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Integrating GWAS and gene expression data for functional characterization of resistance to white mould in soya bean.
Published in:
Plant Biotechnology Journal, 2018, v. 16, n. 11, p. 1825, doi. 10.1111/pbi.12918
By:
- Wen, Zixiang;
- Tan, Ruijuan;
- Zhang, Shichen;
- Collins, Paul J.;
- Yuan, Jiazheng;
- Du, Wenyan;
- Gu, Cuihua;
- Ou, Shujun;
- Song, Qijian;
- An, Yong‐Qiang Charles;
- Boyse, John F.;
- Chilvers, Martin I.;
- Wang, Dechun
Publication type:
Article
Chromosome-Scale Genome for a Red-Fruited, Perpetual Flowering and Runnerless Woodland Strawberry (Fragaria vesca).
Published in:
Frontiers in Genetics, 2021, v. 12, p. 1, doi. 10.3389/fgene.2021.671371
By:
- Alger, Elizabeth I.;
- Platts, Adrian E.;
- Deb, Sontosh K.;
- Luo, Xi;
- Ou, Shujun;
- Cao, Yao;
- Hummer, Kim E.;
- Xiong, Zhiyong;
- Knapp, Steven J.;
- Liu, Zhongchi;
- McKain, Michael R.;
- Edger, Patrick P.
Publication type:
Article
Assessing genome assembly quality using the LTR Assembly Index (LAI).
Published in:
Nucleic Acids Research, 2018, v. 46, n. 21, p. e126, doi. 10.1093/nar/gky730
By:
- Ou, Shujun;
- Chen, Jinfeng;
- Jiang, Ning
Publication type:
Article
Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies.
Published in:
Nature Genetics, 2015, v. 47, n. 7, p. 834, doi. 10.1038/ng.3337
By:
- Hu, Bin;
- Tang, Jiuyou;
- Che, Ronghui;
- Wang, Yiqin;
- Liang, Chengzhen;
- Xu, Chi;
- Chu, Chengcai;
- Wang, Wei;
- Li, Hua;
- Zhang, Zhihua;
- Wang, Hongru;
- Liang, Yan;
- Ou, Shujun;
- Chai, Xuyang;
- Li, Legong;
- Liu, Linchuan;
- Piao, Zhongze;
- Deng, Qiyun;
- Deng, Kun;
- Zhang, Lianhe
Publication type:
Article
Construction of a chromosome-scale long-read reference genome assembly for potato.
Published in:
GigaScience, 2020, v. 9, n. 9, p. 1, doi. 10.1093/gigascience/giaa100
By:
- Pham, Gina M;
- Hamilton, John P;
- Wood, Joshua C;
- Burke, Joseph T;
- Zhao, Hainan;
- Vaillancourt, Brieanne;
- Ou, Shujun;
- Jiang, Jiming;
- Buell, C Robin
Publication type:
Article
Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry.
Published in:
GigaScience, 2019, v. 8, n. 3, p. N.PAG, doi. 10.1093/gigascience/giz012
By:
- Colle, Marivi;
- Leisner, Courtney P;
- Wai, Ching Man;
- Ou, Shujun;
- Bird, Kevin A;
- Wang, Jie;
- Wisecaver, Jennifer H;
- Yocca, Alan E;
- Alger, Elizabeth I;
- Tang, Haibao;
- Xiong, Zhiyong;
- Callow, Pete;
- Ben-Zvi, Gil;
- Brodt, Avital;
- Baruch, Kobi;
- Swale, Thomas;
- Shiue, Lily;
- Song, Guo-qing;
- Childs, Kevin L;
- Schilmiller, Anthony
Publication type:
Article
Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity.
Published in:
GigaScience, 2018, v. 7, n. 2, p. 1, doi. 10.1093/gigascience/gix124
By:
- Edger, Patrick P.;
- VanBuren, Robert;
- Colle, Marivi;
- Poorten, Thomas J.;
- Ching Man Wai;
- Niederhuth, Chad E.;
- Alger, Elizabeth I.;
- Shujun Ou;
- Acharya, Charlotte B.;
- Jie Wang;
- Callow, Pete;
- McKain, Michael R.;
- Jinghua Shi;
- Collier, Chad;
- Zhiyong Xiong;
- Mower, Jeffrey P.;
- Slovin, Janet P.;
- Hytönen, Timo;
- Ning Jiang;
- Childs, Kevin L.
Publication type:
Article
A haplotype resolved chromosome‐scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus.
Published in:
Plant Journal, 2023, v. 116, n. 4, p. 989, doi. 10.1111/tpj.16433
By:
- Mansfeld, Ben N.;
- Yocca, Alan;
- Ou, Shujun;
- Harkess, Alex;
- Burchard, Erik;
- Gutierrez, Benjamin;
- van Nocker, Steve;
- Gottschalk, Christopher
Publication type:
Article
Distinct composition and amplification dynamics of transposable elements in sacred lotus (Nelumbo nucifera Gaertn.).
