Srivastava A - 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. Among authors: srivastava a. 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. Bioinformatics. 2016 Jun 15;32(12):i192-i200. doi: 10.1093/bioinformatics/btw277. Bioinformatics. 2016. PMID: 27307617 Free PMC article.

3

Improved data-driven likelihood factorizations for transcript abundance estimation.

Zakeri M, Srivastava A, Almodaresi F, Patro R. Zakeri M, et al. Among authors: srivastava a. Bioinformatics. 2017 Jul 15;33(14):i142-i151. doi: 10.1093/bioinformatics/btx262. Bioinformatics. 2017. PMID: 28881996 Free PMC article.

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: srivastava a. Bioinformatics. 2018 Jul 1;34(13):i169-i177. doi: 10.1093/bioinformatics/bty292. Bioinformatics. 2018. PMID: 29949982 Free PMC article.

5

Alevin efficiently estimates accurate gene abundances from dscRNA-seq data.

Srivastava A, Malik L, Smith T, Sudbery I, Patro R. Srivastava A, et al. Genome Biol. 2019 Mar 27;20(1):65. doi: 10.1186/s13059-019-1670-y. Genome Biol. 2019. PMID: 30917859 Free PMC article.

6

Nonparametric expression analysis using inferential replicate counts.

Zhu A, Srivastava A, Ibrahim JG, Patro R, Love MI. Zhu A, et al. Among authors: srivastava a. Nucleic Acids Res. 2019 Oct 10;47(18):e105. doi: 10.1093/nar/gkz622. Nucleic Acids Res. 2019. PMID: 31372651 Free PMC article.

7

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. Among authors: srivastava a. Bioinformatics. 2019 Jul 15;35(14):i136-i144. doi: 10.1093/bioinformatics/btz351. Bioinformatics. 2019. PMID: 31510649 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. Bioinformatics. 2020 Jul 1;36(Suppl_1):i292-i299. doi: 10.1093/bioinformatics/btaa450. Bioinformatics. 2020. PMID: 32657394 Free PMC article.

9

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. Genome Biol. 2020 Sep 7;21(1):239. doi: 10.1186/s13059-020-02151-8. Genome Biol. 2020. PMID: 32894187 Free PMC article.

10

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data.

Soneson C, Srivastava A, Patro R, Stadler MB. Soneson C, et al. Among authors: srivastava a. PLoS Comput Biol. 2021 Jan 11;17(1):e1008585. doi: 10.1371/journal.pcbi.1008585. eCollection 2021 Jan. PLoS Comput Biol. 2021. PMID: 33428615 Free PMC article.

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