Bartoš, Jan, Paux, Etienne, Kofler, Robert, Havránková, Miroslava, Kopecký, David, Suchánková, Pavla, ...
Abstract Background Rye ( Secale cereale L.) belongs to tribe Triticeae and is an important temperate cereal. It is one of the parents of man-made species Triticale and has been used as a source of...
Kakar, Klementina, Wandrey, Maren, Czechowski, Tomasz, Gaertner, Tanja, Scheible, Wolf-Rüdiger, Stitt, Mark, ...
Abstract Background Medicago truncatula is a model legume species that is currently the focus of an international genome sequencing effort. Although several different oligonucleotide and cDNA arrays...
Mian, MA Rouf, Zhang, Yan, Wang, Zeng-Yu, Zhang, Ji-Yi, Cheng, Xiaofei, Chen, Lei, ...
Abstract Background Tall fescue ( Festuca arundinacea Schreb) is a major cool season forage and turf grass species grown in the temperate regions of the world. In this paper we report the generation...
Sequencing and analysis of the gene-rich space of cowpea (2008)
Timko, Michael P, Rushton, Paul J, Laudeman, Thomas W, Bokowiec, Marta T, Chipumuro, Edmond, Cheung, Foo, ...
Abstract Background Cowpea, Vigna unguiculata (L.) Walp., is one of the most important food and forage legumes in the semi-arid tropics because of its drought tolerance and ability to grow on poor...
Insights into the Musa genome: Syntenic relationships to rice and between Musa species (2008)
Lescot, Magali, Piffanelli, Pietro, Ciampi, Ana Y, Ruiz, Manuel, Blanc, Guillaume, Leebens-Mack, Jim, ...
Abstract Background Musa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa...
A BAC end view of the Musa acuminatagenome (2007)
Cheung, Foo, Town, Christopher D
Abstract Background Musa species contain the fourth most important crop in developing countries. Here, we report the analysis of 6,252 BAC end-sequences, in order to view the sequence composition of...
Spotted cotton oligonucleotide microarrays for gene expression analysis (2007)
Udall, Joshua A, Flagel, Lex E, Cheung, Foo, Woodward, Andrew W, Hovav, Ran, Rapp, Ryan A, ...
Abstract Background Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on...
Moskal, William A, Wu, Hank C, Underwood, Beverly A, Wang, Wei, Town, Christopher D, Xiao, Yongli
Abstract Background Several lines of evidence support the existence of novel genes and other transcribed units which have not yet been annotated in the Arabidopsis genome. Two gene prediction...
Sequencing Medicago truncatulaexpressed sequenced tags using 454 Life Sciences technology (2006)
Cheung, Foo, Haas, Brian J, Goldberg, Susanne MD, May, Gregory D, Xiao, Yongli, Town, Christopher D
Abstract Background In this study, we addressed whether a single 454 Life Science GS20 sequencing run provides new gene discovery from a normalized cDNA library, and whether the short reads produced...
Ruhlman, Tracey, Lee, Seung-Bum, Jansen, Robert K, Hostetler, Jessica B, Tallon, Luke J, Town, Christopher D, ...
Abstract Background Carrot ( Daucus carota ) is a major food crop in the US and worldwide. Its capacity for storage and its lifecycle as a biennial make it an attractive species for the introduction...
Lee, Seung-Bum, Kaittanis, Charalambos, Jansen, Robert K, Hostetler, Jessica B, Tallon, Luke J, Town, Christopher D, ...
Abstract Background Cotton ( Gossypium hirsutum ) is the most important fiber crop grown in 90 countries. In 2004–2005, US farmers planted 79% of the 5.7-million hectares of nuclear transgenic...
Mudge, Joann, Cannon, Steven B, Kalo, Peter, Oldroyd, Giles ED, Roe, Bruce A, Town, Christopher D, ...
Abstract Background Recent genome sequencing enables mega-base scale comparisons between related genomes. Comparisons between animals, plants, fungi, and bacteria demonstrate extensive synteny...
Haas, Brian J, Wortman, Jennifer R, Ronning, Catherine M, Hannick, Linda I, Smith, Roger K, Maiti, Rama, ...