Published in:
Plant Journal, 2022, v. 112, n. 1, p. 172, doi. 10.1111/tpj.15938
By:
- Cerbin, Stefan;
- Ou, Shujun;
- Li, Yang;
- Sun, Yanni;
- Jiang, Ning
Publication type:
Article
Large structural variations in the haplotype‐resolved African cassava genome.
Published in:
Plant Journal, 2021, v. 108, n. 6, p. 1830, doi. 10.1111/tpj.15543
By:
- Mansfeld, Ben N.;
- Boyher, Adam;
- Berry, Jeffrey C.;
- Wilson, Mark;
- Ou, Shujun;
- Polydore, Seth;
- Michael, Todd P.;
- Fahlgren, Noah;
- Bart, Rebecca S.
Publication type:
Article
Genomic variation within the maize stiff‐stalk heterotic germplasm pool.
Published in:
Plant Genome, 2021, v. 14, n. 3, p. 1, doi. 10.1002/tpg2.20114
By:
- Bornowski, 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.;
- de Leon, Natalia
Publication type:
Article
Author Correction: Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline.
Published in:
2022
By:
- Ou, Shujun;
- Su, Weijia;
- Liao, Yi;
- Chougule, Kapeel;
- Agda, Jireh R. A.;
- Hellinga, Adam J.;
- Lugo, Carlos Santiago Blanco;
- Elliott, Tyler A.;
- Ware, Doreen;
- Peterson, Thomas;
- Jiang, Ning;
- Hirsch, Candice N.;
- Hufford, Matthew B.
Publication type:
Correction Notice
How the pan-genome is changing crop genomics and improvement.
Published in:
Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02224-8
By:
- Della Coletta, Rafael;
- Qiu, Yinjie;
- Ou, Shujun;
- Hufford, Matthew B.;
- Hirsch, Candice N.
Publication type:
Article
Correction to: OsbZIP71, a bZIP transcription factor, confers salinity and drought tolerance in rice.
Published in:
2018
By:
- Liu, Citao;
- Mao, Bigang;
- Ou, Shujun;
- Wang, Wei;
- Liu, Linchuan;
- Wu, Yanbin;
- Chu, Chengcai;
- Wang, Xiping
Publication type:
Correction Notice
OsbZIP71, a bZIP transcription factor, confers salinity and drought tolerance in rice.
Published in:
Plant Molecular Biology, 2014, v. 84, n. 1-2, p. 19, doi. 10.1007/s11103-013-0115-3
By:
- Liu, Citao;
- Mao, Bigang;
- Ou, Shujun;
- Wang, Wei;
- Liu, Linchuan;
- Wu, Yanbin;
- Chu, Chengcai;
- Wang, Xiping
Publication type:
Article
Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.
Published in:
Molecular Biology & Evolution, 2024, v. 41, n. 5, p. 1, doi. 10.1093/molbev/msae095
By:
- Hu, Guanjing;
- Grover, Corrinne E;
- Vera, Daniel L;
- Lung, Pei-Yau;
- Girimurugan, Senthil B;
- Miller, Emma R;
- Conover, Justin L;
- Ou, Shujun;
- Xiong, Xianpeng;
- Zhu, De;
- Li, Dongming;
- Gallagher, Joseph P;
- Udall, Joshua A;
- Sui, Xin;
- Zhang, Jinfeng;
- Bass, Hank W;
- Wendel, Jonathan F
Publication type:
Article
Expression of the Nitrate Transporter Gene OsNRT1.1A/OsNPF6.3 Confers High Yield and Early Maturation in Rice.
Published in:
Plant Cell, 2018, v. 30, n. 3, p. 638, doi. 10.1105/tpc.17.00809
By:
- Wang, Wei;
- Hu, Bin;
- Yuan, Dingyang;
- Liu, Yongqiang;
- Che, Ronghui;
- Hu, Yingchun;
- Ou, Shujun;
- Liu, Yongxin;
- Zhang, Zhihua;
- Wang, Hongru;
- Li, Hua;
- Jiang, Zhimin;
- Zhang, Zhengli;
- Gao, Xiaokai;
- Qiu, Yahong;
- Meng, Xiangbing;
- Bai, Yang;
- Liang, Yan;
- Wang, Yiqin;
- Zhang, Lianhe
Publication type:
Article
Accelerating de novo SINE annotation in plant and animal genomes.
Published in:
Mobile DNA, 2024, v. 15, n. 1, p. 1, doi. 10.1186/s13100-024-00331-y
By:
- Liao, Herui;
- Sun, Yanni;
- Ou, Shujun
Publication type:
Article
LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons.
Published in:
Mobile DNA, 2019, v. 10, n. 1, p. 1, doi. 10.1186/s13100-019-0193-0
By:
- Ou, Shujun;
- Jiang, Ning
Publication type:
Article
Response to Commentary: Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies.
Published in:
2024
By:
- Ou, Shujun;
- Jiang, Ning;
- Hirsch, Candice N.;
- Hufford, Matthew B.
Publication type:
Letter
Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing.
