Delorenzi M, Fajas L, Held W, Dormond O, Romero P (2016) Modulation of mTOR Signalling Triggers the Formation of Stem Cell-like Memory T Cells. EBioMedicine 4:50-61 [PMID:26981571]

Towhidi L, Khodadadi D, Maimari N, Pedrigi RM, Ip H, Kis Z, Kwak BR, Petrova TW, Delorenzi M, Krams R (2016) Comparison between direct and reverse electroporation of cells in situ: a simulation study. Physiol Rep 4: [PMID:27009275]

Utzschneider DT, Alfei F, Roelli P, Barras D, Chennupati V, Darbre S, Delorenzi M, Pinschewer DD, Zehn D (2016) High antigen levels induce an exhausted phenotype in a chronic infection without impairing T cell expansion and survival. J Exp Med 213:1819-1834 [PMID:27455951]

Vallois D, Dobay MP, Morin RD, Lemonnier F, Missiaglia E, Juilland M, Iwaszkiewicz J, Fataccioli V, Bisig B, Roberti A, Grewal J, Bruneau J, Fabiani B, Martin A, Bonnet C, Michielin O, Jais JP, Figeac M, Bernard OA, Delorenzi M, Haioun C, Tournilhac O, Thome M, Gascoyne RD, Gaulard P, de Leval L (2016) Activating mutations in genes related to TCR signaling in angioimmunoblastic and other follicular helper T-cell-derived lymphomas. Blood 128:1490-1502 [PMID:27369867]

Vecchione L, Gambino V, Raaijmakers J, Schlicker A, Fumagalli A, Russo M, Villanueva A, Beerling E, Bartolini A, Mollevi DG, El-Murr N, Chiron M, Calvet L, Nicolazzi C, Combeau C, Henry C, Simon IM, Tian S, in 't Veld S, D'ario G, Mainardi S, Beijersbergen RL, Lieftink C, Linn S, Rumpf-Kienzl C, Delorenzi M, Wessels L, Salazar R, Di Nicolantonio F, Bardelli A, van Rheenen J, Medema RH, Tejpar S, Bernards R (2016) A Vulnerability of a Subset of Colon Cancers with Potential Clinical Utility. Cell 165:317-330 [PMID:27058664]

Yan P, Klingbiel D, Saridaki Z, Ceppa P, Curto M, McKee TA, Roth A, Tejpar S, Delorenzi M, Bosman FT, Fiocca R (2016) Reduced Expression of SMAD4 Is Associated with Poor Survival in Colon Cancer. Clin Cancer Res 22:3037-3047 [PMID:26861460]

Articles 2015

De Meyer T, Bady P, Trooskens G, Kurscheid S, Bloch J, Kros JM, Hainfellner JA, Stupp R, Delorenzi M, Hegi ME, Van Criekinge W (2015) Genome-wide DNA methylation detection by MethylCap-seq and Infinium HumanMethylation450 BeadChips: an independent large-scale comparison. Sci Rep 5:15375 [PMID:26482909]

Fischer U, Forster M, Rinaldi A, Risch T, Sungalee S, Warnatz HJ, Bornhauser B, Gombert M, Kratsch C, Stutz AM, Sultan M, Tchinda J, Worth CL, Amstislavskiy V, Badarinarayan N, Baruchel A, Bartram T, Basso G, Canpolat C, Cario G, Cave H, Dakaj D, Delorenzi M, Dobay MP, Eckert C, Ellinghaus E, Eugster S, Frismantas V, Ginzel S, Haas OA, Heidenreich O, Hemmrich-Stanisak G, Hezaveh K, Holl JI, Hornhardt S, Husemann P, Kachroo P, Kratz CP, Kronnie GT, Marovca B, Niggli F, McHardy AC, Moorman AV, Panzer-Grumayer R, Petersen BS, Raeder B, Ralser M, Rosenstiel P, Schafer D, Schrappe M, Schreiber S, Schutte M, Stade B, Thiele R, Weid Nv, Vora A, Zaliova M, Zhang L, Zichner T, Zimmermann M, Lehrach H, Borkhardt A, Bourquin JP, Franke A, Korbel JO, Stanulla M, Yaspo ML (2015) Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options. Nat Genet 47:1020-1029 [PMID:26214592]

Franzini A, Baty F, Macovei II, Durr O, Droege C, Betticher D, Grigoriu BD, Klingbiel D, Zappa F, Brutsche MH (2015) Gene Expression Signatures Predictive of Bevacizumab/Erlotinib Therapeutic Benefit in Advanced Nonsquamous Non-Small Cell Lung Cancer Patients (SAKK 19/05 trial). Clin Cancer Res 21:5253-5263 [PMID:25922429]

Fuertes Marraco SA, Soneson C, Cagnon L, Gannon PO, Allard M, Abed Maillard S, Montandon N, Rufer N, Waldvogel S, Delorenzi M, Speiser DE (2015) Long-lasting stem cell-like memory CD8+ T cells with a naive-like profile upon yellow fever vaccination. Sci Transl Med 7:282ra48 [PMID:25855494]

Fuertes Marraco SA, Soneson C, Delorenzi M, Speiser DE (2015) Genome-wide RNA profiling of long-lasting stem cell-like memory CD8 T cells induced by Yellow Fever vaccination in humans. Genom Data 5:297-301 [PMID:26484272]

Guinney J, Dienstmann R, Wang X, de Reynies A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, Bot BM, Morris JS, Simon IM, Gerster S, Fessler E, De Sousa E Melo F, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam GC, Broom B, Boige V, Perez-Villamil B, Laderas T, Salazar R, Gray JW, Hanahan D, Tabernero J, Bernards R, Friend SH, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L, Tejpar S (2015) The consensus molecular subtypes of colorectal cancer. Nat Med 21:1350-1356 [PMID:26457759]

Hingorani P, Missiaglia E, Shipley J, Anderson JR, Triche TJ, Delorenzi M, Gastier-Foster J, Wing M, Hawkins DS, Skapek SX (2015) Clinical Application of Prognostic Gene Expression Signature in Fusion Gene-Negative Rhabdomyosarcoma: A Report from the Children's Oncology Group. Clin Cancer Res 21:4733-4739 [PMID:26473193]

Jensen NF, Stenvang J, Beck MK, Hanakova B, Belling KC, Do KN, Viuff B, Nygard SB, Gupta R, Rasmussen MH, Tarpgaard LS, Hansen TP, Budinska E, Pfeiffer P, Bosman F, Tejpar S, Roth A, Delorenzi M, Andersen CL, Romer MU, Brunner N, Moreira JM (2015) Establishment and characterization of models of chemotherapy resistance in colorectal cancer: Towards a predictive signature of chemoresistance. Mol Oncol 9:1169-1185 [PMID:25759163]

Klingbiel D, Saridaki Z, Roth AD, Bosman FT, Delorenzi M, Tejpar S (2015) Prognosis of stage II and III colon cancer treated with adjuvant 5-fluorouracil or FOLFIRI in relation to microsatellite status: results of the PETACC-3 trial. Ann Oncol 26:126-132 [PMID:25361982]

Kurscheid S, Bady P, Sciuscio D, Samarzija I, Shay T, Vassallo I, Criekinge WV, Daniel RT, van den Bent MJ, Marosi C, Weller M, Mason WP, Domany E, Stupp R, Delorenzi M, Hegi ME (2015) Chromosome 7 gain and DNA hypermethylation at the HOXA10 locus are associated with expression of a stem cell related HOX-signature in glioblastoma. Genome Biol 16:16 [PMID:25622821]

Moor AE, Anderle P, Cantu C, Rodriguez P, Wiedemann N, Baruthio F, Deka J, Andre S, Valenta T, Moor MB, Gyorffy B, Barras D, Delorenzi M, Basler K, Aguet M (2015) BCL9/9L-beta-catenin Signaling is Associated With Poor Outcome in Colorectal Cancer. EBioMedicine 2:1932-1943 [PMID:26844272]

Paquet ER, Cui J, Davidson D, Pietrosemoli N, Hassan HH, Tsofack SP, Maltais A, Hallett MT, Delorenzi M, Batist G, Aloyz R, Lebel M (2015) A 12-gene signature to distinguish colon cancer patients with better clinical outcome following treatment with 5-fluorouracil or FOLFIRI. J Pathol Clin Res 1:160-172 [PMID:27499901]

Sabine A, Bovay E, Demir CS, Kimura W, Jaquet M, Agalarov Y, Zangger N, Scallan JP, Graber W, Gulpinar E, Kwak BR, Makinen T, Martinez-Corral I, Ortega S, Delorenzi M, Kiefer F, Davis MJ, Djonov V, Miura N, Petrova TV (2015) FOXC2 and fluid shear stress stabilize postnatal lymphatic vasculature. J Clin Invest 125:3861-3877 [PMID:26389677]

