Sarkar Lab

Ph.D. Computer Science

1400 18th Ave S.

Nashville, TN 37240

I am an Assistant Professor in the newly established College of Connected Computing and a faculty member of the Center for Computational Systems Biology at Vanderbilt University. Our research focuses on deciphering the spatial architecture of complex diseases such as cancer using machine learning and artificial intelligence. We develop computational methods, sometimes it involves inventing entirely new inference algorithms, other times we refine and accelerate existing ones — pushing them to keep pace with the next generation of sequencing and imaging technologies. ✨ Stay tuned for our latest discoveries on
Google Scholar 📖

🚀 Join Me at Vanderbilt! I’m recruiting a few graduate students for Fall 2026. Email me at <firstname>.<lastname>@vanderbilt.edu if you’d like to explore possibilities, and click below

🚀 Apply to the CS/CCC Graduate Program at Vanderbilt

💡 BS/MS students at Vanderbilt interested in independent research projects or research credits (e.g., CS 3860 / CS 8390) are also welcome to reach out. 💡

Brief Bio

I obtained my Ph.D. in Computer Science from the University of Maryland, College Park , where I worked with Prof. Robert Patro . Prior to joining Vanderbilt University, I was a Ludwig Princeton Scholar at Princeton University with Prof. Ben Raphael and Prof. Yibin Kang .

Research Highlights

News

Oct 24, 2025	🎤 Hirak Sarkar presented on multi-omics spatial integration at the NIH-CZI Junior Investigators Atlas Building Meeting ✨
Oct 17, 2025	🎤 Hirak Sarkar presented on multi-omics spatial integration at the Vanderbilt Symposium on AI & Spatial Systems Biology 2025 ✨
Oct 09, 2025	🧬 Journal version of SIID is now published in Genome Research 🎉
Sep 03, 2025	🧬 *Our paper on tumor hijacking macrophages* is now published in Cell!** 🎉 Read the paper →
Aug 15, 2025	🎉 Big news! Hirak joined Vanderbilt University to start his own lab 🧠✨

Latest Posts

Sep 21, 2025	Method development in computational biology
Jun 08, 2021	Theory of variational inference

Selected Publications

Genes & Dev

Deciphering normal and cancer stem cell niches by spatial transcriptomics: opportunities and challenges

Hirak Sarkar, Eunmi Lee , Sereno L Lopez-Darwin , and 1 more author

Genes & Dev, 2025
RECOMB Genome Res

Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms

Hongyu Zheng* , Hirak Sarkar*, and Benjamin J Raphael

bioRxiv, 2025
Cancer Res

Comparative Single-Cell Transcriptomics of Human Neuroblastoma and Preclinical Models Reveals Conservation of an Adrenergic Cell State

Bethel Tesfai Embaie* , Hirak Sarkar*, Adele Mirna Alchahin , and 14 more authors

Cancer Research, 2025
ISMB Bioinformatics

A count-based model for delineating cell–cell interactions in spatial transcriptomics data

Hirak Sarkar, Uthsav Chitra , Julian Gold , and 1 more author

Bioinformatics, 2024
RECOMB

Mapping the topography of spatial gene expression with interpretable deep learning

Uthsav Chitra , Brian J Arnold , Hirak Sarkar, and 4 more authors

bioRxiv, 2023

ISMB Bioinformatics

Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data

Hirak Sarkar, Avi Srivastava , Héctor Corrada Bravo , and 2 more authors

Bioinformatics, 2020

Bib

@article{sarkar2020terminus,
  abbr2 = {Bioinformatics},
  title = {Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data},
  author = {Sarkar, Hirak and Srivastava, Avi and Bravo, H{\'e}ctor Corrada and Love, Michael I and Patro, Rob},
  journal = {Bioinformatics},
  volume = {36},
  number = {Supplement\_1},
  pages = {i102--i110},
  year = {2020},
  publisher = {Oxford University Press},
}

ISMB Bioinformatics

A space and time-efficient index for the compacted colored de Bruijn graph

Fatemeh Almodaresi* , Hirak Sarkar*, Avi Srivastava , and 1 more author

Bioinformatics, 2018