User profiles for R. Ounit

Rachid Ounit

University of California, Riverside
Verified email at cs.ucr.edu
Cited by 3237

[HTML][HTML] A chromosome conformation capture ordered sequence of the barley genome

…, J Vrána, S Chan, M Muñoz-Amatriaín, R Ounit… - Nature, 2017 - nature.com
… Contact probability matrices were plotted using standard R functions 69 . Principal
component analysis was performed with the R function prcomp() on the matrix of log-transformed …

[HTML][HTML] CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

R Ounit, S Wanamaker, TJ Close, S Lonardi - BMC genomics, 2015 - Springer
Background The problem of supervised DNA sequence classification arises in several fields
of computational molecular biology. Although this problem has been extensively studied, it …

[HTML][HTML] Comprehensive benchmarking and ensemble approaches for metagenomic classifiers

ABR McIntyre, R Ounit, E Afshinnekoo, RJ Prill… - Genome biology, 2017 - Springer
Background One of the main challenges in metagenomics is the identification of microorganisms
in clinical and environmental samples. While an extensive and heterogeneous set of …

The genome of cowpea (Vigna unguiculata [L.] Walp.)

…, T Zhu, MC Luo, H Alhakami, R Ounit… - The Plant …, 2019 - Wiley Online Library
… The linear model R function lm was used to compute the linear regression. The R function
predict was used to create the raster objects, and the R function polynomial yielded the …

[HTML][HTML] Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

…, J Vrána, S Chan, M Muñoz-Amatriaín, R Ounit… - Scientific Data, 2017 - nature.com
… We converted the overlap information between BACs in a graph structure using the R package
‘igraph’ 48 . Nodes represented BACs. An edge was drawn between two nodes (BACs) if …

Higher classification sensitivity of short metagenomic reads with CLARK-S

R Ounit, S Lonardi - Bioinformatics, 2016 - academic.oup.com
… Briefly, it assigns a read r to a reference genome G if r and G share more discriminative k-mers
(ie k-mers that appear exclusively in one reference genome) than other genomes in the …

[HTML][HTML] Metagenomic characterization of ambulances across the USA

…, N Caplan, G Rosen, B Frye, S Woloszynek, R Ounit… - Microbiome, 2017 - Springer
… We found that the pair that had the highest correlation (r = 0.81, p < 0.01) was Rothia
mucilaginosa and Streptococcus mitis, bacteria species that inhabit the mouth. R. mucilaginosa has …

[HTML][HTML] rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison

L Hahn, CA Leimeister, R Ounit, S Lonardi… - PLoS computational …, 2016 - journals.plos.org
… We consider sets of binary patterns, where ℓ r is the length of pattern P r and ℓ = max rr .
That is, each P r is a word of length ℓ r over the alphabet {1, 0}. A ‘1’ in a pattern P r represents …

Sequencing of 15 622 gene‐bearing BAC s clarifies the gene‐dense regions of the barley genome

…, S Bozdag, F Cordero, H Mirebrahim, R Ounit… - The Plant …, 2015 - Wiley Online Library
Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that
has hindered the development of a complete sequence. In 2012, the International Barley …

[HTML][HTML] Detection of Mpox virus using microbial cell-free DNA: the potential of pathogen-agnostic sequencing for rapid identification of emerging pathogens

…, R Ounit, LJ Noa, R Sabzwari, R Trible… - The Journal of …, 2023 - academic.oup.com
Background The 2022 global outbreak of mpox virus (MPXV) highlighted challenges with PCR
detection as divergent strains emerged and atypical presentations limited the applicability …