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Yuko Yoshinaga

Lawrence Berkeley National Laboratory

37H-index
104Paper Count
1.3WCitation Count
Published Papers 38
Publication Date
Multi-season analysis reveals hundreds of drought-responsive genes in sorghum
err2026-02-02
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errBenjamin Cole; Wenxin Zhang; Junming Shi; Hao Wang; Christopher Baker; Nelle Varoquaux; Joy Hollingsworth; Robert Hutmacher; Jeffery Dahlberg; Grady Pierroz; Kerrie W. Barry; Vasanth Singan; Yuko Yoshinaga; Christopher Daum; Matthew Zane; Matthew Blow; Ronan O’Malley; Shengqiang Shu; Jerry W. Jenkins; John T. Lovell; Jeremy Schmutz; John W. Taylor; Devin Coleman-Derr; Axel Visel; Peggy G. Lemaux; Elizabeth Purdom; John P. Vogel
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The genomic footprints of wild Saccharum species trace domestication, diversification, and modern breeding of sugarcane
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IF42.5
err2025-10-14
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errOlivier Garsmeur; Simon Rio; Nicolas Pompidor; Anna Lipzen; Catherine Hervouet; Théo Durand; Chris Daum; Yuko Yoshinaga; Mike Butterfield; Alexander Sanchez; George Piperidis; Noa Lincoln; Anna Hale; Jean Yves Hoarau; Yoshifumi Terajima; Prakash Lakshmanan; Erik Sacks; Shailendra Sharma; Marotea Vitrac; Kerrie Barry; Jeremy Schmutz; Angélique D’Hont
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Recruitment, rewiring and deep conservation in flowering plant gene regulation
err2025-07-15
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PREAI
errLeo A. Baumgart; Sharon I. Greenblum; Abraham Morales-Cruz; Peng Wang; Yu Zhang; Lin Yang; Cindy Chen; David J. Dilworth; Alexis C. Garretson; Nicolas Grosjean; Guifen He; Emily Savage; Yuko Yoshinaga; Ian K. Blaby; Chris G. Daum; Ronan C. O’Malley
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Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti
err2025-01-01
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PREAI
errNybo, J. L.; Vesth, T. C.; Theobald, S.; Frisvad, J. C.; Larsen, T. O.; Kjaerboelling, I.; Rothschild-Mancinelli, K.; Lyhne, E. K.; Barry, K.; Clum, A.; Yoshinaga, Y.; Ledsgaard, L.; Daum, C.; Lipzen, A.; Kuo, A.; Riley, R.; Mondo, S.; Labutti, K.; Haridas, S.; Pangalinan, J.; Salamov, A. A.; Simmons, B. A.; Magnuson, J. K.; Chen, J.; Drula, E.; Henrissat, B.; Wiebenga, A.; Lubbers, R. J. M.; Muller, A.; Gomes, A. C. dos Santos; Makela, M. R.; Stajich, J. E.; Grigorie, I., V; Mortensen, U. H.; Andersen, M. R.
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A large sequenced mutant library - valuable reverse genetic resource that covers 98% of sorghum genes
err2023-12-15
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errJiao, Yinping; Nigam, Deepti; Barry, Kerrie; Daum, Chris; Yoshinaga, Yuko; Lipzen, Anna; Khan, Adil; Parasa, Sai-Praneeth; Wei, Sharon; Lu, Zhenyuan; Tello-Ruiz, Marcela K.; Dhiman, Pallavi; Burow, Gloria; Hayes, Chad; Chen, Junping; Brandizzi, Federica; Mortimer, Jenny; Ware, Doreen; Xin, Zhanguo
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Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi
err2023-09-18
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errLongley, Reid; Robinson, Aaron; Liber, Julian A.; Bryson, Abigail E.; Morales, Demosthenes P.; Labutti, Kurt; Riley, Robert; Mondo, Stephen J.; Kuo, Alan; Yoshinaga, Yuko; Daum, Chris; Barry, Kerrie; Grigoriev, Igor V.; Desiro, Alessandro; Chain, Patrick S. G.; Bonito, Gregory
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Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii
err2023-04-05
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errWeng, Xiaoyu; Song, Haili; Sreedasyam, Avinash; Haque, Taslima; Zhang, Li; Chen, Cindy; Yoshinaga, Yuko; Williams, Melissa; O'Malley, Ronan C.; Grimwood, Jane; Schmutz, Jeremy; Juenger, Thomas E.
