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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64
Citations
6717
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Recent Articles
1.
Khan J, Dhulipala L, Patro R
bioRxiv
. 2025 Feb;
PMID: 39975203
The rapid growth of genomic data over the past decade has made scalable and efficient sequence analysis algorithms, particularly for constructing de Bruijn graphs and their colored and compacted variants...
2.
Singh N, Khan J, Patro R
bioRxiv
. 2024 Dec;
PMID: 39677745
Ultrafast mapping of short reads via lightweight mapping techniques such as pseudoalignment has significantly accelerated transcriptomic and metagenomic analyses, often with minimal accuracy loss compared to alignment-based methods. However, applying...
3.
Gao Y, Patro R, Jiang P
Bioinformatics
. 2024 Oct;
40(11).
PMID: 39460943
Motivation: A crucial component of intuitive data visualization is presenting a hierarchical tree structure with interactive functions. For example, single-cell transcriptomics studies may generate gene expression values with developmental trajectories...
4.
Campanelli A, Pibiri G, Fan J, Patro R
J Comput Biol
. 2024 Oct;
31(10):1022-1044.
PMID: 39381838
We describe lossless compressed data structures for the de Bruijn graph (or c-dBG). Given a collection of reference sequences, a c-dBG can be essentially regarded as a map from -mers...
5.
Campanelli A, Pibiri G, Fan J, Patro R
bioRxiv
. 2024 Jul;
PMID: 39026859
Software: The implementation of the indexes used for all experiments in this work is written in C++17 and is available at https://github.com/jermp/fulgor .
6.
Robinson W, Stone J, Schischlik F, Gasmi B, Kelly M, Seibert C, et al.
Sci Adv
. 2024 Jul;
10(27):eadj7402.
PMID: 38959321
The study of the tumor microbiome has been garnering increased attention. We developed a computational pipeline (CSI-Microbes) for identifying microbial reads from single-cell RNA sequencing (scRNA-seq) data and for analyzing...
7.
He D, Gao Y, Chan S, Quintana-Parrilla N, Patro R
Bioinformatics
. 2024 Jun;
40(Suppl 1):i297-i306.
PMID: 38940130
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...
8.
Tiberi S, Meili J, Cai P, Soneson C, He D, Sarkar H, et al.
Biostatistics
. 2024 Jun;
25(4):1079-1093.
PMID: 38887902
Although transcriptomics data is typically used to analyze mature spliced mRNA, recent attention has focused on jointly investigating spliced and unspliced (or precursor-) mRNA, which can be used to study...
9.
Khan J, Rubel T, Molloy E, Dhulipala L, Patro R
Algorithms Mol Biol
. 2024 Apr;
19(1):16.
PMID: 38679714
Purpose: String indexes such as the suffix array (SA) and the closely related longest common prefix (LCP) array are fundamental objects in bioinformatics and have a wide variety of applications....
10.
Karami M, Soltani Mohammadi A, Martin M, Ekim B, Shen W, Guo L, et al.
Bioinformatics
. 2024 Apr;
40(4).
PMID: 38579261
Motivation: Substrings of length k, commonly referred to as k-mers, play a vital role in sequence analysis. However, k-mers are limited to exact matches between sequences leading to alternative constructs....