Sinicrope FA, Shi Q, Smyrk TC, Thibodeau SN, Dienstmann R, Guinney J, Bot BM, Tejpar S, Delorenzi M, Goldberg RM, Mahoney M, Sargent DJ, Alberts SR (2015) Molecular markers identify subtypes of stage III colon cancer associated with patient outcomes. Gastroenterology 148:88-99 [PMID:25305506]

Articles 2014

Barras D, Chevalier N, Zoete V, Dempsey R, Lapouge K, Olayioye MA, Michielin O, Widmann C (2014) A WXW motif is required for the anticancer activity of the TAT-RasGAP317-326 peptide. J Biol Chem 289:23701-23711 [PMID:25008324]

Barras D, Lorusso G, Ruegg C, Widmann C (2014) Inhibition of cell migration and invasion mediated by the TAT-RasGAP317-326 peptide requires the DLC1 tumor suppressor. Oncogene 33:5163-5172 [PMID:24213569]

Barras D, Widmann C (2014) GAP-independent functions of DLC1 in metastasis. Cancer Metastasis Rev 33:87-100 [PMID:24338004]

Belmont PJ, Budinska E, Jiang P, Sinnamon MJ, Coffee E, Roper J, Xie T, Rejto PA, Derkits S, Sansom OJ, Delorenzi M, Tejpar S, Hung KE, Martin ES (2014) Cross-species analysis of genetically engineered mouse models of MAPK-driven colorectal cancer identifies hallmarks of the human disease. Dis Model Mech 7:613-623 [PMID:24742783]

Bonhoure N, Bounova G, Bernasconi D, Praz V, Lammers F, Canella D, Willis IM, Herr W, Hernandez N, Delorenzi M (2014) Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Res 24:1157-1168 [PMID:24709819]

Bossard C, Dobay MP, Parrens M, Lamant L, Missiaglia E, Haioun C, Martin A, Fabiani B, Delarue R, Tournilhac O, Delorenzi M, Gaulard P, de Leval L (2014) Immunohistochemistry as a valuable tool to assess CD30 expression in peripheral T-cell lymphomas: high correlation with mRNA levels. Blood 124:2983-2986 [PMID:25224410]

Di Narzo AF, Tejpar S, Rossi S, Yan P, Popovici V, Wirapati P, Budinska E, Xie T, Estrella H, Pavlicek A, Mao M, Martin E, Scott W, Bosman FT, Roth A, Delorenzi M (2014) Test of four colon cancer risk-scores in formalin fixed paraffin embedded microarray gene expression data. J Natl Cancer Inst 106: [PMID:25246611]

Favre P, Bapaume L, Bossolini E, Delorenzi M, Falquet L, Reinhardt D (2014) A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants. BMC Plant Biol 14:333 [PMID:25465219 ]

Gilardi F, Migliavacca E, Naldi A, Baruchet M, Canella D, Le Martelot G, Guex N, Desvergne B (2014) Genome-wide analysis of SREBP1 activity around the clock reveals its combined dependency on nutrient and circadian signals. PLoS Genet 10:e1004155 [PMID:24603613]

Joerger M, Baty F, Fruh M, Droege C, Stahel RA, Betticher DC, von Moos R, Ochsenbein A, Pless M, Gautschi O, Rothschild S, Brauchli P, Klingbiel D, Zappa F, Brutsche M (2014) Circulating microRNA profiling in patients with advanced non-squamous NSCLC receiving bevacizumab/erlotinib followed by platinum-based chemotherapy at progression (SAKK 19/05). Lung Cancer 85:306-313 [PMID:24928469]

Missiaglia E, Jacobs B, D'Ario G, Di Narzo AF, Soneson C, Budinska E, Popovici V, Vecchione L, Gerster S, Yan P, Roth AD, Klingbiel D, Bosman FT, Delorenzi M, Tejpar S (2014) Distal and proximal colon cancers differ in terms of molecular, pathological, and clinical features. Ann Oncol 25:1995-2001 [PMID:25057166]

Ozdemir BC, Hensel J, Secondini C, Wetterwald A, Schwaninger R, Fleischmann A, Raffelsberger W, Poch O, Delorenzi M, Temanni R, Mills IG, van der Pluijm G, Thalmann GN, Cecchini MG (2014) The molecular signature of the stroma response in prostate cancer-induced osteoblastic bone metastasis highlights expansion of hematopoietic and prostate epithelial stem cell niches. PLoS One 9:e114530 [PMID:25485970]

Ragusa S, Cheng J, Ivanov KI, Zangger N, Ceteci F, Bernier-Latmani J, Milatos S, Joseph JM, Tercier S, Bouzourene H, Bosman FT, Letovanec I, Marra G, Gonzalez M, Cammareri P, Sansom OJ, Delorenzi M, Petrova TV (2014) PROX1 promotes metabolic adaptation and fuels outgrowth of Wnt(high) metastatic colon cancer cells. Cell Rep 8:1957-1973 [PMID:25242332]

Schou JV, Rossi S, Jensen BV, Nielsen DL, Pfeiffer P, Hogdall E, Yilmaz M, Tejpar S, Delorenzi M, Kruhoffer M, Johansen JS (2014) miR-345 in metastatic colorectal cancer: a non-invasive biomarker for clinical outcome in non-KRAS mutant patients treated with 3rd line cetuximab and irinotecan. PLoS One 9:e99886 [PMID:24940606]

Sistigu A, Yamazaki T, Vacchelli E, Chaba K, Enot DP, Adam J, Vitale I, Goubar A, Baracco EE, Remedios C, Fend L, Hannani D, Aymeric L, Ma Y, Niso-Santano M, Kepp O, Schultze JL, Tuting T, Belardelli F, Bracci L, La Sorsa V, Ziccheddu G, Sestili P, Urbani F, Delorenzi M, Lacroix-Triki M, Quidville V, Conforti R, Spano JP, Pusztai L, Poirier-Colame V, Delaloge S, Penault-Llorca F, Ladoire S, Arnould L, Cyrta J, Dessoliers MC, Eggermont A, Bianchi ME, Pittet M, Engblom C, Pfirschke C, Preville X, Uze G, Schreiber RD, Chow MT, Smyth MJ, Proietti E, Andre F, Kroemer G, Zitvogel L (2014) Cancer cell-autonomous contribution of type I interferon signaling to the efficacy of chemotherapy. Nat Med 20:1301-1309 [PMID:25344738]

Soneson C, Gerster S, Delorenzi M (2014) Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation. PLoS One 9:e100335 [PMID:24967636]

Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S, Bougueleret L, Bucher P, Delorenzi M, Lane L, Le Mercier P, Lisacek F, Michielin O, Palagi PM, Rougemont J, Schwede T, von Mering C, van Nimwegen E, Walther D, Xenarios I, Zavolan M, Zdobnov EM, Zoete V, Appel RD (2014) Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. Nucleic Acids Res 42:W436-41 [PMID:24792157]

Tremblay AM, Missiaglia E, Galli GG, Hettmer S, Urcia R, Carrara M, Judson RN, Thway K, Nadal G, Selfe JL, Murray G, Calogero RA, De Bari C, Zammit PS, Delorenzi M, Wagers AJ, Shipley J, Wackerhage H, Camargo FD (2014) The Hippo transducer YAP1 transforms activated satellite cells and is a potent effector of embryonal rhabdomyosarcoma formation. Cancer Cell 26:273-287 [PMID:25087979]

Articles 2013

Budinska E, Popovici V, Tejpar S, D'Ario G, Lapique N, Sikora KO, Di Narzo AF, Yan P, Hodgson JG, Weinrich S, Bosman F, Roth A, Delorenzi M (2013) Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer. J Pathol 231:63-76 [PMID:23836465]

De Vriendt V, De Roock W, Di Narzo AF, Tian S, Biesmans B, Jacobs B, Budinska E, Sagaert X, Rossi S, D'Ario G, Delorenzi M, Simon I, Vecchione L, Tejpar S (2013) DUSP 4 expression identifies a subset of colorectal cancer tumors that differ in MAPK activation, regardless of the genotype. Biomarkers 18:516-524 [PMID:23875912]

Ivanov KI, Agalarov Y, Valmu L, Samuilova O, Liebl J, Houhou N, Maby-El Hajjami H, Norrmen C, Jaquet M, Miura N, Zangger N, Yla-Herttuala S, Delorenzi M, Petrova TV (2013) Phosphorylation regulates FOXC2-mediated transcription in lymphatic endothelial cells. Mol Cell Biol 33:3749-3761 [PMID:23878394]

Popovici V, Budinska E, Bosman FT, Tejpar S, Roth AD, Delorenzi M (2013) Context-dependent interpretation of the prognostic value of BRAF and KRAS mutations in colorectal cancer. BMC Cancer 13:439 [PMID:24073892]

