Instructors
Her research is focused on understanding intratumoral heterogeneity, tumor evolution, and the tumor microenvironment at single cell resolution. She uses computational approaches to analyze, integrate, and interpret large-scale genomic data, with an emphasis on single-cell RNA-sequencing data. She completed a PhD in Genetics in the laboratory of George Church at Harvard Medical School, and a postdoctoral fellowship in Systems Biology with David Botstein at Princeton University. She was Research Faculty under the mentorship of Tim Ley at Washington University and the McDonnell Genome Institute.
I conduct interdisciplinary research that integrates techniques and methods from machine learning, human computer interaction, and data visualization. I analyze data, build tools, and conduct evaluative studies. My research focuses on the intersection of Data Science and Data Visualization. I am especially interested in the way humans can collaboratively work together with ML/AI systems through visual interfaces. I completed my PhD in Computer Science at the University of British Columbia, where I was jointly advised by Tamara Munzner and Jennifer Gardy. Prior to my PhD, I was a research scientist at the British Columbia Centre for Disease Control and Decipher Biosciences, where I conducted research machine learning and data visualization research toward applications in infectious disease and cancer genomics. My research has appeared in publications of the ACM (CHI), IEEE (TVCG, CG&A), Oxford Bioinformatics, and Nature.
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.
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.
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.
Boris Steipe was born in Munich, Germany where he graduated from the medical school of the Ludwig-Maximilians University in 1985. He joined Andreas Plückthun’s lab at the Gene Center of the University for his PhD thesis on the recombinant expression and structure determination of an immunoglobulin fragment. Subsequently, his interests turned to protein engineering, and he joined Robert Huber’s Department at the Max-Planck Institute for Biochemistry in Martinsried, Germany in 1990. It was there that his “Canonical Sequence Approximation” – the hypothesis that sequence propensities can be used to predict stability changes in a very general way was first formulated.
Steipe was appointed Research Fellow at the Gene Center of the University, in 1990 and where his group worked on the rational stabilisation of immunoglobulin domains, on sequence determinants of protein folding and on the interplay of the protein matrix with the fluorophore in Green Fluorescent Protein; he was awarded his Habilitation in Biochemistry at the Faculty for Chemistry and Pharmacy of the University in 2000, when he was appointed as lecturer.
In 2001 Steipe moved to Toronto where he holds an appointment as associate professor in the Department for Biochemistry and the Department for Molecular Genetics, University of Toronto. His directed the University’s Specialist Program in Bioinformatics and Computational Biology from 2004 to 2019.
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.
Dr. Wishart has active research programs in structural biology, nanobiology, synthetic biology, prion biology, bioinformatics and metabolomics. Some of his lab’s most significant contributions have been in the area of protein chemical shift analysis and the prediction of protein structure. Using advanced methods in NMR spectroscopy, mass spectrometry, multi-dimensional chromatography and machine learning Dr. Wishart and his colleagues identified or found evidence for more than 8000 endogenous metabolites (Human Metabolome Database).