Molecular Biology

Refer to Wikipedia for basic information

High throughput sequencing (HTS)

The sequence of sequencers: The history of sequencing DNA, Heather JM et. al., Genomics 2016

High-Throughput Sequencing Technologies, Reuter JA et. al., Molecular Cell 2015

Sequencing depth and coverage: key considerations in genomic analyses, Sims D et. al., Nature Reviews 2014

RNA-seq differential expression studies: more sequence or more replication?, Liu Y et. al., Bioinformatics 2014

De novo genome assembly

A field guide to whole‐genome sequencing, assembly and annotation, Ekblom and Wolf, Evolutionary Applications 2014

The Theory and Practice of Genome Sequence Assembly, Simpson and Pop, Annual Review of Genomics and Human Genetics 2015

Variant Calling

Genotype and SNP calling from next-generation sequencing data. Nielsen et al., Nature Reviews Genetics 2011. This is a review paper that should be easily understandable once the student has taken the variant calling module.

Exome sequencing identifies the cause of a mendelian disorder. Ng et al., Nature Genetics 2010. A paper reporting the first resolution of a mendelian disorder using exome capture.

Statistical genomics

Ten Simple Rules for Reproducible Computational Research, Sandve et. al., PLoS Computational Biology 2013

The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment, Subhajyoti et. al., Briefings in Bioinformatics 2013

GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome, Simovski et. al., GigaScience 2107

Hypothesis testing, McDonald, Handbook of Biological Statistics

Multiple testing, McDonald, Handbook of Biological Statistics

From 2016

Coming of age: ten years of next-generation sequencing technologies, Goodwin et. al., Nature Reviews Genetics 2016

Figures 1-4 from Sequencing technologies — the next generation, Metzker, Nature Reviews Genetics 2009

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis, Fabbro et. al., PLoS ONE 2013

Benchmarking short sequence mapping tools , Hatem et. al., BMC Bioinformatics 2013

Genotype and SNP calling from next-generation sequencing data, Nielsen et. al., Nature Reviews Genetics 2011

The power and promise of RNA‐seq in ecology and evolution, Todd et. al., Molecular Ecology 2016