Items where Subject is "06 BIOLOGICAL SCIENCES > 0601 Biochemistry and Cell Biology > 060102 Bioinformatics"

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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.

Jiang, Simon, Athanasopoulos, Vicki, Ellyard, Julia, Chuah, Aaron, Cappello, Jean, Cook, Amelia, Prabhu, Savit B., Cardenas, Jacob, Gu, Jinghua, Stanley, Maurice, Roco, Jonathan A., Papa, Ilenia, Yabas, Mehmet, Walters, Giles D., Burgio, Gaetan, McKeon, Kathryn, Byers, James M., Burrin, Charlotte, Enders, Anselm, Miosge, Lisa A., Canete, Pablo F., Jelusic, Marjia, Tasic, Velibor, Lungu, Adrian C., Alexander, Stephen I., Kitching, Arthur R., Fulcher, David, Shen, Nan, Arsov, Todor, Gatenby, Paul A., Babon, Jeff J., Mallon, Dominic F., de Lucas Collantes, Carmen, Stone, Eric A., Wu, Philip, Field, Matt, Andrews, Thomas D., Cho, Eun, Pascual, Virginia, Cook, Matthew, and Vinuesa, Carola G. (2019) Functional rare and low frequency variants in BLK and BANK1 contribute to human lupus. Nature Communications, 10. 2201.

Anuar, Nur Diana, Kurscheid, Sebastian, Field, Matt, Zhang, Lei, Rebar, Edward, Gregory, Philip, Buchou, Thierry, Bowles, Josephine, Koopman, Peter, Tremethick, David J., and Soboleva, Tatiana A. (2019) Gene editing of the multi-copy H2A.B gene and its importance for fertility. Genome Biology, 20. 23.

Field, Matthew A., Burgio, Gaetan, Chuah, Aaron, Al Shekaili, Jalila, Hassan, Batool, Al Sukaiti, Nashat, Foote, Simon J., Cook, Matthew C., and Andrews, Daniel T. (2019) Recurrent miscalling of missense variation from short-read genome sequence data. BMC Genomics, 20 (Suppl 8). 546.

Whitelaw, Brooke L., Cooke, Ira R., Finn, Julian, Zenger, Kyall, and Strugnell, J.M. (2019) The evolution and origin of tetrodotoxin acquisition in the blue-ringed octopus (genus Hapalochlaena). Aquatic Toxicology, 206. pp. 114-122.

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. (In Press)

Ying, Hua, Cooke, Ira, Sprungala, Susanne, Wang, Weiwen, Hayward, David C., Tang, Yurong, Huttley, Gavin, Ball, Eldon E., Forêt, Sylvain, and Miller, David J. (2018) Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages. Genome Biology, 19. 175.

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.

Cardinez, Chelisa, Miraghzadeh, Bahar, Tanita, Kay, da Silva, Elizabeth, Hoshino, Akihiro, Okada, Satoshi, Chand, Rochna, Asano, Takaki, Tsumura, Miyuki, Yoshida, Kenichi, Ohnish, Hidenori, Kato, Zenichiro, Yamazki, Masahide, Okuno, Yusuke, Miyano, Satoru, Kojima, Seiji, Ogawa, Seishi, Andrews, T. Daniel, Field, Matthew A., Burgio, Gaetan, Morio, Tomohiro, Vinuesa, Carola G., Kanegane, Hirokazu, and Cook, Matthew C. (2018) Gain-of-function IKBKB mutation causes human combined immune deficiency. The Journal of Experimental Medicine, 215 (11). pp. 2715-2724.

Nuez-Ortín, Waldo G., Carter, Chris G., Nichols, Peter D., Cooke, Ira R., and Wilson, Richard (2018) Liver proteome response of pre-harvest Atlantic salmon following exposure to elevated temperature. BMC Genomics, 19. 133.

Maroso, F., Hillen, J.E.J., Pardo, B.G., Gkagkavouzis, K., Coscia, I., Hermida, M., Franch, R., Hellemans, B., Van Houdt, J., Simionati, B., Taggart, J.B., Nielsen, E.E., Maes, G.E., Ciavaglia, S.A., Webster, L.M., Volckaert, F.A.M., Martínez, P., Bargelloni, Luca, Ogden, R., and AquaTrace Consortium, (2018) Performance and precision of double digestion RAD (ddRAD) genotyping in large multiplexed datasets of marine fish species. Marine Genomics, 39. pp. 64-72.

Nugraha, Roni, Kamath, Sandip D., Johnston, Elecia, Zenger, Kyall R., Rolland, Jennifer M., O’Hehir, Robyn E., and Lopata, Andreas L. (2018) Rapid and comprehensive discovery of unreported shellfish allergens using large-scale transcriptomic and proteomic resources. Journal of Allergy and Clinical Immunology, 141 (4). e8. pp. 1501-1504.

