Dr Ryan Taft

Senior Research Fellow

Institute for Molecular Bioscience
r.taft@imb.uq.edu.au
+61 7 334 62080

Overview

Qualifications

  • Doctor of Philosophy, The University of Queensland

Publications

  • Ulrick, Nicole, Goldstein, Amy, Simons, Cas, Taft, Ryan J., Helman, Guy, Pizzino, Amy, Bloom, Miriam, Vogt, Julie, Pysden, Karen, Diodato, Daria, Martinelli, Diego, Monavari, Ahmad, Buhas, Daniela, van Karnebeek, Clara D. M., Dorboz, Imen, Boespflug-Tanguy, Odile, Rodriguez, Diana, Tetreault, Martine, Majewski, Jacek, Bernard, Genevieve, Ng, Yi Shiau, McFarland, Robert and Vanderver, Adeline (2017) RMND1-related leukoencephalopathy with temporal lobe cysts and hearing loss—another mendelian mimicker of congenital cytomegalovirus infection. Pediatric Neurology, 66 59-62. doi:10.1016/j.pediatrneurol.2016.09.003

  • Crawford, Joanna, Bower, Neil I., Hogan, Benjamin M., Taft, Ryan J., Gabbett, Michael T., McGaughran, Julie and Simons, Cas (2016) Expanding the genotypic spectrum of CCBE1 mutations in Hennekam syndrome. American Journal of Medical Genetics, Part A, 170 10: 2694-2697. doi:10.1002/ajmg.a.37803

  • Vanderver, Adeline, Simons, Cas, Helman, Guy, Crawford, Joanna, Wolf, Nicole I., Bernard, Genevieve, Pizzino, Amy, Schmidt, Johanna L., Takanohashi, Asako, Miller, David, Khouzam, Amirah, Rajan, Vani, Ramos, Erica, Chowdhury, Shimul, Hambuch, Tina, Ru, Ke-Lin, Baillie, Gregory J., Grimmond, Sean M., Caldovic, Ljubica, Devaney, Joseph, Bloom, Miriam, Evans, Sarah H., Murphy, Jennifer L. P., McNeill, Nathan, Fogel, Brent L., Schiffmann, Raphael, van der Knaap, Marjo S. and Taft, Ryan J. (2016) Whole exome sequencing in patients with white matter abnormalities. Annals of Neurology, 79 6: 1031-1037. doi:10.1002/ana.24650

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Supervision

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Publications

Journal Article

  • Ulrick, Nicole, Goldstein, Amy, Simons, Cas, Taft, Ryan J., Helman, Guy, Pizzino, Amy, Bloom, Miriam, Vogt, Julie, Pysden, Karen, Diodato, Daria, Martinelli, Diego, Monavari, Ahmad, Buhas, Daniela, van Karnebeek, Clara D. M., Dorboz, Imen, Boespflug-Tanguy, Odile, Rodriguez, Diana, Tetreault, Martine, Majewski, Jacek, Bernard, Genevieve, Ng, Yi Shiau, McFarland, Robert and Vanderver, Adeline (2017) RMND1-related leukoencephalopathy with temporal lobe cysts and hearing loss—another mendelian mimicker of congenital cytomegalovirus infection. Pediatric Neurology, 66 59-62. doi:10.1016/j.pediatrneurol.2016.09.003

  • Crawford, Joanna, Bower, Neil I., Hogan, Benjamin M., Taft, Ryan J., Gabbett, Michael T., McGaughran, Julie and Simons, Cas (2016) Expanding the genotypic spectrum of CCBE1 mutations in Hennekam syndrome. American Journal of Medical Genetics, Part A, 170 10: 2694-2697. doi:10.1002/ajmg.a.37803

  • Vanderver, Adeline, Simons, Cas, Helman, Guy, Crawford, Joanna, Wolf, Nicole I., Bernard, Genevieve, Pizzino, Amy, Schmidt, Johanna L., Takanohashi, Asako, Miller, David, Khouzam, Amirah, Rajan, Vani, Ramos, Erica, Chowdhury, Shimul, Hambuch, Tina, Ru, Ke-Lin, Baillie, Gregory J., Grimmond, Sean M., Caldovic, Ljubica, Devaney, Joseph, Bloom, Miriam, Evans, Sarah H., Murphy, Jennifer L. P., McNeill, Nathan, Fogel, Brent L., Schiffmann, Raphael, van der Knaap, Marjo S. and Taft, Ryan J. (2016) Whole exome sequencing in patients with white matter abnormalities. Annals of Neurology, 79 6: 1031-1037. doi:10.1002/ana.24650

