Friday, December 11, 2015

Dusting off the blog site...Newsletter time

Greetings and Salutations oh Minions of Bioinformatics...

So in keeping with the premise of this blog as you'll notice - I haven't exactly gone anywhere or done anything meriting a hash on this site. Well that's not totally true - I did once again give my Phylogenetics/Sequence Analysis workshop in January 2015 - this time in Peru and I am shamefully delinquent on posting the materials for that but it's on the list.

My excuse? Well I had just found out I was pregnant. That being said I spent the following 9 mos alternately excited, busy attempting to thwart morning sickness and keep up with work and fretting about 10 pound baby head nightmares. Then I was on maternitiy leave. I just recently returned from leave and have a healthy gorgeous baby girl who lights me up no matter how freaking tired I am...and I am tired.

Thus! I have attended no conferences although my work has appeared at conferences with others presenting. Nor have I attended any workshops. I did have two papers accepted (Huzzah!) and 2 more that'll go into submission before the end of the year - so it hasn't been a total intellectual loss.

As part of my return I emailed my Bioinformatics Enthusiasts listserve with the monthly offering in the form of a Bioinformatics Newsletter that I've been putting together and sharing for the past 3 years. Why haven't I posted it here? Because for the past 3 years the institution I work for has blocked this site as a 'blog' site. I don't know why they suddenly unblocked it but I'll take it! And so here I will post my monthly one-hit-wonder for those that are interested in what I find interesting in the world of virolgy and bioinformatics.

Many thanks to my utterly fabulous colleague Nick Loman for encouraging me to start posting these online - here's the shameless plug to his site: Go Here I am Nick Loman's Awesome Lab Site. If I were on twitter right now I'd be hash-tagging that sentence with #scigroupie

Many thanks to my tens of followers of this blog, I hope you find it's content useful and now in the stead of all the conferences and workshops I am not currently attending - 
I shall post my newsletter instead.

Happy Holidays!
Online Short Course:
Pathogen evolution, selection and immunity
Latest and greatest in the Lit
Darriba, Flouri and Stamatakis. 2015. The state of software in evolutionary biology. bioRxiv. 
Khang and Lau. 2015. Getting the most out of RNA-seq data analysis. PeerJ.  
Wang et al., 2015. Reemergence of autochthonous transmission of dengue virus, Eastern China, 2014. EID
Duong et al., 2015. Asymptomatic humans transmit dengue virus to mosquiotes. PNAS.
Jennifer Doody. 2015. Ebola outbreak: a system that failed. Harvard Gazette.
Lau et al., 2015. A systematic Bayesian integration of epidemiological and genetic data. PLoS Comp Biol
Bowers et al., 2015. Impact of library preparation protocols on the metagenomic reconstruction of a mock microbial community. BMC Genomics.
Worby, Lipsitch and Hanage. 2015. Shared genomic variants: identification of transmission routes using pathogen deep sequencing data. bioRxiv
Scientific Internet Chatter
Tutorial: RNA-seq differential expression & pathway analysis with Sailfish, DESeq2, GAGE and Pathview. (Getting Genetics Done)

A computational pipeline for cross-species analysis of RNA-seq data using R and Bioconductor. (RNAseq Blog)

How to extract FASTQ from the new MinION FAST5 format using poRe. (Opiniomics)

“Do demons dreams of phylogeny packages?” (Omics Omics)

“The five habits of bad bioinformaticians” (Opiniomics)

“DENGVAXIA®, worlds first dengue vaccine, approved in Mexico” (Sanofi Pasteur)

MinION and time to result” (Omics Omics)

“Oxford Nanopore’s Software Side.” (BioIT World)

Software Notes:

The HGAP assembler is actually an elaborate front-end hiding 
three thousand slave labourers all running GAP4!
You can also find a totally exhaustive listing of my internet bioinformatic trolling spoils at where I link to research in general virology, dengue, influenza, bioinformatic software that's published or coming out as well as post job openings and trainings I come across so feel free to hit that up if you desire more bioinformatic madness.