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.

Liu, Huanle, Stephens, Timothy G., González-Pech, Raúl A., Beltran, Victor H., Lapeyre, Bruno, Bongaerts, Pim, Cooke, Ira, Aranda, Manuel, Bourne, David G., Forêt, Sylvain, Miller, David J., van Oppen, Madeleine J.H., Voolstra, Christian R., Ragan, Mark A., and Chan, Cheong Xin (2018) Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis. Communications Biology, 1. 95.

Hayward, Nicholas K., Wilmott, James S., Waddell, Nicola, Johansson, Peter A., Field, Matthew A., Nones, Katia, Patch, Ann-Marie, Kakavand, Hojabr, Alexandrov, Ludmil B., Burke, Hazel, Jakrot, Valerie, Kazakoff, Stephen, Holmes, Oliver, Leonard, Conrad, Sabarinathan, Radhakrishnan, Mularoni, Loris, Wood, Scott, Xu, Qinying, Waddell, Nick, Tembe, Varsha, Pupo, Gulietta M., De Paoli-Iseppi, Ricardo, Vilain, Ricardo E., Shang, Ping, Lau, Loretta M.S., Dagg, Rebecca A., Schramm, Sarah-Jane, Pritchard, Antonia, Dutton-Regester, Ken, Newell, Felicity, Fitzgerald, Anna, Shang, Catherine A., Grimmond, Sean M., Pickett, Hilda A., Yang, Jean Y., Stretch, Jonathan R., Behren, Andreas, Kefford, Richard F., Hersey, Peter, Long, Georgina V., Cebon, Jonathan, Shackleton, Mark, Spillane, Andrew J., Saw, Robyn P.M., López-Bigas, Núria, Pearson, John V., Thompson, John F., Scolyer, Richard A., and Mann, Graham J. (2017) Whole-genome landscapes of major melanoma subtypes. Nature, 545. pp. 175-180.

Stephen, J.N., Sharp, M.F., Ruethers, T., Taki, A., Campbell, D.E., and Lopata, A.L. (2017) Allergenicity of bony and cartilaginous fish – molecular and immunological properties. Clinical & Experimental Allergy, 47 (3). pp. 300-312.

Sukaiti, Nashat Al, AbdelRahman, Khwater, AlShekaili, Jalila, Al Oraimi, Sumaya, Al Sinani, Aisha, Al Rahbi, Nasser, Cho, Vicky, Field, Matt, and Cook, Matthew C. (2017) Agammaglobulinaemia despite terminal B-cell differentiation in a patient with a novel LRBA mutation. Clinical & Translational Immunology, 6 (5). e144.

Lin, Mei-Fang, Moya, Aurelie, Ying, Hua, Chen, Chaolun Allen, Cooke, Ira, Ball, Eldon E., Forȇt, Sylvain, and Miller, David J. (2017) Analyses of corallimorpharian transcriptomes provide new perspectives on the evolution of calcification in the Scleractinia (corals). Genome Biology and Evolution, 9 (1). pp. 150-160.

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.

Dagonnier, Marie, Cooke, Ira Robin, Faou, Pierre, Sidon, Tara Kate, Dewey, Helen Margaret, Donnan, Geoffrey Alan, and Howells, David William (2017) Discovery and longitudinal evaluation of candidate biomarkers for ischaemic stroke by mass spectrometry-based proteomics. Biomarker Insights, 12.

Schneider, Maria Victoria, Griffin, Phillippa C., Tyagi, Sonika, Flannery, Madison, Dayalan, Saravanan, Gladman, Simon, Watson-Haigh, Nathan, Bayer, Philipp E., Charleston, Michael, Cooke, Ira, Cook, Rob, Edwards, Richard J., Edwards, David, Gorse, Dominique, McConville, Malcolm, Powell, David, Wilkins, Marc R., and Lonie, Andrew (2017) Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. Briefings in Bioinformatics, 2017.

FitzGerald, Liesel M., Raspin, Kelsie, Marthick, James R., Field, Matt A., Malley, Roslyn C., Thomson, Russell J., Blackburn, Nicholas B., Banks, Annette, Charlesworth, Jac C., Donovan, Shaun, and Dickinson, Joanne L. (2017) Impact of the G84E variant on HOXB13 gene and protein expression in formalin-fixed, paraffin-embedded prostate tumours. Scientific Reports, 7. 17778.

Bottje, Walter, Kong, Byung-Whi, Reverter, Antonio, Waardenberg, Ashley J., Lassiter, Kentu, and Hudson, Nicholas J. (2017) Progesterone signalling in broiler skeletal muscle is associated with divergent feed efficiency. BMC Systems Biology, 11. 29.

