Bioinformatics Newsletter 1: 22 Jan 2016

Announcements:

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 http://journal.frontiersin.org/article/10.3389/fgene.2015.00348/full

Brierley et al., 2016. Quantifying global drivers of zoonotic bat viruses: a process-based perspective. Amer Naturalist. http://www.journals.uchicago.edu/doi/abs/10.1086/684391?journalCode=an

Borucki et al., 2016. Middle east respiratory syndrome coronavirus intra-host populations are characterized by numerous high frequency variants. PLOS ONE. http://dx.doi.org/10.1371/journal.pone.0146251

Didelot et al., 2016. Within-host evolution of bacterial pathogens. Nature Reviews http://www.nature.com/nrmicro/journal/vaop/ncurrent/abs/nrmicro.2015.13.html

Metcalf et al., 2016. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science. http://science.sciencemag.org/content/351/6269/158.full

Gill et al., 2016. Understanding past population dynamics: Bayesian coalescent-based modeling with covariates. arXiv http://arxiv.org/abs/1601.05078

Ziegenhain et al., 2016. Comparative analysis of single-cell RNA-sequencing methods. bioRxiv http://biorxiv.org/content/early/2016/01/05/035758

Parekh et al., 2016. The impact of amplification on differential expression analyses by RNA-seq. bioRxiv http://biorxiv.org/content/early/2016/01/15/035493

Kim et al., 2016. Host specific and segment-specific evolutionary dynamics of avian and human influenza A viruses: A systematic review. PLOS ONE. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147021

Scientific Internet Chatter

“CDC Zika press conference: Audio and Transcript” (Avian Flu Diary) http://afludiary.blogspot.com/2016/01/cdc-zika-press-conference-audio.html

“Will Zika become the 2016 NTD of the Year?” (PLOS Blogs) http://blogs.plos.org/blog/2016/01/07/will-zika-become-the-2016-ntd-of-the-year/

“Almost everything you wanted to know about Illumina HiSeq 4000” (Core Genomics) http://core-genomics.blogspot.com/2016/01/almost-everything-you-wanted-to-know.html

“Databases in Bioinformatics” (YouTube) Hours 1 and 2: https://www.youtube.com/watch?v=CHwTpBQBwbM and https://www.youtube.com/watch?v=vOcLJkfbX60

“BIOM23: a 16S Practical” (Loman Lab) http://lab.loman.net/2016/01/22/biom25-16s-practical/

“Paper summary: fast and accurate single-cell RNA-seq analysis using equivalence class counts” (NextGenSeek) http://nextgenseek.com/2016/01/paper-summary-fast-and-accurate-single-cell-rna-seq-analysis-using-equivalence-class-counts/

Software Notes:

Blischak, Daveport and Wilson. 2016. A quick introduction to version control with Git and Github. PLOS Comp Biol http://dx.doi.org/10.1371/journal.pcbi.1004668

“RNA-seq Analysis Pipeline – TUXEDO protocol” (YouTube) http://www.rna-seqblog.com/rna-seq-analysis-pipeline-tuxedo-protocol/

Bens et al., 2016. FRAMA: from RNA-seq data to annotated mRNA assemblies. BMC Genomics.  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4712544/

“BroadE- GATK/Mapping and processing RNAseq” (RNAseq Blog) http://www.rna-seqblog.com/broade-gatkmapping-and-processing-rnaseq/

Medina et al., 2016. HPGAlign: Highly sensitive and ultrafast read mapping for RNA-seq analysis. DNA Res http://dnaresearch.oxfordjournals.org/content/early/2016/01/05/dnares.dsv039.long

Korthauer et al., 2016. scDD: A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. bioRxiv http://biorxiv.org/content/early/2015/12/29/035501

Gu et al., 2015. Depletion of abundant sequences by hybridization (DASH): Using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. bioRxiv. http://dx.doi.org/10.1101/031708

101 Fun Bioinformatics Facts!

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