TIGR Plant Genomics Group Publications
Alfano JR, Buell, C. R., Chancey, S. T., Collmer, A., Espinosa, A, Guo, M., Hanks, M., Jamir, Y, Janes, M. D., Schneider, D. J., Shan, L., Petnicki-Ocwieja, T., Schechter, L. M., Tam, V. C. and Tang, X. (2003) Genomic mining for substrates of the type III secretion system of Pseudomonas syringae pv. tomato DC3000: New insights into mechanisms of pathogenesis. In NS Iacobellis, ed, Pseudomonas syringae and related pathogens. Kluwer Academic Publishers, Dordrecht, pp 363-372
Avila-Adame C, Gómez-Alpizar, L., Zismann, V., Jones, K. M., Buell, C. R., Ristaino, J.B. (2005) Mitochondrial genome sequences and molecular evolution of the Irish potato famine pathogen, Phytophthora infestans. Current Genetics
Ayele M, Haas BJ, Kumar N, Wu H, Xiao Y, Van Aken S, Utterback TR, Wortman JR, White OR, Town CD (2005) Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis. Genome Res 15: 487-495 - Pubmed Abstract
Barbazuk WB, Bedell JA, Rabinowicz PD (2005) Reduced representation sequencing: a success in maize and a promise for other plant genomes. Bioessays 27: 839-848 - Pubmed Abstract
Bedell JA, Budiman MA, Nunberg A, Citek RW, Robbins D, Jones J, Flick E, Rholfing T, Fries J, Bradford K, McMenamy J, Smith M, Holeman H, Roe BA, Wiley G, Korf IF, Rabinowicz PD, Lakey N, McCombie WR, Jeddeloh JA, Martienssen RA (2005) Sorghum genome sequencing by methylation filtration. PLoS Biol 3: e13 - Pubmed Abstract
Bradeen JM, Naess SK, Song J, Haberlach GT, Wielgus SM, Buell CR, Jiang J, Helgeson JP (2003) Concomitant reiterative BAC walking and fine genetic mapping enable physical map development for the broad-spectrum late blight resistance region, RB. Mol Genet Genomics 269: 603-611 - Pubmed Abstract
Brown DW, Cheung F, Proctor RH, Butchko RA, Zheng L, Lee Y, Utterback T, Smith S, Feldblyum T, Glenn AE, Plattner RD, Kendra DF, Town CD, Whitelaw CA (2005) Comparative analysis of 87,000 expressed sequence tags from the fumonisin-producing fungus Fusarium verticillioides. Fungal Genet Biol 42: 848-861 - Pubmed Abstract
Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, Pontaroli AC, Wei F, Haberer G, Fuks G, Du C, Raymond C, Estep MC, Liu R, Bennetzen JL, Chan AP, Rabinowicz PD, Quackenbush J, Barbazuk WB, Wing RA, Birren B, Nusbaum C, Rounsley S, Mayer KF, Messing J (2006) Uneven chromosome contraction and expansion in the maize genome. Genome Res - Pubmed Abstract
Buell CR (2002) Current status of the sequence of the rice genome and prospects for finishing the first monocot genome. Plant Physiol 130: 1585-1586 - Pubmed Abstract
Buell CR (2002) Interactions between Xanthomonas species and Arabidopsis thaliana. In CRSaEM Meyerowitz, ed, The Arabidopsis Book. American Society of Plant Biologists, Rockville, MD, p DOI 10.119/tab.0031
Buell CR (2002) Obtaining the sequence of the rice genome and lessons learned along the way. Trends Plant Sci 7: 538-542 - Pubmed Abstract
Buell CR (2004) A survey of plant pathogen genomes. In TR C. Fraser, and K. Nelson, ed, Microbial Genomes. Humana Press Inc, Totowa NJ, pp 213-223
Buell CR, Joardar V, Lindeberg M, Selengut J, Paulsen IT, Gwinn ML, Dodson RJ, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Daugherty S, Brinkac L, Beanan MJ, Haft DH, Nelson WC, Davidsen T, Zafar N, Zhou L, Liu J, Yuan Q, Khouri H, Fedorova N, Tran B, Russell D, Berry K, Utterback T, Van Aken SE, Feldblyum TV, D'Ascenzo M, Deng WL, Ramos AR, Alfano JR, Cartinhour S, Chatterjee AK, Delaney TP, Lazarowitz SG, Martin GB, Schneider DJ, Tang X, Bender CL, White O, Fraser CM, Collmer A (2003) The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci U S A 100: 10181-10186 - Pubmed Abstract