  • Mallett, Andrew, Patel, Chirag, Maier, Barbara, McGaughran, Julie, Gabbett, Michael, Takasato, Minoru, Cameron, Anne, Trnka, Peter, Alexander, Stephen I., Rangan, Gopala, Tchan, Michel C., Caruana, Georgina, John, George, Quinlan, Cathy, McCarthy, Hugh J., Hyland, Valentine, Hoy, Wedy E., Wolvetang, Ernst, Taft, Ryan, Simons, Cas, Healy H. and Little, Melissa (2015) A protocol for the identification and validation of novel genetic causes of kidney disease. BMC Nephrology, 16 152: . doi:10.1186/s12882-015-0148-8

  • Koltowska, Katarzyna, Paterson, Scott, Bower, Neil I., Baillie, Gregory J., Lagendijk, Anne K., Astin, Jonathan W., Chen, Huijun, Francois, Mathias, Crosier, Philip S., Taft, Ryan J., Simons, Cas, Smith, Kelly A. and Hogan, Benjamin M. (2015) mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish. Genes and Development, 29 15: 1618-1630. doi:10.1101/gad.263210.115

  • Lavergne, Vincent, Harliwong, Ivon, Jones, Alun, Miller, David, Taft, Ryan and Alewood, Paul F. (2015) Optimised deep-targeted proteotranscriptomic profiling reveals unexplored conus toxin diversity and novel cysteine frameworks. Proceedings of the National Acadamy of Sciences of the United States of America, 112 29: E3782-E3791. doi:10.1073/pnas.1501334112

  • Thiffault, Isabelle, Wolf, Nicole I., Forget, Diane, Guerrero, Kether, Tran, Luan T., Choquet, Karine, Lavallee-Adam, Mathieu, Poitras, Christian, Brais, Bernard, Yoon, Grace, Sztriha, Laszlo, Webster, Richard I., Timmann, Dagmar, van de Warrenburg, Bart P., Seeger, Jurgen, Zimmermann, Aliz, Mate, Adrienn, Goizet, Cyril, Fung, Eva, van der Knaap, Marjo S., Fribourg, Sebastien, Vanderver, Adeline, Simons, Cas, Taft, Ryan J., Yates III, John R., Coulombe, Benoit and Bernard, Genevieve (2015) Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III. Nature Communications, 6 7623: 1-9. doi:10.1038/ncomms8623

  • Simons, Cas, Griffin, Laurie B., Helman, Guy, Golas, Gretchen, Pizzino, Amy, Bloom, Miriam, Murphy, Jennifer L. P., Crawford, Joanna, Evans, Sarah H., Topper, Scott, Whitehead, Matthew T., Schreiber, John M., Chapman, Kimberly A., Tifft, Cyndi, Lu, Katrina B., Gamper, Howard, Shigematsu, Megumi, Taft, Ryan J., Antonellis, Anthony, Hou, Ya-Ming and Vanderver, Adeline (2015) Loss-of-Function Alanyl-tRNA Synthetase Mutations Cause an Autosomal-Recessive Early-Onset Epileptic Encephalopathy with Persistent Myelination Defect. American Journal of Human Genetics, 96 4: 675-681. doi:10.1016/j.ajhg.2015.02.012

  • Parikh, Sumit, Bernard, Geneviève, Leventer, Richard J., van der Knaap, Marjo S., van Hove, Johan, Pizzino, Amy, McNeill, Nathan H., Helman, Guy, Simons, Cas, Schmidt, Johanna L., Rizzo, William B., Patterson, Marc C., Taft, Ryan J., Vanderver, Adeline and on behalf of the GLIA Consortium (2015) A clinical approach to the diagnosis of patients with leukodystrophies and genetic leukoencephelopathies. Molecular Genetics and Metabolism, 114 4: 501-515. doi:10.1016/j.ymgme.2014.12.434

