Publications

  • Larrainzar E, Hwang HJ, Riely BK, Kim SC, Yu HJ, Oh M, Park SG, Lee KS, Rao A, Datta J, Greenspan A, Mun JH, Cook DR (2015) Deep sequencing of the Medicago truncatula transcriptome reveals a massive early response to Nod factor and ethylene signals. Plant Physiology 169:233-265.
  • R. Varma Penmetsa, Noelia Carrasquilla-Garcia, Emily M Bergmann, Lisa Vance, Brenna Castro, Mulualem T. Kassa, Birinchi K. Sarma, Subhojit Datta, Anuja Dubey, Neha Gujaria, Jong-Min Baek1, Jimmy E Woodward, Andrew D Farmer, Clarice J Coyne, Eric J.B. von Wettberg, Rajeev K Varshney, Douglas R Cook (201x). Multiple post-domestication origins of kabuli chickpea through allelic variation in a diversification-associated transcription factor. In review.
  • Friesen ML, von Wettberg EJB, Badri M, Moriuchi KS, Barhoumi F, Cuellar-Ortiz C, Chang PL, Cordeiro MA, Vu WT, Arraouadi S, Djebali N, Zribi K, Badri Y, Porter SS, Aouani MA, Cook DR, Strauss SY, Nuzhdin SV. (2014). The ecological and genomics basis of salinity adaptation in Tunisian Medicago truncatula. BMC Genomics, 15:1160.
  • Leal-Bertioli, SCM, Santos, SP, Dantas, KM, Inglis, P, Nielen, S, Araújo, ACG, Joseane, JP, Cavalcante, U, Guimarães, PM, Brasileiro, AM, Carrasquilla-Garcia, N, Penmetsa, RV, Cook, D, Morezsohn, MC, Bertioli, DJ (2014) Arachis batizocoi: a study of its relationship to cultivated peanut (A. hypogaea L.) and its potential for introgression of wild genes into the peanut crop using induced allotetraploids. Annals of Botany, in press.
  • Gujaria-Verma, N, Vail, SL, Carrasquilla-Garcia, N, Penmetsa, RV, Cook, DR, Farmer, AD, Vandenberg, A, Bett, KE (2014) Genetic mapping of legume orthologs reveals high conservation of synteny among wild and cultivated lentil species and the sequenced genomes of Medicago and chickpea. Frontiers in Plant Science, in press.
  • Warschefsky E, Penmetsa RV, Cook DR, von Wettberg EJ (2014). Back to the wilds: tapping evolutionary adaptations for resilient crops through systematic hybridization with crop wild relatives. Am J. of Botany (in press).
  • Cordeiro, MA, Moriuchi, KS, Fotinos, T, Miller, KE, Badri, M, Friesen, ML, Nuzhdin, SV, Strauss, SY, von Wettberg, E, Cook, DR (2014) Population differentiation for germination and early seedling root growth traits under saline conditions in the annual legume Medicago truncatula (Fabaceae). American Journal of Botany 101(3):488-498.
  • Laporte, P., Lepage, A., Fournier, J., Catrice, O., Moreau, S., Jardinaud, M-F., Mun, J-H., Larrainzar, E., Cook, D.R., Gamas, P. and Niebel A. (2014) The CCAAT box-binding transcription factor MtNF-YA1 controls rhizobial infection. Journal of Experimental Botany 65:481-94.
  • Choi, HK, Iandolino, A, Goes da Silva, F, Cook, DR (2013) Water deficit modulates the response of Vitis vinifera to the Pierce's disease pathogen Xylella fastidiosa. MPMI 26:643-657.
  • Castro B. M., K. S. Moriuchi, M. L. Friesen, M. Badri, S.V. Nuzhdin, S.Y. Strauss, D. R. Cook and E. von Wettberg. (2013) Effects of history of selection in saline environments, competition, and parental environment on performance of the annual Medicago truncatula. J. Ecology 101: 1281-1287. 
  • Varshney, R.K. et al., & Cook, D.R. (2013) Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology 31:240-246.
  • Garzón, LN, Oliveros, OA, Rosen, B, Ligarreto, GA, Cook, DR, and Blair, MW (2013) Isolation and Characterization of Nucleotide-Binding Site Resistance Gene Homologues in Common Bean (Phaseolus vulgaris). Phytopathology 103:156-168.
  • Riely, BK, Larrainzar, E, Mun, JH, Gil-Quintana, E, González, EM, Tricoli, D, Yu, HJ, Cook, DR (2013) Development of tools for the biochemical characterization of the symbiotic receptor-like kinase DMI2. MPMI 26:216-226.
