Canadian Bioinformatics Workshops: Summer 2019

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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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    Robert Beiko, PhD

    • Associate Professor and Canada Research Chair in Bioinformatics, 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

    Website:
    http://kiwi.cs.dal.ca/~beiko
    Location:
    Halifax, NS
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    Misha Bilenky

    • Staff Scientist, Canada's Michael Smith Genome Sciences Centre

    For a number of years Misha was involved in studies of cellular gene expression regulation in collaboration with biomedical researchers, performing data analysis and developing recourses. He has developed tools for quality assessment and analysis of NGS data. More recently Misha is interested in the analysis of NGS experiments that involve data from a single-cell or small amount of cells.

    Research Interests:

    Computational Biology, Bioinformatics, Gene regulation, Epigenomics

    Contact Details

    Location:
    Vancouver, BC
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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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    Paul Boutros, PhD

    • Principal Investigator, Ontario Institute for Cancer Research

    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
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    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; metagenomics; microbiome analysis; bacterial protein subcellular localization; genome annotation; ontologies and data standards; data integration

    Contact Details

    Website:
    Homepage
    Location:
    Greater Vancouver, BC
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    Michael Brudno

    • Director, Hospital for Sick Children

    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.

    Contact Details

    Website:
    http://www.cs.toronto.edu/~brudno
    Location:
    TorontoCa
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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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    Florence Cavalli, PhD

    • Postdoctoral Fellow, University of Toronto

    Dr. Cavalli works on cancer genomics analyzing methylation and next-generation sequencing data. Her current research focuses on understanding the gene expression regulation behind different medulloblastoma subgroups and subtypes.

    Contact Details

    Location:
    Toronto
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    Anamaria Crisan

    • PhD Student, University of British Columbia

    Anamaria is a PhD student in Computer Science at the University of British Columbia, co-supervised by Drs. Tamara Munzner and Jennifer Gardy. She studies how datasets with thousands of patients and heterogeneous data types (genomic, demographic, outcomes, treatments etc.) can be integrated and effectively visualized. Her work aims to contribute methodological guidance and visualization tools to both public health and information visualization research and practitioner communities. Prior to starting a PhD in information visualization, she worked as a bioinformatician developing cancer biomarkers.

    Contact Details

    Location:
    BC
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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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    Anna Goldenberg, PhD

    • Scientist, Sick Kids

    Assistant Professor, Department of Computer Science, University of Toronto

    Dr. Goldenberg trained in machine learning and statistics at Carnegie Mellon University, with a post-doctoral focus in computational biology. She is an expert in developing machine learning approaches for biological data, network methods and most recently, data integration of -omics and clinical data. The current focus of her lab is on developing methods that capture heterogeneity and identify disease mechanisms in complex human diseases. Her translational focus is on methods that efficiently combine many types of patient measurements to refine diagnosis, improve prognosis and personalize drug response prediction for cancer patients.

    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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    Brian Haas

    • Senior Computational Biologist, Broad Institute

    Brian is a Senior Computational Biologist at the Broad Institute and lead developer of the popular Trinity RNA-Seq de novo assembly software. Brian’s research focuses on efforts to leverage transcriptome data to further improve our understanding of cancer biology and to build a cancer transcriptome analysis toolkit that leverages Trinity.

    Contact Details

    Website:
    Homepage
    Location:
    MA, us
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    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

    Website:
    http://www.reactome.org
    Location:
    Toronto
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    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.

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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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    Morgan Langille, PhD

    • Assistant Professor, Dalhousie University

    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
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    Andrew McArthur, PhD

    • Associate Professor, McMaster University

    The McArthur laboratory’s research program is rooted in bioinformatics, functional genomics, and computational biology. It spans complex informatics approaches to the functional genomics of microbial drug resistance, development of biological databases, next generation sequencing for genome assembly and molecular epidemiology, automated literature curation approaches, controlled vocabularies for biological knowledge integration, and functional genomics approaches in environmental toxicology. As part of our Cisco funded program, we additionally research the use and generation of ‘Big Data’ in the biomedical sciences, with the goal of integrating biomedical research and clinical healthcare.

