Hirak Sarkar

35 Olden St

Princeton, NJ 08540

Hi I am Hirak, a Ludwig Princeton Scholar at the Princeton University. I work in the field of cancer-genomics under the guidance of Prof. Ben Raphael, and Prof. Yibin Kang. I also collaborate with Prof. Eileen White’s lab at the Cancer Institute of New Jersey.

Previously, I was a postdoctoral researcher at Harvard with Prof. Peter Kharchenko (till mid-2022) until his departure to Altos. I completed my PhD in Computer Science from the University of Maryland under the guidance of Prof. Rob Patro.

The following are broadly my current research interests. See also my list of publications.

Computational Biology
Spatial Transcriptomics
Machine Learning
Algorithms

News

Feb 17, 2025	Presented `SIID` in CINJ as a part of quarterly meeting of Ludwig Instutute.
Dec 17, 2024	`SIID` is accepted in RECOMB
Apr 01, 2024	Will be presenting `Copulacci` in NCI Spring School of Algorithms at Bethesda, Maryland
Feb 24, 2024	`Copulacci` is accepted in ISMB
Dec 24, 2023	`GASTON` by Uthsav is accepted in RECOMB

Latest Posts

Jun 08, 2021	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