  • Nagy, ED, Guo, Y, Tang, S, Bowers, JE, Okashah, RA, Taylor, CA, Zhang, D, Khanal, S, Heesaker, AF, Khalilian, N, Farmer, AD, Carrasquilla-Garcia, N, Penmetsa, RV, Cook, D, Stalker, HT, Ozias-Akins, P, and Knapp, SJ (2012) A high-density map of Arachis duranensis, a diploid ancestor of cultivated peanut. BMC Genomics 13:469-479.
  • Blair, MW, Corte´s, AJ, Penmetsa, RV, Farmer, A, Carrasquilla-Garcia, N and Cook, DR (2012) A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.) Theoretical and Applied Genetics 126:535-548.
  • Rachit K Saxena, R Varma Penmetsa, Hari D Upadhyaya, Ashish Kumar, Noelia Carrasquilla-Garcia, Jessica A. Schlueter, Andrew Farmer, Adam M. Whaley, Birinchi K. Sarma, Gregory D May, Douglas R Cook and Rajeev K Varshney (2012) Large-scale development of cost-effective SNP marker assays for genetic mapping in pigeonpea and comparative mapping in legumes. DNA Research 19:449-461.
  • Kassa, M.T., Penmetsa, R.V., Carrasquilla-Garcia, N., Sarma, B.K., Datta, S., Upadhyaya, H.D., Varshney, R.K., von Wettberg, E.J.B., Cook, D.R. (2012) Genetic patterns of domestication in pigeonpea (Cajanus cajan (L.) Millsp.) and wild Cajanus relatives. PLoS ONE 7(6):e39563.
  • Bohra A, Saxena RK, Gnanesh BN, Saxena K, Byregowda M, Rathore A, Kavikishor PB, Cook DR, Varshney RK (2012) An intra-specific consensus genetic map of pigeonpea [Cajanus cajan (L.) Millspaugh] derived from six mapping populations. Theor Appl Genet 125:1325-1338.
  • Hiremath PJ, Kumar A, Penmetsa RV, Farmer A, Schlueter JA, Chamarthi SK, Whaley AM, Carrasquilla-Garcia N, Gaur PM, Upadhyaya HD, Kavi Kishor PB, Shah TM, Cook DR, Varshney RK (2012) Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. Plant Biotechnol J. 10:716-32.
  • Wang H, Penmetsa RV, Yuan M, Gong L, Zhao Y, Guo B, Farmer AD, Rosen BD, Gao J, Isobe S, Bertioli DJ, Varshney RK, Cook DR, He G (2012) Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.). BMC Plant Biology 12(1):10.
  • Zhai, J, Jeong, DH, De Paoli, E, Park, S, Rosen, BD, Li, Y, González, AJ, Yan, Z, Kitto, SL, Grusak, MA, Jackson, SA, Stacey, G, Cook, DR, Green, PJ, Sherrier, DJ, and Meyers, BC (2011) microRNAs as Master Regulators of the Plant NB-LRR Defense Gene Family via the Production of Phased, Trans-acting siRNAs. Genes and Development 25:2540-53.
  • Young, N.D et al. (2011) The Genome Sequence of Medicago truncatula and the Evolution of Nodulation. Nature 480:520-4.
  • Varshney, R, et al. (2011) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nature Biotechnology 30(1):83-9.
  • Cara H. Haney, Brendan K. Riely, David Tricoli, Doug R. Cook, David W. Ehrhardt, Sharon R. Long (2011) Symbiotic Rhizobia Bacteria Trigger a Change in Localization and Dynamics of the Medicago truncatula Receptor Kinase LYK3. Plant Cell 23:2774.
  • Javot H, Penmetsa RR, Breuillin F, Bhattarai KK, Noar RD, Karen Gomez S, Zhang Q, Cook DR, Harrison MJ (2011). Medicago truncatula mtpt4 mutants reveal a role for nitrogen in the regulation of arbuscule degeneration in arbuscular mycorrhizal symbiosis. Plant J. 68:954-965.
