A

Alharbi, Adel B., Schmitz, Ulf, Marshall, Amy D., Vanichkina, Darya, Nagarajah, Rajini, Vellozzi, Melissa, Wong, Justin J.L., Bailey, Charles G., and Rasko, John E.J. (2020) Ctcf haploinsufficiency mediates intron retention in a tissue-specific manner. RNA Biology, 18 (1). pp. 93-103.

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.

B

Ballard, J. William O., Field, Matt A., Edwards, Richard J., Wilson, Laura A.B., Koungoulos, Loukas G., Rosen, Benjamin D., Chernoff, Barry, Dudchenko, Olga, Omer, Arina, Keilwagen, Jens, Skvortsova, Ksenia, Bogdanovic, Ozren, Chan, Eva, Zammit, Robert, Hayes, Vanessa, and Aiden, Erez Lieberman (2023) The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology. GigaScience, 12. giad018.

Brown, Grant J., Cañete, Pablo F., Wang, Hao, Medhavy, Arti, Bones, Josiah, Roco, Jonathan A., He, Yuke, Qin, Yuting, Cappello, Jean, Ellyard, Julia I., Bassett, Katharine, Shen, Qian, Burgio, Gaetan, Zhang, Yaoyuan, Turnbull, Cynthia, Meng, Xiangpeng, Wu, Phil, Cho, Eun, Miosge, Lisa A., Andrews, T. Daniel, Field, Matt A., Tvorogov, Denis, Lopez, Angel F., Babon, Jeffrey J., López, Cristina Aparicio, Gónzalez-Murillo, África, Garulo, Daniel Clemente, Pascual, Virginia, Levy, Tess, Mallack, Eric J., Calame, Daniel G., Lotze, Timothy, Lupski, James R., Ding, Huihua, Ullah, Tomalika R., Walters, Giles D., Koina, Mark E., Cook, Matthew C., Shen, Nan, de Lucas Collantes, Carmen, Corry, Ben, Gantier, Michael P., Athanasopoulos, Vicki, and Vinuesa, Carola G. (2022) TLR7 gain-of-function genetic variation causes human lupus. Nature, 605. pp. 349-356.

Brohus, Malene, Arsov, Todor, Wallace, David A., Jensen, Helene Halkjær, Nyegaard, Mette, Crotti, Lia, Adamski, Marcin, Zhang, Yafei, Field, Matt A., Athanasopoulo, Vicki, Baró, Isabelle, Ribeiro de Oliveira-Mendes, Bárbara B., Redon, Richard, Charpentier, Flavien, Raju, Hariharan, DiSilvestre, Deborah, Wei, Jinhong, Wang, Ruiwu, Rafehi, Haloom, Kaspi, Antony, Bahlo, Melanie, Dick, Ivy E., Chen, Sui Rong Wayne, Cook, Matthew C., Vinuesa, Carola G., Overgaard, Michael Toft, and Schwartz, Peter J. (2021) Infanticide vs. inherited cardiac arrhythmias. Europace, 23 (3). pp. 441-450.

C

Chng, Lena, Holt, Deborah C., Field, Matt, Francis, Joshua R., Tilakaratne, Dev, Dekkers, Milou H., Robinson, Greg, Mounsey, Kate, Pavlos, Rebecca, Bowen, Asha C., Fischer, Katja, Papenfuss, Anthony T., Gasser, Robin B., Korhonen, Pasi K., Currie, Bart J., McCarthy, James S., and Pasay, Cielo (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.

Calcino, Andrew D., Kenny, Nathan J., and Gerdol, Marco (2021) Single individual structural variant detection uncovers widespread hemizygosity in molluscs. Philosophical Transactions of the Royal Society B: Biological Sciences, 376 (1825). 20200153.

Calcino, Andrew, Fernandez-Valverde, Selene L., Taft, Ryan J., and Degnan, Bernard M. (2018) Diverse RNA interference strategies in early-branching metazoans. BMC Evolutionary Biology, 18. 160.

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.

D

Dinh, Xuyen T., Stanley, Dragana, Smith, Letitia D., Moreau, Morgane, Berzins, Stuart P., Gemiarto, Adrian, Baxter, Alan G., and Jordan, Margaret A. (2021) Modulation of TCR signalling components occurs prior to positive selection and lineage commitment in iNKT cells. Scientific Reports, 11. 23650.

