Benjamin Haibe-Kains

I am currently Research Fellow in the Computational Biology and Functional Genomics Laboratory, headed by Professor John Quackenbush, at the Dana-Farber Cancer Institute, Harvard School of Public Health. My primary research interests concern the development and application of machine learning algorithms to analyze high-throughput genomic data in biomedicine, mostly in cancer studies. My ultimate goal is to translate my findings into the clinic, thus really affecting patients' lives. I am currently working on extending network inference from gene expression data to predict the complex behavior of biological systems such as the response of multiple targeted anticancer therapies. My long-term research focuses on the integration of high-throughput data from various sources (DNA, RNA, methylation or proteins) to simultaneously analyze multiple facets of carcinogenesis; next-generation sequencing technologies are particularly promising to leverage the data required to achieve this goal. I was awarded a prestigious Fulbright grant-in-aid for my postdoctoral research (2009-2010).

Prior to joining Professor Quackenbush's laboratory, I earned my PhD in bioinformatics at the Université Libre de Bruxelles (ULB), Belgium (2005-2009). I worked both in the Machine Learning Group (MLG, ULB), headed by Professor Gianluca Bontempi, and the Breast Cancer Translational Research Laboratory (BCTRL, Institut Jules Bordet, Belgium), headed by Professor Christos Sotiriou. In my doctoral work, I gained exposure to biomedical research which, combined with my background in computer science, allowed me to develop novel methodologies for prognostication of breast cancer patients using gene expression profiling. My interdisciplinary contributions have brought new insights in biological processes critical to a patient's clinical outcome and have been published both in top bioinformatics journals such as Bioinformatics, Genome Biol, PNAS, and BMC Genomics, and clinical journals such as Nat Med, Lancet Oncol, J Natl Cancer Inst, J Clin Oncol, Clin Cancer Res and Breast Cancer Res. I received a distinguished Solvay award for my doctoral research in 2010.

As a native of Brussels, Belgium, I received my degree in computer science at ULB. I consequently earned a master's degree both in bioinformatics (2004) and advanced studies in science (2005) from ULB. Accomplished in interdisciplinary challenges, I have gained broad expertise over the years in machine learning and bioinformatics, as well as in oncology and translational research. I will pursue my research in the Clinical Research Institute of Montreal as Assistant Professor and head of the Bioinformatics and Computational Genomics Laboratory.

Editorials

Time to move forward from "first generation" prognostic gene signatures in early breast cancer. Desmedt C, Michiels S, Haibe-Kains B, Loi S, Sotiriou C, Editorial in Breast Cancer Research and Treatment, 124(2), November 2010. [PDF]

Classification models for breast cancer molecular subtyping: What is the best candidate for a translation into clinic? Haibe-Kains B, Editorial in Women’s Health, 6(5):623-625, September 2010. [PDF]

Peer Reviewed Publications

A Three-Gene Model to Robustly Identify Breast Cancer Molecular Subtypes. Haibe- Kains B, Desmedt C, Culhane A, Loi SM, Bontempi G, Quackenbush J, Sotiriou C. J. Natl. Cancer Inst., in press.

Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer. Bentink S, Haibe-Kains B, Risch T, Fan J-B, Hirsch MS, Holton K, Rubio R, Aprils C, Chen J, Wickham-Garcia E, Liu J, Culhane AC, Drapkin R, Quackenbush J, Matulonis UA. PLoS One, in press.

Characterization and clinical evaluation of CD10+ stroma cells in the breast cancer microenvironment. Desmedt C, Majjaj S, Kheddoumi N, Singhal SK, Haibe-Kains B, El Ouriaghli F, Chaboteaux C, Michiels S, Lallemand F, Journe F, Loi S, Quackenbush J, Duvillier H, Dekoninck S, Blanpain C, Lagneaux L, Houhou N, Delorenzi M, Larsimont DP, Piccart MJ, Sotiriou C. Clin Cancer Res. 2012 Jan 10.

Modeling invasive breast cancer: growth factors propel progression of HER2-positive premalignant lesions. Pradeep CR, Zeisel A, Köstler WJ, Lauriola M, Jacob-Hirsch J, Haibe-Kains B, Amariglio N, Ben-Chetrit N, Emde A, Solomonov I, Neufeld G, Piccart M, Sagi I, Sotiriou C, Rechavi G, Domany E, Desmedt C, Yarden Y. Oncogene. 2011 Dec 5. doi: 10.1038/onc.2011.547. [PDF]

Multiple-input multiple-output causal strategies for gene selection. Bontempi G, Haibe-Kains B, Desmedt C, Sotiriou C, Quackenbush J. BMC Bioinformatics. 2011 Nov 25;12(1):458. [PDF]