  • Pandey MK, Monyo E, Ozias-Akins P, Liang X, Guimarães P, Nigam SN, Upadhyaya HD, Janila P, Zhang X, Guo B, Cook DR, Bertioli DJ, Michelmore R, Varshney RK. (2011) Advances in Arachis genomics for peanut improvement. Biotechnol Adv. PMID: 22094114
  • Thudi M, Bohra A, Nayak SN, Varghese N, Shah TM, Penmetsa RV, Thirunavukkarasu N, Gudipati S, Gaur PM, Kulwal PL, Upadhyaya HD, Kavikishor PB, Winter P, Kahl G, Town CD, Kilian A, Cook DR, Varshney RK. (2011) Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.). PLoS One 6:e27275
  • Choi HK and Cook DR (2011) Bridging Comparative Genomics and DNA Marker-aided Molecular Breeding. Kor. J. Breed. Sci. 43: 103-120.
  • Bohra A, Dubey A, Sazena RK, Penmetsa RV, Poornima KN, Kumar N, Farmer AD, Srivani G, Upadhyaya HD, Gothalwal R, Ramesh R, Singh D, Saxena KB, Kavikishor PB, Cook DR and Varshney RV (2011) Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.). BMC Plant Biology 11:56.
  • Gujaria N, Kumar A, Dauthal P, Dubey A, Hiremath P, Prakash AB, Farmer, A, Bhide M, Shah T, Gaur PM, Upadhyaya HD, Bhatia S, Cook DR, May GD, Varshney RK (2011) Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.) Theor Appl Genet 122:1577-1589.
  • Dutta, S, Kumawat, G, Singh, BP, Gupta DK, Singh, S, Dogra, V, Gaikwad, K, Sharma, TR, Raje, RS, Bandhopadhya, T, Datta, S, Singh, MN, Bashasab, F, Kulwal, P, Wanjari, KB, Varshney, RK, Cook, DR, Singh, NK (2011) Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus Cajan (L.) Millspaugh]. BMC Plant Biology 11:17.
  • Riely, BK, He H, Venkateshwaran M, Sarma B, Schraider J, Ane JM and Cook DR (2011) Identification of legume RopGEF gene families and characterization of a Medicago truncatula RopGEF mediating polar growth of root hairs. Plant Journal 65:230-243.
  • Stephens, BW, Cook, DR, and Grusak, MA (2011) Characterization of zinc transport by divalent metal transporters of the ZIP family from the model legume Medicago truncatula. BioMetals 24 51-58.
  • H.-K. Choi , F. Goes da Silva, H.-J. Lim, A. Iandolino, Y.-S. Seo, S.-W. Lee and D. R. Cook (2010) Diagnosis of Pierce’s Disease using biomarkers specific to Xylella fastidiosa rRNA and Vitis vinifera gene expression. Phytopathology 100:1089-1099.
  • Friesen ML, Cordeiro MA, Penmetsa RV, Badri M, Huguet T, Aouani ME, Cook DR, Nuzhdin SV. (2010) Population genomic analysis of Tunisian Medicago truncatula reveals candidates for local adaptation. The Plant Journal 63:623-635.
  • Varshney, R.K. and Cook, D.R. (2010) From genome studies to agricultural biotechnology: closing the gap between basic plant science and applied agriculture. Current Opinion in Plant Biology 13:115-118.
  • Nayak SN, Zhu H, Varghese N, Datta S, Choi HK, Horres R, Jüngling R, Singh J, Kishor PB, Sivaramakrishnan S, Hoisington DA, Kahl G, Winter P, Cook DR, Varshney RK (2010) Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome. Theoret and Appl Genet 120:1415-1441.
  • Varshney, R.K., et al and Cook, D.R. (2009) Pigeonpea genomics initiative: an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.) Mol Breeding, DOI 10.1007/s11032-009-9327-2.
  • Wang Y, Rosen B, Scoffield J, Egnin M, Mortley D, Steiner S, Cook DR and He G (2009) Isolation and analysis of resistance gene homologs in sweetpotato. Plant Breeding doi:10.1111/j.1439-0523.2009.01711.x
  • Varshney RK, Close TJ, Singh NK, Hoisington DA, Cook DR. (2009) Orphan legume crops enter the genomics era! Curr Opin Plant Biol. 2009 12:202-10.
  • Dhandaydham M, Charles L, Zhu H, Starr JL, Huguet T, Cook DR, Prosperi JM, Opperman C. (2008) Characterization of Root-Knot Nematode Resistance in Medicago truncatula. J Nematology 40:46-54.
  • Penmetsa, R.V. Uribe, P., Anderson, J., Lichtenzveig, J., Gish, J-C., Nam, Y-W., Engstrom, E., Xu, K., Siskel, G., Pereira, M., Baek, J-M., Lopez-Meyer, M., Long, SR, Harrison, M.J., Singh, J.B., Kiss, G.B., and Cook, D.R. (2008) The Medicago truncatula ortholog of Arabidopsis EIN2, sickle, is a negative regulator of symbiotic and pathogenic microbial associations. Plant Journal 55:580-595.
