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Cataloguing the Gene Expression Patterns of Dental Plaque Biofilms: A Reference Dental Plaque Transcriptome
The RNA-Seq method has been widely adopted as an alternative to the use of DNA microarrays. In most contexts, the RNA-Seq method is implemented when a single reference organism is being studied. Our project endeavored to establish working methods to enable the generation of cDNA libraries that were depleted of contaminating human mRNA and host/microbiome rRNA sequences that would otherwise represent over 95% of the total sequence reads obtained. We have also made significant efforts to define...
Surrogate Methods for Profiling Species of the Oral and Gut Microbiome
We engaged in an effort focused on alleviating a substantial barrier facing the human microbiome research community. While powerful, the 16S rDNA gene is insufficiently divergent to allow discrimination of many species and essentially no strains present within communities. The increasing costs of Sanger sequencing has forced most investigators to adopt the use of the Roche, 454 sequencing platform to address the question, “who’s there?” The benefits of the 454 sequence data are...
Sequencing of high yield influenza reassortants at JCVI
As part of the Influenza Genome Sequencing Project, JCVI will be sequencing a large number of high yield influenza reassortants created in the lab of Dr. Doris Bucher at New York Medical College. Dr. Bucher’s lab has prepared the type A H3N2 high yield reassortants (hyrs) for the influenza vaccine for the past several years, both within the US and world wide. The Bucher lab continues the tradition of preparing the hyrs as developed by preeminent influenza virologist Dr. Edwin D....
Scientist Spotlight: Meet Vanessa Hayes
Geneticist Vanessa Hayes does not think small nor move slowly—from completing her post doc in six months (the US National average is 3 to 7 years) to completing the first South African Genome Project in 2010 with her goal set on defining the extent of human diversity in all populations, she is on a mission. Just 11 years outside her post doc she has the credentials of someone who has been in science much longer. Her work and talent has taken her to remote regions of Southern Africa, all...
Lucene Revolution Conference 2010
I arrived late in Boston after my plane from Washington DC was delayed. On the agenda - the next four days the Lucene Revolution conference and a Solr application development workshop organized by Lucid Imagination. The conference promised a unique venue (the first of its kind in the US) to meet developers that all share the same challenge: to enable users to find relevant information in growing bodies of data quickly and intuitively. I was looking forward to hearing many interesting talks...
Virtual Comparative Metagenomics
We have created an open virtualization format (OVF) package of JCVI's Metagenomics Reports (METAREP)- a high performance comparative metagenomics analysis tool. The software runs on a web server, retrieves data from two different database systems and uses R for statistical analysis. The new OVF package bundles all these 3rd party tools and is configured to run out of the box in a virtual machine. To run a virtual version of METAREP on your machine, follow these steps download the...
Sampling of Lake Banyoles, The Home of the Olympic Rowing in 1992
May 9th 2010 Sunday May 9th was a much better morning than the previous one. Emilio had taken us out to one of the best dinners I have ever eaten, plus the German teenagers were no longer patrolling the hallways all night long. So after a great seafood dinner and a good nights rest we drove back to Lake Banyoles to sample Basin C-III, Basin C-III is a meromictic area of the lake. Basin C-III in Lake Banyoles Like in Lake Siso, a dinghy was rowed out to the long term research site...
AGBT, Marco Island 2010
I just got back from AGBT in Marco Island, Florida and I am still in awe. As noted in the name, this conference highlights advances in both genome biology and technology. The biology seemed to be very human genome centric. Many of the talks presented full genome sequences of cancer genomes or familial cohorts. Some of the numbers that people threw around were shocking. It was only a short time ago that Craig Venter came out with the first personal genome, and now sequencing centers like...