Drane, Kezia, Huerlimann, Roger, Jones, Rhondda, Whelan, Anna, Sheehan, Madoc, Ariel, Ellen, and Kinobe, Robert (2025) Concordance in molecular methods for detection of antimicrobial resistance: A cross sectional study of the influent to a wastewater plant. Journal of Microbiological Methods, 228. 107069.

Shen, Xueyan, Hu, Jie, Yáñez, José M., Bastos Gomes, Giana, Poon, Zhi Weng Josiah, Foster, Derick, Alarcon, Jorge F., Shao, Libin, Guo, Xinyu, Shao, Yunchang, Huerlimann, Roger, Li, Chengze, Goulden, Evan, Anderson, Kelli, Fan, Guangyi, and Domingos, Jose A. (2024) Exploring the cobia (Rachycentron canadum) genome: unveiling putative male heterogametic regions and identification of sex-specific markers. GigaScience, 13. giae034.

Mason, Benjamin, Hayward, David C., Moya, Aurelie, Cooke, Ira, Sorenson, Alanna, Brunner, Ramona, Andrade Rodriguez, Natalia, Huerlimann, Roger, Bourne, David G., Schaeffer, Patrick, Grinblat, Mila, Ravasi, Timothy, Ueda, Nobuo, Tang, Sen-Lin, Ball, Eldon E., and Miller, David J. (2024) Microbiome manipulation by corals and other Cnidaria via quorum quenching. Current Biology, 34. pp. 3226-3232.

Simpson, Tiffany J.S., Wellington, Claire M., Lukehurst, Sherralee S., Huerlimann, Roger, Veilleux, Heather, Snow, Michael, Dias, Joana, and McDonald, Justin I. (2023) Development of a real-time PCR (qPCR) method for the identification of the invasive paddle crab Charybdis japonica (Crustacea, Portunidae). PeerJ, 11. e15522.

Budd, Alyssa M., Schils, Tom, Cooper, Madalyn K., Lyons, Mitchell B., Mills, Matthew S., Deinhart, Mari E., Le Port, Agnes, Huerlimann, Roger, and Strugnell, Jan M. (2023) Monitoring threatened species with environmental DNA and open ecological data: Local distribution and habitat preferences of scalloped hammerhead sharks (Sphyrna lewini). Biological Conservation, 278 (February 2023). 109881.

Westaway, Jacob A.F., Huerlimann, Roger, Kandasamy, Yogavijayan, Miller, Catherine M., Norton, Robert, Watson, David, Infante-Villamil, Sandra, and Rudd, Donna (2022) Exploring the long-term colonisation and persistence of probiotic-prophylaxis species on the gut microbiome of preterm infants: a pilot study. European Journal of Pediatrics, 181 (9). pp. 3389-3400.

Huerlimann, Roger, Cowley, Jeff A., Wade, Nicholas M., Wang, Yinan, Kasinadhuni, Naga, Chan, Chon Kit Kenneth, Jabbari, Jafar S., Siemering, Kirby, Gordon, Lavinia, Tinning, Matthew, Montenegro, Juan D., Maes, Gregory E., Sellars, Melony J., Coman, Gregory J., McWilliam, Sean, Zenger, Kyall R., Khatkar, Mehar S., Raadsma, Herman W., Donovan, Dallas, Krishna, Gopala, and Jerry, Dean R. (2022) Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence. G3: Genes, Genomes, Genetics, 12 (4). jkac034.

Westaway, Jacob A.F., Huerlimann, Roger, Kandasamy, Yoga, Miller, Catherine M., Norton, Robert, Watson, David, Infante-Vilamil, Sandra, and Rudd, Donna (2022) To Probiotic or Not to Probiotic: A Metagenomic Comparison of the Discharge Gut Microbiome of Infants Supplemented With Probiotics in NICU and Those Who Are Not. Frontiers in Pediatrics, 10. 838559.

