Rob Patro
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Explore the profile of Rob Patro including associated specialties, affiliations and a list of published articles.
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Recent Articles
11.
Jousheghani Z, Patro R
bioRxiv
. 2024 Mar;
PMID: 38464200
Motivation: Long read sequencing technology is becoming an increasingly indispensable tool in genomic and transcriptomic analysis. In transcriptomics in particular, long reads offer the possibility of sequencing full-length isoforms, which...
12.
He D, Gao Y, Chan S, Quintana-Parrilla N, Patro R
bioRxiv
. 2024 Feb;
PMID: 38370848
Motivation: Short-read single-cell RNA-sequencing (scRNA-seq) has been used to study cellular heterogeneity, cellular fate, and transcriptional dynamics. Modeling splicing dynamics in scRNA-seq data is challenging, with inherent difficulty in even...
13.
He D, Mount S, Patro R
bioRxiv
. 2024 Feb;
PMID: 38352549
Single-cell RNA-sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity. Although scRNA-seq reads from most prevalent and popular tagged-end protocols are expected to arise from the 3 end of polyadenylated RNAs,...
14.
Fan J, Khan J, Singh N, Pibiri G, Patro R
Algorithms Mol Biol
. 2024 Jan;
19(1):3.
PMID: 38254124
The problem of sequence identification or matching-determining the subset of reference sequences from a given collection that are likely to contain a short, queried nucleotide sequence-is relevant for many important...
15.
Singh N, Wu E, Fan J, Love M, Patro R
bioRxiv
. 2024 Jan;
PMID: 38234739
Identifying differentially expressed transcripts poses a crucial yet challenging problem in transcriptomics. Substantial uncertainty is associated with the abundance estimates of certain transcripts which, if ignored, can lead to the...
16.
He D, Patro R
Bioinformatics
. 2023 Oct;
39(10).
PMID: 37802884
Summary: The alevin-fry ecosystem provides a robust and growing suite of programs for single-cell data processing. However, as new single-cell technologies are introduced, as the community continues to adjust best...
17.
Tiberi S, Meili J, Cai P, Soneson C, He D, Sarkar H, et al.
bioRxiv
. 2023 Aug;
PMID: 37645841
Motivation: Although transcriptomics data is typically used to analyse mature spliced mRNA, recent attention has focused on jointly investigating spliced and unspliced (or precursor-) mRNA, which can be used to...
18.
Pibiri G, Fan J, Patro R
bioRxiv
. 2023 Aug;
PMID: 37546988
Motivation: The colored compacted de Bruijn graph (c-dBG) has become a fundamental tool used across several areas of genomics and pangenomics. For example, it has been widely adopted by methods...
19.
Wu E, Singh N, Choi K, Zakeri M, Vincent M, Churchill G, et al.
Genome Biol
. 2023 Jul;
24(1):165.
PMID: 37438847
Detecting allelic imbalance at the isoform level requires accounting for inferential uncertainty, caused by multi-mapping of RNA-seq reads. Our proposed method, SEESAW, uses Salmon and Swish to offer analysis at...
20.
Singh N, Love M, Patro R
iScience
. 2023 Jun;
26(6):106961.
PMID: 37378336
A certain degree of uncertainty is always associated with the transcript abundance estimates. The uncertainty may make many downstream analyses, such as differential testing, difficult for certain transcripts. Conversely, gene-level...