genomic

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.

Tatiana Tatusova of NCBI discusses "Annotations in Refseq" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009.

Dawn Field of the NERC Centre for Ecology & Hydrology briefly introduces the GEM Catalogue, followed by Susanna Sansone of the European Bioinformatics Institute who talks about the ISA-GCDML workshop at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

Pelin Yilmaz of the Max Planck Institute-Bremen talks about the MIENS specification and Eugene Kolker of Seattle Children's Hospital discusses the GSC's non-for-profit at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

Dawn Field of the NERC Centre for Ecology & Hydrology briefly describes RCN4GSC and Peter Sterk of the NERC Centre for Ecology & Hydrology follows with a talk on curation of MIGS-compliant data at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

Genomic association study (CHIP-Seq) of Liver X receptors beta in combination with gene expression analysis presented by Lana Garmire, Bioengineering, UC San Diego

Comprehensive characterization of genomic composition in environmental microbial samples has been challenging, because the majority of microorganisms are difficult to culture. Additional challenges include a high degree of genetic diversity between and within species, various level of relative abundance and ubiquitous presence of cell-free DNA. Single cells or single molecules genomic assays hold great promise for tackling these challenges. Recent progresses in the developments of these...

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...

Since the first metagenomics study was published 17 years ago, the ability to make ecological inferences has been limited by sequencing throughput and the ability to analyze the data. Yet, if the potential of metagenomics to help us decipher the structure and function of microbial ecosystems is to be realized, it is essential that our bioinformatics tools motivate our sequencing efforts. This is analogous to the bioinformatics advances that were made to accelerating the sequencing of the...

The MIGS/MIMS checklist developed by the Genomic Standards Consortium (GSC) aims to enrich our ever growing data collection of genomic and metagenomic sequences. Therefore, the checklist defines what minimal list of contextual data attributes has to be added to the sequences in order to conform to the MIGS/MIMS specification. However, MIGS/MIMS itself does not specify how the contextual data should be documented; thus the GSC is developing the Genomic Contextual Data Markup Language (GCDML),...