Soneson C, Delorenzi M (2013) A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics 14:91 [PMID:23497356]

Articles 2012

Anghel SI, Correa-Rocha R, Budinska E, Boligan KF, Abraham S, Colombetti S, Fontao L, Mariotti A, Rimoldi D, Ghanem GE, Fisher DE, Levy F, Delorenzi M, Piguet V (2012) Breast cancer suppressor candidate-1 (BCSC-1) is a melanoma tumor suppressor that down regulates MITF. Pigment Cell Melanoma Res 25:482-487 [PMID:22594792]

Anghel SI, Correa-Rocha R, Budinska E, Boligan KF, Abraham S, Colombetti S, Fontao L, Mariotti A, Rimoldi D, Ghanem GE, Fisher DE, Levy F, Delorenzi M, Piguet V (2012) Breast cancer suppressor candidate-1 (BCSC-1) is a melanoma tumor suppressor that down regulates MITF. Pigment Cell Melanoma Res 25:482-487 [PMID:22594792 ]

Bady P, Diserens AC, Castella V, Kalt S, Heinimann K, Hamou MF, Delorenzi M, Hegi ME (2012) DNA fingerprinting of glioma cell lines and considerations on similarity measurements. Neuro Oncol 14:701-711 [PMID:22570425]

Bady P, Sciuscio D, Diserens AC, Bloch J, van den Bent MJ, Marosi C, Dietrich PY, Weller M, Mariani L, Heppner FL, Mcdonald DR, Lacombe D, Stupp R, Delorenzi M, Hegi ME (2012) MGMT methylation analysis of glioblastoma on the Infinium methylation BeadChip identifies two distinct CpG regions associated with gene silencing and outcome, yielding a prediction model for comparisons across datasets, tumor grades, and CIMP-status. Acta Neuropathol 124:547-560 [PMID:22810491]

Canella D, Bernasconi D, Gilardi F, LeMartelot G, Migliavacca E, Praz V, Cousin P, Delorenzi M, Hernandez N (2012) A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver. Genome Res 22:666-680 [PMID:22287103]

Carrascosa C, Obula RG, Missiaglia E, Lehr HA, Delorenzi M, Frattini M, Ruegg C, Mariotti A (2012) MFG-E8/lactadherin regulates cyclins D1/D3 expression and enhances the tumorigenic potential of mammary epithelial cells. Oncogene 31:1521-1532 [PMID:21841820]

Christensen J, El-Gebali S, Natoli M, Sengstag T, Delorenzi M, Bentz S, Bouzourene H, Rumbo M, Felsani A, Siissalo S, Hirvonen J, Vila MR, Saletti P, Aguet M, Anderle P (2012) Defining new criteria for selection of cell-based intestinal models using publicly available databases. BMC Genomics 13:274 [PMID:22726358]

Desmedt C, Majjaj S, Kheddoumi N, Singhal SK, Haibe-Kains B, El Ouriaghli F, Chaboteaux C, Michiels S, Lallemand F, Journe F, Duvillier H, Loi S, Quackenbush J, Dekoninck S, Blanpain C, Lagneaux L, Houhou N, Delorenzi M, Larsimont D, Piccart M, Sotiriou C (2012) Characterization and clinical evaluation of CD10+ stroma cells in the breast cancer microenvironment. Clin Cancer Res 18:1004-1014 [PMID:22235100]

Hegi ME, Janzer RC, Lambiv WL, Gorlia T, Kouwenhoven MC, Hartmann C, von Deimling A, Martinet D, Besuchet Schmutz N, Diserens AC, Hamou MF, Bady P, Weller M, van den Bent MJ, Mason WP, Mirimanoff RO, Stupp R, Mokhtari K, Wesseling P (2012) Presence of an oligodendroglioma-like component in newly diagnosed glioblastoma identifies a pathogenetically heterogeneous subgroup and lacks prognostic value: central pathology review of the EORTC_26981/NCIC_CE.3 trial. Acta Neuropathol 123:841-852 [PMID:22249618]

Le Martelot G, Canella D, Symul L, Migliavacca E, Gilardi F, Liechti R, Martin O, Harshman K, Delorenzi M, Desvergne B, Herr W, Deplancke B, Schibler U, Rougemont J, Guex N, Hernandez N, Naef F (2012) Genome-wide RNA polymerase II profiles and RNA accumulation reveal kinetics of transcription and associated epigenetic changes during diurnal cycles. PLoS Biol 10:e1001442 [PMID:23209382]

Missiaglia E, Williamson D, Chisholm J, Wirapati P, Pierron G, Petel F, Concordet JP, Thway K, Oberlin O, Pritchard-Jones K, Delattre O, Delorenzi M, Shipley J (2012) PAX3/FOXO1 fusion gene status is the key prognostic molecular marker in rhabdomyosarcoma and significantly improves current risk stratification. J Clin Oncol 30:1670-1677 [PMID:22454413]

Popovici V, Budinska E, Tejpar S, Weinrich S, Estrella H, Hodgson G, Van Cutsem E, Xie T, Bosman FT, Roth AD, Delorenzi M (2012) Identification of a poor-prognosis BRAF-mutant-like population of patients with colon cancer. J Clin Oncol 30:1288-1295 [PMID:22393095]

Rossi S, Di Narzo AF, Mestdagh P, Jacobs B, Bosman FT, Gustavsson B, Majoie B, Roth A, Vandesompele J, Rigoutsos I, Delorenzi M, Tejpar S (2012) microRNAs in colon cancer: a roadmap for discovery. FEBS Lett 586:3000-3007 [PMID:23166923]

Roth AD, Delorenzi M, Tejpar S, Yan P, Klingbiel D, Fiocca R, d'Ario G, Cisar L, Labianca R, Cunningham D, Nordlinger B, Bosman F, Van Cutsem E (2012) Integrated analysis of molecular and clinical prognostic factors in stage II/III colon cancer. J Natl Cancer Inst 104:1635-1646 [PMID:23104212]

Sartore-Bianchi A, Delorenzi M, Gagnon-Kugler T, Rousseau C, Batist G (2012) New frontiers in therapeutic resistance in cancer. Expert Rev Anticancer Ther 12:877-879 [PMID:22845402]

Shchepachev V, Wischnewski H, Missiaglia E, Soneson C, Azzalin CM (2012) Mpn1, mutated in poikiloderma with neutropenia protein 1, is a conserved 3'-to-5' RNA exonuclease processing U6 small nuclear RNA. Cell Rep 2:855-865 [PMID:23022480]

Tian S, Roepman P, Popovici V, Michaut M, Majewski I, Salazar R, Santos C, Rosenberg R, Nitsche U, Mesker WE, Bruin S, Tejpar S, Delorenzi M, Bernards R, Simon I (2012) A robust genomic signature for the detection of colorectal cancer patients with microsatellite instability phenotype and high mutation frequency. J Pathol 228:586-595 [PMID:22926706]

Xie T, D' Ario G, Lamb JR, Martin E, Wang K, Tejpar S, Delorenzi M, Bosman FT, Roth AD, Yan P, Bougel S, Di Narzo AF, Popovici V, Budinska E, Mao M, Weinrich SL, Rejto PA, Hodgson JG (2012) A comprehensive characterization of genome-wide copy number aberrations in colorectal cancer reveals novel oncogenes and patterns of alterations. PLoS One 7:e42001 [PMID:22860045]

Zaric J, Joseph JM, Tercier S, Sengstag T, Ponsonnet L, Delorenzi M, Ruegg C (2012) Identification of MAGI1 as a tumor-suppressor protein induced by cyclooxygenase-2 inhibitors in colorectal cancer cells. Oncogene 31:48-59 [PMID:21666716]

Articles 2011

Barras D, Widmann C (2011) Promises of apoptosis-inducing peptides in cancer therapeutics. Curr Pharm Biotechnol 12:1153-1165 [PMID:21470140]

Chaignat E, Yahya-Graison EA, Henrichsen CN, Chrast J, Schutz F, Pradervand S, Reymond A (2011) Copy number variation modifies expression time courses. Genome Res 21:106-113 [PMID:21084671]

Hegi ME, Diserens AC, Bady P, Kamoshima Y, Kouwenhoven MC, Delorenzi M, Lambiv WL, Hamou MF, Matter MS, Koch A, Heppner FL, Yonekawa Y, Merlo A, Frei K, Mariani L, Hofer S (2011) Pathway analysis of glioblastoma tissue after preoperative treatment with the EGFR tyrosine kinase inhibitor gefitinib--a phase II trial. Mol Cancer Ther 10:1102-1112 [PMID:21471286]