    Research Interests:

    Biological database design and predictive analytics, particularly in the areas of antimicrobial drug resistance and molecular epidemiology; Comprehensive Antibiotic Resistance Database (arpcard.mcmaster.ca); Development of Integrated Health Biosystems research at McMaster University, bridging data-intensive biomedical research and clinical healthcare; Bioinformatics workflows and Cloud computing for gene expression, gene regulation, and population genomics; Next generation DNA sequence analysis, genome assembly, and genome annotation; Molecular phylogenetics and phylogenomics; Ecotoxicogenomics of environmental contaminants (metals, organics, pharmaceuticals) using zebrafish, mouse, and other model systems.

    Contact Details

    Website:
    mcarthurbioinformatics.ca
    Location:
    Hamilton
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    Andrew McPherson, PhD

    • Post Doctoral Fellow, BC Cancer Agency

    Andrew’s research focuses on the development of algorithms and computational methods for understanding cancer genome sequence data. He is interested in genome rearrangements, copy number variation and relevant mutational mechanisms including genomic instability. Additionally, Andrew’s work focuses on understanding tumour evolution, with specific application to ovarian 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
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    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.

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    Quaid Morris

    • Principal Investigator, 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

    Website:
    http://morrislab.med.utoronto.ca
    Location:
    Toronto
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    Sorana Morrissy, PhD

    • Post-Doctoral Fellow, Hospital for Sick Children

    Dr. Morrissy works on the genomics and transcriptomics of medulloblastoma using next-gen 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. Sorana will be starting her own lab at the University of Calgary in January 2018.

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    BF Francis Ouellette

    • Scientific Coordinator, 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:
    CSB University of Toronto
    Twitter:
    @bffo
    Location:
    Montreal, QC
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    John Parkinson, PhD

    • Senior Scientist, 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

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    Mark Phillips

    • Academic Associate, McGill University

    I hold an LL.B. and a B.C.L. from McGill University’s Faculty of Law, as well as a B.Sc. (Honours) in Computer Science from the University of Manitoba. My research interests include comparative data-privacy law and policy, open data, open standards, personal identifiability of data, unique personal identifiers, cloud computing, Big Data, bioinformatics, surveillance, dynamic consent, and health information commons and co-operatives. I am a former editor of both the McGill Journal of Law and Health and of the McGill Law Journal.

    Research Interests:

    data privacy, comparative law, open data, cloud computing, de-identification, unique identifiers

    Contact Details

    Location:
    Montreal, QC
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    Trevor Pugh, PhD

    • Scientist, University Health Network

    Assistant Professor, Department of Medical Biophysics, University of Toronto

    I am focused on the application of genome sequence analysis as a routine clinical test, particularly as modern cancer treatments are predicated on genetic information. I am particularly interested in genome analysis of serial biopsies and circulating tumour DNA collected during clinical trials (particularly immunotherapies), genetic relationships amongst metastatic sites suggestive of effective combination therapies, and oncogenic mechanisms underlying rare tumours of unknown etiology including pediatric, breast, neuroendocrine, and gynecologic cancers. I also spend part of my time supporting diagnostic testing as a clinical molecular geneticist in the University Health Network Laboratory Medicine Program.

    Research Interests:

    cancer genomics, clinical molecular genetics, data sharing

    Contact Details

    Website:
    UHN homepage Cancer Genomics Program
    Location:
    Toronto
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    Jüri Reimand, PhD

    • Principal Investigator, Ontario Institute for Cancer Research

    Assistant Professor, Department of Medical Biophysics, 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.

    Contact Details

    Location:
    Toronto
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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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    Lincoln Stein

    • Director, Senior Principal Investigator, 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

    Website:
    http://oicr.on.ca/person/researcher/lincoln-stein
    Location:
    Toronto
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    Boris Steipe

    • Associate Professor, 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

    Website:
    http://biochemistry.utoronto.ca/steipe/
    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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    Fouad Yousif

    • Research Associate, Informatics and Biocomputing, Ontario Institute for Cancer Research

    Fouad is a member of the Informatics and Biocomputing team at OICR. His current role in Paul Boutros’s team involves algorithm development and biomarker discovery analysis for different types of cancers including Prostate and Breast. Fouad was also a member of the sequencing production team that is responsible for the optimization and parallelization of algorithms for the analysis of genome-sequencing data. His work has been focused on the assembly, evaluation and assessment of the RNA-seq pipeline at OICR. He is also involved in the development of sequencing QC methods, downstream expression analyses and the integration of the RNA-seq data with other data sets.