  • Clark, Michael B., Mercer, Tim R., Bussotti, Giovanni, Leonardi, Tommaso, Haynes, Katelin R., Crawford, Joanna, Brunck, Marion E., Cao, Kim-Anh Le, Thomas, Gethin P., Chen, Wendy Y., Taft, Ryan J., Nielsen, Lars K., Enright, Anton J., Mattick, John S. and Dinger, Marcel E. (2015) Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing. Nature Methods, 12 4: 339-342. doi:10.1038/nmeth.3321

  • Mercer, Tim R., Clark, Michael B., Anderson, Stacey B., Brunck, Marion E., Haerty, Wilifried, Crawford, Joanna, Taft, Ryan J., Nielsen, Lars K., Dinger, Marcel E. and Mattick, John S. (2015) Genome-wide discovery of human splicing branchpoints. Genome Research, 25 2: 290-303. doi:10.1101/gr.182899.114

  • Wolf, Nicole I., Toro, Camilo, Kister, Ilya, Abd Latif, Kartikasalwah, Leventer, Richard, Pizzino, Amy, Simons, Cas, Abbink, Truus E. M., Taft, Ryan J., van der Knaap, Marjo S. and Vanderver, Adeline (2015) DARS-associated leukoencephalopathy can mimic a steroid-responsive neuroinflammatory disorder. Neurology, 84 3: 226-230. doi:10.1212/WNL.0000000000001157

  • Helman, Guy, Caldovic, Ljubica, Whitehead, Matthew T., Simons, Cas, Brockmann, Knut, Edvardson, Simon, Bai, Renkui, Moroni, Isabella, Taylor, J. Michael, Van Haren, Keith, The SDH Study Group, Taft, Ryan, Vanderver, Adeline and van der Knaap, Marjo S. (2015) MRI spectrum of Succinate Dehydrogenase-related infantile leukoencephalopathy. Annals of Neurology, 79 3: 379-386. doi:10.1002/ana.24572

  • Simons Cas, Rash, Lachlan D., Crawford, Joanna, Ma, Linlin, Cristofori-Armstrong, Ben, Miller, David, Ru, Kelin, Baillie, Gregory J., Alanay, Yasemin, Jacquinet, Adeline, Debray, François-Guillaume, Verloes, Alain, Shen, Joseph, Yesil, Gözde, Guler, Serhat, Yuksel, Adnan, Cleary, John G., Grimmond, Sean M., McGaughran, Julie, King, Glenn F., Gabbett, Michael T. and Taft, Ryan J. (2015) Mutations in the voltage-gated potassium channel gene KCNH1 cause Temple-Baraitser syndrome and epilepsy. Nature Genetics, 47 1: 73-77. doi:10.1038/ng.3153

  • Hunt, David, Leventer, Richard J., Simons, Cas, Taft, Ryan, Swodboda, Kathryn J., Gwan-Cain, Mary, The DDD study, Magee, Alex C., Turnpenny, Peter D. and Baralle, Diana (2014) Whole exome sequencing in family trios reveals de novo mutations in PURA as a cause of severe neurodevelopmental delay and learning disability. Journal of Medical Genetics, 51 12: 806-813. doi:10.1136/jmedgenet-2014-102798

  • Pizzino, Amy, Pierson, Tyler Mark, Guo, Yiran, Helman, Guy, Fortini, Sebastian, Guerrero, Kether, Saitta, Sulagna, Murphy, Jennifer Louise Patrick, Padiath, Quasar, Xie, Yi, Hakonarson, Hakon, Xu, Xun, Funari, Tara, Fox, Michelle, Taft, Ryan J., van der Knaap, Marjo S., Bernard, Genevieve, Schiffmann, Raphael, Simons, Cas and Vanderver, Adeline (2014) TUBB4A de novo mutations cause isolated hypomyelination. Neurology, 83 10: 898-902. doi:10.1212/WNL.0000000000000754

  • Miller, David K, Menezes, Minal J., Simons, Cas, Riley, Lisa G., Cooper, Sandra T., Grimmond, Sean M., Thorburn, David R., Christodoulou, John and Taft, Ryan J. (2014) Rapid identification of a novel complex I MT-ND3 m.10134C>A mutation in a Leigh syndrome patient. PLoS One, 9 8: e104879.1-e104879.6. doi:10.1371/journal.pone.0104879

