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
Jared Simpson, PhD
Research Fellow, Informatics and Biocomputing, Ontario Institute for Cancer Research
Research Interests: 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.
Richard de Borja
Bioinformatician, Informatics and Biocomputing, OICR
The Ontario Institute for Cancer Research.
Richard has been involved in the implementation and use of high-throughput sequencing analysis pipelines for genomic and transcriptome data sets. Currently, he is analyzing structural variations in prostate cancer.
Daniele Merico, PhD
Informatics Facility Manager, The Centre for Applied Genomics
Dr. Merico’s current work focuses on rare genetic variation detection, annotation and prioritization for disease gene discovery and clinical diagnostics. Daniele has also worked on pathway/network analysis for a wide range of -omics data.
Graduate Student, Molecular Oncology and Centre for Translational and Applied Genomics, BC Cancer Agency
Andrew is working towards completing a PhD in computational biology focusing on genome rearrangements in cancer. Andrew's initial PhD work focused on identifying gene fusions from RNA-Seq data, and is the author of the well known fusion discovery package named deFuse.
Dr. Michael Hoffman, PhD
Scientist (Principal Investigator), Princess Margaret Cancer Centre
I serve as principal investigator of a new computational research group focusing on the application of machine learning techniques to epigenomic data in mammalian cancer systems. We will develop dynamic Bayesian network (DBN) techniques to analyze genome-scale chromatin and functional genomics data.
Research Interests: My research group develops machine learning techniques to better understand chromatin biology. These models and algorithms transform high-dimensional functional genomics data into interpretable patterns and lead to new biological insight.
Research Interests: epigenomics; functional genomics; machine learning; dynamic Bayesian networks; chromatin; graphical models; ChIP-seq; DNase-seq; cancer
Associate Professor, Department of Statistics and Michael Smith Laboratories, UBC
Jennifer Bryan is an Associate Professor in the Statistics Department and the Michael Smith Laboratories at the University of British Columbia in Vancouver. She's a biostatistician specialized in genomics and takes a special interest and delight in data analysis and statistical computing.
Morgan Langille, PhD
Assistant Professor, Department of Pharmacology,
Our lab is interested in improving human health by looking at personal genomic and microbiome differences and how those relate to various diseases and drug metabolism.
Research Interests: genomics, microbiome, drug metabolism
Dr. William Hsiao, PhD
Chief Bioinformatician, BC Public Health Microbiology & Reference Laboratory, 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
Jianguo (Jeff) Xia, PhD
Assistant Professor, Animal Science, 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: microbiome, big data, bioinformatics, statistics
Matei David, PhD
Postdoctoral Fellow, Informatics and Biocomputing, Ontario Institute for Cancer Research
Dr. David is developing new algorithms and software for the analysis of
second- and third-generation sequencing data. He is interested in read
mapping, de novo assembly, and combining data produced by different
sequencing technologies to improve variation detection.
Post-doctoral Fellow, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto
Jüri is a computational biologist working on functional interpretation of cancer genomics data. He has previously developed tools for pathway and network analysis and studied transcription regulatory networks. Juri is the author of g:profiler.
Gary Bader, PhD
Principal Investigator, The Donnelly Centre, 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
Michelle Brazas, PhD
Manager of Research and Knowledge Exchange, Informatics & Biocomputing, Ontario Institute for Cancer Research
Dr. Brazas is involved in the development and implementation of advanced bioinformatics education programs for the Canadian Bioinformatics Workshops (CBW) series, as well as other outreach science education programs for the Ontario Institute for Cancer Research.
Research Interests: higher learning, cancer genomics, expression technologies, bioinformatics
Principal Investigator, Informatics and Biocomputing, Ontario Institute for Cancer Research
Research Interests: Dr. Boutros’ team focuses on using high-throughput genomic datasets to develop clinical tools. In particular, they work on evaluating and developing techniques for the pre-processing and machine-learning analysis of microarray and next-generation sequencing data. Their work focuses on lung, prostate, and head-and-neck cancers, amongst others.
Research Faculty at the Genome Institute, School of Medicine, University of Washington
Dr. Griffith is involved in the development and application of next-generation sequencing analysis methods for the study of cancer genomes and transcriptomes. He created and maintains the tool 'ALEXA-Seq' for alternative expression analysis by RNA sequencing (www.alexaplatform.org). His research current focus is on the integration of RNA-seq and whole genome sequence data sets and the interpretation of these data in a clinical context.
Obi Griffith, PhD
Assistant Professor of Medicine, Assistant Director, Genome Institute, Washington University School of Medicine
Research Interests: Dr. Griffith's research is focused on the development of personalized medicine strategies for cancer using genomic technologies with a particular focus on gene regulatory changes associated with breast cancer. 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 DGIdb (www.dgidb.org), ORegAnno (www.oreganno.org), CIViC (www.civicdb.org) and more.
Head Bioinformatics Scientist, Prostate Centre/Vancouver General Hospital
Dr. Lapuk's main research interest is the development of bioinformatics approaches for whole genome and transcriptome studies of human cancers. Over the last few years her research was focused on the alternative and aberrant splicing in cancer using sub-gene microarray platforms and WTSS. She is also developing methods for integration of whole genome/transcriptome data from different platforms and systems to facilitate discovery of novel predictive/prognostic biomarkers and therapeutic targets for more efficacious therapy and patient stratification.
Director, Genome Technologies, Ontario Institute for Cancer Research
New sequencing technologies have made possible the systematic identification of genetic mutations and other genomic changes in large sample sets. The Genome Technologies Platform led by Dr. John McPherson catalogues genetic alterations that occur in different types of cancers to better classify tumours and refine and develop new targeted treatments and diagnostic tools. Pancreatic ductal carcinoma and prostate cancer are major research targets. In addition, the Genome Technologies platform is participating in a pilot project to use next-generation sequencing as a clinical tool in the treatment of cancer.
