Patro R - Search Results

1

Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections.

Khan J, Patro R. Khan J, et al. Among authors: patro r. Bioinformatics. 2021 Jul 12;37(Suppl_1):i177-i186. doi: 10.1093/bioinformatics/btab309. Bioinformatics. 2021. PMID: 34252958 Free PMC article.

2

Tree-based differential testing using inferential uncertainty for RNA-Seq.

Singh NP, Wu EY, Fan J, Love MI, Patro R. Singh NP, et al. Among authors: patro r. bioRxiv [Preprint]. 2023 Dec 25:2023.12.25.573288. doi: 10.1101/2023.12.25.573288. bioRxiv. 2023. PMID: 38234739 Free PMC article. Preprint.

3

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.

4

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.

5

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.

6

Data-dependent bucketing improves reference-free compression of sequencing reads.

Patro R, Kingsford C. Patro R, et al. Bioinformatics. 2015 Sep 1;31(17):2770-7. doi: 10.1093/bioinformatics/btv248. Epub 2015 Apr 24. Bioinformatics. 2015. PMID: 25910696 Free PMC article.

7

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: patro r. Bioinformatics. 2016 Jun 15;32(12):i192-i200. doi: 10.1093/bioinformatics/btw277. Bioinformatics. 2016. PMID: 27307617 Free PMC article.

8

deBGR: an efficient and near-exact representation of the weighted de Bruijn graph.

Pandey P, Bender MA, Johnson R, Patro R. Pandey P, et al. Among authors: patro r. Bioinformatics. 2017 Jul 15;33(14):i133-i141. doi: 10.1093/bioinformatics/btx261. Bioinformatics. 2017. PMID: 28881995 Free PMC article.

9

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

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

10

Squeakr: an exact and approximate k-mer counting system.

Pandey P, Bender MA, Johnson R, Patro R, Berger B. Pandey P, et al. Among authors: patro r. Bioinformatics. 2018 Feb 15;34(4):568-575. doi: 10.1093/bioinformatics/btx636. Bioinformatics. 2018. PMID: 29444235

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