Published in:
Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02823-7
By:
- Alonge, Michael;
- Lebeigle, Ludivine;
- Kirsche, Melanie;
- Jenike, Katie;
- Ou, Shujun;
- Aganezov, Sergey;
- Wang, Xingang;
- Lippman, Zachary B.;
- Schatz, Michael C.;
- Soyk, Sebastian
Publication type:
Article
Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus.
Published in:
New Phytologist, 2021, v. 230, n. 1, p. 354, doi. 10.1111/nph.17137
By:
- Bird, Kevin A.;
- Niederhuth, Chad E.;
- Ou, Shujun;
- Gehan, Malia;
- Pires, J. Chris;
- Xiong, Zhiyong;
- VanBuren, Robert;
- Edger, Patrick P.
Publication type:
Article
Variations in CYP 78 A 13 coding region influence grain size and yield in rice.
Published in:
Plant, Cell & Environment, 2015, v. 38, n. 4, p. 800, doi. 10.1111/pce.12452
By:
- XU, FAN;
- FANG, JUN;
- OU, SHUJUN;
- GAO, SHAOPEI;
- ZHANG, FENGXIA;
- DU, LIN;
- XIAO, YUNHUA;
- WANG, HONGRU;
- SUN, XIAOHONG;
- CHU, JINFANG;
- WANG, GUODONG;
- CHU, CHENGCAI
Publication type:
Article
Extreme haplotype variation in the desiccation-tolerant clubmoss Selaginella lepidophylla.
Published in:
Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-017-02546-5
By:
- Ching Man Wai;
- Buren, Robert Van;
- Shujun Ou;
- Jiang, Ning;
- Edger, Patrick;
- Pardo, Jeremy;
- Bryant, Doug;
- Mockler, Todd C.;
- Michae, Todd P.
Publication type:
Article
LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons.
Published in:
Plant Physiology, 2018, v. 176, n. 2, p. 1410, doi. 10.1104/pp.17.01310
By:
- Shujun Ou;
- Ning Jiang
Publication type:
Article
Gapless assembly of maize chromosomes using long-read technologies.
Published in:
Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02029-9
By:
- Liu, Jianing;
- Seetharam, Arun S.;
- Chougule, Kapeel;
- Ou, Shujun;
- Swentowsky, Kyle W.;
- Gent, Jonathan I.;
- Llaca, Victor;
- Woodhouse, Margaret R.;
- Manchanda, Nancy;
- Presting, Gernot G.;
- Kudrna, David A.;
- Alabady, Magdy;
- Hirsch, Candice N.;
- Fengler, Kevin A.;
- Ware, Doreen;
- Michael, Todd P.;
- Hufford, Matthew B.;
- Dawe, R. Kelly
Publication type:
Article
Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline.
Published in:
Genome Biology, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s13059-019-1905-y
By:
- Ou, Shujun;
- Su, Weija;
- Liao, Yi;
- Chougule, Kapeel;
- Agda, Jireh R. A.;
- Hellinga, Adam J.;
- Lugo, Carlos Santiago Blanco;
- Elliott, Tyler A.;
- Ware, Doreen;
- Peterson, Thomas;
- Jiang, Ning;
- Hirsch, Candice N.;
- Hufford, Matthew B.
Publication type:
Article
Natural variations of SLG1 confer high-temperature tolerance in indica rice.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-19320-9
By:
- Xu, Yufang;
- Zhang, Li;
- Ou, Shujun;
- Wang, Ruci;
- Wang, Yueming;
- Chu, Chengcai;
- Yao, Shanguo
Publication type:
Article
Effect of sequence depth and length in long-read assembly of the maize inbred NC358.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-16037-7
By:
- Ou, Shujun;
- Liu, Jianing;
- Chougule, Kapeel M.;
- Fungtammasan, Arkarachai;
- Seetharam, Arun S.;
- Stein, Joshua C.;
- Llaca, Victor;
- Manchanda, Nancy;
- Gilbert, Amanda M.;
- Wei, Sharon;
- Chin, Chen-Shan;
- Hufnagel, David E.;
- Pedersen, Sarah;
- Snodgrass, Samantha J.;
- Fengler, Kevin;
- Woodhouse, Margaret;
- Walenz, Brian P.;
- Koren, Sergey;
- Phillippy, Adam M.;
- Hannigan, Brett T.
Publication type:
Article
A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.).
Published in:
DNA Research, 2023, v. 30, n. 1, p. 1, doi. 10.1093/dnares/dsac033
By:
- McGrath, J Mitchell;
- Funk, Andrew;
- Galewski, Paul;
- Ou, Shujun;
- Townsend, Belinda;
- Davenport, Karen;
- Daligault, Hajnalka;
- Johnson, Shannon;
- Lee, Joyce;
- Hastie, Alex;
- Darracq, Aude;
- Willems, Glenda;
- Barnes, Steve;
- Liachko, Ivan;
- Sullivan, Shawn;
- Koren, Sergey;
- Phillippy, Adam;
- Wang, Jie;
- Liu, Tiffany;
- Pulman, Jane
Publication type:
Article

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