Lambiv WL, Vassallo I, Delorenzi M, Shay T, Diserens AC, Misra A, Feuerstein B, Murat A, Migliavacca E, Hamou MF, Sciuscio D, Burger R, Domany E, Stupp R, Hegi ME (2011) The Wnt inhibitory factor 1 (WIF1) is targeted in glioblastoma and has a tumor suppressing function potentially by induction of senescence. Neuro Oncol 13:736-747 [PMID:21642372]

Planche A, Bacac M, Provero P, Fusco C, Delorenzi M, Stehle JC, Stamenkovic I (2011) Identification of prognostic molecular features in the reactive stroma of human breast and prostate cancer. PLoS One 6:e18640 [PMID:21611158 ]

Popovici V, Budinska E, Delorenzi M (2011) Rgtsp: a generalized top scoring pairs package for class prediction. Bioinformatics 27:1729-1730 [PMID:21505033]

Rossi S, Christ-Neumann M, Ruping S, Buffa F, Wegener D, McVie G, Coveney P, Graf N, Delorenzi M (2011) p-Medicine: From data sharing and integration via VPH models to personalized medicine. Ecancermedicalscience 5:218 [PMID:22276060]

Tejpar S, Saridaki Z, Delorenzi M, Bosman F, Roth AD (2011) Microsatellite instability, prognosis and drug sensitivity of stage II and III colorectal cancer: more complexity to the puzzle. J Natl Cancer Inst 103:841-844 [PMID:21597023]

Wirapati P, Forner K, Delgado-Vega A, Alarcon-Riquelme M, Delorenzi M, Wojcik J (2011) Detecting epistasis with restricted response patterns in pairs of biallelic loci. Ann Hum Genet 75:133-145 [PMID:21118193]

Articles 2010

Antonov J, Popovici V, Delorenzi M, Wirapati P, Baltzer A, Oberli A, Thurlimann B, Giobbie-Hurder A, Viale G, Altermatt HJ, Aebi S, Jaggi R (2010) Molecular risk assessment of BIG 1-98 participants by expression profiling using RNA from archival tissue. BMC Cancer 10:37 [PMID:20144231]

Berger F, De Meulder B, Gaigneaux A, Depiereux S, Bareke E, Pierre M, De Hertogh B, Delorenzi M, Depiereux E (2010) Functional analysis: evaluation of response intensities--tailoring ANOVA for lists of expression subsets. BMC Bioinformatics 11:510 [PMID:20942918]

Bouchal P, Struharova I, Budinska E, Sedo O, Vyhlidalova T, Zdrahal Z, van Spanning R, Kucera I (2010) Unraveling an FNR based regulatory circuit in Paracoccus denitrificans using a proteomics-based approach. Biochim Biophys Acta 1804:1350-1358 [PMID:20116460]

De Roock W, Claes B, Bernasconi D, De Schutter J, Biesmans B, Fountzilas G, Kalogeras KT, Kotoula V, Papamichael D, Laurent-Puig P, Penault-Llorca F, Rougier P, Vincenzi B, Santini D, Tonini G, Cappuzzo F, Frattini M, Molinari F, Saletti P, De Dosso S, Martini M, Bardelli A, Siena S, Sartore-Bianchi A, Tabernero J, Macarulla T, Di Fiore F, Gangloff AO, Ciardiello F, Pfeiffer P, Qvortrup C, Hansen TP, Van Cutsem E, Piessevaux H, Lambrechts D, Delorenzi M, Tejpar S (2010) Effects of KRAS, BRAF, NRAS, and PIK3CA mutations on the efficacy of cetuximab plus chemotherapy in chemotherapy-refractory metastatic colorectal cancer: a retrospective consortium analysis. Lancet Oncol 11:753-762 [PMID:20619739]

Deka J, Wiedemann N, Anderle P, Murphy-Seiler F, Bultinck J, Eyckerman S, Stehle JC, Andre S, Vilain N, Zilian O, Robine S, Delorenzi M, Basler K, Aguet M (2010) Bcl9/Bcl9l are critical for Wnt-mediated regulation of stem cell traits in colon epithelium and adenocarcinomas. Cancer Res 70:6619-6628 [PMID:20682801]

Harewood L, Schutz F, Boyle S, Perry P, Delorenzi M, Bickmore WA, Reymond A (2010) The effect of translocation-induced nuclear reorganization on gene expression. Genome Res 20:554-564 [PMID:20212020]

Jedlickova H, Hlubinka M, Pavlik T, Semradova V, Budinska E, Vlasin Z (2010) Bullous pemphigoid and internal diseases - A case-control study. Eur J Dermatol 20:96-101 [PMID:19797038]

Liechti R, Csardi G, Bergmann S, Schutz F, Sengstag T, Boj SF, Servitja JM, Ferrer J, Van Lommel L, Schuit F, Klinger S, Thorens B, Naamane N, Eizirik DL, Marselli L, Bugliani M, Marchetti P, Lucas S, Holm C, Jongeneel CV, Xenarios I (2010) EuroDia: a beta-cell gene expression resource. Database (Oxford) 2010:baq024 [PMID:20940178]

LopezJimenez N, Gerber S, Popovici V, Mirza S, Copren K, Ta L, Shaw GM, Trueb B, Slavotinek AM (2010) Examination of FGFRL1 as a candidate gene for diaphragmatic defects at chromosome 4p16.3 shows that Fgfrl1 null mice have reduced expression of Tpm3, sarcomere genes and Lrtm1 in the diaphragm. Hum Genet 127:325-336 [PMID:20024584]

Popovici V, Chen W, Gallas BG, Hatzis C, Shi W, Samuelson FW, Nikolsky Y, Tsyganova M, Ishkin A, Nikolskaya T, Hess KR, Valero V, Booser D, Delorenzi M, Hortobagyi GN, Shi L, Symmans WF, Pusztai L (2010) Effect of training-sample size and classification difficulty on the accuracy of genomic predictors. Breast Cancer Res 12:R5 [PMID:20064235]

Ricard G, Molina J, Chrast J, Gu W, Gheldof N, Pradervand S, Schutz F, Young JI, Lupski JR, Reymond A, Walz K (2010) Phenotypic consequences of copy number variation: insights from Smith-Magenis and Potocki-Lupski syndrome mouse models. PLoS Biol 8:e1000543 [PMID:21124890]

Roth AD, Tejpar S, Delorenzi M, Yan P, Fiocca R, Klingbiel D, Dietrich D, Biesmans B, Bodoky G, Barone C, Aranda E, Nordlinger B, Cisar L, Labianca R, Cunningham D, Van Cutsem E, Bosman F (2010) Prognostic role of KRAS and BRAF in stage II and III resected colon cancer: results of the translational study on the PETACC-3, EORTC 40993, SAKK 60-00 trial. J Clin Oncol 28:466-474 [PMID:20008640]

Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD Jr, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukherjee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD (2010) The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol 28:827-838 [PMID:20676074]

Soulard A, Cremonesi A, Moes S, Schutz F, Jeno P, Hall MN (2010) The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates. Mol Biol Cell 21:3475-3486 [PMID:20702584]

Tejpar S, Bertagnolli M, Bosman F, Lenz HJ, Garraway L, Waldman F, Warren R, Bild A, Collins-Brennan D, Hahn H, Harkin DP, Kennedy R, Ilyas M, Morreau H, Proutski V, Swanton C, Tomlinson I, Delorenzi M, Fiocca R, Van Cutsem E, Roth A (2010) Prognostic and predictive biomarkers in resected colon cancer: current status and future perspectives for integrating genomics into biomarker discovery. Oncologist 15:390-404 [PMID:20350999]

Vasikova A, Belickova M, Budinska E, Cermak J (2010) A distinct expression of various gene subsets in CD34+ cells from patients with early and advanced myelodysplastic syndrome. Leuk Res 34:1566-1572 [PMID:20303173]

Articles 2009

Bengtsson H, Wirapati P, Speed TP (2009) A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. Bioinformatics 25:2149-2156 [PMID:19535535]

Djojosubroto M, Bollotte F, Wirapati P, Radtke F, Stamenkovic I, Arsenijevic Y (2009) Chromosomal number aberrations and transformation in adult mouse retinal stem cells in vitro. Invest Ophthalmol Vis Sci 50:5975-5987 [PMID:19628750]

Farmer P, Bonnefoi H, Anderle P, Cameron D, Wirapati P, Becette V, Andre S, Piccart M, Campone M, Brain E, Macgrogan G, Petit T, Jassem J, Bibeau F, Blot E, Bogaerts J, Aguet M, Bergh J, Iggo R, Delorenzi M (2009) A stroma-related gene signature predicts resistance to neoadjuvant chemotherapy in breast cancer. Nat Med 15:68-74 [PMID:19122658]

