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Hirak Sarkar
Hirak Sarkar
Ludwig Scholar at Princeton University
Verified email at hms.harvard.edu - Homepage
Title
Cited by
Cited by
Year
Best practices for single-cell analysis across modalities
L Heumos, AC Schaar, C Lance, A Litinetskaya, F Drost, L Zappia, ...
Nature Reviews Genetics 24 (8), 550-572, 2023
4202023
Alignment and mapping methodology influence transcript abundance estimation
A Srivastava, L Malik, H Sarkar, M Zakeri, F Almodaresi, C Soneson, ...
Genome biology 21, 1-29, 2020
1622020
RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes
A Srivastava, H Sarkar, N Gupta, R Patro
Bioinformatics 32 (12), i192-i200, 2016
1382016
A space and time-efficient index for the compacted colored de Bruijn graph
F Almodaresi*, H Sarkar*, A Srivastava, R Patro
Bioinformatics 34 (13), i169-i177, 2018
912018
Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses
T Hirz, S Mei, H Sarkar, Y Kfoury, S Wu, BM Verhoeven, AO Subtelny, ...
Nature Communications 14 (1), 663, 2023
812023
Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes
T Gao, R Soldatov, H Sarkar, A Kurkiewicz, E Biederstedt, PR Loh, ...
Nature Biotechnology 41 (3), 417-426, 2023
662023
Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data
D He, M Zakeri, H Sarkar, C Soneson, A Srivastava, R Patro
Nature Methods 19 (3), 316-322, 2022
582022
Voronoi game on graphs
S Bandyapadhyay, A Banik, S Das, H Sarkar
Theoretical Computer Science 562, 270-282, 2015
512015
Epigenetic regulation during cancer transitions across 11 tumour types
NV Terekhanova, A Karpova, WW Liang, A Strzalkowski, S Chen, Y Li, ...
Nature 623 (7986), 432-441, 2023
392023
Towards selective-alignment: Bridging the accuracy gap between alignment-based and alignment-free transcript quantification
H Sarkar, M Zakeri, L Malik, R Patro
Proceedings of the 2018 ACM International Conference on Bioinformatics …, 2018
262018
A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification
A Srivastava, L Malik, H Sarkar, R Patro
Bioinformatics 36 (Supplement_1), i292-i299, 2020
202020
Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level
H Sarkar, A Srivastava, R Patro
Bioinformatics 35 (14), i136-i144, 2019
192019
Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets
W Mu, H Sarkar, A Srivastava, K Choi, R Patro, MI Love
Bioinformatics 38 (10), 2773-2780, 2022
162022
Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data
H Sarkar, A Srivastava, HC Bravo, MI Love, R Patro
Bioinformatics 36 (Supplement_1), i102-i110, 2020
132020
Social media attributions in the context of water crisis
R Sarkar, H Sarkar, S Mahinder, AR KhudaBukhsh
arXiv preprint arXiv:2001.01697, 2020
122020
Accurate, fast and lightweight clustering of de novo transcriptomes using fragment equivalence classes
A Srivastava, H Sarkar, L Malik, R Patro
arXiv preprint arXiv:1604.03250, 2016
112016
Single-cell analysis of immune and stroma cell remodeling in clear cell renal cell carcinoma primary tumors and bone metastatic lesions
S Mei, AM Alchahin, I Tsea, Y Kfoury, T Hirz, NE Jeffries, T Zhao, Y Xu, ...
Genome Medicine 16 (1), 1, 2024
82024
Mapping the topography of spatial gene expression with interpretable deep learning
U Chitra, BJ Arnold, H Sarkar, C Ma, S Lopez-Darwin, K Sanno, ...
International Conference on Research in Computational Molecular Biology, 368-371, 2024
62024
Haplotype-enhanced inference of somatic copy number profiles from single-cell transcriptomes
T Gao, R Soldatov, H Sarkar, A Kurkiewicz, E Biederstedt, PR Loh, ...
bioRxiv, 2022.02. 07.479314, 2022
62022
refine. bio: A resource of uniformly processed publicly available gene expression datasets
CS Greene, D Hu, RWW Jones, S Liu, DS Mejia, R Patro, SR Piccolo, ...
Google Scholar, 2023
52023
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