User profiles for R. Ounit
Rachid OunitUniversity 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 …
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
Background The problem of supervised DNA sequence classification arises in several fields
of computational molecular biology. Although this problem has been extensively studied, it …
of computational molecular biology. Although this problem has been extensively studied, it …
[HTML][HTML] Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
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 …
in clinical and environmental samples. While an extensive and heterogeneous set of …
The genome of cowpea (Vigna unguiculata [L.] Walp.)
… 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 …
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 …
‘igraph’ 48 . Nodes represented BACs. An edge was drawn between two nodes (BACs) if …
Higher classification sensitivity of short metagenomic reads with CLARK-S
… 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 …
(ie k-mers that appear exclusively in one reference genome) than other genomes in the …
[HTML][HTML] Metagenomic characterization of ambulances across the USA
… 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 …
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
… We consider sets of binary patterns, where ℓ r is the length of pattern P r and ℓ = max r ℓ r .
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 …
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
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 …
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 …
detection as divergent strains emerged and atypical presentations limited the applicability …