  • Baek, J.M., Han, P., and Cook, D.R. (2008) Characterization of intron structure and alternative splicing in Medicago truncatula, and comparison to Arabidopsis and rice. Plant Molecular Biology 67:499-510
  • Iandolino, A., Nobuta, K., Goes da Silva, F., Wu, H., Cook, D.R., and Meyers, B.C. (2008) Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures. BMC Plant Biology 8:53 doi:10.1186/1471-2229-8-53.
  • Goudeau, D, Uratsu, S.L., Inoue, K., Goes daSilva, F., Leslie, A., Cook, D., Regan, R.L., Dandekar, A.M. (2008) Tunning the orchestra: Selective gene regulation and orange fruit quality. Plant Science 174:310-320.
  • Middleton, P., Jakab, J., Penmetsa, R.V., Starker, C., Doll, J., Kalo, P., Prabu, R., Marsh, J., Mitra, R., Kereszt, A., Dudas, B., VandenBosch, K., Long, S., Cook, D., Kiss, G., and Oldroyd, G. (2007) An ERF transcription factor in Medicago truncatula that is essential for Nod factor signal transduction. The Plant Cell 19:1-14.
  • Messinese, E., Mun, J.H., Yeun, L.H., Jayaraman, D., Lougnon, G., Rougé, P., Barre, A., Bono, J.J., Cook, D.R., and Ané, J.M. (2007) A novel nuclear protein interacting with the symbiotic DMI3 CCaMK. MPMI 20:912-21.
  • Peiter, E, Sun, J, Heckmann, AB, Venkateshwaran, M, Riley, BK, Otegui, MJ, Edwards, A, Freshour, G, Hahn, MG, Cook, DR, Sanders, D, Oldroyd, GED, Downie, JA, Ané, JM (2007) The Medicago truncatula DMI1 Protein Modulates Cytosolic Calcium Signaling. Plant Physiol 145: 192-203.
  • Javot, H., Penmetsa, R.V., Terzaghi, N., Cook, D.R., and Harrison, M.J. (2007) Phosphate delivery by MtPT4 is indispensable for the arbuscular mycorrhizal symbiosis. Proc. Natl. Acad. Sci. USA Proc. Natl. Acad. Sci. USA 104:1720-1725.
  • Riely, B.K., Lougnon, G., Ané, J.-M., Cook, D.R. (2007) The symbiotic ion channel homolog DMI1 functions in the nuclear membrane of Medicago truncatula roots. The Plant Journal 49:208-216.
  • Cannon, SB, Sterck, L, Rombauts, S, Sato, S, Wang, X, Mudge, J, Vasdewani, J, Cheung, F, Gouzy, JP, Schiex, T, Spanngl, M, Schoof, H, Nicholson, C, Humphays, S, Mayer, K, Rogers, J, Quetier, F, Oldroyd, GE, Debelle, F, Cook, DR, Town, CD, Roe, BA, Tabata, S, Van de Peer, Y, Young, ND (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc. Natl. Acad. Sci. USA Proc. Natl. Acad. Sci. USA 103:14959-14964.
  • Hunter-Cevera, J., Cantor, C.R., Chiu, W., Cook, D.R., Kaler, E.W., Kalil, T., Kingsbury, D.T., Neuhauser, C., Petsko, G.A., Sticklen, M., Walker, L.P., and Westpheling, J. (2006) Committee on review of the Department of Energy's Genomics: GTL Program. The National Academies Press, Washington, D.C.
  • Choi, H.K., Luckow, M.A., Doyle, J., and Cook, D.R. (2006) Development of nuclear gene-derived molecular markers linked to legume genetic maps. Molecular Genetics and Genomics. 276:56-70.
  • Mun, JH, Kim, DJ, Choi, HK, Gish, J, Debellé, F, Mudge, J., Denny, R., Endré, G, Dénarié, J, Kiss, GB, Roe, B, Young, ND, and Cook , DR (2006) Distribution of microsatellites in the genome of Medicago truncatula: A resource of genetic markers that integrate genetic and physical maps. Genetics 172: 2541-2555.
  • Debolt, S, Cook, DR, and Ford, CM (2006) L-Tartaric acid synthesis from vitamin C in higher plants. Proc. Natl. Acad. Sci. USA 103:5608-5613.
