Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning

por Ho, Harrison, Chovatia, Mansi, Egan, Rob, He, Guifen, Yoshinaga, Yuko, Liachko, Ivan, O’Malley, Ronan, Wang, Zhong
Publicado 2023

The Genetic Architecture of Shoot and Root Trait Divergence Between Mesic and Xeric Ecotypes of a Perennial Grass

por Khasanova, Albina, Lovell, John T., Bonnette, Jason, Weng, Xiaoyu, Jenkins, Jerry, Yoshinaga, Yuko, Schmutz, Jeremy, Juenger, Thomas E.
Publicado 2019

Genomic prediction of switchgrass winter survivorship across diverse lowland populations

por Tilhou, Neal W, Poudel, Hari P, Lovell, John, Mamidi, Sujan, Schmutz, Jeremy, Daum, Christopher, Zane, Matthew, Yoshinaga, Yuko, Lipzen, Anna, Casler, Michael D
Publicado 2023

Draft Genome Sequence of a Rare Smut Relative, Tilletiaria anomala UBC 951

por Toome, Merje, Kuo, Alan, Henrissat, Bernard, Lipzen, Anna, Tritt, Andrew, Yoshinaga, Yuko, Zane, Matthew, Barry, Kerrie, Grigoriev, Igor V., Spatafora, Joseph W., Aime, M. Catherine
Publicado 2014

Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii

por Weng, 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
Publicado 2023

Marking Embryonic Stem Cells with a 2A Self-Cleaving Peptide: A NKX2-5 Emerald GFP BAC Reporter

por Hsiao, Edward C., Yoshinaga, Yuko, Nguyen, Trieu D., Musone, Stacy L., Kim, Judy E., Swinton, Paul, Espineda, Isidro, Manalac, Carlota, deJong, Pieter J., Conklin, Bruce R.
Publicado 2008

Reciprocal knock-in mice to investigate the functional redundancy of lamin B1 and lamin B2

por Lee, John M., Tu, Yiping, Tatar, Angelica, Wu, Daniel, Nobumori, Chika, Jung, Hea-Jin, Yoshinaga, Yuko, Coffinier, Catherine, de Jong, Pieter J., Fong, Loren G., Young, Stephen G.
Publicado 2014

High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

por Shulse, Christine N., Cole, Benjamin J., Ciobanu, Doina, Lin, Junyan, Yoshinaga, Yuko, Gouran, Mona, Turco, Gina M., Zhu, Yiwen, O’Malley, Ronan C., Brady, Siobhan M., Dickel, Diane E.
Publicado 2019

Deficiencies in lamin B1 and lamin B2 cause neurodevelopmental defects and distinct nuclear shape abnormalities in neurons

por Coffinier, Catherine, Jung, Hea-Jin, Nobumori, Chika, Chang, Sandy, Tu, Yiping, Barnes, Richard H., Yoshinaga, Yuko, de Jong, Pieter J., Vergnes, Laurent, Reue, Karen, Fong, Loren G., Young, Stephen G.
Publicado 2011

High-resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpa

por Abeyratne, Chanaka Roshan, Macaya-Sanz, David, Zhou, Ran, Barry, Kerrie W, Daum, Christopher, Haiby, Kathy, Lipzen, Anna, Stanton, Brian, Yoshinaga, Yuko, Zane, Matthew, Tuskan, Gerald A, DiFazio, Stephen P
Publicado 2022

Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives

por Iwata, Mana, Gutiérrez, 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
Publicado 2021

A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism

por Cooper, Elizabeth A., Brenton, Zachary W., Flinn, Barry S., Jenkins, Jerry, Shu, Shengqiang, Flowers, Dave, Luo, Feng, Wang, Yunsheng, Xia, Penny, Barry, Kerrie, Daum, Chris, Lipzen, Anna, Yoshinaga, Yuko, Schmutz, Jeremy, Saski, Christopher, Vermerris, Wilfred, Kresovich, Stephen
Publicado 2019

Comparative genomics of Mollicutes-related endobacteria supports a late invasion into Mucoromycota fungi

por Longley, 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., Desirò, Alessandro, Chain, Patrick S. G., Bonito, Gregory
Publicado 2023

Near-complete genome sequence of Lipomyces tetrasporous NRRL Y-64009, an oleaginous yeast capable of growing on lignocellulosic hydrolysates

por Jagtap, Sujit Sadashiv, Liu, Jing-Jing, Walukiewicz, Hanna E., Pangilinan, Jasmyn, Lipzen, Anna, Ahrendt, Steven, Koriabine, Maxim, Cobaugh, Kelly, Salamov, Asaf, Yoshinaga, Yuko, Ng, Vivian, Daum, Chris, Grigoriev, Igor V., Slininger, Patricia J., Dien, Bruce S., Jin, Yong-Su, Rao, Christopher V.
Publicado 2023

Near-Complete Genome Sequence of Zygosaccharomyces rouxii NRRL Y-64007, a Yeast Capable of Growing on Lignocellulosic Hydrolysates

por Jagtap, Sujit Sadashiv, Liu, Jing-Jing, Walukiewicz, Hanna E., Pangilinan, Jasmyn, Lipzen, Anna, Ahrendt, Steven, Koriabine, Maxim, Cobaugh, Kelly, Salamov, Asaf, Yoshinaga, Yuko, Ng, Vivian, Daum, Chris, Grigoriev, Igor V., Slininger, Patricia J., Dien, Bruce S., Jin, Yong-Su, Rao, Christopher V.
Publicado 2022

Multiplex knockout of trichome-regulating MYB duplicates in hybrid poplar using a single gRNA

por Bewg, William P, 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
Publicado 2022

The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory

por Craig, Rory J, Gallaher, Sean D, Shu, Shengqiang, Salomé, 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
Publicado 2022

DOE JGI Metagenome Workflow

por Clum, 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.
Publicado 2021

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

por Van 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.
Publicado 2021

The genomic landscape of molecular responses to natural drought stress in Panicum hallii

por Lovell, John T., Jenkins, Jerry, Lowry, David B., Mamidi, Sujan, Sreedasyam, Avinash, Weng, Xiaoyu, Barry, Kerrie, Bonnette, Jason, Campitelli, Brandon, Daum, Chris, Gordon, Sean P., Gould, Billie A., Khasanova, Albina, Lipzen, Anna, MacQueen, Alice, Palacio-Mejía, Juan Diego, Plott, Christopher, Shakirov, Eugene V., Shu, Shengqiang, Yoshinaga, Yuko, Zane, Matt, Kudrna, Dave, Talag, Jason D., Rokhsar, Daniel, Grimwood, Jane, Schmutz, Jeremy, Juenger, Thomas E.
Publicado 2018