Patro R - Search Results

1

Forseti: A mechanistic and predictive model of the splicing status of scRNA-seq reads.

He D, Gao Y, Chan SS, Quintana-Parrilla N, Patro R. He D, et al. Among authors: patro r. bioRxiv [Preprint]. 2024 Feb 5:2024.02.01.577813. doi: 10.1101/2024.02.01.577813. bioRxiv. 2024. Update in: Bioinformatics. 2024 Jun 28;40(Suppl 1):i297-i306. doi: 10.1093/bioinformatics/btae207 PMID: 38370848 Free PMC article. Updated. Preprint.

2

Improved data-driven likelihood factorizations for transcript abundance estimation.

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

3

An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search.

Almodaresi F, Pandey P, Ferdman M, Johnson R, Patro R. Almodaresi F, et al. Among authors: patro r. J Comput Biol. 2020 Apr;27(4):485-499. doi: 10.1089/cmb.2019.0322. Epub 2020 Mar 16. J Comput Biol. 2020. PMID: 32176522 Free PMC article.

4

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

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

5

Global network alignment using multiscale spectral signatures.

Patro R, Kingsford C. Patro R, et al. Bioinformatics. 2012 Dec 1;28(23):3105-14. doi: 10.1093/bioinformatics/bts592. Epub 2012 Oct 9. Bioinformatics. 2012. PMID: 23047556 Free PMC article.

6

Reference-based compression of short-read sequences using path encoding.

Kingsford C, Patro R. Kingsford C, et al. Among authors: patro r. Bioinformatics. 2015 Jun 15;31(12):1920-8. doi: 10.1093/bioinformatics/btv071. Epub 2015 Feb 2. Bioinformatics. 2015. PMID: 25649622 Free PMC article.

7

Salmon provides fast and bias-aware quantification of transcript expression.

Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Patro R, et al. Nat Methods. 2017 Apr;14(4):417-419. doi: 10.1038/nmeth.4197. Epub 2017 Mar 6. Nat Methods. 2017. PMID: 28263959 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: patro r. Bioinformatics. 2020 Jul 1;36(Suppl_1):i292-i299. doi: 10.1093/bioinformatics/btaa450. Bioinformatics. 2020. PMID: 32657394 Free PMC article.

9

Algorithms meet sequencing technologies - 10th edition of the RECOMB-Seq workshop.

Patro R, Salmela L. Patro R, et al. iScience. 2020 Dec 17;24(1):101956. doi: 10.1016/j.isci.2020.101956. eCollection 2021 Jan 22. iScience. 2020. PMID: 33437938 Free PMC article. Review.

10

Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis.

Malik L, Almodaresi F, Patro R. Malik L, et al. Among authors: patro r. Bioinformatics. 2018 Oct 1;34(19):3265-3272. doi: 10.1093/bioinformatics/bty378. Bioinformatics. 2018. PMID: 29746620

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