Current Lab Members
Kieran R Campbell
Canada Research Chair in Machine Learning for Translational Biomedicine, Principal Investigator (LTRI) & Assistant Professor (University of Toronto)
Kieran received his BSc from the University of Edinburgh in Mathematical Physics followed by a masters in Computational Biology at Cambridge University and a DPhil (PhD) in statistical genomics at Oxford University. He was subsequently a Banting postdoctoral fellow at the University of British Columbia and BC Cancer Agency (2017-2019). He is now Principal Investigator & Scientist at the Lunenfeld-Tanenbaum Research Institute, an Assistant Professor in the Departments of Molecular Genetics and Statistical Sciences, University of Toronto, and affiliate faculty at the Ontario Institute for Cancer Research.
Michael Geuenich
PhD Student Molecular Genetics (CBMG Track)
Michael received a BA & Sc. from Quest University Canada where he worked on a phylogenetic analysis of two genes that have been linked to Shwachman-Diamond syndrome. As part of his thesis he also created an assignment aimed at introducing biology majors to the real of computational biology. Before graduating he joined the Eisenman lab at the Fred Hutchinson Cancer Research Center for a year where he worked on analyzing data genomic occupancy data surrounding the MYC transcription factor network. Now his work involves building machine learning models to better understand immune escape mechanisms in PDAC using all kinds of omics data.
Shanza Ayub
PhD Student Molecular Genetics (CBMG Track)
Shanza received her HBSc from University of Toronto Mississauga majoring in Biology for Health Science and Mathematics. During her undergrad, Shanza undertook a bioinformatics and genomics research project with the Ness Lab at UTM looking at polymorphic transposable elements in the green algae, C. reinhardtii, which then became her senior thesis. She also worked on a Math research project with Dr. Jacopo De Simoi investigating the dynamical spectral rigidity of ellipses. Currently, Shanza is a PhD student in the Computational Biology for Molecular Genetics track at UofT and a Graduate Student at the Lunenfeld-Tanenbaum Research Institute. She is supervised by Kieran Campbell and works in close collaboration with the Jackson lab. Her work involves the development of machine learning models for Imaging Mass Cytometry (IMC) data.
Chengxin Yu
PhD Student Molecular Genetics (CBMG Track)
Chengxin received his BSc from McGill University majoring in Neuroscience and minoring in Computer Science. During his undergrad, Chengxin undertook a behavioral research project with the Britt Lab at McGill looking at the impact of nucleus accumbens dopamine signaling on the saliency of external cues. He also worked on a simulation project with Dr. Sjöström, exploring the pedagogical potential of the LIF and the HH model. Currently, Chengxin is a PhD student in the Computational Biology for Molecular Genetics track at University of Toronto and a Graduate Student at the Lunenfeld-Tanenbaum Research Institute.
Alina Selega
Postdoctoral Fellow (Machine Learning)
Alina received a BSc in Computer Science and Mathematics from the University of York, UK. She then earned an MSc in Computational Neuroscience and Neuroinformatics from the University of Edinburgh, UK, where she investigated functional hippocampal-cortical connectivity. Following this, Alina completed her PhD at the School of Informatics, University of Edinburgh. During her PhD studies, she developed machine learning methods for the analysis of high-throughput sequencing data focusing on RNA biology, e.g. RNA secondary structure and RNA-protein interactions. In 2019, Alina started her postdoctoral training in the lab of Dr. Quaid Morris at the University of Toronto and Vector Institute. Alina's postdoctoral work involved segmentation methods for copy number inference from single-cell RNA-sequencing (scRNA-seq) data, linking genotype and phenotype in tumour cells. Currently, Alina is a postdoctoral fellow in Campbell Lab at the Lunenfeld-Tanenbaum Research Institute and is working on automatic machine learning methods for recommending optimal workflows for scRNA-seq analysis.
Cait Harrigan
PhD Student (Computer Science)
Cait earned her BSc. in Computational Biology, and MSc. in Computer Science at the University of Toronto. Her research interests are centered on machine learning, cancer evolution, and mutational signatures. Cait is co-supervised by Quaid Morris and Kieran Campbell, currently working on applying topic modeling approaches to understand mutational signatures in pan-cancer whole genome sequencing data.
Morris Greenberg
PhD Student (Statistical Sciences)
Morris earned his BA in Mathematics and Quantitative Economics at Tufts University, and MSc. in Statistical Science at Duke University. His research interests center around Bayesian modeling and Bayesian nonparametrics for high dimensional health care data. While at Duke, he worked on developing Gaussian Process models for microbiome data from cell transplantation patients with Professor Li Ma. Morris is co-advised by Radu Craiu and Kieran Campbell of the Statistical Sciences department.
