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2012 Journal Article Analyses of pig genomes provide insight into porcine demography and evolutionGroenen, Martien A. M., Archibald, Alan L., Uenishi, Hirohide, Tuggle, Christopher K., Takeuchi, Yasuhiro, Rothschild, Max F., Rogel-Gaillard, Claire, Park, Chankyu, Milan, Denis, Megens, Hendrik-Jan, Li, Shengting, Larkin, Denis M., Kim, Heebal, Frantz, Laurent A. F., Caccamo, Mario, Ahn, Hyeonju, Aken, Bronwen L., Anselmo, Anna, Anthon, Christian, Auvil, Loretta, Badaoui, Bouabid, Beattie, Craig W., Bendixen, Christian, Berman, Daniel, Blecha, Frank, Blomberg, Jonas, Bolund, Lars, Bosse, Mirte, Botti, Sara ... Schook, Lawrence B. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491 (7424), 393-398. doi: 10.1038/nature11622 |
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Featured 2012 Journal Article Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophagesSchroder, Kate, Irvine, Katharine M., Taylor, Martin S., Bokil, Nilesh J., Le Cao, Kim-Anh, Masterman, Kelly-Anne, Labzin, Larisa I., Semple, Colin A., Kapetanovic, Ronan, Fairbairn, Lynsey, Akalin, Altuna, Faulkner, Geoffrey J., Baillie, John Kenneth, Gongora, Milena, Daub, Carsten O., Kawaji, Hideya, McLachlan, Geoffrey J., Goldman, Nick, Grimmond, Sean M., Carninci, Piero, Suzuki, Harukazu, Hayashizaki, Yoshihide, Lenhard, Boris, Hume, David A. and Sweet, Matthew J. (2012). Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. Proceedings of the National Academy of Sciences of the USA, 109 (16), E944-E953. doi: 10.1073/pnas.1110156109 |
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2012 Journal Article Promoter architecture of mouse olfactory receptor genesPlessy, Charles, Pascarella, Giovanni, Bertin, Nicolas, Akalin, Altuna, Carrieri, Claudia, Vassalli, Anne, Lazarevic, Dejan, Severin, Jessica, Vlachouli, Christina, Simone, Roberto, Faulkner, Geoffrey J., Kawai, Jun, Daub, Carsten O., Zucchelli, Silvia, Hayashizaki, Yoshihide, Mombaerts, Peter, Lenhard, Boris, Gustincich, Stefano and Carninci, Piero (2012). Promoter architecture of mouse olfactory receptor genes. Genome Research, 22 (3), 486-497. doi: 10.1101/gr.126201.111 |
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2011 Journal Article Is somatic retrotransposition a parasitic or symbiotic phenomenon?Upton, Kyle R., Baillie, J. Kenneth and Faulkner, Geoffrey J. (2011). Is somatic retrotransposition a parasitic or symbiotic phenomenon?. Mobile Genetic Elements, 1 (4), 279-282. doi: 10.4161/mge.18422 |
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2011 Journal Article Somatic retrotransposition alters the genetic landscape of the human brainBaillie, J. Kenneth, Barnett, Mark W., Upton, Kyle R., Gerhardt, Daniel J., Richmond, Todd A., De Sapio, Fioravante, Brennan. Paul M., Rizzu, Patrizia, Smith, Sarah, Fell, Mark, Talbot, Richard T., Gustincich, Stefano, Freeman, Thomas C., Mattick, John S., Hume, David A., Heutink, Peter, Carninci, Piero, Jeddeloh, Jeffrey A. and Faulkner, Geoffrey J. (2011). Somatic retrotransposition alters the genetic landscape of the human brain. Nature, 479 (7374), 534-537. doi: 10.1038/nature10531 |
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2011 Journal Article Retrotransposons: mobile and mutagenic from conception to deathFaulkner, Geoffrey J. (2011). Retrotransposons: mobile and mutagenic from conception to death. FEBS Letters, 585 (11), 1589-1594. doi: 10.1016/j.febslet.2011.03.061 |
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2011 Conference Publication Retrotransposition and the genetic identity of human neuronsFaulkner, G. J. (2011). Retrotransposition and the genetic identity of human neurons. 36th FEBS Congress of the Biochemistry for Tomorrows Medicine, Torino Italy, Jun 25-30, 2011. MALDEN: WILEY-BLACKWELL. |
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2010 Journal Article Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing librariesde 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 |
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2010 Journal Article A global view of genomic information - moving beyond the gene and the master regulatorMattick, 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 |