Meier P, Antonov J, Zbinden R, Kuhn A, Zbinden S, Gloekler S, Delorenzi M, Jaggi R, Seiler C (2009) Non-invasive gene-expression-based detection of well-developed collateral function in individuals with and without coronary artery disease. Heart 95:900-908 [PMID:18728069]

Murat A, Migliavacca E, Hussain SF, Heimberger AB, Desbaillets I, Hamou MF, Ruegg C, Stupp R, Delorenzi M, Hegi ME (2009) Modulation of angiogenic and inflammatory response in glioblastoma by hypoxia. PLoS One 4:e5947 [PMID:19536297]

Norrmen C, Ivanov KI, Cheng J, Zangger N, Delorenzi M, Jaquet M, Miura N, Puolakkainen P, Horsley V, Hu J, Augustin HG, Yla-Herttuala S, Alitalo K, Petrova TV (2009) FOXC2 controls formation and maturation of lymphatic collecting vessels through cooperation with NFATc1. J Cell Biol 185:439-457 [PMID:19398761]

Parisi F, Sonderegger B, Wirapati P, Delorenzi M, Naef F (2009) Relationship between estrogen receptor alpha location and gene induction reveals the importance of downstream sites and cofactors. BMC Genomics 10:381 [PMID:19689805]

Popovici V, Goldstein DR, Antonov J, Jaggi R, Delorenzi M, Wirapati P (2009) Selecting control genes for RT-QPCR using public microarray data. BMC Bioinformatics 10:42 [PMID:19187545]

Pradervand S, Weber J, Thomas J, Bueno M, Wirapati P, Lefort K, Dotto GP, Harshman K (2009) Impact of normalization on miRNA microarray expression profiling. RNA 15:493-501 [PMID:19176604]

Articles 2008

Brembilla NC, Weber J, Rimoldi D, Pradervand S, Schutz F, Pantaleo G, Ruegg C, Quadroni M, Harshman K, Doucey MA (2008) c-Cbl expression levels regulate the functional responses of human central and effector memory CD4 T cells. Blood 112:652-660 [PMID:18505781]

Colzani M, Schutz F, Potts A, Waridel P, Quadroni M (2008) Relative protein quantification by isobaric SILAC with immonium ion splitting (ISIS). Mol Cell Proteomics 7:927-937 [PMID:18165257]

Desmedt C, Haibe-Kains B, Wirapati P, Buyse M, Larsimont D, Bontempi G, Delorenzi M, Piccart M, Sotiriou C (2008) Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clin Cancer Res 14:5158-5165 [PMID:18698033]

Guipponi M, Toh MY, Tan J, Park D, Hanson K, Ballana E, Kwong D, Cannon PZ, Wu Q, Gout A, Delorenzi M, Speed TP, Smith RJ, Dahl HH, Petersen M, Teasdale RD, Estivill X, Park WJ, Scott HS (2008) An integrated genetic and functional analysis of the role of type II transmembrane serine proteases (TMPRSSs) in hearing loss. Hum Mutat 29:130-141 [PMID:17918732]

Kuhn A, Luthi-Carter R, Delorenzi M (2008) Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics 9:26 [PMID:18201381]

Loi S, Haibe-Kains B, Desmedt C, Wirapati P, Lallemand F, Tutt AM, Gillet C, Ellis P, Ryder K, Reid JF, Daidone MG, Pierotti MA, Berns EM, Jansen MP, Foekens JA, Delorenzi M, Bontempi G, Piccart MJ, Sotiriou C (2008) Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics 9:239 [PMID:18498629]

Michaud J, Simpson KM, Escher R, Buchet-Poyau K, Beissbarth T, Carmichael C, Ritchie ME, Schutz F, Cannon P, Liu M, Shen X, Ito Y, Raskind WH, Horwitz MS, Osato M, Turner DR, Speed TP, Kavallaris M, Smyth GK, Scott HS (2008) Integrative analysis of RUNX1 downstream pathways and target genes. BMC Genomics 9:363 [PMID:18671852]

Monnier Y, Farmer P, Bieler G, Imaizumi N, Sengstag T, Alghisi GC, Stehle JC, Ciarloni L, Andrejevic-Blant S, Moeckli R, Mirimanoff RO, Goodman SL, Delorenzi M, Ruegg C (2008) CYR61 and alphaVbeta5 integrin cooperate to promote invasion and metastasis of tumors growing in preirradiated stroma. Cancer Res 68:7323-7331 [PMID:18794119]

Murat A, Migliavacca E, Gorlia T, Lambiv WL, Shay T, Hamou MF, de Tribolet N, Regli L, Wick W, Kouwenhoven MC, Hainfellner JA, Heppner FL, Dietrich PY, Zimmer Y, Cairncross JG, Janzer RC, Domany E, Delorenzi M, Stupp R, Hegi ME (2008) Stem cell-related "self-renewal" signature and high epidermal growth factor receptor expression associated with resistance to concomitant chemoradiotherapy in glioblastoma. J Clin Oncol 26:3015-3024 [PMID:18565887]

Oberli A, Popovici V, Delorenzi M, Baltzer A, Antonov J, Matthey S, Aebi S, Altermatt HJ, Jaggi R (2008) Expression profiling with RNA from formalin-fixed, paraffin-embedded material. BMC Med Genomics 1:9 [PMID:18423048]

Pradervand S, Paillusson A, Thomas J, Weber J, Wirapati P, Hagenbuchle O, Harshman K (2008) Affymetrix Whole-Transcript Human Gene 1.0 ST array is highly concordant with standard 3' expression arrays. Biotechniques 44:759-762 [PMID:18476829]

Sauvain MO, Dorr AP, Stevenson B, Quazzola A, Naef F, Wiznerowicz M, Schutz F, Jongeneel V, Duboule D, Spitz F, Trono D (2008) Genotypic features of lentivirus transgenic mice. J Virol 82:7111-7119 [PMID:18463153]

Schutz F, Delorenzi M (2008) MAMOT: hidden Markov modeling tool. Bioinformatics 24:1399-1400 [PMID:18440999]

Vlassenbroeck I, Califice S, Diserens AC, Migliavacca E, Straub J, Di Stefano I, Moreau F, Hamou MF, Renard I, Delorenzi M, Flamion B, DiGuiseppi J, Bierau K, Hegi ME (2008) Validation of real-time methylation-specific PCR to determine O6-methylguanine-DNA methyltransferase gene promoter methylation in glioma. J Mol Diagn 10:332-337 [PMID:18556773]

Voelter V, Diserens AC, Moulin A, Nagel G, Yan P, Migliavacca E, Rimoldi D, Hamou MF, Kaina B, Leyvraz S, Hegi ME (2008) Infrequent promoter methylation of the MGMT gene in liver metastases from uveal melanoma. Int J Cancer 123:1215-1218 [PMID:18546261]

Willi-Monnerat S, Migliavacca E, Surdez D, Delorenzi M, Luthi-Carter R, Terskikh AV (2008) Comprehensive spatiotemporal transcriptomic analyses of the ganglionic eminences demonstrate the uniqueness of its caudal subdivision. Mol Cell Neurosci 37:845-856 [PMID:18316204]

Wirapati P, Sotiriou C, Kunkel S, Farmer P, Pradervand S, Haibe-Kains B, Desmedt C, Ignatiadis M, Sengstag T, Schutz F, Goldstein DR, Piccart M, Delorenzi M (2008) Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures. Breast Cancer Res 10:R65 [PMID:18662380]

Articles 2007

Bonnefoi H, Potti A, Delorenzi M, Mauriac L, Campone M, Tubiana-Hulin M, Petit T, Rouanet P, Jassem J, Blot E, Becette V, Farmer P, Andre S, Acharya CR, Mukherjee S, Cameron D, Bergh J, Nevins JR, Iggo RD (2007) Validation of gene signatures that predict the response of breast cancer to neoadjuvant chemotherapy: a substudy of the EORTC 10994/BIG 00-01 clinical trial. Lancet Oncol 8:1071-1078 [PMID:18024211]

Desmedt C, Piette F, Loi S, Wang Y, Lallemand F, Haibe-Kains B, Viale G, Delorenzi M, Zhang Y, d'Assignies MS, Bergh J, Lidereau R, Ellis P, Harris AL, Klijn JG, Foekens JA, Cardoso F, Piccart MJ, Buyse M, Sotiriou C (2007) Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series. Clin Cancer Res 13:3207-3214 [PMID:17545524]

Kapp E, Schutz F (2007) Overview of tandem mass spectrometry (MS/MS) database search algorithms. Curr Protoc Protein Sci Chapter 25:Unit25.2 [PMID:18429324]