Jett (Yuju) Lee
PhD Student (Computer Science)
Jett earned his BS in Statistics and Mathematics & Economics, and MS in Statistics and Computer Science at the University of California, Los Angeles (UCLA). His research interests are center around single-cell image mass cytometry (IMC) data and statistical machine learning. Currently, he is developing generative probabilistic models for IMC. Jett is co-advised by Bo Wang and Kieran Campbell of the Computer Science department.
Darren Chan
PhD Student Molecular Genetics (CBMG Track)
Darren received his BSc from the University of Toronto with majors in Biochemistry and Computer Science. He is co-supervised by Hartland Jackson and Kieran Campbell, and is currently investigating machine learning methods for denoising highly multiplexed imaging data.
Matthew Watson
Programmer
Matt received his BSc in Biology from Queen's University and is currently pursuing evening courses in the Master of Data Science program at UT Austin. Upon graduation from Queen's, Matt worked in the Genomics department at OICR where he was first exposed to bioinformatics and programming. After spending a period of time studying post-graduate bioinformatics courses in Leuven, Belgium (2019-2020), Matt joined PHO in 2021 to assist in developing analysis and visualization tools for the Ontario COVID-19 public health response. He also spent several months in 2022 helping to develop pipelines for the analysis of multi-omics single cell data with the lab of Federico Gaiti at UHN. He has contributed software features to several commonly used bioinformatics and data science tools, and is passionate about software development, pipeline standardization, and collaborative science.
Tiak Ju Tan
PhD Student Molecular Genetics
Tiak received received his BSc in Medical Biosciences from Imperial College London (UK) in 2021, majoring in Immunology and Inflammation. Tiak undertook a multiple projects at the Immunomodulation and Tolerance group at the NHLI in his undergraduate analyzing single cell multiomic data to investigate mechanisms of immune tolerance in allergen immunotherapy. In 2021, Tiak joined the Lab of Neurogenetics at Genome Institute Singapore to functionally characterize SMPD1 variants identified from whole-exome sequencing data of Parkinson's disease patients in dopaminergic cell models. Currently, he is a PhD student co-supervised by Dr Hartland Jackson at LTRI. His research focus is to develop in-situ hybridization methods for Imaging Mass Cytometry.
Haifen Chen
Research Associate (Computational Biology)
Haifen obtained her Bachelor's and Master's degrees in Computer Science, both from Harbin Institute of Technology, China. Then she went to Singapore to pursue her Ph.D in Computational Biology, at Nanyang Technological University. With her Ph.D degree, she moved to Montreal Canada in October 2016 as a postdoctoral fellow in the Majewski lab, where she focused on the analysis of next generation sequencing data (e.g. ChIP/RNA-seq, WGBS) to uncover the crosstalk of epigenetic modifications and its impact on chromatin landscape and gene expression leading to cell fate decisions in tumorigenesis. Haifen recently joined the Campbell Lab at the Lunenfeld-Tanenbaum Research Institute to embark on an exciting journey in single-cell analysis!
Hassaan Maan
PhD Candidate (Medical Biophysics)
Hassaan received his BSc from the University of Waterloo in Biomedical Science, and a Master of Bioinformatics from the University of Guelph. For his Master's, he worked at the Ontario Institute for Cancer Research with Dr. Jüri Reimand on the study of enhancers and long non-coding RNAs and their interactions with promoter regions in tumor-tissue. Subsequently, he joined the labs of Dr. Bo Wang and Dr. Kieran Campbell for his PhD in the Department of Medical Biophysics at the University of Toronto, where his research involves the development and application of machine learning and computational biology methods in single-cell genomics, particularly on integrating disparate and multi-modal single-cell datasets.
Vesal Kasmaeifar
PhD Student Molecular Genetics (CBMG Track)
Vesal obtained his BSc from the University of Guilan in Cell and Molecular Biology. During his bachelor his research was focused on structural bioinformatics and molecular dynamics. He is co-supervised by Anne-Cluade Gingras and Kieran Campbell, and is currently investigating computational methods for analyzing mass spectrometry data
Sarah Asbury
PhD Student Molecular Genetics (CBMG Track)
Sarah earned her BSc and MSc in Biochemistry at McMaster University. Following graduation, she worked as a Bioinformatics Research Assisstant and later as a Clinical Data Manager. Sarah's academic projects have covered a wide-range of topics including RNA-seq to functionally characterize T cell subsets in allogeneic CAR-T cell therapies, 16S microbiome network-based analysis, polygenic risk score analysis, and machine learning for biomarker discovery in clinical psychiatry. At the Campbell lab, Sarah uses machine learning to identify tumor microenvironment biomarkers predicting patient response to cancer immunotherapy.
