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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » People & Locations » Mary Duke
Mary V Duke
Genomics and Bioinformatics Research
Molecular Biologist

Phone: (662) 686-5453
Fax: (662) 686-3567

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Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions Reprint Icon - (Peer Reviewed Journal)
Waldbieser, G.C., Liu, S., Yuan, Z., Older, C.E., Gao, D., Shi, C., Bosworth, B.G., Li, N., Boa, L., Kirby, M.A., Jin, Y., Wood, M.L., Scheffler, B.E., Simpson, S.A., Youngblood, R.C., Duke, M.V., Ballard, L.L., Phillipy, A., Koren, S., Liu, Z. 2023. Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions. BMC Biology. 21:67. https://doi.org/10.1186/s12915-023-01556-8.
Transcriptomic response of Fusarium verticillioides to variably inhibitory environmental isolates of Streptomyces Reprint Icon - (Peer Reviewed Journal)
Satterlee, T.R., Williams, F.N., Nadal, M., Glenn, A.E., Lofton, L., Duke, M.V., Scheffler, B.E., Gold, S.E. 2022. Transcriptomic response of Fusarium verticillioides to variably inhibitory environmental isolates of Streptomyces. Frontiers in Fungal Biology. https://doi.org/10.3389/ffunb.2022.894590.
Transcriptomic Responses of Fusarium verticillioides to Lactam and Lactone Xenobiotics Reprint Icon - (Peer Reviewed Journal)
Gao, M., Gold, S.E., Gu, X., Satterlee, T.R., Duke, M.V., Scheffler, B.E., Glenn, A.E. 2022. Transcriptomic Responses of Fusarium verticillioides to Lactam and Lactone Xenobiotics. Frontiers in Fungal Biology. https://doi.org/10.3389/ffunb.2022.923112.
Development of nuclear microsatellite markers to facilitate germplasm conservation and population genetics studies of five groups of tropical perennial plants with edible fruits and shoots: ranbutan (Nephelium lappaceumt) Reprint Icon - (Peer Reviewed Journal)
Arias De Ares, R.S., Ballard, L.L., Duke, M.V., Simpson, S.A., Liu, X.F., Orner, V.A., Sobolev, V., Scheffler, B.E., Martinez-Castillo, J. 2020. Development of nuclear microsatellite markers to facilitate germplasm conservation and population genetics studies of five groups of tropical perennial plants with edible fruits and shoots: ranbutan (Nephelium lappaceumt). Genetic Resources and Crop Evolution. https://doi.org/10.1007/s10722-020-00965-w.
Pyrrocidine, a molecular off switch for fumonisin biosynthesis Reprint Icon - (Peer Reviewed Journal)
Gao, M., Glenn, A.E., Gu, X., Mitchell, T.R., Satterlee, T., Duke, M.V., Scheffler, B.E., Gold, S.E. 2020. Pyrrocidine, a molecular off switch for fumonisin biosynthesis. PLoS Pathogens. 6;16(7):e1008595. https://doi.org/10.1371/journal.ppat.1008595.
Transcriptome and binding data indicate that citral inhibits single strand DNA-binding proteins Reprint Icon - (Peer Reviewed Journal)
Grana, E., Diaz-Tielas, C., Sanchez-Moreiras, A.M., Reigosa, M.J., Celeirao, M., Abagyan, R., Teijeira, M., Duke, M.V., Clerk, T., Pan, Z., Duke, S.O. 2019. Transcriptome and binding data indicate that citral inhibits single strand DNA-binding proteins. Physiologia Plantarum. 169(1):99-109. https://doi.org/10.1111/ppl.13055.
Mitogenome and nuclear-encoded fungicide-target genes of Thecaphora frezii- causal agent of peanut smut Reprint Icon - (Peer Reviewed Journal)
Arias De Ares, R.S., Cazon, I., Massa, A.N., Scheffler, B.E., Sobolev, V., Lamb, M.C., Duke, M.V., Simpson, S.A., Conforto, C., Paredes, J., Soave, J., Buteler, M., Rago, A.M. 2019. Mitogenome and nuclear-encoded fungicide-target genes of Thecaphora frezii- causal agent of peanut smut. Fungal Genomics and Biology. (9)1:160. https://doi.org/10.35248/2165-8056.19.9.160.