Chambers, Matthew C., Jagtop, Pratik D., Johnson, James E., McGowan, Thomas, Kumar, Praveen, Onsongo, Getiria, Guerrero, Candace R., Barsnes, Harald, Vaudel, Marc, Martens, Lennart, Grüning, Björn, Cooke, Ira, Heydarian, Mohammad, Reddy, Karen L., and Griffin, Timothy J. (2017) An accessible proteogenomics informatics resource for cancer researchers. Cancer Research, 77 (21). E43-E46.

Whitelaw, Brooke Lauren, Strugnell, Jan M., Faou, Pierre, da Fonseca, Rute R., Hall, Nathan, Norman, Mark, Finn, Julian, and Cooke, Ira Robin (2016) Combined transcriptomic and proteomic analysis of the posterior salivary gland from the southern blue-ringed octopus and the southern sand octopus. Journal of Proteome Research, 15 (9). pp. 3284-3297.

Lee, Ping-Shin, Gan, Han Ming, Clements, Gopalasamy Reuben, and Wilson, John-James (2016) Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests. Genome, 59 (11). pp. 1008-1022.

Sabouri, Zahra, Perotti, Samuel, Spierings, Emily, Humburg, Peter, Yabas, Mehmet, Bergmann, Hannes, Horikawa, Keisuke, Roots, Carla, Lambe, Samantha, Young, Clara, Andrews, T. Dan, Field, Matthew, Enders, Anselm, Reed, Joanne H., and Goodnow, Christopher C. (2016) IgD attenuates the IgM-induced anergy response in transitional and mature B cells. Nature Communications, 7. 13381. pp. 1-11.

Waardenberg, Ashley J., Homan, Bernou, Mohamed, Stephanie, Harvey, Richard P., and Bouveret, Romaric (2016) Prediction and validation of protein–protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach. Open Biology, 6. 160183.

Caruana, Nikeisha J., Cooke, Ira R., Faou, Pierre, Finn, Julian, Hall, Nathan E., Norman, Mark, Pineda, Sandy S., and Strugnell, Jan M. (2016) A combined proteomic and transcriptomic analysis of slime secreted by the southern bottletail squid, Sepiadarium austrinum (Cephalopoda). Journal of Proteomics, 148. pp. 170-182.

Nguyen, Vinh A., Carey, Leeanne M., Giummarra, Loretta, Faou, Pierre, Cooke, Ira, Howells, David W., Tse, Tamara, Macaulay, S. Lance, Ma, Henry, Davis, Stephen M., Donnan, Geoffrey A., and Crewther, Sheila G. (2016) A pathway proteomic profile of ischemic stroke survivors reveals innate immune dysfunction in association with mild symptoms of depression: a pilot study. Frontiers in Neurology, 7. 85. pp. 1-16.

Wilmott, James S., Field, Matthew A., Johansson, Peter A., Kakavand, Hojabr, Shang, Ping, De Paoli-Iseppi, Ricardo, Vilain, Ricardo E., Pupo, Gulietta M., Tembe, Varsha, Jakrot, Valerie, Shang, Catherine A., Cebon, Jonathan, Shackleton, Mark, Fitzgerald, Anna, Thompson, John F., Hayward, Nichoas K., Mann, Graham J., and Scolyer, Richard A. (2015) Tumour procurement, DNA extraction, coverage analysis and optimisation of mutation-detection algorithms for human melanoma genomes. Pathology, 47 (7). pp. 683-693.

Field, Matthew A., Cho, Vicky, Andrews, T. Daniel, and Goodnow, Chris C. (2015) Reliably detecting clinically important variants requires both combined variant calls and optimized filtering strategies. PLoS ONE, 10 (11). e0143199. pp. 1-19.

Dunkerton, Sophie, Field, Matthew, Cho, Vicki, Bertram, Edward, Whittle, Belinda, Groves, Alexandra, and Goel, Himanshu (2015) A de novo Mutation in KMT2A (MLL) in monozygotic twins with Wiedemann–Steiner Syndrome. American Journal of Medical Genetics: Part A, 167 (9). pp. 2182-2187.

Murugesan, Selvaraaju, Tay, David B.H., Cooke, Ira, and Faou, Pierre (2015) Application of dual tree complex wavelet transform in tandem mass spectrometry. Computers in Biology and Medicine, 63. pp. 36-41.

Field, Matthew A., Cho, Vicky, Cook, Matthew C., Enders, Anselm, Vinuesa, Carola G., Whittle, Belinda, Andrews, T. Daniel, and Goodnow, Chris C. (2015) Reducing the search space for causal genetic variants with VASP. Bioinformatics, 31 (14). pp. 2377-2379.