Dhungel, Bijay P., Monteuuis, Geoffray, Giardina, Caroline, Tabar, Mehdi S., Feng, Yue, Metierre, Cynthia, Ho, Sarah, Nagarajah, Rajini, Fontaine, Angela R.M., Shah, Jaynish S., Gokal, Divya, Bailey, Charles G., Schmitz, Ulf, and Rasko, John E.J. (2021) The fusion of CLEC12A and MIR223HG arises from a trans‐splicing event in normal and transformed human cells. International Journal of Molecular Sciences, 22. 12178.

de Oliveira, AndréLuiz, Calcino, Andrew, and Wanninger, Andreas (2019) Ancient origins of arthropod moulting pathway components. eLife, 8. e46113.

De Oliveira, A.L., Calcino, A., and Wanninger, A. (2019) Extensive conservation of the proneuropeptide and peptide prohormone complement in mollusks. Scientific Reports, 9. 4846.

E

Edwards, Richard J., Field, Matt A., Ferguson, James M., Dudchenko, Olga, Keilwagen, Jens, Rosen, Benjamin D., Johnson, Gary S., Rice, Edward S., Hillier, La Deanna, Hammond, Jillian M., Towarnicki, Samuel G., Omer, Arina, Khan, Ruqayya, Skvortsova, Ksenia, Bogdanovic, Ozren, Zammit, Robert A., Aiden, Erez Lieberman, Warren, Wesley C., and Ballard, J. William O. (2021) Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. BMC Genomics, 22. 188.

Edwards, Christopher R., Ritchie, William, Wong, Justin J-L., Schmitz, Ulf, Middleton, Robert, An, Xiuli, Mohandas, Narla, Rasko, John E.J., and Blobel, Gerd A. (2016) A dynamic intron retention program in the mammalian megakaryocyte and erythrocyte lineages. Blood, 127 (17). e24-e34.

F

Field, Matt A., Rosen, Benjamin D., Dudchenko, Olga, Chan, Eva K. F., Minoche, Andre E., Edwards, Richard J., Barton, Kirston, Lyons, Ruth J., Tuipulotu, Daniel Enosi, Hayes, Vanessa M., Omer, Arina D., Colaric, Zane, Keilwagen, Jens, Skvortsova, Ksenia, Bogdanovic, Ozren, Smith, Martin A., Aiden, Erez Lieberman, Smith, Timothy P. L., Zammit, Robert A., and Ballard, J. William O. (2020) Canfam GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C. GigaScience, 9 (4). pp. 1-12.

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.

G

Gillman, Rhys, Field, Matt A., Schmitz, Ulf, Karamatic, Rozemary, and Hebbard, Lionel (2023) Identifying cancer driver genes in individual tumours. Computational and Structural Biotechnology Journal, 21. pp. 5028-5038.

Gastineau, Romain, Winsor, Leigh, and Justine, Jean-Lou (2022) The complete mitogenome of the potentially invasive flatworm Australopacifica atrata (Platyhelminthes, Geoplanidae) displays unusual features common to other Rhynchodeminae. ZooKeys, 1110. pp. 121-133.

Gurdek Bas, Rodrigo (2020) Coral reef fish larval connectivity in the Great Barrier Reef from biophysical modelling and genomics. PhD thesis, James Cook University.

H

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.

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.

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.

I

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, The (2020) Pan-cancer analysis of whole genomes. Nature, 578. pp. 82-93.

J

Justine, Jean-lou, Marie, Amandine Delphine, Gastineau, Romain, Fourcade, Yoan, and Winsor, Leigh (2022) The invasive land flatworm Obama nungara in La Reunion, a French island in the Indian Ocean, the first report of the species for Africa. Zootaxa, 5154 (4). pp. 469-476.

Jones, Kathryn Maxson, Cook-Deegan, Robert, Rotimi, Charles N., Callier, Shawneequa L., Bentley, Amy R., Stevens, Hallam, Phillips, Kathryn A., Jansen, Jeroen P., Weyant, Christopher F., Roberts, Dorothy E., Zielinski, Dina, Erlich, Yaniv, Garrison, Nanibaa' A., Carroll, Stephanie Russo, Ossorio, Pilar N., Moreau, Yves, and Wang, Maya (2021) Complicated legacies: the human genome at 20. Science, 371 (6529). pp. 564-569.

