Canadian Bioinformatics Workshops: Summer 2020

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Instructors

Along with the CBW Scientific Committee, the core faculty members are responsible for the ongoing curriculum development and the management of the CBW workshops. The following is a list of the CBW core faculty, and past and present instructors and invited lecturers.

Current Faculty and Instructors

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    Gary Bader, PhD

    • Principal Investigator, University of Toronto

    Dr. Bader develops biological network analysis and pathway information resources. He created the Biomolecular Interation Network Database (BIND, http://bind.ca) while working on his PhD and currently helps lead development of the free Cytoscape network visualization and analysis software (http://cytoscape.org/).

    Research Interests:

    Biological network and pathway analysis

    Contact Details

    Website:
    baderlab.org
    Location:
    Toronto
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    Mathieu Bourgey, PhD

    • Bioinformatics Manager, Canadian Centre for Computational Genomics

    Mathieu Bourgey is the manager of the Research and Development team at the Montreal node of the Canadian Centre for Computational Genomics. He has worked on developing evolution models of genomics large repeats, modeling risk of developing the Coeliac disease based on genetic and familial information, and modeling gene-gene interactions and foeto-maternal interactions in the susceptibility to childhood leukemia. Currently, he manages software and analysis pipeline development on a wide range of next‐generation sequencing platforms technologies as well as taking part in national and international projects studying cancer genomics, genome assembly and transcriptomics at the McGill University and Genome Quebec Innovation Centre. Mathieu also organizes international genomics workshops.

    Research Interests:

    Genomics, Bioinformatics, Next-Generation sequencing, Cancer

    Contact Details

    Website:
    http://computationalgenomics.ca/
    Location:
    Montreal, QC
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    Guillaume Bourque, PhD

    • Associate Professor and Director of Bioinformatics, McGill University and Genome Quebec Innovation Centre

    Guillaume leads the Canadian Center for Computational Genomics (C3G), a Genome Canada bioinformatics platform, and the Epigenomics Mapping Center at McGill, a project that oversees data generation and processing as part of the Canadian Epigenetics, Environment and Health Research Consortium (CEEHRC), which is associated with the International Human Epigenome Consoritum (IHEC). He is also the chair of the Integrative Analysis working group of IHEC, is responsible for the IHEC Data Portal and has undertaken genome-wide epigenetic analysis in a range of conditions. His research interests are in comparative and functional genomics with a special emphasis on applications of next-generation sequencing technologies.

    Contact Details

    Website:
    http://www.computationalgenomics.ca/BourqueLab/
    Location:
    Montreal, QC
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    David Bujold

    • Bioinformatics Manager, McGill University

    David works in Guillaume Bourque’s lab on software solutions in bioinformatics for organizing, visualizing and analyzing datasets produced by large-scale projects such as the International Human Epigenome Consortium (IHEC), which maps human epigenomes for a broad spectrum of cell types and diseases. He is also involved in the development of GenAP, a platform that leverages Compute Canada infrastructure to make bioinformatics analysis more accessible to non-bioinformaticians, and reduces data processing bottlenecks.

    Research Interests:

    Data visualization, Software infrastructure, Data collection and archival, Epigenomics

    Contact Details

    Location:
    Montreal, QC
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    Lauren Erdman

    • Graduate Student, University of Toronto

    Lauren has an MSc in Biostatistics from the University of Toronto and has previously worked as a Biostatitician for two pediatric psychiatric genetics labs at SickKids. She is currently an MSc student in Dr. Anna Goldenberg’s lab. In her work, Lauren is focused on developing and applying statistical machine learning methods primarily in the area of data integration for improved translational discovery in the fields of genetics and genome biology. Lauren has also created custom R programming and data analysis courseware and taught over 200 trainees and scientists in the SickKids research program.

