Science Friday rocks!

I caught part of todays Science Friday on NPR and they were talking with Julie Segre about the work going on with the human microbiome (also reference to their recent paper in Science).
Who says scientists aren't famous? Rock on Julie!

Assessing biodiversity in nematodes

An interesting paper coming out in Mol Ecol Res: "Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity".

Normalization and rarefaction in gene discovery.

A new paper, "Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery" in BMC Genomics.

Jonathan Eisen's blog

It's always fun to see what he's up to.

FLX/Ti test fragments

Some people have asked for information on the test fragment sequences. If you look in the dataRunParams.xml, the sequences for all 6 TFs are listed for FLX and the 6 AVTFs are listed for Titanium.

Flow cytometry for enrichment/titration

A nice new method paper "Flow cytometry for enrichment and titration in massively parallel DNA sequencing" in NAR.

Titanium (Ti) cDNA protocol

A huge thank you to Misha Matz and his lab who have recently released a protocol using suppression PCR to create cDNA for Titanium (Ti) Roche/454 Life Sciences pyrosequencing.
They have a new paper in BMC Genomics detailing the use of this protocol for FLX.

effect of PCR amplicon size on microbial diversity

A nice new paper out by Julie Huber out in Environmental Microbiology: "Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure."

Metastats paper

A nice new paper came out recently allowing a more statistical analysis of metagenome samples. They have their software available at http://metastats.cbcb.umd.edu

@454Sequencing

I don't use twitter, but you may be interested in following 454

454 transcript sequences are now searchable through BLAST

A new option through BLAST specifically for 454.

Pyrosequencing pipeline at RDP

An awesome tool at the RDP for pyrosequencing. Many thanks to my friends at harvards for letting me know about this.