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Phone: (662) 686-5454Fax:     (662) 686-3567

JWDSRC, Bldg.1, Room 229141 Experiment Station Road

PO Box 36Stoneville, MS 38776-0036

Dr. Scheffler is the director of the SEA's Genomics and Bioinformatics Research Unit which serves a majority of the genomics needs for the entire SEA and also helps with other genomics needs of the Agency.  In conjunction with ARS scientists, he and his team help in the analysis of a wide range of important species including catfish, soybean, cotton, sugarcane, rice, sweet potato and various insects.   The Laboratory specializes in DNA sequencing, DNA marker technology and subsequent bioinformatic analysis.

- Projects Integrative Applied Agricultural ‘Omics and Bioinformatics ResearchIn-House Appropriated (D) Accession Number:444279Utilization of Cutting Edge Real Time Sensor Technology in Sugarcane BreedingNon-Assistance Cooperative Agreement (S) Accession Number:444548Genomes of Agriculturally Important Insects and PollinatorsNon-Assistance Cooperative Agreement (S) Accession Number:436423Next Generational Agricultural Research - Through the Use of High Performance ComputingNon-Assistance Cooperative Agreement (S) Accession Number:437257Computational Biology: Studying Species of Agronomic, Ecological, and Evolutionary ImportanceNon-Assistance Cooperative Agreement (S) Accession Number:438850Genomics of MalvaceaeNon-Assistance Cooperative Agreement (S) Accession Number:438861USDA ARS Research Apprenticeship Program at University of Texas at ArlingtonNon-Assistance Cooperative Agreement (S) Accession Number:442862
- Publications - (Clicking on the reprint icon  will take you to the publication reprint.)  
- Long-read sequencing  broadens access to genetic and transcript diversity for high-value traits in sorghum -(Abstract Only)     
- Genome report: chromosome-scale genome assembly of the West Indian fruit fly Anastrepha obliqua(Diptera: Tephritidae)  -(Peer Reviewed Journal)   Sim, S.B., Congrains, C., Velasco-Cuervo, S., Corpuz, R.L., Kauwe, A.N., Scheffler, B.E., Geib, S.M. 2024. Genome report: chromosome-scale genome assembly of the West Indian fruit fly Anastrepha obliqua(Diptera: Tephritidae). G3, Genes/Genomes/Genetics. 14(4). https://doi.org/10.1093/g3journal/jkae024.   
- Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in Saccharum spp. and Tripidium spp.  -(Peer Reviewed Journal)   Pan, Y., Todd, J.R., Lomax, L.E., White Jr, P.M., Simpson, S.A., Scheffler, B.E. 2023. Molecular Dissection of the 5S Ribosomal RNA-Intergenic Transcribed Spacers in Saccharum spp. and Tripidium spp.. Agronomy Journal. https://doi.org/10.3390/agronomy13112728.   
- Discovery of a resistance gene cluster associated with smut resistance in peanut -(Peer Reviewed Journal)     
- Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa  -(Peer Reviewed Journal)   Huff, M., Babiker, E.M., Hulse-Kemp, A.M., Scheffler, B.E., Youngblood, R.C., Simpson, S.A., Staton, M. 2023. Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa. BMC Genomics. https://doi.org/10.1186/s12864-023-09514-y.   
- The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50K SNP array for the St John River aquaculture strain of North American Atlantic salmon  -(Peer Reviewed Journal)   Gao, G., Waldbieser, G.C., Ramey, Y.C., Zaho, D., Pietrak, M.R., Stannard, J.A., Buchman, J.T., Scheffler, B.E., Peterson, B.C., Palti, Y., Rexroad III, C.E., Long, R., Burr, G.S., Milligan, M.T. 2023. The generation of the first chromosome-level de-novo genome assembly and the development and validation of a 50K SNP array for the St John River aquaculture strain of North American Atlantic salmon. G3, Genes/Genomes/Genetics. jkad138. https://doi.org/10.1093/g3journal/jkad138.   
- Chromosome-scale genome assembly of the rusty patched bumble bee, Bombus affinis (Cresson)(Hymenoptera: Apidae), an endangered North American pollinator  -(Peer Reviewed Journal)   Koch, J., Sim, S.B., Scheffler, B.E., Geib, S.M., Smith, T.A. 2023. Chromosome-scale genome assembly of the rusty patched bumble bee, Bombus affinis (Cresson)(Hymenoptera: Apidae), an endangered North American pollinator. G3, Genes/Genomes/Genetics. 13(8). Article jkad119. https://doi.org/10.1093/g3journal/jkad119.   
- Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions  -(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.   
- Detecting cotton leaf curl virus resistance quantitative trait Loci in Gossypium hirsutum and iCottonQTL a new R/Shiny app to streamline genetic mapping in cotton  -(Peer Reviewed Journal)   Schoonmaker, A., Hulse-Kemp, A.M., Youngblood, R.C., Rahmat, M., Iqbal, M., Mehboob-Ur-, R., Kochan, K.J., Scheffler, B.E., Scheffler, J.A. 2023. Detecting cotton leaf curl virus resistance quantitative trait Loci in Gossypium hirsutum and iCottonQTL a new R/Shiny app to streamline genetic mapping in cotton. Plants.  https://doi.org/10.3390/plants12051153.   
- Whole-genome resequencing data support a single introduction of the invasive white pine sawfly, Diprion similis  -(Peer Reviewed Journal)   Davis, J.S., Sim, S.B., Geib, S.M., Scheffler, B.E., Linnen, C.R. 2023. Whole-genome resequencing data support a single introduction of the invasive white pine sawfly, Diprion similis. Journal of Heredity. 114(3):246-258. https://doi.org/10.1093/jhered/esad012.   
- Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella, a global pest of cotton  -(Peer Reviewed Journal)   Stahlke, A.R., Chang, J., Chudalayandi, S., Heu, C.C., Geib, S.M., Scheffler, B.E., Childers, A.K., Fabrick, J.A. 2023. Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella, a global pest of cotton. G3, Genes/Genomes/Genetics. 13(4). Article jkad040. https://doi.org/10.1093/g3journal/jkad040.   
- Initiation of genomics-assisted breeding in virginia-type peanuts through the generation of a de novo reference genome and informative markers  -(Peer Reviewed Journal)   Newman, C.S., Andres, R.J., Youngblood, R.C., Campbell, J.D., Simpson, S.A., Cannon, S.B., Scheffler, B.E., Oakley, A.T., Hulse-Kemp, A.M., Dunne, J.C. 2023. Initiation of genomics-assisted breeding in Virginia-type peanuts through the generation of a de novo reference genome and informative markers. Frontiers in Plant Science. 13.Article 1073542. https://doi.org/10.3389/fpls.2022.1073542.   
- A chromosome-scale genome assembly of a Helicoverpa zea strain resistant to Bacillus thuringiensis Cry1Ac insecticidal protein  -(Peer Reviewed Journal)   Stahlke, A.R., Chen, J., Tembrock, L.R., Sim, S.B., Chudalayandi, S., Geib, S.M., Scheffler, B.E., Perera, O.P., Gilligan, T.M., Childers, A.K., Hackett, K.J., Coates, B.S. 2022. A chromosome-scale genome assembly of a Helicoverpa zea strain resistant to Bacillus thuringiensis Cry1Ac insecticidal protein. Genome Biology and Evolution. 15(3). Article evac131. https://doi.org/10.1093/gbe/evac131.   
- Transcriptomic response of Fusarium verticillioides to variably inhibitory environmental isolates of Streptomyces  -(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  -(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.   
- A chromosome-scale genome assembly of a Bacillus thuringiensis Cry1Ac insecticidal protein resistant strain of Helicoverpa zea  -(Pre-print Publication)   Stahlke, A.R., Chen, J.M., Tembrock, L.R., Sim, S.B., Chudalayandi, S., Geib, S.M., Scheffler, B.E., Perera, O.P., Gilligan, T.M., Childers, A.K., Hackett, K.J., Coates, B.S. 2022. A chromosome-scale genome assembly of a Bacillus thuringiensis Cry1Ac insecticidal protein resistant strain of Helicoverpa zea. bioRxiv. 1-23. https://doi.org/10.1101/2022.04.12.488070.   
- Analysis of a tetraploid cotton line Mac7 transcriptome reveals mechanisms underlying resistance against the whitefly Bemisia tabaci  -(Peer Reviewed Journal)   Aslam, M.Q., Naqvi, R.Z., Asif, M., Akhter, K.P., Scheffler, B.E., Scheffler, J.A., Liu, S., Amin, I., Mansoor, S. 2022. Analysis of a tetraploid cotton line Mac7 transcriptome reveals mechanisms underlying resistance against the whitefly Bemisia tabaci. Gene. 820:146200. https://doi.org/10.1016/j.gene.2022.146200.   
- Legacy genetics of arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange  -(Peer Reviewed Journal)   Bertioli, D.J., Clevenger, J., Godoy, I., Stalker, T., Wood, S., Santos, J., Ballen-Taborda, C., Abernathy, B., Azevedo, V., Campbell, J.D., Chavarro, C., Chu, Y., Farmer, A.D., Fonceka, D., Gao, D., Grimwood, J., Halpin, N., Korani, W., Michelotto, M.D., Ozias-Akins, P., Vaughn, J.N., Youngblood, R., Moretzsohn, M.C., Wright, G.C., Jackson, S.A., Cannon, S.B., Scheffler, B.E., Leal-Bertioli, S.M. 2021. Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange. Proceedings of the National Academy of Sciences(PNAS). 118(38). Article e2104899118. https://doi.org/10.1073/pnas.2104899118.   
- The USDA-ARS Ag100Pest Initiative: High-quality genome assemblies for agricultural pest Arthropod research  -(Peer Reviewed Journal)   Childers, A.K., Geib, S.M., Sim, S.B., Poelchau, M.F., Coates, B.S., Simmonds, T.J., Scully, E.D., Smith, T.P.L., Childers, C., Corpuz, R.L., Hackett, K.J., Scheffler, B.E. 2021. The USDA-ARS Ag100Pest Initiative: High-quality genome assemblies for agricultural pest insect research. Insects. 12(7):626. https://doi.org/10.3390/insects12070626.   
- ‘Jumping Jack’: Genomic microsatellites underscore the distinctiveness of closely related Pseudoperonospora cubensis and Pseudoperonospora humuli and provide new insights into their evolutionary past  -(Peer Reviewed Journal)   Nowicki, M., Hadziabdic-Guerry, D., Trigiano, R.N., Boggess, S.L., Kanetis, L., Wadl, P.A., Ojiambo, P.S., Cubeta, M.A., Spring, O., Thines, M., Runge, F., Scheffler, B.E. 2021. ‘Jumping Jack’: Genomic microsatellites underscore the distinctiveness of closely related Pseudoperonospora cubensis and Pseudoperonospora humuli and provide new insights into their evolutionary past. Molecular Plant Pathology. 12:686759. https://doi.org/10.3389/fmicb.2021.686759.   
- New reference genomes and comparative genomics analyses in Aspergillus flavus -(Abstract Only)     
- Identification of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) that are associated with nectariless trait of Gossypium hirsutum L.  -(Peer Reviewed Journal)   Park, S., Scheffler, J.A., Ray, J.D., Scheffler, B.E. 2021. Identification of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) that are associated with nectariless trait of Gossypium hirsutum L.. Euphytica. 217:78. https://doi.org/10.1007/s10681-021-02799-8.   
- A long reads-based De novo assembly of the genome of the Arlee homozygous line reveals structural genome variance in rainbow trout  -(Peer Reviewed Journal)   Gao, G., Magadan, S., Waldbieser, G.C., Youngblood, R., Wheeler, P., Scheffler, B.E., Thorgaard, G., Palti, Y. 2021. A long reads-based De novo assembly of the genome of the Arlee homozygous line reveals structural genome variance in rainbow trout. Genes, Genomes, and Genomics. https://doi.org/10.1093/g3journal/jkab052.   
- Gene disruption by structural mutations drives selection in US rice breeding over the last century  -(Peer Reviewed Journal)   Vaughn, J.N., Korani, W., Stein, J.C., Edwards, J., Peterson, D.G., Simpson, S.A., Youngblood, R.C., Grimwood, J., Ware, D., Mcclung, A.M., Scheffler, B.E. 2021. Gene disruption by structural mutations drives selection in US rice breeding over the last century. PLoS Genetics. 17(3): e1009389. https://doi.org/10.1371/journal.pgen.1009389.   
- A long reads-based De novo assembly of the genome of the Arlee homozygous line reveals structural genome variance in rainbow trout  -(Pre-print Publication)   Gao, G., Magadan, S., Waldbieser, G.C., Youngblood, R., Wheeler, P., Scheffler, B.E., Thorgaard, G., Palti, Y. 2021. A long reads-based De novo assembly of the genome of the Arlee homozygous line reveals structural genome variance in rainbow trout. bioRxiv. https://doi.org/10.1101/2020.12.28.424581.   
- Two new Aspergillus flavus reference genomes reveal a large insertion potentially contributing to isolate stress tolerance and aflatoxin production  -(Peer Reviewed Journal)   Fountain, J.C., Clevenger, J.P., Nadon, B.D., Youngblood, R.C., Chang, P., Starr, D., Wang, H., Wiggins, R., Kemerait, R.C., Bhatnagar, D., Ozias-Akins, P., Varshney, R.K., Scheffler, B.E., Vaughn, J.N., Guo, B. 2020. Two new Aspergillus flavus reference genomes reveal a large insertion potentially contributing to isolate stress tolerance and aflatoxin production. Genes, Genomes, and Genomics. 10(9). https://doi.org/10.1534/g3.120.401405.   
- 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)  -(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  -(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.   
- Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement  -(Peer Reviewed Journal)   Chen, Z., Sreedasyam, A., Ando, A., Song, Q., De Santiago, L., Hulse-Kemp, A.M., Ding, M., Ye, W., Kirkbride, R., Jenkins, J., Plott, C., Lovell, J., Yu-Ming, L., Vaughn, R., Liu, B., Simpson, S.A., Scheffler, B.E. 2020. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nature Genetics. https://doi.org/10.1038/s41588-020-0614-5.   
- Gene disruption by structural mutations drives selection in U.S. rice breeding over the last century -(Proceedings)   Vaughn, J.N., Stein, J.C., Korani, W., Edwards, J., Peterson, D.G., Simpson, S.A., Grimwood, J., Ware, D., McClung, A.M., Scheffler, B.E. 2021. Gene disruption by structural mutations drives selection in U.S. rice breeding over the last century. Proceedings of 38th Rice Technical Working Group Meeting, February 24-27, 2020, Orange Beach, Alabama. p 77. Electronic Publication.   
- Genetic diversity among geographically separated Cyperus rotundus accessions based on RAPD markers and morphological characteristics -(Peer Reviewed Journal)   Molin, W.T., Kronfol, R.R., Ray, J.D., Scheffler, B.E., Bryson, C.T. 2019. Genetic diversity among geographically separated Cyperus rotundus accessions based on RAPD markers and morphological characteristics. American Journal of Plant Sciences. 10:2034-2046.   
- A long reads-based De-novo assembly of the rainbow trout Arlee-line genome -(Abstract Only)   Gao, G., Waldbieser, G.C., Youngblood, R.C., Wheeler, P.A., Scheffler, B.E., Thorgaard, G.H., Palti, Y. 2020. A long reads-based De-novo assembly of the rainbow trout Arlee-line genome. In Proceedings of the Plant and Animal Genome Conference. International Plan and Animal Genome Conference,January 11, 2020, San Diego, CA. P.No.PE0432.   
- A long reads-based trio-binning De-novo assembly of the North American Atlantic salmon genome -(Abstract Only)   Gao, G., Waldbieser, G.C., Youngblood, R.C., Pietrak, M.R., Scheffler, B.E., Rexroad III, C.E., Peterson, B.C., Palti, Y. 2020. A long reads-based trio-binning De-novo assembly of the North American Atlantic salmon genome. Plant and Animal Genome Conference. 28th International Plant and Animal Genome Conference held in San Diego, CA, January 11, 2020. P.No.PO0425.   
- A long reads-based De-novo assembly of the rainbow trout Arlee-line genome -(Abstract Only)   Gao, G., Waldbieser, G.C., Youngblood, R.C., Wheeler, P.A., Scheffler, B.E., Thorgaard, G.H., Palti, Y. 2019. A long reads-based De-novo assembly of the rainbow trout Arlee-line genome. International Conference on Integrative Salmonid Biology. In: Proceedings of International Conference on Integrative Salmonid Biology,November 17,2019, Edinburgh, Scotland, UK. P.No.ORAL-1.4   
- A long reads-based trio-binning De-novo assembly of the North American Atlantic salmon genome -(Abstract Only)   Gao, G., Waldbieser, G.C., Youngblood, R.C., Pietrak, M.R., Scheffler, B.E., Rexroad Iii, C.E., Peterson, B.C., Palti, Y. 2019. A long reads-based trio-binning De-novo assembly of the North American Atlantic salmon genome. In:Proceedings of International Conference on Integrative Salmonid Biology. Fourth International Conference on Integrative Salmonid Biology, November 17, 2019, Edinburgh, Scotland, UK. P.No.Poster - 1   
- A high-quality genome assembly from a single, field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System  -(Peer Reviewed Journal)   Kingan, S.B., Urban, J., Lambert, C.C., Baybayan, P., Childers, A.K., Coates, B.S., Scheffler, B.E., Hackett, K.J., Korlack, J., Geib, S.M. 2019. A high-quality genome assembly from a single, field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System. Gigascience. 8(10):1-10. https://doi.org/10.1093/gigascience/giz122.   
