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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » People & Locations » Yong Gu

Yong Qiang Gu
Crop Improvement and Genetics Research
Research Leader

Phone: (510) 559-5732
Fax: (510) 559-5818

USDA, ARS, PWA, WRRC-CIG
800 BUCHANAN STREET
ALBANY, CA 94710
Projects
New Genetic Resources for Breeding Better Wheat and Bioenergy Crops
In-House Appropriated (D)
  Accession Number: 434193
Molecular Genetic Tools Advancing the Application of Biotechnology for Crop Improvement
In-House Appropriated (D)
  Accession Number: 434430
GrainGenes: Enabling Data Access and Sustainability for Small Grains Researchers
In-House Appropriated (D)
  Accession Number: 434601
A Genomics-Based Approach to the Improvement of Agronomically Important Traits in Wheat
Non-Assistance Cooperative Agreement (S)
  Accession Number: 433561
Characterization of the Complete Set of Prolamin Genes and Proteins Expressed in the Korean Wheat ‘Keumkang’
Trust Fund Cooperative Agreement (T)
  Accession Number: 434220

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Low prevalence of mobile colistin-resistance in U.S. meat, catfish, poultry and genomic characterization of a mcr-1 positive Escherichia coli strain Reprint Icon - (Peer Reviewed Journal)
Wang, Y., Hou, N., Johnston, J., Sarreal, C., Jarosh, J., Hughes, A.C., Gu, Y.Q., He, X. 2020. Low prevalence of mobile colistin-resistance in U.S. meat, catfish, poultry and genomic characterization of a mcr-1 positive Escherichia coli strain. Food Control. 118:10734. https://doi.org/10.1016/j.foodcont.2020.107434.
A rare single nucleotide variant in Pm5e confers powdery mildew resistance in common wheat Reprint Icon - (Peer Reviewed Journal)
Xie, J., Guo, G., Wang, Y., Hu, T., Wang, L., Li, J., Qiu, D., Li, Y., Wu, Q., Lu, P., Chen, Y., Dong, L., Li, M., Zhang, H., Zhang, P., Zhu, K., Li, B., Deal, K., Huo, N., Zhang, Y., Luo, M., Liu, S., Gu, Y.Q., Li, H., Liu, Z. 2020. A rare single nucleotide variant in Pm5e confers powdery mildew resistance in common wheat. New Phytologist. https://doi.org/10.1111/nph.16762.
A rare gain of function mutation in a wheat tandem kinase confers resistance to powdery mildew Reprint Icon - (Peer Reviewed Journal)
Lu, P., Guo, L., Wang, Z., Li, B., Li, J., Li, Y., Qiu, D., Shi, W., Yang, L., Wang, N., Guo, G., Xie, J., Wu, Q., Chen, Y., Li, M., Zhang, H., Dong, L., Zhang, P., Zhu, K., Yu, D., Zhang, Y., Deal, K., Huo, N., Liu, C., Luo, M., Dvorak, J., Gu, Y.Q., Li, H., Liu, Z. 2020. A rare gain of function mutation in a wheat tandem kinase confers resistance to powdery mildew. Nature Communications. 11. https://doi.org/10.1038/s41467-020-14294-0.
Molecular characterization of Hessian fly resistance genes in Aegilops tauschii - (Abstract Only)
Long, Y., Zhang, Q., Anderson, K.M., Yu, G., Arora, S., Steuernagel, B., Luo, M., Cai, X., Gu, Y.Q., Wuddineh, W., Faris, J.D., Chen, M., Xu, S.S., Wulff, B.H., Lagudah, E.S., Harris, M.O. 2020. Molecular characterization of Hessian fly resistance genes in Aegilops tauschii [abstract]. Plant and Animal Genome Conference XXVIII. W809.
Draft genome sequence of Agrobacterium tumefaciens strain 1D1526 Reprint Icon - (Peer Reviewed Journal)
Huo, N., Gu, Y.Q., Mc Cue, K.F., Alabed, D., Thomson, J.G. 2019. Draft genome sequence of Agrobacterium tumefaciens strain 1D1526. Microbiology Resource Announcements. 8(45). https://doi.org/10.1128/MRA.01084-19.
Exploiting the reference genome sequence of hexaploid wheat: a proteomic study of flour proteins from the cultivar Chinese Spring Reprint Icon - (Peer Reviewed Journal)
Altenbach, S.B., Chang, H., Simon-Buss, A., Mohr, T.J., Huo, N., Gu, Y.Q. 2019. Exploiting the reference genome sequence of hexaploid wheat: a proteomic study of flour proteins from the cultivar Chinese Spring. Functional and Integrative Genomics. 1-16. https://doi.org/10.1007/s10142-019-00694-z.
Rapid evolution of alpha-gliadin gene family revealed by analyzing Gli-2 locus regions of wild emmer wheat Reprint Icon - (Peer Reviewed Journal)
Huo, N., Zhu, T., Zhang, S., Mohr, T.J., Luo, M., Lee, J., Distelfeld, A., Altenbach, S.B., Gu, Y.Q. 2019. Rapid evolution of alpha-gliadin gene family revealed by analyzing Gli-2 locus regions of wild emmer wheat. Functional and Integrative Genomics. https://doi.org/10.1007/s10142-019-00686-z.
OrthoVenn2: a web server for the whole-genome comparison and annotation of orthologous clusters across multiple species Reprint Icon - (Peer Reviewed Journal)
Xu, L., Dong, Z., Fang, L., Luo, Y., Wei, Z., Guo, H., Zhang, G., Gu, Y.Q., Coleman-Derr, D.A., Xia, Q., Wang, Y. 2019. OrthoVenn2: a web server for the whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Research. 47(W1):W52-W58. https://doi.org/10.1093/nar/gkz333.
GrainGenes: centralized small grain resources and digital platform for geneticists and breeders - (Peer Reviewed Journal)
Blake, V.C., Woodhouse, M.R., Lazo, G.R., Odell, S.G., Wight, C.W., Tinker, N.A., Wang, Y., Gu, Y.Q., Birkett, C.L., Jannink, J., Matthews, D.E., Hane, D.L., Michel, S.L., Yao, E., Sen, T.Z. 2019. GrainGenes: centralized small grain resources and digital platform for geneticists and breeders. Database: The Journal of Biological Databases and Curation. 2019.
Complete genome sequence of Agrobacterium fabrum strain 1D159 Reprint Icon - (Peer Reviewed Journal)
Huo, N., Gu, Y.Q., McCue, K.F., Alabed, D., Thomson, J.G. 2019. Complete genome sequence of Agrobacterium fabrum strain 1D159. Microbiology Resource Announcements. 8(19):e00207-19. https://doi.org/10.1128/MRA.00207-19.
Draft genome sequence of serratia sp. 1D1416 Reprint Icon - (Peer Reviewed Journal)
Alabed, D.F., Huo, N., Gu, Y.Q., McCue, K.F., Thomson, J.G. 2019. Draft genome sequence of serratia sp. 1D1416. Microbiology Resource Announcements. 8(3):e01354-18. https://doi.org/10.1128/MRA.01354-18.
Towards reducing the immunogenic potential of wheat flour: Omega gliadins encoded by the D genome of hexaploid may also harbor epitopes for the serious food allergy WDEIA Reprint Icon - (Peer Reviewed Journal)
Altenbach, S.B., Chang, H., Simon-Buss, A., Jang, Y., Denery-Papini, S., Pineau, F., Gu, Y.Q., Huo, N., Lim, S., Kang, C., Lee, J. 2018. Towards reducing the immunogenic potential of wheat flour: Omega gliadins encoded by the D genome of hexaploid may also harbor epitopes for the serious food allergy WDEIA. Biomed Central (BMC) Plant Biology. 18:291. https://doi.org/10.1186/s12870-018-1506-z.