Buell CR, Sundaresan V (2003) A workshop on establishing a rice resource center in the United States. Plant Physiol 132: 1137 - Pubmed Abstract
Cannon SB, Crow JA, Heuer ML, Wang X, Cannon EK, Dwan C, Lamblin AF, Vasdewani J, Mudge J, Cook A, Gish J, Cheung F, Kenton S, Kunau TM, Brown D, May GD, Kim D, Cook DR, Roe BA, Town CD, Young ND, Retzel EF (2005) Databases and information integration for the Medicago truncatula genome and transcriptome. Plant Physiol 138: 38-46 - Pubmed Abstract
Chan A, Pertea, G, Cheung, F, Lee, D, Zheng, L, Pontaroli, AC, SanMiguel, P, Yuan, Y, Bennetzen, JL, Barbazuk, WB, Quackenbush, J, Rabinowicz, PD (2006) The TIGR Maize Database. Nucleic Acids Res. 34: D771-776 - Pubmed Abstract
Cheng Z, Buell CR, Wing RA, Gu M, Jiang J (2001) Toward a cytological characterization of the rice genome. Genome Res 11: 2133-2141 - Pubmed Abstract
Cheng Z, Buell CR, Wing RA, Jiang J (2002) Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers. Chromosome Res 10: 379-387 - Pubmed Abstract
Cheng Z, Dong F, Langdon T, Ouyang S, Buell CR, Gu M, Blattner FR, Jiang J (2002) Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14: 1691-1704 - Pubmed Abstract
Cheng Z, Presting GG, Buell CR, Wing RA, Jiang J (2001) High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics 157: 1749-1757 - Pubmed Abstract
Fedorova M, van de Mortel J, Matsumoto PA, Cho J, Town CD, VandenBosch KA, Gantt JS, Vance CP (2002) Genome-wide identification of nodule-specific transcripts in the model legume Medicago truncatula. Plant Physiol 130: 519-537 - Pubmed Abstract
Fei Z, Tang X, Alba RM, White JA, Ronning CM, Martin GB, Tanksley SD, Giovannoni JJ (2004) Comprehensive EST analysis of tomato and comparative genomics of fruit ripening. Plant J 40: 47-59 - Pubmed Abstract
Fouts DE, Abramovitch RB, Alfano JR, Baldo AM, Buell CR, Cartinhour S, Chatterjee AK, D'Ascenzo M, Gwinn ML, Lazarowitz SG, Lin NC, Martin GB, Rehm AH, Schneider DJ, van Dijk K, Tang X, Collmer A (2002) Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor. Proc Natl Acad Sci U S A 99: 2275-2280 - Pubmed Abstract
Gardiner JM, C. R. Buell, R. Elumalai, D. W. Galbraith, D. A. Henderson, A. L. Iniguez, S. M. Kaeppler, J. J. Kim, J. Liu, L. Zheng, and V. L. Chandler. (2005) Design, production, and utilization of long oligonucleotide microarrays for expression analysis in maize. Maydica
Gill BS, Appels R, Botha-Oberholster AM, Buell CR, Bennetzen JL, Chalhoub B, Chumley F, Dvorak J, Iwanaga M, Keller B, Li W, McCombie WR, Ogihara Y, Quetier F, Sasaki T (2004) A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics 168: 1087-1096 - Pubmed Abstract
Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK, Jr., Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, Salzberg SL, White O (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31: 5654-5666 - Pubmed Abstract
Haas BJ, Volfovsky N, Town CD, Troukhan M, Alexandrov N, Feldmann KA, Flavell RB, White O, Salzberg SL (2002) Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol 3: RESEARCH0029 - Pubmed Abstract
Haas BJ, Wortman JR, Ronning CM, Hannick LI, Smith RK, Jr., Maiti R, Chan AP, Yu C, Farzad M, Wu D, White O, Town CD (2005) Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biol 3: 7 - Pubmed Abstract
Huala E, Dickerman AW, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, Hanley D, Kiphart D, Zhuang M, Huang W, Mueller LA, Bhattacharyya D, Bhaya D, Sobral BW, Beavis W, Meinke DW, Town CD, Somerville C, Rhee SY (2001) The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res 29: 102-105 - Pubmed Abstract
