Publications

Neil J Gemmell, Kim Rutherford, Stefan Prost, Marc Tollis, David Winter, J Robert Macey, David L Adelson, Alexander Suh, Terry Bertozzi, José H Grau, Chris Organ, Paul P Gardner, Matthieu Muffato, Mateus Patricio, Konstantinos Billis, Fergal J Martin, Paul Flicek, Bent Petersen, Lin Kang, Pawel Michalak, Thomas R. Buckley, Melissa Wilson, Yuanyuan Cheng, Hilary Miller, Ryan K Schott, Melissa D Jordan, Richard D Newcomb, José Ignacio Arroyo, Nicole Valenzuela, Tim A Hore, Jaime Renart, Valentina Peona, Claire R Peart, Vera M Warmuth, Lu Zeng, R Daniel Kortschak, Joy M Raison, Valeria Velásquez Zapata, Zhiqiang Wu, Didac Santesmasses, Marco Mariotti, Roderic Guigó, Shawn M Rupp, Victoria G Twort, Nicolas Dussex, Helen Taylor, Hideaki Abe, Donna M Bond, James M Paterson, Daniel G Mulcahy, Vanessa L Gonzalez, Charles G Barbieri, Dustin P DeMeo, Stephan Pabinger, Tracey Van Stijn, Shannon Clarke, Oliver Ryder, Scott V Edwards, Steven L Salzberg, Lindsay Anderson, Nicola Nelson, Clive Stone, Ngatiwai Trust Board (2020). The tuatara genome reveals ancient features of amniote evolution. Nature 584:403-09.

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Jian Cui, Zhipeng Qu, Yuka Harata-Lee, Hanyuan Shen, Thazin Nwe Aung, Wei Wang, R Daniel Kortschak, David L Adelson (2020). The effect of compound kushen injection on cancer cells: Integrated identification of candidate molecular mechanisms. PLoS ONE 15(7):e0236395.

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Atma M Ivancevic, R Daniel Kortschak, Terry Bertozzi, David L Adelson (2018). Horizontal transfer of BovB and L1 retrotransposons in eukaryotes. Genome biology 19:85.

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Lu Zeng, Stephen M Pederson, R Daniel Kortschak, David L Adelson (2018). Transposable elements and gene expression during the evolution of amniotes. Mobile DNA 9:17.

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Reuben M Buckley, R Daniel Kortschak, David L. Adelson (2018). Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse. PLoS computational biology 14:e1006091.

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Lu Zeng, R Daniel Kortschak, Joy M Raison, Terry Bertozzi, David L Adelson (2018). Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies. PLoS One 13:e0193588.

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Eleftheria Palkopoulou, Mark Lipson, Swapan Mallick, Svend Nielsen, Nadin Rohland, Sina Baleka, Emil Karpinski, Atma M Ivancevic, Thu-Hien To, R Daniel Kortschak, Joy M Raison, Zhipeng Qu, Tat-Jun Chin, Kurt W Alt, Stefan Claesson, Love Dalén, Ross DE MacPhee, Harald Meller, Alfred L Roca, Oliver A Ryder, David Heiman, Sarah Young, Matthew Breen, Christina Williams, Bronwen L Aken, Magali Ruffier, Elinor Karlsson, Jeremy Johnson, Federica Di Palma, Jessica Alfoldi, David L Adelson, Thomas Mailund, Kasper Munch, Kerstin Lindblad-Toh, Michael Hofreiter, Hendrik Poinar, David Reich (2018). A comprehensive genomic history of extinct and living elephants. PNAS 115:E2566-E2574.

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R Daniel Kortschak (2018). arrgh: a Go interface to the OpenCPU R server system. The Journal of Open Source Software.

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Reuben M Buckley, R Daniel Kortschak, Joy M Raison, David L Adelson (2017). Similar evolutionary trajectories for retrotransposon accumulation in mammals. Genome Biology and Evolution 9:2336-2353.

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R Daniel Kortschak, David L Adelson (2017). bíogo/ncbi: interfaces to NCBI services for the Go language. The Journal of Open Source Software.

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Thazin Nwe Aung, Zhipeng Qu, R Daniel Kortschak, David L Adelson (2017). Understanding the effectiveness of natural compound mixtures in cancer through their molecular mode of action. Int. J. Mol. Sci. 18:656.