Cloning and characterization of the homoeologous genes for the Rec8-like meiotic cohesin in polyploid wheat Reprint Icon - (Peer Reviewed Journal)
Ma, G., Zhang, W., Liu, L., Chao, W.S., Gu, Y.Q., Qi, L., Xu, S.S., Cai, X. 2018. Cloning and characterization of the homoeologous genes for the Rec8-like meiotic cohesin in polyploid wheat. Biomed Central (BMC) Plant Biology. 18:224. https://doi.org/10.1186/s12870-018-1442-y.
Reassessment of the evolution of wheat chromosomes 4A, 5A, and 7B Reprint Icon - (Peer Reviewed Journal)
Dvorak, J., Wang, L., Zhu, T., Jorgensen, C.M., Luo, M., Deal, K.R., Gu, Y.Q., Gill, B.S., Distelfeld, A., Devos, K.M., Qi, P., Mcguire, P.E. 2018. Reassessment of the evolution of wheat chromosomes 4A, 5A, and 7B. Theoretical and Applied Genetics. https://doi: 10.1007/s00122-018-3165-8.
Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size Reprint Icon - (Peer Reviewed Journal)
Dvorak, J., Wang, L., Zhu, T., Jorgensen, C.M., Dai, X., Muller, H., Luo, M., Dehghani, H., Gu, Y.Q., Salzberg, S., Gill, B.S., Distelfeld, A., Devos, K.M., Bennetzen, J.L., You, F.M., McGuire, P.E. 2018. Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size. Plant Journal. 95(3):487-503. https://doi.org/10.1111/tpj.13964.
Gene duplication and evolution dynamics in the homeologous regions harboring multiple prolamin and resistance gene families in hexaploid wheat Reprint Icon - (Peer Reviewed Journal)
Huo, N., Zhang, S., Zhu, T., Dong, L., Wang, Y., Mohr, T.J., Hu, T., Liu, Z., Dvorak, J., Luo, M., Wang, D., Lee, J., Altenbach, S.B., Gu, Y.Q. 2018. Gene duplication and evolution dynamics in the homeologous regions harboring multiple prolamin and resistance gene families in hexaploid wheat. Frontiers in Plant Science. 9:673. https://doi.org/10.3389/fpls.2018.00673.
Analysis of Gli-D2 locus identifies a genetic target for simultaneously improving the breadmaking and health related traits of common wheat Reprint Icon - (Peer Reviewed Journal)
Li, D., Jin, H., Zhang, K., Wang, Z., Wang, F., Zhao, Y., Huo, N., Liu, X., Gu, Y.Q., Wang, D., Dong, L. 2018. Analysis of Gli-D2 locus identifies a genetic target for simultaneously improving the breadmaking and health related traits of common wheat. Plant Journal. 95(3):414-426. https://doi.org/10.1111/tpj.13956.
Dynamic evolution of alpha-gliadin prolamin gene family in homeologous genomes of hexaploid wheat Reprint Icon - (Peer Reviewed Journal)
Huo, N., Zhu, T., Altenbach, S.B., Dong, L., Wang, W., Mohr, T.J., Liu, Z., Dvorak, J., Wang, D., Luo, M., Gu, Y.Q. 2018. Dynamic evolution of alpha-gliadin prolamin gene family in homeologous genomes of hexaploid wheat. Scientific Reports. 8:5181. https://doi.org/10.1038/s41598-018-23570-5.
Genome sequence of the progenitor of the wheat D genome Aegilops tauschii Reprint Icon - (Peer Reviewed Journal)
Luo, M., Gu, Y.Q., Daniela, P., Hao, W., Deal, K., Huo, N., Zhu, T., Wang, L., Wang, Y., Mcguire, P., Liu, S., Long, H., Ramasamy, R., Rodriguez, J., Sonny, V., Yuan, L., Wang, Z., Xia, Z., Xiao, L., Anderson, O.D., Ouyang, S., Liang, Y., Zimin, A., Pertea, G., Dai, X., Dawson, M., Muller, H., Twardziok, S., Kugler, K., Spannagl, M., Mayer, K., Leroy, P., Li, P., You, F., Sun, Q., Li, Z., Lyons, E., Wicker, T., Salzberg, S., Devos, K., Dvorak, J., Bennetzen, J. 2017. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature. 551:498-502. doi:10.1038/nature24486.
New insights into structural organization and gene duplication in a 1.75-Mb chromosomal region harboring the alpha-gliadin gene family in Aegilops tauschii Reprint Icon - (Peer Reviewed Journal)
Huo, N., Dong, L., Zhang, S., Wang, Y., Zhu, T., Mohr, T.J., Altenbach, S.B., Liu, Z., Dvorak, J., Anderson, O.D., Luo, M., Wang, D., Gu, Y.Q. 2017. New insights into structural organization and gene duplication in a 1.75-Mb chromosomal region harboring the alpha-gliadin gene family in Aegilops tauschii. Plant Journal. 92(4):571–583. https://doi.org/10.1111/tpj.13675.
Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection - (Peer Reviewed Journal)
Hsia, M., O'Malley, R., Cartwright, A., Nieu, R., Gordon, S., Kelly, S., Williams, T.G., Wood, D.F., Zhao, Y., Bragg, J.N., Jordan, M., Pauly, M., Ecker, J., Gu, Y.Q., Vogel, J.P. 2017. Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection. Plant Journal. doi: 10.1111/tpj.13582.
A TRIM insertion in the promoter of Ms2 causes male sterility in wheat - (Peer Reviewed Journal)
Xia, C., Zhang, L., Zou, C., Gu, Y.Q., Duan, J., Zhao, G., Wu, J., Liu, Y., Fang, X., Gao, L., Jiao, Y., Sun, J., Pan, Y., Liu, X., Jia, J., Kong, X. 2017. A TRIM insertion in the promoter of Ms2 causes male sterility in wheat. Nature Communications. 8:15407. doi: 10:1038/ncomms15407
Deep sequencing and transcriptome analyses to identify genes involved in secoiridoid biosynthesis in Tibetan medicinal plant Sewertia mussotii - (Peer Reviewed Journal)
Liu, Y., Wang, Y., Guo, F., Zhan, L., Mohr, T.J., Cheng, P.K., Huo, N., Gu, R., Pei, D., Sun, J., Tang, L., Long, C., Huang, L., Gu, Y.Q. 2017. Deep sequencing and transcriptome analyses to identify genes involved in secoiridoid biosynthesis in Tibetan medicinal plant Sewertia mussotii. Scientific Reports. 7:43108. doi: 10.1038/srep43108.
Genome resources for climate-resilient cowpea, an essential crop for food security - (Peer Reviewed Journal)
Munoz-Amatriain, M., Mirebrahim, H., Xu, P., Wannamaker, S., Luo, M., Alhakami, H., Alpert, M., Atokple, I.K., Batieno, J., Boukar, O., Bozdag, S., Cisse, N., Drabo, I., Ehlers, J., Farmer, A., Fatokun, C., Gu, Y.Q., Guo, Y., Huynh, B., Jackson, S., Kusi, F., Lawley, C.T., Lucas, M.R., Ma, Y., Timko, M.P., Wu, J., You, F., Barkley, N.L., Roberts, P.A., Lonardi, S., Close, T.J. 2017. Genome resources for climate-resilient cowpea, an essential crop for food security. Plant Journal. 89:1042-1054 doi: 10.1111/tpj.13404.
PIECE 2.0: an update for the plant gene structure comparison and evolution database Reprint Icon - (Peer Reviewed Journal)
Wang, Y., Xu, L., Thilmony, R.L., You, F., Gu, Y.Q., Coleman-Derr, D.A. 2016. PIECE 2.0: an update for the plant gene structure comparison and evolution database. Nucleic Acids Research. 45(D1):1015-1020. https://doi.org/10.1093/nar/gkw935.
Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS revealed rapid evolution of Triticeae genome - (Peer Reviewed Journal)
Xie, J., Huo, X., Zhou, S., Wang, Y., Guo, G., Deal, K., Ouyang, S., Liang, Y., Wang, Z., Xiao, L., Zhu, T., Hu, G., Tiwari, V., Zhang, J., Li, H., Ni, Z., Yao, Y., Peng, H., Zhang, S., Anderson, O.D., McGuire, P., Dvorak, J., Luo, M., Liu, Y., Gu, Y.Q., Sun, Q. 2017. Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS revealed rapid evolution of Triticeae genome. Journal of Genetics and Genomics. 44:51-61.
Rapid evolutionary dynamics in a 2.8-Mb chromosomal region containing multiple prolamin and resistance gene families in Aegilops tauschii - (Peer Reviewed Journal)
Dong, L., Huo, N., Wang, Y., Deal, K., Wang, D., Hu, D., Dvorak, J., Anderson, O.D., Luo, M., Gu, Y.Q. 2016. Rapid evolutionary dynamics in a 2.8-Mb chromosomal region containing multiple prolamin and resistance gene families in Aegilops tauschii. Plant Journal. doi: 10.111/tpi.13214.
Glutamine synthetase in durum wheat: Genotypic variation and relationship with grain protein content - (Peer Reviewed Journal)
Nigro, D., Fortunate, S., Giove, S., Paradiso, A., Gu, Y.Q., Blanco, A., Concetta de Pinto, M., Gadaleta, A. 2016. Glutamine synthetase in durum wheat: genotypic variation and relationship with grain protein content. Frontiers in Plant Science. doi: 10.3389lfpls.2016.00971.
Draft genome sequence of Agrobacterium rhizogenes strain NCPPB2659 - (Peer Reviewed Journal)
Valdes, J., Collier, R.A., Wang, Y., Huo, N., Gu, Y.Q., Thilmony, R.L., Thomson, J.G. 2002. Draft genome sequence of Agrobacterium rhizogenes strain NCPPB2659. Genome Announcements. 4:1-2.
MetaCoMET: a web platform for discovery and visualization of the core microbiome - (Peer Reviewed Journal)
Wang, Y., Xu, L., Gu, Y.Q., Coleman-Derr, D.A. 2016. MetaCoMET: a web platform for discovery and visualization of the core microbiome. Bioinformatics. 32(22):3469-3470. doi:10.1093/bioinformatics/btw507.
GSP: A web-based platform for designing genome-specific primers in polyploids - (Peer Reviewed Journal)
Wang, Y., Tiwari, T., Coleman-Derr, D.A., Rawda, N., Gill, B., Huo, N., You, F., Gu, Y.Q. 2016. GSP: A web-based platform for designing genome-specific primers in polyploids. Bioinformatics. doi: 10.1093/bioinformatics/btw/34.
GSP: a web-based platform for designing genome-specific primers in polyploids - (Peer Reviewed Journal)
Wang, Y., Tiwari, V.K., Rawat, N., Gill, B.S., Huo, N., You, F.M., Coleman-Derr, D.A., Gu, Y.Q. 2016. GSP: a web-based platform for designing genome-specific primers in polyploids. Bioinformatics. 32(15):2382-2383.
A rhomboid gene controls speciation through regulation of nuclear-mitochondrial compatibility in Triticum - (Peer Reviewed Journal)
Bassi, F.M., Ghavami, F., Hayden, M.J., Wang, Y., Forrest, K., Kong, S., Dizon, R.G., Michalak De Jimenez, M.K., Meinhardt, S., Mergoum, M., Gu, Y.Q., Kianian, S. 2016. A rhomboid gene controls speciation through regulation of nuclear-mitochondrial compatibility in Triticum. Plant Biotechnology Journal. 14(8):1716-26.
A whole-genome, radiation hybrid map of wheat - (Peer Reviewed Journal)
Tiwari, V., Heesacker, A., Riera-Lizarazu, O., Gunn, H., Wang, S., Wang, Y., Gu, Y.Q., Paux, E., Koo, D.H., Luo, M.C., Lazo, G.R., Akhunov, E., Friebe, B., Poland, J.A., Gill, B., Kianian, S., Leonard, J. 2016. A whole-genome, radiation hybrid map of wheat. Plant Journal. doi: 10.1111/tpj.13513.
WheatExp: an RNA-seq expression database for polypoid wheat - (Peer Reviewed Journal)
Pearce, S., Vazquez-Cross, H., Herin, S.Y., Hane, D., Wang, Y., Gu, Y.Q., Dubcovsky, J. 2015. WheatExp: an RNA-seq expression database for polypoid wheat. Biomed Central (BMC) Plant Biology. 15:299.
Radiation hybrid maps of D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes - (Peer Reviewed Journal)
Kumar, A., Seetan, R., Mergoum, M., Tiwari, V., Iqbal, M.J., Wang, Y., Al-Assam, O., Simkova, H., Luo, M., Dvorak, J., Gu, Y.Q., Denton, A.M., Kilian, A., Lazo, G.R., Kianian, S.F. 2015. Radiation hybrid maps of D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes. BMC Genomics. 16:800.
Toward a better understanding of the genomic region harboring Fusarium head blight resistance QTL Qfhs.ndsu-3AS in durum wheat Reprint Icon - (Peer Reviewed Journal)
Zhu, X., Zhong, S., Chao, S., Gu, Y.Q., Kianian, S.F., Elias, E., Cai, X. 2016. Toward a better understanding of the genomic region harboring Fusarium head blight resistance QTL Qfhs.ndsu-3AS in durum wheat. Theoretical and Applied Genetics. 129:31-43.
Brachypodium seed - a potential model for studying grain development of cereal crops ()
Wu, J., Thilmony, R.L., Gu, Y.Q. 2016. Brachypodium seed - a potential model for studying grain development of cereal crops. In:Vogel, J., editor. Genetics and Genomics of Brachypodium. Cham, Switzerland:Springer International Publishing. p. 219-243. doi: 10.1007/7397.2015.12.
GrainGenes: Changing Times, Changing Databases, Digital Evolution. Reprint Icon - (Abstract Only)
Tobias, C.M., Lazo, G.R., Gu, Y.Q., Matthews, D.E. 2015. GrainGenes: Changing Times, Changing Databases, Digital Evolution. Meeting Abstract. scisoc.confex.com/scisoc/2015am/webprogram/Paper94726.html.
Development of a D genome specific marker resource for diploid and hexaploid wheat - (Peer Reviewed Journal)
Wang, Y., Drader, T., Tiwari, V.K., Dong, L., Kumar, A., Huo, N., Ghavami, F., Iqbal, M.J., Lazo, G.R., Gill, B., Kianian, S., Luo, M., Gu, Y.Q. 2015. Development of a D genome specific marker resource for diploid and hexaploid wheat. Biomed Central (BMC) Genomics. doi: 10.11861S12864-015-1852-2.
OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species - (Peer Reviewed Journal)
Wang, Y., Coleman-Derr, D.A., Chen, G., Gu, Y.Q. 2015. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Research. 43(W1):W78-W84. doi: 10.1093/nar/gkv487.
Dynamic evolution of resistance gene analogs in the orthologous genomic regions of powdery mildew resistance gene MlIW170 in Triticum dicoccoides and Aegilops tauschii - (Peer Reviewed Journal)
Liang, Y., Zhang, D., Ouyang, S., Xie, J., Wu, Q., Wang, Z., Cui, Y., Liu, Z., Chen, Y., Zhang, Y., Luo, M., Dvorak, J., Huo, N., Sun, Q., Gu, Y.Q., Liu, Z. 2015. Dynamic evolution of resistance gene analogs in the orthologous genomic regions of powdery mildew resistance gene MlIW170 in Triticum dicoccoides and Aegilops tauschii. Theoretical and Applied Genetics. 128:1617-1629.