  • Scherson, R., Choi, H-K., Cook, D. R., and Sanderson, M. (2005). Phylogenetics of New World Astragalus: screening of novel nuclear loci for the reconstruction of phylogenies at low taxonomic levels. Brittonia 57: 56-66.
  • Goes da Silva, F., Iandolino, A., Al-Kayal, F., Bohlmann, M.C., Cushman, M.A., Lim, H., Figueroa, R., Leslie, A., Xu, J., Kabuloglu, E.K., Tattersall, E., Ergul, A., Baek, J.M., Cramer, G.R., Cushman, J.C.,Cook, D.R. (2005) Characterizing the grape transcriptome. Analysis of expressed sequence tags from multiple Vitis species and development of a compendium of expression during berry development. Plant Physiology 139: 574-597.
  • Nevin D. Young, Steven B. Cannon, Shusei Sato, Dongjin Kim, Douglas R. Cook, Chris D. Town, Bruce A. Roe, and Satoshi Tabata (2005) Sequencing the Genespaces of Medicago truncatula and Lotus japonicus. Plant Physiol. 137: 1174-1181.
  • Steven B. Cannon, John A. Crow, Michael L. Heuer, Xiaohong Wang, Ethalinda K.S. Cannon, Christopher Dwan, Anne-Francoise Lamblin, Jayprakash Vasdewani, Joann Mudge, Andrew Cook, John Gish, Foo Cheung, Steve Kenton, Timothy M. Kunau, Douglas Brown, Gregory D. May, Dongjin Kim, Douglas R. Cook, Bruce A. Roe, Chris D. Town, Nevin D. Young, and Ernest F. Retzel. (2005). Databases and Information Integration for the Medicago truncatula Genome and Transcriptome. Plant Physiol. 138: 38-46.
  • Zhu, H., Choi, H-K., Cook, D.R. and Shoemaker, R.C. (2005). Bridging Model and Crop Legumes through Comparative Genomics. Plant Physiology 137: 1189-1196.
  • Iandolino, A.B., Goes da Silva, F., Lim, H.J., Choi, H.K., Williams, L.E., and Cook, D.R. (2004). A rapid and efficient protocol for the isolation of high-quality total RNA from grapevine (Vitis vinifera L.) tissues containing high concentrations of polylphenols, polysaccharides and proteins. Plant Molecular Biology Reporter 22:269-278.
  • Veereshlingam, H., Haynes, J.G., Sherrier, D.J., Penmetsa, R.V., Cook, D.R., and Rebecca Dickstein (2004) nip, a symbiotic Medicago truncatula mutant that forms root nodules with aberrant infection threads and exhibits an altered defense response. Plant Physiology 136:3692-3702.
  • Kulikova, O., Geurts, R., Lamine, M., Kim, D.J., Cook D.R., Leunissen, J., de Hong, H., Roe, B.A. and Bisseling, T. (2004) Satellite repeats in the functional centromere and pericentromeric heterochromatin of Medicago truncatula. Chromosoma 113:276-283.
  • Kuppusamy, K.T., Endre, G., Prabhu, R., Penmetsa, R.V., Veereshlingam, H., Cook, D.R., Dickstein, R., and VandenBosch, K.A. (2004) LIN, a Medicago truncatula gene required for nodule differentiation and persistence of rhizobial infections. Plant Physiology 136:3682-3691.
  • Choi, H.-K., Mun, J.-H., Kim, D.-J., Zhu, H., Baek, J.-M., Mudge, J., Roe, B., Ellis, T.H.N., Doyle, J., Kiss, G.B., Young, N.D., and Cook, D.R. (2004) Estimating genome conservation between crop and model legume species. Proc. Natl. Acad. Sci. USA 101:15289-15294.
  • Riely, B., Ane, J-M., Penmetsa, R.V., and Cook, D.R. (2004) Genetic and genomic analysis in model legume systems bring Nod factor signaling to center stage. Current Opinion in Plant Biology 7:408-413.
  • Choi, H.K., Kim, D., Uhm, T., Limpens, E., Lim, H., Mun, J.H., Kalo, P., Penmetsa, R.V., Seres, A., Kulikova, O., Bisseling, T., Kiss, G.B., and Cook, D.R. (2004). A Sequence-based Genetic Map of Medicago truncatula and comparison of marker co-linearity with Medicago sativa. Genetics 166:1463-1502.
  • Cook, D.R. (2004) Unraveling the mystery of Nod factor signaling by a genomic approach in Medicago trunactula. Proc. Natl. Acad. Sci. USA 101:4339-4340.
