CTBMB Publications

Andrade RN, Moya A, Jones R, Miller DJ, Cooke IR (2021) The Significance of Genotypic Diversity in Coral Competitive Interaction: A Transcriptomic Perspective, Frontiers in Ecology and Evolution 9 pp.294.

Chng L, Holt DC, Field M, Francis JR, Tilakaratne D, et al. (2021) Molecular diagnosis of scabies using a novel probe-based polymerase chain reaction assay targeting high-copy number repetitive sequences in the Sarcoptes scabiei genome. PLOS Neglected Tropical Diseases 15(2): e0009149.

Cooper MK, Huerlimann R, Edmunds RC, et al. (2021) Improved detection sensitivity using an optimal eDNA preservation and extraction workflow and its application to threatened sawfishes. Aquatic Conservation: Marine Freshwater Ecosystems, pp.1-18.

Edwards RJ, Field MA, Ferguson JM et al. (2021) Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. BMC Genomics 22 p.188.

Field, MA (2021) Detecting pathogenic variants in autoimmune diseases using high-throughput sequencing. Immunology and Cell Biology, 99 pp.146-156.

Luz BLP, Miller DJ, Kitahara MV (2021) High regenerative capacity is a general feature within colonial dendrophylliid corals (Anthozoa, Scleractinia). JEZ-B Molecular and Developmental Evolution, 336(3)  pp. 281– 292.

O’Brien PA, Andreakis N, Tan S, Miller DJ, Webster NS, Zhang G, & Bourne DG (2021). Testing cophylogeny between coral reef invertebrates and their bacterial and archaeal symbionts. Molecular Ecology, 00, pp.1-15.

Raspin K, FitzGerald LM, Marthick JR, et al. A rare variant in EZH2 is associated with prostate cancer risk. International Journal of Cancer; 1– 11.

Rodriguez-Rodriguez N, Gogoi M, McKenzie ANJ (2021) Group 2 Innate Lymphoid Cells: Team Players in Regulating Asthma, Annual Review of Immunology 39:1, pp.167-198

Ryan RYM, Fernandez A, Wong Y. et al. (2021) The medicinal plant Tabebuia impetiginosa potently reduces pro-inflammatory cytokine responses in primary human lymphocytes. Scientific Reports 11, p. 5519. https://doi.org/10.1038/s41598-021-85211-8

Sathkumara HD, Eaton JL, Field MA, et al. (2021) A murine model of tuberculosis/type 2 diabetes comorbidity for investigating the microbiome, metabolome and associated immune parameters. Animal Models and Experimental Medicine; 4 pp.181-188.

Cooke I, Ying H, Forêt S, Bongaerts P, Strugnell J, Simakov O, Zhang J, Field MA, Rodriguez-Lanetty M, Bell SC, Bourne DG, van Oppen MJH, Ragan MA, Miller MJ (2020) Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts, Scientific Advances, 6(48) eabc6318.

Elliman RJ, Owens L (2020), Confirmation that candidatus Coxiella cheraxi from redclaw crayfish (Cherax quadricarinatus) is a close relative of Coxiella burnetii, the agent of Q-fever. Letters in Applied Microbiology, 71 pp.320-326.

Fingerhut LCH, Miller DJ, Strugnell JM, Daly NL, Cooke IR (2020) ampir: an R package for fast genome-wide prediction of antimicrobial peptides, Bioinformatics, 36(21) pp.5262–5263

Hays R, Pierce D, Giacomin P, Loukas A, Bourke P, McDermott R (2020) Helminth coinfection and COVID-19: An alternate hypothesis. PLoS Neglected Tropical Diseases 14(8): e0008628.

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

Jones K, Burgess G, Budd AM, Huerlimann R, Mashkour N, et al. (2020) Molecular evidence for horizontal transmission of chelonid alphaherpes virus 5 at green turtle (Chelonia mydas) foraging grounds in Queensland, Australia. PLOS ONE 15(1): e0227268.

Lima FD, Strugnell JM, Leite TS, Lima SMQ. (2020). A biogeographic framework of octopod species diversification: the role of the Isthmus of Panama. PeerJ 8:e8691.

Loughland JR, Woodberry T, Field M, Andrew DW, Nair SA, Dooley NL, Piera KA, Amante FH, Kenangalem E, Price RN, Engwerda CR, Anstey NM, McCarthy JS, Boyle MJ and Minigo G (2020), Transcriptional profiling and immunophenotyping show sustained activation of blood monocytes in subpatent Plasmodium falciparum infection. Clinical Translational Immunology, 9: e1144.

Nauheimer L, Weigner N, Joyce E, Crayn D, Clarke C, Nargar K (2020) HybPhaser: a workflow for the detection and phasing of hybrids in target capture datasets,  bioRxiv,10.27.354589.

