Dr Pratyaksha "Asa" Wirapati Bioinformatics Core Facility SIB Batiment Génopode, Quartier Sorge Université de Lausanne CH-1015 Lausanne, Switzerland Pratyaksha.Wirapati@isb-sib.ch Tel: +41 21 692 4098 Fax: +41 21 692 4055

I am a biostatistician/bioinformatician in Dr. Mauro Delorenzi's research group, specializing in omics biomarker development in cancer.

Topics

1. Meta-analysis/systematic reviews of clinical and omics data
2. Discovery, implementation and validation of prognostic nomograms involving molecular profiles
3. High-performance statistical computing for large, heterogenous population data

Publications

• 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
• 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(4):262-272. [pdf]
• 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(26):4245-4253.
• Parisi F, Wirapati P, Naef F. (2007) Identifying synergistic regulation involving c-Myc and sp1 in human tissues. Nucleic Acid Res 35(4):1098-1107
• 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 Research 9:R33 (29 May 2007)
• 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 Acad Sci Natl USA 10.1073/pnas.0703652104
• Pradervand S, Paillusson A, Thomas J, Weber J, Wirapati P, Hagenbüchle O, Harshman K (2008) Affymetrix whole-transcript Human Gene 1.0 ST array is highly concordant with standard 3' expression arrays. Biotechniques 44:756-762.
• 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.
• 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 sub-typing and prognosis signatures. Breast Cancer Research 10:R65

  Additional results can be found here.

• 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, Clinical Cancer Research 14:5158-5165
• 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. Nature Medicine 15:68-74.
• 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 Journal.
• 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.
• 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.
• 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, 23 July 2009.
• 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
• 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
• 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.
• 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 imporoves current risk stratification. J Clin Oncol 30:1670-1677.
• 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) J Natl Cancer Inst 106(10): dju247.

Patent

• Missiaglia E, Wirapati P, Rossi S, Kroll W (2012) Biomarkers for Lung Cancer. Patent No: WO/2012/160177

Technical Reports

• Wirapati P, Speed TP (2002) An algorithm to fit a simplex to a set of multidimensional points. WEHI Bioinformatics technical notes.
• Wirapati P et al. "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.

Teaching

• Microarray data analysis in functional genomics. PhD Course in Functional Genomics, EPFL, 22 January 2009.
• " An Introduction to Analysis of Multiple Gene Expression Datasets ", a part of EMBnet Course: Statistical Analysis Applied to Genome and Proteome Analysis, Lausanne 5 February 2008

Talks

• "Identifying Differential Joint Expression in Microarray Data"
  2004 Statistics in Functional Genomics Workshop, Ascona, Switzerland. [pdf]
• "Integrative Analysis of Genomic Properties"
  2007 Statistics for Biomolecular Data Integration and Modeling, Ascona, Switzerland. [pdf]
• "Computational and statistical issues in co-analyzing gene expression data from multiple studies and platforms"
  10 October 2007, Nederlands Kanker Instituut Seminar. [Abstract]
• "Co-analyzing datasets from multiple cancer studies: incorporating hierarchical models into differential expression, prediction and cluster analysis"
  4 June 2008, Emerging Statistical Challenges in Genome and Translational Research, Banff, Canada [Abstract]

PhD Thesis

• "An automated allele-calling system for high-throughput microsatellite genotyping"
  University of Melbourne, 2003. Advisor: Prof. Terry Speed. [pdf 7.9 Mb]

Education