A Reference Genome for US Rice - (Abstract Only)
Scheffler, B.E., Edwards, J., Stein, J., Ware, D., Vaughn, J.N., Schmutz, J., Peterson, D., Youngblood, C., Duke, M.V., Grimwood, J., Simpson, S.A., Mcclung, A.M. 2018. A Reference Genome for US Rice. Meeting Abstract. 37th Rice Technical Working Group.p.50.
Genome sequences of three strains of Aspergillus flavus for the biological control of Aflatoxin Reprint Icon - (Peer Reviewed Journal)
Weaver, M.A., Scheffler, B.E., Duke, M.V., Ballard, L.L., Abbas, H.K., Grodowitz, M.J. 2017. Genome sequences of three strains of Aspergillus flavus for the biological control of Aflatoxin. American Society for Microbiology, Genome Announcements. 5(44):e01204-e01217x. https://doi:10.1128/genomeA.01204-17.
The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts - (Peer Reviewed Journal)
Liu, Z., Liu, S., Yao, J., Bao, L., Jiang, C., Want, R., Sun, L., Li, Y., Zhang, Y., Zhang, J., Zhou, T., Zeng, Q., Fu, Q., Gao, S., Li, N., Koren, S., Jiang, Y., Zimim, A., Xu, P., Phillippy, A., Geng, X., Song, L., Sun, F., Li, C., Want, X., Chen, A., Jin, Y., Yuan, Z., Yang, Y., Tan, S., Peatman, E., Lu, J., Qin, Z., Dunham, R., Li, Z., Sonstegard, T.S., Feng, J., Danzmann, R.G., Schroeder, S.G., Scheffler, B.E., Duke, M.V., Ballard, L.L., Kucuktas, H., Kaltenboeck, L., Liu, H., Armbruster, J., Xie, Y., Kirby, M.A., Tian, Y., Moore Flanagan, M.E., Mu, W., Waldbieser, G.C. 2016. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nature Communications. 7:11757.
Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall sythesis, represses lignification, and prolongs elongation Reprint Icon - (Peer Reviewed Journal)
Tuttle, J.R., Nah, G., Duke, M.V., Alexander, D.C., Guan, X., Song, Q., Chen, Z.J., Scheffler, B.E., Haigler, C.H. 2015. Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall sythesis, represses lignification, and prolongs elongation. Biomed Central (BMC) Genomics. 16:477. doi:10.1186/s12864-015-1708-9.
Development of a large set of microsatellite markers in Zapote Maney (Pouteria sapota (Jacq.) (H.E. Moore & Stearn) and their potential use in the study of the species - (Peer Reviewed Journal)
Arias De Ares, R.S., Castillo, J.M., Sobolev, V., Blancarte-Jasso, N.H., Simpson, S.A., Ballard, L.L., Duke, M.V., Liu, X.F., Irish, B.M., Scheffler, B.E. 2015. Development of a large set of microsatellite markers in Zapote Maney (Pouteria sapota (Jacq.) (H.E. Moore & Stearn) and their potential use in the study of the species. Molecules. 20(60):11400-11417.
Effects on specific promoter DNA methylation in zebrafish embryos and larvae following benzo[a]pyrene exposure - (Peer Reviewed Journal)
Corrales, J., Fang, X., Thornton, C., Mei, W., Barbazuk, B.W., Duke, M.V., Scheffler, B.E., Willett, K.L. 2014. Effects on specific promoter DNA methylation in zebrafish embryos and larvae following benzo[a]pyrene exposure. Comparative Biochemistry and Physiology. Part C 163 (2014): 37-46.
The haustorial transcriptomes of Uromyces appendiculatus and Phakopsora pachyrhizi and their candidate effector families - (Peer Reviewed Journal)
Link, T.I., Lang, P., Scheffler, B.E., Duke, M.V., Graham, M.A., Cooper, B., Tucker, M.L., Van De Mortel, M., Voegele, R.T., Mendgen, K., Baum, T.J., Whitham, S.A. 2014. The haustorial transcriptomes of Uromyces appendiculatus and Phakopsora pachyrhizi and their candidate effector families. Molecular Plant Pathology. 15(4):379-393. DOI:10.1111/mpp.12099.