    Research Interests:

    Cancer research, biomarker discovery, algorithm Development , RNA-seq, Teaching, Biostatistics

    Contact Details

    Location:
    Toronto
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    Christina Yung, PhD

    • Project Manager, Ontario Institute for Cancer Research

    Christina has a PhD in Biomedical Engineering from the John Hopkins University School of Medicine. She is currently the project manager of the technical working group of the PanCancer Analysis of Whole Genomes (PCAWG). She has coordinated the analysis of 800TB of sequencing reads from over 2800 patients utilizing 14 compute environments including Amazon Web Services, Microsoft Azure, Sun Grid Engine and OpenStack. Christina is also the project manager of the Cancer Genome Collaboratory, an academic cloud newly built in Canada for cancer research.

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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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    Peter Ronning

    • Graduate student, McDonnell Genome Institute, Washington University in St. Louis

    Peter is a 2nd year PhD student in the Molecular Genetics and Genomics program at Washington University in St. Louis. He is a member of the Griffith lab and is in the Precision Medicine pathway. He using “omics” data to study tumor immunology and predict personalized immunotherapy treatments through bioinformatic analysis and machine learning models. He is currently focused on characterizing the tumor/immunologic profile of immuno-humanized mice.

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    Heather Gibling

    • PhD Candidate, Ontario Institute for Cancer Research

    Heather is a PhD candidate in the Awadalla and Simpson labs at OICR in Toronto. Her research focuses on developing computational approaches to improve sequencing read alignment and variant detection to better study genomic polymorphisms relevant to cancer.

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    Christopher Miller, PhD

    • Assistant Professor, McDonnell Genome Institute, Washington University School of Medicine

    Dr. Miller’s research focuses on developing and applying computational tools to provide insight into the origins and progression of cancer. He has particular interest in understanding the clonal architecture of tumors and how they evolve in response to therapy.

    Contact Details

    Website:
    http://chrismiller.science/
    Location:
    St. Louis, MO, US
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    Megan Richters

    • PhD candidate in Molecular Genetics and Genomics, Washington University School of Medicine

    Megan is a PhD student in Molecular Genetics and Genomics at Washington University School of Medicine, where she is supervised by Dr. Malachi Griffith. Her research is focused on analyzing tumor-specific alternative splicing patterns and hotspot mutations in cancer genomic sequencing data to discover immunogenic neoantigen sources. The goal of this work is to improve the efficacy of personalized immunotherapies by increasing the amount of predicted neoantigens available for use in cancer vaccines.

    Contact Details

    Location:
    St. Louis, MO, US
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    Michelle Brazas, PhD

    • Senior Program Manager, Adaptive Oncology, Ontario Institute for Cancer Research

    Dr. Michelle Brazas is the Senior Program Manager for Adaptive Oncology at the Ontario Institute for Cancer Research (OICR), a program encompassing a wide variety of projects from imaging, informatics, genomics and diagnostic development. She is also the Project Manager for the Cancer Genome Collaboratory project (cancercollaboratory.org), an academic compute cloud environment for analysis across the ICGC dataset. Previously, she was the Lead for Bioinformatics.ca, a national bioinformatics continuing education program and a faculty member in Biotechnology at BCIT. She founded and runs the Toronto Bioinformatics User Group (TorBUG), and plays an active role in the International Society of Computational Biology where she sits on the Board of Directors. She is also on the Executive Board of the Global Organisation for Bioinformatics Learning, Education & Training (GOBLET), where she helps coordinate bioinformatics training endeavours worldwide. She completed a PhD in Microbiology at the University of British Columbia and an undergraduate degree in Pharmacology from McMaster University.

    Research Interests:

    Higher learning, cancer genomics, expression technologies, bioinformatics

    Contact Details

    Location:
    Toronto, ON, CA
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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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    Pascale Marquis

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

    Pascale works in Guillaume Bourque’s lab, she provides services for client and users at the Canadian Centre for Computational Genomics (C3G) at McGill University. Processing, mainly of large-scale whole genome sequencing project.

    Contact Details

    Location:
    Montreal, QC, CA
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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.

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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

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
  • 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