Vincent Ferretti

Overview

Dr. Vincent Ferretti's expertise is in bioinformatics with experience in both large-scale software development and computational genomics.

As Associate Director, Bioinformatics Software Development, Ferretti is co-heading the International Cancer Genome Consortium (ICGC) Data Coordination Center, which is responsible for building the consortium‘s databases and public data web portal (dcc.icgc.org). Ferretti is also co-PI of NCI Genomic Data Commons (GDC) in which he is developing the GDC data portal user interfaces (gdc-portal.nci.nih.gov).

Ferretti is also co-PI of the Cancer Genome Collaboratory (cancercollaboratory.org), an infrastructure project which aims to provide the research community with a bio-medical compute cloud resource hosting ICGC data on 25,000 tumor genomes. Ferretti’s team is building the compute infrastructure and developing software solutions for searching and accessing efficiently ICGC protected data hosted on the Collaboratory.

Ferretti also conducts an independent research program with the objective of developing innovative genome-wide bioinformatics tools to identify new viruses as causative agents in human cancer. His laboratory is developing the CaPSID platform allowing the identification of viral sequences in tumour genomes and transcriptomes generated by next generation sequencing technologies.

Finally, Ferretti is contributing to several research projects in genomic epidemiology. He is Co-Principal Investigator of the Maelstrom Research program (maelstrom-research.org). Within this context, he currently leads an independent software development program, called OBiBa (obiba.org), which aims to provide the biobanking community with a free and high-quality open source biobank information management system. OBiBa software is used by several worldwide and Canadian cohort studies including the Canadian Longitudinal Study on Aging (CLSA) and the Canadian Partnership for Tomorrow Project (CPTP).

RESEARCH INTERESTS

  • Cancer
  • Genomics
  • Bioinformatics
  • Big Data
  • Software Development

SOFTWARE

Contact Information

Dr. Vincent Ferretti

vincent [dot] ferrettiatoicr [dot] on [dot] ca

Affiliations

2008 - OICR Senior Investigator and Associate Director, Bioinformatics Software Development, Informatics and Biocomputing, Ontario Institute for Cancer Research (OICR).
2007 - 2010Honorary Research Fellow in the Genomic Epidemiology Research Group within, The School of Translational Medicine, University of Manchester.
2005 - 2008Adjunct Professor, School of Computer Science, McGill University.
2002 - 2008Chief Bioinformatician, Génome Québec.
1998 - 2002Director of Bioinformatics, Targanta Therapeutics Inc..
1994 - 1997Postdoctoral fellow in computational biology, Mathematical Research Center of Université de Montréal.
1994PhD in Mathematics, Université de Montréal.

Research Output

  • Robert L. Grossman, Allison P. Heath, Ferretti,V Harold E. Varmus., Douglas R. Lowy, Warren A. Kibbe, Louis M. Staudt.
    Toward a Shared Vision for Cancer Genomic Data.
    • N Engl J Med, September 22, 2016, DOI: 10.1056/NEJMp16075912016;2016
  • Fortier I, Raina P, van den Heuvel E, Griffith LE, Craig C, Saliba M, Doiron D, Stolk R, Knoppers BM, Ferretti V, Granda P, Burton P.
    Maelstrom Research Guidelines for Rigorous Retrospective Data Harmonization.
    • Int. J. Epidemiol. June 6, 2016 doi:10.1093/ije/dyw075
  • Borozan I, Ferretti V.
    CSSSCL: a python package that uses Combined Sequence Similarity Scores for accurate taxonomic Classification of long and short sequence reads.
    • Bioinformatics. October 2015. doi: 10.1093/bioinformatics/btv587
  • Borozan I, Watt S, Ferretti V.
    Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification.
    • Bioinformatics. Jan 7 2015. Doi: 10.1093/bioinformatics/btv006
  • Doiron D, Burton P, Marcon Y, Gaye A, Wolffenbutter BHR, Perola M, Stolk RP, Foco L, Minelli C, Waldenberger M, Holle R, Kvaloy K, HIllege HL, Tasse AM, Ferretti V, Fortier I.
    Data harmonization and federated analysis of population-based studies: the BioSHaRE project.
    • Emerging Themes in Epidemiology. 2013 Nov. DOI: 10.1186/10.1186/1742-7622-10-12.