    Contact Details

    Location:
    Toronto
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    Malachi Griffith, PhD

    • Assistant Professor (Medicine), Assistant Director (McDonnell Genome Institute), Washington University

    Dr. Griffith’s research is focused on the development of genomics and bioinformatics methods as they apply to the study of cancer biology and medicine. A particular focus of his work is in the translation of genomics data from whole genome, exome and transcriptome sequencing into clinically actionable observations and personalized cancer therapies. He has led the development of key online informatics resources for cancer precision medicine such DGIdb, DoCM, CIViC and more.

    Contact Details

    Website:
    http://griffithlab.org/
    Location:
    St. Louis, MO, US
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    Obi Griffith, PhD

    • Assistant Professor of Medicine, Assistant Director, Washington University School of Medicine

    Dr. Griffith’s research is focused on the development of personalized medicine strategies for cancer using genomic technologies. He develops and uses bioinformatics, machine learning and clinical statistics for the analysis of high throughput sequence data and identification of biomarkers for diagnostic, prognostic and drug response prediction. He has led the development of key online informatics resources such as DGIdb, CIViC, GenVisR and more.

    Contact Details

    Website:
    http://www.griffithlab.org
    Location:
    St. Louis, MO, US
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    Michael Hoffman, PhD

    • Scientist, Princess Margaret Cancer Centre

    Assistant Professor, Departments of Medical Biophysics and Computer Science, University of Toronto
    Faculty Affiliate, Vector Institute

    Michael Hoffman creates predictive computational models to understand interactions between genome, epigenome, and phenotype in human cancers. He implemented the genome annotation method Segway, which simplifies interpretation of large multivariate genomic datasets, and was a linchpin of the NIH ENCODE Project analysis. He was named a CIHR New Investigator and has received several awards for his academic work, including the NIH K99/R00 Pathway to Independence Award, and the Ontario Early Researcher Award.

    Research Interests:

    Epigenomics; functional genomics; machine learning; dynamic Bayesian networks; chromatin; graphical models; ChIP-seq; DNase-seq; cancer

    Contact Details

    Website:
    Hoffman Lab web site
    Location:
    Toronto
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    William Hsiao, PhD

    • Chief Bioinformatician, BC Centre for Disease Control

    I joined BCCDC Public Health Microbiology & Reference Laboratory in September 2011 as the lead bioinformatician. My goal is to apply microbial genomics and bioinformatics in public health setting to improve health care. I completed my PhD at Simon Fraser University in the laboratory of Dr. Fiona Brinkman and a post-doctoral fellowship in the laboratory of Dr. Claire Fraser-Liggett at the Institute for Genome Sciences, University of Maryland School of Medicine. During my training, I focused on whole genome sequence analysis and comparative genomics. I also have published and continue to work in the new field of metagenomics. Currently, my research focus on improving methodologies for conducting infectious disease surveillance and outbreak investigations by using next-generation sequencing technology and developing robust bioinformatics analysis platform.

    Research Interests:

    public health, microboial genomics, bioinformatics

    Contact Details

    Website:
    Clinical Assistant Professor
    Location:
    BC
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    Jared Simpson, PhD

    • Principal Investigator, Ontario Institute for Cancer Research

    Assistant Professor, Department of Computer Science, University of Toronto

    Dr. Simpson develops algorithms and software for the analysis of high-throughput sequencing data. He is interested in de novo assembly, the detection of sequence variation in individuals, cancers and populations and the application of compressed data structures to large analysis problems. Dr. Simpson developed the ABYSS and SGA software packages.

    Contact Details

    Location:
    Toronto
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    Veronique Voisin, PhD

    • Research Associate, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto

    Veronique is currently a bioinformatician applying pathway and networks analyses to highthrouput genomics data for OICR cancer stem cell program. Previously, she worked on characterizing the gene signatures of different types of leukemias using a murine model.

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    David Wishart

    • Professor, University of Alberta

    Dr. Wishart is currently working in four areas: 1) Protein folding and protein structure prediction; 2) Automated genome/proteome annotation; 3) Developing software tools to facilitate metabolomics and cheminformatics; and 4) Developing software tools to improve NMR-based protein structure determination. More recently his research has moved towards systems biology and synthetic biology.