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Targeted Disruption of the Idol Gene Alters Cellular Regulation of the Low-Density Lipoprotein Receptor by Sterols and Liver X Receptor Agonists
err2023-03-20
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errScotti, Elena; Hong, Cynthia; Yoshinaga, Yuko; Tu, Yiping; Hu, Yan; Zelcer, Noam; Boyadjian, Rima; de Jong, Pieter J.; Young, Stephen G.; Fong, Loren G.; Tontonoz, Peter
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A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen
err2023-02-24
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errFeurtey, Alice; Lorrain, Cecile; McDonald, Megan C.; Milgate, Andrew; Solomon, Peter S.; Warren, Rachael; Puccetti, Guido; Scalliet, Gabriel; Torriani, Stefano F. F.; Gout, Lilian; Marcel, Thierry C.; Suffert, Frederic; Alassimone, Julien; Lipzen, Anna; Yoshinaga, Yuko; Daum, Christopher; Barry, Kerrie; Grigoriev, Igor V.; Goodwin, Stephen B.; Genissel, Anne; Seidl, Michael F.; Stukenbrock, Eva H.; Lebrun, Marc-Henri; Kema, Gert H. J.; McDonald, Bruce A.; Croll, Daniel
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Speciation Underpinned by Unexpected Molecular Diversity in the Mycorrhizal Fungal Genus Pisolithus
err2023-02-22
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errPlett, Jonathan M.; Miyauchi, Shingo; Morin, Emmanuelle; Plett, Krista; Wong-Bajracharya, Johanna; de Freitas Pereira, Maira; Kuo, Alan; Henrissat, Bernard; Drula, Elodie; Wojtalewicz, Dominika; Riley, Robert; Pangilinan, Jasmyn; Andreopoulos, William; LaButti, Kurt; Daum, Chris; Yoshinaga, Yuko; Fauchery, Laure; Ng, Vivian; Lipzen, Anna; Barry, Kerrie; Singan, Vasanth; Guo, Jie; Lebel, Teresa; Costa, Mauricio Dutra; Grigoriev, Igor, V; Martin, Francis; Anderson, Ian C.; Kohler, Annegret
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The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory
err2022-12-23
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errCraig, Rory J.; Gallaher, Sean D.; Shu, Shengqiang; Salome, Patrice A.; Jenkins, Jerry W.; Blaby-Haas, Crysten E.; Purvine, Samuel O.; O'Donnell, Samuel; Barry, Kerrie; Grimwood, Jane; Strenkert, Daniela; Kropat, Janette; Daum, Chris; Yoshinaga, Yuko; Goodstein, David M.; Vallon, Olivier; Schmutz, Jeremy; Merchant, Sabeeha S.
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The landscape of Chlamydomonas histone H3 lysine 4 methylation reveals both constant features and dynamic changes during the diurnal cycle
err2022-09-20
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errStrenkert, Daniela; Yildirim, Asli; Yan, Juying; Yoshinaga, Yuko; Pellegrini, Matteo; O'Malley, Ronan C.; Merchant, Sabeeha S.; Umen, James G.
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Genetic mapping and prediction of flowering time and plant height in a maize Stiff Stalk MAGIC population
err2022-04-20
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errMichel, Kathryn J.; Lima, Dayane C.; Hundley, Hope; Singan, Vasanth; Yoshinaga, Yuko; Daum, Chris; Barry, Kerrie; Broman, Karl W.; Buell, C. Robin; de Leon, Natalia; Kaeppler, Shawn M.
