Found: 18

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  • A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset.

    Published in:
    BMC Biology, 2024, v. 22, n. 1, p. 1, doi. 10.1186/s12915-024-01820-5
    By:
    • Zhou, Yong;
    • Kathiresan, Nagarajan;
    • Yu, Zhichao;
    • Rivera, Luis F.;
    • Yang, Yujian;
    • Thimma, Manjula;
    • Manickam, Keerthana;
    • Chebotarov, Dmytro;
    • Mauleon, Ramil;
    • Chougule, Kapeel;
    • Wei, Sharon;
    • Gao, Tingting;
    • Green, Carl D.;
    • Zuccolo, Andrea;
    • Xie, Weibo;
    • Ware, Doreen;
    • Zhang, Jianwei;
    • McNally, Kenneth L.;
    • Wing, Rod A.
    Publication type:
    Article

  • Ensembl 2024.

    Published in:
    Nucleic Acids Research, 2024, v. 52, n. D1, p. D891, doi. 10.1093/nar/gkad1049
    By:
    • Harrison, Peter W;
    • Amode, M Ridwan;
    • Austine-Orimoloye, Olanrewaju;
    • Azov, Andrey G;
    • Barba, Matthieu;
    • Barnes, If;
    • Becker, Arne;
    • Bennett, Ruth;
    • Berry, Andrew;
    • Bhai, Jyothish;
    • Bhurji, Simarpreet Kaur;
    • Boddu, Sanjay;
    • Branco Lins, Paulo R;
    • Brooks, Lucy;
    • Ramaraju, Shashank Budhanuru;
    • Campbell, Lahcen I;
    • Martinez, Manuel Carbajo;
    • Charkhchi, Mehrnaz;
    • Chougule, Kapeel;
    • Cockburn, Alexander
    Publication type:
    Article

  • Engineering homoeologs provide a fine scale for quantitative traits in polyploid.

    Published in:
    Plant Biotechnology Journal, 2023, v. 21, n. 12, p. 2458, doi. 10.1111/pbi.14141
    By:
    • Lee, Eun Song;
    • Heo, Jung;
    • Bang, Woo Young;
    • Chougule, Kapeel M.;
    • Waminal, Nomar Espinosa;
    • Hong, Nguyen Thi;
    • Kim, Min Ji;
    • Beak, Hong Kwan;
    • Kim, Yong Jun;
    • Priatama, Ryza A.;
    • Jang, Ji In;
    • Cha, Kang Il;
    • Son, Seung Han;
    • Rajendran, Sujeevan;
    • Choo, Young‐Kug;
    • Bae, Jong Hyang;
    • Kim, Chul Min;
    • Lee, Young Koung;
    • Bae, Sangsu;
    • Jones, Jonathan D. G.
    Publication type:
    Article

  • Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud.

    Published in:
    G3: Genes | Genomes | Genetics, 2023, v. 13, n. 10, p. 1, doi. 10.1093/g3journal/jkad174
    By:
    • Ntakirutimana, Fabrice;
    • Tranchant-Dubreuil, Christine;
    • Cubry, Philippe;
    • Chougule, Kapeel;
    • Zhang, Jianwei;
    • Wing, Rod A.;
    • Adam, Hélène;
    • Lorieux, Mathias;
    • Jouannic, Stefan
    Publication type:
    Article

  • Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice.

    Published in:
    Nature Communications, 2023, p. 1, doi. 10.1038/s41467-023-37004-y
    By:
    • Zhou, Yong;
    • Yu, Zhichao;
    • Chebotarov, Dmytro;
    • Chougule, Kapeel;
    • Lu, Zhenyuan;
    • Rivera, Luis F.;
    • Kathiresan, Nagarajan;
    • Al-Bader, Noor;
    • Mohammed, Nahed;
    • Alsantely, Aseel;
    • Mussurova, Saule;
    • Santos, João;
    • Thimma, Manjula;
    • Troukhan, Maxim;
    • Fornasiero, Alice;
    • Green, Carl D.;
    • Copetti, Dario;
    • Kudrna, David;
    • Llaca, Victor;
    • Lorieux, Mathias
    Publication type:
    Article

  • Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes.

    Published in:
    Frontiers in Plant Science, 2023, v. 13, p. 1, doi. 10.3389/fpls.2022.1040909
    By:
    • Voelker, William G.;
    • Krishnan, Krittika;
    • Chougule, Kapeel;
    • Alexander Jr., Louie C.;
    • Zhenyuan Lu;
    • Olson, Andrew;
    • Ware, Doreen;
    • Songsomboon, Kittikun;
    • Ponce, Cristian;
    • Brenton, Zachary W.;
    • Boatwright, J. Lucas;
    • Cooper, Elizabeth A.
    Publication type:
    Article

  • Sorghum root epigenetic landscape during limiting phosphorus conditions.

    Published in:
    Plant Direct, 2022, v. 6, n. 5, p. 1, doi. 10.1002/pld3.393
    By:
    • Gladman, Nicholas;
    • Hufnagel, Barbara;
    • Regulski, Michael;
    • Liu, Zhigang;
    • Wang, Xiaofei;
    • Chougule, Kapeel;
    • Kochian, Leon;
    • Magalhães, Jurandir;
    • Ware, Doreen
    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

  • SorghumBase: a web-based portal for sorghum genetic information and community advancement.