AIM: A comprehensive Arabidopsis Interactome Module database and related interologs in plants - (Peer Reviewed Journal)
Wang, Y., Thilmony, R.L., Zhao, Y., Chen, G., Gu, Y.Q. 2014. AIM: A comprehensive Arabidopsis Interactome Module database and related interologs in plants. Database: The Journal of Biological Databases and Curation. doi: 10.1093/database/bau117.
Fine physical and genetic mapping of powdery mildew resistance gene MlIW172 originating from wild emmer(Triticum dicoccoides) - (Peer Reviewed Journal)
Ouyang, S., Zhang, D., Han, J., Zhao, X., Cui, Y., Song, W., Huo, N., Liang, Y., Xie, J., Wang, Z., Wu, Q., Chen, Y., Lu, P., Zhang, D., Wang, L., Sun, H., Yang, T., Keeble-Gagnere, G., Appels, R., Dolezel, J., Ling, H., Luo, M., Gu, Y.Q., Sun, X., Liu, Z. 2014. Fine physical and genetic mapping of powdery mildew resistance gene MlIW172 originating from wild emmer (Triticum dicoccoides). PLoS One. 9:e100160.
Net Venn - An integrated network analysis web platform for gene lists - (Peer Reviewed Journal)
Wang, Y., Thilmony, R.L., Gu, Y.Q. 2014. Net Venn - An integrated network analysis web platform for gene lists. Nucleic Acids Research. DOI: 10.1093/narlgku331.
Transposable element junctions in marker development and genomic characterization of barley - (Peer Reviewed Journal)
Maazaheri, M., Kianian, P., Mergoum, M., Valentini, G., Seetan, R., Pirseyedi, S., Kumar, A., Gu, Y.Q., Stein, N., Kubalakova, M., Dolezel, J., Denton, A., Kianian, S. 2014. Transposable element junctions in marker development and genomic characterization of barley. The Plant Genome. 7:1-8.
Characterization of reniform nematode genome through shotgun sequencing - (Peer Reviewed Journal)
Nyaku, S.T., Sripathi, V.R., Kateny, R.V., Cseke, S.B., Buyyarapu, R., Mcewan, R., Gu, Y.Q., Lawrence, K., Sripathi, P., George, P., Sharma, G.C. 2014. Characterization of reniform nematode genome through shotgun sequencing. Genome. DOI: 10.1139/gen-20140019.
Accelerated evolution of the mitochondrial genome in an alloplasmic line of durum wheat Reprint Icon - (Peer Reviewed Journal)
Noyszewski, A., Ghavami, F., Al-Nimer, L., Soltani, A., Gu, Y.Q., Huo, N., Meinhardt, S., Kianian, P., Kianian, S. 2014. Accelerated evolution of the mitochondrial genome in an alloplasmic line of durum wheat. Biomed Central (BMC) Genomics. 15:67.
Dynamic evolution of Rht-1 homologous regions in grass genomes - (Peer Reviewed Journal)
Wu, J., Kong, X., Shi, C., Gu, Y.Q., Jin, C., Gao, L., Jia, J. 2013. Evolutionary dynamics of Rht-1, a "green revolution" gene homologous regions across the subgenomes, ploids and related grass genomes. PLoS One. 8(9):e75544.
Developing improved durum wheat germplasm by altering the cytoplasmic genome - (Proceedings)
Ghavami, F., Bassi, F., Burciaga, R., Soltani, A., Noyszewski, A., Michalak, D., Gu, Y.Q., Meinhardt, S., Elias, E., Kianian, P., Mergoum, M., Mann, S., Kianian, S. 2014. Developing improved durum wheat germplasm by altering the cytoplasmic genome. Symposium Proceedings. 110:177-188.
Haplotype variation of Glu-D1 locus and the origin of Glu-D1d allele conferring superior end-use qualities in common wheat - (Peer Reviewed Journal)
Dong, G., Yang, Y., Li, Y., Lou, H., An, X., Dong, L., Gu, Y.Q., Anderson, O.D., Liu, X., Qin, H., Zhang, K., Wang, D. 2013. Haplotype variation of Glu-D1 locus and the origin of Glu-D1d allele conferring superior end-use qualities in common wheat. PLoS One. 8(9):e74859.
Sequence organization and evolutionary dynamics of Brachypodium-specific centromere retrotransposons - (Peer Reviewed Journal)
Qi, L.L., Wu, J.J., Friebe, B., Qian, C., Gu, Y.Q., Fu, D.L., Gill, B.S. 2013. Sequence organization and evolutionary dynamics of Brachypodium-specific centromere retrotransposons. Chromosome Research. 21(5):507-521.
Structural analysis of the wheat genes encoding NADH-dependent glutamine-2-oxoglutarate amidotransferases genes and correlation with grain protein content - (Peer Reviewed Journal)
Nigro, D., Gu, Y.Q., Huo, N., Marcotuli, I., Blanco, A., Gadaleta, A., Anderson, O.D. 2013. Structural analysis of the wheat genes encoding NADH-dependent glutamine-2-oxoglutarate amidotransferases genes and correlation with grain protein content. PLoS One. 8(9):e73751.
Genetic association and disassociation of OPR and LOX genes with resistance to Hessian fly in hexaploid wheat - (Peer Reviewed Journal)
Tan, C.T., Carver, B., Chen, M., Gu, Y.Q., Yan, L. 2013. Genetic association and disassociation of OPR and LOX genes with resistance to Hessian fly in hexaploid wheat. Biomed Central (BMC) Genomics. 14:369.
The gene space in wheat: the complete y-gliadin gene family from the wheat cultivar Chinese Spring - (Peer Reviewed Journal)
Anderson, O.D., Huo, N., Gu, Y.Q. 2013. The gene space in wheat: the complete y-gliadin gene family from the wheat cultivar Chinese Spring. Functional and Integrative Genomics. 10.1007/s10142-013-0321-8.
A 4-gigbase physical map unlocks the structure and evolution of the complex genome of Aegilop tauschii, the wheat D-genome progenitor - (Peer Reviewed Journal)
Luo, M., Gu, Y.Q., You, F., Deal, K.R., Ma, Y., Hu, N., Huo, N., Wang, Y., Wang, J., Chen, S., Jorgensen, C.M., Zhang, Y., Mcguire, P.E., Pastrnak, S., Stein, J.C., Ware, D.H., Mccombie, W.R., Juanuan, S.F., Martis, M.M., Mayer, K.F., Sehgal, S., Gill, B.S., Bevan, M.W., Dolezel, J., Lazo, G.R., Anderson, O.D., Dvorak, J. 2013. A 4-gigbase physical map unlocks the structure and evolution of the complex genome of Aegilop tauschii, the wheat D-genome progenitor. Proceedings of the National Academy of Sciences. 110:7940-7945.
A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor Reprint Icon - (Peer Reviewed Journal)
Lou, M., Gu, Y.Q., You, F., Deal, K., Ma, Y., Hu, Y., Huo, N., Wang, Y., Wang, J., Chen, S., Jorgensen, C., Zhang, Y., Mcguire, P., Pasternak, S., Stein, J., Ware, D., Kramer, M., Mccombie, W., Kianian, S., Martis, M., Mayer, K., Sehgal, K., Li, W., Gill, B., Bevan, M., Simkova, H., Dolezel, J., Weining, S., Lazo, G.R., Anderson, O.D., Dvorak, J. 2013. A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proceedings of the National Academy of Sciences. 110(19):7940-7945.
Sequencing and characterization of full-length sequence of 18S rRNA gene from the reniform nematode - (Peer Reviewed Journal)
Nyaku, S.T., Kantety, R.V., Gu, Y.Q., Venkateswara, S.R., Sharma, G.V., Lawrence, K. 2013. Sequencing and characterization of full-length sequence of 18S rRNA gene from the reniform nematode. PLoS One. 8:e60891.