Johar, Angad S., Anaya, Juan-Manuel, Andrews, Dan, Patel, Hardip R., Field, Matthew, Goodnow, Chris, and Arcos-Burgos, Mauricio (2015) Candidate gene discovery in autoimmunity by using extreme phenotypes, next generation sequencing and whole exome capture. Autoimmunity Reviews, 14 (3). pp. 204-209.

Waardenberg, Ashley J., Bassett, Samuel D., Bouveret, Romaric, and Harvey, Richard P. (2015) CompGO: an R package for comparing and visualizing gene ontology enrichment differences between DNA binding experiments. BMC Bioinformatics, 16. 275.

Miosge, Lisa A., Field, Matthew A. , Sontani, Yovina, Cho, Vicky, Johnson, Simon, Palkova, Anna, Balakishnan, Bhavani, Liang, Rong, Zhang, Yafei, Lyon, Stephen, Beutler, Bruce, Whittle, Belinda, Bertram, Edward M., Enders, Anselm, Goodnow, Christopher C., and Andrews, T. Daniel (2015) Comparison of predicted and actual consequences of missense mutations. Proceedings of the National Academy of Sciences of the United States of America, 112 (37). E5189-E5198.

Shiel, Brett P., Hall, Nathan E., Cooke, Ira R., Robinson, Nicholas A, and Strugnell, Jan M. (2015) De novo characterisation of the greenlip abalone transcriptome (Haliotis laevigata) with a focus on the heat shock protein 70 (HSP70) family. Marine Biotechnology, 17. pp. 23-32.

Boekel, Jorrit, Chilton, John, Cooke, Ira, Horvatovich, Peter, Jagtap, Pratik, Kall, Lukas, Lehtiö, Janne, Lukasse, Pieter, Moerland, Perry, and Griffin, Timothy (2015) Multi-omic data analysis using Galaxy. Nature Biotechnology, 33. pp. 137-139.

Johar, Angad S., Mastronardi, Claudio, Rojas-Villarraga, Adriana, Patel, Hardip R., Chuah, Aaron, Peng, Kaiman, Higgins, Angela, Milburn, Peter, Palmer, Stephanie, Silva-Lara, Maria Fernanda, Velez, Jorge I., Andrews, Dan, Field, Matthew, Huttley, Gavin, Goodnow, Chris, Anaya, Juan-Manuel, and Arcos-Burgos, Mauricio (2015) Novel and rare functional genomic variants in multiple autoimmune syndrome and Sjögren's syndrome. Journal of Translational Medicine, 13 (173). pp. 1-11.

Allcock, A. Louise, Lindgren, A., and Strugnell, J.M. (2015) The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review. Journal of Natural History, 49 (21-24). pp. 1373-1421.

Taupin, Douglas, Lam, Wesley, Rangiah, David, McCallum, Larissa, Whittle, Belinda, Zhang, Yafei, Andrews, Daniel, Field, Matthew, Goodnow, Christopher C., and Cook, Matthew C. (2015) A deleterious RNF43 germline mutation in a severely affected serrated polyposis kindred. Human Genome Variation, 2. 15013. pp. 1-3.

Ellyard, Julia I., Jerjen, Rebekka, Martin, Jaime L., Lee, Adrian Y.S., Field, Matthew A., Jiang, Simon H., Cappello, Jean, Naumann, Svenja K., Andrews, T. Daniel, Scott, Hamish S., Casarotto, Marco G., Goodnow, Christopher C., Chaitow, Jeffrey, Pascual, Virginia, Hertzog, Paul, Alexander, Stephen I., Cook, Matthew C., and Vinuesa, Carola G. (2014) Identification of a pathogenic variant in TREX1 in early-onset cerebral systemic lupus erythematosus by whole-exome sequencing. Arthritis & Rheumatism, 66 (12). pp. 3382-3386.

Lee, Cindy Eunhee, Fulcher, David A., Whittle, Belinda, Chand, Rochna, Fewings, Nicole, Field, Matthew, Andrews, Daniel, Goodnow, Christopher C., and Cook, Matthew C. (2014) Autosomal-dominant B-cell deficiency with alopecia due to a mutation in NFKB2 that results in nonprocessable p100. Blood, 124 (19). pp. 2964-2972.

Moxon, Joseph V., Liu, Dawei, Moran, Corey S., Crossman, David J., Krishna, Smriti M., Yonglitthipagon, Ponlapat, Emeto, Theophilus I., Morris, Dylan R., Padula, Matthew P., Mulvenna, Jason P., Rush, Catherine M., and Golledge, Jonathan (2014) Proteomic and genomic analyses suggest the association of Apolipoprotein C1 with abdominal aortic aneurysm. Proteomics Clinical Applications, 8 (10). pp. 762-772.