Joardar V, Lindeberg M, Jackson RW, Selengut J, Dodson R, Brinkac LM, Daugherty SC, Deboy R, Durkin AS, Giglio MG, Madupu R, Nelson WC, Rosovitz MJ, Sullivan S, Crabtree J, Creasy T, Davidsen T, Haft DH, Zafar N, Zhou L, Halpin R, Holley T, Khouri H, Feldblyum T, White O, Fraser CM, Chatterjee AK, Cartinhour S, Schneider DJ, Mansfield J, Collmer A, Buell CR (2005) Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J Bacteriol 187: 6488-6498 - Pubmed Abstract
Joardar V, Lindeberg, M., Collmer, A. Buell, C. R. (2005) Lineage specific regions in Pseudomonas syringae pv tomato DC3000 are associated with features of lateral gene transfer. Molecular Plant Pathology 6: 53-64
Kim H, Snesrud EC, Haas B, Cheung F, Town CD, Quackenbush J (2003) Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray. Genome Res 13: 327-340 - Pubmed Abstract
Kim H, Zhao B, Snesrud EC, Haas BJ, Town CD, Quackenbush J (2002) Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses. Biotechniques 33: 924-930 - Pubmed Abstract
Kuang H, Wei F, Marano MR, Wirtz U, Wang X, Liu J, Shum WP, Zaborsky J, Tallon LJ, Rensink W, Lobst S, Zhang P, Tornqvist CE, Tek A, Bamberg J, Helgeson J, Fry W, You F, Luo MC, Jiang J, Robin Buell C, Baker B (2005) The R1 resistance gene cluster contains three groups of independently evolving, type I R1 homologues and shows substantial structural variation among haplotypes of Solanum demissum. Plant J 44: 37-51 - Pubmed Abstract
Kuhl JC, Cheung F, Yuan Q, Martin W, Zewdie Y, McCallum J, Catanach A, Rutherford P, Sink KC, Jenderek M, Prince JP, Town CD, Havey MJ (2004) A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales. Plant Cell 16: 114-125 - Pubmed Abstract
Lin H, Zhu W, Silva JC, Gu X, Buell CR (2006) Intron gain and loss in segmentally duplicated genes in rice. Genome Biol 7: R41 - Pubmed Abstract
Lin X, Kaul S, Rounsley S, Shea TP, Benito MI, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, Feldblyum TV, Buell CR, Ketchum KA, Lee J, Ronning CM, Koo HL, Moffat KS, Cronin LA, Shen M, Pai G, Van Aken S, Umayam L, Tallon LJ, Gill JE, Adams MD, Carrera AJ, Creasy TH, Goodman HM, Somerville CR, Copenhaver GP, Preuss D, Nierman WC, White O, Eisen JA, Salzberg SL, Fraser CM, Venter JC (1999) Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402: 761-768 - Pubmed Abstract
Liu J, Blaylock LA, Endre G, Cho J, Town CD, VandenBosch KA, Harrison MJ (2003) Transcript profiling coupled with spatial expression analyses reveals genes involved in distinct developmental stages of an arbuscular mycorrhizal symbiosis. Plant Cell 15: 2106-2123 - Pubmed Abstract
Ludwig-Muller J, Vertocnik A, Town CD (2005) Analysis of indole-3-butyric acid-induced adventitious root formation on Arabidopsis stem segments. J Exp Bot 56: 2095-2105 - Pubmed Abstract
Luo MC, Thomas C, You FM, Hsiao J, Ouyang S, Buell CR, Malandro M, McGuire PE, Anderson OD, Dvorak J (2003) High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82: 378-389 - Pubmed Abstract
Martin WJ, McCallum J, Shigyo M, Jakse J, Kuhl JC, Yamane N, Pither-Joyce M, Gokce AF, Sink KC, Town CD, Havey MJ (2005) Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity. Mol Genet Genomics 274: 197-204 - Pubmed Abstract
McNally KL, Bruskiewich R, Mackill D, Buell CR, Leach JE, Leung H (2006) Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes. Plant Physiol 141: 26-31 - Pubmed Abstract
Mudge J, Cannon SB, Kalo P, Oldroyd GE, Roe BA, Town CD, Young ND (2005) Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana. BMC Plant Biol 5: 15 - Pubmed Abstract