    Contact Details

    Website:
    http://wishartlab.com/
    Location:
    Edmonton, AB
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    Jianguo (Jeff) Xia, PhD

    • Assistant Professor, McGill University

    His research focuses on statistics and bioinformatics for metabolomics, microarray and next generation sequencing (RNA-seq) data analysis and integration. Some of the tools he developed in the past include MetaboAnalyst for statistical analysis of metabolomics data, MSEA for metabolite set enrichment analysis, MetPA for metabolic pathway analysis, ROCCET for ROC curve based biomarker analysis, and NetworkAnalyst for data integration and network analysis. His general interest is high-throughput omics data analysis using a variety of statistics, machine learning and data visualization technologies.

    Research Interests:

    bioinformatics, statistics, metabolomics, transcriptomics, network biology

    Contact Details

    Website:
    http://www.xialabresearch.com
    Location:
    QC
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    Kelsy Cotto

    • Graduate student, Washington University in St. Louis

    Kelsy is a PhD candidate in the Molecular Cell Biology program at Washington University in St. Louis. She completed her undergraduate degree at Mercer University in 2016, where she earned a B.S. in Biochemistry and Molecular Biology. She is interested in developing methods to analyze multiple types of sequencing data in order to better understand regulatory mutations and splicing within cancer, particularly with respect to personalized cancer vaccine design. Currently, she is involved with [2]DGIdb, [3]RegTools, ORegAnno and analysis of several breast cancer clinical cohorts. She is also part of the Precision Medicine Pathway and Cancer Biology Pathway at WashU, which allows to better understand how she can translate genomics and informatics into the clinic more efficiently.

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    Rob Syme, PhD

    • Bioinformatics Consultant, Canadian Centre for Computational Genomics, McGill University

    Dr. Syme has a background in the integration of diverse ‘omics approaches in non-model organisms with a specialisation in crops and associated phytopathogens. He is interested in encouraging research groups who might be new to bioinformatics and computational methods to adopt open and reproducible approaches to their work.

    Contact Details

    Twitter:
    @robsyme
    Location:
    Montreal, QC, CA
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    Ruth Isserlin

    • Research data analyst, Donnelly Centre for Cellular and Bimolecular Research, University of Toronto

    Bioinformatician and data analyst in the Bader lab applying pathway and data analysis to varied data types. Developed Enrichment Map App for Cytoscape, an app to visually translate functional enrichment results from popular enrichment tools like GSEA to networks. Further developed the Enrichment Map Pipeline including development of additional Apps to help summarize and analyze resulting Enrichment Maps, including PostAnalysis, WordCloud, and AutoAnnotate App.

    Research Interests:

    statistics, bioinformatics, -omics, network biology

    Contact Details

    Website:
    www.baderlab.org
    Location:
    Toronto, ON, CA
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    BF Francis Ouellette

    • Scientific Director, Canadian Bioinformatics Workshops (CBW)

    Francis was one of the co-founders of the CBW in 1998. His teams were involved in the development of high throughput sequence analysis methods, as well as the development of platforms to integrate data from various open databases. Francis continues to be interested in computational biology and genomics, and the integration of all data types to help our understanding of biology

    Research Interests:

    Open Data, Open Source, Open Access and Open Courseware. Providing data provenance and openness of code, data and literature is essential to doing science.

    Contact Details

    Website:
    Twitter:
    @bffo
    Location:
    Montreal, QC
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    Rachade Hmamouchi

    • Program Manager, Canadian Bioinformatics Workshops (CBW) & McGill initiative in Computational Medicine (MiCM)

    Rachade is a bioinformatician by training, and over the span of her career, she has worked at universities, biotech, and industry fields. She is leading the organisation of the workshops at the CBW and at the MiCM.

