Publications

Journal Articles

Da Fonseca Santos M., Möller M., Clough S.J., Pinheiro J.B. (2018) Heritability of agronomic traits correlated with reduced stink bug damage in an F_2:3 soybean population derived from IAC-100. Journal of Crop Improvement 32(1):1-18.

Ghandchi F.P., Caetano-Anolles G., Clough S.J., Ort D.R. (2016) Investigating the Control of Chlorophyll Degradation by Genomic Correlation Mining. PLoS One 11(9):e0162327.

Castro L.H.S., Figueiro A.A., Nogueira A.P.O., Clough S.J., Fernando C. J. (2016) Resistance of soybean genotypes to Sclerotinia sclerotiorum isolates in different incubation environments. Genetics and Molecular Research 15(4):gmr15049061.

Siddappaji M.H., Scholes D.R., Krishnankutty S.M., Calla B., Clough S.J., Zielinski R.E., Paige K.N. (2015) The role of invertases in plant compensatory responses to simulated herbivory. BMC Plant Biol 15:278.

Zhu J., Li M., Clough S.J. (2015) Similarities and Differences in Global Gene Expression Profiles between Herbicide and Pathogen-Induced PSII Inhibition. J Plant Biochem Physiol 3: 157.

Zhu J., Neece D.J., Calla B., Clough S.J. (2015) If Photoinhibition of Soybean Photosystem II Enhances the Hypersensitive Response, It is Not Solely Due to Blockage of Electron Transfer Flow at D1. J Plant Biochem Physiol 3: 156.

Calla B., Blahut-Beatty L., Koziol L., Zhang Y., Neece D.J., Carbajulca D., Garcia A., Simmonds D.H., and Clough S.J. (2014). Genomic evaluation of oxalate-degrading transgenic soybean in response to Sclerotinia sclerotiorum infection. Mol. Plant Pathol. 15:563-575.

Calla B., Blahut-Beatty L., Koziol L., Simmonds D., Clough S.J. (2014) Transcriptome analyses suggest a disturbance of iron homeostasis in soybean leaves during white mold disease establishment. Mol. Plant Pathol. 15:576-588.

Radwan O., Wu X., Govindarajulu M., Libault M., Neece D.J., Oh M-H., Berg R.H., Stacey G., Taylor C.G., Huber S.C., and Clough S.J. (2012). 14-3-3 proteins SGF14c and SGF14l play critical roles during soybean nodulation. Plant Physiol. 160:2125-2136.

Radwan O., Li M., Calla B., Li S., Hartman G.L., Clough, S.J. (2012). Effect of Fusarium virguliforme phytotoxin on soybean gene expression suggests a multi-dimensional defense approach. Mol. Plant Pathol. 14:293-307.

Zabala G., Campos E.,Varala K.K., Bloomfield S., Jones S.I., Win H., Tuteja J.H., Calla B., Clough S.J., Hudson M. Vodkin L.O. (2012). Divergent Patterns of Endogenous Small RNA Populations from Seed and Vegetative Tissues of Glycine max. BMC Plant Biol. 12:177.

Wang D., Qi M., Calla B., Korban S.S., Clough S.J., Sundin G.W., Toth I., Cock P.J.A., Zhao Y. (2011). Genome-wide identification of genes regulated by the Rcs phosphorelay system in Erwinia amylovora. Mol. Plant-Microbe Interact. 25:6-17. 2012.

Wang, D., B. Calla, S. Vimolmangkang, X. Wu, S.S. Korban, S.C. Huber, S.J. Clough, and Y. Zhao (2011). The orphan gene ybjN conveys pleiotropic effects on multicellular behavior and survival of Escherichia coli. PLoS ONE 6(9): e25293. doi:10.1371/journal.pone.0025293.

Radwan, O., Y. Liu, and S.J. Clough (2011).Transcriptional analysis of soybean roots response to Fusarium virguliforme, the causal agent of sudden death syndrome. Mol. Plant-Microbe Interact. 24:958-972.

Bilgin, D.D., J.A. Zavala, J. Zhu, S.J. Clough, D.R. Ort, and E.H. DeLucia (2010). Biotic stress globally down-regulates photosynthesis genes. Plant Cell Environ. 33:1597-1613.a

Libault, M., A. Farmer, L. Brechenmacher, J. Drnevich, R.J. Langley, D.D. Bilgin, O. Radwan, D. Neece, S.J. Clough, G.D. May, and G. Stacey (2010). Complete transcriptome of the soybean root hair cell, a single cell model, and its alteration in response to Bradyrhizobium japonicum infection. Plant Physiol. 152:541-552.a

Zhu, J., W.L. Patzoldt, O. Radwan, P.J. Tranel, and S.J. Clough (2009). Effects of photosystem II interfering herbicides atrazone and bentazon on the soybean transcriptome. The Plant Genome 2:191-205.

Calla, B., T. Vuong, O. Radwan, G.L. Hartman, and S.J. Clough (2009). Gene expression profiling soybean stem tissue early response to Sclerotinia sclerotiorum and in silico mapping in relation to resistance markers. The Plant Genome 2:149-166.

