SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data von Cox, Murray P, Peterson, Daniel A, Biggs, Patrick J

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Multiple Deeply Divergent Denisovan Ancestries in Papuans von Jacobs, Guy S., Hudjashov, Georgi, Saag, Lauri, Kusuma, Pradiptajati, Darusallam, Chelzie C., Lawson, Daniel J., Mondal, Mayukh, Pagani, Luca, Ricaut, François-Xavier, Stoneking, Mark, Metspalu, Mait, Sudoyo, Herawati, Lansing, J. Stephen, Cox, Murray P.

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Denisovan introgression has shaped the immune system of present-day Papuans von Vespasiani, Davide M, Jacobs, Guy S, Cook, Laura E, Brucato, Nicolas, Leavesley, Matthew, Kinipi, Christopher, Ricaut, François-Xavier, Cox, Murray P, Gallego Romero, Irene

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Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae von Winter, David J, Ganley, Austen R D, Young, Carolyn A, Liachko, Ivan, Schardl, Christopher L, Dupont, Pierre-Yves, Berry, Daniel, Ram, Arvina, Scott, Barry, Cox, Murray P

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Comparative genomics reveals a core gene toolbox for lifestyle transitions in Hypocreales fungi von Wu, Baojun, Cox, Murray P.

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Tradition and change: celebrating food systems resilience at two Indigenous Māori community events von Wehi, Priscilla, Cox, Murray, Whaanga, Hēmi, Roa, Tom

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Fungal endophyte infection of ryegrass reprograms host metabolism and alters development von Dupont, Pierre‐Yves, Eaton, Carla J, Wargent, Jason J, Fechtner, Susanne, Solomon, Peter, Schmid, Jan, Day, Robert C, Scott, Barry, Cox, Murray P

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Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi von Wu, Baojun, Hao, Weilong, Cox, Murray P

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Greater genetic and regulatory plasticity of retained duplicates in Epichloë endophytic fungi von Wu, Baojun, Cox, Murray P.

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Papuan mitochondrial genomes and the settlement of Sahul von Pedro, Nicole, Brucato, Nicolas, Fernandes, Veronica, André, Mathilde, Saag, Lauri, Pomat, William, Besse, Céline, Boland, Anne, Deleuze, Jean-François, Clarkson, Chris, Sudoyo, Herawati, Metspalu, Mait, Stoneking, Mark, Cox, Murray P, Leavesley, Matthew, Pereira, Luisa, Ricaut, François-Xavier

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Woven languages: understanding Indigenous socioecological systems von Wehi, Priscilla M., Whaanga, Hēmi, Roa, Tom, Cox, Murray P.

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Archaic mitochondrial DNA inserts in modern day nuclear genomes von Bücking, Robert, Cox, Murray P, Hudjashov, Georgi, Saag, Lauri, Sudoyo, Herawati, Stoneking, Mark

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Malagasy Genetic Ancestry Comes from an Historical Malay Trading Post in Southeast Borneo von Brucato, Nicolas, Kusuma, Pradiptajati, Cox, Murray P, Pierron, Denis, Purnomo, Gludhug A, Adelaar, Alexander, Kivisild, Toomas, Letellier, Thierry, Sudoyo, Herawati, Ricaut, François-Xavier

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Episodes of Diversification and Isolation in Island Southeast Asian and Near Oceanian Male Lineages von Karmin, Monika, Flores, Rodrigo, Saag, Lauri, Hudjashov, Georgi, Brucato, Nicolas, Crenna-Darusallam, Chelzie, Larena, Maximilian, Endicott, Phillip L, Jakobsson, Mattias, Lansing, J Stephen, Sudoyo, Herawati, Leavesley, Matthew, Metspalu, Mait, Ricaut, François-Xavier, Cox, Murray P

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Complex Patterns of Admixture across the Indonesian Archipelago von Hudjashov, Georgi, Karafet, Tatiana M, Lawson, Daniel J, Downey, Sean, Savina, Olga, Sudoyo, Herawati, Lansing, J Stephen, Hammer, Michael F, Cox, Murray P

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Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover von Griffiths, Andrew G, Moraga, Roger, Tausen, Marni, Gupta, Vikas, Bilton, Timothy P, Campbell, Matthew A, Ashby, Rachael, Nagy, Istvan, Khan, Anar, Larking, Anna, Anderson, Craig, Franzmayr, Benjamin, Hancock, Kerry, Scott, Alicia, Ellison, Nick W, Cox, Murray P, Asp, Torben, Mailund, Thomas, Schierup, Mikkel H, Andersen, Stig Uggerhøj

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Sex-biased evolutionary forces shape genomic patterns of human diversity von Hammer, Michael F, Mendez, Fernando L, Cox, Murray P, Woerner, August E, Wall, Jeffrey D

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Deep ancestry of Bornean hunter-gatherers supports long-term local ancestry dynamics von Kusuma, Pradiptajati, Cox, Murray P., Barker, Graeme, Sudoyo, Herawati, Lansing, J. Stephen, Jacobs, Guy S.

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Genomic insights into the peopling of the Southwest Pacific von Skoglund, Pontus, Posth, Cosimo, Sirak, Kendra, Spriggs, Matthew, Valentin, Frederique, Bedford, Stuart, Clark, Geoffrey R., Reepmeyer, Christian, Petchey, Fiona, Fernandes, Daniel, Fu, Qiaomei, Harney, Eadaoin, Lipson, Mark, Mallick, Swapan, Novak, Mario, Rohland, Nadin, Stewardson, Kristin, Abdullah, Syafiq, Cox, Murray P., Friedlaender, Françoise R., Friedlaender, Jonathan S., Kivisild, Toomas, Koki, George, Kusuma, Pradiptajati, Merriwether, D. Andrew, Ricaut, Francois-X., Wee, Joseph T. S., Patterson, Nick, Krause, Johannes, Pinhasi, Ron, Reich, David

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Host Tissue Environment Directs Activities of an Epichloë Endophyte, While It Induces Systemic Hormone and Defense Responses in Its Native Perennial Ryegrass Host von Schmid, Jan, Day, Robert, Zhang, Ningxin, Dupont, Pierre-Yves, Cox, Murray P, Schardl, Christopher L, Minards, Niki, Truglio, Mauro, Moore, Neil, Harris, Daniel R, Zhou, Yanfei

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