Nagaki K, Cheng Z, Ouyang S, Talbert PB, Kim M, Jones KM, Henikoff S, Buell CR, Jiang J (2004) Sequencing of a rice centromere uncovers active genes. Nat Genet 36: 138-145 - Pubmed Abstract
Nagaki K, Neumann P, Zhang D, Ouyang S, Buell CR, Cheng Z, Jiang J (2005) Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice. Mol Biol Evol 22: 845-855 - Pubmed Abstract
Nagaki K, Song J, Stupar RM, Parokonny AS, Yuan Q, Ouyang S, Liu J, Hsiao J, Jones KM, Dawe RK, Buell CR, Jiang J (2003) Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres. Genetics 163: 759-770 - Pubmed Abstract
Ouyang S, Buell CR (2004) The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res 32: D360-363 - Pubmed Abstract
Petnicki-Ocwieja T, Schneider DJ, Tam VC, Chancey ST, Shan L, Jamir Y, Schechter LM, Janes MD, Buell CR, Tang X, Collmer A, Alfano JR (2002) Genomewide identification of proteins secreted by the Hrp type III protein secretion system of Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci U S A 99: 7652-7657 - Pubmed Abstract
Rabinowicz PD, Bennetzen JL (2006) The maize genome as a model for efficient sequence analysis of large plant genomes. Curr Opin Plant Biol 9: 149-156 - Pubmed Abstract
Rabinowicz PD, Citek R, Budiman MA, Nunberg A, Bedell JA, Lakey N, O'Shaughnessy AL, Nascimento LU, McCombie WR, Martienssen RA (2005) Differential methylation of genes and repeats in land plants. Genome Res 15: 1431-1440 - Pubmed Abstract
Rabinowicz PD, Rensink W (2005) Ways to get from plant genomes to phenomes: via yeast. Genome Biol 6: 310 - Pubmed Abstract
Redman JC, Haas BJ, Tanimoto G, Town CD (2004) Development and evaluation of an Arabidopsis whole genome Affymetrix probe array. Plant J 38: 545-561 - Pubmed Abstract
Rensink W, Hart A, Liu J, Ouyang S, Zismann V, Buell CR (2005) Analyzing the potato abiotic stress transcriptome using expressed sequence tags. Genome 48: 598-605 - Pubmed Abstract
Rensink WA, Buell CR (2004) Arabidopsis to rice. Applying knowledge from a weed to enhance our understanding of a crop species. Plant Physiol 135: 622-629 - Pubmed Abstract
Rensink WA, Buell CR (2005) Microarray expression profiling resources for plant genomics. Trends Plant Sci 10: 603-609 - Pubmed Abstract
Rensink WA, Iobst S, Hart A, Stegalkina S, Liu J, Buell CR (2005) Gene expression profiling of potato responses to cold, heat, and salt stress. Funct Integr Genomics 5: 201-207 - Pubmed Abstract
Rensink WA, Lee Y, Liu J, Iobst S, Ouyang S, Buell CR (2005) Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts. BMC Genomics 6: 124 - Pubmed Abstract
Restrepo S, Myers KL, del Pozo O, Martin GB, Hart AL, Buell CR, Fry WE, Smart CD (2005) Gene profiling of a compatible interaction between Phytophthora infestans and Solanum tuberosum suggests a role for carbonic anhydrase. Mol Plant Microbe Interact 18: 913-922 - Pubmed Abstract
Ronning CM, Stegalkina SS, Ascenzi RA, Bougri O, Hart AL, Utterbach TR, Vanaken SE, Riedmuller SB, White JA, Cho J, Pertea GM, Lee Y, Karamycheva S, Sultana R, Tsai J, Quackenbush J, Griffiths HM, Restrepo S, Smart CD, Fry WE, Van Der Hoeven R, Tanksley S, Zhang P, Jin H, Yamamoto ML, Baker BJ, Buell CR (2003) Comparative analyses of potato expressed sequence tag libraries. Plant Physiol 131: 419-429 - Pubmed Abstract