Condon, Kelly, Huerlimann, Roger, Charles, Tony, Lowrey, Ryan, Arbon, Phoebe, and Jerry, Dean R. (2022) Using bacterial whole genome sequencing to identify toxin genes associated with disease outbreaks in black tiger shrimp (Penaeus monodon) aquaculture production. Aquaculture, 546. 737255.

Westaway, Jacob A.F., Huerlimann, Roger, Kandasamy, Yoga, Miller, Catherine M., Norton, Robert, Staunton, Kyran M., Watson, David, and Rudd, Donna (2022) The bacterial gut microbiome of probiotic-treated very-preterm infants: changes from admission to discharge. Pediatric Research, 92. pp. 142-150.

McKnight, Donald T., Huerlimann, Roger, Bower, Deborah S., Schwarzkopf, Lin, Alford, Ross A., and Zenger, Kyall R. (2022) The interplay of fungal and bacterial microbiomes on rainforest frogs following a disease outbreak. Ecosphere, 13 (7). e4037.

Tsang, Hin Hung, Domingos, Jose A., Westaway, Jacob A.F., Kam, Maximilian H.Y., Huerlimann, Roger, and Bastos Gomes, Giana (2021) Digital droplet PCR-based environmental DNA tool for monitoring Cryptocaryon irritans in a marine fish farm from Hong Kong. Diversity, 13 (8). 350.

Budd, Alyssa M., Cooper, Madalyn K., Le Port, Agnès, Schils, Tom, Mills, Matthew S., Deinhart, Mari E., Huerlimann, Roger, and Strugnell, Jan M. (2021) First detection of critically endangered scalloped hammerhead sharks (Sphyrna lewini) in Guam, Micronesia, in five decades using environmental DNA. Ecological Indicators, 127. 107649.

Cooper, Madalyn K., Huerlimann, Roger, Edmunds, Richard C., Budd, Alyssa M., Le Port, Agnes, Kyne, Peter M., Jerry, Dean R., and Simpfendorfer, Colin A. (2021) Improved detection sensitivity using an optimal eDNA preservation and extraction workflow and its application to threatened sawfishes. Aquatic Conservation: marine and freshwater ecosystems, 31 (8). pp. 2131-2148.

Westaway, Jacob A.F, Huerlimann, Roger, Miller, Catherine M., Kandasamy, Yoga, Norton, Robert, and Rudd, Donna (2021) Methods for exploring the faecal microbiome of premature infants: a review. Maternal health, neonatology and perinatology, 7 (11).

Infante Villamil, Sandra, Huerlimann, Roger, and Jerry, Dean R. (2021) Microbiome diversity and dysbiosis in aquaculture. Reviews in Aquaculture, 13 (2). pp. 1077-1096.

Pewan, Shedrach Benjamin, Otto, John Roger, Huerlimann, Roger, Budd, Alyssa Marie, Mwangi, Felista Waithira, Edmunds, Richard Crawford, Holman, Benjamin William Behrens, Henry, Michelle Lauren Elizabeth, Kinobe, Robert Tumwesigye, Adegboye, Oyelola Abdulwasiu, and Malau-Aduli, Aduli Enoch Othniel (2021) Next generation sequencing of single nucleotide polymorphic DNA-markers in selecting for intramuscular fat, fat melting point, omega-3 long-chain polyunsaturated fatty acids and meat eating quality in Tattykeel Australian White MARGRA lamb. Foods, 10 (10). 2288.

Karnaneedi, Shaymaviswanathan, Huerlimann, Roger, Johnston, Elecia B., Nugraha, Roni, Ruethers, Thimo, Taki, Aya C., Kamath, Sandip D., Wade, Nicholas M., Jerry, Dean R., and Lopata, Andreas L. (2021) Novel allergen discovery through comprehensive de novo transcriptomic analyses of five shrimp species. International Journal of Molecular Sciences, 22 (1). 32.

Drane, Kezia, Huerlimann, Roger, Power, Michelle, Whelan, Anna, Ariel, Ellen, Sheehan, Madoc, and Kinobe, Robert (2021) Testudines as sentinels for monitoring the dissemination of antibiotic resistance in marine environments: an integrative review. Antibiotics, 10 (7). 775.

