Curriculum¶
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
RNA-seq analysis¶
A survey of best practices for RNA-seq data analysis, Conesa A et. al., Genome Biology 2016
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Trapnell C et. al., Nature Protocol 2014
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Hass BJ et. al., Nature Protocol 2013
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Love MI et. al., Genome Biology 2014
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Robinson MD et. al., Bioinformatics 2010
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