Instructors
Dr. Benjamin Haibe-Kains is a Senior Scientist at the Princess Margaret Cancer Centre (PM), University Health Network, and Professor in the Medical Biophysics Department of the University of Toronto. Dr. Haibe-Kains earned his PhD in Bioinformatics at the Université Libre de Bruxelles (Belgium). Supported by a Fulbright Award, he did his postdoctoral fellowship at the Dana-Farber Cancer Institute and Harvard School of Public Health (USA). He is now the Canada Research Chair in Computational Pharmacogenomics and the Scientific Director of the Cancer Digital Intelligence Program at PM. Dr. Haibe-Kains’ research focuses on the integration of high-throughput data from various sources to simultaneously analyze multiple facets of carcinogenesis. Dr. Haibe-Kains’ team analyzes large-scale radiological and (pharmaco)genomic datasets to develop new prognostic and predictive models to improve cancer care.
Dr. Bernard Lam holds a graduate degree in Plant Molecular Biology from the University of Toronto and completed a Postdoctoral appointment at Massachusetts General Hospital, Harvard Medical School. With over 13 years of experience as a Senior Research Scientist, he specialized in product and assay development for molecular biology and genomics applications within an ISO13485 and ISO15189-accredited company. In his current role as Associate Director of the Translational Genomics Laboratory, Dr. Lam oversees the day-to-day operations of the high-throughput next generation sequencing laboratory in the Genomics program of OICR.
University of Munich School of Medicine (1978-1985); Max-Planck Institute for Biochemistry (1985-1994); Gene Center of the University of Munich (1995-2001); University of Toronto (since 2001). I wish to understand complexity in adaptive systems. Complexity arises from the context dependent behaviour of system components, and in biochemistry we observe it in the hierarchies of structure formation, and the generation of function, across molecular, cellular and organismal scales. Recent scholarly work (since 2017, with Yi CHEN) has focussed on complexity in human relationality, ethics and aesthetics. Most recently (2022) I have founded the “Sentient Syllabus Project” as an international, public-good collaborative to address how academia can re-imagine itself in the face of our new wave of Artificial Intelligence capabilities. My teaching focuses on inquiry.
Caryn Geady is a graduate researcher specializing in quantitative imaging and data science. With a Bachelor’s degree in Physics (Medical Physics and Imaging) from Toronto Metropolitan University (TMU) and a Master’s degree in Medical Biophysics from the University of Toronto (UofT), she brings a strong foundation in both theoretical and practical aspects of medical imaging. Caryn is passionate about teaching, having helped launch Supported Learning Groups at TMU to aid students in mastering challenging course concepts. Currently pursuing a Ph.D. at UofT, her research focuses on machine learning techniques for assessing treatment response in advanced cancers.
Chaitra is a computational biologist with experience in software development. During her PhD, she applied mathematical modelling, network analysis and multi-omics integration to study complex diseases. She has contributed to open-source toolboxes (openCOBRA) and developed softwares (EFMviz & ComMet) to analyse genome-scale metabolic models. She currently works in the Bader lab’s MODiL team (Multi Omics Data Integration and Analysis) and with groups at PMCC, where she develops pipelines to analyse various omics data types and discover new drug targets in cancer.
I’m an Assistant Professor in the Division of Oncology, where my focus is on developing and applying computational tools to provide insight into the origins and progression of cancer. I earned Bachelor degrees in Biology and Computer Science from Truman State University and my PhD in Computational Biology from Baylor College of Medicine.
My core research interests include understanding the clonal architecture of tumors and how they evolve in response to therapy, with a special focus on hematologic cancers. I also study effective design and targeting of cancer immunotherapies, developing open-source software for interpreting and visualizing genomic data, and integrative analysis that translates multi-dimensional genomic data into both functional and actionable contexts.
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.
Over the past 30 years Dr. Wishart has conducted world-leading research in many areas, including bioinformatics, metabolomics, structural biology and machine learning. He has also made important contributions to medical diagnostics, agri-food research, environmental science and analytical chemistry. Dr. Wishart is considered one of the early pioneers in the field of metabolomics and has played a foundational role in the development of bioinformatics and cheminformatics in North America.
Based on his many important contributions to metabolomics, Dr. Wishart was made a lifetime fellow of the Metabolomics Society in 2014, the society’s highest honour. In recognition of his outstanding accomplishments in bioinformatics, metabolomics and structural biology, he was elected as a Fellow of the Royal Society of Canada (2017), received a University of Alberta Alumni award (2018) and was appointed as a Distinguished University Professor (2018).
He has developed a number of techniques based on NMR spectroscopy, mass spectrometry, liquid chromatography and gas chromatography to characterize the structures of both small and large molecules. As part of this effort, Dr. Wishart has led the “Human Metabolome Project” (HMP), a multi-university, multi-investigator project that is cataloguing all theknown chemicals in human tissues and biofluids. Using a variety of analytical chemistry techniques along with text mining and machine learning, Dr. Wishart and his colleagues have identified or found evidence for more than 250,000 metabolites in the human body.
This information has been archived on a freely accessible web resource called the Human Metabolome Database (HMDB). Dr. Wishart has also been using machine learning and artificial intelligence to help create other useful chemistry databases, such as DrugBank, FooDB and ContaminantDB and software tools (such as MetaboAnalyst, CFM-ID and BioTransformer) to help with the characterization and identification of metabolites, drugs, pesticides and natural products. Over the course of his career Dr. Wishart has published more than 500 research papers in high profile journals on a wide variety of subject areas. These papers have been cited over 120,000 times.
Dr. Eduardo Taboada is an internationally recognized expert on the molecular epidemiology and genomics of Campylobacter jejuni. In 1999 he completed a Ph.D. in molecular genetics at the University of Ottawa and joined the National Research Council, to work on C. jejuni genomics. Since joining the Public Health Agency of Canada’s as a Research Scientist in 2006, he has developed a research programme focusing on bacterial comparative genomics, genome dynamics and the application of genomics approaches towards the study of the molecular surveillance and epidemiology of priority food- and water-borne bacterial pathogens. He leads the Campylobacter Genomics Laboratory at the National Microbiology Laboratory and is head of the Genomic Epidemiology Research Unit. In addition of being a co-principal investigator of a Genome Alberta-funded project on large-scale sequencing on Campylobacter in the Canadian poultry chain, he is a co-investigator on a Genome Canada-funded project on AMR emergence, transmission and ecology and a work package leader in the Government of Canada’s Genomics Research Development Initiative interdepartmental project on AMR.