Drane, Kezia, Huerlimann, Roger, Power, Michelle, Ariel, Ellen, Sheehan, Madoc, and Kinobe, Robert (2021) Using Green sea turtles (Chelonia mydas) as essential bio-indicators for monitoring antibiotic resistance in marine environments worldwide: a critical appraisal. FASEB Journal, 35 (S1). 03303-03303.

Bolte, Brett, Goldsbury, Julie, Huerlimann, Roger, Jerry, Dean, and Kingsford, Mike (2021) Validation of eDNA as a viable method of detection for dangerous cubozoan jellyfish. Environmental DNA, 3 (4). pp. 769-779.

Trujillo-González, A., Becker, J.A., Huerlimann, R., Saunders, R.J., and Hutson, K.S. (2020) Can environmental DNA be used for aquatic biosecurity in the aquarium fish trade? Biological Invasions, 22. pp. 1011-1025.

Huerlimann, R., Cooper, M.K., Edmunds, R.C., Villacorta-Rath, C., Le Port, A., Robson, H.L.A., Strugnell, J.M., Burrows, D., and Jerry, D.R. (2020) Enhancing tropical conservation and ecology research with aquatic environmental DNA methods: an introduction for non-environmental DNA specialists. Animal Conservation, 23 (6). pp. 632-645.

Pewan, Shedrach, Otto, John Roger, Huerlimann, Roger, Budd, Alyssa Marie, Mwangi, Felista Waithira, Edmunds, Richard Crawford, Holman, Benjamin William Behrens, Henry, Michelle Lauren Elizabeth, Kinobe, Robert Tumwesigye, Adegboye, Oyelola Abdulwasiu, and Malau-Aduli, Aduli Enoch Othniel (2020) Genetics of omega-3 long-chain polyunsaturated fatty acid metabolism and meat eating quality in Tattykeel Australian White lambs. Genes, 11 (5). 587.

McKnight, Donald T., Zenger, Kyall R., Alford, Ross A., and Huerlimann, Roger (2020) Microbiome diversity and composition varies across body areas in a freshwater turtle. Microbiology, 166 (5). pp. 440-452.

Jones, K., Burgess, G., Budd, A.M., Huerlimann, R., Mashkour, N., and Ariel, E. (2020) Molecular evidence for horizontal transmission of chelonid alphaherpesvirus 5 at green turtle (Chelonia mydas) foraging grounds in Queensland, Australia. PLoS ONE, 15 (1). e0227268.

Huerlimann, Roger, Maes, Gregory E., Maxwell, Michael J., Mobli, Mehdi, Launikonis, Bradley S., Jerry, Dean R., and Wade, Nicholas M. (2020) Multi-species transcriptomics reveals evolutionary diversity in the mechanisms regulating shrimp tail muscle excitation-contraction coupling. Gene, 752. 144765.

Mendoza-Porras, Omar, Kamath, Sandip, Harrison, James O., Colgrave, Michelle L., Huerlimann, Roger, Lopata, Andreas L., and Wade, Nicholas M. (2020) Resolving hemocyanin isoform complexity in haemolymph of black tiger shrimp Penaeus monodon - implications in aquaculture, medicine and food safety. Journal of Proteomics, 218. 103689.

Infante-Villamil, Sandra, Huerlimann, Roger, Condon, Kelly, Maes, Gregory E., and Jerry, Dean R. (2019) Bacterial signatures of productivity decay in Penaeus monodon ponds infected with PirA toxin. Aquaculture, 511. 734202.

Ahasan, Md. Shamim, Kinobe, Robert, Elliott, Lisa, Owens, Leigh, Scott, Jenni, Picard, Jacqueline, Huerlimann, Roger, and Ariel, Ellen (2019) Bacteriophage versus antibiotic therapy on gut bacterial communities of juvenile green turtle, Chelonia mydas. Environmental Microbiology, 21 (8). pp. 2871-2885.