Bilgin, D.D., E.H. DeLucia, and S.J. Clough (2009). A robust plant RNA isolation method suitable for Affymetrix GeneChip analysis and quantitative real-time RT-PCR. Nature Protocols. 4:333-340.a

Bilgin, D.D., M. Aldea, B.F. O'Neill, M. Benitez, M. Li, S.J. Clough, and E.H. DeLucia (2008). Elevated ozone alters soybean-virus interaction. Mol. Plant-Microbe Interact 21:1297-1308.

Zhu, J., W.L. Patzoldt, R.T. Shealy, L.O. Vodkin, S.J. Clough, and P.J. Tranel (2008). Transcriptional profiling in response to glyphosate in sensitive and resistant soybean. J. Agricul. Food Chem. 56:6355-6363.

Libault, M., S. Thibivilliers, O. Radwan, S.J. Clough, and G. Stacey (2008). Identification of four soybean reference genes for gene expression normalization. The Plant Genome 1:44-54.

Li, Y., J. Zou, M. Li, D.D. Bilgin, L.O. Vodkin, G.L. Hartman, and S.J. Clough (2008). Soybean defense responses to the soybean aphid. New Phytologist 179:185-195.

Wan, J., X. Zhang, D. Neece, K.M. Ramonell, S.J. Clough, S-Y. Kim, M.G. Stacey, and G. Stacey (2008). A LysM receptor-like kinase mediates chitin perception and fungal resistance in Arabidopsis. The Plant Cell 20:471-481.

Brechenmacher, L., M.-Y. Kim, M. Benitez, M. Li, T. Joshi, B. Calla, M.P. Lee, M. Libault, L.O. Vodkin, D. Xu, S.-H. Lee, S.J. Clough, and G. Stacey (2008). Transcription profiling of soybean nodulation by Bradyrhizobium japonicum. Mol. Plant-Microbe Interact 21:631-645.

Vodkin, L.O.. F. Thibaud-Nissen, D.O. Gonzalez, G. Zabala, S.J. Clough, and R. Shealy (2007). An update on soybean functional genomics and microarray resources for gene discovery and crop improvement. Petria 17:43-53.

Zabala, G. J. Zou, J. Tuteja, D.O. Gonzalez, S.J. Clough, and L.O. Vodkin (2006). Transcription changes in the phenylpropanoid pathway of Glycine max in response to Pseudomonas syringae infection. BMC Genomics 6:26.

Zou, J., S. Rodriguez-Zas, M. Aldea, M. Li, J. Zhu, D. O. Gonzales, L. O. Vodkin, E. DeLucia, and S. J. Clough (2005). Expression profiling soybean response to Pseudomonas syringae reveals new defense-related genes and rapid HR-specific down regulation of photosynthesis. Mol. Plant-Microbe Interact 18:1161-1174.

Vodkin, L. O., A. Khanna, R. T. Shealy, S. J. Clough, D. O. Gonzales, R. Philip, G. C. Zabala, F. Thibaud-Nissen, M. Sidarous, M. V. Stromvik, E. G. Shoop, C. Schmidt, E. Retzel, J. Erpelding, R. C. Shoemaker, A. M. Rodrizues-Huete, J. C. Polacco, V. Coryell, P. Keim, G. Gong, L. Lui, J. L. Pardinas, and P. Schweitzer (2004). Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant. BMC Genomics. 5:73.

Clough, S. J., J. Tuteja, M. Li, L. F. Marek, R. C. Shoemaker, and L. O. Vodkin (2004). Features of a 103-kb, gene-rich region in soybean include an inverted perfect repeat cluster of CHS genes comprising the I locus. Genome 47:819-831.

Tuteja, J. H., S. J. Clough, W.-C. Chan, and L. O. Vodkin (2004). Tissue specific gene silencing mediated by a naturally occurring chalcone synthase gene cluster in Glycine max. Plant Cell 16: 819-835.

Clough, S. J., K. A. Fengler, B. Lippok, R. K. Smith, I-c. Yu, and A. F. Bent (2000). The Arabidopsis dnd1 "defense, no death" gene encodes a mutated cyclic nucleotide-gated ion channel. Proc. Nat. Acad. Sci. 97:9323-9328.

Desfeux, C., S. J. Clough, and A. F. Bent (2000). Female reproductive tissues are the primary target of Agrobacterium-mediated transformation in the Arabidopsis floral-dip method. Plant Physiol. 123:895-904.

Palanichelvam, K., P. Oger, S. J. Clough, C. E. Cha, A. F. Bent, and S. K. Farrand (2000). A second T-region of the soybean-supervirulent chrysopine-type Ti plasmid pTIChry5, and construction of a fully disarmed vir helper plasmid. Mol. Plant Microbe Interact. 13:1081-1091.

Yu, I-c., K. A. Fengler, S. J. Clough, and A. F. Bent (2000). Identification of Arabidopsis mutants exhibiting an altered hypersensitive response in gene-for-gene disease resistance. Mol. Plant Microbe Interact. 13:277-286.

