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
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.
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
Graduate Student, Molecular Oncology and Centre for Translational and Applied Genomics, BC Cancer Agency
Aaron Quinlan, PhD
Assistant Professor, Center for Public Health Genomics, University of Virginia
Dr. Quinlan's laboratory develops and applies new computational methods towards the understanding of genetic variation and genome biology in diverse contexts. His laboratory is particularly interested in the mechanisms that drive variation in chromosome structure in the germline and the soma. Current research projects include: (1) the origins of genome instability in glioblastoma, (2) improved methods for detecting structural variants with modern sequencing technologies, (3) new statistical approaches to exploring and interpreting high-dimension genomics datasets (e.g., ENCODE), and (4) software for mining genetic variation in the context of human disease.
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.
Nicholas Harding, PhD
Postdoctoral Fellow, Informatics and Biocomputing, Ontario Institute for Cancer Research
Dr. Harding primarily works with developing and evaluating computational pipelines for the analysis of next-generation sequencing (NGS) data, in the context of a large prostate cancer study. Recently he has carried out analysis of microarray data examining how transcription of ER proteins in liver and colorectal cancer cells changes in the absence of oxygen.
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.
Senior Scientist, Terry Fox Laboratory, BC Cancer Research Centre
Research Interests: My group is focused on applying bioinformatics techniques to flow cytometry data. Flow cytometry is a technique that is widely used within the biomedical community. New high throughput methods can generate up to a thousand flow cytometry data files per day and each data file can consist of millions of multiparametric descriptions of individual cells. We are leading an international effort to develop a systemic approach to modeling, capturing, analyzing and disseminating flow cytometry data.
Faculty Member/Group Leader Academic, Computer Science, University of Toronto
Dr. Brudno works on genome assembly and discovery of variation using Next Generation Sequencing data. He is also interested in development of bioinformatics tools and population genomics.
Research Interests: Comparative genomics; Algorithms for biological data.
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
Research Assistant Professor, Genome Institute, Washington University School of Medicine
Research Interests: Dr. Griffith is involved in the development and application of clinical statistics, machine-learning and next-generation sequencing analysis methods for the study of cancer. He has worked on tools for annotation of the regulatory genome (ORegAnno) and subspace clustering of large-scale gene expression data (KiWi) and has developed molecular signatures for diagnostic, prognostic and drug sensitivity prediction with specific focus on thyroid and breast cancer.
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
Associate Director, Principal Investigator, 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. People in my group will strive to doing this at all time. We will do it for our analysis of Cancer genomic data, or for linking genes and diseases together.
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
Bioinformatics scientist, illumina
Dr. Strömberg develops core algorithms and software workflow spanning base-calling, reference-guided alignment, de novo assembly, and variant calling for upcoming sequencing platforms. Previously while working in the Marth Lab at Boston College, Dr. Strömberg developed a reference-guided aligner, MOSAIK, while analyzing sequencing data in the 1000 Genomes Project.
Professor, Department of Medical Genetics, Senior Scientist, Centre for Molecular Medicine and Therapeutics,, University of British Columbia
Centre for Molecular Medicine and Therapeutics, University of British Columbia
Dr. Wasserman develops algorithms for the analysis of regulatory sequences, with the goal of understanding how, when and where each gene will be expressed. His group creates community resources like the JASPAR and PAZAR databases.
Research Interests: Genome sequence analysis, identification of regions regulating transcription, gene expression
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.
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.
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
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
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
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
Gary Van Domselaar (Past Faculty)
Bioinformatics Scientist, Genetics Institute, Cambridge, MA.