People
Andrew McPherson is an Assistant Laboratory Member at the Memorial Sloan Kettering Cancer Center in the Department of Epidemiology and Biostatistics under the supervision of Dr. Sohrab Shah. Andrew completed a PhD in computing science at Simon Fraser University under the supervision of Dr. Cenk Sahinalp and Dr. Sohrab Shah, focusing on methods for sequencing analysis, including detection and characterization of genome rearrangements, and inference of clonal phylogenies. During his post-doctoral research at University of British Columbia with Dr. Sohrab Shah, Andrew focused on the development of computational methods and infrastructure for a novel single cell sequencing plaform, Direct Library Preparation. Andrew moved to MSKCC in May of 2019 and plans to build on his post-doctoral work in single cell genomics to understand genomic instability, mutational processes, clonal evolution and the role of the microenvironment in cancer development and progression.
Dr Goldenberg is a Senior Scientist in Genetics and Genome Biology program at SickKids Research Institute, recently appointed as the first Varma Family Chair in Biomedical Informatics and Artificial Intelligence. She is also an Associate Professor in the Department of Computer Science at the University of Toronto, faculty member and an Associate Research Director, Health at Vector Institute and a fellow at the Canadian Institute for Advanced Research (CIFAR), Child and Brain Development group. Dr Goldenberg trained in machine learning at Carnegie Mellon University, with a post-doctoral focus in computational biology and medicine. The current focus of her lab is on developing machine learning methods that capture heterogeneity and identify disease mechanisms in complex human diseases as well as developing risk prediction and early warning clinical systems. Dr Goldenberg is a recipient of the Early Researcher Award from the Ministry of Research and Innovation and a Canada Research Chair in Computational Medicine. She is strongly committed to creating responsible AI to benefit patients across a variety of conditions.
Anna Panchenko completed her PhD at Lomonosov Moscow State University in Russia and pursued post-doctoral research at the University of Illinois at Urbana-Champaign and the National Center for Biotechnology Information (NCBI) at the National Institutes of Health in the USA. As a Lead Scientist at NCBI, her focus was on creating computational methods for the analysis of protein interactions, cancer driver events, and chromatin dynamics. In 2019, she joined Queen’s University as a professor and as a Canada Research Chair Tier 1, alongside a Senior Investigator role at the Ontario Institute of Cancer Research in Toronto. Her research lab delves into the links between essential epigenomic elements to uncover how their disturbances may cause cancer. Anna has authored a book on protein interactions and over 100 peer-reviewed articles. She is an editor for several scientific journals, including the Journal of Molecular Biology, eLife, and Chromosoma.
Anthony Kusalik received his M.Sc. and Ph.D. from the University of British Columbia in Vancouver, B.C., Canada in 1982 and 1988, respectively. Dr. Kusalik began a faculty position at the University of Saskatchewan in 1985. He is now a professor emeritus in the Department of Computer Science at the University of Saskatchewan. Dr. Kusalik has served on NIH/NIAAD, NSERC, and CIHR grant review panels, and on program committees of numerous bioinformatics conferences. He is a member of the ISCB.
Arnaud Droit is a full professor in bioinformatics in the Faculty of Medicine of Laval University. He is the director of the bioinformatics and proteomics platforms of the Research Center of the CHU de Québec – Université Laval. His laboratory focuses on the development of tools dedicated to the analysis of omics-type massive data, including genomics, transcriptomics, proteomics and metabolomics. His work provides a better understanding of the complex biological mechanisms of different diseases or biological phenomena. His team develops various approaches to identify multi-omics signatures using multivariate-driven methods such as machine learning and knowledge-based methods such as interaction networks.
Arneet Saltzman is an Assistant Professor in the Department of Cell and Systems Biology at the University of Toronto. Her lab uses the model organism C. elegans to study how different layers of regulation work together to control gene expression and ultimately cell fate, development and epigenetic inheritance. Current projects use genetics, cell biology and genomics approaches to understand how chromatin regulators ensure robust neuronal development and maintain the immortality of the germline.
Arvind Gupta has served as President and Vice-Chancellor of UBC and Scientific Director of Mitacs Inc. His research focuses on theoretical computer science, computational genomics and national innovation strategies. He was instrumental in creating Mitacs, the Pacific Institute for the Mathematical Sciences (PIMS), the Banff International Research Station (BIRS), and Palette Skills Inc. He serves on the Boards of IC-IMPACTS, BIRS, Simpson Centre, and Digital Health Circle. He served as a lead for the Federal Innovation Agenda, sat on the Federal blue-ribbon innovation panel (Jenkins panel), served on the national Science, Technology, and Innovation Council (STIC), and was a member of BC’s Food Security Task Force.
Dr. Zovoilis is since January 2024 an Associate Professor of Bioinformatics at the Department of Biochemistry and Medical Genetics at the University of Manitoba and a senior scientist at the Paul Albrechtsen Research Institute at CCMB. Dr Zovoilis holds a doctorate from the University of Goettingen (Germany), postgraduate training in bioinformatics from the University of Manchester (UK), and expertise in bioinformatics of next generation sequencing from his time as research fellow at Vancouver Genome Sciences Centre (Canada), a research fellow at Harvard Medical School (USA), a Canada Research Chair in RNA Bioinformatics and Genomics at the University of Lethbridge and the director of its bioinformatics core facility. He has been the founding director of the Southern Alberta Genome Sciences Center (SAGSC) and also the academic lead of the Alberta Bioinformatics Network (BioNet), and currently of its successor, the Bioinformatics Network (BioNet) Prairie. He is the director of the Bioinformatics Platform at Cancer Care Manitoba Research Institute and co-director of the Statistical Genomics and Bioinformatics Platform at the Rady Faculty of Health Sciences at the University of Manitoba. Dr. Zovoilis’ research combines translational research in medicine, in particular aging associated diseases such as cancer and dementia, with basic research in bioinformatics. His expertise in bioinformatics of next-generation sequencing (NGS) is demonstrated by multiple leading or senior author scientific publications in distinguished journals such as Cell, Science, Elife, PNAS and EMBO Reports. Being the Academic Lead of BioNet Prairie, he works to foster research collaborations and partnerships in the fields of bioinformatics and computational biology in the prairie provinces and across Canada.
Themes
Symbiotic bacteria and fungi
Genome and gene evolution
Bioinformatics, Genomics, Transcriptomics and Proteomics
SYMBIOTIC BACTERIA AND FUNGI
Multicellular organisms like plants and animals frequently interact with symbiotic microbes. They range from beneficial to pathogenic, and may live within tissues, within cells, or be in external contact. We are particularly interested in beneficial plant symbionts, to understand how they cooperate with their host, by sequencing and analyzing their genomes, transcriptomes and proteomes. This project is far-reaching for sustainable agriculture – replacement of agrochemicals by bio-pesticides, and mineral fertilizers by biofertilization.
GENOME AND GENE EVOLUTION
Understanding genome architecture, gene content and gene expression – in an evolutionary context – is the basis for understanding living organisms. We are interested in a wide range of bacteria, fungi and unicellular eukaryotes, in particular plant symbiotic species, and primitive eukaryotes that allow tracing back the origin of eukaryotes. Our comparative genomics approach regularly permits to identify innovative molecular mechanisms, such as RNA editing, trans-splicing or ribosomal hopping.
BIOINFORMATICS TOOLS FOR GENOME ANALYSIS
We are developing bioinformatics approaches for genome assembly, gene finding and functional annotation.
Our research is multi-disciplinary, based on national and international collaborations.
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.
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.