  • Yan, H.H., Mudge, J., Kim, D.J., Larsen, D., Denny, R., Shoemaker, R.C., Cook, D.R., Young, N.D. (2004) Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana. Genome 47:141-155.
  • Ecker, J. and Cook, D. (2004) Genome studies and molecular genetics: Unwrapping new layers of complexity in plant genomes. Current Opinion in Plant Biology 7:99-101.
  • Ané, J.M., Kiss, G.B., Riely, B.K., Penmetsa, R.V., Ayax, C., Lévy, J., Debellé, F., Baek, J.M., Kalo, P., Roseberg, C., Roe, B.A., Long, S.R., Dénarié, J., and Cook, D.R. (2004). Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes. Science 303:1364-1367.
  • Schnabel, E., Kulikova, O., Penmetsa, R.V., Bisseling, T., Cook, D., Frugoli, J. (2003) An integrated physical, genetic and cytogenetic map around the sunn locus of M. truncatula. Genome 46: 665-672.
  • Ben Amor, B., Shaw, S.L. Oldroyd, G.E.D., Maillet, F., Penmetsa, R.V., Cook, D., Long, S.R., Dénarié, J., and Gough, C. (2003) The NFP locus of Medicago truncatula controls an early step of Nod factor signal transduction upstream of a rapid calcium flux and root hair deformation. The Plant J. 34: 495-506.
  • Zhu, HY, Kim, DJ, Baek, JM, Choi, HK, Ellis, L., Kuester, H., McCombie, W.R., Peng, H.M. and Cook, D.R. (2003). Syntenic Relationships between Medicago truncatula and Arabidopsis thaliana Reveal Extensive Divergence of Genome Organization. Plant Physiology, 131:1018-1026.
  • Yan, H., Mudge, J., Kim, D.J., Shoemaker, R.C., Cook, D.R., and Young, N.D. (2003). Global estimates of conserved microsynteny among the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana. Theoretical and Applied Genetics. 106:1256-1265.
  • Donald A. Phillips, Howard Ferris, Douglas R. Cook and Donald R. Strong. (2003) Rhizosphere control points: molecules to food webs. Ecology 84:816-826.
  • Penmetsa, R.V., Frugoli, J.A., Smith, L., Long, S.R., and Cook, D.R. (2003). Dual Genetic Pathways Controlling Nodule Number In Medicago truncatula. Plant Physiology 131:998-1008.
  • Lamblin, AJ, Crow, JA, Johnson, JE, Silverstein, KAT, Kunau, TM, Endre, G, Stromvik, M, VandenBosch, KA, Cook, DR, and Retzel, EF (2003) MtDB: A database for personalized data mining of the model legume Medicago truncatula transcriptome. NAR 31:196-201.
  • Dangl, J., Cook, D., Haselkorn, R., Kellog, E., Last, R., Martienssen, R., McCouch, S., Retzel, E. F., Somerville, C.R., Wessler, S., Yates, J. (2002) The National Plant Genome Initiative: Objectives for 2003-2008. The National Academies Press, Washington, D.C.
  • Ané, J-M., Lévy, J., Thoquet, P., Kulikova, O., de Billy, F., Penmetsa, V., Debellé, F., Rosenberg, C., Kim, D.J., Cook, D., Bisseling, T., Huguet, T., and Dénarié, J. (2002). Genetic and cytogenetic mapping of dmi1, dmi2 and dmi3 genes of Medicago truncatula involved in Nod factor transduction, nodulation and mycorrhization. MPMI 15: 1108-1118.
  • Dickstein, R., Hu, X., Yang, J., Ba, L., Coque, L., Kim, D.J., Cook, D.R., Yeung, A. (2002). Differential expression of tandemly duplicated ENOD8 genes in Medicago truncatula. Plant Science 163, 333-343.
  • Zhu, H.Y., Cannon, S., Young, N.D., and Cook, D.R. (2002). Phylogeny and Genomic Organization of the TIR and non-TIR NBS-LRR Resistance Gene Family in Medicago truncatula, MPMI 15:529-539.
  • Gualtieri, G., Kulikova, O., Limpens, E., Kim, DJ, Cook, DR, Bisseling, T., Geurts, R. (2002). Microsynteny between pea and Medicago truncatula in the SYM2 region. Plant Molecular Biology 50: 225-235.
  • Ramu, S.R., Peng, H., and Cook, D.R. (2002). Nod factor induction of reactive oxygen species production is correlated with early nodulin gene expression. MPMI 15: 522-528.