Kuhn A, Goldstein DR, Hodges A, Strand AD, Sengstag T, Kooperberg C, Becanovic K, Pouladi MA, Sathasivam K, Cha JH, Hannan AJ, Hayden MR, Leavitt BR, Dunnett SB, Ferrante RJ, Albin R, Shelbourne P, Delorenzi M, Augood SJ, Faull RL, Olson JM, Bates GP, Jones L, Luthi-Carter R (2007) Mutant huntingtin's effects on striatal gene expression in mice recapitulate changes observed in human Huntington's disease brain and do not differ with mutant huntingtin length or wild-type huntingtin dosage. Hum Mol Genet 16:1845-1861 [PMID:17519223]

Loi S, Haibe-Kains B, Desmedt C, Lallemand F, Tutt AM, Gillet C, Ellis P, Harris A, Bergh J, Foekens JA, Klijn JG, Larsimont D, Buyse M, Bontempi G, Delorenzi M, Piccart MJ, Sotiriou C (2007) Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. J Clin Oncol 25:1239-1246 [PMID:17401012]

Parisi F, Wirapati P, Naef F (2007) Identifying synergistic regulation involving c-Myc and sp1 in human tissues. Nucleic Acids Res 35:1098-1107 [PMID:17264126]

Prandini P, Deutsch S, Lyle R, Gagnebin M, Delucinge Vivier C, Delorenzi M, Gehrig C, Descombes P, Sherman S, Dagna Bricarelli F, Baldo C, Novelli A, Dallapiccola B, Antonarakis SE (2007) Natural gene-expression variation in Down syndrome modulates the outcome of gene-dosage imbalance. Am J Hum Genet 81:252-263 [PMID:17668376]

Runne H, Kuhn A, Wild EJ, Pratyaksha W, Kristiansen M, Isaacs JD, Regulier E, Delorenzi M, Tabrizi SJ, Luthi-Carter R (2007) Analysis of potential transcriptomic biomarkers for Huntington's disease in peripheral blood. Proc Natl Acad Sci U S A 104:14424-14429 [PMID:17724341]

Schmid CD, Sengstag T, Bucher P, Delorenzi M (2007) MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data. Nucleic Acids Res 35:W201-5 [PMID:17526516]

Vuaroqueaux V, Urban P, Labuhn M, Delorenzi M, Wirapati P, Benz CC, Flury R, Dieterich H, Spyratos F, Eppenberger U, Eppenberger-Castori S (2007) Low E2F1 transcript levels are a strong determinant of favorable breast cancer outcome. Breast Cancer Res 9:R33 [PMID:17535433]

Articles 2006

Bacac M, Migliavacca E, Stehle JC, McKee T, Delorenzi M, Coindre JM, Guillou L, Stamenkovic I (2006) A gene expression signature that distinguishes desmoid tumours from nodular fasciitis. J Pathol 208:543-553 [PMID:16440290]

Buyse M, Loi S, van't Veer L, Viale G, Delorenzi M, Glas AM, d'Assignies MS, Bergh J, Lidereau R, Ellis P, Harris A, Bogaerts J, Therasse P, Floore A, Amakrane M, Piette F, Rutgers E, Sotiriou C, Cardoso F, Piccart MJ (2006) Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J Natl Cancer Inst 98:1183-1192 [PMID:16954471]

Gotthardt D, Blancheteau V, Bosserhoff A, Ruppert T, Delorenzi M, Soldati T (2006) Proteomics fingerprinting of phagosome maturation and evidence for the role of a Galpha during uptake. Mol Cell Proteomics 5:2228-2243 [PMID:16926386]

Hodges A, Strand AD, Aragaki AK, Kuhn A, Sengstag T, Hughes G, Elliston LA, Hartog C, Goldstein DR, Thu D, Hollingsworth ZR, Collin F, Synek B, Holmans PA, Young AB, Wexler NS, Delorenzi M, Kooperberg C, Augood SJ, Faull RL, Olson JM, Jones L, Luthi-Carter R (2006) Regional and cellular gene expression changes in human Huntington's disease brain. Hum Mol Genet 15:965-977 [PMID:16467349]

Jagannathan V, Roulet E, Delorenzi M, Bucher P (2006) HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites. Nucleic Acids Res 34:D90-4 [PMID:16381982]

Leupin N, Kuhn A, Hugli B, Grob TJ, Jaggi R, Tobler A, Delorenzi M, Fey MF (2006) Gene expression profiling reveals consistent differences between clinical samples of human leukaemias and their model cell lines. Br J Haematol 135:520-523 [PMID:17061979]

Menzel O, Migliaccio M, Goldstein DR, Dahoun S, Delorenzi M, Rufer N (2006) Mechanisms regulating the proliferative potential of human CD8+ T lymphocytes overexpressing telomerase. J Immunol 177:3657-3668 [PMID:16951325]

Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, Nordgren H, Farmer P, Praz V, Haibe-Kains B, Desmedt C, Larsimont D, Cardoso F, Peterse H, Nuyten D, Buyse M, Van de Vijver MJ, Bergh J, Piccart M, Delorenzi M (2006) Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst 98:262-272 [PMID:16478745]

Urban P, Vuaroqueaux V, Labuhn M, Delorenzi M, Wirapati P, Wight E, Senn HJ, Benz C, Eppenberger U, Eppenberger-Castori S (2006) Increased expression of urokinase-type plasminogen activator mRNA determines adverse prognosis in ErbB2-positive primary breast cancer. J Clin Oncol 24:4245-4253 [PMID:16963728]

Articles 2005

Anderle P, Sengstag T, Mutch DM, Rumbo M, Praz V, Mansourian R, Delorenzi M, Williamson G, Roberts MA (2005) Changes in the transcriptional profile of transporters in the intestine along the anterior-posterior and crypt-villus axes. BMC Genomics 6:69 [PMID:15882471]

Beckmann JS, Maurer F, Delorenzi M, Falquet L (2005) On ubiquitin ligases and cancer. Hum Mutat 25:507-512 [PMID:15880746]

Farmer P, Bonnefoi H, Becette V, Tubiana-Hulin M, Fumoleau P, Larsimont D, Macgrogan G, Bergh J, Cameron D, Goldstein D, Duss S, Nicoulaz AL, Brisken C, Fiche M, Delorenzi M, Iggo R (2005) Identification of molecular apocrine breast tumours by microarray analysis. Oncogene 24:4660-4671 [PMID:15897907]

Jongeneel CV, Delorenzi M, Iseli C, Zhou D, Haudenschild CD, Khrebtukova I, Kuznetsov D, Stevenson BJ, Strausberg RL, Simpson AJ, Vasicek TJ (2005) An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res 15:1007-1014 [PMID:15998913]

Articles 2004

de Kruijf WJM, Sengstag T, de Haas, DW, van der Hagen THJJ (2004) Experimental thermohydraulic stability map of a Freon-12 Boiling Water Reactor facility with high exit friction. Nuclear Engineering and Design 229:75-80

Anderle P, Farmer P, Berger A, Roberts MA (2004) Nutrigenomic approach to understanding the mechanisms by which dietary long-chain fatty acids induce gene signals and control mechanisms involved in carcinogenesis. Nutrition 20:103-108 [PMID:14698023]

Bourgon R, Delorenzi M, Sargeant T, Hodder AN, Crabb BS, Speed TP (2004) The serine repeat antigen (SERA) gene family phylogeny in Plasmodium: the impact of GC content and reconciliation of gene and species trees. Mol Biol Evol 21:2161-2171 [PMID:15306658]

Schmid CD, Praz V, Delorenzi M, Perier R, Bucher P (2004) The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Nucleic Acids Res 32:D82-5 [PMID:14681364]

de Fourmestraux V, Neubauer H, Poussin C, Farmer P, Falquet L, Burcelin R, Delorenzi M, Thorens B (2004) Transcript profiling suggests that differential metabolic adaptation of mice to a high fat diet is associated with changes in liver to muscle lipid fluxes. J Biol Chem 279:50743-50753 [PMID:15377667]

Articles ≤2003

Migliavacca E, Carrupt PA, Testa B (1997) Theoretical Parameters to Characterize Antioxidants. Part 1. The Case of Vitamin E and Analogs Helvetica Chimica Acta 80(5):1613-1626

Migliavacca E, Ancerewicz J, Carrupt PA, Testa B (1998) Theoretical Parameters to Characterize Antioxidants. Part 1. The Cases of Melatonin and Carvedilol Helvetica Chimica Acta 81(7):1337-1348

Salvi A, Bruhlmann C, Migliavacca E, Carrupt PA, Hostettmann K, Testa B (2002) Protein Protection by Antioxidants: Development of a Convenient Assay and Structure-Activity Relationships of Natural Polyphenols Helvetica Chimica Acta 85(3):867-881