- Mitogenome and nuclear-encoded fungicide-target genes of Thecaphora frezii- causal agent of peanut smut  -(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.   
- Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum)  -(Peer Reviewed Journal)   Zaidi, S., Naqvi, R., Asif, M., Strickler, S., Shakir, S., Woldemariam, M., Shafiq, M., Khan, A.M., Amin, I., Mishra, B., Mukhtar, S., Jander, G., Scheffler, B.E., Scheffler, J.A., Mueller, L.A., Mansoor, S. 2019. Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum). Plant Biotechnology Journal. Volume 18, Issue 3.   
- Microsatellite markers in Spanish lime (Melicoccus bijugatus Jacq., Sapindaceae), a neglected Neotropical fruit crop  -(Peer Reviewed Journal)   Martinez-Castillo, J., Arias De Ares, R.S., Andueza-Noh, R.H., Ortiz-Garcia, M.M., Irish, B.M., Scheffler, B.E. 2019. Microsatellite markers in Spanish lime (Melicoccus bijugatus Jacq., Sapindaceae), a neglected Neotropical fruit crop. Genetic Resources and Crop Evolution. 66(7):1371-1377. https://doi.org/10.1007/s10722-019-00815-4.   
- Whole genome sequencing of Asia II 1 species of whitefly reveals that genes involved in virus transmission and insecticide resistance have genetic variances between Asia II 1 and MEAM1 species  -(Peer Reviewed Journal)   Hussain, S., Farooq, M., Malik, H., Amin, I., Scheffler, B.E., Scheffler, J.A., Liu, S., Mansoor, S. 2019. Whole genome sequencing of Asia II 1 species of whitefly reveals that genes involved in virus transmission and insecticide resistance have genetic variances between Asia II 1 and MEAM1 species. BMC Genomics. 20:507. https://doi.org/10.1186/s12864-019-5877-9.   
- Non-cultivated cotton species (Gossypium spp.) act as a reservoir for cotton leaf curl begomoviruses and associated satellites  -(Peer Reviewed Journal)   Shakir, S., Zaidi, S., Farooq, M., Amin, I., Scheffler, J.A., Scheffler, B.E., Nawaz-Ul-Rehman, M., Mansoor, S., Atiq, U. 2019. Non-cultivated cotton species (Gossypium spp.) act as a reservoir for cotton leaf curl begomoviruses and associated satellites. Plants. 8:127.  https://doi.org/10.3390/plants8050127.   
- Dissecting the role of oxidative stress in host-Aspergillus flavus interactions using genomics and genetic engineering -(Abstract Only)     
- Chemical defense responses of upland cotton, Gossypium hirsutum L. to physical wounding  -(Peer Reviewed Journal)   Park, S., Scheffler, J.A., Scheffler, B.E., Cantrell, C.L., Pauli, C.S. 2019. Chemical defense responses of upland cotton, Gossypium hirsutum L. to physical wounding. Plant Direct. 3:5. https://doi.org/10.1002/pld3.141.   
- The genome sequence of segmental allotetraploid peanut Arachis hypogaea  -(Peer Reviewed Journal)   Bertioli, D.J., Jenkins, J., Clevenger, J., Dudchenko, O., Gao, D., Seijo, G., Leal-Bertioli, S., Ren, L., Farmer, A., Pandey, M., Samoluk, S.S., Abernathy, B., Agarwal, G., Ballen-Taborda, C., Cameron, C., Campbell, J., Chavarro, C., Chitikineni, A., Chu, Y., Dash, S., El Baidouri, M., Guo, B., Huang, W., Kim, K.D., Korani, W., Lanciano, S., Lui, C.G., Mirouze, M., Moretzsohn, M.C., Pham, M., Shin, J.H., Shirasawa, K., Sinharoy, S., Sreedasyam, A., Weeks, N.T., Zhang, X., Zheng, Z., Sun, Z., Froenicke, L., Aiden, E.L., Michelmore, R., Varshney, R.K., Holbrook Jr, C.C., Cannon, E.K., Scheffler, B.E., Grimwwood, J., Ozias-Akins, P., Cannon, S.B., Jackson, S.A., Schmutz, J. 2019. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nature Genetics. 51:877-884. https://doi.org/10.1038/s41588-019-0405-z.   
- Insights into the evolution of the New World diploid cottons (Gossypium, subgenus Houzingenia) based on genome sequencing  -(Peer Reviewed Journal)   Grover, C.E., Arick, M.A., Thrash, A., Conover, J.L., Sanders, W.S., Peterson, D.G., Frelichowski, J.E., Scheffler, J.A., Scheffler, B.E., Wendel, J.F. 2018. Insights into the evolution of the New World diploid cottons (Gossypium, subgenus Houzingenia) based on genome sequencing. Genome Biology and Evolution. 11(1):53-71. https://doi.org/10.1093/gbe/evy256.   
- Peanut germplasm screening for aflatoxin accumulation and genetic fingerprinting -(Abstract Only)     
- New tools to screen wild peanut species for aflatoxin accumulation and genetic fingerprinting  -(Peer Reviewed Journal)   Arias De Ares, R.S., Sobolev, V., Massa, A.N., Orner, V.A., Walk, T., Simpson, S.A., Ballard, L.L., Puppala, N., Scheffler, B.E., De Blass, F., Tallury, S.P., Guillermo, S. 2018. New tools to screen wild peanut species for aflatoxin accumulation and genetic fingerprinting. Biomed Central (BMC) Plant Biology. https://doi.org/10.1186/s12870-018-1355-9.   
- The hunt for the "silver bullet": Reference genome development and comparative genomics analysis of field isolates of Aspergillus flavus for identification of aflatoxin regulators -(Abstract Only)     
- Maximizing Utility of Community-based Resources -(Abstract Only)     
- Lessons from Cotton: Research Projects Following Development of a Community-based Genotyping Array -(Abstract Only)     
- 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.   
- Gene space and transcriptome assemblies of leafy spurge (Euphorbia esula) identify promoter sequences, repetitive elements, high-quality markers, and a full-length chloroplast genome  -(Peer Reviewed Journal)   Horvath, D.P., Patel, S., Dogramaci, M., Chao, W.S., Anderson, J.V., Foley, M.E., Scheffler, B., Lazo, G., Dorn, K., Yan, C., Childers, A., Schatz, M., Marcus, S. 2018. Gene space and transcriptome assemblies of leafy spurge (Euphorbia esula) identify promoter sequences, repetitive elements, high-quality markers, and a full-length chloroplast genome. Weed Science. 66(3):355-367. https://doi.org/10.1017/wsc.2018.2.   
- Evaluation of carbon nanotube based copper nanoparticle composite for the efficient detection of agroviruses  -(Peer Reviewed Journal)   Tahir, M.A., Bajwa, S.Z., Mansoor, S., Briddon, R.W., Khan, W.S., Scheffler, B.E., Amin, I. 2018. Evaluation of carbon nanotube based copper nanoparticle composite for the efficient detection of agroviruses. Journal of Hazardous Materials. 346:27–35.  doi: 10.1016/j.jhazmat.2017.12.007.   
- Transcriptomics reveals multiple resistance mechanisms against cotton leaf curl disease in a naturally immune cotton species, Gossypium arboreum  -(Peer Reviewed Journal)   Naqvi, R., Zaidi, S., Akhtar, K.P., Strickler, S., Woldemariam, M., Mishra, B., Mukhtar, M., Scheffler, B.E., Scheffler, J.A., Jander, G., Mueller, L.A., Asif, M., Mansoor, S. 2017. Transcriptomics reveals multiple resistance mechanisms against cotton leaf curl disease in a naturally immune cotton species, Gossypium arboreum. Scientific Reports. 7:15880. https://doi:10.1038/s41598-017-15963-9.   
- Subgenome-anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids  -(Peer Reviewed Journal)   Saski, C.A., Scheffler, B.E., Hulse-Kemp, A.M., Liu, B., Song, Q., Stelly, D.M., Scheffler, J.A., Jones, D.C., Peterson, D.G., Haigler, C., Schmutz, J., Chen, Z.J. 2017. Subgenome-anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids. Scientific Reports. 7:15274. https://doi:10.1038/s41598-017-14885-w.   
- Genome sequences of three strains of Aspergillus flavus for the biological control of Aflatoxin  -(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.   
- Length and nucleotide sequence polymorphism at the trnL and trnF non-coding regions of chloroplast genomes among Saccharum and Erianthus species -(Abstract Only)   Pan, Y., Todd, J.R., Scheffler, B.E., Hale, A.L., Lomax, L.E., Simpson, S.A., Liu, F., Grisham, M.P. 2017. Length and nucleotide sequence polymorphism at the trnL and trnF non-coding regions of chloroplast genomes among Saccharum and Erianthus species [abstract]. Journal of the American Society of Sugar Cane Technologists. 37:32.   
- Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton -(Peer Reviewed Journal)   Zubair, M., Zaidi, S., Shakir, S., Farooq, M., Amin, I., Scheffler, J.A., Scheffler, B.E., Mansoor, S. 2017. Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton. Scientific Reports. 7:article number 680. doi:10.1038/s41598-017-00727-2.   
- Study of the genetic diversity of the aflatoxin biosynthesis cluster in Aspergillus section Flavi using insertion/deletion markers in peanut seeds from Georgia, USA -(Peer Reviewed Journal)   Faustinelli, P.C., Palencia, E.R., Wang, X.M., Sobolev, V., Horn, B.W., Sheppard, H.T., Lamb, M.C., Scheffler, B.E., Martinez-Castillo, J., Arias De Ares, R.S. 2017. Study of the genetic diversity of the aflatoxin biosynthesis cluster in Aspergillus section Flavi using insertion/deletion markers in peanut seeds from Georgia, USA. Mycologia. doi:10.1080/00275514.2017.1307095.   
- Naturally occurring high oleic acid cottonseed oil: identification and functional analysis of a mutant allele of Gossypium barbadense fatty acid desaturase-2 -(Peer Reviewed Journal)   Shockey, J., Dowd, M., Mack, B., Gilbert, M., Scheffler, B., Ballard, L., Frelichowski, J., Mason, C. 2017. Naturally occurring high oleic acid cottonseed oil: identification and functional analysis of a mutant allele of Gossypium barbadense fatty acid desaturase-2. Planta. 245:611-622.   
- RNAi-mediated mortality of the whitefly through transgenic expression of double-stranded RNA homologous to acetylcholinesterase and ecdysone receptor in tobacco plants -(Peer Reviewed Journal)   Malik, H.J., Raza, A., Amin, I., Scheffler, J.A., Scheffler, B.E., Brown, J.K., Mansoor, S. 2016. RNAi-mediated mortality of the whitefly through transgenic expression of double-stranded RNA homologous to acetylcholinesterase and ecdysone receptor in tobacco plants. Scientific Reports. 6. doi:10.1038/srep38469.   
- Amplicon based RNA interference targeting V2 gene of cotton leaf curl Kokhran virus-Burewala strain can provide resistance in transgenic cotton plants -(Peer Reviewed Journal)   Yasmeen, A., Kiani, S., Butt, A., Rao, A.Q., Akram, F., Ahmad, A., Nasir, I.A., Husnain, T., Mansoor, S., Amin, I., Zubair, M., Tahir, M.N., Akhtar, S., Scheffler, J.A., Scheffler, B.E. 2016. Amplicon based RNA interference targeting V2 gene of cotton leaf curl Kokhran virus-Burewala strain can provide resistance in transgenic cotton plants. Molecular Biotechnology. doi:10.1007/s12033-016-9980-8.   
- A developmental transcriptome map for allotetraploid arachis hypogaea  -(Peer Reviewed Journal)   Clevenger, J., Chu, Y., Scheffler, B.E., Ozias-Akins, P. 2016. A developmental transcriptome map for allotetraploid arachis hypogaea. Frontiers in Plant Science. 7:1446. doi: 10.3389/fpls.2016.01446.   
- Colistin resistance mcr-1 gene bearing Escherichia coli from the United States -(Peer Reviewed Journal)   Meinersmann, R.J., Ladely, S.R., Plumblee Lawrence, J.R., Hall, M.C., Simpson, S.A., Ballard, L.L., Scheffler, B.E., Genzlinger, L.L., Cook, K.L. 2016. Colistin resistance mcr-1 gene bearing Escherichia coli from the United States. Genome Announcements. 4(5):898-16.   
- Frequent occurrence of tomato leaf curl New Delhi virus in cotton leaf curl disease affected cotton in Pakistan -(Peer Reviewed Journal)   Zaidi, S.S., Shafiq, M., Amin, I., Scheffler, B.E., Scheffler, J.A., Briddon, R.W., Mansoor, S. 2016. Frequent occurrence of tomato leaf curl New Delhi virus in cotton leaf curl disease affected cotton in Pakistan. PLoS One. doi:10.1371/journal.pone.0155520.   
- 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.   
- Development and characterization of 12 polymorphic microsatellite loci for pityopsis graminifolia var. latifolia -(Abstract Only)   Boggess, S., Wadl, P.A., Hadziabdic, D., Scheffler, B.E., Windham, A., Klingeman, W., Trigiano, R. 2016. Development and characterization of 12 polymorphic microsatellite loci for pityopsis graminifolia var. latifolia. HortScience. 51:S101.   
- RNA Interference Based Approach to Down Regulate Osmoregulators of Whitefly (Bemisia tabaci): Potential Technology for the Control of Whitefly  -(Peer Reviewed Journal)   Raza, A., Malik, H., Shafiq, M., Amin, I., Scheffler, J.A., Scheffler, B.E., Mansoor, S. 2016. RNA Interference Based Approach to Down Regulate Osmoregulators of Whitefly (Bemisia tabaci): Potential Technology for the Control of Whitefly. PLoS One. 11:e0153883.   
- Workflow to study genetic biodiversity of aflatoxigenic Aspergillus spp. in Georgia, USA -(Abstract Only)     
- The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut -(Peer Reviewed Journal)   Bertioli, D., Cannon, S.B., Froenicke, L., Huang, G., Farmer, A.D., Cannon, E., Dash, S., Liu, X., Barkley, N.L., Guo, B., Scheffler, B.E., et al. 2016. The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nature Genetics. 48:438-446. doi: 10.1038/ng.3517.   
- Genetic diversity of the two commercial tetraploid cotton species in the Gossypium Diversity Reference Set -(Peer Reviewed Journal)   Hinze, L.L., Gazave, E., Gore, M.A., Fang, D.D., Scheffler, B.E., Yu, J., Jones, D.C., Frelichowski, J.E., Percy, R.G. 2016. Genetic diversity of the two commercial tetraploid cotton species in the Gossypium Diversity Reference Set. Journal of Heredity. 107(3):274-286.   
- Genetic and environmental effects in the TeQing-into-Lemont (TIL) population under flooded and alternating wet-dry conditions -(Proceedings)   Edwards, J., Teaster, N.D., Scheffler, B.E., McClung, A.M. 2017. Genetic and environmental effects in the TeQing-into-Lemont (TIL) population under flooded and alternating wet-dry conditions. Proc. 36th Rice Technical Working Group Meeting, Galveston, TX, p. 69-70. March 1-4, 2016. CDROM.   
- Sesbania bispinosa, a new host of a begomovirus-betasatellite complex in Pakistan -(Peer Reviewed Journal)   Zaidi, S.S., Amin, I., Iqbal, Z., Akhtar, K.P., Scheffler, B.E., Mansoor, S. 2016. Sesbania bispinosa, a new host of a begomovirus-betasatellite complex in Pakistan. Canadian Journal of Plant Pathology. 38:1, 107-111, DOI:10.1080/07060661.2015.1128980.   
- Application of genomic, transcriptomic and metabolomic technologies in Arachis species -(Book / Chapter)   Chu, Y., Clevenger, J., Hovav, R., Wang, J., Scheffler, B.E., Jackson, S., Ozias-Akins, P. 2016. Peanuts: genetics, processing, and utilization. In: Elsevier. Application of genomic, transcriptomic and metabolomic technologies in Arachis species. San Diego, CA. p.209-239.   
- Virus-induced gene silencing in cultivated cotton (Gossypium spp.) using Tobacco rattle virus  -(Peer Reviewed Journal)   Mustafa, R., Shafiq, M., Mansoor, S., Briddon, R.W., Scheffler, B.E., Scheffler, J.A., Amin, I. 2016. Virus-induced gene silencing (VIGS) in cultivated cotton (Gossypium spp.) using Tobacco rattle virus (TRV). Molecular Biotechnology. 58:65–72. doi: 10.1007/s12033-015-9904-z.   
- Analysis of genetic diversity and population structure for the native tree Viburnum rufidulum occurring in Kentucky and Tennessee -(Peer Reviewed Journal)     
- Genomic resources for water yam (Dioscorea alata L.): analyses of EST-Sequences, De Novo sequencing and GBS libraries -(Peer Reviewed Journal)   Saski, C.A., Bhattacharjee, R., Scheffler, B.E., Asiedu, R. 2015. Genomic resources for water yam (Dioscorea alata L.): analyses of EST-Sequences, De Novo sequencing and GBS libraries. PLoS One. doi:10.1371/journal.pone.0134031.   
- Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall sythesis, represses lignification, and prolongs elongation  -(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.   
- Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences -(Peer Reviewed Journal)   Gardner, E.M., Laricchia, K.M., Murphy, M., Ragone, D., Scheffler, B.E., Simpson, S.A., Williams, E., Zerega, N.C. 2015. Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences. Applications in Plant Sciences. 3(9):1500049. doi:10.3732/apps.1500049.   
