Bioinformatics Books!

With the start of 2017 Fall semester, the same standard stream of queries on twitter and linkedin comes along - what are some good reference books for bioinformatics Now that is indeed a good question. Bioinformatics itself is something that elicits wows from new acquaintances showing complete ignorance at the term. Moreover folks from all sorts [...]

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Bioinformatics tools for VCF files

With the ever growing abundance of Next Generation Sequencing (NGS) data there continues to be a challenge faced by the research community to not only standardize best practices and analysis methods, but to embrace the foray of open-source tools and file formats. Having been engaged since almost the beginning of this NGS data outburst with [...]

The Ebola outbreak of 2014 (Contd.)

Following up on the previous post here are some more detail on the recent Science paper along with a round-up of "what do we know, what have we learned" thus far. The Gire et al paper in Science was huge amount of work and a giant collaborative research effort. Being a computational biology researcher, I [...]

Solving the Ebola Virus Genome and Identifying Possible Diagnosis

If you have ever played the card game Killer Bunnies and your Bunnies in the Bunny circle have died because of the Level 11 Weapon of Ebola Virus you want to read this. Research community is making strides to understand whether the virus is adapting to its host or changing as it spreads through the [...]

Exomes vs Genomes (re-visited)

The paper by Lupski et al in Genome Medicine provides fuel to the perpetual debate of Whole Exome Sequencing (WES) vs Whole Genome Sequencing (WGS). It takes me down the memory lane to my own presentation "Genomes or Exomes: evaluation of cost, time and coverage" at Beyond the Genome 2011 conference. (If you would like [...]

Mitochondrial Gold Rush

Mitochondrial genomes can be extracted from Whole Exome Sequencing (WES) data as outlined by this paper in Nature methods by Ernesto Picardi & Graziano Pesole. Tools like Mito Seek are now available that gather mitochondrial read sequences from NGS data and perform high throughput sequence analysis. Availability of mitochondrial genomes is important as genomic variation in mitochondria has [...]

#ASHG2013 Platform and Poster abstract tag-clouds

With more than 6000 scientists (genetics, bioinformatics, clinicians, statistics, genetic counselor...) and more than 200 companies at Boston for this year's American Society for Human Genetics conference, there is a lot of great science to catch up on. Very quickly, I just pulled out the selected platform talk abstracts, and the poster abstracts (too many [...]