People

Audrey is an M.Sc. student in the lab of Dr. Guillaume Bourque, in the Department of Human Genetics at McGill. She specializes in bioinformatics, more specifically on how genomic architecture and transcription are interrelated.

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.

Cancer genomics researcher working on pediatric leukemia.

My group’s research focuses on the regulation of gene expression, which is fundamental to our efforts to understand and engineer biological systems, and is a critical aspect of nearly every disease. Our research includes DNA synthesis and omics technology development, algorithm and computer model design, and drug design and discovery.

Dr. Carolina Tropini is an Assistant Professor at UBC in the Department of Microbiology and Immunology, and School of Biomedical Engineering. She is recognized as a Paul Allen Distinguished Investigator and, in 2020, became the first Canadian to receive the Johnson & Johnson Women in STEM2D Scholar award in Engineering. She’s the inaugural Alan Bernstein CIFAR Fellow in the Humans & the Microbiome Program and a Michael Smith Foundation for Health Research Scholar. In 2019, she was selected as a CIFAR Azrieli Global Scholar. Her lab explores the impact of disrupted physical environments, like altered nutrition or intestinal diseases, on microbiota and hosts across multiple scales. This cross-disciplinary team integrates microbiology, bioengineering, and biophysics to study bacterial and microbial community functions, aiming to enhance human health. Dr. Tropini completed her Ph.D. in Biophysics at Stanford University, where she combined computational and experimental methods to study bacterial mechanics and morphogenesis. As a postdoc in Dr. Justin Sonnenburg’s lab at Stanford, she focused on the effects of physical disruptions on gut-associated microbial communities, supported by a James S. McDonnell Foundation Postdoctoral Fellowship Award.

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.