Alumni
Matthew T Warkentin
PhD candidate (Epidemiology)
Matt received his BSc in Medical Sciences and MSc in Epidemiology from Brock University. Matt is currently a PhD candidate in Epidemiology at the Dalla Lana School of Public Health at the University of Toronto and a Doctoral Fellow at the Lunenfeld-Tanenbaum Research Institute. Matt is co-supervised by Kieran Campbell and Rayjean Hung. Briefly, his research focuses on the molecular epidemiology of cancers. In particular, his work includes integrating genomics into high-risk stratification models for lung cancer screening, and using deep learning to analyze biomedical images to aid in the clinical-management of screen-detected pulmonary lesions.
Aisha Faruqui
Undergrad student
Aisha Faruqui is a fourth year undergrad student pursuing a double major in Neuroscience and Ecology and Evolutionary Biology at the University of Toronto. She previously held an NSERC award to explore DNA binding activity of proteins involved with DNA repair in the Pearson Lab at the Peter Gilgan Centre for Research and Learning. More recently, she conducted an independent research project at the Rollinson Lab, where she focused on the evolution of sex-determining mechanisms in reptile species. Aisha is currently a student in the Campbell Lab for the 2020-2021 year. Her project aims to explore the effects of copy number aberrations on signalling networks in cancer. Being a passionate supporter of the arts, Aisha is also a piano teacher and has been the pianist for the Hart House Jazz Ensemble since 2018, frequently playing at The Rex Hotel Jazz and Blues Bar.
Joanne Leung
Postdoctoral Fellow (Immunology)
Joanne received her HBSc from the University of Toronto in 2009 as an Immunology specialist with a minor in French. During the swine-flu pandemic of 2009, Joanne was selected as one of ten Canadian students to participate in the Emerging & Infectious Disease program in Shantou University, China, hosted by the International Institute of Infection & Immunity. She then completed her PhD in 2016 at McGill University where she examined the regulation of anti-tumor T cell immunity by the co-inhibitor B7-H4 under the guidance of Dr. Woong-Kyung Suh at the Montreal Clinical Research Institute. In 2017, Joanne began her postdoctoral studies at Memorial Sloan Kettering Cancer Center, New York, where she investigated the anti-tumor responses in long-term survivors of human pancreatic ductal adenocarcinoma in the lab of Dr. Vinod Balachandran. There, she sought to understand how cancer neoantigens define T cell function based on a neoantigen quality fitness model established with computational scientists Dr. Benjamin Greenbaum and Dr. Marta Luksza from the Icahn School of Medicine at Mount Sinai. In 2019, Joanne joined Dr. Michele Anderson’s team at Sunnybrook Research Institute (affiliated with U of T) to continue examining T cell immunity in the context of fundamental immunology. In 2021, Joanne received the AAI Intersect Fellowship, which aims to connect immunology researchers and computational scientists, and is currently being co-supervised by Dr. Kieran Campbell from the Lunenfeld-Tanenbaum Research Institute to further elucidate the developmental patterning in the generation of long-term T cell immunity using in silico modeling approaches.
Benjamin Zheng
2021 Amgen Scholars Research Intern
Benjamin received is BA & Sc. from the University of Toronto where he worked on a variety of research projects ranging from structural biology to organic synthesis. For the past two years, Benjamin has worked in the Nitz Lab in the Department of Chemistry at UofT where he worked on the synthesis and computational design of small molecule inhibitors against various bacterial enzymes involved in biofilm formation. For the summer of 2021, Benjamin will be working in the Campbell lab helping develop a Python package used to supplement the capabilities of imaging mass cytometry in the detection of cancer cells. In September 2021, Benjamin will be starting graduate studies in the Department of Chemistry at UofT.
Kevin Sun
NSERC Summer Student
Kevin is a fourth year undergraduate student pursuing mathematical applications in economics and finance specialist and computer science major at the University of Toronto. His research interests focus on machine learning applications. Kevin is supervised by Dr. Kieran Campbell and Jett Lee, currently working on learning cellular representations from highly multiplexed imaging data that are robust to segmentation errors.