Publications

* denotes joint first authorship, † denotes joint last (senior) authorship. Underline indicates member of Chitra Lab or trainee mentored/co-mentored

Preprints

Decoding the causal drivers of spatial cellular topology
Prannav Shankar, Huan Liang, Uthsav Chitra†, Rohit Singh†
RECOMB Satellite Conference on Biological Sequence Analysis (RECOMB-seq 2025)
Spatial metabolic gradients in the liver and small intestine
Laith Samarah, Clover Zheng, ..., Uthsav Chitra, ..., Benjamin J. Raphael, Joshua Rabinowitz
In review

2025

Resolving discrepancies between chimeric and multiplicative measures of higher-order epistasis
Uthsav Chitra*, Brian J. Arnold*, Benjamin J. Raphael
Nature Communications
Mapping the topography of spatial gene expression with interpretable deep learning
Uthsav Chitra, Brian J. Arnold, Hirak Sarkar, Kohei Sanno, Cong Ma, Sereno Lopez-Darwin, Benjamin J. Raphael
Nature Methods / RECOMB 2024
[slides] [talk]
GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts
Uthsav Chitra, Shu Dan, Fenna Krienen, Benjamin J. Raphael
Bioinformatics / ISMB 2025, to appear
Anomaly Detection in Spatial Transcriptomics via Spatially Localized Density Comparison
Gary Hu, Julian Gold, Uthsav Chitra, Sunay Joshi, Benjamin J. Raphael
Bioinformatics / ISMB 2025, to appear

2024

A count-based model for delineating cell-cell interactions in spatial transcriptomics data
Hirak Sarkar*, Uthsav Chitra*, Julian Gold, Benjamin J. Raphael
Bioinformatics / 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

2022

NetMix2: Unifying network propagation and altered subnetworks
Uthsav Chitra*, Tae Yoon Park*, Benjamin J. Raphael
Journal of Computational Biology / RECOMB 2022
[slides]
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 / RECOMB 2022

2021

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 / RECOMB 2020
[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] [talk]

2020

Analyzing the Impact of Filter Bubbles on Social Network Polarization
Uthsav Chitra, Christopher Musco
ACM Conference on Web Search and Data Mining (WSDM 2020)
[slides]
Preliminary version presented at KDD WISDOM 2019 workshop

2019

Committee Selection is More Similar Than You Think: Evidence from Avalanche and Stellar
Tarun Chitra, Uthsav Chitra
Manuscript
Random Walks on Hypergraphs with Edge-Dependent Vertex Weights
Uthsav Chitra, Benjamin J. Raphael
International Conference on Machine Learning (ICML 2019)
[slides] [talk]
Talk @ 55:27