Clough, S. J. and A. F. Bent (1998). Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. The Plant J. 16:735-743.

Flavier, A. B., S. J. Clough, M. A. Schell, and T. P. Denny (1997). Identification of 3-hydroxypalmitic acid methyl ester as a novel autoregulator controlling virulence in Ralstonia solanacearum. Mol. Microbiol. 26:251-259.

Clough, S. J. , K.-E. Lee, M. A. Schell, and T. P. Denny (1997). A two-component system in Ralstonia (Pseudomonas) solanacearum modulates production of PhcA-regulated virulence factors in response to 3-hydroxypalmitic acid methyl ester. J. Bacteriol. 179:3639-3648.

Clough, S. J. , A.B. Flavier, M. A. Schell, and T. P. Denny (1996). Differential expression of virulence genes and motility in Ralstonia (Pseudomonas) solanacearum during exponential growth. Appl. Environ. Microbiol. 63:844-850.

Clough, S. J., M. A. Schell, and T. P. Denny (1994). Evidence for the involvement of a volatile extracellular factor in Pseudomonas solanacearum virulence gene expression. Mol. Plant Microbe Interact. 7:621-630.

Book Chapters

Wei Wei and Steven J. Clough. (2016) Sclerotinia sclerotiorum: Molecular Aspects in Plant-Pathogenic Interactions. Revisão Anual de Patologia de Plantas 24:174-189.

Wan, J., K. Ramonell, X. Zhang, S. Clough, R. Zhang, M. Libault, G.H. Son, M.G. Stacey, J.C. Hong and G. Stacey. 2008. Chitin signaling in Arabidopsis . pp 1-4 In: Biology of Plant Microbe Interactions, Vol. 6. M. Lorito, S.L. Woo, and F. Scala, eds. The American Phytopathological Society, St. Paul, MN.

Clough, S. J., and L. O. Vodkin. 2004. Soybean microarrays: a genomic tool for crop improvement. pp. 267-282. In: Legume Crop Genomics. R. F. Wilson, H. T. Stalker, and E. C. Brummer, eds. American Oil Chemists Society Press, Urbana, IL.

Clough, S. J. 2004. Floral dip: Agrobacterium-mediated germ-line transformation. pp. 91-101. In: Transgenic plants: methods and protocols. Methods in Molecular Biology. L. Pena, ed. The Humana Press, Inc., Totowa, NJ.

Bent, A. F. and S. J. Clough. 1998. Agrobacterium germ-line transformation: Transformation of Arabidopsis without tissue culture. pp. 1-14. In: Plant Molecular Biology Manual (2nd ed). S. B. Gelvin and R. A. Schilperoort, eds. Kluwer Academic Publishers, Dordrech, The Netherlands.

Denny, T. P., E. Saile, A. B. Flavier, S. J. Clough, L. M. Ganova-Raeva and M. A. Schell. 1998. The role of extracellular polysaccharide and regulated gene expression in invasion and colonization of tomato by Ralstonia solanacearum. pp. 263-270. In: Molecular approaches in biological control. B. K. Duffy, U. Rosenberger, and G. Défago, eds. IOBC Bulletin Vol. 21(9).

Denny, T. P., A. B. Flavier, S. J. Clough, E. Saile, L. M. Ganova-Raeva and M. A. Schell. 1998. Regulation of virulence by endogenous signal molecules and the importance of extracellular polysaccharide during infection and colonization. pp. 164-170. In: Bacterial wilt disease: molecular and ecological aspects. P. Prior, C. Allen, and J. Elphinstone, eds. Springer-Verlag, Berlin, Germany.

Denny, T. P., S. M. Brumbley, B. F. Carney, S. J. Clough, and M. A. Schell. 1994. Phenotype conversion of Pseudomonas solanacearum: its molecular basis and potential function. pp. 137-143. In: Bacterial Wilt: the disease and its causative agent, Pseudomonas solanacearum. A. C. Hayward and G. L. Hartman, eds. CAB International, Wallingford, UK.

Schell, M. A., T. P. Denny, S. J. Clough, and J. Huang. 1993. Further characterization of genes encoding extracellular polysaccharide of Pseudomonas solanacearum and their regulation. pp. 231-239. In: Advances in molecular genetics of plant-microbe interactions. E. W. Nester and D. P. S. Verma, eds. Kluwer Academic Publishers, Dordrecht, The Netherlands.

Denny, T. P., S. M. Brumbley, B. F. Carney, S. J. Clough, and M. A. Schell. 1993. Regulation of virulence in Pseudomonas solanacearum. Pages 252-256 in: Bacterial Wilt: proceedings of an international conference held at Kaohsiung, Taiwan, 28-31 October 1992, G.L. Hartman and A.C. Hayward, eds., ACIAR Proceedings No. 45. Watson Ferguson and Co., Australia.

Denny, T. P., S. M. Brumbley, B. F. Carney, and S. J. Clough. 1991. Regulation of virulence in Pseudomonas solanacearum. In: Proceedings UM-USDA-Monsanto 4th International Symposium Biotechnology and Plant Protection, 21-23 October, 1991.