- Transcriptomic changes in zebrafish embryos and larvae following benzo[a]pyrene exposure -(Peer Reviewed Journal)   Fang, X., Corrales, J., Thornton, C., Clerk, T., Scheffler, B.E., Willett, K.L. 2015. Transcriptomic changes in zebrafish embryos and larvae following benzo[a]pyrene exposure. Toxicological Sciences. 146(2):395-411. doi: 10.1093/toxsci/kfv105..   
- The first nearly cryptic Scorpionfly (Mecoptera: Panorpidae) from North America -(Peer Reviewed Journal)   Bicha, W., Schiff, N., Lancaster, A., Scheffler, B.E. 2015. The first nearly cryptic Scorpionfly (Mecoptera: Panorpidae) from North America. Zootaxa. 3973(3):591–600. doi.org/10.11646/zootaxa.3973.3.12.   
- Fluorescence- and capillary electrophoresis (CE)-based SSR DNA fingerprinting and a molecular identity database for the Louisiana sugarcane industry -(Abstract Only)   Pan, Y., Scheffler, B.E., Dufrene Jr, E.O., Waguespack, H., Grisham, M.P. 2015. Fluorescence- and capillary electrophoresis (CE)-based SSR DNA fingerprinting and a molecular identity database for the Louisiana sugarcane industry. Journal of the American Society of Sugar Cane Technologists. 35:51.   
- Ecology, Behavior and Bionomics: First Genotyping of Spodoptera frugiperda (J. E. Smith)(Lepidoptera: Noctuidae) Progeny from Crosses between Bt-Resistant and Bt-Susceptible Populations, and 65-Locus Discrimination of Isofami -(Peer Reviewed Journal)   Arias De Ares, R.S., Portilla, M., Ray, J.D., Blanco, C.A., Simpson, S.A., Scheffler, B.E. 2015. Ecology, Behavior and Bionomics: First Genotyping of Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) Progeny from Crosses between Bt-Resistant and Bt-Susceptible Populations, and 65-Locus Discrimination of Isofamilies. The Journal of Botanical Society. 4:18-29.   
- BAC-end sequence-based SNP mining in Allotetraploid Cotton (Gossypium) utilizing re-sequencing data, phylogenetic inferences and perspectives for genetic mapping -(Peer Reviewed Journal)   Hulse-Kemp, A.M., Hamid, A., Stoffel, K., Pepper, A.E., Saski, C., Scheffler, B.E., Fang, D.D., Chen, Z., Van Deynze, A., Zheng, X., Stelly, D.M. 2015. BAC-end sequence-based SNP mining in Allotetraploid Cotton (Gossypium) utilizing re-sequencing data, phylogenetic inferences and perspectives for genetic mapping. Genes, Genomes, and Genomics. 5:1095-1105. doi:10.1534/g3.115.017749/-/DC1.   
- Biotechnology in weed control -(Book / Chapter)   Duke, S.O., Scheffler, B.E., Boyette, C.D., Dayan, F.E. 2015. Biotechnology in weed control. In: Kirk Othmer Encyclopedia for Technical Technology, Wiley Interscience, New York. p. 1-25. DOI: 10.1002/0471238961.   
- Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement -(Peer Reviewed Journal)   Zhang, T., Hu, Y., Jiang, W., Fang, L., Guan, X., Chen, J., Zhang, J., Saski, C., Scheffler, B.E., Stelly, D.M., Hulse-Kemp, A.M., Wan, Q., Liu, B., Liu, C., Wang, S., Pan, M., Wang, Y., Wang, D., Ye, W., Chang, L., Zhang, W., Song, Q., Kirkbride, R.C., Chen, X., Dennis, E., Llewellyn, D.J., Peterson, D.G., Thaxton, P., Jones, D.C., Wang, Q., Xu, X., Zhang, H., Wu, H., Zhou, L., Mei, G., Chen, S., Tian, Y., Xiang, D., Li, X., Ding, J., Zuo, Q., Tao, L., Liu, Y., Li, J., Lin, Y., Hui, Y., Cao, Z., Cai, C., Zhu, X., Jiang, Z., Zhou, B., Guo, W., Li, R., Chen, Z. 2015. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nature Biotechnology. 33(5):531-537. doi:10.1038/nbt.3207.   
- Development of microsatellites from Fothergilla xintermedia (Hamamelidaceae) and cross transfer to four other genera within Hamamelidaceae  -(Peer Reviewed Journal)   Hatmaker, E., Wadl, P.A., Mantooth, K., Scheffler, B.E., Ownley, B.H., Trigiano, R.N. 2015. Development of microsatellites from Fothergilla xintermedia (Hamamelidaceae) and cross transfer to four other genera within Hamamelidaceae. Applications in Plant Sciences. 3(4):1400123. doi.org/10.3732/apps.1400123. Availiable: http://www.bioone.org/doi/full/10.3732/apps.1400123.   
- Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection -(Peer Reviewed Journal)   Duitama, J., Silva, A., Sanabria, Y., Cruz, D., Quintero, C., Ballen, C., Lorieux, M., Scheffler, B.E., Farmer, A., Torres, E., Oard, J., Tohme, J. 2015. Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection. PLoS One. 10(4):e0124617. doi:10.1371/journal.pone.0124617.   
- RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean  -(Peer Reviewed Journal)   Horvath, D.P., Hansen, S.A., Moriles-Miller, J.C., Pierik, R., Yan, C., Clay, D.E., Scheffler, B., Clay, S.A. 2015. RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean. New Phytologist. 207:196-210. https://doi.org/10.1111/nph.13351.   
- Diversity of the breadfruit complex (Artocarpus, Moraceae): Genetic characterization of critical germplasm -(Peer Reviewed Journal)   Zerega, N., Wiesner-Hanks, T., Ragone, D., Irish, B.M., Scheffler, B.E., Simpson, S.A., Zee, F.T. 2015. Diversity of the breadfruit complex (Artocarpus, Moraceae): Genetic characterization of critical germplasm. Tree Genetics and Genomes. doi: 10.1007/s11295-014-0824-z.   
- Molecular characterization of the Gossypium diversity reference set of the US National Cotton Germplasm Collection -(Peer Reviewed Journal)   Hinze, L.L., Fang, D.D., Gore, M.A., Scheffler, B.E., Yu, J., Frelichowski, J.E., Percy, R.G. 2015. Molecular characterization of the Gossypium diversity reference set of the US National Cotton Germplasm Collection. Theoretical and Applied Genetics. 128(2):313-327.   
- Development of microsatellites from Cornus mas L. (Cornaceae) and characterization of genetic diversity of cornelian cherries from China, central Europe, and the United States  -(Peer Reviewed Journal)   Wadl, P.A., Szyp-Borowska, I., Piórecki, N., Schlarbaum, S.E., Scheffler, B.E., Trigiano, R.N. 2014. Development of microsatellites from Cornus mas L. (Cornaceae) and characterization of genetic diversity of cornelian cherries from China, central Europe, and the United States. Scientia Horticulturae. 179:314-320.   
- Characterization of 12 polymorphic microsatellite loci of Pityopsis graminifolia var. latifolia  -(Peer Reviewed Journal)   Boggess, S.L., Wadl, P.A., Hadziabdic, D., Scheffler, B.E., Windham, A.S., Klingeman, W.E., Trigiano, R.N. 2014. Characterization of 12 polymorphic microsatellite loci of Pityopsis graminifolia var. latifolia. Conservation Genetics. 6(4):1043-1045. DOI: 10.1007/s12686-014-0282-9.   
- Extensive and biased intergenomic nonreciprocal DNA exchanges shaped a nascent polyploid genome, Gossypium (cotton) -(Peer Reviewed Journal)   Guo, H., Wang, X., Gundlach, H., Mayer, K.F., Peterson, D.G., Scheffler, B.E., Chee, P.W., Paterson, A.H. 2014. Extensive and biased intergenomic nonreciprocal DNA exchanges shaped a nascent polyploid genome, Gossypium (cotton). Genetics. 197:1153-1163. do1 1 0.1 534/genetics.114.1 66124/-/DC 1.   
- Musa spp. germplasm management: microsatellite fingerprinting of USDA-ARS National Plant Germplasm System (NPGS) collection -(Peer Reviewed Journal)   Irish, B.M., Cuevas, H.E., Simpson, S.A., Scheffler, B.E., Sardos, J., Ploetz, R., Goenaga, R.J. 2014. Musa spp. germplasm management: microsatellite fingerprinting of USDA-ARS National Plant Germplasm System (NPGS) collection. Crop Science. 54:2140-2151.   
- Complete genome sequence of an attenuated Sparfloxacin-resistant Streptococcus agalactiae strain 138spar -(Other)   Wei Pridgeon, Y., Zhang, D., Zhang, L., Ballard, L.L., Scheffler, B.E. 2014. Complete genome sequence of an attenuated Sparfloxacin-resistant Streptococcus agalactiae strain 138spar. Genbank. Accession No. CP007565.1.   
- 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.   
- Using RNA-seq transcriptome profiling in support of field based strategies to improve cotton productivity under water deficit stress -(Abstract Only)   Campbell, B.T., Bowman, M., Park, W., Bauer, P.J., Scheffler, B.E., Udall, J., Jones, D.C. 2014. Using RNA-seq transcriptome profiling in support of field based strategies to improve cotton productivity under water deficit stress. In: Proceeedings of the Plant and Animal Genome XXII Conference, January 10-15, San Diego, CA. p918.   
- RNA-seq transcriptome profiling of upland cotton (Gossypium hirsutum) root tissue under water-deficit stress -(Peer Reviewed Journal)   Bowman, M.J., Park, W., Bauer, P.J., Udall, J.A., Page, J.T., Raney, J., Scheffler, B.E., Jones, D.C., Campbell, B.T. 2013. RNA-seq transcriptome profiling of upland cotton (Gossypium hirsutum) root tissue under water-deficit stress. PLoS One. 8:e82634.   
- 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  -(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.   
- Candidate gene association mapping of Sclerotinia stalk rot resistance in sunflower (Helianthus annuus L.) uncovers the importance of COI1 homologs -(Peer Reviewed Journal)   Talukder, Z.I., Hulke, B.S., Qi, L., Scheffler, B.E., Pegadaraju, V., McPhee, K., Gulya, T.J. 2014. Candidate gene association mapping of Sclerotinia stalk rot resistance in sunflower (Helianthus annuus L.) uncovers the importance of COI1 homologs. Theoretical and Applied Genetics. 127:193-209.   
- 'Ebony Embers', 'Ebony Fire', 'Ebony Flame','Ebony Glow' and 'Ebony and Ivory' Dark-Leaf Crapemyrtles  -(Peer Reviewed Journal)   Pounders Jr, C.T., Scheffler, B.E., Rinehart, T.A. 2013. 'Ebony Embers', 'Ebony Fire', 'Ebony Flame','Ebony Glow' and 'Ebony and Ivory' Dark-Leaf Crapemyrtles. HortScience. 48(12)1568-1570.   
- Integrated genomic and phenomic approaches for improving cotton productivity under water deficit stress -(Proceedings)   Campbell, B.T., Park, W., Bowman, M.J., Bauer, P.J., Scheffler, B.E., Udall, J., Jones, D.C. 2013. Integrated genomic and phenomic approaches for improving cotton productivity under water deficit stress. In: Proceedings of the Interdrought-IV Research conference, September 6-8, Perth, australia. 2013 CDROM.   
- Developmental regulation of diacylglycerol acyltransferase family gene expression in tung tree tissues -(Peer Reviewed Journal)   Cao, H., Shockey, J.M., Klasson, K.T., Chapital, D.C., Mason, C.B., Scheffler, B.E. 2013. Developmental regulation of diacylglycerol acyltransferase family gene expression in tung tree tissues. PLoS ONE 8(10):e76946. doi: 10.1371/journal.pone.0076946.   
- Submission to NCBI Sequence Read Archive (SRA): Raw read files from manuscript “RNA-seq transcriptome profiling of upland cotton (Gossypium hirsutum) root tissue under water deficit stress” NCBI SRA Accession No. PRJNA210770 -(Other)   Bowman, M.J., Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T., Page, J.T., Udall, J.A., Raney, J. 2013. Submission to NCBI Sequence Read Archive (SRA): Raw read files from manuscript “RNA-seq transcriptome profiling of upland cotton (Gossypium hirsutum) root tissue under water deficit stress” NCBI SRA Accession No. PRJNA210770. National Center for Biotechnology Information (NCBI). National Center for Biotechnology Information. SRA PRJNA210770.   
- Transcriptome sequencing of Hydrangea macrophylla to uncover genes related to reblooming and powdery mildew resistance -(Proceedings)   Rinehart, T.A., Reed, S.M., Scheffler, B.E. 2013. Transcriptome sequencing of Hydrangea macrophylla to uncover genes related to reblooming and powdery mildew resistance. Acta Horticulture Proceedings. 3:30-37.   
- Global and gene specific DNA methylation changes during zebrafish development -(Peer Reviewed Journal)   Fang, X., Corrales, J., Thornton, C., Scheffler, B.E., Willett, K.L. 2013. Global and gene specific DNA methylation changes during zebrafish development. Comparative Biochemistry and Physiology. Part B. 166:99-108. DOI.org/10.1016/j.cbpb.2013.07.007.   
- Drought stress related gene expression patterns and sub-genome localization of five aquaporin genes in upland cotton (Gossypium hirsutum) -(Abstract Only)   Bowman, M.J., Park, W., Bauer, P.J., Udall, J.A., Page, J.T., Scheffler, B.E., Campbell, B.T. 2013. Drought stress related gene expression patterns and sub-genome localization of five aquaporin genes in upland cotton (Gossypium hirsutum). In: Proceedings of the 2013 Joint Annual Meeting of the National Association of Plant Breeders and the Plant Breeding Coordinating Committee, Tampa, FL. June 2-5. 20.   
- Molecular characterization of Uzbekistan isolates of fusarium oxysporum f. sp. vasinfectum -(Peer Reviewed Journal)   Egamberdiev, S.S., Ulloa, M., Saha, S., Salakhudinov, I.B., Abdullaev, A., Glukhova, L.A., Adylova, A.T., Scheffler, B.E., Jenkins, J.N., Abdurakhmonov, I.Y. 2013. Molecular characterization of Uzbekistan isolates of fusarium oxysporum f. sp. vasinfectum. Journal of Plant Science and Molecular Breeding. 2:3.   
- Isolation and characterization of microsatellite Loci for Cornus sanguniea (Cornaceae) 1 -(Peer Reviewed Journal)   Wadl, P.A., Hatmaker, A., Fussi, B., Scheffler, B.E., Trigiano, R.N. 2013. Isolation and characterization of microsatellite Loci for Cornus sanguniea (Cornaceae) 1. American Journal of Botany. 1(9):1300012. doi:10.3732/apps.1300012.   
- The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color -(Peer Reviewed Journal)   Motamayor, J.C., Mockaitis, K., Schmutz, J., Haiminen, N., Livinstone Iii, D., Cornejo, O., Findley, S., Zheng, P., Utro, F., Royaert, S., Saski, C., Jenkins, J., Podicheti, R., Zhao, M., Scheffler, B.E., Stack, J.C., Feltus, A., Mustiga, G., Amores, F., Phillips, W., Marelli, J., May, G.D., Shapiro, H., Ma, J., Bustamante, C.D., Schnell, R.J., Main, D., Gilbert, D., Parida, L., Kuhn, D.N. 2013. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biology. Genome Biology 2013, 14:R53 doi:10.1186/gb-2013-14-6-r53.   
- Development and characterization of simple sequence repeats for Bipolaris sokiniana and cross transferability to related species -(Peer Reviewed Journal)   Fajolu, O.L., Wadl, P.A., Vu, A.L., Gwinn, K.D., Scheffler, B.E., Trigiano, R.N., Ownley, B.H. 2013. Development and characterization of simple sequence repeats for Bipolaris sokiniana and cross transferability to related species. Mycologia. 105(5):1164-1173. DOI: 10.3852/12-210.   
- Development and characterization of seashore paspalum SSR markers -(Peer Reviewed Journal)   Harris-Shultz, K.R., Raymer, P., Scheffler, B.E., Arias De Ares, R.S. 2013. Development and characterization of seashore paspalum SSR markers. Crop Science. 53:2679-2685.   
- Camelina seed transcriptome: Tool for meal and oil improvement and translational research -(Peer Reviewed Journal)   Nguyen, T., Collins-Silva, J.E., Macrander, J., Yang, W., Nazarenus, T.J., Nam, J., Jaworski, J.G., Lu, C., Scheffler, B.E., Mockaitis, K., Cahoon, E.B. 2013. Camelina seed transcriptome: Tool for meal and oil improvement and translational research. Plant Biotechnology Journal. pp. 1-11.   
- Benzo[a]pyrene decreases global and gene specific DNA methylation during zebrafish development -(Peer Reviewed Journal)   Fang, X., Thornton, C., Scheffler, B.E., Willett, K.L. 2013. Benzo[a]pyrene decreases global and gene specific DNA methylation during zebrafish development. Environmental Toxicology and Pharmacology. p. 40-50.   
- Tissue specific transcriptome changes during water deficit stress in tetraploid cotton -(Abstract Only)   Bowman, M.J., Park, W., Bauer, P.J., Udall, J.A., Page, J.T., Raney, J., Scheffler, B.E., Campbell, B.T. 2013. Tissue specific transcriptome changes during water deficit stress in tetraploid cotton [Abstract]. In: Proceedings of the National Cotton Council Beltwide Cotton Conference, January 7-10, San Antonio, Texas. 1255.   