  • Wong, Justin J. L., Ritchie, William, Gao, Dadi, Lau, Katherine A., Gonzalez, Maria, Choudhary, Anupma, Taft, Ryan J., Rasko, John E. J. and Holst, Jeff (2014) Identification of nuclear-enriched miRNAs during mouse granulopoiesis. Journal of Hematology and Oncology, 7 1: 1-15. doi:10.1186/1756-8722-7-42

  • Hamilton, Eline M., Polder, Emiel, Vanderver, Adeline, Naidu, Sakkubai, Schiffmann, Raphael, Fisher, Kate, Raguz, Ana Boban, Blumkin, Luba, H-ABC Research Group, van Berkel, Carola G. M., Waisfisz, Quinten, Simons, Cas, Taft, Ryan J., Abbink, Truus E. M., Wolf, Nicole I. and van der Knapp, Marjo S. (2014) Hypomyelination with atrophy of the basal ganglia and cerebellum: further delineation of the phenotype and genotype-phenotype correlation. Brain, 137 7: 1921-1930. doi:10.1093/brain/awu110

  • Hudson, Nicholas J., Porto-Neto, Laercio R., Kijas, James, McWilliam, Sean, Taft, Ryan J. and Reverter, Antonio (2014) Information compression exploits patterns of genome composition to discriminate populations and highlight regions of evolutionary interest. BMC Bioinformatics, 15 Article ID.66: . doi:10.1186/1471-2105-15-66

  • Mercer, Tim R., Clark, Michael B., Crawford, Joanna, Brunck, Marion E., Gerhardt, Daniel J., Taft, Ryan J., Nielsen, Lars K., Dinger, Marcel E. and Mattick, John S. (2014) Targeted sequencing for gene discovery and quantification using RNA CaptureSeq. Nature Protocols, 9 5: 989-1009. doi:10.1038/nprot.2014.058

  • Vanderver, Adeline, Simons, Cas, Schmidt, Johanna L., Pearl, Philip L., Bloom, Miriam, Lavenstein, Bennett, Miller, David, Grimmond, Sean M. and Taft, Ryan J. (2013) Identification of a novel de novo p.Phe932Ile KCNT1 mutation in a patient with leukoencephalopathy and severe epilepsy. Pediatric Neurology, In Press, Corrected Proof 1-3. doi:10.1016/j.pediatrneurol.2013.06.024

  • Lavergne, Vincent, Dutertre, Sebastien, Jin, Ai-hua, Lewis, Richard J., Taft, Ryan J. and Alewood, Paul F. (2013) Systematic interrogation of the Conus marmoreus venom duct transcriptome with ConoSorter reveals 158 novel conotoxins and 13 new gene superfamilies. Bmc Genomics, 14 1: 708.1-708.11. doi:10.1186/1471-2164-14-708

  • Wainwright, Elanor N., Jorgensen, Joan S., Kim, Youngha, Truong, Vy, Bagheri-Fam, Stefan, Davidson, Tara, Svingen, Terje, Fernandez-Valverde, Selene L., McClelland, Kathryn S., Taft, Ryan J., Harley, Vincent R., Koopman, Peter and Wilhelm, Dagmar (2013) SOX9 Regulates MicroRNA miR-202-5p/3p expression during mouse testis differentiation. Biology of Reproduction, 89 2: . doi:10.1095/biolreprod.113.110155

  • Liu, Ganqiang, Mattick, John S. and Taft, Ryan (2013) A meta-analysis of the genomic and transcriptomic composition of complex life. Cell Cycle, 12 13: 2061-2072. doi:10.4161/cc.25134

  • Rakoczy, Joanna, Fernandez-Valverde, Selene L., Glazov, Evgeny A., Wainwright, Elanor N., Sato, Tempei, Takada, Shuji, Combes, Alexander N., Korbie, Darren J., Miller, David, Grimmond, Sean M., Little, Melissa H., Asahara, Hiroshi, Mattick, John S., Taft, Ryan J. and Wilhelm, Dagmar (2013) MicroRNAs-140-5p/140-3p modulate leydig cell numbers in the developing mouse testis. Biology of Reproduction, 88 6: . doi:10.1095/biolreprod.113.107607