Past Faculty and Instructors

  • Robert Beiko (Past Faculty)
    Associate Professor and Canada Research Chair in Bioinformatics, Dalhousie University
    • Misha Bilenky (Past Faculty)
      Staff Scientist, Canada's Michael Smith Genome Sciences Centrey
      • Paul Boutros (Past Faculty)
        Principal Investigator, Ontario Institute for Cancer Research
        • Fiona Brinkman, (Past Faculty)
          Professor, Molecular Biology and Biochemistry, SFU
          • Michael Brudno (Past Faculty)
            Director, Hospital for Sick Children
            • Florence Cavalli (Past Faculty)
              Postdoctoral Fellow, University of Toronto
              • Anamaria Crisan (Past Faculty)
                PhD Student, University of British Columbia
                • Anna Goldenberg (Past Faculty)
                  Assistant Professor, Department of Computer Science, University of Toronto
                  • Brian Haas (Past Faculty)
                    Senior Computational Biologist, Broad Institute
                    • Robin Haw (Past Faculty)
                      Manager of Reactome Outreach and Scientific Associate, OICR
                      • Martin Hirst (Past Faculty)
                        Assistant Professor, University of British Columbia, Centre for Hightroughput Biology (CHiBi)
                        • Morgan Langille (Past Faculty)
                          Assistant Professor, Dalhousie University
                          • Andrew McArthur (Past Faculty)
                            Associate Professor, McMaster University
                            • Andrew McPherson (Past Faculty)
                              Post Doctoral Fellow, BC Cancer Agency
                              • George Mihaiescu (Past Faculty)
                                Senior Cloud Architect, Informatics and Biocomputing, Ontario Institute for Cancer Research
                                • Quaid Morris (Past Faculty)
                                  Principal Investigator, University of Toronto
                                  • John Parkinson (Past Faculty)
                                    Senior Scientist, Hospital for Sick Children
                                    • Mark Phillips (Past Faculty)
                                      Academic Associate, McGill University
                                      • Trevor Pugh (Past Faculty)
                                        Scientist, University Health Network
                                        • Jüri Reimand (Past Faculty)
                                          Principal Investigator, Ontario Institute for Cancer Research
                                          • Lincoln Stein (Past Faculty)
                                            Director, Senior Principal Investigator, Ontario Institute for Cancer Research
                                            • Boris Steipe (Past Faculty)
                                              Associate Professor, University of Toronto
                                              • Fouad Yousif (Past Faculty)
                                                Research Associate, Informatics and Biocomputing, Ontario Institute for Cancer Research
                                                • Christina Yung (Past Faculty)
                                                  Project Manager, Ontario Institute for Cancer Research
                                                  • Peter Ronning (Past Faculty)
                                                    Graduate student, McDonnell Genome Institute, Washington University in St. Louis
                                                    • Heather Gibling (Past Faculty)
                                                      PhD Candidate, Ontario Institute for Cancer Research
                                                      • Christopher Miller (Past Faculty)
                                                        Assistant Professor, McDonnell Genome Institute, Washington University School of Medicine
                                                        • Megan Richters (Past Faculty)
                                                          PhD candidate in Molecular Genetics and Genomics, Washington University School of Medicine
                                                          • Michelle Brazas (Past Faculty)
                                                            Senior Program Manager, Adaptive Oncology, Ontario Institute for Cancer Research
                                                            • Pascale Marquis (Past Faculty)
                                                              Bioinformatics Consultant, McGill University
                                                              • David Baillie (Past Faculty)
                                                                Professor, Simon Fraser University
                                                              • Andreas Baxevanis (Past Faculty)
                                                                Director, Computational Genomics and Associate Director for Intramural Research, National Human Genome Research Institute, Bethesda, MD; Adjunct Professor, The Johns Hopkins University.
                                                              • Yoshua Bengio (Past Faculty)
                                                                Professeur Agrégé/Associate Professor, Département d'Informatique et Recherche Opérationnelle, Université de Montréal.
                                                              • Ryan Brinkman (Past Faculty)
                                                                Senior Scientist, Terry Fox Laboratory, BC Cancer Research Centre, Vancouver, BC
                                                              • Stefanie Butland (Past Faculty)
                                                                Research Associate, Centre for Molecular Medicine and Therapeutics, University of British Columbia
                                                              • Jennifer Bryan (Past Faculty)
                                                                Associate Professor, Department of Statistics and Michael Smith Laboratories, UBC.
                                                              • Fong Chun Chan (Past Faculty)