Abstract Background Since the initial publication of its complete genome sequence, Arabidopsis thaliana has become more important than ever as a model for plant research. However, the initial genome...
Full-length messenger RNA sequences greatly improve genome annotation (2002)
Haas, Brian J, Volfovsky, Natalia, Town, Christopher D, Troukhan, Maxim, Alexandrov, Nickolai, Feldmann, Kenneth A, ...
Abstract Background Annotation of eukaryotic genomes is a complex endeavor that requires the integration of evidence from multiple, often contradictory, sources. With the ever-increasing amount of...
Full-length messenger RNA sequences greatly improve genome annotation (2002)
Haas, Brian J, Volfovsky, Natalia, Town, Christopher D, Troukhan, Maxim, Alexandrov, Nickolai, Feldman, Kenneth A, ...
Background: Annotation of eukaryotic genomes is a complex endeavor that requires the integration of evidence from multiple, often contradictory, sources. With the ever-increasing amount of genome...
Kreps, Joel A., Town, Christopher D.
Mutants of Arabidopsis thaliana have been selected for resistance to growth inhibition at the seedling stage by alpha-methyltryptophan (aMT). One mutant, amt-1 has been characterized in detail. The...
Campell, Bruce R., Town, Christopher D.
To investigate the molecular mechanisms of hormonal control of growth, we constructed a subtracted cDNA library enriched for sequences expressed more in a hormone-autonomous, radiation-induced tumor...
Campell, Bruce R., Town, Christopher D.
gamma-Radiation-induced tumors of Arabidopsis thaliana L. have been produced as a novel approach to isolation of genes that regulate plant development. Tumors excised from irradiated plants are...
Huala, Eva, Dickerman, Allan W., Garcia-Hernandez, Margarita, Weems, Danforth, Reiser, Leonore, LaFond, Frank, ...
Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic,...
Stupar, Robert M., Lilly, Jason W., Town, Christopher D., Cheng, Zhukuan, Kaul, Samir, Buell, C. Robin, ...
Previously conducted sequence analysis of Arabidopsis thaliana (ecotype Columbia-0) reported an insertion of 270-kb mtDNA into the pericentric region on the short arm of chromosome 2. DNA fiber-based...
Full-length messenger RNA sequences greatly improve genome annotation
Haas, Brian J, Volfovsky, Natalia, Town, Christopher D, Troukhan, Maxim, Alexandrov, Nickolai, Feldmann, Kenneth A, ...
Genome-Wide Identification of Nodule-Specific Transcripts in the Model Legume Medicago truncatula1
Fedorova, Maria, Van De Mortel, Judith, Matsumoto, Peter A., Cho, Jennifer, Town, Christopher D., VandenBosch, Kathryn A., ...
The Medicago truncatula expressed sequence tag (EST) database (Gene Index) contains over 140,000 sequences from 30 cDNA libraries. This resource offers the possibility of identifying previously...
Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis1[w]
Xiao, Yong-Li, Malik, Mukesh, Whitelaw, Catherine A., Town, Christopher D.
About 25% of the genes in the fully sequenced and annotated Arabidopsis genome have structures that are predicted solely by computer algorithms with no support from either nucleic acid or protein...
Annotation of the Arabidopsis Genome1
Wortman, Jennifer R., Haas, Brian J., Hannick, Linda I., Smith, Roger K., Maiti, Rama, Ronning, Catherine M., ...
Liu, Jinyuan, Blaylock, Laura A., Endre, Gabriella, Cho, Jennifer, Town, Christopher D., VandenBosch, Kathryn A., ...
The formation of symbiotic associations with arbuscular mycorrhizal (AM) fungi is a phenomenon common to the majority of vascular flowering plants. Here, we used cDNA arrays to examine transcript...
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
Haas, Brian J., Delcher, Arthur L., Mount, Stephen M., Wortman, Jennifer R., Smith, Roger K., Hannick, Linda I., ...
The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble...
Town, Christopher D., Smith, Kendric C., Kaplan, Henry S.
Late log-phase Escherichia coli B/r cells are 1.6 times more sensitive to killing by X rays than are stationary-phase cells when grown in Brain Heart Infusion (BHI) + glucose. The number of...
Kuhl, Joseph C., Cheung, Foo, Yuan, Qiaoping, Martin, William, Zewdie, Yayeh, McCallum, John, ...
