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.
Online Short Course:
Pathogen evolution, selection and immunity http://bedford.io/projects/sismid/
Latest and greatest in the Lit
Darriba, Flouri and Stamatakis. 2015. The state of software in evolutionary biology. bioRxiv. http://dx.doi.org/10.1101/031930
Khang and Lau. 2015. Getting the most out of RNA-seq data analysis. PeerJ. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631466/
Wang et al., 2015. Reemergence of autochthonous transmission of dengue virus, Eastern China, 2014. EID http://wwwnc.cdc.gov/eid/article/21/9/15-0622_article
Duong et al., 2015. Asymptomatic humans transmit dengue virus to mosquiotes. PNAS. http://www.pnas.org/content/112/47/14688.abstract
Jennifer Doody. 2015. Ebola outbreak: a system that failed. Harvard Gazette. http://news.harvard.edu/gazette/story/2015/11/ebola-outbreak-a-system-that-failed/
Lau et al., 2015. A systematic Bayesian integration of epidemiological and genetic data. PLoS Comp Biol http://dx.doi.org/10.1371/journal.pcbi.1004633
Bowers et al., 2015. Impact of library preparation protocols on the metagenomic reconstruction of a mock microbial community. BMC Genomics. http://www.biomedcentral.com/1471-2164/16/856
Worby, Lipsitch and Hanage. 2015. Shared genomic variants: identification of transmission routes using pathogen deep sequencing data. bioRxiv http://dx.doi.org/10.1101/032458
Scientific Internet Chatter
Tutorial: RNA-seq differential expression & pathway analysis with Sailfish, DESeq2, GAGE and Pathview. (Getting Genetics Done) http://www.gettinggeneticsdone.com/2015/12/tutorial-rna-seq-differential.html
A computational pipeline for cross-species analysis of RNA-seq data using R and Bioconductor. (RNAseq Blog) http://www.rna-seqblog.com/a-computational-pipeline-for-cross-species-analysis-of-rna-seq-data-using-r-and-bioconductor/
How to extract FASTQ from the new MinION FAST5 format using poRe. (Opiniomics) https://biomickwatson.wordpress.com/2015/11/23/how-to-extract-fastq-from-the-new-minion-fast5-format-using-pore/
“Do demons dreams of phylogeny packages?” (Omics Omics) http://omicsomics.blogspot.com/2015/11/do-demons-dream-of-phylogeny-packages.html
“The five habits of bad bioinformaticians” (Opiniomics) https://biomickwatson.wordpress.com/2015/11/16/the-five-habits-of-bad-bioinformaticians/
“DENGVAXIA®, worlds first dengue vaccine, approved in Mexico” (Sanofi Pasteur) http://sanofipasteur.com/en/articles/dengvaxia-world-s-first-dengue-vaccine-approved-in-mexico.aspx
“MinION and time to result” (Omics Omics) http://omicsomics.blogspot.com/2015/12/minion-and-time-to-result.html
“Oxford Nanopore’s Software Side.” (BioIT World) http://www.bio-itworld.com/2015/11/19/oxford-nanopores-software-side.html
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 http://www.scoop.it/u/mel-melendrez-vallard 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.