                                                                PhD Candidate, University of British Columbia.
                                                              • A. Jamie Cuticchia (Past Faculty)
                                                                Department of Medical Biophysics, University of Toronto
                                                              • Axel Ducret (Past Faculty)
                                                                Sr. Research Biologist, Merck Frosst Center for Therapeutic Research
                                                              • Daniel Figeys (Past Faculty)
                                                                Senior Scientist, MDS Ocata Inc.
                                                              • Joanne Fox (Past Faculty)
                                                                Instructor, University of British Columbia
                                                              • Warren Gish (Past Faculty)
                                                                Associate Professor, Genetics, Washington University, St. Louis
                                                              • Raphael Gottardo (Past Faculty)
                                                                Associate Member, Fred Hutchinson Cancer Research Center
                                                              • Larry D. Greller (Past Faculty)
                                                                Director of Mathematical Biology and Systems Modeling, Molecular Mining Corporation, Kingston, Ontario
                                                              • Mike Hallett (Past Faculty)
                                                                Director, McGill Centre for Bioinformatics, Associate Professor, School of Computer Science, Associate Member, Department of Biochemistry.
                                                              • Donal Hickey (Past Faculty)
                                                                Professor, Biology, University of Ottawa.
                                                              • Phil Hieter (Past Faculty)
                                                                Michael Smith Laboratories, Vancouver, BC
                                                              • Christopher Hogue(Past Faculty)
                                                              • Walid Houry (Past Faculty)
                                                                Assistant Professor, Department of Biochemistry, University of Toronto, Toronto, ON.
                                                              • Steve Jones (Past Faculty)
                                                                Director of Data Analysis and Informatics Group, BC Genome Sequencing Centre, Vancouver, BC
                                                              • Igor Jurisica (Past Faculty)
                                                                Senior Scientist, Princess Margaret Cancer Centre, IBM Life Sciences Discovery Center, Toronto, ON
                                                              • Anna Lapuk (Past Faculty)
                                                                Head Bioinformatics Scientist, Prostate Centre/Vancouver General Hospital.
                                                              • Franois Major (Past Faculty)
                                                                Professeur Agrégé/Associate Professor, Département d'Informatique et Recherche Opérationnelle, Université de Montréal
                                                              • Marco Marra (Past Faculty)
                                                                BC Genome Sequencing Centre, Vancouver, BC
                                                              • John McPherson (Past Faculty)
                                                                Director, Ontario Institute for Cancer Research.
                                                              • David Morais, PhD (Past Faculty)
                                                                Bioinformatician and software developer, Universite de Sherbrooke.
                                                              • Aaron Quinlan (Past Faculty)
                                                                Assistant Professor, Center for Public Health Genomics, University of Virginia, USA
                                                              • Joseph Ryan (Past Faculty)
                                                                National Human Genome Research Institute, Bethesda, MD.
                                                              • Roberto Sanchez (Past Faculty)
                                                                Medical Biophysics, Rockefeller University, New York
                                                              • Steve Scherer (Past Faculty)
                                                                Senior Scientist, Department of Genetics and Associate Director, The Centre for Applied Genomics at The Hospital for Sick Children, Associate Professor, Faculty of Medicine, University of Toronto, Canada
                                                              • Sohrab Shah (Past Faculty)
                                                                Bioinformatics group leader, BC Cancer Agency.
                                                              • Michael Stromberg (Past Faculty)
                                                                Bioinformatics scientist, Illumina, San Diego, CA
                                                              • Carl Virtanen (Past Faculty)
                                                                Director, Research Lead UHN Digital, Associate Director, HPC4Health.
                                                              • Wyeth Wasserman (Past Faculty)
                                                                Professor, Department of Medical Genetics, Senior Scientist, Centre for Molecular Medicine and Therapeutics,, University of British Columbia, Vancouver, BC