CV

Education

2012 – present: Ph.D. in Biostatistics
Johns Hopkins Bloomberg School of Public Health (Baltimore, MD)
Advisor: Kasper Daniel Hansen, Ph.D.

2008 – 2012: B.Sc. in Mathematics (Honours), Minor in Physics
McGill University (Montreal, QC)
First-Class Honours and Distinction

2006 – 2008: Diploma of Collegial Studies
CEGEP Sainte-Foy (Quebec City, QC)

Research Experience

06/2013 – present: Research Internship in Oncology Biostatistics
Johns Hopkins Sidney Kimmel Comprehensive Cancer Center (Baltimore, MD)
Advisor: Elana J. Fertig, Ph.D.

2012 – 2013: Research Assistantship in Biostatistics
Lady Davis Institute for Medical Research and McGill University (Montreal, QC)
Advisors: Celia M.T. Greenwood, Ph.D., & Aurélie Labbe, Ph.D.

2011 – 2012: Summer Internship in Mathematics
McGill University (Montreal, QC)
Advisors: Dmitry Jakobson, Ph.D., & Louigi Addario-Berry, Ph.D.

Scholarships

2012 – 2014: FQRNT Scholarship (ES M)
Fonds québécois de la recherche sur la nature et les technologies

2012 – 2013: NSERC Scholarship (PGS M)
Natural Sciences and Engineering Research Council of Canada

2013 Travel Scholarship, Bioconductor Conference 2013

2011 Undergraduate Research Scholarship
Institut des sciences mathématiques (ISM), Montréal

2008: Narcissa Farrand Entrance Scholarship, McGill University

Awards

2014
Hopkins Genetics Research Day, Johns Hopkins University

2013 PhD Comprehensive Examination Award
Johns Hopkins University, Department of Biostatistics

2012 Best Research Trainee Presentation Award
Canadian Human and Statistical Genetics Meeting, Niagara Falls, Canada

2012 Poster Award, 2nd place
Annual Undergraduate Research Conference, McGill University

2011-2012 Dean’s Honours List
McGill University

2008: Governor General’s Academic Medal, La Malbaie, Québec, Canada

Publications

2015 Jean-Philippe Fortin , Kasper D. Hansen
Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data
bioRxiv doi:

2014 Jean-Philippe Fortin , Aurelie Labbe, Mathieu Lemire, Brent W. Zanke, Thomas J. Hudson, Elana J. Fertig, Celia M.T. Greenwood, Kasper D. Hansen
Functional normalization of 450k methylation array data improves replication in large cancer studies
Genome Biology doi: 10.1186/s13059-014-0503-2

2014 Jean-Philippe Fortin , Elana J. Fertig, Kasper D. Hansen
shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R
F1000Research doi: 10.12688/f1000research.4680.1

2014 Jean-Philippe Fortin , Aurelie Labbe, Mathieu Lemire, Brent W. Zanke, Thomas J. Hudson, Elana J. Fertig, Celia M.T. Greenwood, Kasper D. Hansen
Functional normalization of 450k methylation array data improves replication in large cancer studies
bioRxiv doi: 10.1101/002956

2013 Jean-Philippe Fortin , Samantha Rudinsky
Asymptotic eigenvalue distribution of random lifts
Waterloo Mathematics Review

2011 Jean-Philippe Fortin

Delta-Epsilon Magazine

Presentations

Minfi tutorial
450K Workshop, University College London
May 2014, London, UK

shinyMethyl: interactive tool for 450K arrays (Poster)
450K Workshop, University College London
May 2014, London, UK

About Hi-C and other high-dimensional beverages
Genomics Working Group, Johns Hopkins University
April 2014, Baltimore, MD

Functional normalization (FunNorm): A better alternative to quantile normalization for methylation data (Poster)
ENAR spring meeting
March 2014, Baltimore, MD

Functional normalization of 450k methylation array data improves replication in large cancer studies
Hopkins Genetics Day, Johns Hopkins University
February 2014, Baltimore, MD
First place

Functional normalization: a method to keep large-scale biological differences in methylation data
Joint Genomics Meeting, Johns Hopkins University
January 2014, Baltimore, MD

Functional normalization for methylation data (poster)
Program in Quantitative Genomics Conference, Harvard School of Public Health
November 2013, Boston, MA

Adaptive Resistant Regression Method (ARRm): A Better Alternative to Quantile Normalization for Methylation Data
Joint Statistical Meetings (JSM)
August 2013, Montréal, Canada

Functional Normalization (FunNorm): A New Approach for Batch Correction of DNA Methylation Data
PennSIVE group, University of Pennsylvania
July 2013, Philadelphia, PA

minfi and shinyMethyl: a Winning Pair of R-packages for the Analysis of Methytlation Data
Bioconductor Conference, Fred Hutchinson Center
July 2013, Seattle, WA


Genomics Working Group, Johns Hopkins University
May 2013, Baltimore, MD

Statistical Methods for Analysis of Illumina Infinium Methylation Arrays in a Case-Control Study of Colorectal Cancer
Poster, Third Annual Lady Davis Institute Scientific Retreat
May 2012, Montréal, Canada

Normalization Method for Illumina Infinium Methylation Arrays in a Case-Control Study of Colorectal Cancer
Canadian Human and Statistical Genetics Meeting
April 2012, Niagara Falls, Canada
Best Research Trainee Presentation Award

Asymptotic Eigenvalue Distribution of Random Lifts
Poster, Ottawa Undergraduate Research Poster Competition
January 2012, University of Ottawa, Canada

Asymptotic Eigenvalue Distribution of Random Lifts
Poster, Annual Faculty of Science Undergraduate Research Conference
October 2011, McGill University, Montréal, Canada
Second prize

Geometric Interpretation of the Uniformly Minimum-Variance Unbiased Estimator
Canadian Undergraduate Mathematics Conference
June 2011, Université Laval, Québec, Canada

Représentations de nombres premiers par des formes quadratiques binaires
Colloque pan-québécois des étudiants de l’Institut des sciences mathématiques
May 2011, Université de Montréal, Canada

Peer Review Activities

Peer Reviewer for Bioinformatics

Software

shinyMethyl: an interactive R application for visualization of methylation data

ARRmNormalization: Adaptive Robust Regression normalization for Illumina methylation data