Genomics & Bioinformatics
Selection of Scripps Oceanography & UC San Diego research & resources
UC San Diego and Scripps are world-leaders in microbiome research, biomedical engineering, quantitative measurements and modeling, cellular and chemical imaging, drug discovery, “omics” sciences and much more. The UCSD Center for Microbiome Innovation draws interdisciplinary teams of these researchers together to push the boundaries of human understanding of microbiomes — the distinct constellations of bacteria, viruses and other microorganisms that live within and around humans, other species and the environment. Scripps researchers are specifically looking at environmental microbiomes of marine sponges and other invertebrates, fish, deep sea habitats, ocean spray aerosols and numerous other marine microbial communities.
PIs: Eric Allen, Bradley Moore, Paul Jensen, Robert Knight, Pieter Dorrestein, Douglas Bartlett, Jeffrey Bowman, William Fenical, William Gerwick, Jules Jaffe, Brian Palenik, Kimberly Prather, Lahini Aluwihare, Davey Smith
Metagenomic analysis of complex marine communities
Marine metagenomics is a burgeoning field with the capacity to facilitate discoveries of intricate interactions within microbial communities. Using metagenomic analysis, Scripps researchers examine diverse questions in ecology, evolution, functional genomics and drug discovery. Scripps labs have unique access to marine microbial communities from the deepest ocean trenches to marine invertebrates to water off the Scripps Pier and develop sequenced-based approaches to make discoveries about the complex microbial communities of the oceans.
PIs: Eric Allen, Douglas Bartlett, Ronald Burton, Brian Palanik, Jeffrey Bowman, Andrew Allen, William Gerwick, Farooq Azam, Bradley Moore
Analysis of bioactive molecule-producing microbes- genome-driven discovery
Microbial biodiversity remains one of the last great biotic frontiers, and developing effective strategies to discover and exploit new small molecules from this resource is integral to the success of future drug discovery efforts. Microbes hold the blueprints for the molecules they make within their genomes, and Scripps scientists work to decode these instructions to discover and engineer new medicines. Scripps researchers have developed high-throughput methods to “mine” microbial genomes to determine their potential as producers of novel molecules and have discovered numerous bioactive molecules using genetic information. This genome driven discovery is the future of natural product research, and Scripps is at the cutting-edge of this developing field.
PIs: Bradley Moore, Paul Jensen, William Gerwick, Eric Allen, William Fenical
De novo sequencing and analysis of marine invertebrates, transcriptomics
Eukaryotic genomes prove a much more difficult challenge than microbial genomics, and Scripps researchers are developing computational methods to assemble and analyze the complex genomes of marine invertebrates. A collaborative team including Scripps researchers has recently decoded the genome of a copepod that serves as a model system for speciation research, allowing for a genetic understanding of speciation. Scripps scientists have also undertaken the enormous task of assembling a transcriptome of the California Market Squid in low oxygen and low pH conditions. Understanding the underlying genetics of such important species will inform regulation and help mitigate the biological impacts of climate change.
PI: Terry Gaasterland, Eric Allen, Ron Burton
Work with Scripps
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