Members

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Quaid Morris

Principal Investigator

PhD, Massachusetts Institute of Technology

Our lab uses machine learning and artificial intelligence to do biomedical research, focusing on cancer evolution, gene regulation, clinical informatics, and gene function prediction. A key interest is the role of RNA-binding proteins (RBPs) in post-transcriptional regulation. We focus on developing computational and experimental techniques to determine the RNA specificities of RBPs (both sequence and structural) and use these specificities to predict their target transcripts, determine RBP function, and ultimately decipher the regulatory code. Another focus is reconstructing and modelling somatic evolution (pre- and post-cancer) using bulk and single-cell genomic data. In general, we are focused on using large, heterogeneous functional genomic datasets to uncover insights about gene function. Recently, we have becoming increasingly interested in using artificial intelligence and predictive analytics, along with electronic medical records, to inform patient care, particularly in the domain of auto-immune disease.

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Hussein Mohsen

Postdoctoral Fellow

PhD, Yale University

Hussein is a Postdoctoral Research Fellow in the lab. His main research interests are centered on interpretable machine learning and somatic-germline interactions in cancer. He earned his PhD/MA in Computational Biology/History of Science from Yale University, MS in Bioinformatics from Indiana University (IU), and BS in Computer Science from the Lebanese American University (LAU).

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Niklas von Krosigk

Graduate Student

BS, University of British Columbia

Nik is a PhD student in the Computational Biology in Molecular Genetics track at the University of Toronto, and is co-supervised by Quaid Morris and Lincoln Stein. He earned a B.Sc (Honours) in Cell and Developmental Biology from the University of British Columbia in 2018. He is working on applying machine learning approaches to single cell sequencing data.

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Jarry Barber

Graduate Student

BScH, Queen's University

Jarry is a PhD student in the CBMG program at the University of Toronto. He earned his Bachelor in Astrophysics from Queen's University in 2013. His research interests include applications of machine learning methods and cancer genetics. He is currently developing tools to reconstruct the evolutionary history of cancers using single-cell sequencing data.

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Kaitlin U Laverty

Graduate Student

BS, University of Toronto

Kaitlin is a PhD student in the Department of Molecular Genetics at U of T. She also completed her B.Sc. degree at U of T, with a major in Molecular Genetics and minor in both Statistics and Computer Science. She is interested in the application of machine learning methods to functional genomics data. Kaitlin is particularly interested in post-transcriptional gene regulation.

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Jingping Qiao

Graduate Student

MS, Northeastern University (Boston)

Jingping is working on multi-omics integration of breast cancer involving genomics, transcriptomics, proteomics and radiomics. She earned BS degree in Applied Mathematics from Saint Louis University, and MS degree in Bioinformatics from Northeastern University. Her interest including Machine Learning and Cancer Genetics.

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Caitlin Harrigan

Graduate Student

MS, University of Toronto

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 and cancer evolution. Cait is co-supervised by Quaid Morris and Kieran Campbell, currently working on applying topic modeling approaches to understand mutational signatures in cancer evolution.

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Ruian (Ian) Shi

Graduate Student

MSc, University of Toronto

Ian is a PhD student in the University of Toronto's Department of Computer Science. He previously earned his BSc in Computer Science and Bioinformatics and MSc in Computer Science at the University of Toronto. Ian is interested in deep time series methods, deep generative models, and machine learning applications in the health and biology domains.

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Olga Lyudovyk

Graduate Student

MA, Columbia University

Olga is a PhD student in the Tri-I CBM program. She earned a Master degree in Biomedical Informatics from Columbia University in 2018, an MBA from INSEAD, and a Bachelor degree from New Mexico State University. She is building NLP-inspired deep learning models to understand the specificity of the adaptive immune system in order to design cancer cell therapies.

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Madison Darmofal

Graduate Student

BS, Massachusetts Institute of Technology

Madison graduated from MIT in 2019 with a degree in Computer Science and Biology. She then entered the Tri-Institutional Computational Biology & Medicine program, and is co-supervised by Quaid Morris and Mike Berger. She is interested in the field of precision oncology, specifically in using machine learning techniques to improve cancer treatment and patient outcomes. Madison is currently working on developing models for cancer diagnosis and detection using clinical genomic assays.

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Cyrus Tam

Graduate Student

BA, New York University

Cyrus Tam is a student in the CBM program with a BA in Biology from NYU. He is interested in understanding how in vivo RNA structures impact RBP binding and their applications in cancer progression.