Salanoubat M, Lemcke K, Rieger M, Ansorge W, Unseld M, Fartmann B, Valle G, Blocker H, Perez-Alonso M, Obermaier B, Delseny M, Boutry M, Grivell LA, Mache R, Puigdomenech P, De Simone V, Choisne N, Artiguenave F, Robert C, Brottier P, Wincker P, Cattolico L, Weissenbach J, Saurin W, Quetier F, Schafer M, Muller-Auer S, Gabel C, Fuchs M, Benes V, Wurmbach E, Drzonek H, Erfle H, Jordan N, Bangert S, Wiedelmann R, Kranz H, Voss H, Holland R, Brandt P, Nyakatura G, Vezzi A, D'Angelo M, Pallavicini A, Toppo S, Simionati B, Conrad A, Hornischer K, Kauer G, Lohnert TH, Nordsiek G, Reichelt J, Scharfe M, Schon O, Bargues M, Terol J, Climent J, Navarro P, Collado C, Perez-Perez A, Ottenwalder B, Duchemin D, Cooke R, Laudie M, Berger-Llauro C, Purnelle B, Masuy D, de Haan M, Maarse AC, Alcaraz JP, Cottet A, Casacuberta E, Monfort A, Argiriou A, flores M, Liguori R, Vitale D, Mannhaupt G, Haase D, Schoof H, Rudd S, Zaccaria P, Mewes HW, Mayer KF, Kaul S, Town CD, Koo HL, Tallon LJ, Jenkins J, Rooney T, Rizzo M, Walts A, Utterback T, Fujii CY, Shea TP, Creasy TH, Haas B, Maiti R, Wu D, Peterson J, Van Aken S, Pai G, Militscher J, Sellers P, Gill JE, Feldblyum TV, Preuss D, Lin X, Nierman WC, Salzberg SL, White O, Venter JC, Fraser CM, Kaneko T, Nakamura Y, Sato S, Kato T, Asamizu E, Sasamoto S, Kimura T, Idesawa K, Kawashima K, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Muraki A, Nakayama S, Nakazaki N, Shinpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S (2000) Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature 408: 820-822 - Pubmed Abstract
Song J, Bradeen JM, Naess SK, Raasch JA, Wielgus SM, Haberlach GT, Liu J, Kuang H, Austin-Phillips S, Buell CR, Helgeson JP, Jiang J (2003) Gene RB cloned from Solanum bulbocastanum confers broad spectrum resistance to potato late blight. Proc Natl Acad Sci U S A 100: 9128-9133 - Pubmed Abstract
Sorghum Genomics Planning Workshop Participants (2005) Toward sequencing the sorghum genome. A U.S. National Science Foundation-sponsored workshop report. Plant Physiol 138: 1898-1902 - Pubmed Abstract
Stupar RM, Lilly JW, Town CD, Cheng Z, Kaul S, Buell CR, Jiang J (2001) Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: implication of potential sequencing errors caused by large-unit repeats. Proc Natl Acad Sci U S A 98: 5099-5103 - Pubmed Abstract
The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815 - Pubmed Abstract
The International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800 - Pubmed Abstract
Theologis A, Ecker JR, Palm CJ, Federspiel NA, Kaul S, White O, Alonso J, Altafi H, Araujo R, Bowman CL, Brooks SY, Buehler E, Chan A, Chao Q, Chen H, Cheuk RF, Chin CW, Chung MK, Conn L, Conway AB, Conway AR, Creasy TH, Dewar K, Dunn P, Etgu P, Feldblyum TV, Feng J, Fong B, Fujii CY, Gill JE, Goldsmith AD, Haas B, Hansen NF, Hughes B, Huizar L, Hunter JL, Jenkins J, Johnson-Hopson C, Khan S, Khaykin E, Kim CJ, Koo HL, Kremenetskaia I, Kurtz DB, Kwan A, Lam B, Langin-Hooper S, Lee A, Lee JM, Lenz CA, Li JH, Li Y, Lin X, Liu SX, Liu ZA, Luros JS, Maiti R, Marziali A, Militscher J, Miranda M, Nguyen M, Nierman WC, Osborne BI, Pai G, Peterson J, Pham PK, Rizzo M, Rooney T, Rowley D, Sakano H, Salzberg SL, Schwartz JR, Shinn P, Southwick AM, Sun H, Tallon LJ, Tambunga G, Toriumi MJ, Town CD, Utterback T, Van Aken S, Vaysberg M, Vysotskaia VS, Walker M, Wu D, Yu G, Fraser CM, Venter JC, Davis RW (2000) Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature 408: 816-820 - Pubmed Abstract
The Rice Chromosome 3 Sequencing Consortium (2005) Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Res 15: 1284-1291 - Pubmed Abstract
The Rice Chromosome 10 Sequencing Consortium (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300: 1566-1569 - Pubmed Abstract
The Rice Chromosomes 11 and 12 Sequencing Consortia (2005) The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biol 3: 20
