Microbiomics and Functional Genomics Core

The Microbiomics and Functional Genomics Core in the San Diego Digestive Diseases Research Center provides advanced microbiomics and genomics services to Center members, and offer consultation and training in genomics technologies to enhance the ability of members to implement these technologies in their research.

Specifically, the Core will:

  1. Conduct sequencing-based assays for microbiomics and functional genomics 
  2. Perform bioinformatics analyses of sequencing-based assays 
  3. Consult and advise in studies involving microbiomics and functional genomics
  4. Provide validated experimental protocols and training 

The Core will be directed by Dr. Rob Knight, an internationally recognized experts in microbiomics, and co-directed by Dr. Christopher Glass, an expert in functional genomics.  Dr. Kristen Jepsen serves as co-investigator and is the Director of the IGM Genomics Center at UCSD, which will perform all sequencing-based assays for the Core.  Dr. Kathleen Fisch serves as co-investigator and she is the Executive Director of the Center for Computational Biology and Bioinformatics (CCBB), which will provide all bioinformatics analyses that result from the sequencing-based assays.

Services Offered:

  • 16S rRNA and metagenomic shotgun sequencing of microbial communities
  • RNA-seq (including single-cell transcriptomics), ChIP-seq, miRNA-Seq, GRO-Seq, Ribo-Seq, ATAC-Seq, Whole Genome Sequencing, and Exome sequencing
  • Bioinformatics analyses of sequencing-based assays
  • Consultation and training in specific experimental and analytical techniques related to microbiomics and functional genomics.


For obtaining services, Center members can make an online request: sddrc@ucsd.edu