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R Daniel Kortschak, Josh Bleecher Snyder, Manolis Maragkakis, David L Adelson (2017). bíogo: a simple high-performance bioinformatics toolkit for the Go language. The Journal of Open Source Software.

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R Daniel Kortschak, Brent S Pedersen, David L Adelson (2017). bíogo/hts: high throughput sequence handling for the Go language. The Journal of Open Source Software.

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Atma M Ivancevic, R Daniel Kortschak, Terry Bertozzi, David L Adelson (2016). LINEs between species: Evolutionary dynamics of LINE-1 retrotransposons across the eukaryotic tree of life. Genome Biology and Evolution 8:3301-3322.

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Zhipeng Qu, Jian Cui, Yuka Harata-Lee, Thazin Nwe Aung, Qianjin Feng, Joy M Raison, R Daniel Kortschak, David L Adelson (2016). Identification of candidate anti-cancer molecular mechanisms of Compound Kushen Injection using functional genomics. Oncotarget 7:66003–66019.

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Shu Ly Lim, Zhi Peng Qu, R Daniel Kortschak, David M Lawrence, Joel Geoghegan, Anna-Lena Hempfling, Martin Bergmann, Christopher C Goodnow, Christopher J Ormandy, Lee Wong, Jeff Mann, Hamish S Scott, Duangporn Jamsai, David L Adelson, Moira K O'Bryan (2015). HENMT1 and piRNA stability are required for adult male germ cell transposon repression and to define the spermatogenic program in the mouse. PLoS Genetics 11:e1005620.

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Atma M Ivancevic, Ali M Walsh, R Daniel Kortschak, David L Adelson (2013). Jumping the fine LINE between species: Horizontal transfer of transposable elements in animals catalyses genome evolution. BioEssays 35:1071–1082.

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Kirsty Kitto, R Daniel Kortschak (2013). Contextual models and the non-Newtonian paradigm. Progress in Biophysics and Molecular Biology 112:97-107.

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Nicola D Roberts, R Daniel Kortschak, Wendy T Parker, Andreas W Schreiber, Susan Branford, Hamish S Scott, Garique Glonek, David L Adelson (2013). A comparative analysis of algorithms for somatic SNV detection in cancer. Bioinformatics 29:2223-2230.

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Ali Morton Walsh, R Daniel Kortschak, Michael G Gardner, Terry Bertozzi, David L Adelson (2012). Widespread horizontal transfer of retrotransposons. PNAS 110:1012-1016.

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Enkhjargal Tsend-Ayush, R Daniel Kortschak, Pascal Bernard, Shu Ly Lim, Janelle Ryan, Ruben Rosenkranz, Tatiana Borodina, Juliane C Dohm, Heinz Himmelbauer, Vincent R Harley, Frank Grützner (2012). Identification of mediator complex 26 (Crsp7) gametologs on platypus X1 and Y5 sex chromosomes: a candidate testis-determining gene in monotremes?. Chromosome Research 20:127-138.

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R Daniel Kortschak, Enkhjargal Tsend-Ayush, Frank Grützner (2009). Analysis of SINE and LINE repeat content of Y chromosomes in the platypus, Ornithorhynchus anatinus. Reproduction, Fertility and Development 21:964-975.

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R Daniel Kortschak, Gabrielle Samuel, Robert Saint, David J Miller (2003). EST analysis of the Cnidarian Acropora millepora reveals extensive gene loss and rapid sequence divergence in the model invertebrates. Current Biology 13:2190-2195.

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R Daniel Kortschak, Richard Tamme, Michael Lardelli (2001). Evolutionary analysis of vertebrate Notch genes. Development Genes and Evolution 211:350-354.

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R Daniel Kortschak, Philip W Tucker, Robert Saint (2000). ARID proteins come in from the desert. Trends in Biochemical Sciences 25:294-299.

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Stephen L Gregory, R Daniel Kortschak, Bill Kalionis, Robert Saint (1996). Characterization of the dead ringer gene identifies a novel, highly conserved family of sequence-specific DNA-binding proteins. Molecular and Cellular Biology 16:792-799.

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