Jiang, Simon H., Mercan, Sevcan, Papa, Ilenia, Moldovan, Max, Walters, Giles D., Koina, Mark, Fadia, Mitali, Stanley, Maurice, Lea-Henry, Tom, Cook, Amelia, Ellyard, Julia, McMorran, Brendan, Sundaram, Madhivanan, Thomson, Russell, Canete, Pablo F., Hoy, Wendy, Hutton, Holly, Srivastava, Monika, McKeon, Kathryn, de la Ru´a Figueroa, In˜igo, Cervera, Ricard, Faria, Raquel, D'Alfonso, Sandra, Gatto, Mariele, Athanasopoulos, Vicki, Field, Matthew, Mathews, John, Cho, Eun, Andrews, Thomas D., Kitching, A. Richard, Cook, Matthew C., Alarcon Riquelme, Marta, Bahlo, Melanie, and Vinuesa, Carola G. (2021) Deletions in VANGL1 are a risk factor for antibody-mediated kidney disease. Cell Reports Medicine, 2. 100475.

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.

K

Karimi, Mohammad Reza, Karimi, Amir Hossein, Abolmaali, Shamsozoha, Mehdi, Sadeghi, and Schmitz, Ulf (2022) Prospects and challenges of cancer systems medicine: from genes to disease networks. Briefings in Bioinformatics, 23 (1). bbab343.

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.

L

Lim, Ee Chen, Lim, Shu Wen, Tan, Kenneth JunKai, Sathiya, Maran, Cheng, Wan Hee, Lai, Kok-Song, Loh, Jiun-Yan, and Yap, Wai-Sum (2022) In-Silico Analysis of Deleterious SNPs of FGF4 Gene and Their Impacts on Protein Structure, Function and Bladder Cancer Prognosis. Life, 12 (7). 1018.

Leow, Melvin Khee Shing, Dogra, Shaillay, Ge, Xiaojia, Chuah, Khoon Leong, Liew, Huiling, Loke, Kelvin Siu Hoong, and McFarlane, Craig (2021) Paraneoplastic secretion of multiple phosphatonins from a deep fibrous histiocytoma causing oncogenic osteomalacia. The Journal of Clinical Endocrinology & Metabolism, 106 (5). e2299-e2308.

Loughland, Jessica R., Woodberry, Tonia, Field, Matt, Andrew, Dean W., SheelaNair, Arya, Dooley, Nicholas L., Piera, Kim A., Amante, Fiona H., Kenangalem, Enny, Price, Ric N., Engwerda, Christian R., Anstey, Nicholas M., McCarthy, James S., Boyle, Michelle J., and Minigo, Gabriela (2020) Transcriptional profiling and immunophenotyping show sustained activation of blood monocyte in subpatent Plasmodium falciparum infection. Clinical & Translational Immunology, 9. pp. 1-18.

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.

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.

M

McGowan, Alexandra M., Lanyon, Janet M., Clark, Nicholas, Blair, David, Marsh, Helene, Wolanski, Eric, and Seddon, Jennifer M. (2023) Cryptic marine barriers to gene flow in a vulnerable coastal species, the dugong (Dugong dugon). Marine Mammal Science, 39 (3). pp. 918-939.

Moxon, Joseph V., Calcino, Andrew, Kraeuter, Ann-Katrin, Phie, James, Anderson, Georgina, Standley, Glenys, Sealey, Cindy, Jones, Rhondda E., Field, Matt A., and Golledge, Jonathan (2023) A case-control comparison of acute-phase peripheral blood gene expression in participants diagnosed with minor ischaemic stroke or stroke mimics. Human Genomics, 17. 106.

Mekonnen, Gebeyaw G., Tedla, Bemnet A., Pearson, Mark S., Becker, Luke, Field, Matt, Amoah, Abena S., van Dam, Govert, Corstjens, Paul L.A.M., Mduluza, Takafira, Mutapi, Francisca, Loukas, Alex, and Sotillo, Javier (2022) Characterisation of tetraspanins from Schistosoma haematobium and evaluation of their potential as novel diagnostic markers. PLoS Neglected Tropical Diseases, 16 (1). e0010151.

Marthick, James R., Raspin, Kelsie, Foley, Georgea R., Blackburn, Nicholas B., Banks, Annette, Donovan, Shaun, Malley, Roslyn C., Field, Matthew A., Stanford, Janet L., Ostrander, Elaine A., FitzGerald, Liesel M., and Dickinson, Joanne L. (2021) Massively parallel sequencing in hereditary prostate cancer families reveals a rare risk variant in the DNA repair gene, RAD51C. European Journal of Cancer, 159. pp. 52-55.

