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 [...]

R Line Plots – the easiest fastest plot ever

What you need: Data R Eager Bioinformatician For data I used a file with 7 columns where the first column was a counter and the other columns (2-7) had different values that I would like to compare across using a line plot to visualize the variation in my data points Serves: As many data points [...]

How recent are rare variants?

The Department of Genome Sciences at the University of Washington in Seattle, in a multi-institutional effort sequenced 15,336 genes for the NHLBI sponsored ESP project from a total of 6515 individuals of European American and African American descent.To identify approaches for disease-gene discovery, its important to understand evolutionary history of homosapiens and identify the age [...]