A

Aibinu, Ibukun E., Smooker, Peter M., and Lopata, Andreas L. (2019) Anisakis nematodes in fish and shellfish- from infection to allergies. International Journal for Parasitology: Parasites and Wildlife, 9. pp. 384-393.

B

Buraphaka, Hathairat, Dobutr, Theerawat, Wiese, Michael D., Lopata, Andreas L., and Daduang, Sakda (2024) Structure-based epitope prediction and assessment of cross-reactivity of Myrmecia pilosula venom-specific IgE and recombinant Sol g proteins (Solenopsis geminata). Scientific Reports, 14. 11145.

Bourquin, Rebecca Ashleigh (2023) Development of a high-throughput HIV-1 integrase drug screening platform. Masters (Research) thesis, James Cook University.

Brunner, Ramona (2023) Investigating receptors and signalling pathways of coral settlement and metamorphosis using proteomics, transcriptomics and phylogenetics. PhD thesis, James Cook University.

Bailey, Charles G., Gupta, Shailendra, Metierre, Cynthia, Amarasekera, Punkaja M.S., O'Young, Patrick, Kyaw, Wunna, Laletin, Tatyana, Francis, Habib, Semaan, Crystal, Sharifi Tabar, Mehdi, Singh, Krishna P., Mullighan, Charles G., Wolkenhauer, Olaf, Schmitz, Ulf, and Rasko, John (2021) Structure–function relationships explain CTCF zinc finger mutation phenotypes in cancer. Cellular and Molecular Life Sciences, 78. pp. 7519-7536.

C

Caruana, Nikeisha J., Strugnell, Jan M., Finn, Julian, Faou, Pierre, Plummer, Kim M., and Cooke, Ira R. (2020) Quantitative proteomic analysis of the slime and ventral mantle glands of the Striped Pyjama squid (Sepioloidea lineolata). Journal of Proteome Research, 19. pp. 1491-1501.

Caruana, Nikeisha J., Strugnell, Jan M., Faou, Pierre, Finn, Julian, and Cooke, Ira R. (2019) Comparative proteomic analysis of slime from the striped pyjama squid, Sepioloidea lineolata, and the southern bottletail squid, Sepiadarium austrinum (Cephalopoda: Sepiadariidae). Journal of Proteome Research, 18 (3). pp. 890-899.

Cameron, Timothy C., Cooke, Ira, Faou, Pierre, Toet, Hayley, Piedrafita, David, Young, Neil, Rathinasamy, Vignesh, Beddoe, Travis, Anderson, Glenn, Dempster, Robert, and Spithill, Terry W. (2017) A novel ex vivo immunoproteomic approach characterising Fasciola hepatica tegumental antigens identified using immune antibody from resistant sheep. International Journal for Parasitology, 47 (9). pp. 555-567.

Chaiyadet, Sujittra, Smout, Michael, Laha, Thewarach, Sripa, Banchob, Loukas, Alex, and Sotillo, Javier (2017) Proteomic characterization of the internalization of Opisthorchis viverrini excretory/secretory products in human cells. Parasitology International, 66 (4). pp. 494-502.

Chaiyadet, Sujittra, Krueajampa, Watchara, Hipkaeo, Wiphawi, Plosan, Yada, Piratae, Supawadee, Sotillo, Javier, Smout, Michael, Sripa, Banchob, Brindley, Paul J., Loukas, Alex, and Laha, Thewarach (2017) Suppression of mRNAs encoding CD63 family tetraspanins from the carcinogenic liver fluke Opisthorchis viverrini results in distinct tegument phenotypes. Scientific Reports, 7. 14342.

Cortés, Alba, Sotillo, Javier, Muñoz-Antolí, Carla, Martín-Grau, Carla, Esteban, J. Guillermo, and Toledo, Rafael (2016) Resistance against Echinostoma caproni (Trematoda) secondary infections in mice is not dependent on the ileal protein production. Journal of Proteomics, 140. pp. 37-47.

Cortés, Alba, Sotillo-Gallego, Javier, Muñoz-Antolí, Carla, Trelis, Maria, Esteban, J. Guillermo, and Toledo, Rafael (2016) Definitive host influences the proteomic profile of excretory/secretory products of the trematode Echinostoma caproni. Parasites & Vectors, 9. 185. pp. 1-10.

D

Del Cid, Joselyn S., Isik Reed, Nilgun, Molnar, Kathleen, Liu, Sean, Dang, Bobo, Jensen, Sacha A., DeGrado, William, Handford, Penny, Sheppard, Dean, and Sundaram, Aparna B. (2019) A disease associated mutation in fibrillin-1 differentially regulates integrin mediated cell adhesion. Journal of Biological Chemistry, 294 (48). pp. 18232-18243.