Wheat Zapper: a flexible online tool for colinearity studies in plants - (Peer Reviewed Journal)
Alnemer, L.M., Seetan, R., Bassi, F.M., Chitaranjan, C., Helsene, A., Loree, P., Goshn, S.B., Gu, Y.Q., Luo, M.C., Iqbal, M., Lazo, G.R., Kianian, S.F., Denton, A.M. 2013. Wheat Zapper: a flexible online tool for colinearity studies in plants. Functional and Integrative Genomics. 13:11-17.
A radiation hybrid map of chromosome ID reveals synteny conservation at a wheat speciation locus. - (Peer Reviewed Journal)
Michalak De Jimenez, M.K., Bassi, F.M., Ghavami, F.G., Simons, K., Dizon, R., Setan, R.I., Alnemer, L.M., Denstin, A.M., Dogramaci, M., Simkova, H., Dolezel, J., Seth, K., Luo, M., Dvorak, J., Gu, Y.Q., Kianian, S.F. 2013. Accelerated evolution of the mitochondrial genome in an alloplasmic line of durum wheat. Functional and Integrative Genomics. 13:19-32.
Rapid genome mapping in nano channel array for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome - (Peer Reviewed Journal)
Hastie, A., Dong, L., Luo, M., Huo, N., Gu, Y.Q., Xiao, M. 2013. Rapid genome mapping in nano channel array for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome. PLoS One. 8:e55864.
Phylogenetic, molecular, and biochemical characterization of caffeic aicd O-methyltransferase (COMT) gene family in Brachypodium distachyon - (Peer Reviewed Journal)
Wu, X., Ju, J., Bragg, J.N., Vogel, J.P., Anderson, O.D., Gu, Y.Q. 2013. Phylogenetic, molecular, and biochemical characterization of caffeic aicd O-methyltransferase (COMT) gene family in Brachypodium distachyon. International Journal of Plant Genomics. doi.org/10.1155/2013/423189.
A new class of wheat gliadin genes and proteins - (Peer Reviewed Journal)
Anderson, O.D., Dong, L., Huo, N., Gu, Y.Q. 2012. A new class of wheat gliadin genes and proteins. PLoS One. 7:e52139.
Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor aegilops tauschii accession AL8/78 - (Peer Reviewed Journal)
Kumar, A., Simons, K., Iqbal, M.J., Jimenez, M., Bassi, F.M., Ghavami, F., Al, A., Wang, Y., Luo, M., Gu, Y.Q., Denton, A., Xu, S.S., Dvorak, J., Kianian, P., Kianian, S.F. 2012. Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor aegilops tauschii. Biomed Central (BMC) Genomics. 13:597.
PIECE: A database for plant gene structure comparison and evolution - (Peer Reviewed Journal)
Wang, Y., You, F., Lazo, G.R., Luo, M., Thilmony, R.L., Gordon, S.P., Gu, Y.Q., Kianian, S. 2012. PIECE: A database for plant gene structure comparison and evolution. Nucleic Acids Research. D1159-D1166.
Analysis of the allohexaploid bread wheat genome (Triticum aestivum) using comparative whole genome shotgun sequencing - (Peer Reviewed Journal)
Brenchley, R., Spannagl, M., Pfeifer, M., Baker, G., D'Amore, R., Gu, Y.Q., Luo, M., Huo, N., Anderson, O.D., Dvorak, J., Hall, A., Mayer, K., Edward, K.J., Hall, N. 2012. Analysis of the allohexaploid bread wheat genome (Triticum aestivum) using comparative whole genome shotgun sequencing. Nature. 491:705-710.
Exploring the diploid wheat ancestral A genome through sequence comparison at the High-Molecular-Weight glutenin locus region - (Peer Reviewed Journal)
Dong, L., Huo, N., Wang, Y., Deal, K., Luo, M., Wang, D., Anderson, O.D., Gu, Y.Q. 2012. Exploring the diploid wheat ancestral A genome through sequence comparison at the High-Molecular-Weight glutenin locus region. Molecular Genetics and Genomics. 287:855-866.
DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum - (Peer Reviewed Journal)
Kumar, A., Bassi, F.M., Gu, Y.Q., Dogramaci, M., Kianian, S. 2012. DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum. Biomed Central (BMC) Genomics. doi 10.1186/1471-2164-13-339.
Generation and characterization of the Western Regional Research Center brachypodium T-DNA insertional mutant collection - (Peer Reviewed Journal)
Bragg, J., Wu, J., Gordon, S.P., Guttman, M.E., Thilmony, R.L., Lazo, G.R., Gu, Y.Q., Vogel, J.P. 2012. Generation and characterization of the Western Regional Research Center brachypodium T-DNA insertional mutant collection. PLoS One. 7(9):e41916. doi:10.1371/journal.pone.0041916.
A tandem segmental duplication (TSD) in the green revolution gene Rht-D1b region underlies plant height variation - (Peer Reviewed Journal)
Li, Y., Xioa, J., Wu, J., Gu, Y.Q., Kong, X. 2012. A tandem segmental duplication (TSD) in the green revolution gene Rht-D1b region underlies plant height variation. New Phytologist. doi: 10.1111/j.1469-8137.2012.04243.x.
Fine mapping of the Bsrl barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. - (Peer Reviewed Journal)
Cui, Y., Lee, M.Y., Huo, N., Bragg, J., Yan, L., Yuan, C., Li, C., Holditch, S.J., Xie, J., Luo, M.C., Li, D., Yu, J., Martin, J., Schackwitz, W., Gu, Y.Q., Vogel, J.P., Jackson, A.O., Liu, Z., Garvin, D.F. 2012. Fine mapping of the Bsrl barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS One. 7:e38333.
New cis-regulatory elements in the Rht-D1b locus region of wheat - (Peer Reviewed Journal)
Duan, J., Wu, J., Gu, Y.Q., Kong, X. 2012. New cis-regulatory elements in the Rht-D1b locus region of wheat. Functional and Integrative Genomics. Available at: http://rd.springer.com/article/10.2007/s10142-012-0283-2. DOI 10.1007/s10142-012-0283-2.
Characterizing the walnut genome through analyses of BAC end sequences - (Peer Reviewed Journal)
Wu, J., Gu, Y.Q., Hu, Y., You, F.M., Dandekar, A.M., Leslie, C.A., Aradhya, M.K., Dvorak, J., Luo, M. 2011. Characterizing the walnut genome through analyses of BAC end sequences. Plant Molecular Biology. 78:95-107.
Characterizing the walnut genome through analyses of BAC end sequences - (Peer Reviewed Journal)
Wu, J., Gu, Y.Q., Hu, Y., You, F.M., Dandekar, A.M., Leslie, C., Aradhya, M.K., Dvorak, J., Luo, M. 2011. Characterizing the walnut genome through analyses of BAC end sequences. Plant Molecular Biology. 78:95-107.
Characterizing the citrus variety Carrizo genome through 454 shotgun sequencing - (Peer Reviewed Journal)
Belknap, W.R., Wang, Y., Wu, J., Huo, N., Rockhold, D.R., Gu, Y.Q., Stover, E.W. 2011. Characterizing the citrus variety Carrizo genome through 454 shotgun sequencing. Genome. 54:1005-1015. doi:10.1139/G11-070.
Brachypodium as a model for the grasses: today and the future Reprint Icon - (Peer Reviewed Journal)
Brkljacic, J., Grotewold, E., Scholl, R., Mockler, T., Garvin, D.F., Vain, P., Brutnell, T., Sibout, R., Bevan, M., Budak, H., Caicedo, A.L., Gao, C., Gu, Y.Q., Hazen, S.P., Holt, B.F., Hong, S., Jordan, M., Manzaneda, A.J., Mitchell-Olds, T., Mochida, K., Mur, L.A., Park, C., Sedbrook, J., Watt, M., Zheng, S., Vogel, J.P. 2011. Brachypodium as a model for the grasses: today and the future. Plant Physiology. 157(1):3-13.
Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon - (Peer Reviewed Journal)
Huo, N., Garvin, D.F., You, F., McMahon, S.A., Luo, M., Gu, Y.Q., Lazo, G.R., Vogel, J.P. 2011. Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon. Theoretical and Applied Genetics. 123(3):455-464.
Gene Space Dynamics during the Evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor Genomes - (Peer Reviewed Journal)
Massa, A.N., Wanjugi, H., Deal, K.R., Chan, A.P., Gu, Y.Q., Luo, M., Anderson, O.D., Rabinomics, P.D., Dvorak, J., Devos, K.M., O'Brien, K., Maiti, R., You, F. 2011. Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes. Molecular Biology and Evolution. Available at: http://mbe.oxfordjournalsorg/content/early/2011/04/06/molbev.msr080.long. DOI: 10.1093/molbev/msr080.
Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence - (Peer Reviewed Journal)
You, F., Huo, N., Deal, K., Gu, Y.Q., Luo, M., Mcguire, P., Dvorak, J., Anderson, O.D. 2011. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. Biomed Central (BMC) Genomics. 12:59.
Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes - (Peer Reviewed Journal)
Akhunov, E.D., Akhunova, A., Anderson, O.D., Anderson, J., Blake, N., Clegg, M., Coleman-Derr, D., Conley, E., Crossman, C., Deal, K., Dubcovsky, J., Gill, B., Gu, Y.Q., Hadam, J., Heo, H., Huo, N., Lazo, G.R., Luo, M., Ma, Y., Matthews, D.E., Mcguire, P., Morrell, P., Qualset, C., Renfro, J., Tabanao, D., Talbert, L., Tian, C., Toleno, D., Warburton, M., You, F., Zhang, W., Dvorak, J. 2010. Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. Biomed Central (BMC) Genomics. 11:702-710.
The compact Brachypodium genome conserves centromeric regions of a common ancestor with wheat and rice - (Peer Reviewed Journal)
Qi, L., Friebe, B., Wu, J., Gu, Y., Qian, C., Gill, B.S. 2010. The compact Brachypodium genome conserves centromeric regions of a common ancestor with wheat and rice. Functional and Integrative Genomics. 10:477-492.
Structural and transcriptional analysis of plant genes encoding the bifunctional lysine ketoglutarate reductase saccharopine dehydrogenase enzyme - (Peer Reviewed Journal)
Anderson, O.D., Coleman-Derr, D., Gu, Y.Q., Heath, S. 2010. Structural and transcriptional analysis of plant genes encoding the bifunctional lysine ketoglutarate reductase saccharopine dehydrogenase enzyme. Biomed Central (BMC) Genomics. 10:113.
Inferring geographic origin of barley accessions using molecular markers - (Peer Reviewed Journal)
Bonman, J.M., Gu, Y.Q., Coleman Derr, D., Jackson, E.W., Bockelman, H.E. 2010. Inferring geographic origin of barley accessions using molecular markers. Genetic Resources and Crop Evolution. DOI: 10.1007/s10722-010-9574-4.
RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development - (Peer Reviewed Journal)
You, F., Wanjugi, H., Huo, N., Lazo, G.R., Luo, M., Anderson, O.D., Dvorak, J., Gu, Y.Q. 2010. RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development. Nucleic Acids Research. 38:Suppl:W310-320.
Development of PCR-based Markers for Marker-Assisted Selection of H26 and H32 for Hessian Fly Resistance - (Abstract Only)
Yu, G.T., S.S. Xu, M.O. Harris, X. Cai, C.E. Williams, Y.-Q. Gu, and M.-C. Luo. 2010. Development of PCR-based markers for marker-assisted selection of H26 and H32 for Hessian fly resistance. p. 328. In: Abstract of Oral and Poster Presentations, 8th International Wheat Conference, June 1 - 4, St. Petersburg, Russia.
Genome Sequencing and Analysis of the Model Grass Brachypodium Distachyon. - (Peer Reviewed Journal)
Vogel, J.P., Garvin, D.F., Gu, Y.Q., Lazo, G.R., Anderson, O.D., Bragg, J.N., Chingcuanco, D.L., Weng, Y., Belknap, W.R., Thomson, J.G., Dardick, C.D., Baxter, I.R. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 463:763-768.
Evolutionary relationship of nuclear genes encoding mitochondrial proteins across grasses - (Peer Reviewed Journal)
Michalak, M.K., Ghavami, F., Lazo, G.R., Gu, Y.Q., Kianian, S.F. 2009. Evolutionary relationship of nuclear genes encoding mitochondrial proteins across grasses. Maydica. 54: 471-483
A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat - (Peer Reviewed Journal)
Gu, Y.Q., Ma, Y., Huo, N., Vogel, J.P., You, F., Lazo, G.R., Nelson, W., Soderlund, C., Dvorak, J. 2009. A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. Biomed Central (BMC) Genomics. 10:496
ConservedPrimers 2.0: A high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery - (Peer Reviewed Journal)
You, F., Huo, N., Gu, Y.Q., Lazo, G.R., Dvorak, J., Anderson, O.D. 2009. ConservedPrimers 2.0: A high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery. BMC Bioinformatics. 10:331.
Genome-Wide Sequence Comparison of Centromeric Regions and BAC-Landing on Chromosomes Provide New Insights into Centromere Evolution Among Wheat, Brachypodium, and Rice - (Abstract Only)
Qi, L., Friebe, B., Gu, Y.Q., Qian, C., Gill, B.S. 2010. Genome-Wide Sequence Comparison of Centromeric Regions and BAC-Landing on Chromosomes Provide New Insights into Centromere Evolution Among Wheat, Brachypodium, and Rice. Plant and Animal Genome XVIII Conference, January 9-13, 2010, San Diego, CA. P236. Available: http://www.intl-pag.org/18/abstracts/P05a_PAGXVIII_236.html
An SSR-Based Genetic Linkage Map of the Model Grass Brachypodium distachyon - (Peer Reviewed Journal)
Garvin, D.F., Mckenzie, N., Vogel, J.P., Mockler, T.C., Blankenheim, Z., Wright, J., Huo, N., Cheema, J.J., Dicks, J., Hayden, D.M., Gu, Y.Q., Tobias, C.M., Chang, J.H., Chu, A., Trick, M., Michael, T.P., Bevan, M.W., Snape, J.W. 2010. An SSR-Based Genetic Linkage Map of the Model Grass Brachypodium distachyon. Genome. 53(1):1-13.
Conserved globulin gene across eight grass genomes identify fundamental units of the loci encoding seed storage proteins - (Peer Reviewed Journal)
Gu, Y.Q., Wanjugi, H., Coleman-Derr, D., Kong, X., Anderson, O.D. 2009. Conserved globulin gene across eight grass genomes identify fundamental units of the loci encoding seed storage proteins. Functional and Integrative Genomics. 10:111-122.
Genome Comparisons Reveal a Dominant Mechanism of Chromosome Number Reduction in Grasses and Accelerated Genome Evolution in Triticeae - (Peer Reviewed Journal)
Luo, M.C., Deal, K.R., Akhunov, E.D., Akhunova, A.R., Anderson, O.D., Anderson, J.A., Blake, N., Clegg, M.T., Coleman-Derr, D., Conley, E.E., Crossman, C.C., Dubcovsky, J., Gill, B.S., Gu, Y.Q., Hadam, J., Heo, H., Huo, N., Lazo, G.R., Lundy, K.E., Ma, Y., Matthews, D.E., Mcguire, P.E., Morrell, P.L., Nicolet, C.M., Qualset, C.O., Renfro, J., Tabano, D., Talbert, L.E., Tian, A., Toleno, D.M., Warburton, M.L., You, F.M., Zhang, W.J., Dvorak, J. 2009. Genome Comparisons Reveal a Dominant Mechanism of Chromosome Number Reduction in Grasses and Accelerated Genome Evolution in Triticeae. Proceedings of the National Academy of Sciences. 106:15780-15785.
Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon - (Peer Reviewed Journal)
Vogel, J.P., Metin, T., Budak, H., Huo, N., Gu, Y.Q., Steinwand, M.A. 2009. Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon Biomed Central (BMC) Plant Biology. 9:Article 88. Available: http://www.biomedcentral.com/1471-2229/9/88/abstract
Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv - (Peer Reviewed Journal)
Bai, W., Cai, A., Rz, Z., Li, A., Huo, N., Li, S., Gu, Y.Q., Yabut, L., Jia, J., Qi, Y. 2009. Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Functional and Integrative Genomics. 9:532-541.
Structure of the omega-gliadin gene family - (Peer Reviewed Journal)
Anderson, O.D., Gu, Y.Q., Kong, K., Lazo, G.R., Wu, J. 2009. Structure of the omega-gliadin gene family. Functional and Integrative Genomics. 9: 397-410.
Saturation and comparative mapping of genomic region harboring Hessian fly resistance gene H26 in wheat - (Peer Reviewed Journal)
Yu, G., Cai, X., Harris, M., Gu, Y.Q., Luo, M., Xu, S.S. 2009. Saturation and comparative mapping of genomic region harboring Hessian fly resistance gene H26 in wheat. Theoretical and Applied Genetics. 118(8):1589-1599.
Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat - (Peer Reviewed Journal)
Wanjugi, H., Coleman-Derr, D., Huo, N., Kianian, S.F., Luo, M., Wu, J., Anderson, O.D., Gu, Y.Q. 2009. Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. Genome. 52:576-587.
Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat - (Peer Reviewed Journal)
Huo, N., Vogel, J.P., Lazo, G.R., You, F., Ma, Y., McMahon, S.A., Dvorak, J., Anderson, O.D., Luo, M., Gu, Y.Q. 2009. Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat. Plant Molecular Biology. 70: 47-61.
Radiation hybrid mapping in crop plants ()
Kalavachrla, V., Hossia, K., Gu, Y.Q., Maan, S., Kianian, S. 2009. Radiation hybrid mapping in crop plants. Advances in Agronomy. 102:199-219.
The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes - (Peer Reviewed Journal)
Bortiri, E., Coleman-Derr, D., Lazo, G.R., Anderson, O.D., Gu, Y.Q. 2008. The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes. BMC Research Notes. 1:61.
BatchPrimer3: A high throughput web application for PCR and sequencing primer design - (Peer Reviewed Journal)
You, F.M., Huo, N., Gu, Y.Q., Luo, M., Ma, Y., Hane, D., Lazo, G.R., Dvorak, J., Anderson, O.D. 2008. BatchPrimer3: A high throughput web application for PCR and sequencing primer design. BMC Bioinformatics. 9:253.
The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. - (Peer Reviewed Journal)
Huo, N., Lazo, G.R., Vogel, J.P., You, F., Ma, Y., Hayden, D.M., Coleman-Derr, D., Hill, T., Dvorak, J., Anderson, O.D., Luo, M., Gu, Y.Q. 2007. Characterizing the nuclear genome structure of Brachypodium distachyon using BAC end sequences. Functional and Integrative Genomics. 8:135-147.
Development of genetic and genomic research resources for Brachypodium distachyon, a new model system for grass crop research - (Peer Reviewed Journal)
Garvin, D.F., Gu, Y.Q., Hasterok, R., Hazen, S.P., Jenkins, G., Mockler, T.C., Mur, L.A., Vogel, J.P. 2008. Development of genetic and genomic research resources for Brachypodium distachyon, a new model system for grass crop research. The Plant Genome. 48:S69-S84.
Rapid evolution and complex structural organization in genomic regions harboring multiple prolamin genes in the polyploid wheat genome - (Peer Reviewed Journal)
Gao, S., Gu, Y.Q., Wu, J., Huo, N., Crossman, C., Jia, J., Ren, Z., Anderson, O.D., Xiuying, K. 2007. Rapid evolution and complex structural organization in genomic regions harboring multiple prolamin genes in the polyploid wheat genome. Plant Molecular Biology. 65:189-203.
New insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification - (Peer Reviewed Journal)
Zhang, S., Gu, Y., Singh, J., Coleman-Derr, D., Brar, D., Jiang, N., Lemaux, P. 2007. New Insights into Oryza genome evolution: high gene colinearity and differential retrotransposon amplification. Plant Molecular Biology. 64:589-600.
Geno Profiler: Automated processing of high throughput capillary fingerprinting data - (Peer Reviewed Journal)
You, F., Ming-Cheng, L., Gu, Y.Q., Lazo, G.R., Thomas, C., Mcguire, P.E., Dvorak, J., Anderson, O.D. 2006. Geno Profiler: Automated Processing of High Throughput Capillary Fingerprinting Data. Bioinformatics. 2:240-242.
GENO PROFILER: BATCH PROCESSING OF HIGH THROUGHPUT CAPILLARY FINGERPRINTING DATA - (Peer Reviewed Journal)
You, F.M., Luo, M.C., Gu, Y.Q., Lazo, G.R., Thomas, C., McGuire, P.E., Dvorak, J., and Anderson, O.D. 2007. Genoprofiler: Automated processing of high throughput capillary fingerprinting data. Bioinformatics. 23:240-242.
TYPES AND RATES OF SEQUENCE EVOLUTION AT HMW-GLUTENIN LOCUS IN HEXAPLOID WHEAT AND ITS ANCESTRAL GENOMES - (Peer Reviewed Journal)
Gu, Y., Salse, J., Coleman-Derr, D., Dupin, A., Crossman, C., Lazo, G., Huo, N., Belcram, H., Ravel, C., Charmet, G., Charles, M., Anderson, O., Chalhoub, B. 2006. Types and Rates of Sequence Evolution at the HMW-Glutenin Locus in Hexaploid Wheat and Its Ancestral Genomes. Genetics. 174:1493-1504.
CONSTRUCTION AND CHARACTERIZATION OF TWO BAC LIBRARIES FROM BRACHYPODIUM DISTACHYPON, A NEW MODEL FOR GRASS GENOMICS - (Peer Reviewed Journal)
Gu, Y., Lazo, G., Vogel, J., Coleman-Derr, D., Luo, M.C., Thilmony, R., Garvin, D., Anderson, O., Huo, N. 2006. Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome. 49(9):1099-1108.
HIGH-RESOLUTION RADIATION HYBRID MAP OF WHEAT CHROMOSOME 1D - (Peer Reviewed Journal)
Kalavacharla, V., Hossain, K., Gu, Y.Q., Riera, L.O., Isabel, V.M., Bhamidimarri, S., Gonzalez-Hernandez, J., Maan, S., Kianian, S. 2006. High-resolution radiation hybrid map of wheat chromosome 1d. Genetics. 173:1-11.
EST SEQUENCING AND PHYLOGENETIC ANALYSIS OF THE MODEL GRASS BRACHYPODIUM DISTACHYON - (Peer Reviewed Journal)
Vogel, J.P., Gu, Y.Q., Twigg, P., Lazo, G.R., Chingcuanco, D.L., Hayden, D.M., Donze, T., Vivia-Lindsay, A., Stamova, B., Coleman-Derr, D. 2006. EST sequencing and phylogenetic analysis of the model grass brachypodium distachyon. Theoretical and Applied Genetics. 113: 186-195.
