Sarkar H - Search Results

1

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

Sarkar H, Srivastava A, Bravo HC, Love MI, Patro R. Sarkar H, et al. Bioinformatics. 2020 Jul 1;36(Suppl_1):i102-i110. doi: 10.1093/bioinformatics/btaa448. Bioinformatics. 2020. PMID: 32657377 Free PMC article.

2

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

Srivastava A, Sarkar H, Gupta N, Patro R. Srivastava A, et al. Among authors: sarkar h. Bioinformatics. 2016 Jun 15;32(12):i192-i200. doi: 10.1093/bioinformatics/btw277. Bioinformatics. 2016. PMID: 27307617 Free PMC article.

3

Quark enables semi-reference-based compression of RNA-seq data.

Sarkar H, Patro R. Sarkar H, et al. Bioinformatics. 2017 Nov 1;33(21):3380-3386. doi: 10.1093/bioinformatics/btx428. Bioinformatics. 2017. PMID: 29077806

4

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

Almodaresi F, Sarkar H, Srivastava A, Patro R. Almodaresi F, et al. Among authors: sarkar h. Bioinformatics. 2018 Jul 1;34(13):i169-i177. doi: 10.1093/bioinformatics/bty292. Bioinformatics. 2018. PMID: 29949982 Free PMC article.

5

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

Sarkar H, Srivastava A, Patro R. Sarkar H, et al. Bioinformatics. 2019 Jul 15;35(14):i136-i144. doi: 10.1093/bioinformatics/btz351. Bioinformatics. 2019. PMID: 31510649 Free PMC article.

6

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

Srivastava A, Malik L, Sarkar H, Patro R. Srivastava A, et al. Among authors: sarkar h. Bioinformatics. 2020 Jul 1;36(Suppl_1):i292-i299. doi: 10.1093/bioinformatics/btaa450. Bioinformatics. 2020. PMID: 32657394 Free PMC article.

7

Alignment and mapping methodology influence transcript abundance estimation.

Srivastava A, Malik L, Sarkar H, Zakeri M, Almodaresi F, Soneson C, Love MI, Kingsford C, Patro R. Srivastava A, et al. Among authors: sarkar h. Genome Biol. 2020 Sep 7;21(1):239. doi: 10.1186/s13059-020-02151-8. Genome Biol. 2020. PMID: 32894187 Free PMC article.

8

Compression of quantification uncertainty for scRNA-seq counts.

Van Buren S, Sarkar H, Srivastava A, Rashid NU, Patro R, Love MI. Van Buren S, et al. Among authors: sarkar h. Bioinformatics. 2021 Jul 19;37(12):1699-1707. doi: 10.1093/bioinformatics/btab001. Bioinformatics. 2021. PMID: 33471073 Free PMC article.

9

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

He D, Zakeri M, Sarkar H, Soneson C, Srivastava A, Patro R. He D, et al. Among authors: sarkar h. Nat Methods. 2022 Mar;19(3):316-322. doi: 10.1038/s41592-022-01408-3. Epub 2022 Mar 11. Nat Methods. 2022. PMID: 35277707 Free PMC article.

10

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

Mu W, Sarkar H, Srivastava A, Choi K, Patro R, Love MI. Mu W, et al. Among authors: sarkar h. Bioinformatics. 2022 May 13;38(10):2773-2780. doi: 10.1093/bioinformatics/btac212. Bioinformatics. 2022. PMID: 35561168 Free PMC article.

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