L. J. Grenville-Briggs and P. Van West, “The Biotrophic Stages of Oomycete-Plant Interactions,” Advances in Applied Microbiology, Vol. 57, 2005, pp. 217-243.
 R. J. O'Connell and R. Panstruga, “Tête à Tête inside a Plant Cell: Establishing Compatibility between Plants and Biotrophic Fungi and Oomycetes,” New Phytologist, Vol. 171, No. 4, 2006, pp. 699-718.
 J. T. Greenberg and N. Yao, “The Role and Regulation of Programmed Cell Death in Plant-Pathogen Interactions,” Cellular Microbiology, Vol. 6, No. 3, 2004, pp. 201-211.
 R. A. Dixon, M. J. Harrison and C. J. Lamb, “Early Events in the Activation of Plant Defense Responses,” Annual Review of Phytopathology, Vol. 32, 1994, pp. 479-501.
 J. F. Miller, J. J. Mekalanos and S. Falkow, “Coordinate Regulation and Sensory Transduction in the Control of Bacterial Virulence,” Science, Vol. 243, No. 4893, 1989, pp. 916-922. http://dx.doi.org/10.1126/science.2537530
 J. Ma, X. Huang, X. Wang, X. Chen, Z. Qu, L. Huang and Z. Kang, “Identification of Expressed Genes during Compatible Interaction between Stripe Rust (Puccinia striiformis) and Wheat Using a cDNA Library,” BMC Genomics, Vol. 10, 2009, pp. 586-597.
 M. Polesani, F. Desario, A. Ferrarini, A. Zamboni, M. Pezzoti, A. Kortekamp and A. Polverari, “cDNA-AFLP Analysis of Plant and Pathogen Genes Expressed in Grapevine Infected with Plasmopara viticola,” BMC Genomics, Vol. 9, 2008, pp. 142-155.
 E. J. Nestler and S. E., “Hyman Regulation of Gene Expression,” In: K. L. Davis, D. Charney, J. T. Coyle and C. B. N., Eds., Neuropsychopharmacology: The Fifth Generation of Progress, Philadelphia, 2002, Chapter 17.
 K. Al-Taweel and W. G. D. Fernando, “Differential Gene Expression Is a Promising Tool for Understanding of Host-Pathogen Interactions,” The Americas Journal of Plant Science and Biotechnology, Vol. 5, Special Issue, No. 1, 2011, pp. 1-10.
 P. Moy, D. Qutob, B. P. Chapman, I. Atkinson and M. Gijzen, “Patterns of Gene Expression upon Infection of Soybean Plants by Phytophthora sojae,” Molecular Plant-Microbe Interactions, Vol. 17, No. 10, 2004, pp. 1051-1062. http://dx.doi.org/10.1094/MPMI.2004.17.10.1051
 H. Yamane, Y. Kashima, T. Ooka, R. Tao and K. Yonemori, “Suppression Subtractive Hybridization and Differential Screening Reveals Endodormancy-Associated Expression of an SVP/AGL24-Type MADS-Box Gene in Lateral Vegetative Buds of Japanese Apricot,” Journal of the American Society for Horticultural Science, Vol. 133, No. 5, 2008, pp. 708-716.
 S. Nascimento, E. R. Suarez and M. A. S. Pinhal, “Real Time PCR and RT-PCR Technology and Its Applications in the Medicine Field,” Revista Brasileira de Medicina, Vol. 67, 2010, pp. 7-19.
 J. DeRisi, L. Penland, P. O. Brown, M. L. Bittner, P. S. Meltzer, M. Ray, Y. Chen, Y. A. Su and J. M. Trent, “Use of cDNA Microarray to Analyse Gene Expression Patterns in Human Cancer,” Nature Genetics, Vol. 14, No. 4, 1996, pp. 457-460.
 R. P. Wise, M. J. Moscou, A. J. Bogdanove and S. A. Whitham, “Transcript Profiling in Host-Pathogen Interactions,” Annual Review of Phytopathology, Vol. 45, 2007, pp. 329-369.
 R. Guigo, P. Agarwal, J. F. Abril, M. Burset and J. W. Fickett, “An Assessment of Gene Prediction Accuracy in Large DNA Sequences,” Genome Research, Vol. 10, No. 10, 2000, pp. 1631-1642.