SUBTRACTIVE CDNA LIBRARIES IDENTIFY DIFFERENTIALLY EXPRESSED GENES IN DORMANT AND GROWING BUDS OF LEAFY SPURGE (EUPHORBIA ESULA) - (Peer Reviewed Journal)
Jia, Y., Anderson, J.V., Horvath, D.P., Gu, Y.-Q., Lym, R.G., Chao, W.S. 2006. Subtractive cDNA libraries identify differentially expressed genes in dormant and growing buds of leafy spurge (Euphorbia esula). Plant Molecular Biology. 61:329-344.
POSITIONAL RELATIONSHIP BETWEEN PHOTOPERIOD RESPONSE QTL AND PHOTORECEPTOR AND VERNALIZATION GENES IN BARLEY - (Peer Reviewed Journal)
Szucs, P., Karsai, I., Von Zitzewitz, J., Meszaros, K., Copper, L., Gu, Y.Q., Chen, T., Hayes, P., Skinner, J. 2006. Positional relationship between photoperiod response qtl and photoreceptor and vernalization genes in barley. Theoretical and Applied Genetics. 112: 1,277-1,285.
POSITIONAL RELATIONSHIP BETWEEN PHOTOPERIOD RESPONSE QTL AND PHOTORECEPTOR AND VERNALIAZATION GENES IN BARLEY - (Peer Reviewed Journal)
Szucs, P., Karsai, I., Von Zitzewitz, J., Meszaros, K., Cooper, L., Gu, Y.Q., Chen, T., Hayes, P., Skinner, J. 2006. Positional relationship between photoperiod response qtl and photoreceptor and vernaliazation genes in barley. Theoretical and Applied Genetics. 112: 1,277-1,285.
SUBTRACTIVE CDNA LIBRARIES IDENTIFY DIFFERENTIALLY-EXPRESSED GENES IN DORMANT AND GROWING BUDS OF LEAFY SPURGE (EUPHORBIA ESULA) - (Abstract Only)
Jia, Y., Anderson, J.V., Horvath, D.P., Gu, Y.Q., Lym, R.G., Chao, W.S. 2006. Subtractive cDNA libraries identify differentially-expressed genes in dormant and growing buds of leafy spurge (Euphorbia esula). [Abstract]. Weed Science Society of America Abstracts 46:30.
IDENTIFICATION OF DIFFERENTIALLY-EXPRESSED GENES IN DORMANT AND GROWING BUDS OF LEAFY SPURGE (EUPHORBIA ESULA L.) - (Abstract Only)
Jia, Y., Gu, Y.Q., Horvath, D.P., Anderson, J.V., Chao, W.S. 2005. Identification of differentially-expressed genes in dormant and growing buds of leafy spurge (Euphorbia esula L.). [Abstract]. Annual Meeting of the American Society of Plant Biologists. Final Program and Abstract Supplement, Poster 670, Page 225.
HYBSWEEPER: A RESOURCE FOR DETECTING HIGH-DENSITY PLATE COORDINATES - (Peer Reviewed Journal)
Lazo, G.R., Lui, N., Gu, Y.Q., Kong, X., Coleman Derr, D., Anderson, O.D. 2005. Hybsweeper: a resource for detecting high-density plate coordinates. Biotechniques. 39:320-324.
SUBTRACTIVE HYBRIDIZATION AS A TOOL TO SCREEN FOR GENES INVOLVED IN DORMANCY AND GROWTH IN UNDERGROUND ADVENTITIOUS BUDS OF LEAFY SPURGE (EUPHORBIA ESULA) - (Abstract Only)
Jia, Y., Gu, Y., Horvath, D.P., Anderson, J.V., Chao, W.S. 2005. Subtractive hybridization as a tool to screen for genes involved in dormancy and growth in underground adventitious buds of leafy spurge (Euphorbia esula). [Abstract]. Weed Science Society of America. Page No. 120.
GENOMIC ORGANIZATION OF THE COMPLEX A-GLIADIN GENE LOCI IN WHEAT - (Peer Reviewed Journal)
Gu, Y.Q., Crossman, C.C., Kong, X., Luo, M., You, F.M., Coleman Derr, D., Dubcovsky, J., Anderson, O.D. 2004. Genomic organization of the complex a-gliadin gene loci in wheat. Theoretical and Applied Genetics. 109:648-657.
Rapid genome evolution as revealed by comparative sequence analysis of orthologous regions from four triticeae genomes - (Peer Reviewed Journal)
Gu, Y.Q., Coleman-Derr, D., Kong, X., Anderson, O.D. 2004. Dynamics and rapid genome evolution in allopolyploid wheat as revealed by comparative sequence analysis of the complex hmw-glutenin locus regions. Plant Physiology. 135:459-470.
DYNAMICS OF THE EVOLUTION OF ORTHOLOGOUS AND PARALOGOUS PORTIONS OF A COMPLEX LOCUS REGION IN TWO GENOMES OF ALLOPOLYPLOID WHEAT - (Peer Reviewed Journal)
Kong, X., Gu, Y.Q., You, F.M., Dubcovsky, J., Anderson, O.D. 2004. Dynamics of the evolution of orthologous and paralogous portions of a complex locus region in two genomes of allopolyploid wheat. Plant Molecular Biology. 54:55-69.
CONSTRUCTION OF CONTIGS OF AEGILOPS TAUSCHII GENOMIC DNA FRAGMENTS CLONED IN BAC AND BIBAC VECTORS - (Proceedings)
LUO, M., THOMAS, C.S., DEAL, K.R., YOU, F., ANDERSON, O.D., GU, Y.Q., LI, W., KURAPARTHY, V., GILL, B.S., MCGUIRE, P.E. 2003. CONSTRUCTION OF CONTIGS OF AEGILOPS TAUSCHII GENOMIC DNA FRAGMENTS CLONED IN BAC AND BIBAC VECTORS. WHEAT GENETICS INTERNATIONAL SYMPOSIUM PROCEEDINGS. 1:293-296.
Structure organization of barley D-hordein locus in comparison with its orthologous regions of wheat genomes - (Peer Reviewed Journal)
Gu, Y.Q., Anderson, O.D., Kong, X., Lazo, G.R., Wilson, C. 2003. Structure organization of barley D-hordein locus in comparison with its orthologous regions of wheat genomes. Genome. 46:1084-1097.
Construction and characterization of a half million clones BAC library of durum wheat (Triticum Turdigum SSP. durum). - (Peer Reviewed Journal)
Cenci, A., Chantret, N., Kong, X., Gu, Y.Q., Anderson, O.D., Fahima, T., Distelfeld, A., Dubcovsky, J. 2003. Construction and Characterization of a half-million clones BAC library of durum wheat (Triticum Turdigum SSP. Durum). Theoretical and Applied Genetics. 107:931-939.
SILENCING OF SUBFAMILY I OF PROTEIN PHOSPHATASE 2A CATALYTIC SUBUNITS RESULTS IN ACTIVATION OF PLANT DEFENSE RESPONSES AND LOCALIZED CELL DEATH. - (Peer Reviewed Journal)
He, X., Anderson, J.C., Del Pozo, O., Gu, Y.Q., Tang, X., Martin, G.B. 2004. Silencing of subfamily I of protein phosphatase 2A catalytic subunits results in activation of plant defense responses and localized cell death. Plant Journal. 38:563-577.
ASSESSMENT OF THE INSULAR ORGANIZATION OF THE WHEAT D GENOME BY PHYSICAL MAPPING - (Abstract Only)
DVORAK, J., ANDERSON, O.D., GILL, B.S., LUO, M., ZHANG, H., DEAL, K., LI, W., YOU, F., GU, Y.Q., MCGUIRE, P.E. ASSESSMENT OF THE INSULAR ORGANIZATION OF THE WHEAT D GENOME BY PHYSICAL MAPPING. Annual International Plant & Animal Genome Conference. 2003.
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