Godard S, Getz G, Delorenzi M, Farmer P, Kobayashi H, Desbaillets I, Nozaki M, Diserens AC, Hamou MF, Dietrich PY, Regli L, Janzer RC, Bucher P, Stupp R, de Tribolet N, Domany E, Hegi ME (2003) Classification of human astrocytic gliomas on the basis of gene expression: a correlated group of genes with angiogenic activity emerges as a strong predictor of subtypes. Cancer Res 63:6613-6625 [PMID:14583454]

Hodder AN, Drew DR, Epa VC, Delorenzi M, Bourgon R, Miller SK, Moritz RL, Frecklington DF, Simpson RJ, Speed TP, Pike RN, Crabb BS (2003) Enzymic, phylogenetic, and structural characterization of the unusual papain-like protease domain of Plasmodium falciparum SERA5. J Biol Chem 278:48169-48177 [PMID:13679369]

Migliavacca E (2003) Applied introduction to multivariate methods used in drug discovery. Mini Rev Med Chem 3:831-848 [PMID:14529502]

Delorenzi M, Sexton A, Shams-Eldin H, Schwarz RT, Speed T, Schofield L (2002) Genes for glycosylphosphatidylinositol toxin biosynthesis in Plasmodium falciparum. Infect Immun 70:4510-4522 [PMID:12117963]

Delorenzi M, Speed T (2002) An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. Bioinformatics 18:617-625 [PMID:12016059]

Miller SK, Good RT, Drew DR, Delorenzi M, Sanders PR, Hodder AN, Speed TP, Cowman AF, de Koning-Ward TF, Crabb BS (2002) A subset of Plasmodium falciparum SERA genes are expressed and appear to play an important role in the erythrocytic cycle. J Biol Chem 277:47524-47532 [PMID:12228245]

Migliavacca E, Adzhubei AA, Peitsch MC (2001) MDB: a database system utilizing automatic construction of modules and STAR-derived universal language. Bioinformatics 17:1047-1052 [PMID:11724733]

Triglia T, Thompson J, Caruana SR, Delorenzi M, Speed T, Cowman AF (2001) Identification of proteins from Plasmodium falciparum that are homologous to reticulocyte binding proteins in Plasmodium vivax. Infect Immun 69:1084-1092 [PMID:11160005]

Ancerewicz J, Migliavacca E, Carrupt PA, Testa B, Bree F, Zini R, Tillement JP, Labidalle S, Guyot D, Chauvet-Monges AM, Crevat A, Le Ridant A (1998) Structure-property relationships of trimetazidine derivatives and model compounds as potential antioxidants. Free Radic Biol Med 25:113-120 [PMID:9655529]

Handoko HY, Wirapati PJ, Sudoyo HA, Sitepu M, Marzuki S (1998) Meiotic breakpoint mapping of a proposed X linked visual loss susceptibility locus in Leber's hereditary optic neuropathy. J Med Genet 35:668-671 [PMID:9719375]

Sengstag T, Binggeli N, Baldereschi A (1995) Anomalies in the pressure dependence of the effective charge in cubic semiconductors. Phys Rev B Condens Matter 52:R8613-R8616 [PMID:9979907]

Delorenzi M, Bienz M (1990) Expression of Abdominal-B homeoproteins in Drosophila embryos. Development 108:323-329 [PMID:1972049]

DeLorenzi M, Ali N, Saari G, Henry C, Wilcox M, Bienz M (1988) Evidence that the Abdominal-B r element function is conferred by a trans-regulatory homeoprotein. EMBO J 7:3223-3231 [PMID:2903049]

Thali M, Muller MM, DeLorenzi M, Matthias P, Bienz M (1988) Drosophila homoeotic genes encode transcriptional activators similar to mammalian OTF-2. Nature 336:598-601 [PMID:2904655]

De Lorenzi M, Rohrer U, Birnstiel ML (1986) Analysis of a sea urchin gene cluster coding for the small nuclear U7 RNA, a rare RNA species implicated in the 3' editing of histone precursor mRNAs. Proc Natl Acad Sci U S A 83:3243-3247 [PMID:3458178]

Oral Presentations

Presenter is underlined.

Talks 2008

Wirapati P. "Co-analyzing datasets from multiple cancer studies: incorporating hierarchical models into differential expression, prediction and cluster analysis" June 4 2008, Statistical Challenges in Genome and Translational Research, Banff, [Abstract]

Sengstag T GridR: a grid-enabled R environment, BioConductor Developer Workshop, Lausanne, April 24-25, 2008

Talks 2007

Wirapati, P. "Computational and statistical issues in co-analyzing gene expression data from multiple studies and platforms". 10 October 2007, Nederlands Kanker Instituut Seminar. [Abstract]

Wirapati, P. Integrative Analysis of Genomic Properties. Statistics for Biomolecular Data Integration and Modeling - Workshop, Ascona 2007. [PDF]

S. Matthey, V. Popovici, J.Antonov, A. Oberli, A. Baltzer, M. Delorenzi, H.J. Altermatt, R. Jaggi, "Successful measurement of gene expression by quantitative PCR and DNA chip analysis with RNA derived of FFPE material", 3rd International qPCR Symposium, March 2007, Munich, Germany

Farmer P, Bonnefoi H, Anderle P, Cameron D, Wirapati P, Becette V, André S, Piccart M, Campone M, Tubiana-Hulin M, MacGrogan G, Petit T, Jassem J, Rouanet P, Blot E, Bogaerts J, Bergh J, Iggo R and Delorenzi M. A stroma-related gene signature predicts resistance to epirubicin-containing neoadjuvant chemotherapy in breast cancer, 30th Annual San Antonio Breast Cancer Symposium

Delorenzi M, (Integrative) analysis of breast cancer gene-expression profiles: toward an understanding of (prognosis) signatures, Bugnon Seminar Series, Lausanne, October 2007

Delorenzi M, (Integrative) analysis of breast cancer gene-expression profiles: toward an understanding of (prognosis) signatures, Invited Seminar, Ipsogen, Marseille, December 3, 2007

D. Wegener, T. Sengstag, S. Sfakianakis, S. Rueping, A. Assi, "GridR: An R-based grid-enabled tool for data analysis in ACGT." 3rd IEEE International Conference on e-Science and Grid Computing, Bangalore, India, December 10-13, 2007

Talks 2006

Christine Desmedt, Fanny Piette, Fatima Cardoso, Yixin Wang, Sherene Loi, Françoise Lallemand, Jan Klijn, Benjamin Haibe-Kains, Giuseppe Viale, Mauro Delorenzi, Yi Zhang, Mahasti Saghatchian d'Assignies, Jonas Bergh, Rosette Lidereau, Paul Ellis, Adrian Harris, John Foekens,Marc Buyse, Martine J. Piccart, Christos Sotiriou. TRANSBIG multi-centre independent validation of the Rotterdam 76-geneprognostic signature for patients with node-negative breast cancer. European Breast Cancer Conference, Nice, March 2006.

Christos Sotiriou et al. . Is genomic grading killing histological grading?. European Breast Cancer Conference, Nice, March 2006.

H. Bonnefoi , P. Farmer, V. Becette, M. Piccart, M. Campone, L. Mauriac, J. Jassem, J. Bergh, D. Cameron, and R. Iggo. Stroma related genes signature predicts sensitivity to epirubicin containing neoadjuvant chemotherapy in breast cancer. A microarray study of 102 patients included in EORTC 10994/BIG 00-01 trial. European Breast Cancer Conference, Nice, March 2006.

Anastasia Murat, Eugenia Migliavacca, Tal Shay, Roger Stupp, Eytan Domany, Mauro Delorenzi, and Monika E. Hegi. Molecular profiles of gliomas, mechanistic insights and associations with outcome. ICTR 2006 Third International Conference on Translational Research and Pre-Clinical Strategies in Radiation Oncology, Lugano, March 12-15, 2006

Anastasia Murat, Wanyu L. Lambiv, Eugenia Migliavacca, Tal Shay, Anjan Misra, Burt Feuerstein, Robert C. Janzer, Roger Stupp, Eytan Domany, Mauro Delorenzi, and Monika E. Hegi. Molecular Profiles of Gliomas, Mechanistic Insights and Associations with Outcome. XXIst INTERNATIONAL WINTER MEETING ST. MORITZ, Growth And Death In The Nervous System, MARCH 22– 26 2006

M. Hegi, A. Murat, W. Lambiv, T. Shay, E. Migliavacca, A. Misra, B. Feuerstein, N. de Tribolet, A.-C. Diserens, *M. Delorenzi*, E. Domany, R. Stupp on behalf of the EORTC & NCIC Cooperative Groups. Molecular tumor profiles, mechanistic insights, and associations with outcome in patients treated with TMZ&RT within the EORTC trial for newly diagnosed glioblastoma. International Brain Tumor Research And Therapy Meeting (ASILOMAR), Silverado, USA, April 26-30, 2006

Monika E. Hegi, Anastasia Murat, Wanyu L. Lambiv, Tal Shay, Eugenia Migliavacca, Thierry Gorlia, Anjan Misra, Burt Feuerstein, Nicolas de Tribolet, Annie-Claire Diserens, Mauro Delorenzi, Eytan Domany, and Roger Stupp on behalf of the EORTC & NCIC Cooperative Groups. Predicting Tumor Response to Treatment. Molecular Genetic Studies. Annual Meeting of the British Neuro Oncology Society (BNOS), London, June 21-23, 2006

Wanyu L. Lambiv, Tal Shay, Annie-Claire Diserens Anjan Misra, Mauro Delorenzi, Burt Feuerstein, Eytan Domany, Roger Stupp, Monika E. Hegi. Relationships Among Genomic Copy Number Status, Gene Expression, Outcome and Response to therapy in Glioblastoma. 6th ISREC Conference on Cancer Research, Lausanne, October 11-13, 2006.