Principal Investigator, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto
Dr. Morris uses machine learning and statistical modeling to do research in molecular genetics.
Research Interests: Machine learning and statistical modelling for genomic-scale experimental data; genomic dataset integration; microarray data analysis; protein-protein interaction networks; microRNAs; regulatory networks; transcription factor binding site prediction
CBW Scientific Coordinator, Associate Director, Senior Scientist, Informatics and Bio-computing, Ontario Institute for Cancer Research
Francis Ouellette’s team is involved in developing high throughput sequence analysis methods, as well as developing platforms to integrate data from various open databases. Francis continues to be interested in all databases, and the integration of that data to help our understanding of cancer.
Research Interests: Providing data provenance and openness of code, data and literature is essential to doing science. We work on next-gen sequence analysis pipelines, ICGC database curation and data coordination, Web development, and bioinformatics training and outreach.
Bioinformatics group leader, Molecular Oncology and Centre for Translational and Applied Genomics, BC Cancer Agency
Dr. Shah works on developing analytical methods for interpretation of next generation sequencing and other high dimensional genomic data from breast and ovarian cancer. His work is focused on profiling subtypes of breast and ovarian carcinoma to improve clinical management of these diseases and on discovery of novel genetic alterations. His previous work focused on probabilistic modeling of array comparative genomic hybridization data.
Research Interests: Computer Science/Bioinformatics
Director, Senior Principal Investigator, Informatics and Biocomputing, Ontario Institute for Cancer Research
Dr. Stein integrates and interprets large datasets, developing visualization tools to turn raw data into meaningful information for biologists, clinicians and trainees. Reactome, ModENCODE, and GBrowse are among Lincoln’s projects to make the human genome both accessible and navigable by scientists using the World Wide Web.
Research Interests: Bioinformatics.
Associate Professor, Departments of Biochemistry and Molecular Genetics, Director, Specialist Program in Bioinformatics and Computational Biology, University of Toronto
Director, Specialist Program in Bioinformatics and Computational Biology, University of Toronto
Dr. Steipe is active in structural bioinformatics and protein engineering. His research interests include the discovery of linear and non-linear motifs in protein structure and the application of these motifs to rational protein engineering.
Research Interests: Bioinformatics; protein engineering; motifs in protein structure
Professor, Depts of Computing Science and Biological Sciences, 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.
John Parkinson, PhD
Senior Scientist, Molecular Structure and Function, Hospital for Sick Children
Research in the Parkinson lab is focused on applying computational tools to study the evolution and operation of biological systems, and how changes in these systems can lead to human disease. Specific systems of interests range from those implicated in infectious disease to those that can modify our risk to cardiovascular disease.
Research Interests: Comparative genomics; Genome databases; Partial Genomes; Network analysis; Protein classification; Systems Biology; Dynamic simulations; Computational modelling
Robin Haw, PhD
Manager of Reactome Outreach and Scientific Associate, OICR
Robin is a microbiologist with experience in bioinformatics, curation and outreach. Dr. Haw has a PhD in genetics and was a senior curator at Biomolecular Interaction Network Database (BIND) and managing curator at Science Signaling’s Signal Transduction Knowledge Environment (STKE). He has been responsible for coordinating outreach, Reactome presentations and training at workshops and conferences.
Research Interests: Gene and Protein Annotations; Analysis of Gene Expression data; Network Biology; Database Curation
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.
Robert Beiko, PhD
Associate Professor and Canada Research Chair in Bioinformatics, Computer Science, Dalhousie University
My scientific career began at a time when there were about ten microbial genome sequences available. As this number has grown into tens of thousands, my research has asked questions of these microbes individually, collectively, and most importantly at the level of interacting sets of microorganisms. My lab has looked at evolutionary histories and interactions via processes such as lateral gene transfer, and tried to untangle some of the most complicated relationships in microbial evolution. We have also used a series of approaches to associate variation in microbial genotypes with the corresponding variation in phenotypes. Our work in microbiomics spans the development of algorithms and software for metagenomics and community analysis, the application of metagenomic techniques in model organisms and human populations, and developing views of the “community genome” that mimic those used in community ecology.
Research Interests: Bioinformatics, Comparative genomics and phylogenetics, Machine learning, Visualization of biological data
Guillaume Bourque, PhD
Associate Professor and Director of Bioinformatics, McGill University and Genome Quebec Innovation Centre
The main focus of my group is to explore functional genomics questions that can benefit from a comparative perspective. The topics covered include: the evolution of regulatory sequences, the role of transposable elements in host gene regulation and the impact of genome rearrangements in evolution and in cancer.
Past Faculty and Instructors
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.
Fiona Brinkman (Past Faculty)
Professor, Simon Fraser University, Burnaby, BC
Ryan Brinkman (Past Faculty)
Senior Scientist, Terry Fox Laboratory, BC Cancer Research Centre, Vancouver, BC
Michael Brudno (Past Faculty)
Associate Professor & Canada Research Chair in Computational Biology, University of Toronto, Toronto, ON
Stefanie Butland (Past Faculty)
Research Associate, Centre for Molecular Medicine and Therapeutics, 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
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
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
Michael Stromberg (Past Faculty)
Bioinformatics scientist, Illumina, San Diego, CA
Gary Van Domselaar (Past Faculty)
Bioinformatics Scientist, Genetics Institute, Cambridge, MA.
Wyeth Wasserman (Past Faculty)
Professor, Department of Medical Genetics, Senior Scientist, Centre for Molecular Medicine and Therapeutics,, University of British Columbia, Vancouver, BC