Here are my publications (including preprints).


    Mapping the topography of spatial gene expression with interpretable deep learning
    Uthsav Chitra , Brian J Arnold , Hirak Sarkar, and 4 more authors
    bioRxiv, 2023
  2. Nat Biotech
    Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes
    Teng Gao , Ruslan Soldatov , Hirak Sarkar, and 4 more authors
    Nature Biotechnology, 2023
  3. Nat Comm
    Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses
    Taghreed Hirz , Shenglin Mei , Hirak Sarkar, and 8 more authors
    Nature Communications, 2023
  4. Nat Rev
    Best practices for single-cell analysis across modalities
    Lukas Heumos , Anna C Schaar , Christopher Lance , and 8 more authors
    Nature Reviews Genetics, 2023
  5. DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes
    Simone Tiberi , Joël Meili , Peiying Cai , and 6 more authors
    bioRxiv, 2023


  1. Nat Methods
    Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data
    Dongze He , Mohsen Zakeri , Hirak Sarkar, and 3 more authors
    Nature Methods, 2022
  2. Bioinformatics
    Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets
    Wancen Mu , Hirak Sarkar, Avi Srivastava , and 3 more authors
    Bioinformatics, 2022


  1. Bioinformatics
    Compression of quantification uncertainty for scRNA-seq counts
    Scott Van Buren , Hirak Sarkar, Avi Srivastava , and 3 more authors
    Bioinformatics, 2021
  2. bioRxiv
    A like-for-like comparison of lightweight-mapping pipelines for single-cell RNA-seq data pre-processing
    Mohsen Zakeri , Avi Srivastava , Hirak Sarkar, and 1 more author
    bioRxiv, 2021


  1. 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
  2. Genome Biology
    Alignment and mapping methodology influence transcript abundance estimation
    Avi Srivastava , Laraib Malik , Hirak Sarkar, and 6 more authors
    Genome biology, 2020
  3. EMNLP
    Social media attributions in the context of water crisis
    Rupak Sarkar , Hirak Sarkar, Sayantan Mahinder , and 1 more author
    arXiv preprint arXiv:2001.01697, 2020
  4. ISMB Bioinformatics
    A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification
    Avi Srivastava , Laraib Malik , Hirak Sarkar, and 1 more author
    Bioinformatics, 2020


  1. ISMB Bioinformatics
    Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level
    Hirak Sarkar, Avi Srivastava , and Rob Patro
    Bioinformatics, 2019


  1. Towards selective-alignment: Bridging the accuracy gap between alignment-based and alignment-free transcript quantification
    Hirak Sarkar, Mohsen Zakeri , Laraib Malik , and 1 more author
    In Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics , 2018
  2. 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


  1. Bioinformatics
    Quark enables semi-reference-based compression of RNA-seq data
    Hirak Sarkar, and Rob Patro
    Bioinformatics, 2017
  2. ISMB Bioinformatics
    Towards selective-alignment: producing accurate and sensitive alignments using quasi-mapping
    Hirak Sarkar, Mohsen Zakeri , Laraib Malik , and 1 more author
    bioRxiv, 2017


  1. ISMB Bioinformatics
    RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes
    Avi Srivastava , Hirak Sarkar, Nitish Gupta , and 1 more author
    Bioinformatics, 2016
  2. RECOMB-seq
    Accurate, fast and lightweight clustering of de novo transcriptomes using fragment equivalence classes
    Avi Srivastava , Hirak Sarkar, Laraib Malik , and 1 more author
    arXiv preprint arXiv:1604.03250, 2016


  1. TCS
    Voronoi game on graphs
    Sayan Bandyapadhyay , Aritra Banik , Sandip Das , and 1 more author
    Theoretical Computer Science, 2015


  1. Some geometric and combinatorial properties of binary matrices related to discrete tomography
    Hirak Sarkar
    Indian Statistical Institute-Kolkata , 2013