Complete genome sequence of channel catfish gastrointestinal sepicemia isolate Edwardsiella tarda C07-087 Reprint Icon - (Peer Reviewed Journal)
Tekedar, H.C., Karsi, A., Williams, M.L., Vamenta, S., Banes, M.M., Duke, M.V., Scheffler, B.E., Lawrence, M.L. 2013. Complete genome sequence of channel catfish gastrointestinal sepicemia isolate Edwardsiella tarda C07-087. American Society for Microbiology. 1(6):e00959-13. doi:10.1128/genomeA.00959-13.
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres - (Peer Reviewed Journal)
Paterson, A.H., Wendel, J.F., Gundlach, H., Guo, H., Jenkins, J., Jin, D., Llewellyn, D., Showmaker, K.C., Shu, S., Udall, J., Duke, M.V., Scheffler, B.E., Scheffler, J.A. 2012. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature. 492:423-428.
Development and characterization of seashore paspulum SSR markers and identification of markers associated with salt tolerance - (Abstract Only)
Harris-Shultz, K.R., Raymer, P., Duke, M.V., Ballard, L.L., Scheffler, B.E., Arias De Ares, R.S. 2012. Development and characterization of seashore paspulum SSR markers and identification of markers associated with salt tolerance. Visions for a Sustainable Planet. ASA, CSSA, and SSSA 2012 International Annual Meetings. Oct. 21-24, 2012, Cincinnati, OH. Agronomy Abstracts. p. 143.
Batch Isolation of Microsatellites for Tropical Plant Species Pyrosequencing - (Abstract Only)
Arias De Ares, R.S., Irish, B.M., Ballard, L.L., Duke, M.V., Liu, X.F., Simpson, S.A., Scheffler, B.E. 2010. Batch Isolation of Microsatellites for Tropical Plant Species Pyrosequencing. Plant and Animal Genome. Abstract P089.
Metagenomic analysis of the turkey gut RNA virus community - (Peer Reviewed Journal)
Day, J.M., Ballard, L.L., Duke, M.V., Scheffler, B.E., Zsak, L. 2010. Metagenomic analysis of the turkey gut RNA virus community. Virology Journal. 7:313.
UPIC + GO: Zeroing in on informative markers - (Other)
Ford, D., Arias, R.S., Ballard, L.L., Scheffler, B.E., Duke, M.V., Simpson, S.A., Newsome, A. 2010. UPIC + GO: Zeroing in on informative markers. Eighth Annual Rocky Mountain Bioinformatics Conference, International Society of Computational Biology (ISCB), December 09-11, 2010, Aspen, CO. Meeting Proceedings.
A First Generation Bac-Based Physical Map of the Channel Catfish Genome - (Peer Reviewed Journal)
Quiniou, S.M., Waldbieser, G.C., Duke, M.V. A first generation bac-based physical map of the channel catfish genome. Biomed Central (BMC) Genomics.
AMINO- AND UREA-SUBSTITUTED THIAZOLES INHIBIT PHOTOSYNTHETIC ELECTRON TRANSFER - (Peer Reviewed Journal)
STRATEGIES FOR THE DISCOVERY OF BIOACTIVE PHYTOCHEMICALS - (Book / Chapter)
EVALUATION OF FERULIC ACID FOR CONTROLLING THE MUSTY-ODOR CYANOBACTERIUM OSCILLATORIA PERORNATA IN AQUACULTURE PONDS - (Peer Reviewed Journal)
SEQUESTRATION OF PHYTOTOXINS BY PLANTS: IMPLICATIONS FOR COMMERCIAL BIOSYNTHETIC PRODUCTION - (Proceedings)
SELECTIVE BLUE-GREEN ALGICIDES FOR MANAGEMENT OF THE "OFF FLAVOR" PROBLEM IN CATFISH AQUACULTURE - (Abstract Only)
NATURAL PRODUCTS AS LEADS FOR NEW HERBICIDE MODES OF ACTION - (Proceedings)
PROTOPORPHYRINOGEN OXIDASE INHIBITORS -- THEIR CURRENT AND FUTURE ROLES - (Proceedings)