E

Engholm-Keller, Kasper, Waardenberg, Ashley J., Müller, Johannes A., Wark, Jesse R., Fernando, Rowena N., Arthur, Jonathan W., Robinson, Phillip J., Dietrich, Dirk, Schoch, Susanne, Graham, Mark E., UNSPECIFIED, and UNSPECIFIED (2019) The temporal profile of activity-dependent presynaptic phospho-signalling reveals long-lasting patterns of poststimulus regulation. PLoS Biology, 17 (3). e3000170.

F

Fingerhut, Legana C. H. W. (2022) Identifying antimicrobial peptides in genomes using machine learning. PhD thesis, James Cook University.

Fingerhut, Legana C. H. W., Miller, David J., Strugnell, Jan M., Daly, Norelle L., and Cooke, Ira R. (2020) ampir: an R package for fast genome-wide prediction of antimicrobial peptides. Bioinformatics, 36 (21). btaa653.

Fingerhut, Legana C.H.W., Strugnell, Jan M., Faou, Pierre, Labiaga, Àlvaro Roura, Zhang, Jia, and Cooke, Ira R. (2018) Shotgun proteomics analysis of saliva and salivary gland tissue from the common octopus Octopus vulgaris. Journal of Proteome Research, 17 (11). pp. 3866-3876.

H

Hoffrogge, Raimund, Beyer, Susanne, Hübner, Rayk, Mikkat, Stefan, Mix, Eilhard, Scharf, Christian, Schmitz, Ulf, Pauleweit, Stefan, Berth, Matthias, Zubrzycki, Igor Z., Christoph, Hilmar, Pahnke, Jens, Wolkenhauer, Olaf, Uhrmacher, Adelinde, Völker, Uwe, and Rolfs, Arndt (2007) 2-DE profiling of GDNF overexpression-related proteome changes in differentiating ST14A rat progenitor cells. Proteomics, 7 (1). pp. 33-46.

K

Karnaneedi, Shaymaviswanathan, Limviphuvadh, Vachiranee, Maurer-Stroh, Sebastian, and Lopata, Andreas L. (2024) De Novo Transcriptomic Analyses to Identify and Compare Allergens in Foods. In: Cabanillas, Beatriz, (ed.) Food Allergens: Methods and Protocols. Methods in Molecular Biology, 2717 . Humana Press, New York, NY, USA, pp. 351-365.

Kabasser, Stefan, Pratap, Kunal, Kamath, Sandip, Taki, Aya, Dang, Thanh, Koplin, Jennifer, Perrett, Kirsten, Hummel, Karin, Radauer, Christian, Breiteneder, Heimo, Lopata, Andreas L., and Bublin, Merima (2022) Identification of vicilin, legumin and antimicrobial peptide 2a as macadamia nut allergens. Food Chemistry, 370. 131028.

L

Loke, Paxton, Chebar Lozinsky, Adriana, Orsini, Francesca, Wong, Lydia Su-Yin, Leung, Agnes Sze-Yin, Tham, Elizabeth Huiwen, Lopata, Andreas L., Shek, Lynette Pei-Chi, and Tang, Mimi L.K. (2021) Study protocol of a phase 2, dual-centre, randomised, controlled trial evaluating the effectiveness of probiotic and egg oral immunotherapy at inducing desensitisation or sustained unresponsiveness (remission) in participants with egg allergy compared with placebo (probiotic egg allergen oral immunotherapy for treatment of egg allergy: PEAT study). BMJ Open, 11 (7). e044331.

M

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.

Muñoz-Antoli, Carla, Cortes, Alba, Santano, Rebeca, Sotillo, Javier, Esteban, J. Guillermo, and Toledo, Rafael (2016) Interleukin-25 induces resistance against intestinal trematodes. Scientific Reports, 6. 34142. pp. 1-12.

McCusker, Paul, McVeigh, Paul, Rathinasamy, Vignesh, Toet, Hayley, McCammick, Erin, O’Connor, Anna, Marks, Nikki J., Mousley, Angela, Brennan, Gerard P., Halton, David W., Spithill, Terry W., and Maule, Aaron G. (2016) Stimulating Neoblast-Like Cell Proliferation in Juvenile Fasciola hepatica Supports Growth and Progression towards the Adult Phenotype In Vitro. PLoS Neglected Tropical Diseases, 10 (9). e0004994.

