366 Papers for 2016

I stumbled upon a Twitter hashtag #366papers. The text usually associated with this is a summary or the title of an article they read. Presumably, they have read the paper and will read an article every day of this year (which happens to be a leap year!).

As a graduate student, I find this challenge great. It’ll help me make a habit of reading journal articles. Additionally, I hope to keep a log of the papers I read with this post. So I will regularly update this post with new papers I read and links to them. Enjoy and wish me luck!

Papers Log

1. Feb 20. Mager, J., Bartolomei M. “Strategies for dissecting epigenetic mechanisms in the mouse”. Nature Genetics (2005).
   • Reviews epigenetic modifications and mediators of modifications
   • Overview of epigenetics techniques and methods of analysis
   • Highlights challenges to some of the epigenetic methods, such as sufficient number of cells
   • Summarizes bisulfite sequencings, retriction landscape genome scanning (RLGS), chromatin immunoprecipitation (ChIP), ChIP on chip, and chromatin conformation capture (3C)
2. Feb 07. Clooney, A., et. al. “Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis”. PLoS One (2016).
   • Microbiome research is rapidly changing, different and new methods appear, so comparing analyses is going to be difficult
   • Compares HiSeq, MiSeq, and Ion PGM sequencing and its effects on downstream metagenomic analyses
3. Feb 04. Conesa, A., et.al. “A survey of best practices for RNA-seq analysis”. Genome Biology (2016).
   • Excellent summary roadmap for RNA-seq computational analyses from pre-analysis all the way through advanced analysis of visualization and integrating with other data
   • Covers common pitfalls and lots of reasoning to decisions made in an RNA-seq analysis (e.g. map to the transcriptome versus the genome)
   • Gives references to some computational tools used in each analysis step
4. Feb 03. Bassuk, Alexander G., et. al. “Precision Medicine: Genetic Repair of Retinitis Pigmentosa in Patient-Derived Stem Cells”. Scientific Reports 6 (2016).
   • Uses CRISPR/Cas9 to edit mutation in patients with X-linked retinitis pigmentosa (XLRP)
   • Uses induced pluripotent stem cells (iPSCs) from patient fibroblasts
   • Patient derived cells required no patient immunosuppression
   • Need to be conscious of off-targeting of CRISPR/Cas9
   • Describes methods of narrowing which CRISPR guide RNA to use and validation