  • Cannon, S.B., Zhu, H.Y., Baumgarten, A., Spangler, R., May, G., Cook, D.R., and Young, N.D. (2002). Diversity, distribution and ancient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene subfamilies. Journal of Molecular Evolution 54:548-562.
  • Kim, D., Baek, J-M, Kim, D., Kenerley, C.M., Cook, D.R. (2002). Cloning and characterization of multiple chitinase genes from the mycoparasitic fungus, Trichoderma virens. Current Genetics 40:374-384.
  • Kulikova, O, Gualtieri, G., Geurts, R., Kim, DJ, Cook, DR, Huguet, T., de Jong, J.H., Fransz, P.F., and Bisseling, T. (2001). Integration of the Fish-pachytene and genetic maps of Medicago truncatula. Plant Journal 27, 49-58.
  • Catoira, R., Timmer, A.C.J., Maillet, F., Galear, C., Penmetsa, R.V., Cook, D.R., Gough, C., and Denarie, J. (2001). The HCL gene of Medicago truncatula controls Rhizobium-induced root hair curling. Development 128, 1507-1518.
  • Cohn, J., Ramu, S., Uhm, T., Nam, Y.W., Kim, D.J., Penmetsa, V., Wood, T., Cook, D., and Stacey, G. (2001). Differential regulation of a family of apyrase genes from Medicago truncatula. Plant Physiology 125, 2104-2119.
  • Wais, R.J., Galera, C., Catoira, R., Penmetsa, R.V., Cook, D., Gough, C., Dénarié, J., and Long, S.R. (2000). Early symbiosis mutants of Medicago truncatula show a block in Ca++ spiking. Proc. Natl. Acad. Sci. USA, 97: 13407-13412.
  • Catoira, R., Galera C., de Billy F., Journet E.P., Maillet F., Penmetsa, V., Rosenberg C., Gough, C., Cook D., and Denarie J. (2000). Identification of four genes of Medicago truncatula controlling steps in Nod factor transduction. Plant Cell 12, 1647-1665.
  • Cook, D.R., and Dénarié, J. (2000). Progress in the genomics of Medicago truncatula and the promise for application to grain legume crops. Grain Legumes Magazine, No. 28, 12-13.
  • Cook, D.R., Kim, D., Zhu, H., and Uribe, P. (2000). Plant-Pathogen interactions in Medicago truncatula. Grain Legumes Magazine, No.28, 20.
  • Penmetsa, R.V. and Cook, D.R. (2000). Production and Characterization of Diverse Developmental Mutants of Medicago truncatula. Plant Physiology 123, 1387-1397.
  • Salzer, P., Bonanomi, A., Beyer, K., Vögeli-Lange, R., Aeschbacher, R.A., Lange, J., Wiemken, A., Kim, D., Cook, D.R., and Boller, T. (2000). Differential Expression of Eight Chitinase Genes in Medicago truncatula Roots During Mycorrhiza Formation, Nodulation, and Pathogen Infection". MPMI, 13 763-777.
  • Chory, J., Ecker, J.R., Briggs, S., Caboche, M., Coruzzi, G.M., Cook, D., Dangl, J., Grant, S., Guerinot, L., Henikoff, S., Martienssen, R., Okada, K., Raikhel, N.V., Somerville, C.R., and Weigel, D. (2000). Functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them. Plant Physiol. 123, 423-426.
  • Satcey, G., Day, R.B., Chon, J., Okada, M., Ito, Y., Koh, S., Ramu, S., Uhm, T., Kim, D., Cook, D., and Shibyua, N. (2000). Nod Factor Perception. In, Nitrogen fixation: from molecules to crop productivity, pp. 227-230.
  • Geurts, R. Gualtieri, G., Kulikova, O., Kim, D-J., Cook, D.R., and Bisseling, T. (2000). A region on the upper arm of chromosome 5 of Medicago truncatula is highly syntenic to the sym2 region of pea. In, Nitrogen fixation: from molecules to crop productivity, pp 309-310.
  • Cook, D. (1999). Medicago truncatula - a model in the making! Current Opinion in Plant Biology, 2 (4) 301-304.
  • Nam, Y-W, Penmetsa, R.V., Endre, G., Kim, D., and Cook, D.R. (1999). Construction of a bacterial artificial chromosome library of Medicago truncatula and identification of clones containing ethylene response genes. Theor Appl Genet 98: 638-646.