- The Genome of the Most Widely Cultivated Cacao Type and Its Use to Identify Candidate Genes Regulating Traits:  Pod Color as an Example -(Abstract Only)   Motamayor, J., Mockaitis, K., Schmutz, J., Haiminen, N., Livingstone Iii, D.S., Cornejo, O., Findley, S.D., Zheng, P., Utro, F., Royaert, S., Saski, C., Jenkins, J., Podicheti, R., Zhao, M., Scheffler, B.E., Feltus, A.F., Amores, F.M., Phillips, W., Marelli, J., May, G.D., Shapiro, H., Ma, J., Bustamante, C., Schnell, R.J., Main, D., Gilbert, D., Parida, L., Kuhn, D.N. 2013. The Genome of the Most Widely Cultivated Cacao Type and Its Use to Identify Candidate Genes Regulating Traits:  Pod Color as an Example  . Meeting Abstract. Plant and Animal Genome Meeting XXI, January 12-16, 2013 San Diego, CA.   
- The Genome of the Most Widely Cultivated Cacao Type and Its Use to Identify Candidate Genes Regulating Traits:  Pod Color as an Example -(Abstract Only)   Motamayor Arias, J., Mockaitis, K., Schmutz, J., Haiminen, N., Livingstone Iii, D.S., Cornejo, O., Findley, S.D., Zheng, P., Utro, F., Royaert, S., Saski, C., Jenkins, J., Podicheti, R., Zhao, M., Scheffler, B.E., Feltus, A.F., Amores, F.M., Phillips, W., Marelli, J., May, G., Shapiro, H., Ma, J., Bustamante, C., Schnell, R.J., Main, D., Gilbert, D., Parida, L., Kuhn, D.N. 2013. The Genome of the Most Widely Cultivated Cacao Type and Its Use to Identify Candidate Genes Regulating Traits:  Pod Color as an Example. Meeting Abstract. Plant and Animal Genome Meeting XXI, January 12-16, 2013 San Diego, CA.   
- Molecular diversity among G. hirsutum accessions in the Gossypium Diversity Reference Set -(Abstract Only)     
- Molecular properties of the class III subfamily of acyl-coenyzme A binding proteins from tung tree (Vernicia fordii) -(Peer Reviewed Journal)   Pastor, S., Sethumadhavan, K., Ullah, A.H., Gidda, S., Cao, H., Mason, C., Chapital, D., Scheffler, B., Mullen, R., Dyer, J., Shockey, J. 2013. Molecular properties of the class III subfamily of acyl-coenyzme A binding proteins from tung tree (Vernicia fordii). Plant Science. 203-204:79-88.   
- Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species -(Peer Reviewed Journal)   Witherup, C., Ragone, D., Wiesner-Hanks, T., Irish, B.M., Scheffler, B.E., Simpson, S.A., Zee, F.T., Zuberi, M., Zerega, N. 2013. Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species. Applications in Plant Sciences. 1(7):1200423. doi: org/10.3732/apps.1200423.   
- 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.   
- Sub-genomic level sequence analysis of the aquaporin multi-gene family in cotton -(Proceedings)   Park, W., Bauer, P.J., Scheffler, B.E., Bowman, M.J., Campbell, B.T. 2012. Sub-genomic level sequence analysis of the aquaporin multi-gene family in cotton [Abstract]. In: Proceedings of the International Cotton Genome Initiative 2012 Conference, October 8-12, Raleigh, North Carolina. 50. 2012 CDROM.   
- Submission to GenBank a set of differentially expressed transcript derived fragments (TDFs) upon water deficit stress in Gossypium hirsutum L - GenBank Accession No. JK512212-JK512358 -(Other)   Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T. 2012. Submission to GenBank a set of differentially expressed transcript derived fragments (TDFs) upon water deficit stress in Gossypium hirsutum L - GenBank Accession No. JK512212-JK512358. National Center for Biotechnology Information (NCBI).   
- Transcriptome sequencing of Hydrangea macrophylla to uncover genes related to reblooming and powdery mildew resistance -(Abstract Only)   Rinehart, T.A., Reed, S.M., Scheffler, B.E. 2012. Transcriptome sequencing of Hydrangea macrophylla to uncover genes related to reblooming and powdery mildew resistance. International Hydrangea Conference. vol3, pg 9.   
- Transcriptome sequencing of flowering dogwodd (Cornus florida) for development of EST-SSRs -(Abstract Only)   Wadl, P.A., Rinehart, T.A., Scheffler, B.E., Trigiano, R.N. 2012. Transcriptome sequencing of flowering dogwodd (Cornus florida) for development of EST-SSRs. International Symposium on Woody Ornamentals of the Temperate Zone. vol2, pg 66.   
- Transcriptome sequencing of Hydrangea macrophylla -(Abstract Only)   Rinehart, T.A., Reed, S.M., Scheffler, B.E. 2012. Transcriptome sequencing of Hydrangea macrophylla. International Symposium on Woody Ornamentals of the Temperate Zone. vol 2, pg 67.   
- Transcriptome sequencing of flowering dogwood (Cornus florida) for development of EST-SSRs -(Proceedings)   Wadl, P.A., Rinehart, T.A., Scheffler, B.E., Trigiano, R. 2013. Transcriptome sequencing of flowering dogwood (Cornus florida) for development of EST-SSRs. Acta Horticulture Proceedings. 990:265-270.   
- 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.   
- Genome-wide identification of differentially expressed genes under water deficit stress in Upland cotton (Gossypium hirsutum L.) -(Peer Reviewed Journal)   Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T. 2012. Genome-wide identification of differentially expressed genes under water deficit stress in Upland cotton (Gossypium hirsutum L.). Biomed Central (BMC) Plant Biology. Available: http://www.biomedcentral.com/1471-2229/12/90.   
- Genetic diversity assessment of Musa spp. germplasm using SSR markers -(Abstract Only)   Irish, B.M., Scheffler, B.E., Goenaga, R.J. 2012. Genetic diversity assessment of Musa spp. germplasm using SSR markers. HortScience 47(9):S342.   
- Microsatellite markers in plant pathogenic fungi -(Abstract Only)   Arias, R.S., Ray, J.D., Mengistu, A., Glynn, N.C., Scheffler, B.E. 2012. Microsatellite markers in plant pathogenic fungi. Meeting Proceedings.   
- Analysis of the aquaporin gene family in cotton -(Abstract Only)   Park, W., Bauer, P.J., Scheffler, B.E., Campbell, B.T. 2012. Analysis of the aquaporin gene family in cotton [abstract]. In: Proceedings of the American Society of Plant Biologists Southern Section Annual Meeting, March 3-5, 2012, Myrtle Beach, South Carolina.   
- Transcriptomes of Lolium/Schedonorus/Festuca species -(Book / Chapter)   Dinkins, R.D., Hesse, U., Arnaoudova, E., Nagabhyru, P., Moore, N., Liu, J., Jaromczyk, J., Zeng, Z., Liu, J., Dai, X., Zhao, P.X., Scheffler, B.E., Jaromczyk, J., Schardl, C.L. 2012. Transcriptomes of Lolium/Schedonorus/Festuca species. International Symposium on Fungal Endophytes of Grasses. ISBNL 978-0-9754303-6-1.   
- Development of a core set of SSR markers for the characterization of Gossypium germplasm -(Peer Reviewed Journal)   Yu, J., Fang, D.D., Kohel, R.J., Ulloa, M., Hinze, L.L., Percy, R.G., Zhang, J., Chee, P., Scheffler, B.E., Jones, D.C. 2012. Development of a core set of SSR markers for the characterization of Gossypium germplasm. Euphytica. 187(2):203-213.   
- MiRNAs from cotton roots infected with Meloidogyne incognita -(Abstract Only)   Shapulatov, U.M., Abdusalom, M., Saha, S., Wubben, M., Jenkins, J.N., Buriev, Z.T., Ulloa, M., Scheffler, B.E., Abdurakhmonov, I.Y. 2012. MiRNAs from cotton roots infected with Meloidogyne incognita [abstract]. National Cotton Council Beltwide Cotton Conference. p. 730.   
- Genetic diversity in the U.S. Cotton Germplasm Collection as revealed by SSR markers -(Abstract Only)     
- Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina -(Peer Reviewed Journal)   Trigiano, R.N., Wadl, P.A., Dean, D., Hadziabdic, D., Scheffler, B.E., Runge, F., Telle, S., Thines, M., Ristaino, J., Spring, O. 2012. Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina. Mycological Society of America. 104(3):633-640.   
- High-throughput SNP genotyping for breeding applications in rice using the BeadXpress platform -(Peer Reviewed Journal)     
- High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform -(Peer Reviewed Journal)   Thomson, M.J., Zhao, K., Wright, M., McNally, K.L., Rey, J., Tung, C., Reynolds, A., Scheffler, B.E., Eizenga, G.C., McClung, A.M., Kim, H., Ismail, A.M., Ocampo, M., Mojica, C., Reveche, M., Dilla-Ermita, C.J., Mauleon, R., Leung, H., Bustamante, C., McCouch, S.R. 2011. High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Molecular Breeding. 29:875-886. doi: 10.1007/s11032-011-9663-x.   
- Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina -(Peer Reviewed Journal)   Trigiano, R.N., Wadl, P.A., Dean, D., Hadziabdic, D., Scheffler, B.E., Runge, F., Telle, S., Thines, M., Ristaino, J., Spring, O. 2012. Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina. Mycologia. 104(3):633-640.   
- Development of microsatellite loci for the endangered species Pityopsis ruthii (Asteraceae)1 -(Peer Reviewed Journal)   Wadl, P.A., Dattilo, A.J., Scheffler, B.E., Trigiano, R.N. 2011. Development of microsatellite loci for the endangered species Pityopsis ruthii (Asteraceae)1. American Journal of Botany. 0:e1-e4.   
- Development and characterization of sixteen microsatellite loci for Geosmithia morbida, the causal agent of thousand canker disease in black walnut (Juglans nigra) -(Peer Reviewed Journal)   Hadziabdic, D., Wadl, P.A., Boggess, S.L., Scheffler, B.E., Windham, M.T., Trigiano, R.N. 2011. Development and characterization of sixteen microsatellite loci for Geosmithia morbida, the causal agent of thousand canker disease in black walnut (Juglans nigra). Conservation Genetics. 4(2):287-289.   
- Screening and characterization of eleven novel microsatellite markers from Viburnum dilatatum -(Peer Reviewed Journal)   Dean, D., Wadl, P.A., Trigiano, R., Wang, X., Klingeman, W., Ownley, B.H., Rinehart, T.A., Scheffler, B.E. 2011. Screening and characterization of eleven novel microsatellite markers from Viburnum dilatatum. HortScience. 46(11):1456-1459.   
- QTL mapping for milling quality in elite western U.S. rice germplasm -(Peer Reviewed Journal)   Nelson, J.C., Jodari, F., Roughton, A.I., McKenzie, K.S., McClung, A.M., Fjellstrom, R.G., Scheffler, B.E. 2012. QTL mapping for milling quality in elite western U.S. rice germplasm. Crop Science. 52:242-252.   
- Identification of Candidate Genes in Rice for Resistance to Sheath Blight Disease by Whole Genome Sequencing -(Peer Reviewed Journal)   Silva, J., Scheffler, B.E., Sanabria, Y., De Guzman, C., Galam, D., Farmer, A., Woodward, J., May, G., Oard, J. 2012. Identification of Candidate Genes in Rice for Resistance to Sheath Blight Disease by Whole Genome Sequencing. Journal of Theoretical and Applied Genetics. 124(1):63-74.   
- Registration of "Rex" Southern Long-Grain Rice -(Peer Reviewed Journal)   Solomon, W.L., Kanter, D.G., Walker, T.W., Baird, III, G.E., Scheffler, B.E., Lanford, L.S., Shaifer, S. 2012. Registration of "Rex" Southern Long-Grain Rice. Journal of Plant Registrations. 6(1).   
- Integrating genomics and phenomics to improve abiotic stress tolerance in cotton -(Proceedings)   Campbell, B.T., Park, W., Bauer, P.J., Scheffler, B.E. 2011. Integrating genomics and phenomics to improve abiotic stress tolerance in cotton. In: Proceedings of the 2011 Plant Genomics Eurepean Meeting, May 4-7, 2011, Istanbul, Turkey. 2011 CDROM.   
- Transcriptome sequencing of Hydrangea macrophylla a non-model woody plant and specialty crop -(Abstract Only)   Rinehart, T.A., Reed, S.M., Scheffler, B.E. 2011. Transcriptome sequencing of Hydrangea macrophylla a non-model woody plant and specialty crop. Botanical Society of America Abstracts. vol 1 pg 92.   
- Sheath-blight resistance QTLs and in japonica rice germplasm -(Peer Reviewed Journal)   Nelson, J., Oard, J.H., Groth, D., Utomo, H., Jia, Y., Liu, G., Moldenhauer, K.K., Correa-Victoria, F.J., Fjellstrom, R.G., Scheffler, B.E., Prado, G.A. 2012. Sheath-blight resistance QTLs and in japonica rice germplasm. Euphytica. 184:23-24. 10.1007/s10681-011-0475-1.   
- Comparison of whole-genome amplifications for microsatellite genotyping of Rotylenchulus reniformis -(Peer Reviewed Journal)   Arias, R.S., Stetina, S.R., Scheffler, B.E. 2011. Comparison of whole-genome amplifications for microsatellite genotyping of Rotylenchulus reniformis. Electronic Journal of Biotechnology. DOI:10.2225/vol14-issue3-fulltext-13.   
- Generation and analysis of expressed sequence tags(ESTs) for marker development in yam (Dioscores alata L.) -(Peer Reviewed Journal)   Narina, S.S., Buyyarapu, R., Kottapalli, R., Sartie, A.M., Moahmed, A., Asiedu, R., Mignouna, H., Sayre, B., Scheffler, B.E. 2011. Generation and analysis of expressed sequence tags(ESTs) for marker development in yam (Dioscores alata L.). Biomed Central (BMC) Genomics. 1471-2164.   
- Water deficit stress induced gene expression -(Abstract Only)   Campbell, B.T., Park, W., Bauer, P.J., Scheffler, B.E. 2011. Water deficit stress induced gene expression [abstract]. In: Proceedings of the National Cotton Council Beltwide Cotton Conference, January 4-7, 2011, Atlanta, Georgia. p. 725.   
- Isolation and characterisation of the first microsatellite markers for Cyperus rotundus -(Peer Reviewed Journal)   Arias, R.S., Molin, W.T., Ray, J.D., Peel, M., Scheffler, B.E. 2011. Isolation and characterisation of the first microsatellite markers for Cyperus rotundus. Weed Research. 51:451-460.   
- First microsatellites developed from Spodoptera frugiperda and their potential use for population genetics -(Abstract Only)   Arias De Ares, R.S., Blanco, C.A., Portilla, M., Snodgrass, G.L., Scheffler, B.E. 2011. First microsatellites developed from Spodoptera frugiperda and their potential use for population genetics. Entomology Society America Annual Meeting. 104(3):516-587.   
- First microsatellites from Spodoptera frugiperda (Lepidoptera: Noctuidae) and their potential use for population genetics -(Peer Reviewed Journal)   Arias, R.S., Blanco, C.A., Portilla, M., Snodgrass, G.L., Scheffler, B.E. 2011. First microsatellites from Spodoptera frugiperda (Lepidoptera: Noctuidae) and their potential use for population genetics. Annals of the Entomological Society of America. 104(3):576-587.   
- Cocoa/Cotton Comparative Genomics -(Abstract Only)   ay, G.D., Mudge, J., Crow, J.A., Bharti, A.K., Woodward, J.E., Ramaraj, T., Farmer, A.D., Rice, B.J., Kramer, R.S., Wilkins, T.A., Schmutz, J., Kim, R.W., Mockaitis, K., Saski, C., Scheffler, B.E., Main, D., Jenkins, J., Livingstone, D., Zheng, P., Gilbert, D., Feltus, A., Haiminen, N., Parida, L., Tondo, C.L., Royaert, S.E., Phillips, W., Shapiro, H., Schnell, R.J., Kuhn, D.N., Motamayor, J. 2011. Cocoa/Cotton Comparative Genomics. Annual International Plant & Animal Genome Conference. 2011.   
- Genomic resources for valuable woody ornamental landscape plants such as hydrangea macrophylla -(Abstract Only)   Rinehart, T.A., Reed, S.M., Scheffler, B.E. 2011. Genomic resources for valuable woody ornamental landscape plants such as hydrangea macrophylla. Plant and Animal Genome VX Conference Abstracts. W396.   
- Preliminary assessment of the efficiency of a core marker set in revealing genetic diversity in the U.S. germplasm collection -(Abstract Only)   Percy, R.G., Fang, D.D., Hinze, L.L., Yu, J., Frelichowski, J.E., Scheffler, B.E., Gore, M.A. 2011. Preliminary assessment of the efficiency of a core marker set in revealing genetic diversity in the U.S. germplasm collection. In: Proceedings of the National Cotton Council Beltwide Cotton Conference, January 4-7, 2011, Atlanta, Georgia. 2011 CDROM.   
- Advances in molecular breeding of flowering dogwood (Cornus florida L.) -(Abstract Only)   Wadhl, P.A., Xingwang, X., Saxton, A.M., Rinehart, T.A., Scheffler, B.E., Pantalone, V.R., Trigiano, R.N. 2011. Advances in molecular breeding of flowering dogwood (Cornus florida L.). Plant and Animal Genome Conference. W397.   
- Differentially expressed genes in drought stressed cotton -(Abstract Only)   Park, W., Bauer, P.J., Scheffler, B.E., Campbell, B.T. 2010. Differentially expressed genes in drought stressed cotton. In: Proceedings of the American Society of Agronomy-Crop Science Society of America-Soil Science Society of America International Annual Meetings, October 31-November 4, 2010, Long Beach, California. 2010 CDROM.   