  • Taft, Ryan J., Vanderver, Adeline, Leventer, Richard J., Damiani, Stephen A., Simons, Cas, Grimmond, Sean M., Miller, David, Schmidt, Johanna, Lockhart, Paul J., Pope, Kate, Ru, Kelin, Crawford, Joanna, Rosser, Tena, de Coo, Irenaeus F. M., Juneja, Monica, Verma, Ishwar C., Prabhakar, Prab, Blaser, Susan, Raiman, Julian, Pouwels, Petra J. W., Bevova, Marianna R., Abbink, Truus E. M., van der Knaap, Marjo S. and Wolf, Nicole I. (2013) Mutations in DARS cause hypomyelination with brain stem and spinal cord involvement and leg spasticity. American Journal of Human Genetics, 92 5: 774-780. doi:10.1016/j.ajhg.2013.04.006

  • Simons, Cas, Wolf, Nicole I., McNeil, Nathan, Caldovic, Ljubica, Devaney, Joseph M., Takanohashi, Asako, Crawford, Joanna, Ru, Kelin, Grimmond, Sean M., Miller, David, Tonduti, Davide, Schmidt, Johanna L., Chudnow, Robert S., van Coster, Rudy, Lagae, Lieven, Kisler, Jill, Sperner, Juergen, van der Knaap, Marjo S., Schiffmann, Raphael, Taft, Ryan J. and Vanderver, Adeline (2013) A de novo mutation in the beta-tubulin gene TUBB4A results in the leukoencephalopathy hypomyelination with atrophy of the basal ganglia and cerebellum. American Journal of Human Genetics, 92 5: 767-773. doi:10.1016/j.ajhg.2013.03.018

  • Cattenoz, Pierre B., Taft, Ryan J., Westhof, Eric and Mattick, John S. (2013) Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage. RNA, 19 2: 257-270. doi:10.1261/rna.036202.112

  • Plummer, Prue N., Freeman, Ruth, Taft, Ryan, Vider, Jelena, Sax, Michael, Umer, Brittany, Gao, Dingcheng, Johns, Christopher A., Mattick, John S., Wilton, Stephen D., Ferro, Vito, McMillan, Nigel A, Swarbrick, Alex, Mittal, Vivek and Mellick, Albert S. (2013) MicroRNAs regulate tumor angiogenesis modulated by endothelial progenitor cells. Cancer Research, 73 1: 341-352. doi:10.1158/0008-5472.CAN-12-0271

  • Clark, Michael, Choudhary, Anupma, Smith, Martin Alexander, Taft, Ryan and Mattick, John S. (2013) The dark matter rises: the expanding world of regulatory RNAs. Essays in Biochemistry, 54 1: 1-16. doi:10.1042/BSE0540001

  • Barry, Guy, Briggs, J. A., Vanichkina, D. P., Poth, E. M., Beveridge, N. J., Vikram Ratnu, Nayler, S. P., Nones, K., Hu, J., Timothy Bredy, Nakagawa, S., Rigo, F., Taft, R. J., Cairns, M. J., Blackshaw, S., Wolvetang, E. J. and Mattick, J. S. (2013) The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Molecular Psychiatry, 19 4: 486-494. doi:10.1038/mp.2013.45

  • Gascoigne, Dennis K., Cheetham, Seth W., Cattenoz, Pierre B., Clark, Michael B., Amaral, Paulo P., Taft, Ryan J., Wilhelm, Dagmar, Dinger, Marcel E. and Mattick, John S. (2012) Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes. Bioinformatics, 28 23: 3042-3050. doi:10.1093/bioinformatics/bts582

  • Lavergne, Vincent, Taft, Ryan J. and Alewood, Paul F. (2012) Cysteine-rich mini-proteins in human biology. Current Topics in Medicinal Chemistry, 12 14: 1514-1533. doi:10.2174/156802612802652411

  • Taft, Ryan J., Hawkins, Peter G., Mattick, John S. and Morris, Kevin V. (2011) The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF) localization. Epigenetics and Chromatin, 4 13: 1-13. doi:10.1186/1756-8935-4-13