Migliavacca, Eugenia, Tay, Stacey K.H., Patel, Harnish P., Sonntag, Tanja, Civiletto, Gabriele, McFarlane, Craig McFarlane, Forrester, Terence, Barton, Sheila J., Leow, Melvin K., Antoun, Elie, Charpagne, Aline, Seng Chong, Yap, Descombes, Patrick, Feng, Lei, Francis-Emmanuel, Patrice, Garratt, Emma S., Giner, Maria Pilar, Green, Curtis O., Karaz, Sonia, Kothandaraman, Narasimhan, Marquis, Julien, Metairon, Sylviane, Moco, Sofia, Nelson, Gail, Ngo, Sherry, Pleasants, Tony, Raymond, Frederic, Sayer, Avan A., Ming Sim, Chu, Slater-Jefferies, Jo, Syddall, Holly E., Fang Tan, Pei, Titcombe, Philip, Vaz, Candida, Westbury, Leo D., Wong, Gerard, Wu, Yonghui, Cooper, Cyrus, Sheppard, Allan, Godfrey, Keith M., Lillycrop, Karen, Karnani, Neerja, and Feige, Jerome N. (2019) Mitochondrial oxidative capacity and NAD+ biosynthesis are reduced in human sarcopenia across ethnicities. Nature Communications, 10. 5808.

Marshall, A.D., Bailey, C.G., Champ, K., Vellozzi, M., O'Young, P., Metierre, C., Feng, Y., Thoeng, A., Richards, A.M., Schmitz, U., Biro, M., Jayasinghe, R., Ding, L., Anderson, L., Mardis, E.R., and Rasko, J.E.J. (2017) CTCF genetic alterations in endometrial carcinoma are pro-tumorigenic. Oncogene, 36. pp. 4100-4110.

N

Nargar, Katharina, O'Hara, Kate, Mertin, Allison, Bent, Stephen J., Nauheimer, Lars, Simpson, Lalita, Zimmer, Heidi, Molloy, Brian P.J., and Clements, Mark A. (2022) Evolutionary Relationships and Range Evolution of Greenhood Orchids (Subtribe Pterostylidinae): Insights From Plastid Phylogenomics. Frontiers in Plant Science, 13. 912089.

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.

O

Okoh, God'spower Richard, Ariel, Ellen, Whitmore, David, and Horwood, Paul F. (2023) Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies. EcoHealth, 20. pp. 427-440.

Oehler, Josphine B., Wright, Helen, Stark, Zornitza, Mallett, Andrew, and Schmitz, Ulf (2023) The application of long‑read sequencing in clinical settings. Human Genomics, 17. 73.

P

Poon, Zhi Weng Josiah, Shen, Xueyan, Angelo, Joseph, Terence, Celestine, Chua, Shi Wei Gavin, and Domingos, Jose A. (2022) Comparative transcriptome analysis reveals factors involved in the influence of dietary astaxanthin on body colouration of Malabar Snapper (Lutjanus malabaricus). Aquaculture, 562. 738874.

Petrova, Veronika, Song, Renhua, DEEP Consortium, Nordström, Karl J.V., Walter, Jörn, Wong, Justin J.-L., Armstrong, Nicola J., Rasko, John E.J., and Schmitz, Ulf (2022) Increased chromatin accessibility facilitates intron retention in specific cell differentiation states. Nucleic Acids Research, 50 (20). gkac994. pp. 11563-11579.

Q

Quigley, Kate M., Bay, Line K., and van Oppen, Madeleine J. H. (2019) The active spread of adaptive variation for reef resilience. Ecology and Evolution, 9 (19). pp. 11122-11135.

R

Raghubar, Arti M., Crawford, Joanna, Jones, Kahli, Lam, Pui Y., Andersen, Stacey B., Matigian, Nicholas A., Ng, Monica S.Y., Healy, Helen, Kassianos, Andrew J., and Mallett, Andrew J. (2023) Spatial Transcriptomics in Kidney Tissue. In: Hewitson, Tim D., Toussaint, Nigel D., and Smith, Edward R., (eds.) Kidney Research: Experimental protocols. Methods in Molecular Biology . Springer, New York, NY, USA, pp. 233-282.

Raspin, Kelsie, FitzGerald, Liesel M., Marthick, James R., Field, Matt A., Malley, Roslyn C., Banks, Annette, Donovan, Shaun, Thomson, Russell J., Foley, Georgea R., Stanford, Janet L., and Dickinson, Joanne L. (2021) A rare variant in EZH2 is associated with prostate cancer risk. International Journal of Cancer, 149 (5). pp. 1089-1099.

Rajasekhar, Magha, Schmitz, Ulf, Flamant, Stephane, Wong, Justin J.-L., Bailey, Charles G., Ritchie, Willian, Holst, Jeff, and Rasko, John E.J. (2018) Identifying microRNA determinants of human myelopoiesis. Scientific Reports, 8. 7264.