- Development of Mississippi cotton breeding lines resistant to reniform and root-koot nematodes via marker assisted selection -(Proceedings)   Wallace, T.P., Thaxton, P.S., Gutierrez, O.A., Scheffler, B.E., Stetina, S.R., Scheffler, J.A. 2011. Development of Mississippi cotton breeding lines resistant to reniform and root-koot nematodes via marker assisted selection. National Cotton Council Beltwide Cotton Conference. pp.742.   
- Evaluation of genetic diversity and pedigree within crapemyrtle (Lagerstroemia spp.) cultivars using simple sequence repeat (SSR) markers -(Peer Reviewed Journal)   Wang, X., Wadl, P.A., Cabrera, R.I., Pounders Jr, C.T., Scheffler, B.E., Pooler, M.R., Rinehart, T.A., Trigiano, R.N. 2011. Evaluation of genetic diversity and pedigree within crapemyrtle (Lagerstroemia spp.) cultivars using simple sequence repeat (SSR) markers. Journal of the American Society for Horticultural Science. 136(2):116-128.   
- 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.   
- Major Pesticide Receptors, Detoxification Enzymes, and Transcriptional Profile in Midgut of the Tobacco Budworm, Heliothis virescens (Lepidoptera: Noctuidae) -(Peer Reviewed Journal)   Zhu, Y., Guo, Z., Chen, M., Zhu, K., Liu, X.F., Scheffler, B.E. 2011. Major Pesticide Receptors, Detoxification Enzymes, and Transcriptional Profile in Midgut of the Tobacco Budworm, Heliothis virescens (Lepidoptera: Noctuidae). Insect Molecular Biology. 106:296-307. doi: 10.1016/jip.2010.10.007.   
- Discriminating microsatellites from Macrophomina phaseolina and their potential association to biological functions -(Peer Reviewed Journal)   Arias, R.S., Ray, J.D., Mengistu, A., Scheffler, B.E. 2011. Discriminating microsatellites from Macrophomina phaseolina and their potential association to biological functions. Plant Pathology. 60(4):709-718 DOI:10.1111/j.1365-3059.2010.02421.x.   
- 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.   
- Development of simple sequence repeat markers for Chionanthus retusus (Oleaceae) and effective discrimination of closely related taxa -(Peer Reviewed Journal)   Arias, R.S., Techen, N., Rinehart, T.A., Olsen, R.T., Kirkbride, J.H., Scheffler, B.E. 2010. Development of simple sequence repeat markers for Chionanthus retusus (Oleaceae) and effective discrimination of closely related taxa. HortScience. 46(1):23-29.   
- Interspecific Chromosome Substitution Lines as Genetic Resources for Improvement, Trait Analyses and Genomic Inference -(Abstract Only)     
- Discovering genes with potential abiotic stress tolerance applications in cotton -(Proceedings)   Campbell, B.T., Park, W., Bauer, P.J., Scheffler, B.E. 2010. Discovering genes with potential abiotic stress tolerance applications in cotton [abstract]. In: Proceedings of the International Cotton Genome Initiative Workshop, September 21-23, 2010, Canberra, Australia. p. 39.   
- Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.) -(Peer Reviewed Journal)   Tung, C., Zhao, K., Wright, M.K., Ali, M., Jung, J., Kimball, J.A., Tyagi, W., Thomson, M.J., McNally, K., Leung, H., Kim, H., Ahn, S., Reynolds, A., Scheffler, B.E., Eizenga, G.C., McClung, A.M., Bustamante, C.D., McCouch, S.D. 2010. Development of a research platform for dissecting phenotype-genotype associations in rice (Oryza spp.). Rice. 3:205–217.   
- Development and characterization of microsatellites for switchgrass rust fungus (Puccinia emaculata) -(Peer Reviewed Journal)   Wadl, P.A., Dean, D., Li, Y., Vito, L.M., Scheffler, B.E., Hadziabdic, D., Windham, M.T., Trigiano, R.N. 2011. Development and characterization of microsatellites for switchgrass rust fungus (Puccinia emaculata). Conservation Genetics. 3:185–188.   
- Mapping QTL main and interaction influences on milling quality in elite U.S. rice germplasm -(Peer Reviewed Journal)   Nelson, J.C., McClung, A.M., Fjellstrom, R.G., Moldenhauer, K.K., Boza, E., Jodari, F., Oard, J.H., Linscombe, S., Scheffler, B.E., Yeater, K.M. 2011. Mapping QTL main and interaction influences on milling quality in elite U.S. rice germplasm. Theoretical and Applied Genetics. 122(2):291-309.   
- Characterization of novel blast resistant genes for US rice breeding -(Abstract Only)   Yan, W., Scheffler, B.E., Correll, J.C., Fjellstrom, R.G., Feng, C.D., Jackson, A.K., McClung, A.M. 2010. Characterization of novel blast resistant genes for US rice breeding [abstract]. Proceedings of 5th International Rice Blast Conference, August 11-14, 2010, Little Rock, Arkansas. p. 36.   
- Functional diversity in fungal fatty acid synthesis the first acetylenase from the Pacific Golden Chanterelle Cantharellus formosus -(Peer Reviewed Journal)   Blacklock, B.J., Scheffler, B.E., Shepard, M.R., Jayasuriya, N., Minto, R.E. 2010. Functional diversity in fungal fatty acid synthesis. The first acetylenase from the Pacific Golden Chanterelle, Cantharellus formosus. Journal of Biological Chemistry. 287(37):28442-28449.   
- Identification of the family of aquaporin genes and their expression in Upland cotton (Gossypium hirsutum L.) -(Peer Reviewed Journal)   Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T. 2010. Identification of the family of aquaporin genes and their expression in Upland cotton (Gossypium hirsutum L.). Biomed Central (BMC) Plant Biology. 10:142.   
- Microbial and Antibiotic REsistant Constituents Associated with Biological Aerosols Within A Commercial Poultry House -(Peer Reviewed Journal)   Brooks, J.P., McLaughlin, M.R., Scheffler, B.E., Miles, D.M. 2010. Microbial and antibiotic resistant constituents associated with biological aerosols and poultry litter within a commercial poultry house. Science of the Total Environment. 408:4770-4777.   
- Registration of the MY2 Cypress/LaGrue rice recombinant inbred line mapping population. Journal of Plant Registrations 4(3): 261-265. -(Peer Reviewed Journal)   Oard, J.H., Moldenhauer, K.K., Fjellstrom, R.G., Nelson, J., Linscombe, S.D., Silva, J., May, G.D. 2010. Registration of the MY2 Cypress/LaGrue rice recombinant inbred line mapping population. Journal of Plant Registrations. 4(3):1-5.   
- Submission to GenBank of the Plasma membrane intrinsic protein (PIP) Subfamily in Cotton – GenBank Accession No. GU998827-GU998830 and GenBank Accession TPA;inferential No. BK007045-BK007052 -(Other)   Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T. 2010. Submission to GenBank of the Plasma membrane intrinsic protein (PIP) Subfamily in Cotton – GenBank Accession No. GU998827-GU998830 and GenBank Accession TPA;inferential No. BK007045-BK007052. National Center for Biotechnology Information (NCBI).   
- Submission to GenBank of the X intrinsic protein (XIP) Subfamily in Cotton – GenBank Accession No. GU998849 -(Other)   Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T. 2010. Submission to GenBank of the X intrinsic protein (XIP) Subfamily in Cotton – GenBank Accession No. GU998849. National Center for Biotechnology Information (NCBI).   
- Submission to GenBank of the Nodulin 26-like intrinsic protein (NIP) Subfamily in Cotton – GenBank Accession No. GU998840-GU998845 and GenBank Accession TPA;inferential No. BK007061-BK007062 -(Other)   Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T. 2010. Submission to GenBank of the Nodulin 26-like intrinsic protein (NIP) Subfamily in Cotton – GenBank Accession No. GU998840-GU998845 and GenBank Accession TPA;inferential No. BK007061-BK007062. National Center for Biotechnology Information (NCBI).   
- Submission to GenBank of the Small intrinsic protein (SIP) Subfamily in Cotton – GenBank Accession No. GU998846-GU998848 and GenBank Accession TPA;inferential No. BK007063-BK007064 -(Other)   Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T. 2010. Submission to GenBank of the Small intrinsic protein (SIP) Subfamily in Cotton – GenBank Accession No. GU998846-GU998848 and GenBank Accession TPA;inferential No. BK007063-BK007064. National Center for Biotechnology Information (NCBI).   
- Submission to GenBank of the Tonoplast membrane intrinsic protein (TIP) Subfamily in Cotton – GenBank Accession No. GU998831-GU998839 and GenBank Accession TPA;inferential No. BK007053-BK007060 -(Other)   Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T. 2010. Submission to GenBank of the Tonoplast membrane intrinsic protein (TIP) Subfamily in Cotton – GenBank Accession No. GU998831-GU998839 and GenBank Accession TPA;inferential No. BK007053-BK007060. National Center for Biotechnology Information (NCBI).   
- Characterization of twelve microsatellite markers for the native redbud tree (Cercis canadensis) -(Peer Reviewed Journal)   Rinehart, T.A., Trigiano, R., Wadl, P., Hadziabdic, D., Pooler, M.R., Scheffler, B.E. 2010. Characterization of twelve microsatellite markers for the native redbud tree (Cercis canadensis). Molecular Ecology Resources. 10(4):751-754.   
- Drought-related gene expression in Upland cotton -(Abstract Only)   Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T. 2010. Drought-related gene expression in Upland cotton [abstract]. Proceedings of the nternational Association for Plant Biotechnology Congress, June 6-11, 2010, St. Louis, Missouri. CDROM.   
- Development of microsatellite markers from crape myrtle (Lagerstroemia L.) -(Peer Reviewed Journal)   Wang, X., Dean, D., Wadl, P., Hadziabdic, D., Scheffler, B.E., Rinehart, T.A., Trigiano, R. 2010. Development of microsatellite markers from Crape Myrtle (Lagerstroemia L.). HortScience. 45(5):842-844.   
- Characterization of Two Cotton (Gossypium hirsutum) Invertase Genes -(Peer Reviewed Journal)   Taliercio, E.W., Scheffler, J.A., Scheffler, B.E. 2010. Characterization of Two Cotton (Gossypium hirsutum) Invertase Genes. Molecular Biology Reports. 37:3915-3920.   
- Transcript Analysis of Parasitic Females of the Sedentary Semi-Endoparasitic Nematode Rotylenchulus reniformis -(Peer Reviewed Journal)   Wubben, M., Callahan, F.E., Scheffler, B.E. 2010. Transcript Analysis of Parasitic Females of the Sedentary Semi-Endoparasitic Nematode Rotylenchulus reniformis. Molecular and Biochemical Parasitology. 172:31-40.   
- Toward identification of complete set of aquaporin gene family in cotton - A possible way to improve cotton production -(Abstract Only)   Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T. 2010. Toward identification of complete set of aquaporin gene family in cotton - A possible way to improve cotton production. p. 815. In: Proceedings of the Beltwide Cotton Conference, January 4-7, 2010, New Orleans, Louisiana.   
- DNA Fingerprinting Eastern Redbud Cultivars (Cercis canadensis) Using SSR Markers -(Proceedings)   Rinehart, T.A., Scheffler, B.E., Trigiano, R., Pooler, M.R. 2011. DNA Fingerprinting Eastern Redbud Cultivars (Cercis canadensis) Using SSR Markers. Southern Nursery Association Research Conference. 55:40-45.   
- The need for an assembly pilot project -(Abstract Only)   Kuhn, D.N., Saski, C., Feltus, F.A., Haiminen, N., Main, D., May, G.D., Schnell Ii, R.J., Motamayor, J.C., Mockaitis, K., Scheffler, B.E., Shapiro, H. 2010. The need for an assembly pilot project. Plant and Animal Genome Conference. 1.   
- T. cacao Transcriptome Sequencing -(Abstract Only)   Mockaitis, K., Kuhn, D.N., Main, D., Haiminen, N., May, G., Saski, C., Scheffler, B.E., Schnell Ii, R.J., Harkins, T., Motamayor, J.C., Shapiro, H. 2010. T. cacao Transcriptome Sequencing. Plant and Animal Genome Conference. 1.   
- Functional genomics analysis of horseweed (Conyza canadensis) with special reference to the evolution of non-target-site glyphosate resistance -(Peer Reviewed Journal)   Yuan, J.S., Abercrombie, L., Cao, Y., Halfhill, M.D., Zhou, X., Peng, Y., Hu, J., Rao, M.R., Heck, G.R., Larosa, T.J., Sammons, R.D., Wang, X., Ranjan, P., Johnson, D.H., Wadl, P.A., Scheffler, B.E., Rinehart, T.A., Trigiano, R.N., Stewart, Jr, C.N. 2010. Functional genomics analysis of horseweed (Conyza canadensis) with special reference to the evolution of non-target-site glyphosate resistance. Weed Science. 58:109-117.   
- Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1. -(Peer Reviewed Journal)   Simko, I., Pechenick, D.A., Mchale, L.K., Truco, M.J., Ochoa, O.E., Michelmore, R.W., Scheffler, B.E. 2009. Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1.. Biomed Central (BMC) Plant Biology, Year 2009, volume 9, article number 135.   
- Optimized construction of microsatellite-enriched libraries -(Peer Reviewed Journal)   Techen, N., Arias De Ares, R.S., Pan, Z., Khan, I., Scheffler, B.E. 2010. Optimized construction of microsatellite-enriched libraries. Molecular Ecology. 10:508-515.   
- Transcript Analysis of Sedentary Parastic Female Reniform Nematodes (Rotylenchulus reniformis) Identifies Candidate Parasitism Genes and Targets for RNA-Interference -(Abstract Only)   Wubben, M., Callahan, F.E., Scheffler, B.E. 2010. Transcript analysis of sedentary parastic female reniform nematodes (Rotylenchulus reniformis) identifies candidate parasitism genes and targets for RNA-interference. Proceedings Plant and Animal Genome Conference. CD-ROM.   
- Microsatellites Reveal Genetic Diversity in Reniform Nematode Populations -(Abstract Only)   Arias De Ares, R.S., Stetina, S.R., Tonos, J.L., Scheffler, J.A., Scheffler, B.E. 2010. Microsatellites Reveal Genetic Diversity in Reniform Nematode Populations. National Cotton Council Beltwide Cotton Conference, New Orleans, Louisiana, January 4-7, 2010   
- Optimized Construction of SSR-enriched Libraries -(Peer Reviewed Journal)   Techen, N., Arias De Ares, R.S., Glynn, N.C., Pan, Z., Khan, I.A., Scheffler, B.E. 2010. Optimized Construction of SSR-enriched Libraries. Molecular Ecology Resources. 10(3)508-515   
- Development of molecular markers for marker-assisted selection in lettuce (Lactuca sativa). -(Peer Reviewed Journal)   Simko, I., Pechenick, D.A., Mchale, L.K., Truco, M.J., Ochoa, O.E., Michelmore, R.W., Scheffler, B.E. 2010. Development of molecular markers for marker-assisted selection in lettuce (Lactuca sativa). Acta Horticulture Proceedings, Year 2010, volume 859, pages 401-408.   
- Benzo(A)pyrene induced glycine N-methyltransferase messenger rna expression in Fundulus heteroclitus embryos -(Peer Reviewed Journal)   Fang, X., Dong, W., Thornton, C., Scheffler, B.E., Willet, K. 2010. Benzo(A)pyrene induced glycine N-methyltransferase messenger rna expression in Fundulus heteroclitus embryos. Marine Environmental Research. 69:274-276.   
- Clustering, haplotype diversity and locations of MIC-3: a unique root-specific defense-related gene family in upland cotton (Gossypium hirsutum L.) -(Peer Reviewed Journal)   Buriev, Z.T., Saha, S., Abdurakhmonov, I.Y., Jenkins, J.N., Abdukarimov, A., Scheffler, B.E., Stelly, D.M. 2010. Clustering, haplotype diversity and locations of MIC-3: a unique root-specific defense-related gene family in upland cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics. 120:587-606.   
- Fingerprinting the bad guys, SSR DNA-profiling of Nutsedge -(Abstract Only)     
- Structural and functional properties of the cotton Aquaporin gene family -(Abstract Only)   Park, W., Scheffler, B.E., Bauer, P.J., Campbell, B.T. 2009. Structural and functional properties of the cotton Aquaporin gene family [abstract]. In: Proceedings of the American Society of Agronomy-Crop Science Society of America-Soil Science Society of America International Annual Meetings, November 1-5, 2009, Pittsburg, Pennsylvania. CDROM.   
- RiceCAP: Progress in identifying QTL for sheath blight resistance and milling yield -(Abstract Only)   Mcclung, A.M., Boza, E., Brooks, S.A., Correll, J., Eizenga, G.C., Fjellstrom, R.G., Groth, D.E., Jia, Y., Jodari, F., Linscombe, S.D., Liu, G., Moldenhauer, K.K., Nelson, J.C., Oard, J., Pinson, S.R., Prasad, B., Scheffler, B.E., Yeater, K.M., Wang, Y. 2009. RiceCAP: Progress in identifying QTL for sheath blight resistance and milling yield. American Society of Agronomy Abstracts.   
- Genetic Likage Map for Hydrangea macrophylla Using SSR and AFLP Markers -(Abstract Only)   Rinehart, T.A., Scheffler, B.E., Reed, S.M. 2009. Genetic Likage Map for Hydrangea macrophylla Using SSR and AFLP Markers. Meeting [Abstract]. pg. 75.   
