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Irigoyen, S., Ramasamy, M., Misra, A., McKnight, T.D. and Mandadi, K., (2022). A BTB-TAZ protein is required for gene activation by Cauliflower mosaic virus 35S multimerized enhancers. Plant Physiol.188(1), 397-410.

Bedre, R., Avila, C., Mandadi, K.  (2021). HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis. Sci. Rep., 11(1), 1-7.

Farber, C., Sanchez, L., Pant, S., Scheuring, D., Vales, I., Mandadi, K., & Kurouski, D. (2021). Potential of spatially offset raman spectroscopy for detection of zebra chip and potato virus Y diseases of potatoes (Solanum tuberosum). ACS J. Agric. Sci.

Pant, S.R., Irigoyen, S., Liu, J., Bedre, R., Christensen, S.A., Schmelz, E.A., Sedbrook, J.C., Scholthof, K.B.G. and Mandadi, K.K. (2021) Brachypodium Phenylalanine Ammonia Lyase (PAL) promotes antiviral defenses against Panicum mosaic virus and its Satellites. Mbio, 12(1).

Gautam, S., Solis-Gracia, N., Teale, M. K., Mandadi, K., Silva, J. A. D., & Vales, M. I. (2021). Development of an in vitro microtuberization and temporary immersion bioreactor system to evaluate heat stress tolerance in potatoes (Solanum tuberosum L.). Front. Plant Sci., 1659.

Mora, V., Ramasamy, M., Damaj, M. B., Irigoyen, S., Ancona, V., Ibanez, F., Avila, C., & Mandadi, K. K. (2021). Potato zebra chip: an overview of the disease, control strategies, and prospects. Front. microbiol, 2064.

Kurouski, D., Dou, T., Niraula, P. and Mandadi, K.K. (2021). Biochemical Origin of Raman-Based Diagnostics of Huanglongbing in Grapefruit Trees. Front. Plant Sci.,  12, p.1246.

Bedre, R. H., Avila, C. A., & Mandadi, K. (2021). HTSeqQC: A Flexible and One-Step Quality Control Software for High-throughput Sequence Data Analysis. bioRxiv, 2020-07.

Irigoyen, S., Ramasamy, M., Pant, S., Niraula, P., Bedre, R., Gurung, M., Rossi, D., Laughlin, C., Gorman, Z., Achor, D., Levy, A., Kolomiets, M.V., Setamou, M., Badillo-Vargas, I.E,, Avila, C.A., Irey, M., Mandadi, K.K. (2020). Plant hairy roots enable high throughput identification of new antimicrobials against Candidatus Liberibacter spp. Nature Commun. 11, 5802

Padilla, C.S., Damaj, M.B., Yang, Z-N., Molina, J., Berquist, B.R., White, E.L., Solís-Gracia, N., Da Silva, J., Mandadi, K.K. (2020). High-level production of recombinant snowdrop lectin in sugarcane and energy cane. Front. Bioeng. Biotechnol.8, 977.

Damaj, M.B., Jifon, J.L, Woodard, S.L., Vargas-Bautista, C., Barros, G.O., Molina, J., White, S.G., Damaj, B.B., Nikolov, Z.L., Mandadi, K.K. (2020). Unprecedented enhancement of recombinant protein production in sugarcane culms using a combinatorial promoter stacking system. Sci. Rep. 10, 1-16.

Zuniga C., Peacock B, Liang, B., McCollum, G., Irigoyen, S., Tec-Campos, D., Marotz, C., Weng, N-C., Zepeda, A., Vidalakis, G., Mandadi, K., Borneman, J., Zengler, K. (2020). Linking metabolic phenotypes to pathogenic traits among ‘Candidatus Liberibacter asiaticus’ and its hosts. npj Systems Biology and Applications 6, 1-12.

Petrillo, E., Kalyna, M., Mandadi, K.K., Tu, S-L., and Simpson, C.G. (2020). Alternative splicing regulation in plants. Front. Plant Sci. 11, 913.

Sanchez, L., Pant, S., Mandadi, K., and Kurouski, D. (2020). Raman spectroscopy vs quantitative polymerase chain reaction in early stage Huanglongbing diagnostics. Sci. Rep. 10, 1-10.

Da Silva, J. A.,  Solis-Gracia, N., Jifon, J., Souza, S.C., and  Mandadi, K. (2020). Use of bioreactors for large-scale multiplication of sugarcane (Saccharum spp.), energy cane (Saccharum spp.), and related species. In Vitro Cell. Dev. Biol.-Plant, 1-11.

Awika, H. O., Cochran, K., Joshi, V., Bedre, R., Mandadi, K. K., and Avila, C. A. (2020). Single‐marker and haplotype‐based association analysis of anthracnose (Colletotrichum dematium) resistance in spinach (Spinacia oleracea). Plant Breeding, 139(2), 402-418.

