My main interests lie in the development and application of genomic and bioinformatics tools to answer research questions. Currently I am involved in two major projects.

For TropWater I am developing and optimising metabarcoding protocols. Metabarcoding uses universal PCR primers to simultaneously identify species composition and biodiversity in various sources of enivronmental DNA (eDNA), including water samples, stomach content of fishes, or faecal matter.

I am also involved in the ARC Research Hub for Advanced Prawn Breeding, where I lead the assembly of the Tiger Prawn (Penaeus monodon) genome and transcriptome.

  • BC3101: Genes, Genomes and Development (Level 3; TSV)
  • BC3203: Bioinformatics (Level 3; TSV)
  • BC5101: Advanced Genes, Genomes and Development (Level 5; TSV)
  • BC5203: Advanced Bioinformatics (Level 5; TSV)
  • 2015 to present - Post-doctoral researcher, James Cook University (Townsville, Australia)
  • 2014 to 2015 - Research Assistant, James Cook University (Townsville, Australia)
  • 2009 to 2014 - Doctor of Philosophy. Thesis title: Microalgal lipid biosynthesis - Phylogeny of Acetyl-CoA carboxylase and gene expression patterns of key enzymes, James Cook University (Townsville, Australia)
  • 2007 to 2008 - Master of Applied Science. Major: Marine Biology, James Cook University (Townsville, Australia)
  • 2003 to 2006 - Senior Analyst, Study Director and Deputy Team Leader, MDS Pharma Services Switzerland AG (Fehraltorf, Switzerland)
  • 1999 to 2002 - Bachelor of Chemistry (Biotechnological Engineer). Major: Biological Chemistry, Focus: Biochemistry, Zurich University of Applied Science Winterthur (ZHAW) (Winterthur, Switzerland)
  • 1995 to 1998 - Apprenticeship as Chemical Laboratory Assistant, Swiss Federal Institute of Aquatic Science and Technology (EAWAG) (Duebendorf, Switzerland)
Research Disciplines
  • 2008 - MAppSc: University Medal for Excellence
  • 2002 - BSc: Award for outstanding performance by the Swiss Union of Applied Chemistry (SVC)

These are the most recent publications associated with this author. To see a detailed profile of all publications stored at JCU, visit ResearchOnline@JCU. Hover over Altmetrics badges to see social impact.

Journal Articles
Book Chapters
Conference Papers

ResearchOnline@JCU stores 19+ research outputs authored by Dr Roger Huerlimann from 2010 onwards.

Current Funding

Current and recent Research Funding to JCU is shown by funding source and project.

CRC for Developing Northern Australia Scheme - Projects

Biosecurity in northern Australian prawn aquaculture

Indicative Funding
$441,819 over 3 years
This project addresses biosecurity risk through conducting the first comprehensive and widespread biosecurity audit of Australian prawn farms. This project has two components. The first is to conduct a biosecurity metanalysis using traditional and molecular diagnostic tools to establish what pathogens currently occur on prawn farms and how they relate to productivity. Secondly, once the pathobiome is established the project will formulate a risk management strategy for industry and provide on-farm biosecurity training. Understanding the risk of disease, and increased capacity to detect and monitor on-farm, will lead to more effective management practices for northern Australian prawn aquaculture.
Dean Jerry, Ellen Ariel, Kelly Condon and Roger Huerlimann (College of Science & Engineering, College of Public Health and Medical & Vet Sciences)
Penaeus monodon (Penaidae); Disease; Prawn; Aquaculture

ABRS - National Environmental Science Programme (NESP) - Northern Australia Environmental Resources Hub

The Northern Australia eDNA Program - Revolutionising Aquatic Monitoring and Field Surveys in Tropical Waters

Indicative Funding
$570,000 over 3 years
All organisms shed DNA into their environment. This is termed environment DNA (eDNA). Capture and analysis of eDNA (in soil or water samples) is a highly efficient and sensitive method to detect the presence of a wide range of species without actually requiring physical capture, or sighting of the organisms themselves. eDNA field sampling can involve as little as collecting water samples and
Damien Burrows, Jan Strugnell, Roger Huerlimann, Richard C Edmunds and Dean Jerry (TropWATER and College of Science & Engineering)
eDNA; Threatened Species; Northern Australia; exotic pest species; aquatic monitoring; Genetics

Townsville Hospital and Health Service - Study Education Research Trust Account (SERTA)