Thibaud-Nissen F, Wu H, Richmond T, Redman JC, Johnson C, Green R, Arias J, Town CD (2006) Development of Arabidopsis whole-genome microarrays and their application to the discovery of binding sites for the TGA2 transcription factor in salicylic acid-treated plants. Plant J 47: 152-162 - Pubmed Abstract
Town C (2005) Large-scale DNA Sequencing. In K Meksem, Kahl, G, ed, The Hanbook of Plant Genome Mapping. Wiley-VCH, pp 337-351
Town CD, Cheung F, Maiti R, Crabtree J, Haas BJ, Wortman JR, Hine EE, Althoff R, Arbogast TS, Tallon LJ, Vigouroux M, Trick M, Bancroft I (2006) Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 18: 1348-1359 - Pubmed Abstract
Triwitayakorn K, Njiti VN, Iqbal MJ, Yaegashi S, Town C, Lightfoot DA (2005) Genomic analysis of a region encompassing QRfs1 and QRfs2: genes that underlie soybean resistance to sudden death syndrome. Genome 48: 125-138 - Pubmed Abstract
Van der Hoeven R, Ronning C, Giovannoni J, Martin G, Tanksley S (2002) Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing. Plant Cell 14: 1441-1456 - Pubmed Abstract
Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, Lee Y, Zheng L, van Heeringen S, Karamycheva S, Bennetzen JL, SanMiguel P, Lakey N, Bedell J, Yuan Y, Budiman MA, Resnick A, Van Aken S, Utterback T, Riedmuller S, Williams M, Feldblyum T, Schubert K, Beachy R, Fraser CM, Quackenbush J (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302: 2118-2120 - Pubmed Abstract
Wortman JR, Haas BJ, Hannick LI, Smith RK, Jr., Maiti R, Ronning CM, Chan AP, Yu C, Ayele M, Whitelaw CA, White OR, Town CD (2003) Annotation of the Arabidopsis genome. Plant Physiol 132: 461-468 - Pubmed Abstract
Xiao YL, Malik M, Whitelaw CA, Town CD (2002) Cloning and sequencing of cDNAs for hypothetical genes from chromosome 2 of Arabidopsis. Plant Physiol 130: 2118-2128 - Pubmed Abstract
Xiao YL, Smith SR, Ishmael N, Redman JC, Kumar N, Monaghan EL, Ayele M, Haas BJ, Wu HC, Town CD (2005) Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants. Plant Physiol 139: 1323-1337 - Pubmed Abstract
Yan H, Jin W, Nagaki K, Tian S, Ouyang S, Buell CR, Talbert PB, Henikoff S, Jiang J (2005) Transcription and Histone Modifications in the Recombination-Free Region Spanning a Rice Centromere. Plant Cell - Pubmed Abstract
Young ND, Cannon SB, Sato S, Kim D, Cook DR, Town CD, Roe BA, Tabata S (2005) Sequencing the genespaces of Medicago truncatula and Lotus japonicus. Plant Physiol 137: 1174-1181 - Pubmed Abstract
Yu J, Whitelaw CA, Nierman WC, Bhatnagar D, Cleveland TE (2004) Aspergillus flavus expressed sequence tags for identification of genes with putative roles in aflatoxin contamination of crops. FEMS Microbiol Lett 237: 333-340 - Pubmed Abstract
Yuan Q, Hill J, Hsiao J, Moffat K, Ouyang S, Cheng Z, Jiang J, Buell CR (2002) Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion. Mol Genet Genomics 267: 713-720 - Pubmed Abstract
Yuan Q, Liang F, Hsiao J, Zismann V, Benito MI, Quackenbush J, Wing R, Buell R (2000) Anchoring of rice BAC clones to the rice genetic map in silico. Nucleic Acids Res 28: 3636-3641 - Pubmed Abstract
Yuan Q, Ouyang S, Liu J, Suh B, Cheung F, Sultana R, Lee D, Quackenbush J, Buell CR (2003) The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res 31: 229-233 - Pubmed Abstract
Yuan Q, Ouyang S, Wang A, Zhu W, Maiti R, Lin H, Hamilton J, Haas B, Sultana R, Cheung F, Wortman J, Buell CR (2005) The institute for genomic research Osa1 rice genome annotation database. Plant Physiol 138: 18-26 - Pubmed Abstract
Yuan Q, Quackenbush J, Sultana R, Pertea M, Salzberg SL, Buell CR (2001) Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species. Plant Physiol 125: 1166-1174 - Pubmed Abstract