- Ethanol Disrupts Chondrification of the Neurocranial Cartilages in Medaka Embryos without Affecting Aldehyde Dehydrogenase 1A2 (Aldh1A2) Promoter Methylation -(Peer Reviewed Journal)   Hu, Y., Willett, K.L., Khan, I.A., Scheffler, B.E., Dasmahapatra, A.K. 2009. Ethanol Disrupts Chondrification of the Neurocranial Cartilages in Medaka Embryos without Affecting Aldehyde Dehydrogenase 1A2 (Aldh1A2) Promoter Methylation. Comparative Biochemistry and Physiology. 150(4):495-502.   
- Development of SSR markers for Chionanthus retusus (Oleaceae) and effective discrimination of closely related taxa -(Other)   Arias, R.S., Techen, N., Rinehart, T.A., Olsen, R.T., Kirkbride, J.H., Scheffler, B.E. 2009. Development of SSR markers for Chionanthus retusus (Oleaceae) and effective discrimination of closely related taxa. American Society of Horticulture Science Meeting, July 24-28, 2008, St. Louis, MO. meeting Prodeedings. 44(4):1007.   
- Characterization of Pi-ta Blast resistance gene in an international rice core collection -(Peer Reviewed Journal)   Wang, X., Fjellstrom, R.G., Jia, Y., Yan, W., Jia, M.H., Scheffler, B.E., Wu, D., Shu, Q., McClung, A.M. 2010. Characterization of Pi-ta Blast resistance gene in an international rice core collection. Plant Breeding. 129(5):491-501.   
- UPIC: Perl scripts to determine the number of SSR markers to run -(Other)   Arias, R.S., Ballard, L.L., Scheffler, B.E. 2009. UPIC: Perl scripts to determine the number of SSR markers to run. Molecular markers in Horticulture Symposium, July 29-31, 2009, Corvallis, Oregon State University. Meeting Proceedings.   
- Laser capture microdissection and expressed sequence tag analysis of uredinia formed by Phakopsora pachyrhizi, the causal agent of Asian soybean rust -(Peer Reviewed Journal)   Tremblay, A., Li, S., Scheffler, B.E., Matthews, B.F. 2009. Laser capture microdissection (LCM) and expressed sequence tag analysis of uredinia formed by Phakopsora pachyrhizi, the causal agent of Asian soybean rust. Physiological and Molecular Plant Pathology. 73(6):163-174.   
- Microsatellites Reveal Genetic Diversity in Rotylenchulus reniformis Populations -(Peer Reviewed Journal)   Arias, R.S., Stetina, S.R., Tonos, J.L., Scheffler, J.A., Scheffler, B.E. 2009. Microsatellites Reveal Genetic Diversity in Rotylenchulus reniformis Populations. Journal of Nematology. 41(2): 146-156.   
- Ploidy Variation and Genetic Diversity in Dichroa -(Peer Reviewed Journal)   Rinehart, T.A., Scheffler, B.E., Reed, S.M. 2010. Ploidy Variation and Genetic Diversity in Dichroa. HortScience. 45:208-213.   
- Development of molecular markers for marker-assisted selection in lettuce (Lactuca sativa). -(Abstract Only)     
- Microsatellites from Conyza canadensis (horseweed) -(Peer Reviewed Journal)   Wang, X.W., Good, L.L., Wadl, P.A., Johnson, D.H., Panthee, D., Scheffler, B.E., Rinehart, T.A., Stewart, N.R., Yuan, J., Stewart, N.C., Trigiano, R.N. 2009. Microsatellites from Conyza canadensis (horseweed). Molecular Ecology Resources. 9(5):1375-1379.   
- A Genetic Linkage Map of Louisiana Sugarcane (Saccharum spp. hybrids) using AFLP and SSR Markers -(Abstract Only)   Pan, Y.-B., Suman, A., Zhou, M., Kimbeng, C.A., Scheffler, B.E., Grisham, M.P., Tew, T.L., White, W.H., Richard Jr, E.P. 2009. A Genetic Linkage Map of Louisiana Sugarcane (Saccharum spp. hybrids) using AFLP and SSR Markers. ASA-CSSA-SSSA Annual Meeting Abstracts. Paper 58-1. Available: http://a-c-s.confex.com/crops/2009am/webprogram/Paper52547.html   
- Genomic profile of maize response to Aspergillus flavus infection -(Peer Reviewed Journal)   Kelley, R.Y., Williams, W.P., Mylroie, J.E., Boykin, D.L., Hawkins, L.K., Windham, G.L., Brooks, T.D., Bridges, S.M., Scheffler, B.E., Wilkinson, J.R. 2009. Genomic Profile of Maize Response to Aspergillus flavus Infection. Toxin Reviews. 28:129-141.   
- UPIC: Perl scripts to determine the number of SSR markers to run -(Peer Reviewed Journal)   Arias, R.S., Ballard, L.L., Scheffler, B.E. 2009. UPIC: How Many SSR Markers to Run. Bioinformation 3(8):352-360, http://www.bioinformation.net/003/007800032009.htm   
- SSR-FACILITATED IDENTIFICATION OF INTERSPECIFIC HYPOANEUPLOID HYBRIDS OF GOSSYPIUM HIRSUTUM X G. TOMENTOSUM NUTT. -(Peer Reviewed Journal)   Gutierrez, O.A., Stelly, D.M., Saha, S., Jenkins, J.N., McCarty Jr., J.C., Raska, D.A., Scheffler, B.E. 2009. Integrative placement and orientation of non-redundant SSR loci in cotton linkage groups by deficiency analysis. Molecular Breeding. 23:693-707.   
- Analysis of the RiceCAP germplasm panel for SNP diversity, population structure and seven yield-component traits of rice -(Proceedings)   Solomon, W., Oard, J., McClung, A.M., Wright, M., Zhao, K., Reynolds, A., Bustamante, C., Kanter, D., McCouch, S., Scheffler, B.E. 2009. Analysis of the RiceCAP germplasm panel for SNP diversity, population structure and seven yield-component traits of rice. In: Proceedings of Plant and Animal Genome Conference XVII, January 10-14, 2009, San Diego, CA. P220.   
- Worldwide distribution and origin of rice blast resistance gene Pi-ta -(Proceedings)   Xueyan, W., Fjellstrom, R.G., Jia, Y., Yan, W., Jia, M.H., Scheffler, B.E., Dianxing, W., Qingyao, S., McClung, A.M. 2009. Worldwide distribution and origin of rice blast resistance gene Pi-ta. In: Proceedings of the Plant and Animal Genome Conference XVII, January 10-14-2009, San Diego, CA. P116.   
- Detection of Illicium anisatum as Adulterant of Illicium verum  -(Peer Reviewed Journal)   Techen, N., Pan, Z., Scheffler, B.E., Kahn, I.A. 2009. Detection of Illicium anisatum as Adulterant of Illicium verum. Planta Medica. 75:392–395.   
- Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm -(Peer Reviewed Journal)   Abdurakhmonov, I.Y., Saha, S., Jenkins, J.N., Buriev, Z.T., Shermatov, S.E., Scheffler, B.E., Pepper, A.E., Yu, J., Kohel, R.J., Abdukarimov, A. 2009. Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica. 136:401-417.   
- Transcript analysis of sedentary female reniform nematodes identifies potential targets ofr RNAi-mediated resistance -(Abstract Only)   Wubben, M., Callahan, F.E., Scheffler, B.E., Jenkins, J.N. 2009. Transcript analysis of sedentary female reniform nematodes identifies potential targets ofr RNAi-mediated resistance [abstract]. National Cotton Council Beltwide Cotton Conference. p. 179.   
- A Linkage Map for Flowering Dogwood (Cornus florida L.) Based on Microsatellite Markers -(Peer Reviewed Journal)   Wang, X., Wadl, P.A., Rinehart, T.A., Scheffler, B.E., Windham, M.T., Spiers, J.M., Johnson, D.H., Trigiano, R.N. 2008. A linkage map for flowering dogwood (cornus florida l.) based on microsatellite markers. Euphytica. 165:165-175.   
- Quantitative Proteomic Analysis of Bean Plants Infected by a Virulent and Avirulent Obligate Rust Fungus -(Peer Reviewed Journal)   Lee, J., Campbell, K., Scheffler, B.E., Feng, J., Naiman, D.Q., Garrett, W.M., Thibivilliers, S., Stacey, G., Tucker, M.L., Pastor Corrales, M.A., Cooper, B. 2008. Quantitative Proteomic Analysis of Bean Plants Infected by a Virulent and Avirulent Obligate Rust Fungus. Molecular and Cellular Proteomics. 8:19-31.   
- Identification and Differentiation Between Hoodia gordonii Masson) Sweet ex Decne., Opuntia ficus indica (L.) P. Miller and Other Related Hoodia Species by Microscopy and PCR Methods -(Peer Reviewed Journal)   Joshi, V., Techen, N., Scheffler, B.E., Khan, I.A. 2009. Identification and Differentiation Between Hoodia gordonii Masson) Sweet ex Decne., Opuntia ficus indica (L.) P. Miller and Other Related Hoodia Species by Microscopy and PCR Methods. Journal of Herbs, Spices and Medicinal Plants. 15(3)253-264   
- Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm -(Peer Reviewed Journal)   Abdurakhmonov, I.Y., Kohel, R.J., Yu, J., Pepper, A.E., Abdullaev, A.A., Kushanov, F.N., Salakhutdinov, I.B., Buriev, Z.T., Saha, S., Scheffler, B.E., Jenkins, J.N., Abdukarimov, A. 2008. Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm. Genomics. 92:478-487.   
- Applications of Microsatellites in Two Big Bracted Dogwood Species, Flowering and Kousa Dogwood -(Abstract Only)   Xinwang, W., Scheffler, B.E., Rinehart, T.A., Gann, A.M., Reed, S.M., Windham, M.T., Trigiano, R.N., Wadl, P.A. 2008. Applications of Microsatellites in Two Big Bracted Dogwood Species, Flowering and Kousa Dogwood. American Society of Horticulture Science Meeting.   
- Analysis of expressed sequence tags from Uromyces appendiculatus hyphae and haustoria and their comparison to sequences from other rust fungi -(Peer Reviewed Journal)   Tucker, M.L., Puthoff, D.P., Neelam, A., Ehrenfried, M.L., Scheffler, B.E., Ballard, L.L., Campbell, K.B., Cooper, B. 2008. Analysis of expressed sequence tags from Uromyces appendiculatus hyphae and haustoria and their comparison to sequences from other rust fungi. Phytopathology. 98:1126-1135.   
- Developing a sugarcane molecular identity database for use in breeding -(Abstract Only)   Pan, Y.-B., Scheffler, B.E., Richard Jr, E.P. 2008. Developing a sugarcane molecular identity database for use in breeding [abstract]. Available: http://www.issct.org/past-workshops/pathmbiolreport08.html. Also in: Proceedings IX Plant Pathology and VI Molecular Biology Workshop. June 23-27, 2008. Cali, Colombia. p. 6.   
- Mining novel genes resistant to blast disease for US rice production -(Abstract Only)   Yan, W., Correll, J., Agrama, H., Scheffler, B.E., Fjellstrom, R.G., McClung, A.M. 2008. Mining novel genes resistant to blast disease for US rice production. American Society of Agronomy Abstracts. p. 551-8.   
- Benzo(A)pyrene Decreases Brain and Ovarian Aromatase mRNA Expression -(Peer Reviewed Journal)   Dong, W., Wang, L., Thornton, C., Scheffler, B.E., Willett, K.L. 2008. Benzo(A)pyrene Decreases Brain and Ovarian Aromatase mRNA Expression. Aquatic Toxicology.   
- Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylo-genomic characterization, chromosome localization and linkage mapping -(Peer Reviewed Journal)   An, C., Saha, S., Jenkins, J.N., Ma, D., Scheffler, B.E., Kohel, R.J., Yu, J., Stelly, D.M. 2008. Cotton (Gossypium spp.) R2R3-MYB transcription factors SNP identification, phylogenomic characterization, chromosome localization and linkage mapping. Theoretical and Applied Genetics. 161:1015-1026.   
- Factors contributing to milling quality differences in MY3, a 'RiceCAP' project milling population -(Abstract Only)   Jodari, F., Roughton, A.I., Fjellstrom, R.G., Scheffler, B.E., Nelson, J.C. 2008. Factors contributing to milling quality differences in MY3, a 'RiceCAP' project milling population [abstract]. In: Proceedings of the Thirty-Second Rice Technical Working Group, February 18–21, 2008, San Diego, California. p. 55.   
- Fractionation of Synteny in a Genomic Region Containing Tandemly Duplicated Genes Across Glycine max, Medicago truncatula and Arabidopsis thaliana -(Peer Reviewed Journal)   Schlueter, J.A., Scheffler, B.E., Jackson, S., Shoemaker, R.C. 2008. Fractionation of Synteny in a Genomic Region Containing Tandemly Duplicated Genes Across Glycine max, Medicago truncatula and Arabidopsis thaliana. Journal of Heredity.   
- Microsatellites from Kousa dogwood (Cornus Kousa) -(Peer Reviewed Journal)   Wadl, P., Wang, X., Scheffler, B.E., Rinehart, T.A., Trigiano, R. 2007. Microsatellites from Kousa dogwood (Cornus Kousa). Molecular Ecology Notes, online (doi:10.1111/j.1471-8286.2007.02062.x)   
- Development and Characterization of Simple Sequence Repeats for Flowering Dogwood (Cornus florida L.) -(Peer Reviewed Journal)   Wang, X., Trigiano, R.N., Windham, M.T., Scheffler, B.E., Rinehart, T.A., Spiers, J.M. 2007. Development and Characterization of Simple Sequence Repeats for Flowering Dogwood (Cornus florida L.). Tree Genetics & Genomics  Vol 4, no.3 pp.461-468.   
- BAC-DERIVED SSR CHROMOSOME LOCATIONS IN COTTON -(Peer Reviewed Journal)   Guo, Y., Saha, S., Yu, J., Jenkins, J.N., Kohel, R.J., Scheffler, B.E., Stelly, D.M. 2008. BAC-derived SSR chromosome locations in cotton. Euphytica. 161:361-370.   
- GENE DUPLICATION AND PALEOPOLYPLOIDY IN SOYBEAN AND THE IMPLICATIONS FOR WHOLE GENOME SEQUENCING -(Peer Reviewed Journal)   Schlueter, J., Lin, J., Schlueter, S., Vasylenko-Sanders, I., Deshpandem, S., Yi, J., O'Bleness, M., Roe, B., Nelson, R., Scheffler, B.E., Jackson, S., Shoemaker, R.C. 2007. Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing. Biomed Central (BMC) Genomics. 8:330.   
- Towards Sequencing Cotton (Gossypium) Genomes -(Peer Reviewed Journal)   Chen, Z., Scheffler, B.E., Dennis, E., Triplett, B.A., Zhang, T., Chen, X., Stelly, D., Rabinowicz, P., Town, C., Arioli, T., Brubaker, C., Cantrell, R., Lacape, J., Ulloa, M., Chee, P., Gingle, A.R., Haigler, C.H., Percy, R.G., Saha, S., Wilkins, T., Wright, R.I., Van Deynze, A., Zhu, Y., Yu, S., Guo, W., Abdurakhmonov, I., Katageri, I., Ur-Rahman, M., Zafar, Y., Yu, J., Kohel, R.J., Wendel, J., Paterson, A. 2007. Towards Sequencing Cotton (Gossypium) Genomes. Plant Physiology. 145:1303-1310.   
- Analysis of Transcripts and Proteins Expressed in the Salivary Glands of Hessian Fly (Mayetiola destructor) Larvae -(Peer Reviewed Journal)   Chen, M., Huixian, Z., Zhu, Y., Scheffler, B.E., Liu, X., Liu, X., Hulbert, S., Stuart, J. 2008. Analysis of Transcripts and Proteins Expressed in the Salivary Glands of Hessian Fly (Mayetiola destructor) Larvae. Journal of Insect Physiology.54:1-16.   
- Development and characterization of RiceCAP QTL mapping population for sheath blight resistance -(Abstract Only)   Mcclung, A.M., Groth, D., Oard, J.H., Utomo, H., Moldenhauer, K.K., Boza, E., Scheffler, B.E., Jia, Y., Liu, G., Correa, F., Fjellstrom, R.G. 2007. Development and characterization of RiceCAP QTL mapping population for sheath blight resistance. [abstract] American Society of Agronomy Abstracts. p. 259-4.   
- Development of Reniform Nematode Resistance in Upland Cotton -(Review Article)   Robinson, A.F., Augudelo, P., Avila, C.A., Bell, A.A., Callahan, F.E., Cook, C.G., Dighe, N.D., Gutierrez, O.A., Hayes, R.W., Jenkins, J.N., Johnson, J.T., Kantety, R., Lawrence, G.W., Lawrence, K.S., Mangineni, L., Mccarty, J.C., Menz, M.A., Meredith, W.A., Nichols, R.L., Robbins, R.T., Sacks, E., Scheffler, B., Sciumbato, G.L., Smith, C.W., Starr, J.L., Stelly, D.M., Stetina, S.R., Stewart, J.M., Thaxton, P.M., Wallace, T.P., Weaver, D.B., Wubben, M.J., Young, L.D. 2008.  Development of reniform nematode resistance in Upland cotton. In: Proceedings of the World Cotton Research Conference-4, September 10-14, 2007, Lubbock, Texas. 2008 CDROM.   
- AFLATOXIN FORMATION AND GENE EXPRESSION IN RESPONSE TO CARBON SOURCE MEDIA SHIFT IN ASPERGILLUS PARASITICUS -(Peer Reviewed Journal)   Wilkinson, J.R., Yu, J., Abbas, H.K., Scheffler, B.E., Kim, H.S., Nierman, W.C., Bhatnagar, D., Cleveland, T.E. 2007. Aflatoxin formation and gene expression in response to carbon source media shift in Aspergillus parasiticus. Journal of Food Additives & Contaminants. 24(10):1051-1060.   
