metagenome

Kostas Mavrommatis of the DOE Joint Genome Institute presents at the JGI/Argonne HPC Workshop on January 26, 2010.

Eugene Kolker from Seattle Children's Hospital briefly discusses "The Encyclopedia of Systems Biology and OMICS," followed by Susanna Sansone from the EBI on "The ISA Infrastructure for multi-omics data" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 11, 2009.

George Weinstock from Washington University School of Medicine talks about the Human Microbiome Project (HMP) followed briefly by Jennifer Wortman from the University of Maryland School of Medicine on the Data Analysis and Coordination Center (DACC) portal to the HMP at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

Bob Vaughan of EMBL on submitting MIGS/MIMS/MIENS information to EMBL-EBI's system, followed by a brief talk from Jon Kaye of the Gordon and Betty Moore Foundation on standards and the foundation's sequencing pipelines at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

Victor Markowitz, head of the Biological Data Management and Technology Center at Lawrence Berkeley National Laboratory, talks about the Integrated Microbial Genomes system housed at the DOE JGI at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM on May 29, 2009.

The methodologies used to generate genome and metagenome annotations are diverse and vary between groups and laboratories. Descriptions of the annotation process are helpful in interpreting genome annotation data. Some groups have produced Standard Operating Procedures (SOPs) that describe the annotation process, but standards are lacking for structure and content of these descriptions. A general structure for SOP documents that are relevant to genome annotation, metagenomics, environmental...

Trillions of microbes live in our digestive tract and influence our biology in profound and diverse ways. Several diseases, including obesity and inflammatory bowel diseases, have been associated with large-scale shifts in microbiota composition. The ability to address basic questions concerning community function and plasticity are fundamental to understanding the extent of causal relationships between host biology and microbiota perturbations, and whether the microbiota is a viable...

Jeroen Raes, European Molecular Biology Laboratory Comparative metagenomics is a powerful tool to detect environment-specific adaptation of the communities that inhabit them. However, a wide range of technical and biological interfering factors hamper the correct interpretation of comparative metagenomics results. Here, I will describe some of these factors and pitfalls and propose a minimal metagenome sequence analysis standard (MINIMESS) to cope with these issues. This suggested additional,...

With the MIGS/MIMS specifications the Genomic Standards Consortium has finished the groundwork to enrich our genome and metagenome collections with contextual data. Now, it is time to consider whether these standards could be applied ‘as is’ in the short-term, and ‘with modification/extension’ in the longer-term to any genetic marker sequence retrieved from the environment. To move for ward and leverage existing interest in the community the proposal for MIENS, the ‘Minimum...

Termites and their complex hindgut microbiota are able to convert wood lignocellulose into hydrogen and other products used to fuel their metabolisms. Recent gene and genome and metagenome based analyses on the gut community have revealed novel insights into many bacteria-mediated, important symbiotic functions. The system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation has both basic and applied implications.