Genome_Biology.md

Genome Biology Articles

The following is a list of papers from Genome Biology that seemed interesting.

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Matthew B Hufford 2016. Comparative genomics provides insight into maize adaptation in temperate regions

• Review paper on maize adaptation in temperate regions

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Unterseer et al. 2016. A comprehensive study of the genomic differentiation between temperate Dent and Flint maize

• Aims to understand genomic differences between two pools
• Traits that differentiate between two pools: cold tolerance, early vigor, and flowering time

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Joo et al. 2016. Multiple testing correction in linear mixed models

• GWAS multiple hypothesis testing correction approach
• Reduce amount of time to estimate per-marker thresholds accurately

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Muir et al. 2016. The real cost of sequencing: scaling computation to keep pace with data generation

• Short paper on Sequencing cost decrease & Sequence data generated increases
• Data storage & Analysis
• Scaling behavior changes to accomodate evolving technologies

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Zhang et al. 2016. Genome-wide introgression among distantly related Heliconius butterfly species

• Characterization of genome-wide patterns of introgression between distantly related species of butterfly
• Presents a workflow for gene flow identification in genomic datasets

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Wendel et al. 2016. Evolution of plant genome architecture

• Short review paper on: evolutionary history of all plant genomes, lineage-specific transposable elements, and small RNAs and their contribution to genomic architecture and function.

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Smolka et al. 2015. Teaser: Individualized benchmarking and optimization of read mapping results for NGS data

• Read mapping for low-quality assemblies or high mutation rates. Optimizing mapper choice and parameters.
• Teaser software

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Gentleman et al. 2004. Bioconductor: open software development for computational biology and bioinformatics

• Development and widespread use of software

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Bolisetty, Rajadinakaran and Graveley 2015. Determining exon connectivity in complex mRNAs by nanopore sequencing

• Method for comprehensive transcriptome characterization

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Lawrenson et al. 2015. Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease

• RNA-guided Cas9 system for genome editing in Hordeum vulgare and Brassica oleracea
• Rapid characterization of gene function

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Neil Hall 2014. The Kardashian index: a measure of discrepant social media profile for scientists

• Scientist's social media profile vs Scientist's publication record
• Ratio of number of citation to number of Twitter followers

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Chaparro-Garcia, Kamoun and Nekrasov 2015. Boosting plant immunity with CRISPR/Cas

• Geminivirus resistnce

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