- Microsatellites and Their Appliation in Flowering Dogwood -(Abstract Only)   Wang, X., Trigiano, R., Windham, M., Scheffler, B.E., Rinehart, T.A., Spiers, J.M. 2008. Microsatellites and Their Appliation in Flowering Dogwood. Meeting Abstract.   
- High-throughput genotyping of commercial sugarcane clones with microsatellite (SSR) DNA markers -(Peer Reviewed Journal)   Pan, Y.-B., Scheffler, B.S., Richard, Jr., E.P. 2007. High-throughput genotyping of commercial sugarcane clones with microsatellite (SSR) DNA markers. Sugar Tech. 9:176-181.   
- RiceCAP: Development of molecular markers associated with long grain milling yield -(Abstract Only)   Mcclung, A.M., Boza, E., Fjellstrom, R.G., Guo, Z., Jodari, F., Linscombe, S.D., Moldenhauer, K.K., Nelson, J., Oard, J., Scheffler, B.E., Sun, X. 2007. RiceCAP: Development of molecular markers associated with long grain milling yield. Cereal Foods World 52:A5.   
- Transcriptome profiling, sequence characterization, and assignment to chromosomes of SNP markers for EXPANSIN genes in cotton -(Peer Reviewed Journal)   An, C., Saha, S., Jenkins, J.N., Scheffler, B.E., Wilkins, T.A., Stelly, D.M. 2007. Transcriptome profiling, sequence characterization, and  SNP-based chromosomal assignment of the EXPANSIN genes in cotton. Molecular Genetics and Genomics. 278:539-553.   
- Molecular and SNP characterization of two genome specific transcription factor genes GhMyb8 and GhMyb10 in cotton species -(Peer Reviewed Journal)   Hsu, C., An, C., Saha, S., Ma, D., Jenkins, J.N., Scheffler, B.E., Stelly, D. 2008. Molecular and SNP characterization of two genome specific transcription factor genes GhMyb8 and GhMyb10 in cotton species. Euphytica. 159:259-273.   
- Characterization of Microsatellite Loci in the Western Tarnished Plant Bug, Lygus hesperus Knight (Hemiptera: Miridae) -(Peer Reviewed Journal)   Shrestha, R.B., Parajulee, M.N., Perera, O.P., Scheffler, B.E., Densmore, L.S. 2007. Characterization of Microsatellite Loci in the Western Tarnished Plant Bug, Lygus hesperus Knight (Hemiptera: Miridae). Molecular Ecology Notes. 7:1342-1344. (doi:10.1111/j.147-8286.2007.01875.x)   
- Using microsatellite DNA markers to determine the genetic identity of parental clones used in the Louisiana sugarcane breeding program -(Abstract Only)   Pan, Y.-B., Scheffler, B.E., Richard Jr, E.P. 2007. Using microsatellite DNA markers to determine the genetic identity of parental clones used in the Louisiana sugarcane breeding program. Journal of the American Society of Sugar Cane Technologists. 27:71.   
- Chararacteristics of Thirteen Polymorphic Microsatellite Markers in the Corn Earworm, Helicovepa zea (Lepidoptera : Noctuidae) -(Peer Reviewed Journal)   Perera, O.P., Blanco C.A., SchefflerB.E., and Abel C.A. 2007. Characteristics of 13 ploymorphic microsatellite makers in the corn earworm, Helicovepa zea (Lepidoptera: Noctuidae). Mol. Ecol. Notes. doi: 10.1111/j.147-8286.2007.01806.x   
- Protein Accumulation Changes Associated with Germination of the Uromyces appendiculatus Uredospore -(Peer Reviewed Journal)   Cooper, B., Neelan, A., Campbell, K., Lee, J., Liu, G., Garrett, W.M., Scheffler, B.E., Tucker, M.L. 2007. Protein Accumulation Changes Associated with Germination of the Uromyces appendiculatus Uredospore. Molecular Plant-Microbe Interactions. 20(7):857-866.   
- Characterization of Eight Polymorphic Microsatellite Markers from the Tarnished Plant Bug, Lygus lineolaris (Palisot de Beauvois) -(Peer Reviewed Journal)   Perera O. P., Snodgras G.L., Scheffler B.E., Gore J., and Abel C. A. 2007. characterization of eight ploymorphic microsatelliet markers in the tarnished plant bug, Lygus lineolaris (Palisot de Beauvois). Mol. Ecol. Notes. doi: 10.1111/j.1471-8286.2007.01747.x   
- Aspergillus flavus whole genome and EST sequence releases and construction of homologous gene search blast server -(Germplasm Release)   Yu, J., Moore Flanagan, M.E., Scheffler, B.E., King Jr, E.G., Bhatnagar, D., Cleveland, T.E. 2007. Aspergillus flavus whole genome and EST sequence releases and construction of homologous gene search blast server. Germplasm Release. Web Blast Server for Gene Homology Search and Genome Sequence Releases at USDA/ARS/MSA, Stoneville, MS. (http://199.133.182.124:4443/blast/Unique.html).   
- The R2R3-Myb transcription fators of cotton:  SNP characterization, chromosomal assignment, and phylogenetic analysis -(Abstract Only)   An, C., Saha, S., Jenkins, J.N., Scheffler, B.E., Ma, D-P., Stelly, D.M. 2007. MYB genes, a family of transcription fators:  SNPS characterization, chromosomal location, and phylogenetic analysis [abstract]. National Cotton Council Beltwide Cotton Conference. p. 1620.   
- Genome-wide linkage disequilibruim revealed by microsatellite markers and association study of fiber quality traits in cotton -(Abstract Only)   Abdurakhmonov, I.Y., Kohel, R.J., Saha, S., Pepper, A.E., Yu, J., Buriev, Z.T., Abdullaev, A., Shermatov, S., Jenkins, J.N., Scheffler, B.E., Abdukarimov, A. 2007. Genome-wide linkage disequilibruim revealed by microsatellite markers and association study of fiber quality traits in cotton [abstract]. In: Proceedings of Plant and Animal Genome XV Conference, January 13-17, 2007, San Diego, California. Paper No. W199.   
- EVIDENCE OF CLUSTERING FOR THE MIC-3 ROOT-SPECIFIC GENE FAMILY ASSOCIATED WITH NEMATODE RESISTANCE IN GOSSYPIUM SPP. -(Abstract Only)   Buriev, Z., Saha, S., Abdurakhmonov, I.Y., Jenkins, J.N., Abukarimov, A., Scheffler, B.E., Stelly, D.M., Wubben, M. 2006. Evidence of clustering for the mic-3 root-specific gene family associated with nematode resistance in gossypium spp [abstract]. American Society of Agronomy Abstracts. CDROM.   
- A Simple and Effective Procedure for Discovering Microsatellites from Small Insert Libraries -(Peer Reviewed Journal)   Wang, X., Trigiano, R.N., Windham, M.T., Devries, R., Scheffler, B.E., Rinehart, T.A., Spiers, J.M. 2006. A simple and effective procedure for discovering microsatellites from small insert libraries. Molecular Ecology Notes.  Vol 7. pp 558-561   
- Analysis of ESTs from Multiple Gossypium hirsutum Tissues and Identification of SSRs -(Peer Reviewed Journal)   Taliercio, E.W., Allen, R.D., Essenberg, M., Nguyen, H., Patil, M., Payton, P.R., Phillips, A., Pierce, M., Scheffler, B.E., Turley, R.B., Wang, J., Zhang, D., Scheffler, J.A. 2006. Analysis of ESTs from Multiple Gossypium hirsutum Tissues and Identification of SSRs. Genome.  49:306-319.   
- THE FAD2 GENE FAMILY OF SOYBEAN:INSIGHTS INTO THE STRUCTURAL AND FUNCTIONAL DIVERGENCE OF A PALEOPOLYPLOID GENOME -(Peer Reviewed Journal)   Schlueter, J.A., Sanders, I.F., Deshpande, S., Yi, J., Seigfried, M., Roe, B.A., Schlueter, S.D., Scheffler, B.E., Shoemaker, R.C. 2006. The fad2 gene family of soybean:insights into the structural and functional divergence of a paleopolyploid genome. The Plant Genome. 1:14-26.   
- EVALUATION OF THE CMD PANEL -(Abstract Only)     
- A STRATEGY FOR DEVELOPING SNP MARKERS FOR THE MIC-3 ROOT-SPECIFIC GENE FAMILY ASSOCIATED WITH NEMATODE RESISTANCE IN GOSSYPIUM SPP. -(Abstract Only)   Buriev, Z., Saha, S., Abdurakhmonov, I.Y., Jenkins, J.N., Abdukarimov, A., Scheffler, B.E., Stelly, D.M., Wubben, M. 2006. A strategy for developing snp markers for the mic-3 root-specific gene family associated with nematode resistance in gossypium spp. [abstract]. Proceedings International Cotton Genome Initiative Conference. Available: http:\\cgi.tamu.edu\pds\icgi06-abs-final.   
- Genetic diversity estimates for the genus Hydrangea and development of a molecular key based on SSR -(Peer Reviewed Journal)   Rinehart, T.A., Scheffler, B.E., Reed, S.M. 2006. Genetic diversity estimates for the genus Hydrangea and development of a molecular key based on SSR. Journal of the American Society for Horticultural Science. 131:787-797.   
- Linkage Disequilibrium Based Association Mapping of Fiber Quality Traits in Cotton Using Diverse Cotton Germplasm from Uzbekistan -(Abstract Only)   Abdurakhomonov, I.Y., Kohel, R.J., Saha, S., Pepper, A.E., Yu, J., Buriev, Z.T., Shermatov, S.E., Abdullaev, A.A., Kushanov, F.N., Jenkins, J.N., Scheffler, B.E., Abdukarimov, A. 2006. Linkage disequilibrium based association mapping of fiber quality traits in cotton using diverse cotton germplasm from Uzbekistan [abstract]. In: Proceedings of International Cotton Genome Initiative Workshop, Structural Genomics Session, September 18-20, 2006, Brasilia, Brazil. Paper No. 7.  Available: http://icgi.tamu.edu/pdf/icgi06_abs_final.pdf.   
- Analysis of Genetic Diversity in Selected Cornus Species Using SSR Markers -(Proceedings)   Wang, X., Trigiano, R., Windham, M., Devries, R., Rinehart, T.A., Spiers, J.M., Scheffler, B.E. 2007. Analysis of Genetic Diversity in Selected Cornus Species Using SSR Markers. Southern Nursery Association Research Conference vol.51, pp. 616-617.   
- CMD:  A Cotton Microsatellite Database Resource for Gossypium Genomics -(Peer Reviewed Journal)   Blenda, A.V., Scheffler, J.A., Scheffler, B.E., Palmer, M., Lacape, J., Yu, J., Jesudraui, C., Jung, S., Muthukumar, S., Yellambalase, P., Ficklin, S., Staton, M., Eschelman, R., Ulloa, M., Saha, S., Burr, B., Lui, S., Zhang, T., Fang, D., Pepper, A.E., Kumpatla, S.P., Jacobs, J., Tomkins, J.P., Cantrell, R.G., Main, D. 2006. CMD:  A Cotton Microsatellite Database Resource for Gossypium Genomics. Biomed Central (BMC) Genomics. 7:132.   
- ON THE HUNT FOR NEW MOLECULAR MARKERS:  EVALUATING SOYBEAN (GLYCINE MAX) SSR'S FOR COTTON (GOSSYPIUM HIRSUTUM) -(Peer Reviewed Journal)   Scheffler, J.A., Scheffler, B.E., Ray, J.D., Taliercio, E.W. 2006. On the hunt for new molecular markers:  evaluating soybean (glycine max) ssr's for cotton (gossypium hirsutum). Indian Society for Cotton Improvement.  Vol 31: 79-87   
- MEDIA SHIFT OF ASPERGILLUS PARASITICUS CULTURES FOR STUDYING THE MOLECULAR REGULATION OF AFLATOXIN -(Abstract Only)   Wilkinson, J.R., Yu, J., Abbas, H.K., Scheffler, B.E., Kim, H.S., Nierman, W.C., Bhatnagar, D., Cleveland, T.E. 2006. Media shift of Aspergillus parasiticus cultures for studying the molecular regulation of aflatoxin. In: Proceedings of the American Society for Microbiology Annual Meeting, May 21-26, 2006, Orlando, FL. Abstract #O-064, p. 433.   
- INFLUENCE OF TRYPTOPHAN ON AFLATOXIN BIOSYNTHESIS AND REGULATION IN ASPERGILLUS FLAVUS -(Abstract Only)   Wilkinson, J.R., Yu, J., Bland, J.M., Scheffler, B.E., Kim, H.S., Nierman, W.C., Cleveland, T.E. 2006. Influence of tryptophan on aflatoxin biosynthesis and regulation in Aspergillus flavus. In: Proceedings of the American Society for Microbiology Annual Meeting, May 21-26, 2006, Orlando, FL. Abstract #O-042, p. 429.   
- TRYPTOPHAN’S EFFECTS ON AFLATOXIN BIOSYNTHESIS AND ITS REGULATION IN ASPERGILLUS FLAVUS -(Abstract Only)   Wilkinson, J.R., Yu, J., Bland, J.M., Scheffler, B.E., Kim, H.S., Nierman, W.C., Cleveland, T.E. 2006. Tryptophan’s effects on aflatoxin biosynthesis and its regulation in Aspergillus flavus. In: Proceedings of the 8th European Conference on Fungal Genetics, April 6-12, 2006, Vienna, Austria. p. 68.   
- USING SSR MARKERS TO VERIFY CRAPEMYRTLE HYBRIDS -(Abstract Only)   Rinehart, T.A., Pounders Jr, C.T., Scheffler, B.E. Using ssr markers to verify crapemyrtle hybrids. American Society of Horticulture Science Meeting vol. 41, 1008.   
- ANALYSIS OF GENETIC DIVERSITY IN SELECTED CORNUS SPECIES USING SSR MARKERS -(Abstract Only)   Wang, X., Trigiano, R.N., Windham, M.T., Rinehart, T.A., Spiers, J.M., Scheffler, B.E. 2006. Analysis of genetic diversity in selected cornus species using ssr markers. American Society of Horticulture Science Meeting.   
- Cotton Marker Database -(Abstract Only)     
- SEQUENCE ANALYSIS OF SIX A-EXPANSIN GENES IN COTTON -(Abstract Only)   An, C., Saha, S., Jenkins, J.N., Scheffler, B.E., Wilkins, T.A. 2006. Chromosomal assignment of six alpha-expansin genes using SNP markers in cotton (Gossypium spp.). Beltwide Cotton Conferences. p. 737.   
- EFFECTS OF BENZO(A)PYRENE EXPOSURSE ON KILLFISH (FUNDULUS HETEROCLITUS) AROMATASE ACTIVITIES AND MRNA -(Peer Reviewed Journal)   Patel, M.R., Scheffler, B.E., Wang, L., Willett, K.L. 2006. Effects of benzo(a)pyrene exposure on killfish (fundulus heteroclitus) aromatase activities and mrna. Aquatic Toxicology. 77(3):267-278.   
- IN VIVO AND IN VITRO CYP1B MRNA EXPRESSION IN CHANNEL CATFISH -(Peer Reviewed Journal)   Willett, K.L., Ganesan, S., Patel, M., Metzger, C., Quiniou, S.M., Waldbieser, G.C., Scheffler, B.E. 2005. In vivo and in vitro cyp1b mrna expression in channel catfish. Marine Environmental Research.   
- Characterization of a higher plant herbicide-resistant phytoene desaturase and its use as a selectable marker -(Peer Reviewed Journal)   Arias De Ares, R.S., Dayan, F.E., Albrecht, M., Howell, J., Scheffler, B.E. 2006. Characterization of a higher plant herbicide-resistant phytoene desaturase and its use as a selectable marker. Plant Biotechnology Journal. 4:263-273.   
- CHARACTERIZATION OF A HIGHER PLANT HERBICIDE-RESISTANT PHYTOENE DESATURASE AND ITS USE AS A SELECTABLE MARKER -(Peer Reviewed Journal)   Arias, R.S., Dayan, F.E., Michel, A., Howell, J., Scheffler, B.E. 2006. Characterization of a higher plant herbicide-resistant phytoene desaturase and its use as a selectable marker. Plant Biotechnology Journal. 4: 263-273.   
- THE OPTIMIZATION OF MICROSATELLITE DISCOVERY IN FLOWERING DOGWOOD (CORNUS FLORIDA L.) -(Abstract Only)   Wang, X., Trigiano, R.N., Windham, M.T., Devries, R., Rinehart, T.A., Spiers, J.M., Scheffler, B.E. 2006. The optimization of microsatellite discovery in flowering dogwood (cornus florida l.). Annual International Plant & Animal Genome Conference.   
- GENETIC DIVERSITY IN FLOWERING DOGWOOD (CORNUS FLORIDA L.) USING MICROSATELLITE (SSR) MARKERS -(Abstract Only)   Wang, X., Trigiano, R.N., Windham, M.T., Devries, R., Rinehart, T.A., Spiers, J.M., Scheffler, B.E. 2006. Genetic diversity in flowering dogwood (cornus florida l.) using microsatellite (ssr) markers. Annual International Plant & Animal Genome Conference.   
- CULTIVAR IDENTIFICATION AND INTERSPECIFIC HYBRID VERIFICATION IN LAGERSTROEMIA USING SSR MARKERS -(Abstract Only)   Rinehart, T.A., Pounders Jr, C.T., Scheffler, B.E. 2006. Cultivar identification and interspecific hybrid verification in lagerstroemia using ssr markers. Annual International Plant & Animal Genome Conference.   