  • Faunes, Fernando, Sanchez, Natalia, Moreno, Mauricio, Olivares, Gonzalo H., Lee-Liu, Dasfne, Almonacid, Leonardo, Slater, Alex W., Norambuena, Tomas, Taft, Ryan J., Mattick, John S., Melo, Francisco and Larrain, Juan (2011) Expression of transposable elements in neural tissues during Xenopus development. PLoS One, 6 7: e22569.1-e22569.11. doi:10.1371/journal.pone.0022569

  • Fernandez Valverde, Selene L., Taft, Ryan J. and Mattick, John S. (2011) MicroRNAs in β-cell biology, insulin resistance, diabetes and its complications. Diabetes, 60 7: 1825-1831. doi:10.2337/db11-0171

  • Clark, Michael B., Amaral, Paulo P., Schlesinger, Felix J., Dinger, Marcel E., Taft, Ryan J., Rinn, John L., Ponting, Chris P., Stadler, Peter F., Morris, Kevin V., Morillon, Antonin, Rozowsky, Joel S., Gerstein, Mark B., Wahlestedt, Claes, Hayashizaki, Yoshihide, Carninci, Piero, Gingeras, Thomas R. and Mattick, John S. (2011) The reality of pervasive transcription. PLoS Biology, 9 7: e1000625.1-e1000625.6. doi:10.1371/journal.pbio.1000625

  • Fernandez-Valverde, Selene L., Taft, Ryan J. and Mattick, John S. (2010) Dynamic isomiR regulation in Drosophila development. RNA, 16 10: 1881-1888. doi:10.1261/rna.2379610

  • Taft, Ryan, Simons, Cas, Nahkuri, Satu, Oey, Harald, Korbie, Darren J., Mercer, Timothy R., Holst, Jeff, Ritchie, William, Wong, Justin J-L., Rasko, John E. J., Rokhsar, Daniel S., Degnan, Bernard M. and Mattick, John S. (2010) Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nature Structural and Molecular Biology, 17 8: 1030-1035. doi:10.1038/nsmb.1841

  • de Hoon, Michiel J. L., Taft, Ryan J., Hashimoto, Takehiro, Kanamori-Katayama, Mutsumi, Kawaji, Hideya, Kawano, Mitsuoki, Kishima, Mami, Lassmann, Timo, Faulkner, Geoffrey J., Mattick, John S., Daub, Carsten O., Carninci, Piero, Kawai, Jun, Suzuki, Harukazu and Hayashizaki, Yoshihide (2010) Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Research, 20 2: 257-264. doi:10.1101/gr.095273.109

  • Mattick, John S., Taft, Ryan J. and Faulkner, Geoffrey J. (2010) A global view of genomic information - moving beyond the gene and the master regulator. Trends in Genetics, 26 1: 21-28. doi:10.1016/j.tig.2009.11.002

  • Taft, R. J., Pang, K. C., Mercer, T. R., Dinger, M and Mattick, J. S. (2009) Non-coding RNAs: regulators of disease. Journal of Pathology, 220 2: 126-139. doi:10.1002/path.2638

  • Nahkuri, S, Taft, R. J. and Mattick, J. S. (2009) Nucleosomes are preferentially positioned at exons in somatic and sperm cells. Cell Cycle, 8 20: 3420-3424.

  • Taft, R. J., Kaplan, C. D., Simons, C and Mattick, J. S. (2009) Evolution, biogenesis and function of promoter-associated RNAs. Cell Cycle, 8 15: 2332-2338. doi:10.4161/cc.8.15.9154

  • Taft, Ryan J., Glazov, Evgeny A., Lassmann, Timo, Hayashizaki, Yoshihide, Carninci, Piero and Mattick, John S. (2009) Small RNAs derived from snoRNAs. RNA, 15 7: 1233-1240. doi:10.1261/rna.1528909

