Hirak Sarkar

发表

Accounting for fragments of unexpected origin improves transcript quantification in RNA-seq simulations focused on increased realism

Mohsen Zakeri, C. Soneson, Carl Kingsford, 2021, bioRxiv.

Some Geometric and Combinatorial Properties of Binary Matrices Related to Discrete Tomography

Hirak Sarkar, 2013 .

Alignment and mapping methodology influence transcript abundance estimation

Fatemeh Almodaresi, Mohsen Zakeri, M. Love, 2020, Genome biology.

Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes

Po-Ru Loh, P. Kharchenko, R. Soldatov, 2022, Nature Biotechnology.

Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses

Evan Z. Macosko, Chin-Lee Wu, Evan Murray, 2023, Nature Communications.

Integrated single-cell and spatial transcriptomic analyses unravel the heterogeneity of the prostate tumor microenvironment

Evan Z. Macosko, P. Kharchenko, D. Scadden, 2022, bioRxiv.

A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification

Rob Patro, Avi Srivastava, Hirak Sarkar, 2020, bioRxiv.

RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes

Robert Patro, Nitish Gupta, Avi Srivastava, 2015, bioRxiv.

Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level

Rob Patro, Avi Srivastava, Hirak Sarkar, 2019, Bioinform..

Alignment and mapping methodology influence transcript abundance estimation

Fatemeh Almodaresi, Charlotte Soneson, Carl Kingsford, 2019, Genome Biology.

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

Fatemeh Almodaresi, Robert Patro, Avi Srivastava, 2017, bioRxiv.

Haplotype-enhanced inference of somatic copy number profiles from single-cell transcriptomes

Po-Ru Loh, P. Kharchenko, R. Soldatov, 2022, bioRxiv.

Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq data

Mohsen Zakeri, C. Soneson, Robert Patro, 2021, Nature Methods.

Compression of quantification uncertainty for scRNA-seq counts

Rob Patro, Avi Srivastava, Hirak Sarkar, 2020, bioRxiv.

Accurate, Fast and Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes pdf

Robert Patro, Avi Srivastava, Hirak Sarkar, 2016, ArXiv.

Quark enables semi‐reference‐based compression of RNA‐seq data

Robert Patro, Hirak Sarkar, Robert Patro, 2017, Bioinform..

Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets

M. Love, Kwangbom Choi, Robert Patro, 2021, bioRxiv.

Social Media Attributions in the Context of Water Crisis pdf

Hirak Sarkar, Ashiqur R. KhudaBukhsh, Rupak Sarkar, 2020, EMNLP.

Towards selective-alignment: Bridging the accuracy gap between alignment-based and alignment-free transcript quantification

Robert Patro, Hirak Sarkar, Laraib Malik, 2017, bioRxiv.

Towards Selective-Alignment: Producing Accurate And Sensitive Alignments Using Quasi-Mapping

Hirak Sarkar, Laraib Malik, Rob Patro, 2017 .

DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes

Mark D. Robinson, C. Soneson, Robert Patro, 2023, bioRxiv.

Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets

M. Love, Kwangbom Choi, Robert Patro, 2021, bioRxiv.

Supplementary Methods, Tables, and Figures

M. Love, Kwangbom Choi, Robert Patro, 2022 .

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

Rob Patro, Avi Srivastava, Hirak Sarkar, 2020, bioRxiv.

Mapping the topography of spatial gene expression with interpretable deep learning

Sereno Lopez-Darwin, Uthsav Chitra, Hirak Sarkar, 2023, bioRxiv.