O’Brien PA, Tan S, Yang C et al. (2020) Diverse coral reef invertebrates exhibit patterns of phylosymbiosis. ISME Journal 14, pp.2211–2222.

Ratnatunga CN, Lutzky VP, Kupz A, Doolan DL, Reid DW, Field MA, Bell SC, Thomson RM, Miles JJ (2020), The Rise of Non-Tuberculosis Mycobacterial Lung Disease, Frontiers in Immunology, 11 p. 303.

Schmidt CA, Wilson DT, Cooke IR, Potriquet J, Tungatt K, Muruganandah V, Boote C, Kuek F, Miles JJ, Kupz A, Ryan S, Loukas A, Bansal PS, Takjoo R, Miller DJ, Peigneur S, Tytgat J, and Daly NL (2020), Identification and Characterization of a Peptide from the Stony Coral Heliofungia actiniformis, Journal of Natural Products, 83 (11), pp.3454-3463.

Weerakoon H, Potriquet J, Shah AK et al. (2020) A primary human T-cell spectral library to facilitate large scale quantitative T-cell proteomics. Scientific Data 7, p. 412.

Cooke, I., Mead, O., Whalen, C., Boote, C., Moya, A., Ying, H., ... & Voolstra, C. R. (2019). Molecular techniques and their limitations shape our view of the holobiont. Zoology, 125695.

Cooper M, Loiseau C, McCarthy J and Doolan D (2019) Human challenge models: tools to accelerate the development of malaria vaccines. Expert Review of Vaccines, 18 (3). pp. 241-251

Field M, Burgio G, Chuah A, Al Shekaili J, Hassan B, Al Sukaiti N, Foote S, Cook M and Andrews D (2019) Recurrent miscalling of missense variation from short-read genome sequence data. BMC Genomics, 20 (Suppl 8).

Gan, H. M., Tan, M. H., Austin, C. M., Sherman, C., Wong, Y. T., Strugnell, J., ... & Miller, A. (2019). Best foot forward: Nanopore long reads, hybrid meta-assembly and haplotig purging optimises the first genome assembly for the Southern Hemisphere blacklip abalone (Haliotis rubra).Frontiers in genetics, 10, 889.

Hua, K., Cobcroft, J. M., Cole, A., Condon, K., Jerry, D. R., Mangott, A., ... & Strugnell, J. M. (2019). The Future of Aquatic Protein: Implications for Protein Sources in Aquaculture Diets. One Earth, 1(3), 316-329.

Infante-Villamil, S., Huerlimann, R., Condon, K., Maes, G. E., & Jerry, D. R. (2019). Bacterial signatures of productivity decay in Penaeus monodon ponds infected with PirA toxin. Aquaculture, 734202.

Jiang S, Athanasopoulos V, Ellyard J, Chuah A, Cappello J, Cook A, Prabhu S, Cardenas J, Gu J, Stanley M, Roco J, Papa I, Yabas M, Walters G, Burgio G, McKeon K, Byers J, Burrin C, Enders A, Miosge L, Canete P, Jelusic M, Tasic V, Lungu A, Alexander S, Kitching A, Fulcher D, Shen N, Arsov T, Gatenby P, Babon J, Mallon D, de Lucas Collantes C, Stone E, Wu P, Field M, Andrews T, Cho E, Pascual V, Cook M and Vinuesa C (2019) Functional rare and low frequency variants in BLK and BANK1 contribute to human lupus. Nature Communications, 10.

Kuhn, D. N., Dillon, N., Bally, I., Groh, A., Rahaman, J., Warschefsky, E., Freeman, B., Innes, D. and Chambers, A. H. (2019) Estimation of genetic diversity and relatedness in a mango germplasm collection using SNP markers and a simplified visual analysis method. Scientia Horticulturae, 252 . pp. 156-168. ISSN 0304-4238

Law S, Haigh O, Walpole C, Colm K, Miles J, Ghandi M, Radford K and Steptoe R (2019) Simple, rapid and inexpensive typing of common HLA class I alleles for immunological studies. Journal of Immunological Methods, 465. pp. 72-76

McKnight, D. T., Huerlimann, R., Bower, D. S., Schwarzkopf, L., Alford, R. A., & Zenger, K. R. (2019). Methods for normalizing microbiome data: An ecological perspective. Methods in Ecology and Evolution, 10(3), 389-400.

Nowland, S. J., Silva, C. N., Southgate, P. C., & Strugnell, J. M. (2019). Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development.BMC genomics, 20(1), 711.

Thang, M. W., Chua, X. Y., Price, G., Gorse, D., & Field, M. A. (2019). MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data. F1000Research, 8.

Ying, H., Hayward, D. C., Cooke, I., Wang, W., Moya, A., Siemering, K. R., ... & Miller, D. J. (2019). The whole genome sequence of the coral Acropora millepora. Genome biology and evolution.