Crowdsourcing biomedical research: leveraging communities as innovation engines
The generation of large-scale biomedical data is creating unprecedented opportunities for
basic and translational science. Typically, the data producers perform initial analyses, but it …
basic and translational science. Typically, the data producers perform initial analyses, but it …
[HTML][HTML] Adaptive genomic structural variation in the grape powdery mildew pathogen, Erysiphe necator
Background Powdery mildew, caused by the obligate biotrophic fungus Erysiphe necator, is
an economically important disease of grapevines worldwide. Large quantities of fungicides …
an economically important disease of grapevines worldwide. Large quantities of fungicides …
[HTML][HTML] A comprehensive evaluation of assembly scaffolding tools
Background Genome assembly is typically a two-stage process: contig assembly followed
by the use of paired sequencing reads to join contigs into scaffolds. Scaffolds are usually the …
by the use of paired sequencing reads to join contigs into scaffolds. Scaffolds are usually the …
High-throughput genome scaffolding from in vivo DNA interaction frequency
Despite advances in DNA sequencing technology, assembly of complex genomes remains
a major challenge, particularly for genomes sequenced using short reads, which yield highly …
a major challenge, particularly for genomes sequenced using short reads, which yield highly …
[HTML][HTML] An improved genome assembly uncovers prolific tandem repeats in Atlantic cod
Abstract Background The first Atlantic cod (Gadus morhua) genome assembly published in
2011 was one of the early genome assemblies exclusively based on high-throughput 454 …
2011 was one of the early genome assemblies exclusively based on high-throughput 454 …
Whole-genome sequencing in outbreak analysis
CA Gilchrist, SD Turner, MF Riley… - Clinical microbiology …, 2015 - Am Soc Microbiol
In addition to the ever-present concern of medical professionals about epidemics of
infectious diseases, the relative ease of access and low cost of obtaining, producing, and …
infectious diseases, the relative ease of access and low cost of obtaining, producing, and …
Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution
JW Davey, M Chouteau, SL Barker… - G3: Genes …, 2016 - academic.oup.com
The Heliconius butterflies are a widely studied adaptive radiation of 46 species spread
across Central and South America, several of which are known to hybridize in the wild. Here …
across Central and South America, several of which are known to hybridize in the wild. Here …
Tools and techniques for computational reproducibility
SR Piccolo, MB Frampton - Gigascience, 2016 - academic.oup.com
When reporting research findings, scientists document the steps they followed so that others
can verify and build upon the research. When those steps have been described in sufficient …
can verify and build upon the research. When those steps have been described in sufficient …
[HTML][HTML] Next-generation sequence assembly: four stages of data processing and computational challenges
S El-Metwally, T Hamza, M Zakaria… - PLoS computational …, 2013 - journals.plos.org
Decoding DNA symbols using next-generation sequencers was a major breakthrough in
genomic research. Despite the many advantages of next-generation sequencers, eg, the …
genomic research. Despite the many advantages of next-generation sequencers, eg, the …
In vitro, long-range sequence information for de novo genome assembly via transposase contiguity
We describe a method that exploits c ontiguity p reserving t ransposase seq uencing (CPT-
seq) to facilitate the scaffolding of de novo genome assemblies. CPT-seq is an entirely in …
seq) to facilitate the scaffolding of de novo genome assemblies. CPT-seq is an entirely in …