Discovering the Faecal Microbiome Associated with Pre-Term Birth

Indicative Funding
$9,494 (administered by Townsville Hospital and Health Service)
Development of the pre-term gut microbiome is important for immediate and longer term health outcomes. Much of what is known about the infant and neonatal microbiome has been derived from healthy full term infants. Collecting and understanding the microbiome of the TTH NICU cohort would provide a unique insight into the microbial development and in pre-term babies admitted to the NICU. This information will provide further evidence for interventions currently undertaken in the NICU such as administration of probiotics to infants <32 weeks. This project supports evidence-based multidisciplinary research in a novel way to assess the neonatal microbiome development.
Yoga Kandasamy, Donna Rudd, Robert Norton and Roger Huerlimann (Townsville Hospital and Health Service, College of Public Health, Medical & Vet Sciences, Townsville Health Service District and College of Science & Engineering)
Human; Neonatal; Term or Pre-Term; Microbiome; Probiotics

Department of Agriculture and Water Resources - Research Grant

The validation of molecular diagnostic assays of marine pests of high priority to Australia

Indicative Funding
$45,000 (administered by Department of Fisheries (WA))
Detection of marine pests using traditional methods is notoriously difficult, lacks accuracy and is costly. Molecular methods for detection of marine pests using environmental DNA offers promise of relatively inexpensive, efficient and sensitive sampling to detect the possible presence of marine pests. However, many of these tests have not been validated to give a level of sensitivity and specificity to inform determination of whether an exotic marine species is present. The validation of molecular techniques for marine pests will determine fitness for purpose and performance for that purpose which can then be factored into design of surveillance.
Roger Huerlimann and Dean Jerry (College of Science & Engineering)
Marine Pests; eDNA; Early detection; Northern Australia

United States Navy - Detection of scalloped hammerhead sharks in Apra Harbor and adjacent nearshore waters, Guam using environmental DNA

Detection of scalloped hammerhead sharks in Apra Harbor and adjacent waters, Guam using Environmental DNA

Indicative Funding
$154,074 over 3 years (administered by University of Guam)
Scalloped hammerhead sharks (Sphyrna lewini) are anecdotally reported in Apra Harbor, Guam, but their spatial and temporal patterns of occurrence are not well understood. Lack of knowledge of population abundance, distribution, and habitat use also extends across the geographic range of the Indo-West Pacific subpopulation. All S. lewini are nationally protected under the Endangered Species Act, and their occurrence within Apra Harbor is of concern to management and conservation strategies and mission-essential operations of the U.S. Department of Navy. This project will determine the temporal and spatial distribution and habitat use of the scalloped hammerhead shark within Apra Harbor and Orote Peninsula nearshore waters.
Tom Schils, Jan Strugnell, Agnes Le Port and Roger Huerlimann in collaboration with Madalyn Cooper (University of Guam and College of Science & Engineering)
eDNA; Guam; Sphyrna lewini (Sphyrnidae); scalloped hammerhead shark

Advisory Accreditation: I can be on your Advisory Panel as a Primary or Secondary Advisor.

These Higher Degree Research projects are either current or by students who have completed their studies within the past 5 years at JCU. Linked titles show theses available within ResearchOnline@JCU.

  • Monitoring tropical freshwater biodiversity using environmental DNA (eDNA) (PhD , Secondary Advisor)
  • Genome surveillance of bacterial pathogens (PhD , Secondary Advisor)
  • Discovering Faecal Microbiome Associated with Pre-Term Birth (PhD , Secondary Advisor)
  • Resolving the global occurrence and distribution of sawfishes using genetic techniques (PhD , Secondary Advisor)
  • Intestinal and environmental microbiome community analysis in formed block tiger and banana shrimps as a tool for prawn health and production biomonitoring (PhD , Secondary Advisor)

The map shows research collaborations by institution from the past 7 years.
Note: Map points are indicative of the countries or states that institutions are associated with.

  • 5+ collaborations
  • 4 collaborations
  • 3 collaborations
  • 2 collaborations
  • 1 collaboration
  • Indicates the Tropics (Torrid Zone)

Connect with me
Share my profile
Share my profile:

Advisory Accreditation
Primary Advisor (P)
Find me on…
Icon for Google Scholar profile Icon for Twitter profile page Icon for Scopus Author page Icon for ResearchGate profile

Similar to me

  1. Prof Dean Jerry
    College of Science & Engineering
  2. A/Prof Jan Strugnell
    College of Science & Engineering
  3. A/Prof Ellen Ariel
    College of Public Health, Medical & Vet Sciences
  4. Dr Jennifer Elliman
    College of Public Health, Medical & Vet Sciences
  5. Dr Gregory Maes
    Division of Services & Resources