Faculty

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

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

Contact Details

Jianguo (Jeff) Xia, PhD

Assistant Professor, Institute of Parasitology and Department of 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: bioinformatics, statistics, metabolomics, transcriptomics, network biology

Contact Details

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.

Contact Details

  • Location: ON

Juri Reimand

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.

Irina Kalatskaya, PhD

Project Manager and Computational Biologist, Informatics and Bio-computing, Ontario Institute for Cancer Research

Dr.Kalatskaya’s research focuses on the downstream analysis of the cancer-related high-throughput data (sequencing, gene expression, proteomics) using pathway- and network-based analysis. She is looking for regions of highly interconnected proteins that can help to generate biologically relevant hypothesis and/or serve as prognostic signatures in cancer patient management. She is also providing scientific and management support for the high scale Genome Canada project titled “Early detection of patients at high risk of esophageal adenocarcinoma” in OICR.

Contact Details

  • Location: ON

Junjun Zhang, PhD

Project Leader, Data Centre, Informatics and Bio-computing, Ontario Institute for Cancer Research

Junjun works in the software development team at the Data Coordination Centre, OICR, contributes to developing large-scale data management system for the International Cancer Genome Consortium that is aimed to generate comprehensive catalogues of genomic abnormalities for 50 different cancer types, totaling 2500 patients. Junjun is also interested in developing software tools for integrative data management and analysis for cancer genomics research.

Vincent Ferretti, PhD

Associate Director, Informatics and Bio-computing, Ontario Institute for Cancer Research

Dr. Vincent Ferretti's expertise is in bioinformatics with experience in both large-scale software development and computational genomics. Among numerous other large scale projects, he heads the software infrastructure development of the International Cancer Genome Consortium (ICGC) Data Coordination Center, which is responsible for building the consortium‘s databases and public data web portal.

Sorana Morrissy, PhD

Post-Doctoral Fellow, Hospital for Sick Children

Dr Morrissy works on the genomics and transcriptomics of medulloblastoma using next-gem sequencing data. Her current research focuses on understanding the clonal evolution of recurrent disease, and the on elucidating the transcriptional regulation of clinically distinct medulloblastoma subgroups.

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.

Contact Details

  • Location: Toronto, ON

Fong Chun Chan

PhD Candidate, Department of Bioinformatics, University of British Columbia

Fong is currently undertaking a PhD in Bioinformatics and is co-supervised by Dr. Sohrab Shah and Dr. Christian Steidl. His main research interest is in the implications of tumour genomic diversity on disease progression in B-cell lymphomas. In particular, how tumour evolution plays a role in treatment resistance and how understanding this process may aid in the determination of relevant and precise therapeutic approaches for each cancer patient.

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.

Contact Details

  • Location: Toronto, ON

Philip Awadalla, PhD

Senior Investigator, Informatics and Biocomputing, Ontario Institute for Cancer Research

Philip is a Principal Investigator of the Canadian Partnership for Tomorrow Project and biobank. He is also the Director of the Genome Canada, Canadian Data Integration Centre. His team focuses on the development of next-generation genomics approaches, model-based tools and population-based approaches to study mutation rates, genome biology, and cancer. His team’s research also focuses on systems and population genomics approaches to capture signals in population-based samples or families as well as tools to capture rare or de novo variants, potentially critical to disease phenotypes.

Contact Details

  • Location: AB

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.

Contact Details

  • Location: ON

Martin Hirst, PhD

Assistant Professor, University of British Columbia, Centre for Hightroughput Biology (CHiBi)

The overall objectives of Martin's lab are directed at understanding the role of epigenetics in cancer and to investigate the therapeutic potential of interventions directed at epigenetic processes. We approach this from an epigenomic perspective by combining innovative molecular biology and computational techniques with genome wide detection platforms.

Andrew McPherson

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.

Contact Details

  • Location: BC

George Mihaiescu

Senior Cloud Architect, Informatics and Biocomputing, Ontario Institute for Cancer Research

George specializes in cloud technologies and virtualization with a focus on Openstack and related open-source projects. George has played a lead role in the development of the Cancer Genome Collaboratory and GDC.

Dr. Michael Hoffman, PhD

Scientist (Principal Investigator), Princess Margaret Cancer Centre

Assistant Professor, Department of Medical Biophysics, University of Toronto
Assistant Professor, Department of Computer Science, University of Toronto

I serve as principal investigator of a computational research group focusing on the application of machine learning techniques to epigenomic data in mammalian cancer biology. We develop techniques to analyze genome-scale chromatin, methylation, and 3D genome organization 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

Contact Details

Jennifer Bryan

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.

Contact Details

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

Contact Details

  • Location: NS

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

Contact Details

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

Contact Details

  • Location: Toronto, ON

Dr. Fiona Brinkman, PhD

Professor, Molecular Biology and Biochemistry, SFU

Dr. Brinkman is developing bioinformatic resources to better track infectious diseases using genomic data, and improve prediction of new vaccine/drug targets. Her primary aim is to develop more sustainable, integrated approaches for infectious disease control, however she is also applying her methods to aid allergy and environmental research.

Research Interests: Genomic epidemiology; microbial evolution; bacterial protein subcellular localization; genome annotation; data integration

Contact Details

  • Home page: Homepage
  • Location: Greater Vancouver, BC

Paul Boutros

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.

Contact Details

  • Location: Toronto, ON

Malachi Griffith

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.

Contact Details

Obi Griffith, PhD

Assistant Professor of Medicine, Assistant Director, McDonnell 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.

Contact Details

Anna Lapuk

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.

Contact Details

  • Location: Vancouver, BC

John McPherson

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.

Contact Details

  • Location: Toronto, ON

Quaid Morris

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

Contact Details

Francis Ouellette

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.

Contact Details

Sohrab Shah

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

Contact Details

Lincoln Stein

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.

Contact Details

Boris Steipe

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

Contact Details

David Wishart

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.

Contact Details

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

Contact Details

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

Contact Details

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.

Contact Details

  • Location: ON

Stephen Montgomery, PhD

Assistant Professor, Stanford University

Stephen's lab studies genetic effects on gene regulation and gene expression to identify the molecular and cellular mechanisms which define human traits.

Contact Details

  • Location: AB

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

Contact Details

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.

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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.

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