A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans
Marlétaz, Ferdinand, Peijnenburg, Katja T.C.A., Goto, Taichiro, Satoh, Noriyuki, Rokhsar, Daniel S.
Published in Current biology (21.01.2019)
Published in Current biology (21.01.2019)
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Ancient gene linkages support ctenophores as sister to other animals
Schultz, Darrin T, Haddock, Steven H D, Bredeson, Jessen V, Green, Richard E, Simakov, Oleg, Rokhsar, Daniel S
Published in Nature (London) (01.06.2023)
Published in Nature (London) (01.06.2023)
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The octopus genome and the evolution of cephalopod neural and morphological novelties
Albertin, Caroline B, Simakov, Oleg, Mitros, Therese, Wang, Z Yan, Pungor, Judit R, Edsinger-Gonzales, Eric, Brenner, Sydney, Ragsdale, Clifton W, Rokhsar, Daniel S
Published in Nature (London) (13.08.2015)
Published in Nature (London) (13.08.2015)
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Genomics of the origin and evolution of Citrus
Wu, Guohong Albert, Terol, Javier, Ibanez, Victoria, López-García, Antonio, Pérez-Román, Estela, Borredá, Carles, Domingo, Concha, Tadeo, Francisco R, Carbonell-Caballero, Jose, Alonso, Roberto, Curk, Franck, Du, Dongliang, Ollitrault, Patrick, Roose, Mikeal L, Dopazo, Joaquin, Gmitter, Frederick G, Rokhsar, Daniel S, Talon, Manuel
Published in Nature (London) (15.02.2018)
Published in Nature (London) (15.02.2018)
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Genome and transcriptome mechanisms driving cephalopod evolution
Albertin, Caroline B, Medina-Ruiz, Sofia, Mitros, Therese, Schmidbaur, Hannah, Sanchez, Gustavo, Wang, Z Yan, Grimwood, Jane, Rosenthal, Joshua J C, Ragsdale, Clifton W, Simakov, Oleg, Rokhsar, Daniel S
Published in Nature communications (04.05.2022)
Published in Nature communications (04.05.2022)
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Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
Putnam, Nicholas H, O'Connell, Brendan L, Stites, Jonathan C, Rice, Brandon J, Blanchette, Marco, Calef, Robert, Troll, Christopher J, Fields, Andrew, Hartley, Paul D, Sugnet, Charles W, Haussler, David, Rokhsar, Daniel S, Green, Richard E
Published in Genome research (01.03.2016)
Published in Genome research (01.03.2016)
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Suboptimization of developmental enhancers
Farley, Emma K., Olson, Katrina M., Zhang, Wei, Brandt, Alexander J., Rokhsar, Daniel S., Levine, Michael S.
Published in Science (American Association for the Advancement of Science) (16.10.2015)
Published in Science (American Association for the Advancement of Science) (16.10.2015)
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Phytozome: a comparative platform for green plant genomics
Goodstein, David M., Shu, Shengqiang, Howson, Russell, Neupane, Rochak, Hayes, Richard D., Fazo, Joni, Mitros, Therese, Dirks, William, Hellsten, Uffe, Putnam, Nicholas , Rokhsar, Daniel S.
Published in Nucleic acids research (01.01.2012)
Published in Nucleic acids research (01.01.2012)
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Beyond “living fossils”: Can comparative genomics finally reveal novelty?
Sanchez, Gustavo, Simakov, Oleg, Rokhsar, Daniel
Published in Molecular ecology resources (01.01.2022)
Published in Molecular ecology resources (01.01.2022)
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Journal Article
Genome biology of the paleotetraploid perennial biomass crop Miscanthus
Mitros, Therese, Session, Adam M., James, Brandon T., Wu, Guohong Albert, Belaffif, Mohammad B., Clark, Lindsay V., Shu, Shengqiang, Dong, Hongxu, Barling, Adam, Holmes, Jessica R., Mattick, Jessica E., Bredeson, Jessen V., Liu, Siyao, Farrar, Kerrie, Głowacka, Katarzyna, Jeżowski, Stanisław, Barry, Kerrie, Chae, Won Byoung, Juvik, John A., Gifford, Justin, Oladeinde, Adebosola, Yamada, Toshihiko, Grimwood, Jane, Putnam, Nicholas H., De Vega, Jose, Barth, Susanne, Klaas, Manfred, Hodkinson, Trevor, Li, Laigeng, Jin, Xiaoli, Peng, Junhua, Yu, Chang Yeon, Heo, Kweon, Yoo, Ji Hye, Ghimire, Bimal Kumar, Donnison, Iain S., Schmutz, Jeremy, Hudson, Matthew E., Sacks, Erik J., Moose, Stephen P., Swaminathan, Kankshita, Rokhsar, Daniel S.