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2009 Journal Article Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLiteHashimoto, T, de Hoon, M. J. L., Grimmond, S. M., Daub, C. O., Hayashizaki, Y and Faulkner, G. J. (2009). Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite. Bioinformatics, 25 (19), 2613-2614. doi: 10.1093/bioinformatics/btp438 |
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2009 Journal Article Altruistic functions for selfish DNAFaulkner, Geoffrey J. and Carninci, Piero (2009). Altruistic functions for selfish DNA. Cell Cycle, 8 (18), 2895-2900. doi: 10.4161/cc.8.18.9536 |
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2009 Journal Article RNA-MATE: a recursive mapping strategy for high throughput RNA-sequencing dataCloonan, Nicole, Xu, Qinying, Faulkner, Geoffrey J., Taylor, Darrin F., Tang, Dave T. P., Kolle, Gabriel and Grimmond, Sean M. (2009). RNA-MATE: a recursive mapping strategy for high throughput RNA-sequencing data. Bioinformatics, 25 (19), 2615-2616. doi: 10.1093/bioinformatics/btp459 |
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2009 Journal Article The regulated retrotransposon transcriptome of mammalian cellsFaulkner, Geoffrey J., Kimura, Yasumasa, Daub, Carsten O., Wani, Shivangi, Plessy, Charles, Irvine, Katharine M., Schroder, Kate, Cloonan, Nicole, Steptoe, Anita L., Lassmann, Timo, Waki, Kazunori, Hornig, Nadine, Arakawa, Takahiro, Takahashi, Hazuki, Kawai, Jun, Forrest, Alistair R. R., Suzuki, Harukazu, Hayashizaki, Yoshihide, Hume, David A., Orlando, Valerio, Grimmond, Sean M. and Carninci, Piero (2009). The regulated retrotransposon transcriptome of mammalian cells. Nature Genetics, 41 (5), 563-571. doi: 10.1038/ng.368 |
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2009 Journal Article Tiny RNAs associated with transcription start sites in animalsTaft, 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 |
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2009 Journal Article The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell lineSuzuki, 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 ... 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 |
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2009 Book Chapter Setting CAGE tags in a genomic contextFaulkner, G. J. and Grimmond, S. M. (2009). Setting CAGE tags in a genomic context. Cap- Analysis Gene Expression (Cage): The Science of Decoding Gene Transcription. (pp. 93-100) edited by Carninci, P. Singapore: Pan Stanford Publishing. doi: 10.4032/9789814241359 |
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2008 Journal Article A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGEFaulkner, G. J., Forrest, A. R. R., Chalk, A. M., Schroder, K., Hayashizaki, Y., Carninci, P., Hume, D. A. and Grimmond, S. M. (2008). A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics, 91 (3), 281-288. doi: 10.1016/j.ygeno.2007.11.003 |
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2008 Other Outputs Short sequence tags reveal global transcription of repetitive elements in mammalian genomesFaulkner, Geoffrey (2008). Short sequence tags reveal global transcription of repetitive elements in mammalian genomes. PhD Thesis, Institute for Molecular Bioscience, The University of Queensland. doi: 10.14264/167578 |
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2008 Journal Article Stem cell transcriptome profiling via massive-scale mRNA sequencingCloonan, Nicole, Forrest, Alistair R. R., Kolle, Gabriel, Gardiner, Brooke B. A., Faulkner, Geoffrey J., Brown, Mellissa K., Taylor, Darrin F ., Steptoe, Anita L., Wani, Shivangi, Bethel, Graeme, Robertson, Alan J., Perkins, Andrew C., Bruce, Stephen J., Clarence, C. Lee, Ranade, Swati S., Peckham, Heather E, Manning, Jonathan M, McKernan, Kevin J and Grimmond, Sean M (2008). Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nature Methods, 5 (7), 613-619. doi: 10.1038/nmeth.1223 |
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2007 Journal Article The expression of Clcn7 and Ostm1 in osteoclasts is coregulated by microphthalmia transcription factorMeadows, Nicholas A., Sharma, Sudarshana M., Faulkner, Geoffrey J., Ostrowski, Michael C., Hume, David A. and Cassady, Alan I. (2007). The expression of Clcn7 and Ostm1 in osteoclasts is coregulated by microphthalmia transcription factor. Journal of Biological Chemistry, 282 (3), 1891-1904. doi: 10.1074/jbc.M608572200 |
