Carol Soderlund

Summary

Affiliation: University of Arizona
Country: USA

Publications

  1. pmc SyMAP: A system for discovering and viewing syntenic regions of FPC maps
    Carol Soderlund
    Arizona Genomics Computational Laboratory, The BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA
    Genome Res 16:1159-68. 2006
  2. pmc TCW: transcriptome computational workbench
    Carol Soderlund
    BIO5 Institute, University of Arizona, Tucson, Arizona, USA
    PLoS ONE 8:e69401. 2013
  3. pmc Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids
    Hyun Jo Koo
    School of Plant Sciences and BIO5 Institute, The University of Arizona, Tucson, AZ 85721, USA
    BMC Plant Biol 13:27. 2013
  4. pmc An elm EST database for identifying leaf beetle egg-induced defense genes
    Kerstin Buchel
    Freie Universitat Berlin, Applied Zoology Animal Ecology, Berlin, Germany
    BMC Genomics 13:242. 2012
  5. pmc A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat
    Yong 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
  6. doi Computational techniques for elucidating plant-pathogen interactions from large-scale experiments on fungi and oomycetes
    Carol Soderlund
    BIO5 Institute, 1657 Helen Street, University of Arizona, Tucson AZ 85721, USA
    Brief Bioinform 10:654-63. 2009
  7. ncbi MGOS: A resource for studying Magnaporthe grisea and Oryza sativa interactions
    Carol Soderlund
    Arizona Genomics Computational Laboratory, BIO5 Institute, University of Arizona, Tucson 85721, USA
    Mol Plant Microbe Interact 19:1055-61. 2006
  8. pmc Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs
    Carol Soderlund
    BIO5 Institute, University of Arizona, Tucson, Arizona, USA
    PLoS Genet 5:e1000740. 2009
  9. pmc SyMAP v3.4: a turnkey synteny system with application to plant genomes
    Carol Soderlund
    BIO5 Institute, 1657 Helen Street, University of Arizona, Tucson, AZ 85721, USA
    Nucleic Acids Res 39:e68. 2011
  10. pmc PAVE: program for assembling and viewing ESTs
    Carol Soderlund
    BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
    BMC Genomics 10:400. 2009

Collaborators

Detail Information

Publications21

  1. pmc SyMAP: A system for discovering and viewing syntenic regions of FPC maps
    Carol 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...
  2. pmc TCW: transcriptome computational workbench
    Carol 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...
  3. pmc Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids
    Hyun 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...
  4. pmc An elm EST database for identifying leaf beetle egg-induced defense genes
    Kerstin 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...
  5. pmc A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat
    Yong 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...
  6. doi Computational techniques for elucidating plant-pathogen interactions from large-scale experiments on fungi and oomycetes
    Carol 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...
  7. ncbi MGOS: A resource for studying Magnaporthe grisea and Oryza sativa interactions
    Carol 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...
  8. pmc Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs
    Carol 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)...
  9. pmc SyMAP v3.4: a turnkey synteny system with application to plant genomes
    Carol 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...
  10. pmc PAVE: program for assembling and viewing ESTs
    Carol 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...
  11. pmc Physical and genetic structure of the maize genome reflects its complex evolutionary history
    Fusheng 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...
  12. pmc Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains
    William 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...
  13. pmc 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
    ....
  14. pmc Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza
    Hyeran 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...
  15. ncbi Efficacy of clone fingerprinting methodologies
    William 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...
  16. pmc Integrating sequence with FPC fingerprint maps
    William 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...
  17. pmc FPC Web tools for rice, maize, and distribution
    Vishal Pampanwar
    Arizona Genomic Computational Laboratory, BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA
    Plant Physiol 138:116-26. 2005
    ....
  18. pmc Whole-genome validation of high-information-content fingerprinting
    William 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...
  19. pmc 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 Oryza
    Jetty S S Ammiraju
    Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721 USA
    Genome Res 16:140-7. 2006
    ....
  20. pmc Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization
    Jack 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...
  21. doi MGOS: development of a community annotation database for Magnaporthe oryzae
    Anupreet 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...