Gao, Zeqian, Wang, Miao, Blair, David, Zheng, Yadong, and Dou, Yongxi (2014) Phylogenetic analysis of the endoribonuclease Dicer family. PLoS ONE, 9 (4). e95350. pp. 1-7.

Enders, Anselm, Short, Alanna, Miosge, Lisa A., Bergmann, Hannes, Sontani, Yovina, Bertram, Edward M., Whittle, Belinda, Balakishnan, Bhavani, Yoshida, Kaoru, Sjollema, Geoff, Field, Matthew A., Andrews, T. Daniel, Hagiwara, Hiromi, and Goodnow, Christopher C. (2014) Zinc-finger protein ZFP318 is essential for expression of IgD, the alternatively spliced Igh product made by mature B lymphocytes. Proceedings of the National Academy of Sciences, 111 (12). pp. 4513-4518.

Prasopdee, Sattrachai, Sotillo, Javier, Tesana, Smarn, Laha, Thewarach, Kulsantiwong, Jutharat, Nolan, Matthew J., Loukas, Alex, and Cantacessi, Cinzia (2014) RNA-seq reveals infection-induced gene expression changes in the snail intermediate host of the carcinogenic liver fluke, Opisthorchis viverrini. PLoS Neglected Tropical Diseases, 8 (3). e2765. pp. 1-9.

Luan, Hemi, Meng, Nan, Fu, Jin, Chen, Xiaomin, Xu, Xun, Feng, Qiang, Jiang, Hui, Dai, Jun, Yuan, Xune, Lu, Yanping, Roberts, Alexandra A., Luo, Xiao, Chen, Maoshan, Xu, Shengtao, Li, Jun, Hamilton, Chris J., Fang, Chengxiang, and Wang, Jun (2014) Genome-wide transcriptome and antioxidant analyses on gamma-irradiated phases of Deinococcus Radiodurans R1. PLoS ONE, 9 (1). e85649. pp. 1-11.

Tedersoo, Leho, Bahram, Mohammad, Põlme, Sergei, Kõljalg, Urmas, Yorou, Nourou S., Wijesundera, Ravi, Villarreal Ruiz, Luis, Vasco-Palacios, Aida M., Pham, Quang Thu, Suija, Ave, Smith, Matthew E., Sharp, Cathy, Saluveer, Erki, Saitta, Alessandro, Rosas, Miguel, Riit, Taavi, Ratkowsky, David, Pritsch, Karin, Põldmaa, Kadri, Piepenbring, Meike, Phosri, Cherdchai, Peterson, Marko, Parts, Kaarin, Paertel, Kadri, Otsing, Eveli, Nouhra, Eduardo, Njouonkou, Andre L., Nilsson, R. Henrik, Morgado, Luis N., Mayor, Jordan, May, Tom W., Majuakim, Luiza, Lodge, D. Jean, Lee, Su See, Larsson, Karl-Henrik, Kohout, Petr, Hosaka, Kentaro, Hiiesalu, Indrek, Henkel, Terry W., Harend, Helery, Guo, Liang-dong, Greslebin, Alina, Grelet, Gwen, Geml, Jozsef, Gates, Genevieve, Dunstan, William, Dunk, Chris, Drenkhan, Rein, Dearnaley, John, De Kesel, Andre, Dang, Tan, Chen, Xin, Buegger, Franz, Brearley, Francis Q., Bonito, Gregory, Anslan, Sten, Abell, Sandra, and Abarenkov, Kessy (2014) Global diversity and geography of soil fungi. Science, 346 (6213). pp. 1078-1088.

Cooke, Ira R, Jones, Dan, Bowen, Joanna K, Deng, Cecilia, Faou, Pierre, Hall, Nathan E, Jayachandran, Vignesh, Liem, Michael, Taranto, Adam P, Plummer, Kim M, and Mathivanan, Suresh (2014) Proteogenomic analysis of the Venturia pirina (pear scab fungus) secretome reveals potential effectors. Journal of Proteome Research, 13 (8). pp. 3635-3644.

Daley, Stephen R., Coakley, Kristen M., Hu, Daniel Y., Randall, Katrina L., Jenne, Craig N., Limnander, Andre, Myers, Darienne R., Polakos, Noelle K., Enders, Anselm, Roots, Carla, Balakishnan, Bhavani, Miosge, Lisa A., Sjollema, Geoff, Bertram, Edward M., Field, Matthew A., Shao, Yunli, Andrews, T. Daniel, Whittle, Belinda, Barnes, S. Whitney, Walker, John R., Cyster, Jason G., Goodnow, Christopher C., and Roose, Jeroen P. (2013) Rasgrp1 mutation increases naïve T-cell CD44 expression and drives mTOR-dependent accumulation of Helios⁺ T cells and autoantibodies. eLife, 2. e01020. pp. 1-26.