- Estimating Genetic Diversity within the Hydrangea Genus Using Molecular Markers -(Proceedings)   Rinehart, T.A., Scheffler, B.E., Reed, S.M. 2005. Estimating Genetic Diversity within the Hydrangea Genus Using Molecular Markers. Southern Nursery Association Research Conference. pp. 656-659.   
- APPLICATION OF HIGH-THROUGHPUT DNA MARKER TECHNOLOGY IN SUGARCANE BREEDING: PHASE II - PCR AMPLIFICATION AND CAPILLARY ELECTROPHORESIS -(Abstract Only)   Pan, Y., Scheffler, B.E., Richard Jr, E.P. 2005. Application of High-Throughput DNA Marker Technology in Sugarcane Breeding: Phase II - PCR Amplification and Capillary Electrophoresis. Journal of the American Society of Sugar Cane Technologists. 25:117. Available: http://www.assct.org/journal/journal.htm   
- THE DOMINANT INHIBITORY CHALCONE SYNTHASE ALLELE C2-IDF (INHIBITOR DIFFUSE) FROM ZEA MAYS(L.) ACTS VIA AN ENDOGENOUS RNA SILENCING MECHANISM -(Peer Reviewed Journal)   Della Vedova, C.B., Lorbiecke, R., Kirsch, H., Schulte, M.B., Scheets, K., Borchert, L.M., Scheffler, B.E., Wienand, U., Cone, K.C., Birchler, J.A. 2006. The dominant inhibitory chalcone synthase allele C2-IDF (inhibitor diffuse) from zea mays(L.) acts via an endogenous rna silencing mechanism. Genetics. 170:1989-2002.   
- THE USE OF POLYMERASE CHAIN REACTION (PCR) FOR THE IDENTIFICATION OF EPHEDRA DNA IN DIETARY SUPPLEMENTS -(Peer Reviewed Journal)   Techen, N., Khan, I.A., Pan, Z., Scheffler, B.E. 2006. The use of polymerase chain reaction (pcr) for the identification of ephedra dna in dietary supplements. Planta Medica. 72: 241-247.   
- PATTERNS OF ESSENTIAL OIL RELATIONSHIPS IN PIMPINELLA (UMBELLIFERAE) BASED ON PHLYOGENETIC RELATIONSHIPS USING NUCLEAR AND CHLOROPLAST SEQUENCES -(Peer Reviewed Journal)   Tabanca, N., Douglas, A.W., Bedir, E., Dayan, F.E., Kirimer, N., Baser, H.K., Aytac, Z., Khan, I.A., Scheffler, B.E. 2005. Patterns of essential oil relationships in pimpinella (umbelliferae) based on phlyogenetic relationships using nuclear and chloroplast sequences. Plant Genetic Resources. 3(2):149-169.   
- GENE TRANSCRIPTION PROFILES OF SACCHAROMYCES CEREVISIAE AFTER TREATMENT WITH PLANT PROTECTION FUNGICIDES THAT INHIBIT ERGOSTEROL BIOSYNTHESIS -(Peer Reviewed Journal)   Kagan, I., Michel, A., Prause, A., Scheffler, B.E., Pace, P., Duke, S.O. 2005. Gene transcription profiles of saccharomyces cerevisiae after treatment with plant protection fungicides that inhibit ergosterol biosynthesis. Journal of Pesticide Biochemistry and Physiology.  82(2):133-153.   
- GLOBAL GENE EXPRESSION APPROACHES TO MODE-OF-ACTION STUDIES WITH NATURAL PRODUCT-BASED PESTICIDES -(Book / Chapter)   Kagan, I., Michel, A., Scheffler, B.E., Prause, A., Baerson, S.R., Duke, S.O. Global gene expression approaches to mode-of-action studies with natural product-based pesticides. Rimando, A.M., Duke, S.O., editors. American Chemical Society, Washington, DC. Natural Products for Pest Management. 2006. pp. 255-264.   
- EVALUATION OF SEVEN AB INITIO GENE PREDICTION PROGRAMS FOR THE DISCOVERY OF MAIZE GENES -(Peer Reviewed Journal)   Yao, H., Guo, L., Fu, Y., Wen, T., Borsuk, L.A., Skibbe, D.S., Cui, X., Scheffler, B.E., Cao, J., Ashlock, D.A., Schnable, P.S. 2005. Evaluation of seven ab initio gene prediction programs for the discovery of maize genes. Plant Physiology.  57(3): 445-460.   
- MOLECULAR EVOLUTION OF HERBICIDE RESISTANCE TO PHYTOENE DESATURASE INHIBITORS IN HYDRILLA VERTICILLATA AND ITS POTENTIAL USE TO GENERATE HEBICIDE-RESISTANT CROPS -(Review Article)   Arias, R.S., Netherland, M.D., Scheffler, B.E., Puri, A., Dayan, F.E. 2005. Molecular evolution of herbicide resistance to phytoene desaturase inhibitors in hydrilla verticillata and its potential use to generate hebicide-resistant crops. Pest Management Science.  61:258-268.   
- HERBICIDES, BIOTECHNOLOGY -(Review Article)   Duke, S.O., Scheffler, B.E., Boyette, C.D., Lydon, J., Oliva, A. 2005. Herbicides, biotechnology. In Kirk-Othmer Encyclopedia of Chemical Technology, Wiley-Interscience, New York.  13:346-369.   
- THE SOYBEAN GENOME:  DUPLICATIVE, YET UNIQUE -(Abstract Only)   Shoemaker, R.C., Schlueter, J., Scheffler, B.E. 2005. The soybean genome:  duplicative, yet unique. Plant and Animal Genome Abstracts. W207:Legumes.   
- MOLECULAR MARKERS RUN ON A TEST PANEL: A DATA SOURCE FOR THE COTTON COMMUNITY -(Abstract Only)   Scheffler, B.E., Taliercio, E.W., Scheffler, J.A., Yu, J. 2004. Molecular markers run on a test panel: a data source for the cotton community. International Cotton Genome Initiative Workshop.   
- THE ROADMAP TO THE COTTON GENOME -(Abstract Only)   Scheffler, B.E. 2004. The roadmap to the cotton genome. International Cotton Genome Initiative Workshop.   
- MOLECULAR MARKERS RUN ON A TEST PANEL: A DATA SOURCE FOR THE COTTON COMMUNITY -(Abstract Only)   Scheffler, B.E., Taliercio, E.W., Scheffler, J.A., Yu, J. 2004. Molecular markers run on a test panel: A data source for the cotton community [abstract]. International Cotton Genome Initiative Workshop. Paper No. 18-45.   
- ON THE HUNT FOR NEW MOLECULAR MARKERS -(Abstract Only)     
- HIGHLY POLYMORPHIC MICROSATELLITE DNA MARKERS FOR U.S. SUGARCANE GERMPLASM EVALUATION AND VARIETY FINGERPRINTING -(Abstract Only)   Pan, Y.B., Comstock, J.C., Scheffler, B.E. 2005. Highly Polymorphic Microsatellite DNA Markers for U.S. Sugarcane Germplasm Evaluation and Variety Fingerprinting [abstract]. Guide of Plant and Animal Genome XIII. p. 36.   
- GENETIC PROFILING OF HYPERICUM L. (ST. JOHN'S WORT) SPECIES BY NUCLEAR RIBOSOMAL I.T.S. SEQUENCE ANALYSIS -(Peer Reviewed Journal)   Crockett, S.L., Douglas, A.W., Scheffler, B.E., Khan, I.A. 2004. Genetic profiling of Hypericum L. (St. John's Wort) species by nuclear ribosomal I.T.S. sequence analysis. Planta Medica. 70:929-935.   
- SOR1, A GENE ASSOCIATED WITH BIOHERBICIDE PRODUCTION IN SORGHUM ROOT HAIRS -(Peer Reviewed Journal)   Yang, X., Scheffler, B.E., Weston, L.A. 2004. Sor1, a gene associated with bioherbicide production in sorghum root hairs. Experimental Biology. 55(406):2251-2259.   
- SOMATIC MUTATION-MEDIATED EVOLUTION OF HERBICIDE RESISTANCE IN THE NONINDIGENOUS INVASIVE PLANT HYDRILLA (HYDRILLA VERTICILLATA) -(Peer Reviewed Journal)   Michel, A., Arias De Ares, R.S., Scheffler, B.E., Duke, S.O., Netherland, M., Dayan, F.E. 2004. Somatic mutation-mediated evolution of herbicide resistance in the nonindigenous invasive plant hydrilla (Hydrilla verticillata). Molecular Ecology. 13:3229-3237.   
- APPLICATION OF HIGH-THROUGHPUT DNA MARKER TECHNOLOGY IN SUGARCANE BREEDING: PHASE I - NUCLEIC ACIDS EXTRACTION -(Abstract Only)   Pan, Y., Veremis, J.C., Scheffler, B.E., Tew, T.L., Grisham, M.P., White, W.H., Richard Jr, E.P. 2004. High-throughput application of the DNA marker technology in sugarcane breeding: Phase I - DNA extraction [abstract]. Journal of the American Society of Sugar Cane Technologists. 24:117.   
- DNA MICROARRAY AND PROTEOMIC ANALYSIS OF ROOT HAIR INFECTION -(Proceedings)   Stacey, G., Huang, S., Wan, J., Zou, J., Clough, S.J., Scheffler, B.E., Kim, S., Nguyen, H. 2004. DNA microarray and proteomic analysis of root hair infection. International Conference on Legume Genomics and Genetics. p. 183-184.   
- AUTHENTICATION OF MEDICINAL PLANTS USING MOLECULAR BIOLOGY TECHNIQUES TO COMPLIMENT CONVENTIONAL METHODS -(Peer Reviewed Journal)   Techen, N., Crockett, S.L., Khan, I.A., Scheffler, B.E. Authentication of medicinal plants using molecular biology techniques to compliment conventional methods. Current Medicinal Chemistry. 2004. V. 11.  P. 1391-1401.   
- EVALUATION OF THE TRANSCRIPTOME RESPONSE OF CHANNEL CATFISH TO ENTERIC SEPTICEMIA OF CATFISH -(Proceedings)   Arnizaut, A., Waldbieser, G.C., Scheffler, B.E., Bengten, E., Wilson, M., Wolters, W.R., Hanson, L. 2004. Evaluation of the transcriptome response of channel catfish to enteric septicemia of catfish. 55th Annual Meeting of the Animal Disease Research Workers in Southern States/6th Annual Meeting of the Southern Conference of Researchers in Aquatic Diseases. Biloxi, MS. p. 28.   
- GENOMIC AND PHYLOGENIC COMPARISONS OF THE ALPHA GLOBIN AND BETA GLOBIN INTERGENIC SEQUENCES BETWEEN ZEBRA FISH (DANIO RERIO) AND SIX CLOSELY RELATED CYPRININDAE SPECIES -(Peer Reviewed Journal)   Vidal, G., Scheffler, B.E., Michel, A., D'Surney, S.J. 2004. Genomic and phylogenic comparisons of the alpha globin and beta globin intergenic sequences between zebra fish (danio rerio) and six closely related cyprinindae species. DNA and Cell Biology. V. 23. P. 325-334.   
- MOLECULAR MARKER POSSIBILITIES - GOING BEYOND GOSSYPIUM -(Abstract Only)   Scheffler, J.A., Ray, J.D., Scheffler, B.E., Techan, N. 2004. Molecular marker possibilities - going beyond Gossypium [abstract]. National Cotton Council Beltwide Cotton Conference. p. 1130.   
- NEW POSSIBILITIES FOR SOME OLD GENES: IMPROVED HOST PLANT RESISTANCE IN COTTON -(Proceedings)   Scheffler, J.A., Dowd, M.K., Meredith Jr, W.R., Scheffler, B.E. 2004. New possibilities for some old genes: improved host plant resistance in cotton. In: Proceedings of the World Cotton Research Conference III, March 9-13, 2003, Cape Town, South Africa. p. 175-182.   
- DOSE-RESPONSE RELATIONSHIPS BETWEEN HERBICIDES WITH DIFFERENT MODES OF ACTION AND GROWTH OF LEMNA PAUCICOSTATA: AN IMPROVED ECOTOXICOLOGICAL METHOD -(Peer Reviewed Journal)   Michel, A., Johnson, R.D., Duke, S.O., Scheffler, B.E. Dose-response relationships between herbicides with different modes of action and growth of Lemna paucicostata: an improved ecotoxicological method. Environmental Toxicology and Chemistry.  2004. V. 23(4). P. 1074-1079.   
- Bioengineering resistance to phytoene desaturase inhibitors in Arabidopsis thaliana -(Abstract Only)   Arias, R.S., Netherland, M.D., Michel, A., Duke, S.O., Scheffler, B.E., Dayan, F.E. 2004. Bioengineering resistance to phytoene desaturase inhibitors in Arabidopsis thaliana. Weed Science Society of America (WSSA) Meeting, February 11, 2004, Kansas City, MO.  Meeting Proceedings.   
- MANIPULATION OF ROOT HAIR DEVELOPMENT AND SORGOLEONE PRODUCTION IN SORGHUM SEEDLINGS -(Peer Reviewed Journal)   Yang, X., Owens, T.G., Scheffler, B.E., Weston, L.A. Manipulation of root hair development and Sorgoleone production in sorghum seedlings. Journal of Chemical Ecology. 2004. V. 30(1). P. 199-213.   
- HOW MOLECULAR BIOLOGY METHODS CAN BE USED IN THE AUTHENTICATION OF BOTANICALS -(Abstract Only)   Scheffler, B.E., Tabanca, N., Crockett, S., Douglas, A., Techen, N., Kahn, I. 2003. How molecular biology methods can be used in the authentication of botanicals. American Society for Horticultural Science.   
- ARS RESEARCH ON NATURAL PRODUCTS FOR PEST MANAGEMENT -(Review Article)   DUKE, S.O., BAERSON, S.R., DAYAN, F.E., RIMANDO, A.M., SCHEFFLER, B.E., TELLEZ, M.R., WEDGE, D.E., AKEY, D.H., ARTHUR, F.H., DE LUCCA II, A.J. ARS RESEARCH ON NATURAL PRODUCTS FOR PEST MANAGEMENT. PEST MANAGEMENT SCIENCE. 2003.  V.59:708-717.   
- STRATEGIES FOR THE USE OF NATURAL PRODUCTS FOR WEED MANAGEMENT -(Literature Review)   DUKE, S.O., RIMANDO, A.M., BAERSON, S.R., SCHEFFLER, B.E., OTA, E., BELZ, R.G. STRATEGIES FOR THE USE OF NATURAL PRODUCTS FOR WEED MANAGEMENT. JOURNAL OF PESTICIDE SCIENCE. 2002.  V.27:298-306.   
- BIOACTIVATION OF THE FUNGAL PHYTOTOXIN 2,5-ANHYDRO-D GLUCITOL BY GLYCOLYTIC ENZYMES IS AN ESSENTIAL COMPONENT OF ITS MECHANISM OF ACTION -(Peer Reviewed Journal)     
- THE INHIBITORY ACTIVITY OF NATURAL PRODUCTS ON PLANT P-HYDROXYPHENYL-      PYRUVATE DIOXYGENASE -(Peer Reviewed Journal)     
- MOLECULAR METHODS IN WEED SCIENCE -(Peer Reviewed Journal)     
- STRATEGIES FOR USING TRANSGENES TO PRODUCE ALLELOPATHIC CROPS -(Review Article)     
- BIOTECHNOLOGY FOR CONTROL OF WEEDS -(Book / Chapter)   Duke, S.O., Scheffler, B.E., Boyette, D.C., Lydon, J., Oliva, A. 2003. Biotechnology for control of weeds. In: Plimer, J., Gammon, D.W., Ragsdale, N.N., editors.  Encyclopedia of Agrochemicals, Vol. 2.  New York, NY: John Wiley & Sons.  P. 733-744.   
- MOLECULAR MARKERS: A DIAGNOSTIC TOOL FOR THE ASSESSMENT OF GENETIC         DIVERSITY IN PODOPHYLLUM PELTATUM -(Proceedings)     
- ALLELOCHEMICALS AS HERBICIDES -(Proceedings)   DUKE,S.O., SCHEFFLER,B.E., DAYAN,F.E., ALLELOCHEMICALS AS HERBICIDES, EUROPEAN ALLELOPATHY SYMPOSIUM, 2002.  Book Chapter: "Allelopathy from molecules to ecosystems".  PP. 183-195.   
- STRATEGIES FOR RESEARCH IN APPLIED ASPECTS OF ALLELOPATHY -(Proceedings)   DUKE,S.O., RIMANDO,A.M., SCHEFFLER,B.E., DAYAN,F.E. STRATEGIES FOR RESEARCH IN APPLIED ASPECTS OF ALLELOPATHY.  EUROPEAN ALLELOPATHY SYMPOSIUM.  2002.  Book Chapter: "Allelopathy from molecules to ecosystems".  PP. 139-151.   
- GENETIC FINGERPRINTING OF HYPERICUM SPECIES: TOWARDS CERTIFICATION OF ST.  JOHN'S WORT AT THE SEED LEVEL -(Peer Reviewed Journal)     
- ISOLATION OF TWO NEW CACTA TRANSPOSABLE ELEMENTS FROM ANTHOCYANIN GENES IN MAIZE -(Research Notes)     
- MOLECULAR ANALYSIS OF IN-D; A SEMI-DOMINANT ALLELE OF THE ANTHOCYANIN      REGULATORY GENE INTENSIFIER -(Research Notes)     

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