Devloo-Delva, Floriaan, Huerlimann, Roger, Chua, Gladys, Matley, Jordan K., Heupel, Michelle R., Simpfendorfer, Colin A., and Maes, Gregory E. (2019) How does marker choice affect your diet analysis: comparing genetic markers and digestion levels for diet metabarcoding of tropical-reef piscivores. Marine and Freshwater Research, 70 (1). MF17209. pp. 8-18.

McKnight, Donald T., Huerlimann, Roger, Bower, Deborah S., Schwarzkopf, Lin, Alford, Ross A., and Zenger, Kyall R. (2019) Methods for normalizing microbiome data: an ecological perspective. Methods in Ecology and Evolution, 10 (3). pp. 389-400.

Gomes, Giana Bastos, Hutson, Kate S., Domingos, Jose A., Infante Villamil, Sandra, Huerlimann, Roger, Miller, Terrence L., and Jerry, Dean (2019) Parasitic protozoan interactions with bacterial microbiome in a tropical fish farm. Aquaculture, 502. pp. 196-201.

McKnight, Donald T., Huerlimann, Roger, Bower, Deborah S., Schwarzkopf, Lin, Alford, Ross A., and Zenger, Kyall R. (2019) microDecon: a highly accurate read‐subtraction tool for the post‐sequencing removal of contamination in metabarcoding studies. Environmental DNA, 1 (1). pp. 14-25.

Infante Villamil, Sandra, Huerlimann, Roger, Morianos, Christina, Sarnyai, Zoltan, and Maes, Gregory E. (2018) Adverse effect of early life high-fat/high-carbohydrate ('Western') diet on bacterial community in the distal bowel of mice. Nutrition Research, 50. pp. 25-36.

Ahasan, Md. Shamim, Waltzek, Thomas, Huerlimann, Roger, and Ariel, Ellen (2018) Comparative analysis of gut bacterial communities of green turtles (Chelonia mydas) pre-hospitalization and post-rehabilitation by high-throughput sequencing of bacterial 16S rRNA gene. Microbiological Research, 207. pp. 91-99.

Huerlimann, Roger, Wade, Nicholas M., Gordon, Lavinia, Montenegro, Juan D., Goodall, Jake, McWilliam, Sean, Tinning, Matthew, Siemering, Kirby, Giardina, Erika, Donovan, Dallas, Sellars, Melony J., Cowley, Jeff A., Condon, Kelly, Coman, Greg J., Khatkar, Mehar S., Raadsma, Herman W., Maes, Gregory E., Zenger, Kyall R., and Jerry, Dean R. (2018) De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome. Scientific Reports, 8. 13553.

Le Port, Agnes, Bakker, Judith, Cooper, Madalyn K., Huerlimann, Roger, and Mariani, Stefano (2018) Environmental DNA (eDNA): a valuable tool for ecological inference and management of sharks and their relatives. In: Carrier, Jeffrey C., Heithaus, Michael R., and Simpfendorfer, Colin A., (eds.) Shark Research: emerging technologies and applications for the field and laboratory. Marine Biology Series . CRC Press, Boca Raton, FL, USA, pp. 255-283.

Matley, Jordan K., Maes, Gregory E., Devloo-Delva, Floriaan, Huerlimann, Roger, Chua, Gladys, Tobin, Andrew J., Fisk, Aaron T., Simpfendorfer, Colin A., and Heupel, Michelle R. (2018) Integrating complementary methods to improve diet analysis in fishery‐targeted species. Ecology and Evolution, 8 (18). pp. 9503-9515.

Guppy, Jarrod L., Jones, Dave B., Jerry, Dean R., Wade, Nicholas M., Raadsma, Herman W., Huerlimann, Roger, and Zenger, Kyall R. (2018) The state of "omics" research for farmed penaeids: advances in research and impediments to industry utilization. Frontiers in Genetics, 9. 282.