 A. Tremblay, P. Hosseini, N. W. Alkharouf, S. Li and B. F. Matthews, “Gene Expression in Leaves of Susceptible Glycine max during Infection with Phakopsora pachyrhizi Using Next Generation Sequencing,” Sequencing, Vol. 2011, 2011.
 P. Company and C. González-Bosch, “Identification of a Copper Chaperone from Tomato Fruits Infected with Botrytis cinerea by Differential Display,” Biochemical and Biophysical Research Communications, Vol. 304, No. 4, 2003, pp. 825-830.
 A. Morant, S. Bak, B. L. Moller and D. Werck-Reichhart, “Plant Cytochromes P450: Tools for Pharmacology, Plant Protection and Phytoremediation,” Current Opinion in Biotechnology, Vol. 14, No. 2, 2003, pp. 151-162.
 N. R. Tharanathan and F. S. Kitter, “Chitin-the Undisputed Biomolecule of Great Potential,” Critical Reviews in Food Science and Nutrition, Vol. 43, No. 1, 2003, pp. 61-87. http://dx.doi.org/10.1080/10408690390826455
 C. W. Bachem, R. S. Hoeven Van Der, S. M. de Bruijn, D. Vreugdenhil, M. Zabeau and R. G. Visser, “Visualization of Differential Gene Expression Using a Novel Method of RNA Fingerprinting Based on AFLP: Analysis of Gene Expression during Potato Tuber Development,” The Plant Journal, Vol. 9, No. 5, 1996, pp. 745-753.
 X. Wang, W. Liu, X. Chen, C. Tang, Y. Dong, J. Ma, X. Huang, G. Wei, Q. Han, L. Huang and Z. Kang, “Differential Gene Expression in Incompatible Interaction between Wheat and Stripe Rust Fungus Revealed by cDNA-AFLP and Comparison to Compatible Interaction,” BMC Plant Biology, Vol. 10, 2010, pp. 9-23.
 C. Guindalini and S. Tufik, “Use of Microarrays in the Search of Gene Expression Patterns—Application to the Study of Complex Phenotypes,” Revista Brasileira de Psiquiatria, Vol. 29, No. 4, 2007, pp. 370-374.
 W. P. Kuo, T. K. Jenssen, A. J. Butte, L. Ohno-Machado and I. S. Kohane, “Analisys of Matched mRNA Measurements from Two Different Microarray Technologies,” Bioinformatics, Vol. 18, No. 3, pp. 405-412.
 W. P. Kuo, E. Y. Kim, J. Trimarchi, T. K. Jenssen, S. A. Vinterbo and L. Ohno-Machado, “A Primer on Gene Expression and Microarrays for Machine Learning Researchers,” Journal of Biomedical Informatics, Vol. 37, No. 4, 2004, pp. 293-303.
 S. Golkari, J. Gilbert, S. Prashar and D. Procunier, “Microarray Analysis of Fusarium graminearum-Induced Wheat Genes: Identification of Organ-Specific and Differentially Expressed Genes,” Plant Biotechnology Journal, Vol. 5, 2007, pp. 38-49.
 S. Golkari, J. Gilbert, T. Ban and J. D. Procunier, “QTLSpecific Microarray Gene Expression Analysis of Wheat Resistance to Fusarium Head Blight in Sumai-3 and Two Susceptible NILs,” Genome, Vol. 52, No. 5, 2009, pp. 409-418. http://dx.doi.org/10.1139/G09-018
 B. Fofana, T. W. Banks, B. McCallum, S. E. Strelkov and S. Cloutier, “Temporal Gene Expression Profiling of the Wheat Leaf Rust Pathosystem Using cDNA Microarray Reveals Differences in Compatible and Incompatible Defence Pathways,” International Journal of Plant Genomics, Vol. 2007, 2007, p. 17542.
 G. Hu and F. H. J. Rijkenberg, “Scanning electron Microscopy of Early Infection Structure Formation by Puccinia recondita f. sp. tritici on and in Susceptible and Resistant Wheat Lines,” Mycological Research, Vol. 102, No. 4, 1998, pp. 391-399.
