Affiliation: University of Arizona
- SyMAP: A system for discovering and viewing syntenic regions of FPC mapsCarol Soderlund
Arizona Genomics Computational Laboratory, The BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA
Genome Res 16:1159-68. 2006..The Web-based graphics uses Java for a highly interactive display that allows the user to interrogate the evidence of synteny...
- A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvementRuifeng He
Institute of Biological Chemistry, Washington State University, PO Box 646340, Pullman, WA 99164, USA
BMC Plant Biol 14:46. 2014..Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant...
- TCW: transcriptome computational workbenchCarol Soderlund
BIO5 Institute, University of Arizona, Tucson, Arizona, USA
PLoS ONE 8:e69401. 2013..Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility...
- Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoidsHyun Jo Koo
School of Plant Sciences and BIO5 Institute, The University of Arizona, Tucson, AZ 85721, USA
BMC Plant Biol 13:27. 2013..Despite their importance, relatively little is known regarding gene expression in the rhizomes of ginger and turmeric...
- An elm EST database for identifying leaf beetle egg-induced defense genesKerstin Buchel
Freie Universitat Berlin, Applied Zoology Animal Ecology, Berlin, Germany
BMC Genomics 13:242. 2012..Little is known about the transcriptional changes that insect eggs trigger in plants and how such indirect defense mechanisms are orchestrated in the context of other biological processes...
- A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheatYong Q Gu
1Genomics and Gene Discovery Research Unit, USDA ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
BMC Genomics 10:496. 2009..A BAC-based physical map is one of them. A physical map will facilitate analysis of genome structure, comparative genomics, and assembly of the entire genome sequence...
- Computational techniques for elucidating plant-pathogen interactions from large-scale experiments on fungi and oomycetesCarol Soderlund
BIO5 Institute, 1657 Helen Street, University of Arizona, Tucson AZ 85721, USA
Brief Bioinform 10:654-63. 2009..It discusses how various emerging approaches will increase the power of computers in host-pathogen interaction studies...
- PAVE: program for assembling and viewing ESTsCarol Soderlund
BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
BMC Genomics 10:400. 2009..The new 454 technology has the benefit of high-throughput expression profiling, but introduces time and space problems for assembling large contigs...
- SyMAP v3.4: a turnkey synteny system with application to plant genomesCarol Soderlund
BIO5 Institute, 1657 Helen Street, University of Arizona, Tucson, AZ 85721, USA
Nucleic Acids Res 39:e68. 2011..A project manager is provided to organize and automate the analysis of multi-genome groups. The software is freely distributed at http://www.agcol.arizona.edu/software/symap...
- Sequencing, mapping, and analysis of 27,455 maize full-length cDNAsCarol Soderlund
BIO5 Institute, University of Arizona, Tucson, Arizona, USA
PLoS Genet 5:e1000740. 2009..The libraries, ESTs, and FLcDNA sequences produced from this project are publicly available. The annotated EST and FLcDNA assemblies are available through the maize FLcDNA web resource (www.maizecdna.org)...
- MGOS: A resource for studying Magnaporthe grisea and Oryza sativa interactionsCarol Soderlund
Arizona Genomics Computational Laboratory, BIO5 Institute, University of Arizona, Tucson 85721, USA
Mol Plant Microbe Interact 19:1055-61. 2006..grisea genomic sequence. Community-based annotation is available for the M. grisea genes to aid in the study of the interactions...
- Physical and genetic structure of the maize genome reflects its complex evolutionary historyFusheng Wei
Arizona Genomics Institute, University of Arizona, Tucson, Arizona, United States of America
PLoS Genet 3:e123. 2007..Reconstructing the paleoethnobotany of the maize genome indicates that the progenitors of modern maize contained ten chromosomes...
- Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domainsWilliam Nelson
Arizona Genomics Computational Laboratory, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
BMC Genomics 9:621. 2008..These libraries differ from other gene-rich datasets in having larger insert sizes, and the MSLL clones are designed to provide reads localized to "epigenetic boundaries" where methylation begins or ends...
- Comparative physical mapping between Oryza sativa (AA genome type) and O. punctata (BB genome type)Hyeran Kim
Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721, USA
Genetics 176:379-90. 2007....
- Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus OryzaHyeran Kim
Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
Genome Biol 9:R45. 2008..sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date...
- Efficacy of clone fingerprinting methodologiesWilliam M Nelson
Arizona Genomics Computational Laboratory, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
Genomics 89:160-5. 2007..Our data indicate that the five-enzyme method known as SNaPshot is the most effective and that the assembly can in fact be significantly improved with greater than 10x coverage...
- Integrating sequence with FPC fingerprint mapsWilliam Nelson
Arizona Genomics Computational Laboratory, BIO5 Institute, University of Arizona, Tucson, AZ, USA
Nucleic Acids Res 37:e36. 2009..Simulation results are provided for the MTP, DSI and parallelization. These features are in the FPC V9.3 software package, which is freely available...
- MGOS: development of a community annotation database for Magnaporthe oryzaeAnupreet Kour
School of Plant Sciences, Division of Plant Pathology and Microbiology, The University of Arizona, Tucson 85721, USA
Mol Plant Microbe Interact 25:271-8. 2012..Thus far, 362 M. oryzae genes have associated information on mutants. MGOS is now poised to become a one-stop repository for all structural and functional data available on all genes of this critically important rice pathogen...
- FPC Web tools for rice, maize, and distributionVishal Pampanwar
Arizona Genomic Computational Laboratory, BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA
Plant Physiol 138:116-26. 2005....
- The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus OryzaJetty S S Ammiraju
Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721 USA
Genome Res 16:140-7. 2006....
- Whole-genome validation of high-information-content fingerprintingWilliam M Nelson
Arizona Genomics Computational Laboratory, BIO5 Institute, University of Arizona, Tucson, 85721, USA
Plant Physiol 139:27-38. 2005..Finally, repetitive bands are isolated, and their effect on the assembly is studied...
- Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridizationJack Gardiner
Department of Agronomy, University of Missouri, Columbia, Missouri 65211, USA
Plant Physiol 134:1317-26. 2004..Our results indicate overgos are a powerful approach for generating gene-specific hybridization probes that are facilitating the assembly of an integrated genetic and physical map for maize...