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Multiplex knockout of trichome-regulating MYB duplicates in hybrid poplar using a single gRNA
err2022-03-17
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errBewg, W. Patrick; Harding, Scott A.; Engle, Nancy L.; Vaidya, Brajesh N.; Zhou, Ran; Reeves, Jacob; Horn, Thomas W.; Joshee, Nirmal; Jenkins, Jerry W.; Shu, Shengqiang; Barry, Kerrie W.; Yoshinaga, Yuko; Grimwood, Jane; Schmitz, Robert J.; Schmutz, Jeremy; Tschaplinski, Timothy J.; Tsai, Chung-Jui
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Persistence and plasticity in bacterial gene regulation
err2021-11-25
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errBaumgart, Leo A.; Lee, Ji Eun; Salamov, Asaf; Dilworth, David J.; Na, Hyunsoo; Mingay, Matthew; Blow, Matthew J.; Zhang, Yu; Yoshinaga, Yuko; Daum, Chris G.; O'Malley, Ronan C.
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Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics
err2021-11-18
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errVan Goethem, Marc W.; Osborn, Andrew R.; Bowen, Benjamin P.; Andeer, Peter F.; Swenson, Tami L.; Clum, Alicia; Riley, Robert; He, Guifen; Koriabine, Maxim; Sandor, Laura; Yan, Mi; Daum, Chris G.; Yoshinaga, Yuko; Makhalanyane, Thulani P.; Garcia-Pichel, Ferran; Visel, Axel; Pennacchio, Len A.; O'Malley, Ronan C.; Northen, Trent R.
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Genomic variation within the maize stiff-stalk heterotic germplasm pool
err2021-07-18
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errBornowski, Nolan; Michel, Kathryn J.; Hamilton, John P.; Ou, Shujun; Seetharam, Arun S.; Jenkins, Jerry; Grimwood, Jane; Plott, Chris; Shu, Shengqiang; Talag, Jayson; Kennedy, Megan; Hundley, Hope; Singan, Vasanth R.; Barry, Kerrie; Daum, Chris; Yoshinaga, Yuko; Schmutz, Jeremy; Hirsch, Candice N.; Hufford, Matthew B.; Leon, Natalia; Kaeppler, Shawn M.; Buell, C. Robin
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DOE JGI Metagenome Workflow
err2021-06-29
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errClum, Alicia; Huntemann, Marcel; Bushnell, Brian; Foster, Brian; Foster, Bryce; Roux, Simon; Hajek, Patrick P.; Varghese, Neha; Mukherjee, Supratim; Reddy, T. B. K.; Daum, Chris; Yoshinaga, Yuko; O'Malley, Ronan; Seshadri, Rekha; Kyrpides, Nikos C.; Eloe-Fadrosh, Emiley A.; Chen, I-Min A.; Copeland, Alex; Ivanova, Natalia N.
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Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives
err2021-06-15
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errIwata, Mana; Gutierrez, Ana; Marques, Gisela; Sabat, Grzegorz; Kersten, Philip J.; Cullen, Daniel; Bhatnagar, Jennifer M.; Yadav, Jagjit; Lipzen, Anna; Yoshinaga, Yuko; Sharma, Aditi; Adam, Catherine; Daum, Christopher; Ng, Vivian; Grigoriev, Igor V.; Hori, Chiaki
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101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens
err2020-06-01
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errHaridas, S.; Albert, R.; Binder, M.; Bloem, J.; LaButti, K.; Salamov, A.; Andreopoulos, B.; Baker, S. E.; Barry, K.; Bills, G.; Bluhm, B. H.; Cannon, C.; Castanera, R.; Culley, D. E.; Daum, C.; Ezra, D.; Gonzalez, J. B.; Henrissat, B.; Kuo, A.; Liang, C.; Lipzen, A.; Lutzoni, F.; Magnuson, J.; Mondo, S. J.; Nolan, M.; Ohm, R. A.; Pangilinan, J.; Park, H-J; Ramirez, L.; Alfaro, M.; Sun, H.; Tritt, A.; Yoshinaga, Y.; Zwiers, L-H; Turgeon, B. G.; Goodwin, S. B.; Spatafora, J. W.; Crous, P. W.; Grigoriev, I., V
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