William M Nelson
Affiliation: University of Arizona
- 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...
- 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...
- 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...
- 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...
- 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...
- Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate caveMarianyoly Ortiz
Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, USA
ISME J 8:478-91. 2014..These strategies may provide key insights into other ecosystems dominated by oligotrophy, including aphotic subsurface soils or aquifers and photic systems such as arid deserts. ..
- Profiling bacterial diversity and taxonomic composition on speleothem surfaces in Kartchner Caverns, AZMarianyoly Ortiz
Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ 85721 0038, USA
Microb Ecol 65:371-83. 2013....
- 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...
- 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...
- 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...
- Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expressionCarol A Soderlund
BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
PLoS ONE 9:e115740. 2014..google.com/p/allele-workbench. Additionally, all software is ready for immediate use from an Atmosphere Virtual Machine Image available from the iPlant Collaborative (www.iplantcollaborative.org). ..
- Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, ChileJulia W Neilson
Department of Soil, Water and Environmental Science, University of Arizona, Shantz Bldg Room 429, P O Box 210038, Tucson, AZ 85721 0038, USA
Extremophiles 16:553-66. 2012....