Published in Nature communications (28.10.2020)
Published in Nature communications (28.10.2020)
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The deuterostome context of chordate origins
Lowe, Christopher J, Clarke, D Nathaniel, Medeiros, Daniel M, Rokhsar, Daniel S, Gerhart, John
Published in Nature (London) (23.04.2015)
Published in Nature (London) (23.04.2015)
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A reference genome for common bean and genome-wide analysis of dual domestications
Schmutz, Jeremy, McClean, Phillip E, Mamidi, Sujan, Wu, G Albert, Cannon, Steven B, Grimwood, Jane, Jenkins, Jerry, Shu, Shengqiang, Song, Qijian, Chavarro, Carolina, Torres-Torres, Mirayda, Geffroy, Valerie, Moghaddam, Samira Mafi, Gao, Dongying, Abernathy, Brian, Barry, Kerrie, Blair, Matthew, Brick, Mark A, Chovatia, Mansi, Gepts, Paul, Goodstein, David M, Gonzales, Michael, Hellsten, Uffe, Hyten, David L, Jia, Gaofeng, Kelly, James D, Kudrna, Dave, Lee, Rian, Richard, Manon M S, Miklas, Phillip N, Osorno, Juan M, Rodrigues, Josiane, Thareau, Vincent, Urrea, Carlos A, Wang, Mei, Yu, Yeisoo, Zhang, Ming, Wing, Rod A, Cregan, Perry B, Rokhsar, Daniel S, Jackson, Scott A
Published in Nature genetics (01.07.2014)
Published in Nature genetics (01.07.2014)
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Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals
Bartel, David P, Grimson, Andrew, Srivastava, Mansi, Fahey, Bryony, Woodcroft, Ben J, Chiang, H. Rosaria, King, Nicole, Degnan, Bernard M, Rokhsar, Daniel S
Published in Nature (30.10.2008)
Published in Nature (30.10.2008)
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Acoel genome reveals the regulatory landscape of whole-body regeneration
Gehrke, Andrew R, Neverett, Emily, Luo, Yi-Jyun, Brandt, Alexander, Ricci, Lorenzo, Hulett, Ryan E, Gompers, Annika, Ruby, J Graham, Rokhsar, Daniel S, Reddien, Peter W, Srivastava, Mansi
Published in Science (American Association for the Advancement of Science) (15.03.2019)
Published in Science (American Association for the Advancement of Science) (15.03.2019)
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A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
Chapman, Jarrod A, Mascher, Martin, Buluç, Aydın, Barry, Kerrie, Georganas, Evangelos, Session, Adam, Strnadova, Veronika, Jenkins, Jerry, Sehgal, Sunish, Oliker, Leonid, Schmutz, Jeremy, Yelick, Katherine A, Scholz, Uwe, Waugh, Robbie, Poland, Jesse A, Muehlbauer, Gary J, Stein, Nils, Rokhsar, Daniel S
Published in Genome Biology (31.01.2015)
Published in Genome Biology (31.01.2015)
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Symbiotic organs shaped by distinct modes of genome evolution in cephalopods
Belcaid, Mahdi, Casaburi, Giorgio, McAnulty, Sarah J., Schmidbaur, Hannah, Suria, Andrea M., Moriano-Gutierrez, Silvia, Pankey, M. Sabrina, Oakley, Todd H., Kremer, Natacha, Koch, Eric J., Collins, Andrew J., Nguyen, Hoan, Lek, Sai, Goncharenko-Foster, Irina, Minx, Patrick, Sodergren, Erica, Weinstock, George, Rokhsar, Daniel S., McFall-Ngai, Margaret, Simakov, Oleg, Foster, Jamie S., Nyholm, Spencer V.
Published in Proceedings of the National Academy of Sciences - PNAS (19.02.2019)
Published in Proceedings of the National Academy of Sciences - PNAS (19.02.2019)
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Deeply conserved synteny resolves early events in vertebrate evolution
Simakov, Oleg, Marlétaz, Ferdinand, Yue, Jia-Xing, O'Connell, Brendan, Jenkins, Jerry, Brandt, Alexander, Calef, Robert, Tung, Che-Huang, Huang, Tzu-Kai, Schmutz, Jeremy, Satoh, Nori, Yu, Jr-Kai, Putnam, Nicholas H, Green, Richard E, Rokhsar, Daniel S
Published in Nature ecology & evolution (01.06.2020)
Published in Nature ecology & evolution (01.06.2020)
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Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing
Hellsten, Uffe, Wright, Kevin M., Jenkins, Jerry, Shu, Shengqiang, Yuan, Yaowu, Wessler, Susan R., Schmutz, Jeremy, Willis, John H., Rokhsar, Daniel S.
Published in Proceedings of the National Academy of Sciences - PNAS (26.11.2013)
Published in Proceedings of the National Academy of Sciences - PNAS (26.11.2013)
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