N

Nuez-Ortin, Waldo G., Carter, Chris G., Wilson, Richard, Cooke, Ira R., Amoroso, Gianluca, Cobcroft, Jennifer M., and Nichols, Peter D. (2017) Triploid Atlantic salmon shows similar performance, fatty acid composition and proteome response to diploids during early freshwater rearing. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 22. pp. 67-77.

Neale, Vanessa, Sotillo, Javier, Seymour, Jamie E., and Wilson, David (2017) The venom of the spine-bellied sea snake (Hydrophis curtus): proteome, toxin diversity and intraspecific variation. International Journal of Molecular Sciences, 18 (12).

R

Ramialison, Mirana, Waardenberg, Ashley J., Schonrock, Nicole, Doan, Tram, de Jong, Danielle, Bouveret, Romaric, and Harvey, Richard P. (2017) Analysis of steric effects in DamID profiling of transcription factor target genes. Genomics, 109 (2). pp. 75-82.

S

Sharp, Michael F., Taki, Aya C., Ruethers, Thimo, Stephen, Juan N., Daly, Norelle L., Lopata, Andreas L., and Kamath, Sandip D. (2021) IgE and IgG4 epitopes revealed on the major fish allergen Lat c 1. Molecular Immunology, 131. pp. 155-163.

Sorenson, Alanna E., and Schaeffer, Patrick M. (2020) Electrophoretic mobility shift assays with GFP-tagged proteins (GFP-EMSA). In: Labrou, Nikolaos E., (ed.) Targeting Enzymes for Pharmaceutical Development. Methods in Molecular Biology, 2089 . Springer, New York, NY, USA, pp. 159-166.

Sorenson, Alanna E., and Schaeffer, Patrick M. (2020) High-throughput differential scanning fluorimetry of GFP-tagged proteins. In: Labrou, Nikolaos E., (ed.) Targeting Enzymes for Pharmaceutical Development. Methods in Molecular Biology, 2089 . Springer, New York, NY, USA, pp. 69-85.

Su, Zhiduan, Burchfield, James G., Yang, Pengyi, Humphrey, Sean J., Yang, Guang, Francis, Deanne, Yasmin, Sabina, Shin, Sung-Young, Norris, Dougall M., Kearney, Alison L., Astore, Miro A., Scavuzzo, Jonathan, Fisher-Wellman, Kelsey H., Wang, Qiao-Ping, Parker, Benjamin L., Neely, G. Gregory, Vafaee, Fatemeh, Chiu, Joyce, Yeo, Reichelle, Hogg, Philip J., Fazakerley, Daniel J., Nguyen, Lan K., Kuyucak, Serdar, and James, David E. (2019) Global redox proteome and phosphoproteome analysis reveals redox switch in Akt. Nature Communications, 10. 5486.

Sotillo, Javier, Doolan, Denise, and Loukas, Alex (2017) Recent advances in proteomic applications for schistosomiasis research: potential clinical impact. Expert Review of Proteomics, 14 (2). pp. 171-183.

Suwannatrai, Kulwadee, Suwannatrai, Apiporn, Tabsripair, Pairat, Welbat, Jariya Umka, Tangkawattana, Sirikachorn, Cantacessi, Cinzia, Mulvenna, Jason, Tesana, Smarn, Loukas, Alex, and Sotillo, Javier (2016) Differential protein expression in the hemolymph of Bithynia siamensis goniomphalos infected with Opisthorchis viverrini. PLoS Neglected Tropical Diseases, 10 (11). e0005104.

Sotillo, Javier, Pearson, Mark, Potriquet, Jeremy, Becker, Luke, Pickering, Darren, Mulvenna, Jason, and Loukas, Alex (2016) Extracellular vesicles secreted by Schistosoma mansoni contain protein vaccine candidates. International Journal for Parasitology, 46 (1). pp. 1-5.

T

Toft, Casey J., Sorenson, Alanna E., and Schaeffer, Patrick M. (2022) Rise of the terminator protein tus: A versatile tool in the biotechnologist's toolbox. Analytica Chimica Acta, 1213. 339946.

W

Weerakoon, Harshi, Miles, John J., Lepletier, Ailin, and Hill, Michelle M. (2022) A high-resolution mass spectrometry based proteomic dataset of human regulatory T cells. Data in Brief, 40. 107687.

Wilson, David, and Daly, Norelle L. (2018) Approaches to delineate disulfide connectivities in pharmaceutical peptides. In: Webb, Graham A., (ed.) Modern Magnetic Resonance. Springer International Publishing, Gewerbestrasse, Cham, Switzerland, pp. 2021-2034.