Douglas W Bryant
Affiliation: Oregon State University
- QSRA: a quality-value guided de novo short read assemblerDouglas W Bryant
Department of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
BMC Bioinformatics 10:69. 2009..Since all high-throughput sequencing platforms incorporate errors in their output, short-read assemblers must be designed to account for this error while utilizing all available data...
- Supersplat--spliced RNA-seq alignmentDouglas W Bryant
Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
Bioinformatics 26:1500-5. 2010..Identification of intron/exon boundaries is an essential part of genome annotation, yet remains a challenge. Here, we present supersplat, a method for unbiased splice-junction discovery through empirical RNA-seq data...
- A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag(4) conferring resistance to the aphid Amphorophora agathonicaJill M Bushakra
USDA ARS National Clonal Germplasm Repository, 33447 Peoria Rd, Corvallis, OR, 97333, USA
Theor Appl Genet 128:1631-46. 2015..This is the first linkage map of black raspberry and will aid in developing markers for marker-assisted breeding, comparative mapping with other Rubus species, and enhancing the black raspberry genome assembly...
- Genome-wide mapping of alternative splicing in Arabidopsis thalianaSergei A Filichkin
Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
Genome Res 20:45-58. 2010..Taken together, our results suggest that like in animals, NMD and RUST may be widespread in plants and may play important roles in regulating gene expression...