Chaitra Sarathy - Bioinformatician

Chaitra Sarathy

Bioinformatician

Toronto, Ontario, Canada

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Summary

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Senior

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Top School

Chaitra Sarathy is a bioinformatician and systems biologist with over 10 years of experience developing computational methods for omics integration and metabolic modelling. Holding a PhD in Systems Biology from Maastricht University and an MSc in Bioinformatics, she specializes in algorithm development that bridges transcriptomics and constraint-based metabolic models. Her open-source contributions include enhancing the widely used COBRA Toolbox to map gene expression with significance values into metabolic reactions, enabling more nuanced functional interpretations. Based in Toronto, she combines rigorous academic training with practical data science skills to turn complex multi-omics data into actionable biological insight. Colleagues describe her as methodical and pragmatic, with a knack for translating statistical signals into mechanistic hypotheses.

10 years of coding experience

PhD, Systems Biology, PhD, Systems Biology at Maastricht University

Bachelor of Engineering (B.E.), Biotechnology, Bachelor of Engineering (B.E.), Biotechnology at Visvesvaraya Technological University

Master of Science (MSc) in Bioinformatics and Applied Biotechnology, Bioinformatics and Biotechnology, 87%, Master of Science (MSc) in Bioinformatics and Applied Biotechnology, Bioinformatics and Biotechnology, 87% at Institute of Bioinformatics and Applied Biotechnology

Github Skills (7)

bioinformatics10

constraint-layout10

constraint10

transcriptomics10

constraint-satisfaction10

data-integration10

modeling10

Programming languages (2)

Jupyter NotebookMATLAB

Github contributions (5)

opencobra/cobratoolbox

Oct 2019 - Feb 2020

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Role in this project:

Data Scientist

Contributions:11 commits, 2 PRs, 6 comments in 3 months

Contributions summary:Chaitra primarily contributed to the integration of gene expression data into the COBRA toolbox, specifically for transcriptomics analysis. Their work involved modifying existing functions like `findUsedGenesLevels`, `selectGeneFromGPR`, and `mapExpressionToReactions` to incorporate significance values alongside expression data. This enhancement allows for a more nuanced analysis of gene expression in metabolic models. They also updated the tutorial for expression mapping.

microbiome-analysisgap-fillingmetabolic-reconstructioncobra-toolboxomics-data-integration

macsbio/efmviz

Jan 2019 - Jul 2020

EFM Visualization

Contributions:79 commits, 8 PRs, 63 pushes in 1 year 5 months

visualization

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