Cantacessi, Cinzia, Seddon, Jennifer M., Miller, Terrence L., Leow, Chiuan Yee, Thomas, Laëtitia, Mason, Lyndel, Willis, Charlene, Walker, Giselle, Loukas, Alex, Gasser, Robin B., Jones, Malcolm K., and Hofmann, Andreas (2013) A genome-wide analysis of annexins from parasitic organisms and their vectors. Scientific Reports, 3. 2893. pp. 1-8.

Pujolar, J.M., Jacobsen, M.W., Frydenberg, J., Als, T.D., Larsen, P.F., Maes, G.E., Zane, L., Jian, J.B., Cheng, L., and Hansen, M.M. (2013) A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel. Molecular Ecology Resources, 13 (4). pp. 706-714.

Bergmann, Hannes, Yabas, Mehmet, Short, Alanna, Miosge, Lisa, Barthel, Nadine, Teh, Charis E., Roots, Carla M., Bull, Katherine R., Jeelall, Yogesh, Horikawa, Keisuke, Whittle, Belinda, Balakishnan, Bhavani, Sjollema, Geoff, Bertram, Edward M., Mackay, Fabienne, Rimmer, Andrew J., Cornall, Richard J., Field, Matthew A., Andrews, T. Daniel, Goodnow, Christopher C., and Enders, Anselm (2013) B cell survival, surface BCR and BAFFR expression, CD74 metabolism, and CD8⁻ dendritic cells require the intramembrane endopeptidase SPPL2A. The Journal of Experimental Medicine, 210 (1). pp. 31-40.

Helyar, Sarah J., Limborg, Morten T., Bekkevold, Dorte, Babbucci, Massimiliano, van Houdt, Jeroen, Maes, Gregory E., Bargelloni, Luca, Nielsen, Rasmus O., Taylor, Martin I., Ogden, Rob, Cariani, Alessia, Carvalho, Gary R., Consortium, FishPopTrace, and Panitz, Frank (2012) SNP discovery using next generation transcriptomic sequencing in Atlantic herring (Clupea harengus). PLoS ONE, 7 (8). e42089. pp. 1-11.

Andrews, T.D., Whittle, B., Field, M.A., Balakishnan, B., Zhang, Y., Shao, Y., Cho, V., Kirk, M., Singh, M., Xia, Y., Hager, J., Winslade, S., Sjollema, G., Beutler, B., Enders, A., and Goodnow, C.C. (2012) Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models. Open Biology, 2 (5). 120061. pp. 1-16.

Appleby, Sarah L., Cockshell, Michaelia P., Pippal, Jyotsna B., Thompson, Emma J., Barrett, Jeffrey M., Tooley, Katie, Sen, Shaundeep, Sun, Wai Yan, Grose, Randall, Nicholson, Ian, Levina, Vitalina, Cooke, Ira, Talbo, Gert, Lopez, Angel F., and Bonder, Claudine S. (2012) Characterization of a distinct population of circulating human non-adherent endothelial forming cells and their recruitment via intercellular adhesion molecule-3. PLoS ONE, 7 (11). e46996.

Wang, Conan K., Broder, Ursula, Weeratunga, Saroja K., Gasser, Robin B., Loukas, Alex, and Hofmann, Andreas (2012) SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments. Bioinformatics, 28 (7). pp. 1026-1027.

Sun, Wei, Hudson, Nicholas J., Reverter, Antonio, Waardenberg, Ashley, Tellam, Ross L, Vuocolo, Tony, Byrne, Keren, and Dalrymple, Brian P (2012) An always correlated gene expression landscape for ovine skeletal muscle, lessons learnt from comparison with an “equivalent” bovine landscape. BMC Research Notes, 5. 632.

Morin, Ryan D., Mendez-Lago, Maria, Mungall, Andrew J., Goya, Rodrigo, Mungall, Karen L., Corbett, Richard D., Johnson, Nathalie A., Severson, Tesa M., Chiu, Readman, Field, Matthew, Jackman, Shaun, Krzywinski, Martin, Scott, David W., Trinh, Diane L., Tamura-Wells, Jessica, Li, Sa, Firme, Marlo R., Rogic, Sanja, Griffith, Malachi, Chan, Susanna, Yakovenko, Oleksandr, Meyer, Irmtraud M., Zhao, Eric Y., Smailus, Duane, Moksa, Michelle, Chittaranjan, Suganthi, Rimsza, Lisa, Brooks-Wilson, Angela, Spinelli, John J., Ben-Neriah, Susana, Meissner, Barbara, Woolcock, Bruce, Boyle, Merrill, McDonald, Helen, Tam, Angela, Zhao, Yongjun, Delaney, Allen, Zeng, Thomas, Tse, Kane, Butterfield, Yaron, Birol, Inanç, Holt, Rob, Schein, Jacqueline, Horsman, Douglas E., Moore, Richard, Jones, Steven J.M., Connors, Joseph M., Hirst, Martin, Gascoyne, Randy D., and Marra, Marco A. (2011) Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature, 476 (7360). pp. 298-303.

