Shreejoy Tripathy

Keywords: Neuron Physiology, Single-cell genomics, RNA-seq, Patch-clamp, Patch-seq, Machine learning, Depression, Epilepsy, Alzheimer’s, Cross-species analysis, Collaboration, Neuroinformatics, Bioinformatics, Open-Source Software, Databases, Computational Neuroscience

Collaborators: Drs. Taufik Valiante, Etay Hay, Evelyn Lambe, Steve Prescott

METHODS USED

Data Science, Bioinformatics, Neuroinformatics, Machine Learning, Collaboration, Computer Programming

Programming languages: R, Python

Research Synopsis

Research Divisions: Brain Research and Integrated Neurophysiology

Research Interests: We aim to develop a multi-scale understanding of brain cell type diversity, bridging genetics and gene expression with cell and circuit physiology. We develop machine learning and statistical methods to help neuroscientists translate information at different levels of organization, like gene expression to neuron electrophysiology. Our long-term goal is to better understand the cellular changes that underlie psychiatric and neurological disorders and to ultimately develop approaches that can help guide tailored treatments for mental health patients. Our lab is part of the new Krembil Centre for Neuroinformatics, where we contribute to the building of large-scale computational simulations of the nervous system. We are a computational “dry-lab”, but we collaborate extensively with experimental groups in Toronto and beyond.e

Recent Publications

See this link for a list of up to date publications: https://scholar.google.ca/citations?hl=en&user=dNybyvgAAAAJ&view_op=list_works&sortby=pubdate

Moradi H, Wang L, Zhang L, Carlen P, Tripathy SJ*, Valiante TA*. Sag currents are a major contributor to human pyramidal cell intrinsic diversity across cortical layers and between individuals. In revision. Biorxiv preprint: https://www.biorxiv.org/content/10.1101/748988v2.abstract.

Nagy C, Maitra M, Tanti A, Suderman M, Theroux JF, Davoli MA, Perlman K, Yerko V, Tripathy SJ, Pavlidis P, Mechawar N, Ragoussis J, Turecki G. Single nucleus RNA sequencing implicates OPCs and deep layer excitatory neurons in the pathophysiology of major depression. Nature Neuroscience. April 2020. https://doi.org/10.1038/s41593-020-0621-y

Bomkamp C*, Tripathy SJ*, Bengsston Gonzales C, Hjerling-Leffler J, Craig AM, Pavlidis P. Transcriptomic correlates of electrophysiological and morphological diversity within and across neuron cell types. PLoS Computational Biology, June 2019. https://doi.org/10.1101/524561

Tripathy SJ, Toker L, Bomkamp C, Mancarci O, Belmadani M, Pavlidis P. Assessing transcriptome quality in patch-seq datasets. Frontiers in Molecular Neuroscience, October 2018.

Appointments

Cross-Appointed to Physiology
Cross-Appointed to Institute of Medical Science
Primary: Psychiatry
Independent Scientist, Center for Addiction and Mental Health

Graduate Students

Student Name: Sonny Chen (Post-doc)
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Student Name: Michael Wainberg (Post-doc)
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Student Name: Xiao Luo (Post-doc)
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Student Name: Anukrati Nigam (PhD student)
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Student Name: Isabel Kerrebijn (MSc student)
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