Monika E. Hegi, Anastasia Murat, Wanyu L. Lambiv, Eugenia Migliavacca, Thierry Gorlia, Tal Shay, Anjan Misra, Burt Feuerstein, Robert C. Janzer, Eytan Domany, Mauro Delorenzi, Roger Stupp. Molecular Profiling Of Glioblastoma To Individualize Future Therapies. Japan Neurosurgical Society, 65th Annual Meeting, Kyoto, Japan, October 18-20, 2006

A. Murat, E. Migliavacca, T. Shay, R. Stupp, E. Domany, M. Delorenzi, and M. E. Hegi. Gene expression profiles of glioblastoma, mechanistic insights and associations with outcome. ELTEM Neurogenomics Course 2006, Biozentrum Basel, November 27-December 1, 2006.

Wirapati P. "GlimEx: a unified approach to gene expression analysis." SIB Retreat, Leysin 31 January 2006.

Talks 2005

Sotiriou C, Wirapati P, Loi S, Viale G, Harris A, Bergh J, Smeds J, Farmer P, Praz V, Haibe-Kains B, Lallemand F, Desmedt C, Durbecq V, Larsimont D, Cardoso F, Buyse M, Delorenzi M, Piccart M. Breast tumours with intermediate histological grade can be reclassified into prognostically distinct groups by gene expression profiling. San Antonio Breast Cancer Symposium (SABCS), December 7-10, 2005.

Talks 2004

Wirapati P. Microarray database from the point of view of downstream statistical analysis. Swiss Array Consortium (SAC) Meeting. November 25, 2004. Functional Genomics Center Zürich.

Wirapati P. Identifying Differential Joint Expression in Microarray Data. Statistics in Functional Genomics Workshop, Ascona Switzerland, June 27th — July 2th 2004.

Posters

Posters 2008

Aebi S, Antonov J, Popovici V, Delorenzi M, Giobbie-Hurder A, Viale G, Thürlimann B, Altermatt H-J, Jaggi R. Risk assessment of relapse in Swiss participants of BIG 1-98 with grade 2 early breast cancer by gene expression profiling using RNA from formalin-fixed, paraffin embedded (FFPE) tissue. San Antonio Breast Cancer Symposium (SABCS), San Antonio, USA, December 2008

Sotiriou C, Wirapati P, Farmer P, ... and Delorenzi M. Refining Tumor Grade and its Prognosic Relevance by Expression Profiling. Statistical Challenges in Genome and Translational Research BIRS Conference, Banff, Canada, June 2008.

J. Antonov, V. Popovici, A. Oberli, A. Baltzer, S. Matthey, M. Schobesberger, M. Delorenzi, S. Aebi, H.J. Altermatt, R. Jaggi. "Risk assessment of grade 2 breast cancer patients by reliable expression profiling with RNA from formalin-fixed, paraffin embedded tissue". American Associaton for Cancer Research (AACR) Annual Meeting 2008, Abstract 974, April 12-16, San Diego, CA

Posters 2007

Mara Colzani, Alexandra Potts, Patrice Waridel, Frédéric Schütz, Manfredo Quadroni. Relative protein quantification by isobaric SILAC with immonium ion splitting (ISIS). 55th ASMS (American Society of Mass Spectrometry) Conference on Mass Spectrometry being held in Indianapolis, IN from June 3, 2007 to June 7, 2007.

Sybille Matthey, Vlad Popovici, Andrea Oberli, Anna Baltzer, Janine Antonov, Mauro Delorenzi, Hans Jörg Altermatt, Stefan Aebi1 and Rolf Jaggi, "Microarray and QPCR comparison from fresh frozen and archival breast cancer tissues", Tag der Klinischen Forschung, DKF Univ. of Bern, 2007

Janine Antonov, Andrea Oberli, Vlad Popovici, Anna Baltzer, Sybille Matthey, Martina Schobesberger, Mauro Delorenzi, Stefan Aebi, Hans Jörg Altermatt and Rolf Jaggi, "Reliable Molecular Characterization of Archival Formalin-Fixed Paraffin Embedded Breast Cancer Tissue by QRT-PCR", Tag der Klinischen Forschung, DKF Univ. of Bern, 2007

Anastasia Murat, Eugenia Migliavacca, Wanyu Lambiv, Tal Shay, Thierry Gorlia, Eytan Domany, Roger Stupp, Mauro Delorenzi, Monika E. Hegi. Self renewal signature identified in glioblastoma is associated with resistance to chemoradiation therapy in patients treated within clinical trial. American Association for Cancer Research, Los Angeles, USA, April 2007.

Stephane Califice, Annie-Claire Diserens, Ilse Vlassenbroeck, Eugenia Migliavacca, Josef Straub, Ivano Di Stefano, Fabrice Moreau, Marie-France Hamou, Isabelle Renard, Mauro Delorenzi, Katja Bierau, Monika E. Hegi. A new method for testing MGMT gene promoter methylation status of glioblastoma tissue using a direct real-time fluorescence-based methylation-specific PCR. MGMT Conference, Mainz, Germany, June 2007.

Posters 2006

Frédéric Schütz, Asa Wirapati, Mauro Delorenzi. PGC: Linear models for microarray analysis. SIB retreat, Leysin, 31 January 2006.

Migliavacca E, Bacac M, Delorenzi M, Guillou L, Stamenkovic I. Use of Gene-Expression Profiling to Characterize Desmoid Tumors and Nodular Fasciitis. SIB retreat, Leysin, 31 January 2006.

Susanne Kunkel, Sandra Flores-Urushima, Thierry Sengstag, Mauro Delorenzi, Asa Wirapati. SwissBrod. SIB retreat, Leysin, 31 January 2006.

C. Sotiriou, P Wirapati, S Loi, A Harris, J Bergh, J Smeds, V Praz, P Farmer, B Haibe-Kains, F Lallemand, M Buyse, M Piccart and M Delorenzi. Refining Tumor Grade and its Prognosic Relevance by Expression Profiling. SIB retreat, Leysin, 31 January 2006.

Tal Shay, Wanyu L. Lambiv, Anastasia Murat, Eugenia Migliavacca, Anjan Misra, Burt Feuerstein, Mauro Delorenzi, Roger Stupp, Monika E. Hegi, Eytan Domany. Effects of DNA Copy Number on Gene Expression in Glioblastoma Multiforme (GBM). 5th ECCB 2006, Eilat, Israel.

Sotiriou C, Haibe-KainsB, Desmedt C, Wirapati P , Durbecq V, Harris A, Larsimont D, Bontempi G, Buyse M, Delorenzi M , and Piccart M. Comprehensive molecular analysis of several prognostic signatures using molecular indices related to hallmarks of breast cancer: proliferation index appears to be the most significant component of all signatures. San Antonio Breast Cancer Symposium 2006, December 2006.

Miscellaneous

Rüping S, Wegener D, Sfakianakis S, Sengstag T. Workflows for intelligent monitoring using proxy services. Healthgrid 2009 Conference, Berlin, June 29-July 1, 2009.

Technical Reports

Wirapati P, Kunkel S, Goldstein DR, Farmer P, Pradervand S, Haibe-Kains B, Desmedt C, Sengstag T, Schütz F, Piccart M, Sotiriou C, Delorenzi M. "Integrative analysis of gene-expression profiles in breast cancer: toward a unified understanding of breast cancer sub-typing and prognosis signatures." BCF-SIB Technical Report 2007-1

(Parts of) Books

Goldstein DR, Delorenzi M, Luthy-Carter R, Sengstag T. Statistical design and data analysis for microarray experiments. In: Meta-Analysis and Combining Information in Genetics, Rudy Guerra and David Allison (eds), Chapman and Hall, 2006.

Awards

Nicolas Guex, Eugenia Migliavacca, Ioannis Xenarios. Best performer of the phospho-proteomics challenge in DREAM3 Predictions and Network Inference Challenges 2008. [Bio-ITWorld news]