Sarkar H - Search Results

1

A count-based model for delineating cell-cell interactions in spatial transcriptomics data.

Sarkar H, Chitra U, Gold J, Raphael BJ. Sarkar H, et al. Bioinformatics. 2024 Jun 28;40(Suppl 1):i481-i489. doi: 10.1093/bioinformatics/btae219. Bioinformatics. 2024. PMID: 38940134 Free PMC article.

2

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

3

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.

4

Best practices for single-cell analysis across modalities.

Heumos L, Schaar AC, Lance C, Litinetskaya A, Drost F, Zappia L, Lücken MD, Strobl DC, Henao J, Curion F; Single-cell Best Practices Consortium; Schiller HB, Theis FJ. Heumos L, et al. Nat Rev Genet. 2023 Aug;24(8):550-572. doi: 10.1038/s41576-023-00586-w. Epub 2023 Mar 31. Nat Rev Genet. 2023. PMID: 37002403 Free PMC article. Review.

5

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.

6

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.

7

DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes.

Tiberi S, Meili J, Cai P, Soneson C, He D, Sarkar H, Avalos-Pacheco A, Patro R, Robinson MD. Tiberi S, et al. Among authors: sarkar h. Biostatistics. 2024 Oct 1;25(4):1079-1093. doi: 10.1093/biostatistics/kxae017. Biostatistics. 2024. PMID: 38887902 Free PMC article.

8

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.

9

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.

10

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.

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