Duplessis, Sébastien, Cuomo, Christina A., Lin, Yao-Cheng, Aerts, Andrea, Tisserant, Emilie, Veneault-Fourrey, Claire, Joly, David L., Hacquard, Stéphane, Amselem, Joëlle, Cantarel, Brandi L., Chiu, Readman, Coutinho, Pedro M., Feau, Nicolas, Field, Matt, Frey, Pascal, Gelhaye, Eric, Goldberg, Jonathan, Grabherr, Manfred G., Kodira, Chinnappa D., Kohler, Annegret, Kües, Ursula, Lindquist, Erika A., Lucas, Susan M., Mago, Rohit, Mauceli, Evan, Morin, Emmanuelle, Murat, Claude, Pangilinan, Jasmyn L., Park, Robert, Pearson, Matthew, Quesneville, Hadi, Rouhier, Nicolas, Sakthikumar, Sharadha, Salamov, Asaf A., Schmutz, Jeremy, Selles, Benjamin, Shapiro, Harris, Tanguay, Philippe, Tuskan, Gerald A., Henrissat, Bernard, Van de Peer, Yves, Rouzé, Pierre, Ellis, Jeffrey G., Dodds, Peter N., Schein, Jacqueline E., Zhong, Shaobin, Hamelin, Richard C., Grigoriev, Igor V., Szabo, Les J., and Martin, Francis (2011) Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proceedings of the National Academy of Sciences, 108 (22). pp. 9166-9171.

Nefedov, Mikhail, Carbone, Lucia, Field, Matthew, Schein, Jacquie, and de Jong, Pieter J. (2011) Isolation of specific clones from nonarrayed BAC libraries through homologous recombination. Journal of Biomedicine and Biotechnology, 2011. 560124. pp. 1-8.

Waardenberg, Ashley J., Bernardo, Bianca C., Ng, Dominic C. H., Shepherd, Peter R., Cemerlang, Nelly, Sbroggiò, Mauro, Wells, Christine A., Dalrymple, Brian P., Brancaccio, Mara, Lin, Ruby C. Y., McMullen, Julie R., and UNSPECIFIED (2011) Phosphoinositide 3-Kinase (PI3K(p110α)) directly regulates key components of the Z-disc and cardiac structure. Journal of Biological Chemistry, 286 (35). pp. 30837-30846.

Robertson, Gordon, Schein, Jacqueline, Chiu, Readman, Corbett, Richard, Field, Matthew, Jackman, Shaun D., Mungall, Karen, Lee, Sam, Okada, Hisanaga Mark, Qian, Jenny Q., Griffith, Malachi, Raymond, Anthony, Thiessen, Nina, Cezard, Timothee, Butterfield, Yaron S., Newsome, Richard, Chan, Simon K., She, Rong, Varhol, Richard, Kamoh, Baljit, Prabhu, Anna-Liisa, Tam, Angela, Zhao, YongJun, Moore, Richard A., Hirst, Martin, Marra, Marco A,, Jones, Steven J.M., Hoodless, Pamela A., and Birol, Inanc (2010) De novo assembly and analysis of RNA-seq data. Nature Methods, 7 (11). pp. 909-912.

Eslabão, Marcus R., Dellagostin, Odir A., and Cerqueira, Gustavo M. (2010) LepBank: a Leptospira sequence repository and a portal for phylogenetic studies. Infection, Genetics and Evolution, 10 (4). pp. 586-590.

Cerqueira, Gustavo M., McBride, Alan J.A., Queiroz, Adriano, Pinto, Luciano S., Silva, Éverton F., Hartskeerl, Rudy A., Reis, Mitermayer G., Ko, Albert I., and Dellagostin, Odir A. (2010) Monitoring Leptospira strain collections: the need for quality control. American Journal of Tropical Medicine and Hygiene, 82 (1). pp. 83-87.

Cerqueira, Gustavo M., McBride, Alan J.A., Hartskeerl, Rudy A., Ahmed, Nyiaz, Dellagostin, Odir A., Eslabão, Marcus R., and Nascimento, Ana L.T. (2010) Bioinformatics describes novel Loci for high resolution discrimination of leptospira isolates. PLoS ONE, 5. e15335. pp. 1-7.