S

Schmitz, Ulf (2023) Overview of Computational and Experimental Methods to Identify Tissue-Specific MicroRNA Targets. In: Dalmay, Tamas, (ed.) MicroRNA Detection and Target Identification: Methods and Protocols. Methods in Molecular Biology, 2630 . Humana Press, New York, NY, USA, pp. 155-177.

Swan, Thomas Stanley Tonks (2022) Ecology and population genomics of Aedes albopictus in the Torres Strait, Australia. PhD thesis, James Cook University.

Shah, Jaynish S., Milevskiy, Michael J.G., Petrova, Veronika, Au, Amy Y.M., Wong, Justin J.L., Visvader, Jane E., Schmitz, Ulf, and Rasko, John E.J. (2022) Towards resolution of the intron retention paradox in breast cancer. Breast Cancer Research, 24. 100.

Schmitz, Ulf, Monteuuis, Geoffray, Petrova, Veronika, Shah, Jaynish S., and Rasko, John E.J. (2021) Computational methods for intron retention identification and quantification. In: Wolkenhauer, Olaf, Cai, Yudong, and Rozman, Damjana, (eds.) Systems Medicine: integrative, qualitative and computational approaches. Academic Press, London Wall, United Kingdom, pp. 63-74.

Schmidt, Thomas L., Swan, Tom, Chung, Jessica, Karl, Stephan, Demok, Samuel, Yang, Qiong, Field, Matt, Muzari, Mutizwa Odwell, Ehlers, Gerhard, Brugh, Mathew, Bellwood, Rodney, Horne, Peter, Burkot, Thomas R., Ritchie, Scott, and Hoffmann, Ary A. (2021) Spatial population genomics of a recent mosquito invasion. Molecular Ecology, 30 (5). pp. 1174-1189.

Schmitz, Ulf, Shah, Jaynish S., Dhungel, Bijay P., Monteuuis, Geoffray, Luu, Phuc-Loi, Petrova, Veronika, Metierre, Cynthia, Nair, Shalima S., Bailey, Charles G., Saunders, Verity A., Turhan, Ali G., White, Deborah L., Branford, Susan, Clark, Susan J., Hughes, Timothy P., Wong, Justin J.-L., and Rasko, John E.J. (2020) Widespread aberrant alternative splicing despite molecular remission in chronic myeloid leukaemia patients. Cancers, 12 (12). 3738.

Singh, Mandeep, Jackson, Katherine J.L., Wang, Jing J., Schofield, Peter, Field, Matt A., Koppstein, David, Peters, Timothy J., Burnett, Deborah L., Rizzetto, Simone, Nevoltris, Damien, Masle-Farquhar, Etienne, Faulks, Megan L., Russell, Amanda, Gokal, Divya, Hanioka, Asami, Horikawa, Keisuke, Colella, Alexander D., Chataway, Timothy K., Blackburn, James, Mercer, Tim R., Langley, David B., Goodall, D. Margaret, Jefferis, Roy, Komala, Muralikrishna Gangadharan, Kelleher, Anthony D., Suan, Dan, Rischmueller, Maureen, Christ, Daniel, Brink, Robert, Luciani, Fabio, Gordon, Tom P., Goodnow, Christopher C., and Reed, Joanne H. (2020) Lymphoma driver mutations in the pathogenic evolution of an iconic human autoantibody. Cell, 180 (5). pp. 878-894.

Stevens, Hallam (2018) Globalizing Genomics: The Origins of the International Nucleotide Sequence Database Collaboration. Journal of the History of Biology, 51 (4). pp. 657-691.

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.

Schmitz, Ulf, Pinello, Natalia, Jia, Fangzhi, Alasmari, Sultan, Ritchie, William, Keightley, Maria-Cristina, Shini, Shaniko, Lieschke, Graham J., Wong, Justin J-L., and Rasko, John E.J. (2017) Intron retention enhances gene regulatory complexity in vertebrates. Genome Biology, 18. 216.

Stevens, Hallam (2016) Hadooping the genome: The impact of big data tools on biology. BioSocieties, 11. pp. 352-371.

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.

T

Thomas, Luke, Underwood, Jim N., Rose, Noah H., Fuller, Zachary L., Richards, Zoe T., Dugal, Laurence, Grimaldi, Camille M., Cooke, Ira R., Palumbi, Stephen, and Gilmour, James P. (2022) Spatially varying selection between habitats drives physiological shifts and local adaptation in a broadcast spawning coral on a remote atoll in Western Australia. Science Advances, 8 (17). eabl9185.

W

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.

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.

Y

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.