 X. Chen, R. E. Niks, P. E. Hedley, J. Morris, A. Druka, T. C. Marcel, A. Vels and R. Waugh, “Differential Gene Expression in Nearly Isogenic Lines with QTL for Partial Resistance to Puccinia hordei in Barley,” BMC Genomics, Vol. 11, No. 1, 2010, pp. 629-641.
 L. Diatchenko, S. Lukyanov, Y. F. Lau and P. D. Siebert, “Suppressive Subtraction Hybridization: A Versatile Method for Identifying Differentially Expressed Genes,” Methods in Enzymology, Vol. 303, 1999, pp. 349-380.
 R. S. Goswami, J. R. Xu, F. Trail, K. Hilburn and H. C. Kistler, “Genomic Analysis of Host-Pathogen Interaction between Fusarium graminearum and Wheat during Early Stages of Disease Development,” Microbiology, Vol. 152, No. 6, 2006, pp. 1877-1890.
 L. Kong, J. M. Anderson and H. W. Ohm, “Induction of Wheat Defense and Stress-Related Genes in Response to Fusarium graminearum,” Genome, Vol. 48, No. 1, 2005, pp. 29-40. http://dx.doi.org/10.1139/g04-097
 M. Yang, M. Jiang, Y. Cai, Y. Ye and W. Lihuan, “Construction and Analysis of Suppression Subtractive Hybridization Library for Leymus secalinus Exposed to Drought Stress,” African Journal of Biotechnology, Vol. 11, No. 73, 2012, pp. 13775-13781.
 D. E. Moody, “Genome Techniques: An Overview of Methods for the Study of Gene Expression,” Journal of Animal Science, Vol. 79, 2001, pp. 128-135.
 J. D. Alves, T. T. Vantoai and N. Kaya, “Differential Display: A Novel PCR-Based Method for Gene Isolation and Cloning,” Revista Brasileira de Fisiologia Vegetal, Vol. 10, No. 2, 1998, pp. 161-164.
 P. Liang and A. B. Pardee, “Differential Display of mRNA by PCR,” In: F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith and K. Struhl, Eds., Current Protocols in Molecular Biology, John Wiley and Sons, New York, 1994, pp. 15.8.1-15.8.8.
 O. Bozkurt, T. Unver and M. S. Akkaya, “Genes Associated with Resistance to Wheat Yellow Rust Disease Identified by Differential Display Analysis,” Physiological and Molecular Plant Pathology, Vol. 71, No. 4-6, 2007, pp. 251-259.
 M. Yamamoto, T. Wakatsuki, A. Hada and A. Ryo, “Use of Serial Analysis of Gene Expression (SAGE) Technology,” Journal of Immunological Methods, Vol. 250, No. 1-2, 2001, pp. 45-66.
 N. H. Bhuian, G. Selvaraj, Y. Wei and J. King, “Gene Expression Profiling and Silencing Reveal that Monolignol Biosynthesis Plays a Critical Role in Penetration Defense in Wheat against Powdery Mildew Invasion,” Journal of Experimental Botany, Vol. 60, No. 2, 2009, pp. 509-521. http://dx.doi.org/10.1093/jxb/ern290
 L. D. Bowler, M. Hubank and M. G. Spratt, “Representational Difference Analysis of cDNA for the Detection of Differential Gene Expression in Bacteria; Development Using a Model of Iron-Regulated Gene Expression in Neisseria meningitides,” Microbiology, Vol. 145, No. 12, 1999, pp. 3529-3537.
 M. Hubank and D. G. Schatz, “Identifying Differences in mRNA Expression by Representational Difference Analysis of cDNA,” Nucleic Acids Research, Vol. 22, No. 25, 1994, pp. 5640-5648.
 G. R. D. McGrann, L. D. Martin, C. S. Kingsnorth, M. J. C. Asher, M. J. Adams and E. S. Mutasa-Gö
ttgens, “Screening for Genetic Elements Involved in the Nonhost Response of Sugar Beet to the Plasmodiophorid Cereal Root Parasite Polymyxa graminis by Representational Difference Analysis,” Journal of General Plant Pathology, Vol. 73, No. 4, 2007, pp. 260-265.