  • Suzuki, H, Forrest, ARR, van Nimwegen, E, Daub, CO, Balwierz, PJ, Irvine, KM, Lassmann, T, Ravasi, T, Hasegawa, Y, de Hoon, MJL, Katayama, S, Schroder, K, Carninci, P, Tomaru, Y, Kanamori-Katayama, M, Kubosaki, A, Akalin, A, Ando, Y, Arner, E, Asada, M, Asahara, H, Bailey, T, Bajic, VB, Bauer, D, Beckhouse, AG, Bertin, N, Bjorkegren, J, Brombacher, F, Bulger, E, Chalk, AM, Chiba, J, Cloonan, N, Dawe, A, Dostie, J, Engstrom, PG, Essack, M, Faulkner, GJ, Fink, JL, Fredman, D, Fujimori, K, Furuno, M, Gojobori, T, Gough, J, Grimmond, SM, Gustafsson, M, Hashimoto, M, Hashimoto, T, Hatakeyama, M, Heinzel, S, Hide, W, Hofmann, O, Hornquist, M, Huminiecki, L, Ikeo, K, Imamoto, N, Inoue, S, Inoue, Y, Ishihara, R, Iwayanagi, T, Jacobsen, A, Kaur, M, Kawaji, H, Kerr, MC, Kimura, R, Kimura, S, Kimura, Y, Kitano, H, Koga, H, Kojima, T, Kondo, S, Konno, T, Krogh, A, Kruger, A, Kumar, A, Lenhard, B, Lennartsson, A, Lindow, M, Lizio, M, MacPherson, C, Maeda, N, Maher, CA, Maqungo, M, Mar, J, Matigian, NA, Matsuda, H, Mattick, JS, Meier, S, Miyamoto, S, Miyamoto-Sato, E, Nakabayashi, K, Nakachi, Y, Nakano, M, Nygaard, S, Okayama, T, Okazaki, Y, Okuda-Yabukami, H, Orlando, V, Otomo, J, Pachkov, M, Petrovsky, N, Plessy, C, Quackenbush, J, Radovanovic, A, Rehli, M, Saito, R, Sandelin, A, Schmeier, S, Schonbach, C, Schwartz, AS, Semple, CA, Sera, M, Severin, J, Shirahige, K, Simons, C, Laurent, GS, Suzuki, M, Suzuki, T, Sweet, MJ, Taft, RJ, Takeda, S, Takenaka, Y, Tan, K, Taylor, MS, Teasdale, RD, Tegner, J, Teichmann, S, Valen, E, Wahlestedt, C, Waki, K, Waterhouse, A, Wells, Christine A., Winther, O, Wu, L, Yamaguchi, K, Yanagawa, H, Yasuda, J, Zavolan, M, Hume, DA, Arakawa, T, Fukuda, S, Imamura, K, Kai, C, Kaiho, A, Kawashima, T, Kawazu, C, Kitazume, Y, Kojima, M, Miura, H, Murakami, K, Murata, M, Ninomiya, N, Nishiyori, H, Noma, S, Ogawa, C, Sano, T, Simon, C, Tagami, M, Takahashi, Y, Kawai, J, Hayashizaki, Y, FANTOM Consortium and Riken Omics Science Center (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics, 41 5: 553-562. doi:10.1038/ng.375

  • Taft, RJ, Glazov, EA, Cloonan, N, Simons, C, Stephen, S, Faulkner, GJ, Lassmann, T, Forrest, ARR, Grimmond, SM, Schroder, K, Irvine, K, Arakawa, T, Nakamura, M, Kubosaki, A, Hayashida, K, Kawazu, C, Murata, M, Nishiyori, H, Fukuda, S, Kawai, J, Daub, CO, Hume, DA, Suzuki, H, Orlando, V, Carninci, P, Hayashizaki, Y and Mattick, JS (2009) Tiny RNAs associated with transcription start sites in animals. Nature Genetics, 41 5: 572-578. doi:10.1038/ng.312

  • Guffanti, Alessandro, Iacono, Michele, Pelucchi, Paride, Kim, Namshin, Solda, Giulia, Croft, Larry J., Taft, Ryan J., Rizzi, Ermanno, Askarian-Amiri, Marjan, Bonnal, Raoul J., Callari, Maurizio, Mignone, Flavio, Pesole, Graziano, Bertalot, Giovanni, Bernardi, Luigi Rossi, Albertini, Alberto, Lee, Christopher, Mattick, John S., Zucchi, Ileana and De Bellis, Gianluca (2009) A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. BMC Genomics, 10 163.1-163.17. doi:10.1186/1471-2164-10-163

  • Hussain, Mazhar, Taft, Ryan J. and Asgari, Sassan (2008) An insect virus-encoded microRNA regulates viral replication. Journal of Virology, 82 18: 9164-9170. doi:10.1128/JVI.01109-08

