Wednesday, June 10, 2009

Single Cell Genomics: New PLoS ONE article evaluated at Faculty of 1000

I recently handled an interesting article at PLoS ONE [Assembling the marine metagenome, one cell at a time. Woyke T, et al., PLoS ONE 2009 4(4):e5299].
As for the other high ranking PLoS ONE articles, this article too was evaluated at the Faculty of 1000 Biology and was rated with a F1000 Factor of 6.0 (Must Read). A redacted version of the evaluation by Douglas Bartlett is here: 
'This work details the use of single cell genomics from two uncultured marine Flavobacteria to recruit considerable sequence data from the Global Ocean Survey (GOS) compared to genome sequences from cultured Flavobacteria isolates. The genome reconstruction and stringent quality control of the two SAGs (single amplified genomes) are well handled, considering contamination and chimeras associated with the amplification process. The analyses of the two SAGs indicate unique metabolic features such as hydrogen oxidation, proteorhodopsin photometabolism, and biopolymer hydrolysis. Also of interest is the genome streamlining in the ...' ..... Full evaluation of the article is available here (

BLoG ONE has moved to Word Press

A mirror of BLoG ONE now operates from WordPress. All contents from this site will be mirrored from there.

PLoS ONE Prokaryotic Genome Collection - now launched

I am excited to tell you of the latest collection of some of the high-impact articles, the PLoS ONE Prokaryotic Genome Collection. Liz Allen of PLoS, has some more things to say …read her full blog post here.

There is an editorial overview that accompanies the new collection; it’s written by me. Comments related to the collection and the ‘overview’ have started to trickle in, such as this one by Dr Ramy Aziz:

“This article lists very interesting challenges and questions that will be answered in the next decade of this millennium. With the revolution stirred by next-gen sequencing machines, sequencing/resequencing steps have become quick and cheap. Thus, data generation is the least part to worry about. However, as the article appropriately discusses, the problem is what to sequence and then how to make sense out of the piles.

We will very soon have 5,000 fully sequenced prokaryotic genomes, but, as quick annotation tools are being developed, we realize very well that more genomes annotated = more errors propagated.

In addition to high-speed and high-performance …”
Read more here.