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. Culhane AC, Schröder MS, Sultana R, Picard SC, Martinelli EN, Kelly C, Haibe-Kains B, Kapushesky M, St Pierre AA, Flahive W, Picard KC, Gusenleitner D, Papenhausen G, O'Connor N, Correll M, Quackenbush J. Nucleic Acids Res. 2011 Nov 21. [PDF]

Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. Haibe-Kains B, Olsen C, Djebbari A, Bontempi G, Correll M, Bouton C, Quackenbush J. Nucleic Acids Res. 2011 Nov 16. [PDF]

Low residual proliferation after short-term letrozole therapy is an early predictive marker of response in high proliferative ER-positive breast cancer. Bedard P, Singhal SK, Ignatiadis M, Bradbury I, Haibe-Kains B, Desmedt C, Loi S, Evans D, Michiels S, Dixon JM, Miller WR, Piccart M, Sotiriou C. Endocr Relat Cancer. 2011 Oct 7. [PDF]

DNA methylation profiling reveals a predominant immune component in breast cancers. Dedeurwaerder S, Desmedt C, Calonne E, Singha SK, Haibe-Kains B, Defrance M, Michiels S, Volkmar M, Deplus R, Luciani J, Lallemand F, Larsimont D, Toussaint J, Haussy S, Rothé F, Rouas G, Metzger O, Majjaj S, Saini K, Putmans P, Hames G, Baren NV, Coulie PG, Piccart M, Sotiriou C, Fuks F. EMBO Mol Med. 2011 Sep 12. [PDF]

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models. Schröder MS, Culhane AC, Quackenbush J, Haibe-Kains B. Bioinformatics. 2011 Sep 7. [PDF]

Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. Li Q, Eklund AC, Birkbak NJ, Desmedt C, Haibe-Kains B, Sotiriou C, Symmans WF, Pusztai L, Brunak S, Richardson AL, Szallasi Z. BMC Bioinformatics. 2011 Jul 28;12(1):310. [PDF]

Global MicroRNA Expression Profiling Identifies MiR-210 Associated with Tumor Proliferation, Invasion and Poor Clinical Outcome in Breast Cancer. Rothé F, Ignatiadis M, Chaboteaux C, Haibe-Kains B, Kheddoumi N, Majjaj S, Badran B, Fayyad-Kazan H, Desmedt C, Harris AL, Piccart M, Sotiriou C. PLoS ONE. 2011;6(6):e20980. Epub 2011 Jun 29. [PDF]

Minimising Immunohistochemical False Negative ER Classification Using a Complementary 23 Gene Expression Signature of ER Status. Li Q, Eklund AC, Juul N, Haibe-Kains B, Workman CT, Richardson AL, Szallasi Z, and Swanton C in PLoS ONE; 5(12): e15031, 2010. [PDF]

Low CD10 mRNA expression identifies high-risk ductal carcinoma in situ (DCIS). Toussaint J, Durbecq V, Altintas S, Doriath V, Rouas G, Paesmans M, Bedard P, Haibe-Kains B, Tjalma WA, Larsimont D, Piccart MJ, Sotiriou C in PLoS ONE, 5(8):e12100, 2010. [PDF]

Long term in vitro treatment of human glioblastoma cells with temozolomide increases resistance in vivo through up-regulation of GLUT transporter and aldo-keto reductase enzyme AKR1C expression. Le Calvé B, Rynkowski M, LeMercier M, Bruyère C, Lonez C, Gras T, Haibe-Kains B, Bontempi G, Decaestecker C, Ruysschaert JM, Kiss R and Lefranc F in Neoplasia, 12(9):727-739, 2010. [PDF]

PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor positive breast cancer. Loi S, Haibe-Kains B, Majjaj S, Lallemand F, Durbecq V, Larsimont D, Gonzalez-Angulo AM, Pusztai L, Symmans FW, Bardelli A, Ellis P, Tutt AN, Gillett CE, Mills GB, Hennessy BT, Phillips WA, Piccart MJ, Speed TP, McArthur GA, Sotiriou C in PNAS, 107(22):20208-10213, 2010. [PDF]

Evaluation of an RNA interference screen-derived mitotic and ceramide pathway meta- gene in paclitaxel-treated primary ER-/PR-/ERBB2- breast cancer: a retrospective analysis of five clinical trials. Juul N, Eklund AC, Li Q, Burrell RA, Gerlinger M, Valero V, Andreopoulou E, Esteva FJ, Symmans FW, Desmedt C, Haibe-Kains B, Sotiriou C, Pusztai L, Szallasi Z and Swanton C in Lancet Oncology, 11(4):358-364, 2010. [PDF]

A fuzzy gene expression-based computational approach improves breast cancer prognostication. Haibe-Kains B*, Desmedt C*, Rothé F, Sotiriou C and Bontempi G in Genome Biology 11(2):R18, 2010. [PDF]

Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer. Li Y, Zou L, Li Q, Haibe-Kains B, Tian R, Li Y, Desmedt C, Sotiriou C, Szallasi Z, Iglehart JD, Richardson AL, Wang ZC in Nature Medecine 16(2):214-218, 2010. [PDF]

Comparison of prognostic gene expression signatures for breast cancer. Haibe-Kains B, Desmedt C, Piette F, Buyse M, Cardoso F, Van't Veer L, Piccart M, Bontempi G, Sotiriou C. BMC Genomics. 2008 Aug 21;9:394. [PDF]

Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Desmedt C, Haibe-Kains B, Wirapati P, Buyse M, Larsimont D, Bontempi G, Delorenzi M, Piccart M, Sotiriou C. Clin Cancer Res. 2008 Aug 15;14(16):5158-65. [PDF]

Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures. Wirapati P, Sotiriou C, Kunkel S, Farmer P, Pradervand S, Haibe-Kains B, Desmedt C, Ignatiadis M, Sengstag T, Schütz F, Goldstein DR, Piccart M, Delorenzi M. Breast Cancer Res. 2008;10(4):R65. [PDF]

A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all? Haibe-Kains B, Desmedt C, Sotiriou C, Bontempi G. Bioinformatics. 2008 Oct 1;24(19):2200-8. [PDF]

Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. 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. BMC Genomics. 2008 May 22;9:239. [PDF]

Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. 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. J Clin Oncol. 2007 Apr 1;25(10):1239-46. [PDF]

Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. 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. J Natl Cancer Inst. 2006 Feb 15;98(4):262-72. [PDF]

Conferences

Computational discovery of biological pathways associated to breast cancer molecular subtypes and prognosis. Schröder M,  Gusenleitner D, Culhane AC, Haibe-Kains B, Quackenbush J at the conference Systems Biology of Diversity in Cancer, Rockefeller Research Laboratories, Memorial Sloan-Kettering Cancer Center, New York, USA, 2011. Schröder M received the CCSB Young Scientist Award for this abstract. [PDF]

Meta-analysis  of  gene  expression  and  survival  data  using  the  R  packages SurvComp and  genefu. Schröder M,  Gusenleitner D,  Goesmann A, Culhane AC, Quackenbush J and Haibe-­-Kains B at VIZBI, workshop on visualizing biological data, Broad Institute, Cambridge, USA, 2011. [PDF]

A Robust Breast Cancer Subtype Classifier: A Three-Gene Model To Translate Into the Clinic. Haibe-Kains B, Desmedt C, Culhane AC, Bontempi G, Quackenbush J, Sotiriou C at the Breakthrough Breast Cancer: Triple Negative Breast Cancer Conference, London, UK, 2011. [PDF]

Robustness of breast cancer molecular subtypes identification. Haibe-Kains B, Culhane AC, Desmedt C, Bontempi G, Quackenbush J, Sotiriou C in Annals of Oncology 21(4):iv49-iv59, 2010 (IMPAKT Breast Cancer Conference, Bruxelles, Belgium). [PDF] [PDF]

Invited Talks

Molecular subtypes and gene-expression signatures in breast cancer. Haibe-Kains B in the department of Biochemistry and Bioinformatics at University of Montreal, Montreal, Quebec, Canada, 2011. [PDF]

Molecular subtypes and gene-expression signatures in breast cancer. Haibe-Kains B in the Biostatistics seminar series at McGill University, Montreal, Quebec, Canada, 2011. [PDF]

Cancer subtypes and prognosis: a translational approach. Haibe-Kains B at the Cincinnatti Chrildren's Hospital Medical Center, Cincinnatti, Wisconsin, USA, 2010. [PDF]

Robust Identification of Breast Cancer Molecular Subtypes to Refine Prognosis. Haibe-Kains B in Quackenbush's laboratory at the Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA, USA, 2009. [PDF]

Book Chapters

Computational Intelligence in Clinical Oncology : Lessons Learned from an Analysis of a Clinical Study. Haibe-Kains B, Desmedt C, Loi S, Delorenzi M, Sotiriou C, and Bontempi G, in Applications of Computational Intelligence in Bioinformatics and Biomedicine: Current Trends and Open Problems of Studies in Computational Intelligence, Springer-Verlag, 122(10):237-268, 2008. [PDF]

Labs

Bioinformatics and Computational Genomics Laboratory, Clinical Research Institute of Montreal, Montreal, Quebec, Canada

Computational Biology and Functional Genomics Laboratory, Dana-Farber Cancer Institute, Harvard Schoold of Public Health, Boston, MA, United States

Machine Learning Group, Université Libre de Bruxelles, Bruxelles, Belgium

Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Bruxelles, Belgium

Other personal webpages

Homepage at the Université Libre de Bruxelles