 A. Mehta and Y. B. Rosatto, “Identification of Differentially Expressed Genes of Xanthomonas axonopodis pv. citri by Representational Difference Analysis of cDNA,” Genetics and Molecular Biology, Vol. 28, No. 1, 2005, pp. 140-149.
 C. Howlad, A. Tanzer, J. Chrast, F. Kokocinski, T. Derrien, N. Walters, J. M. Gonzales, A. Frankish, B. L. Aken, T. Hourlier, J.-H. Vogel, S. White, S. Searle, J. Harrow, T. J. Hubbard, R. Guigo and A. Reymond, “Combining RT-PCR-seq and RNA-Seq to Catalog All Genic Elements Encoded in the Human Genome,” Genome Research, Vol. 22, 2012, pp. 1698-1710.
 S. Tarazona, F. García-Alcalde, J. Dopazo, A. Ferrer and A. Conesa, “Differential Expression in RNA-seq: A Matter of Depth,” Genome Research, Vol. 21, No. 12, 2011, pp. 2213-2223. http://dx.doi.org/10.1101/gr.124321.111
 M. A. Busby, C. Stewart, C. A. Miller, K. R. Grzeda and G. T. Marth, “Scotty: A Web Tool for Designing RNASeq Experiments to Measure Differential Gene Expression,” Bioinformathics, Vol. 29, No. 5, 2013, pp. 656-657. http://dx.doi.org/10.1093/bioinformatics/btt015
 E. J. Kok, N. L. W. Franssen-Van Hal, L. N. W. Winnubst, E. H. M. Kramer, W. T. P. Dijksma, H. A. Kuiper and J. Keijer, “Assessment of Representational Difference Analysis (RDA) to Construct Informative cDNA Microarrays for Gene Expression Analysis of Species with Limited Transcriptome Information, Using Red and Green Tomatoes as a Model,” Journal of Plant Physiology, Vol. 164, No. 3, 2007, pp. 337-349.
 M. Hubank and D. G. Schatz, “cDNA Representational Difference Analysis: A Sensitive and Flexible Method for Identification of Differentially Expressed Genes,” Methods in Enzymology, Vol. 303, 1999, pp. 325-349.
 A. Bernardo, G. Bai, P. Guo, K. Xiao, A. C. Guenzi and P. Ayoubi, “Fusarium graminearum-Induced Changes in Gene Expression between Fusarium Head Blight-Resistant and Susceptible Wheat Cultivars,” Functional & Integrative Genomics, Vol. 7, No. 1, 2007, pp. 69-77.
 D. Bauer, P. Warthoe, M. Rohde and M. Stauss, “Detection and Differential Display of Expressed Genes by DDRT-PCR,” PCR Methods and Applications, Vol. 4, No. 2, 1994, pp. 97-108. http://dx.doi.org/10.1101/gr.4.2.S97
 L. Sompayrac, S. Jane, T. C. Burn, D. G. Tenen and K. J. Danna, “Overcoming Limitations of the mRNA Differential Display Technique,” Nucleic Acids Research, Vol. 23, No. 22, 1995, pp. 4738-4739.
 D. J. Bertioli, U. H. A. Schlichter, M. J. Adams, P. R. Burrows, H. H. Steinbin and J. F. Antoniw, “An Analysis of Differential Display Shows a Strong Bias Towards High Copy Number mRNAs,” Nucleic Acids Research, Vol. 23, No. 21, 1995, pp. 4520-4523.
 W. E. Durrant, O. Rowland, P. Piedras, K. E. Hammond-Kosack and J. D. Jones, “cDNA-AFLP Reveals a Striking Overlap in Race-Specific Resistance and Wound Response Gene Expression Profiles,” Plant Cell, Vol. 12, No. 6, 2000, pp. 963-977.
 L. Zhang, H. Meakin and M. Dickinson, “Isolation of Genes Expressed during Compatible Interactions between Leaf Rust (Puccinia triticina) and Wheat Using cDNAAFLP,” Molecular Plant Pathology, Vol. 4, No. 6, 2003, pp. 469-477.