Heindler, Franz M., Alajmi, Fahad, Huerlimann, Roger, Zeng, Chaoshu, Newman, Stephen J., Vamvounis, George, and van Herwerden, Lynne (2017) Toxic effects of polyethylene terephthalate microparticles and Di(2-ethylhexyl)phthalate on the calanoid copepod, Parvocalanus crassirostris. Ecotoxicology and Environmental Safety, 141. pp. 298-305.

Ahasan, Md. Shamim, Waltzek, Thomas B., Huerlimann, Roger, and Ariel, Ellen (2017) Fecal bacterial communities of wild-captured and stranded green turtles (Chelonia mydas) on the Great Barrier Reef. FEMS Microbiology Ecology, 93 (12). fix139.

Chidambarampadmavathy, K., Karthikeyan, O.P., Huerlimann, R., Maes, G.E., and Heimann, K. (2017) Response of mixed methanotrophic consortia to different methane to oxygen ratios. Waste Management, 61. pp. 220-228.

Chidambarampadmavathy, Karthigeyan, Obulisamy, Karthigeyan, Huerlimann, Roger, Maes, Gregory. E., and Heimann, Kirsten (2017) Responses of mixed methanotrophic consortia to variable Cu2+/Fe2+ ratios. Journal of Environmental Management, 197. pp. 159-166.

Razaghi, Ali, Huerlimann, Roger, Owens, Leigh, and Heimann, Kirsten (2015) Increased expression and secretion of recombinant hINFγ through amino acid starvation-induced selective pressure on the adjacent HIS4 gene in Pichia pastoris. Acta Facultatis Pharmaceuticae Universitatis Comenianae, 62 (2). pp. 1-8.

Huerlimann, Roger, Zenger, Kyall R., Jerry, Dean R., and Heimann, Kirsten (2015) Phylogenetic analysis of nucleus-encoded acetyl-CoA carboxylases targeted at the cytosol and plastid of algae. PLoS ONE, 10 (7). e0131099. pp. 1-10.

Heimann, Kirsten, and Huerlimann, Roger (2015) Microalgal classification: major classes and genera of commercial microalgal species. In: Kim, Se-Kwon, (ed.) Handbook of Marine Microalgae: Biotechnolgy Advances. Academic Press, London, UK, pp. 25-41.

Heimann, Kirsten, and Huerlimann, Roger (2015) The benefits and advantages of commercial algal biomass harvesting. In: Proceedings of the Biosafety and the Environmental Uses of Micro-Organisms Conference. pp. 73-92. From: OECD Conference on the Environmental Uses of Micro-organisms, 26-27 March 2012, Paris, France.

Huerlimann, Roger, Steinig, Eike J., Loxton, Heather, Zenger, Kyall R., Jerry, Dean R., and Heimann, Kirsten (2014) Effects of growth phase and nitrogen starvation on expression of fatty acid desaturases and fatty acid composition of Isochrysis aff. galbana (TISO). Gene, 545 (1). pp. 36-44.

Huerlimann, Roger, Steinig, Eike J., Loxton, Heather, Zenger, Kyall, Jerry, Dean R., and Heimann, Kirsten (2014) The effect of nitrogen limitation on acetyl-CoA carboxylase expression and fatty acid content in Chromera velia and Isochrysis aff. galbana (TISO). Gene, 543 (2). pp. 204-211.

Huerlimann, Roger Stephan (2014) Microalgal lipid biosynthesis: phylogeny of acetyl-CoA carboxylase and gene expression patterns of key enzymes. PhD thesis, James Cook University.

Huerlimann, Roger, and Heimann, Kirsten (2013) Comprehensive guide to acetyl-carboxylases in algae. Critical reviews in Biotechnology, 33 (1). pp. 49-65.

Huerlimann, Roger, De Nys, Rocky, and Heimann, Kirsten (2010) Growth, lipid content, productivity, and fatty acid composition of tropical microalgae for scale-up production. Biotechnology and Bioengineering, 107 (2). pp. 245-257.