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PBHoney: identifying genomic variants via long-read discordance and interrupted mapping

Adam C English 0 William J Salerno 0 Jeffrey G Reid 0 0 Human Genome Sequencing Center at Baylor College of Medicine , One Baylor Plaza, Houston 77030, Texas , USA Background: As resequencing

PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations

Background Generation of long (>5 Kb) DNA sequencing reads provides an approach for interrogation of complex regions in the human genome. Currently, large-insert whole genome sequencing (WGS) technologies from Pacific Biosciences (PacBio) enable analysis of chromosomal structural variations (SVs), but the cost to achieve the required sequence coverage across the entire human genome ...

Prevalence of alternative splicing choices in Arabidopsis thaliana

Background Around 14% of protein-coding genes of Arabidopsis thaliana genes from the TAIR9 genome release are annotated as producing multiple transcript variants through alternative splicing. However, for most alternatively spliced genes in Arabidopsis, the relative expression level of individual splicing variants is unknown. Results We investigated prevalence of alternative ...

Assessing structural variation in a personal genome—towards a human reference diploid genome

Background Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and methods are available to detect these structural variants (SVs), they remain less characterized than smaller variants because of SV diversity, complexity, and size. These challenges are exacerbated by the experimental ...

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

Many genomes have been sequenced to high-quality draft status using Sanger capillary electrophoresis and/or newer short-read sequence data and whole genome assembly techniques. However, even the best draft genomes contain gaps and other imperfections due to limitations in the input data and the techniques used to build draft assemblies. Sequencing biases, repetitive genomic ...