Enormous genomic resources have been developed for plants in the monocot order Poales; however, it is not clear how representative the Poales are for the monocots as a whole. The Asparagales are a...
Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray
Kim, Heenam, Snesrud, Erik C., Haas, Brian, Cheung, Foo, Town, Christopher D., Quackenbush, John
The gene predictions and accompanying functional assignments resulting from the sequencing and annotation of a genome represent hypotheses that can be tested and used to develop a more complete...
Ayele, Mulu, Haas, Brian J., Kumar, Nikhil, Wu, Hank, Xiao, Yongli, Van Aken, Susan, ...
Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea, we have identified conserved regions that represent potentially functional sequences...
Campell, Bruce R., Town, Christopher D.
To investigate the molecular mechanisms of hormonal control of growth, we constructed a subtracted cDNA library enriched for sequences expressed more in a hormone-autonomous, radiation-induced tumor...
Isolation and Characterization of a Mutant of Arabidopsis thaliana Resistant to α-Methyltryptophan 1
Kreps, Joel A., Town, Christopher D.
Mutants of Arabidopsis thaliana have been selected for resistance to growth inhibition at the seedling stage by α-methyltryptophan (aMT). One mutant, amt-1 has been characterized in detail. The...
Campell, Bruce R., Town, Christopher D.
γ-Radiation-induced tumors of Arabidopsis thaliana L. have been produced as a novel approach to isolation of genes that regulate plant development. Tumors excised from irradiated plants are hormone...
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release
Haas, Brian J, Wortman, Jennifer R, Ronning, Catherine M, Hannick, Linda I, Smith, Roger K, Maiti, Rama, ...
Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana
Mudge, Joann, Cannon, Steven B, Kalo, Peter, Oldroyd, Giles ED, Roe, Bruce A, Town, Christopher D, ...
Shultz, Jeffry L., Kurunam, Deepak, Shopinski, Kay, Iqbal, M. Javed, Kazi, Samreen, Zobrist, Kimberley, ...
Genomes that have been highly conserved following increases in ploidy (by duplication or hybridization) like Glycine max (soybean) present challenges during genome analysis. At the Soybean Genome...
Lee, Seung-Bum, Kaittanis, Charalambos, Jansen, Robert K, Hostetler, Jessica B, Tallon, Luke J, Town, Christopher D, ...
Ruhlman, Tracey, Lee, Seung-Bum, Jansen, Robert K, Hostetler, Jessica B, Tallon, Luke J, Town, Christopher D, ...
Xiao, Yong-Li, Smith, Shannon R., Ishmael, Nadeeza, Redman, Julia C., Kumar, Nihkil, Monaghan, Erin L., ...
In the fully sequenced Arabidopsis (Arabidopsis thaliana) genome, many gene models are annotated as “hypothetical protein,” whose gene structures are predicted solely by computer algorithms with...
Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology
Cheung, Foo, Haas, Brian J, Goldberg, Susanne MD, May, Gregory D, Xiao, Yongli, Town, Christopher D
Huala, Eva, Dickerman, Allan W., Garcia-Hernandez, Margarita, Weems, Danforth, Reiser, Leonore, LaFond, Frank, ...
Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic,...
Stupar, Robert M., Lilly, Jason W., Town, Christopher D., Cheng, Zhukuan, Kaul, Samir, Buell, C. Robin, ...
Previously conducted sequence analysis of Arabidopsis thaliana (ecotype Columbia-0) reported an insertion of 270-kb mtDNA into the pericentric region on the short arm of chromosome 2. DNA fiber-based...
Full-length messenger RNA sequences greatly improve genome annotation
Haas, Brian J, Volfovsky, Natalia, Town, Christopher D, Troukhan, Maxim, Alexandrov, Nickolai, Feldmann, Kenneth A, ...
Genome-Wide Identification of Nodule-Specific Transcripts in the Model Legume Medicago truncatula1
Fedorova, Maria, Van De Mortel, Judith, Matsumoto, Peter A., Cho, Jennifer, Town, Christopher D., VandenBosch, Kathryn A., ...