  • Nahkuri, S., Taft, R. J., Korbie, D. J. and Mattick, J. S. (2008) Molecular evolution of the HBII-52 snoRNA Cluster. Journal of Molecular Biology, 381 4: 810-815. doi:10.1016/j.jmb.2008.06.057

  • Taft, Ryan J, Pheasant, Michael and Mattick, John S. (2007) The relationship between non-protein-coding DNA and eukaryotic complexity. BioEssays, 29 3: 288-299. doi:10.1002/bies.20544

  • Yount, Garret, Taft, Ryan J., Luu, Tri, Rachlin, Kenneth, Moore, Dan and Zhang, Wei (2007) Independent motile microplast formation correlates with glioma cell invasiveness. Journal of Neuro-Oncology, 81 2: 113-121. doi:10.1007/s11060-006-9211-4

  • McAllister, Sean D., Chan, Calvin, Taft, Ryan J., Luu, Tri, Abood, Mary E., Moore, Dan H., Aldape, Ken and Yount, Garret (2005) Cannabinoids selectively inhibit proliferation and induce death of cultured human glioblastoma multiforme cells. Journal of Neuro-Oncology, 74 1: 31-40. doi:10.1007/s11060-004-5950-2

  • Yount, Garret, Taft, Ryan, West, Jeremy and Moore, Dan (2004) Possible influence of infrasound on glioma cell response to chemotherapy: A pilot study. Journal of Alternative and Complementary Medicine, 10 2: 247-250. doi:10.1089/107555304323062239

  • Taft, Ryan J. and Mattick, John S. (2003) Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences. Genome Biology, 5 1: 1-24. doi:10.1186/gb-2003-5-1-p1

Conference Publication

  • Plummer, Prue N., Balsara, Spenta, Umer, Brittany, Taft, Ryan, Ferro, Vito, Mattick, John S., Swarbrick, Alex, McMillan, Nigel, Mittal, Vivek and Mellick, Albert S. (2013). Micrornas as novel anti-angiogenesis therapeutic targets. In: Abstracts - 8th Australasian Gene Therapy Society Meeting. 8th Meeting of the Australasian GeneTherapy-Society, Sydney, NSW Australia, (321-322). 08-10 May 2013. doi:10.1002/jgm.2740

  • Plummer, P. N., Taft, R., Mattick, J., McMillan, N., Swarbrick, A., Brink, R., Mittal, V. and Mellick, A. S. (2011). MicroRNAs as tools to target bone marrow mediated tumour angiogenesis. In: Abstracts: 7th Australasian gene therapy society meeting. Biennial Meeting of the Australasian Gene Therapy Society (7th, AGTS, 2011), Parkville, VIC, Australia, (430-430). 4-6 May 2011. doi:10.1002/jgm.1582

  • Plummer, P. N., Taft, R., Mattick, J., McMillan, N., Swarbrick, A., Brink, R., Mittal, V. and Mellick, A. S. (2011). MicroRNAs as tools to target bone marrow mediated tumour angiogenesis. In: Abstracts: 7th Australasian gene therapy society meeting. Biennial Meeting of the Australasian Gene Therapy Society (7th, AGTS, 2011), Parkville, VIC, Australia, (443-443). 4-6 May 2011. doi:10.1002/jgm.1582

  • Plummer, P. N., Taft, R., Mattick, J., McMillan, N., Swarbrick, A., Brink, R., Mittal, V. and Mellick, A. S. (2010). Targeting bone marrow mediated tumour angiogenesis. In: Gold Coast Health and Medical Research Conference: Abstract Book. Gold Coast Health and Medical Research Conference, Gold Coast, QLD, Australia, (21-21). 2-3 December 2010.

  • Mattick, JS, Croft, LJ, Dinger, ME, Pheasant, M, Makunin, IV, Amiri, MA, Mercer, TR, Pang, KC, Simons, C and Taft, RJ (2007). The human genome as an RNA machine. In: FEBS JOURNAL. 32nd Congress of the Federation-of-European-Biochemical-Societies (FEBS), Vienna AUSTRIA, (15-15). JUL 07-12, 2007.

Other Outputs

Grants (Administered at UQ)

PhD and MPhil Supervision

Current Supervision

Completed Supervision