Cerqueira, Gustavo M., McBride, Alan J.A., Picardeau, Mathieu, Ribeiro, Samuel G., Moreira, Ângela N., Morel, Viviane, Reis, Mitermayer G., Ko, Albert I., and Dellagostin, Odir A. (2009) Distribution of the leptospiral immunoglobulin-like (lig) genes in pathogenic Leptospira species and application of ligB to typing leptospiral isolates. Journal of Medical Microbiology, 58. pp. 1173-1181.

Cerqueira, Gustavo M., and Picardeau, Mathieu (2009) A century of Leptospira strain typing. Infection, Genetics and Evolution, 9 (5). pp. 760-768.

Voolstra, Christian R., Sunagawa, Shinichi, Schwarz, Jodi A., Coffroth, Mary Alice, Yellowlees, Dave, Leggat, William, and Medina, Monica (2009) Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium). Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 4 (2). pp. 67-74.

Pujolar, J.M., Maes, G.E., Van Houdt, J.K.J., and Zane, L. (2009) Isolation and characterization of expressed sequence tag-linked microsatellite loci for the European eel (Anguilla anguilla). Molecular Ecology Resources, 9 (1). pp. 233-235.

Wood, David L.A., Miljenović, Tomas, Cai, Shuzhi, Raven, Robert J., Kaas, Quentin, Escoubas, Pierre, Herzig, Volker, Wilson, David, and King, Glenn F. (2009) ArachnoServer: a database of protein toxins from spiders. BMC Genomics, 10. 375. pp. 1-8.

Waardenberg, Ashley J., Reverter, Antonio, Wells, Christine A., and Dalrymple, Brian P. (2008) Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle. BMC Systems Biology, 2. 88.

Krzywinski, Martin, Bosdet, Ian, Mathewson, Carrie, Wye, Natasja, Brebner, Jay, Chiu, Readman, Corbett, Richard, Field, Matthew, Lee, Darlene, Pugh, Trevor, Volik, Stas, Siddiqui, Asim, Jones, Steven, Schein, Jacquie, Collins, Collin, and Marra, Marco (2007) A BAC clone fingerprinting approach to the detection of human genome rearrangements. Genome Biology, 8 (10). R224. pp. 1-17.

Margulies, Elliot H., Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Dewey, Colin N., Siepel, Adam, Birney, Ewan, Keefe, Damian, Schwartz, Ariel S., Hou, Minmei, Taylor, James, Nikolaev, Sergey, Montoya-Burgos, Juan I., Löytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Brown, James B., Bickel, Peter, Holmes, Ian, Mullikin, James C., Ureta-Vidal, Abel, Paten, Benedict, Stone, Eric A., Rosenbloom, Kate R., Kent, W. James, Bouffard, G.G., Guan, X., Hansen, N.F., Idol, J.R., Maduro, V.V.B., Maskeri, B., McDowell, J.C., Park, M., Thomas, P.J., Young, A.C., Blakesley, R.W., Muzny, D.M., Sodergren, E., Wheeler, D.A., Worley, K.C., Jiang, H., Weinstock, G.M., Gibbs, R.A., Graves, T., Fulton, R., Mardis, E.R., Wilson, R.K., Clamp, M., Cuff, J., Gnerre, S., Jaffe, D.B., Chang, J.L., Lindblad-Toh, K., Lander, E.S., Hinrichs, A., Trumbower, H., Clawson, H., Zweig, A., Kuhn, R.M., Barber, G., Harte, R., Karolchik, D., Field, Matt, Moore, R.A., Matthewson, C.A., Schein, J.E., Marra, M.A., Antonarakis, Stylianos E., Batzoglou, Serafim, Goldman, Nick, Hardison, Ross, Haussler, David, Miller, Webb, Pachter, Lior, Green, Eric D., and Sidow, Arend (2007) Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research, 17 (6). pp. 760-774.

Rogers, Matthew B., Archibald, John M., Field, Matthew A., Li, Catherine, Striepen, Boris, and Keeling, Patrick J. (2004) Plastid-targeting peptides from the Chlorarachniophyte Bigelowiella natans. Journal of Eukaryotic Microbiology, 51 (5). pp. 529-535.

Conference Item

Boldt, L., Yellowlees, D., and Leggat, W. (2010) Measuring Symbiodinium sp. gene expression patterns with quantitative real-time PCR. In: Proceedings of the 11th International Coral Reef Symposium. pp. 118-122. From: 11th International Coral Reef Symposium, 7 - 11 July 2008, Fort Lauderdale, FL, USA.

Thesis

Lin, Mei-Fang (2016) Corallimorpharian transcriptomes and their use to understand phylogeny and symbiosis in the Hexacorallia. PhD thesis, James Cook University.

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

Zou, Huibin (2011) Characterization of selenium containing proteins in the coral Acropora millepora. PhD thesis, James Cook University.

This list was generated on Fri Nov 15 22:45:28 2019 AEST.