CSO at CLC bio, Bjarne Knudsen and Michael M. Miyamoto from the University of Florida recently wrote an article in BMC Bioinformatics.
The article illustrates how the mutation rate in a population can be efficiently estimated, even with data affected by a number of practical issues such as sequencing errors, missing haplotype information, and missing data. The premise is that sequence errors generally give rise to unique mutations only found in a single sequence. By ignoring such singletons and adjusting the coalescent based calculations accordingly, efficient estimates can be obtained while not loosing too much information.
Click to read the entire “Accurate and fast methods to estimate the population mutation rate from error prone sequences” article
Ed Yong at his Not Exactly Rocket Science blog wrote…
Julie Dunning-Hotopp from the J. Craig Venter Institute and Michael Clark from the University of Rochester have found a drastic strategy used by Wolbachia to preserve its own immortality - inserting its entire genome wholesale into that of another living thing.
Click here to read the exciting article.
In the latest edition of Nature, Technology Editor, Nathan Blow, PhD, published a Technology Feature on how Next Generation Sequencing is changing gene-expression profiling from analog to digital methods.
Our Director of Scientific Solutions, Dr. Roald Forsberg, was interviewed for the article and shares the vision behind our focus within Gene Expression Analysis - both digital and analog.
I recommend reading the feature, which is really thorough in describing the change from analog to digital gene-expression. You can read it here:
Transcriptomics: The digital generation
Recently our Director of Scientific Solutions - and Editor-in-Chief of this blog - Dr. Roald Forsberg, did an online presentation called Comprehensive, Fast, and User-Friendly Downstream Analysis of Illumina Sequencing Data, through Illumina’s webinar series. The presentation was very successful and is now available for everyone, so you can view it her and download the presentation slides. Enjoy!
Click to download the presentation slides or learn more about the solutions mentioned
I once had the pleasure of visiting David Lambert, an expert and pioneer in ancient DNA studies. With Dave I had some of the most interesting and thought provoking discussion about biology, that I have ever had.
Now Dave and his colleagues have a new review out in TREE on New developments in ancient genomics that I can’t wait to read when I get back to work next week.
Here is the abstract:
Ancient DNA research is on the crest of a ‘third wave’ of progress due to the introduction of a new generation of DNA sequencing technologies. Here we review the advantages and disadvantages of the four new DNA sequencers that are becoming available to researchers. These machines now allow the recovery of orders of magnitude more DNA sequence data, albeit as short sequence reads. Hence, the potential reassembly of complete ancient genomes seems imminent, and when used to screen libraries of ancient sequences, these methods are cost effective. This new wealth of data is also likely to herald investigations into the functional properties of extinct genes and gene complexes and will improve our understanding of the biological basis of extinct phenotypes.
