People
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.
Ashleigh is a postdoctoral fellow working in the Miller Lab at the Michael Smith Laboratories, University of British Columbia. Her work aims to understand how neural stem cells of the ventricular-subventricular zone can be activated and recruited for brain repair and remyelination, with a particular interest in the influence of the environment in this process. Ashleigh uses single cell RNA-sequencing and single-cell spatial transcriptomics (including 10X Xenium), combined with in vivo murine models, to address these questions. Her work is currently funded by an endMS fellowship from the MS Society of Canada.
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.
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.
Brian Fristensky attended the College of Arts and Sciences at Cornell University, where he completed his A.B. in Biology in 1980. After graduation he worked as a technician with Dr. Ray Wu. where he authored the Cornell Sequence Analysis Package, one of the first packages of sequence programs. In 1982 he joined the lab of Lee Hadwiger at Washington State University, in one of the first attempts to clone plant defense genes. In 1987 he was awarded his Ph.D. in Genetics and Cell Biology. On a postdoctoral fellowship from the North Carolina Biotechnology Center, he worked on light regulated gene expression with Dr. William F. Thompson at North Carolina State University. In 1990 he joined the University of Manitoba Plant Science Department, where he is currently an Associate Professor. Publications topics include disease resistance in plants, genetic engineering of disease resistance, machine learning and bioinformatics software.
Our research interests are in the area of bioinformatics, molecular evolution and DNA sequence analysis. Our research attempts to understand how the processes of evolution act to cause the changes observed between molecules, between genes and between genomes. The recent advances in molecular genetics provide a storm of new data on DNA sequences, on gene structure and higher order genomic structure. However, the implications of these new data are not always clear.