Bedre, R.,  and Mandadi, K. (2019). GenFam: A web application and database for gene family‐based classification and functional enrichment analysis. Plant Direct, 3, e00191.

Sanchez, L., Pant, S., Irey, M., Mandadi, K., and Kurouski, D. (2019) Detection and identification of canker and blight on orange trees using a hand‐held Raman spectrometer. J Raman Spectrosc. 50: 1875–1880.

Awika, H.O., Marconi, T.G., Bedre, R., Mandadi, K.K., and Avila, C.A. (2019). Minor alleles are associated with white rust (Albugo occidentalis) susceptibility in spinach (Spinacia oleracea). Hort. Research. 6, 1-5.

Pyle, J. D., Mandadi, K. K., and Scholthof, K. B. G. (2019). Panicum mosaic virus and its satellites acquire RNA modifications associated with host-mediated antiviral degradation. mBio, 10, e01900-19

Bedre, R., Irigoyen, S., Schaker, P. D., Monteiro-Vitorello, C. B., Da Silva, J. A., and Mandadi, K. K. (2019). Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen. Sci. Rep., 9, 8876.

Bedre, R., Irigoyen, S., Petrillo, E., and Mandadi, K. (2019). New era in plant alternative splicing analysis enabled by advances in high-throughput sequencing (HTS) technologies. Front. Plant Sci., 10, 740.

Sanchez, L., Pant, S., Xing, Z., Mandadi, K., and Kurouski, D. (2019) Rapid and non-invasive diagnostics of Huanglongbing and nutrient deficits on citrus trees with a hand-held Raman spectrometer. Anal. Bioanal. Chem. 411,3125-3133

Awika, H., Bedre, R., Yeom, J., Marconi, T., Enciso, J., Mandadi K.K., Jung, J., and Avila, C. (2019). Developing growth-associated molecular markers via high-throughput phenotyping in spinach. Plant Genome, 12, 1-19.

Kandel, D. R., Bedre, R. H., Mandadi, K. K., Crosby, K., and Avila, C. A. (2019). Genetic diversity and population structure of tomato (Solanum lycopersicum) germplasm developed by Texas A&M breeding programs. American Journal of Plant Sciences, 10(7), 1154-1180.

Ramasamy, M., Damaj, M.B., Mora, V., Padilla, C., Ramos, N., Gracia, N., Vargas-Bautista, C., Irigoyen, S., daSilva, J., Mirkov, T.E, and Mandadi, K.K. (2018). A high-efficiency biolistic-based genetic transformation system for sugarcane and energycane. GM Crops & Food. 9, 211-227

Scholthof, K.-B.G., Irigoyen, S., Catalan, P., and Mandadi, K.K. (2018). Brachypodium: A monocot grass model system for plant biology. Plant Cell. 30, 1673-1694

Misra, A., McKnight, T.D., and Mandadi, K.K. (2018). Bromodomain proteins GTE9 and GTE11 are essential for specific BT2-mediated sugar and ABA responses in Arabidopsis thaliana. Plant Mol. Biol. 96, 393-402

Chiong, K.T., Damaj, M.B., Padilla, C.S., Avila, C.A., Pant, S.R., Mandadi, K.K., Ramos, N.R., Carvalho, D.V., and Mirkov, T.E. (2017). Reproducible genomic DNA preparation from diverse crop species for molecular genetic applications. Plant Methods 13, 106.

Pant, S.R., Irigoyen, S, Doust, A.N., Scholthof, K-B.G. and Mandadi, K.K. (2016). Setaria: A food crop and translational research model for C4 grasses. Front. Plant Sci. 7, 1885

Mandadi, K.K., Pyle, J.D., and Scholthof, K-B.G. (2015) Characterization of SCL33 splicing patterns during diverse virus infections in Brachypodium distachyon. Plant Sig. Behav. 10:8, e1042641

Mandadi, K.K. and Scholthof, K-B.G. (2015) Genomic architecture and functional relationships of intronless, constitutively- and alternatively-spliced genes in Brachypodium distachyon. Plant Sig. Behav. 10:8, e1042640

Mandadi, K.K. and Scholthof, K-B.G. (2015) Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon. Plant Cell 27, 71-85. COVER FEATURE/LARGE SCALE BIOLOGY

Mandadi, K.K., Pyle, J.D., and Scholthof, K-B.G. (2014) Comparative analysis of antiviral responses in Brachypodium distachyon and Setaria viridis reveal conserved and unique outcomes among C3 and C4 plant defenses. Mol. Plant Microbe Interact. 27, 1277-1290.

