Carol Soderlund

Summary

Affiliation: University of Arizona
Country: USA

Publications

  1. ncbi 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. ncbi 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
  3. ncbi 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
  4. ncbi 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
  5. ncbi PAVE: program for assembling and viewing ESTs
    Carol Soderlund
    BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
    BMC Genomics 10:400. 2009
  6. ncbi 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
  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. ncbi 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
  9. ncbi 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
  10. ncbi 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

Collaborators

Detail Information

Publications18

  1. ncbi 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. ncbi 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...
  3. ncbi 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)...
  4. ncbi 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...
  5. ncbi 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...
  6. ncbi 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...
  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. ncbi 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...
  9. ncbi 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
    ....
  10. ncbi 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...
  11. ncbi 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...
  12. 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...
  13. ncbi 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...
  14. ncbi 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
    ....
  15. ncbi 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
    ....
  16. ncbi 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...
  17. ncbi 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...
  18. ncbi 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...