Friday, January 22, 2016

Bioinformatics Newsletter 1: 22 Jan 2016

East Coasters – Stay Warm! The blizzard LOOMS! Find some of your favorite scientist’s publications and cozy up with a hot beverage, I know I will!
Latest and greatest in the Lit
Escobar-Zepeda et al., 2015. The road to metagenomics: from microbiology to DNA sequencing technologies and bioinformatics. Front in Genet
Brierley et al., 2016. Quantifying global drivers of zoonotic bat viruses: a process-based perspective. Amer Naturalist.
Borucki et al., 2016. Middle east respiratory syndrome coronavirus intra-host populations are characterized by numerous high frequency variants. PLOS ONE.
Didelot et al., 2016. Within-host evolution of bacterial pathogens. Nature Reviews
Metcalf et al., 2016. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science.
Gill et al., 2016. Understanding past population dynamics: Bayesian coalescent-based modeling with covariates. arXiv
Ziegenhain et al., 2016. Comparative analysis of single-cell RNA-sequencing methods. bioRxiv
Parekh et al., 2016. The impact of amplification on differential expression analyses by RNA-seq. bioRxiv
Kim et al., 2016. Host specific and segment-specific evolutionary dynamics of avian and human influenza A viruses: A systematic review. PLOS ONE.
Scientific Internet Chatter
“CDC Zika press conference: Audio and Transcript” (Avian Flu Diary)

“Will Zika become the 2016 NTD of the Year?” (PLOS Blogs)

“Almost everything you wanted to know about Illumina HiSeq 4000” (Core Genomics)

Databases in Bioinformatics” (YouTube) Hours 1 and 2: and

“BIOM23: a 16S Practical” (Loman Lab)

“Paper summary: fast and accurate single-cell RNA-seq analysis using equivalence class counts” (NextGenSeek)

Software Notes:

#14 Velvet is so named because Daniel Zerbino wore velvet gloves when coding it (via Nick Loman)