I am a postdoctoral fellow at the Eric and Wendy Schmidt Center at the Broad Institute. I completed my PhD in Computer Science at Princeton University, where I was very fortunate to be advised by Ben Raphael and generously supported by an NSF Graduate Research Fellowship and a Siebel Scholar award.
I am broadly interested in developing statistical models and algorithms to address problems in biology and machine learning, with a particular interest in problems involving spatial or network structure.
Here is my CV and Google Scholar.
Recent Updates
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(July 2024) New pre-print on measuring higher-order epistasis.
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(July 2024) Started my postdoc at the Eric and Wendy Schmidt Center!
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(June 2024) GASTON was accepted in principle to Nature Methods.
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(May 2024) DIALECT won the Best Paper Award at RECOMB-CCB 2024!
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(March 2024) DIALECT, our method to identify mutually exclusive driver mutations that accounts for passenger mutations, was accepted to RECOMB-CCB 2024.
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(March 2024) Copulacci, our method for learning cell-cell interactions from sparse spatial transcriptomics data, was accepted to ISMB 2024.
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(March 2024) I defended my PhD thesis! Slides available here. Next up: I will join the Eric and Wendy Schmidt Center at the Broad Institute as a postdoctoral fellow.
Papers
* denotes joint first authorship.
Mapping the topography of spatial gene expression with interpretable deep learning.
Uthsav Chitra, Brian J. Arnold, Hirak Sarkar, Cong Ma, Sereno Lopez-Darwin, Kohei Sanno, Benjamin J. Raphael
Nature Methods, accepted in principle. Previously appeared at RECOMB 2024 [slides].
Slaying the chimera: a unified model of higher-order epistasis
Uthsav Chitra*, Brian J. Arnold*, Benjamin J. Raphael
In review.
A count-based model for delineating cell-cell interactions in spatial transcriptomics data.
Hirak Sarkar*, Uthsav Chitra*, Julian Gold, Benjamin J. Raphael
Bioinformatics (2024). To appear at ISMB 2024.
A latent variable model for evaluating mutual exclusivity between driver mutations in cancer.
Ahmed Shuaibi*, Uthsav Chitra*, Benjamin J. Raphael
RECOMB Satellite Workshop on Computational Cancer Biology (RECOMB-CCB 2024).
Best Paper Award.
Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics
Cong Ma*, Uthsav Chitra*, Shirley Zhang, Benjamin J. Raphael
Cell Systems (2022). Previously appeared at RECOMB 2022.
NetMix2: Unifying network propagation and altered subnetworks
Uthsav Chitra*, Tae Yoon Park*, Benjamin J. Raphael
Journal of Computational Biology (2022). Previously appeared at RECOMB 2022 [slides].
Quantifying and Reducing Bias in Maximum Likelihood Estimation of Structured Anomalies
Uthsav Chitra, Kimberly Ding, Jasper C. H. Lee, Benjamin J. Raphael
International Conference on Machine Learning (ICML 2021) [slides, ICML talk].
NetMix: A network-structured mixture model for reducing bias in the identification of altered subnetworks.
Matthew A. Reyna*, Uthsav Chitra*, Rebecca Elyanow, Benjamin J. Raphael
Journal of Computational Biology (2021). Previously appeared at RECOMB 2020 [slides].
Analyzing the Impact of Filter Bubbles on Social Network Polarization
Uthsav Chitra, Christopher Musco
ACM Conference on Web Search and Data Mining (WSDM 2020).
Preliminary version presented at KDD WISDOM 2019 workshop [slides].
Random Walks on Hypergraphs with Edge-Dependent Vertex Weights
Uthsav Chitra, Benjamin J. Raphael
International Conference on Machine Learning (ICML 2019) [slides, ICML talk @ 55:27].
Committee Selection is More Similar Than You Think: Evidence from Avalanche and Stellar
Tarun Chitra, Uthsav Chitra
Manuscript, 2019.
Personal
I like to go bouldering, attempt to do crosswords, and make bad puns.