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Ilyes Baali

Graduate Student

MS, Antalya Bilim University

Ilyes is a PhD student in the Tri-I CBM program. He earned Bachelor of Science degrees in Electrical & Electronics Engineering and in Computer Engineering from Antalya Bilim University (ABU) in 2017. and Master of Science in Electrical and Computer Engineering from ABU. He is interested in the application of machine learning methods to functional genomics, particularly in understanding post-transcriptional regulation.

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Aditya Sinha

Graduate Student

MS, Columbia University

Aditya is a PhD student in Tri-I Computational Biology & Medicine, mainly interested in studying regulation of gene expression using mathematical modeling. He did his B.Tech. and MS in Electrical Engineering.

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Divya Koyyalagunta

Graduate Student

BS, Duke University

Divya is a PhD student in the Tri-Institutional Computational Biology & Medicine program. Prior to entering her PhD, she earned a B.S. in Computer Science at Duke University and then worked as a software engineer on Apple Watch. She is primarily interested in using machine learning methods to understand gene regulatory networks.

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Leah Morales

Graduate Student

MS, New York University

Leah is a PhD student in the Tri-Institutional Computational Biology & Medicine program. She earned a B.S. in Mathematics from the University of Wisconsin-Madison and an M.S. in Bioinformatics from New York University. She is developing a method to infer clonal lineage of tumor cells from single cell RNA-sequencing.

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Aziz Zafar

Undergraduate Student

Aziz is a Biology and Applied Mathematics double major at Colgate University. His research interests lie in the overlap between Statistics, Machine Learning, and Human Diseases, such as cancers, parasitic infections, and mood disorders. His internship at MSK as part of the Morris Lab involves building classification models for predicting rare, out-of-distribution tumor types.

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Ellen Mammen

Administrative Assistant

Alumni

Name

Morris Lab Position

Current Position

Anna Goldenberg Postdoctoral FellowAssociate Professor in Computer Science, Univ Toronto
Shankar Vembu Postdoctoral FellowFounder: argmix a technology consulting firm specializing in machine learning
Gavin Gray Postdoctoral FellowPostdoctoral Research Fellow, Vector Institute, Toronto
Linda SundermannPostdoctoral FellowResearch Scientist, Silicon Valley start-up
Alina Selega Postdoctoral FellowPostdoctoral Research Fellow, Lunenfeld Research Institute, Toronto
Arttu Jolma Postdoctoral FellowPostdoctoral Research Fellow, Hughes Lab, Toronto
Rozita RazaviPostdoctoral FellowAssociate Research Scientist, University Health Network
Debashish Ray Postdoctoral FellowSenior Research Associate, Hughes Lab, Toronto
Gurnit Atwal Graduate StudentPostdoctoral Research Fellow, Memorial Sloan Kettering Cancer Center, New York
Yulia RubanovGraduate StudentResearch Scientist, Deep Mind, London
Chris CremerGraduate StudentResearch Intern, Facebook AI, Pittsburgh
Simon EngGraduate StudentData Scientist, BioSymetrics, Toronto
Kevin Ha Graduate StudentLead Data Scientist, BioSymetrics, Toronto
Amit Deshwar Graduate StudentResearch Scientist, Deep Genomics
Martin H. RadfarGraduate StudentResearch Assistant Professor in Computer Science, Stony Brook University
Xiao Li Graduate StudentAssistant Professor, Case Western University
Hilal Kazan Graduate StudentAssociate Professor, Computer Science, Antalya Bilim University
Gerald Quon Graduate StudentAssistant Professor, Computer Science at University of California Davis
Sara Mostafavi Graduate StudentAssociate Professor, Computer Science, University of Washington, Canada CIFAR AI chair
Amir KhasahmadiGraduate StudentResearch Scientist at Autodesk AI lab
Wei JiaoGraduate StudentResearch Scientist at Ontario Institute for Cancer Research
David Warde-FarleyGraduate StudentResearch Scientist at DeepMind, London
Sepand Mavandadi Graduate StudentSoftware engineer at Amazon
Seong Woo HanComputational BiologistGraduate Student, University of Pennsylvania
Ethan KulmanComputational BiologistGraduate Student, University of Minnesota
Chenlian (Tom) FuUndergraduate StudentGraduate Student, Tri-I CBM
Kimberly SkeadGraduate Student