    Published in:
    Planta: An International Journal of Plant Biology, 2022, v. 255, n. 2, p. 1, doi. 10.1007/s00425-022-03821-6
    By:
    • Gladman, Nicholas;
    • Olson, Andrew;
    • Wei, Sharon;
    • Chougule, Kapeel;
    • Lu, Zhenyuan;
    • Tello-Ruiz, Marcela;
    • Meijs, Ivar;
    • Van Buren, Peter;
    • Jiao, Yinping;
    • Wang, Bo;
    • Kumar, Vivek;
    • Kumari, Sunita;
    • Zhang, Lifang;
    • Burke, John;
    • Chen, Junping;
    • Burow, Gloria;
    • Hayes, Chad;
    • Emendack, Yves;
    • Xin, Zhanguo;
    • Ware, Doreen
    Publication type:
    Article

  • Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.

    Published in:
    Nucleic Acids Research, 2022, v. 50, n. D1, p. D996, doi. 10.1093/nar/gkab1007
    By:
    • Yates, Andrew D;
    • Allen, James;
    • Amode, Ridwan M;
    • Azov, Andrey G;
    • Barba, Matthieu;
    • Becerra, Andrés;
    • Bhai, Jyothish;
    • Campbell, Lahcen I;
    • Carbajo Martinez, Manuel;
    • Chakiachvili, Marc;
    • Chougule, Kapeel;
    • Christensen, Mikkel;
    • Contreras-Moreira, Bruno;
    • Cuzick, Alayne;
    • Da Rin Fioretto, Luca;
    • Davis, Paul;
    • De Silva, Nishadi H;
    • Diamantakis, Stavros;
    • Dyer, Sarah;
    • Elser, Justin
    Publication type:
    Article

  • Gene disruption by structural mutations drives selection in US rice breeding over the last century.

    Published in:
    PLoS Genetics, 2021, v. 17, n. 3, p. 1, doi. 10.1371/journal.pgen.1009389
    By:
    • Vaughn, Justin N.;
    • Korani, Walid;
    • Stein, Joshua C.;
    • Edwards, Jeremy D.;
    • Peterson, Daniel G.;
    • Simpson, Sheron A.;
    • Youngblood, Ramey C.;
    • Grimwood, Jane;
    • Chougule, Kapeel;
    • Ware, Doreen H.;
    • McClung, Anna M.;
    • Scheffler, Brian E.
    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

  • 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

  • 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

  • Double triage to identify poorly annotated genes in maize: The missing link in community curation.

    Published in:
    PLoS ONE, 2019, v. 14, n. 10, p. 1, doi. 10.1371/journal.pone.0224086
    By:
    • Tello-Ruiz, Marcela K.;
    • Marco, Cristina F.;
    • Hsu, Fei-Man;
    • Khangura, Rajdeep S.;
    • Qiao, Pengfei;
    • Sapkota, Sirjan;
    • Stitzer, Michelle C.;
    • Wasikowski, Rachael;
    • Wu, Hao;
    • Zhan, Junpeng;
    • Chougule, Kapeel;
    • Barone, Lindsay C.;
    • Ghiban, Cornel;
    • Muna, Demitri;
    • Olson, Andrew C.;
    • Wang, Liya;
    • Ware, Doreen;
    • Micklos, David A.
    Publication type:
    Article

  • Low-phosphate-selected Auxenochlorella protothecoides redirects phosphate to essential pathways while producing more biomass.

    Published in:
    PLoS ONE, 2018, v. 13, n. 6, p. 1, doi. 10.1371/journal.pone.0198953
    By:
    • Park, Sang-Hyuck;
    • Kyndt, John;
    • Chougule, Kapeel;
    • Park, Jeong-Jin;
    • Brown, Judith K.
    Publication type:
    Article

  • Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length.

    Published in:
    Euphytica, 2018, v. 214, n. 2, p. 1, doi. 10.1007/s10681-018-2119-1
    By:
    • Bhatia, Dharminder;
    • Wing, Rod A.;
    • Yu, Yeisoo;
    • Chougule, Kapeel;
    • Kudrna, Dave;
    • Lee, Seunghee;
    • Rang, Allah;
    • Singh, Kuldeep
    Publication type:
    Article

  • Gramene 2016: comparative plant genomics and pathway resources.

    Published in:
    Nucleic Acids Research, 2016, v. 44, n. 1, p. D1133, doi. 10.1093/nar/gkv1179
    By:
    • Tello-Ruiz, Marcela K.;
    • Stein, Joshua;
    • Wei, Sharon;
    • Preece, Justin;
    • Olson, Andrew;
    • Naithani, Sushma;
    • Amarasinghe, Vindhya;
    • Dharmawardhana, Palitha;
    • Jiao, Yinping;
    • Mulvaney, Joseph;
    • Kumari, Sunita;
    • Chougule, Kapeel;
    • Elser, Justin;
    • Wang, Bo;
    • Thomason, James;
    • Bolser, Daniel M.;
    • Kerhornou, Arnaud;
    • Walts, Brandon;
    • Fonseca, Nuno A.;
    • Huerta, Laura
    Publication type:
    Article