Mandadi, K.K., and Scholthof, K-B.G. (2013) Plant immune responses against viruses: How does a virus cause disease? Plant Cell 25, 1489–1505

Góngora-Castillo, E., Childs, K.L., Fedewa, G., Hamilton, J.P., Liscombe, D.K., Magallanes, M., Mandadi, K., Nims, N.E., Runguphan, W., Vaillancourt, B., Varbanova, M., DellaPenna, D., McKnight, T., O’Connor, S., and Buell, C.R. (2012). Development of transcriptomic resources for interrogating the biosynthesis of monoterpene indole alkaloids in medicinal plant species. PLoS ONE 7(12): e52506

Mandadi, K.K., and Scholthof, K.-B.G. (2012). Characterization of a viral synergism in the monocot Brachypodium reveals distinctly altered host molecular processes associated with disease. Plant Physiol. 160, 1432-1452.

Mandadi, K.K., Misra, A., Ren, S., and McKnight, T.D. (2009) BT2 mediates multiple responses to nutrients, stresses and hormones in Arabidopsis thaliana. Plant Physiol. 150, 1930-1939.

Ren, S., Mandadi, K.K., Boedeker, A.L., Rathore, K.S., and McKnight, T.D. (2007) Regulation of telomerase in Arabidopsis by BT2, an apparent target of the TELOMERASE ACTIVATOR1. Plant Cell 19, 23-31.

Mandadi, K., Ramirez, M., Jayaprakasha, G.K., Faraji, B., Lihono, M., Deyhim, F., and Patil B.S. (2009) Citrus bioactive compounds improve bone quality and plasma antioxidant activity in orchidectomized rats. Phytomedicine 16(6-7), 513-520.

Deyhim, F., Mandadi, K., Faraji, B and Patil B.S. (2008) Grapefruit juice modulates bone quality in rats. J. Med. Food 11, 99-104.

Deyhim, F., Mandadi, K., Faraji, B and Patil B.S. (2008) Grapefruit pulp increases antioxidant status and improves bone quality in orchidectomized rats. Nutrition 24, 1039-1044.

Jayaprakasha, G.K., Mandadi, K.K., Poulose, S.M., Jadegoud, Y., Nagana Gowda, G.A., and Patil, B.S. (2008) Novel triterpinoid from Citrus aurantium L. possess chemopreventive properties against human colon cancer cells. Bioorg. Med. Chem. 16, 5939-5951.

Deyhim, F., Villarreal, A., Garcia, K., Rios, R., Garcia, C., Gonzales, C., Mandadi, K., and Patil, B.S. (2007) Orange pulp improves antioxidant status and suppresses lipid peroxidation in orchidectomized male rats. Nutrition 23, 617-621.

Mandadi, K.K., Jayaprakasha, G.K., Bhat, N., and Patil, B.S. (2007) Red Mexican Grapefruit: A novel source for bioactive limonoids and their antioxidant activity. Z. Naturforschung 62C, 179.

Jayaprakasha, G.K., Mandadi, K.K., Poulose, S.M., Jadegoud, Y., Nagana Gowda, G.A., and Patil, B.S. (2007) Inhibition of colon cancer cell growth and antioxidant activity of bioactive compounds from Poncirus trifoliata (L.) Raf. Bioorg. Med. Chem. 15, 4923-4932.

Villarreal, A., Stoecker, B.J., Garcia, C., Garcia, K., Rios, R., Gonzales, C., Mandadi, K., Faraji, B., Patil, B.S., and Deyhim, F. (2007) Cranberry juice improved antioxidant status without affecting bone quality in orchidectomized male rats. Phytomedicine 10, 49-53.

Deyhim, F., Rios, R., Garcia, C., Villarreal, A., Garcia, K., Gonzales, C., Mandadi, K., Faraji, B., and Patil, B.S. (2007) Orange pulp increases antioxidant status and improves bone quality in orchidectomized rats. Curr. Nutr. Food Sci. 3, 319-323.

Deyhim, F., Garcia, C., Villarreal, A., Garcia, K., Rios, R., Gonzales, C., Mandadi, K., Faraji, B., and Patil, B.S. (2007) Vitamin E does not support bone quality in orchidectomized rats. Curr. Nutr. Food Sci. 3, 300-303.

Deyhim, F., Gonzales, C., Villarreal, A., Garcia, K., Rios, R., Garcia, C., Mandadi, K., and Patil, B.S. (2007) Vitamin E does not modulate plasma cholesterol, triglyceride, or C-reactive protein despite suppressing oxidative stress in orchidectomized rats. J. Med. Food 10, 559-562.

Deyhim, F., Patil, B.S., Villarreal, A., Lopez, E., Garcia, K., Rios, R., Garcia, C., Gonzales, C., and Mandadi, K. (2007) Cranberry juice increases antioxidant status without affecting cholesterol homeostasis in orchidectomized rats. J. Med. Food 10, 49-53.

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