Assigned Reading

Biology

• Quantitative bacterial transcriptomics with RNA-seq
• Studying bacterial transcriptomes using RNA-seq
• Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
• pH Regulates Genes for Flagellar Motility, Catabolism, and Oxidative Stress in Escherichia coli K-12†

Statistics

• Statistical Design and Analysis of RNA Sequencing Data
• Statistical Challenges in Preprocessing in Microarray Experiments in Cancer
• Statistical Considerations for Analysis of Microarray Experiments
• Differential expression analysis for sequence count data

Bioinformatics

• Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
• Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples
• Fast gapped-read alignment with Bowtie 2
• TopHat: discovering splice junctions with RNA-Seq
• Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2