Example RNAseq papers

[k8hertweck]

Let's use this issue to track example papers to use as references in class. Ideally this will include:

• authors from the FH community
• exhibit reproducible methods
• different model systems (human, mouse, etc) and methods

[lakikowolfe]

Used in concepts class 1

• Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap
• Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion

Reviews

• RNA sequencing: advances, challenges and opportunities
• RNA sequencing: the teenage years
• A survey of best practices for RNA-seq data analysis

Applications

• The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
• Understanding mechanisms underlying human gene expression variation with RNA sequencing
• Quantitative bacterial transcriptomics with RNA-seq
• An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

Fred Hutch

• Genomic analyses identify recurrent MEF2D fusions in acute lymphoblastic leukaemia - Radich
• Genetic Ancestry Contributes to Somatic Mutations in Lung Cancers from Admixed Latin American Populations - Ha