  • Penmetsa, R.V. and Cook, D. (1997). A legume ethylene-insensitive mutant hyperinfected by its rhizobial symbiont. Science 275, 527-530
  • Cook, D.R., VandenBosch, K.A., de Bruijn, F.J., and Huguet, T. (1997). Model legumes get the nod. Plant Cell 9, 275-281.
  • Cook, D.R. and VandenBosch, K.A. (1997). International Research Efforts on Medicago truncatula: a model for legume biology. IS-MPMI Reporter May 1997, 10-15.
  • Peng, H.-M., Dreyer, D.A., VandenBosch, K.A., and Cook, D. (1996). Gene structure and differential regulation of the Rhizobium-induced peroxidase gene rip1. Plant Physiology 112, 1437-1446.
  • VandenBosch, K.A., Cook, D., deBruijn, F., and Huguet, T. (1996). Emerging model legume systems: Tools and recent advances. In: Biology of Plant-Microbe Interactions, G. Stacey, B. Mullin and P.M. Gresshoff, ed. ISMPMI. pp. 557-562.
  • Cook, D., Dreyer, D. A., Bonnet, D., Howell, M., Nony, E., and VandenBosch, K.A. (1995). Transient induction of a peroxidase gene in Medicago truncatula precedes infection by Rhizobium meliloti. Plant Cell 7:43-55.
  • Cook, D. (1995). Surprising developments in the legume root nodule. BioEssays 17(3), 191-194.
  • Cook. D. and Sequeira, L. (1994). Strain Differentiation of Pseudomonas solanacearum by Molecular Genetic Methods. In: Bacterial Wilt (Pseudomonas solanacearum) A.C. Hayward and G.L. Hartman, ed. CAB International. pp. 77-93.
  • Raina, R., Cook, D., and Fedoroff, N. (1993). The Maize Spm transposable element has an enhancer-insensitive promoter. PNAS 90:6355-6359.
  • Cook, D. and Fedoroff, N. (1992). Regulation of Spm promoter activity by the Spm encoded tnpA gene product and DNA methylation. Maize Gen. Coop. Newslet. 66:11-12.
  • Fedoroff, N., Schlappi, M., Cook, D., and Kolosha, V. (1992). Regulation of the maize Spm transposable element: an hypothesis. Maize Gen. Coop. Newsletter 66: 13-14.
  • Cook, D. and Sequeira, L. (1991). Genetic and biochemical characterization of a gene cluster from Pseudomonas solanacearum required for extracellular polysaccharide production and for virulence. J. Bacteriol. 173(5):1654-1662.
  • Cook, D. and Sequeira, L. (1991). Use of subtractive hybridization to identify a DNA probe for Pseudomonas solanacearum race 3. Molecular and General Genetics 227:401-410.
  • Cook, D., Barlow, E., and Sequeira, L. (1991). DNA probes for the study of host-pathogen evolution: the example of Pseudomonas solanacearum. Pages 103-108, in: Advances in Molecular Genetics of Plant-Microbe Interactions, v1. H. Henneke and D.P. Verma, ed. Kulwer Academic Publishers.
  • Coplin, D.L. and Cook, D. (1990). Molecular genetics of extracellular polysaccharide biosynthesis in phytopathogenic bacteria. Mol. Plant-Microbe Interact. 3:271-279.
  • Cook, D., Barlow, E., and Sequeira, L. (1989). Genetic diversity of Pseudomonas solanacearum: detection of restriction fragment length polymorphisms with DNA probes that specify virulence and the hypersensitive response. Mol. Plant-Microbe Interact. 2:113-121.
  • Cook, D.R. and Robeson, D.J. (1986). Active resistance of cabbage (Brassica oleracea) to Xanthomonas campestris pv. carotae and protection against the causal agent of black rot, X. campestris pv. campestris, by co-inoculation. Physiological and Molecular Plant Pathology 28:41-52.
  • Robeson, D.J. and Cook, D.R. (1985). Production of low molecular weight carboxylic acids by Xanthomonas capestris pv. carotae in relation to the amino acid composition of the medium and their possible involvement in pathogenesis. Physiological Plant Pathology 26:219-230.
  • Robeson, D.J. and Cook, D.R. (1985). Biotransformation of tryptophan to indole-3-acetic acid by Xanthomonas campestris pv. campestris. Z. Naturforsch 40c:741-742.
  • Cook, D., Rasche, M., and Eisinger, W. (1985). Regulation of ethylene biosynthesis and action in cut carnation flower senescence by cytokinins. J. Amer. Soc. Hort. Sci. 110:241-227.