Applied Genomics and Bioinformatics

Research overview

We are a bioinformatics and molecular lab that combines computational analysis with low- and high-throughput sequencing methods to answer biological questions relevant to the mission of FAU Harbor Branch Oceanographic Institute. Our work is integrated into many aspects the Institute, from ocean exploration and marine ecosystem health, to aquaculture and marine biomedical and biotechnology research.

The overall research area is understanding DNA sequence and the application of this to biological and biomedical research. This is achieved using similarity, clustering and machine learning methods to identify related pieces of DNA, increase or understanding of their function and make predictions.


The main applications of our research are:

  • Using -omics to understand biodiversity and enhance aquaculture; using genome sequencing to improve breeding programs, understand fish populations and identify markers for fish stock enhancement.
  • Molecular exploration; using DNA barcoding and metabarcoding for species identification and discovery. We also apply these methods to track single species in aquatic environments.
  • Functional metagenomics; understanding environmental changes using shotgun metagenomics and the application of these methods to understanding biosynthesis of secondary metabolites for marine natural products and in the toxins produced in harmful algal blooms.


We also have strong interests in the automation of analysis methods for reproducibility and scalability. Some of the computational tools/platforms that we use to achieve this:

aws docker python git ansible bioconda


Current Projects

Marine Ecosystem Health: We are leading the molecular aspects of the HBOI Foundation funded Florida Center for Coastal and Human Health, using metabarcoding and shotgun metagenomics to understand the microbial environment associated with harmful algal blooms in the Indian River Lagoon.

Marine Biomedical: We are in the process of sequencing the genome of the fungal pathogen Paracoccidioides braziliensis variant ceti.

Aquaculture: We are sequencing and assembling the genome of the Florida Pompano (Trachinotus carolinus) using a hybrid Pacific Biosystems SMRT sequencing and Illumina high-throughput sequencing.



HBOI has a long history of outreach and our group has recently taken the scientific lead on a citizen science program to educate people on environmental metagenomics and involve the local community in our research.


HBOI ocean fish