The Medicago truncatula expressed sequence tag (EST) database (Gene Index) contains over 140,000 sequences from 30 cDNA libraries. This resource offers the possibility of identifying previously...
Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis1[w]
Xiao, Yong-Li, Malik, Mukesh, Whitelaw, Catherine A., Town, Christopher D.
About 25% of the genes in the fully sequenced and annotated Arabidopsis genome have structures that are predicted solely by computer algorithms with no support from either nucleic acid or protein...
Annotation of the Arabidopsis Genome1
Wortman, Jennifer R., Haas, Brian J., Hannick, Linda I., Smith, Roger K., Maiti, Rama, Ronning, Catherine M., ...
Liu, Jinyuan, Blaylock, Laura A., Endre, Gabriella, Cho, Jennifer, Town, Christopher D., VandenBosch, Kathryn A., ...
The formation of symbiotic associations with arbuscular mycorrhizal (AM) fungi is a phenomenon common to the majority of vascular flowering plants. Here, we used cDNA arrays to examine transcript...
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
Haas, Brian J., Delcher, Arthur L., Mount, Stephen M., Wortman, Jennifer R., Smith, Roger K., Hannick, Linda I., ...
The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble...
Town, Christopher D., Smith, Kendric C., Kaplan, Henry S.
Late log-phase Escherichia coli B/r cells are 1.6 times more sensitive to killing by X rays than are stationary-phase cells when grown in Brain Heart Infusion (BHI) + glucose. The number of...
Kuhl, Joseph C., Cheung, Foo, Yuan, Qiaoping, Martin, William, Zewdie, Yayeh, McCallum, John, ...
Enormous genomic resources have been developed for plants in the monocot order Poales; however, it is not clear how representative the Poales are for the monocots as a whole. The Asparagales are a...
Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray
Kim, Heenam, Snesrud, Erik C., Haas, Brian, Cheung, Foo, Town, Christopher D., Quackenbush, John
The gene predictions and accompanying functional assignments resulting from the sequencing and annotation of a genome represent hypotheses that can be tested and used to develop a more complete...
Ayele, Mulu, Haas, Brian J., Kumar, Nikhil, Wu, Hank, Xiao, Yongli, Van Aken, Susan, ...
Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea, we have identified conserved regions that represent potentially functional sequences...
Campell, Bruce R., Town, Christopher D.
To investigate the molecular mechanisms of hormonal control of growth, we constructed a subtracted cDNA library enriched for sequences expressed more in a hormone-autonomous, radiation-induced tumor...
Isolation and Characterization of a Mutant of Arabidopsis thaliana Resistant to α-Methyltryptophan 1
Kreps, Joel A., Town, Christopher D.
Mutants of Arabidopsis thaliana have been selected for resistance to growth inhibition at the seedling stage by α-methyltryptophan (aMT). One mutant, amt-1 has been characterized in detail. The...
Campell, Bruce R., Town, Christopher D.
γ-Radiation-induced tumors of Arabidopsis thaliana L. have been produced as a novel approach to isolation of genes that regulate plant development. Tumors excised from irradiated plants are hormone...
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release
Haas, Brian J, Wortman, Jennifer R, Ronning, Catherine M, Hannick, Linda I, Smith, Roger K, Maiti, Rama, ...
Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana
Mudge, Joann, Cannon, Steven B, Kalo, Peter, Oldroyd, Giles ED, Roe, Bruce A, Town, Christopher D, ...
Xiao, Yong-Li, Smith, Shannon R., Ishmael, Nadeeza, Redman, Julia C., Kumar, Nihkil, Monaghan, Erin L., ...
In the fully sequenced Arabidopsis (Arabidopsis thaliana) genome, many gene models are annotated as “hypothetical protein,” whose gene structures are predicted solely by computer algorithms with...
Shultz, Jeffry L., Kurunam, Deepak, Shopinski, Kay, Iqbal, M. Javed, Kazi, Samreen, Zobrist, Kimberley, ...
Genomes that have been highly conserved following increases in ploidy (by duplication or hybridization) like Glycine max (soybean) present challenges during genome analysis. At the Soybean Genome...
Lee, Seung-Bum, Kaittanis, Charalambos, Jansen, Robert K, Hostetler, Jessica B, Tallon, Luke J, Town, Christopher D, ...