Shiguo Zhou

Summary

Affiliation: University of Wisconsin
Country: USA

Publications

  1. pmc Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4.1 and its use for whole-genome shotgun sequence assembly
    Shiguo Zhou
    Laboratory for Molecular and Computational Genomics, University of Wisconsin Madison, UW Biotechnology Center, Madison, Wisconsin 53706, USA
    Genome Res 13:2142-51. 2003
  2. pmc Validation of rice genome sequence by optical mapping
    Shiguo Zhou
    Laboratory for Molecular and Computational Genomics, University of Wisconsin Madison, UW Biotechnology Centre, 425 Henry Mall, Madison, Wisconsin 53706, USA
    BMC Genomics 8:278. 2007
  3. pmc AGORA: Assembly Guided by Optical Restriction Alignment
    Henry C Lin
    Center for Bioinformatics and Computational Biology, University of Maryland College Park, College Park, MD, USA
    BMC Bioinformatics 13:189. 2012
  4. pmc Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association
    John P Bannantine
    National Animal Disease Center, USDA Agricultural Research Service, Ames, Iowa, USA
    BMC Genomics 13:89. 2012
  5. pmc Whole-genome shotgun optical mapping of Rhodospirillum rubrum
    Susan Reslewic
    Laboratory for Molecular and Computational Genomics, University of Wisconsin Madison, UW Biotechnology Center, 425 Henry Mall, Madison, WI 53706, USA
    Appl Environ Microbiol 71:5511-22. 2005
  6. pmc A single molecule scaffold for the maize genome
    Shiguo Zhou
    Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin Madison, Madison, Wisconsin, United States of America
    PLoS Genet 5:e1000711. 2009
  7. pmc Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis
    Mohana Ray
    Department of Chemistry, UW Biotechnology Center, University of Wisconsin Madison, Madison, WI 53706, USA
    BMC Genomics 14:505. 2013
  8. pmc Single-molecule approach to bacterial genomic comparisons via optical mapping
    Shiguo Zhou
    Laboratory for Molecular and Computation Genomics, University of Wisconsin Madison, Madison, WI 53706, USA
    J Bacteriol 186:7773-82. 2004
  9. ncbi request reprint Shotgun optical mapping of the entire Leishmania major Friedlin genome
    Shiguo Zhou
    Laboratory for Molecular and Computational Genomics, UW Biotechnology Center, University of Wisconsin Madison, 425 Henry Mall, Madison, WI 53706, USA
    Mol Biochem Parasitol 138:97-106. 2004
  10. pmc Optical mapping discerns genome wide DNA methylation profiles
    Gene E Ananiev
    Department of Chemistry, Laboratory for Molecular and Computational Genomics, University of Wisconsin Biotechnology Center, University of Wisconsin Madison, Madison, WI 53706, USA
    BMC Mol Biol 9:68. 2008

Collaborators

Detail Information

Publications18

  1. pmc Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4.1 and its use for whole-genome shotgun sequence assembly
    Shiguo Zhou
    Laboratory for Molecular and Computational Genomics, University of Wisconsin Madison, UW Biotechnology Center, Madison, Wisconsin 53706, USA
    Genome Res 13:2142-51. 2003
    ..Our results show that such maps facilitated the closure of sequence gaps by the early detection of nascent sequence contigs during the course of the whole-genome shotgun sequencing process...
  2. pmc Validation of rice genome sequence by optical mapping
    Shiguo Zhou
    Laboratory for Molecular and Computational Genomics, University of Wisconsin Madison, UW Biotechnology Centre, 425 Henry Mall, Madison, Wisconsin 53706, USA
    BMC Genomics 8:278. 2007
    ..Although the rice genome is sequenced, validation and gap closing efforts require purely independent means for accurate finishing of sequence build data...
  3. pmc AGORA: Assembly Guided by Optical Restriction Alignment
    Henry C Lin
    Center for Bioinformatics and Computational Biology, University of Maryland College Park, College Park, MD, USA
    BMC Bioinformatics 13:189. 2012
    ....
  4. pmc Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association
    John P Bannantine
    National Animal Disease Center, USDA Agricultural Research Service, Ames, Iowa, USA
    BMC Genomics 13:89. 2012
    ..To systematically characterize all genomic differences that may be associated with the specific hosts, we sequenced the genomes of three U.S. sheep isolates and also obtained an optical map...
  5. pmc Whole-genome shotgun optical mapping of Rhodospirillum rubrum
    Susan Reslewic
    Laboratory for Molecular and Computational Genomics, University of Wisconsin Madison, UW Biotechnology Center, 425 Henry Mall, Madison, WI 53706, USA
    Appl Environ Microbiol 71:5511-22. 2005
    ..With a resolution ranging from 6.5 kb (previously published) to 45 kb (reported here), optical mapping advances a "molecular cytogenetics" approach to solving problems in genomic analysis...
  6. pmc A single molecule scaffold for the maize genome
    Shiguo Zhou
    Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin Madison, Madison, Wisconsin, United States of America
    PLoS Genet 5:e1000711. 2009
    ....
  7. pmc Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis
    Mohana Ray
    Department of Chemistry, UW Biotechnology Center, University of Wisconsin Madison, Madison, WI 53706, USA
    BMC Genomics 14:505. 2013
    ..In this context, high throughput, single molecule platforms like Optical Mapping offer a unique perspective...
  8. pmc Single-molecule approach to bacterial genomic comparisons via optical mapping
    Shiguo Zhou
    Laboratory for Molecular and Computation Genomics, University of Wisconsin Madison, Madison, WI 53706, USA
    J Bacteriol 186:7773-82. 2004
    ..Our results suggest that genomic rearrangements and chromosomal breakpoints are readily identified and annotated against a prototypic sequenced strain by using the tools of optical mapping...
  9. ncbi request reprint Shotgun optical mapping of the entire Leishmania major Friedlin genome
    Shiguo Zhou
    Laboratory for Molecular and Computational Genomics, UW Biotechnology Center, University of Wisconsin Madison, 425 Henry Mall, Madison, WI 53706, USA
    Mol Biochem Parasitol 138:97-106. 2004
    ..Our results also showed the potential use of optical maps as a means to detect and characterize map segmental duplication within genomes...
  10. pmc Optical mapping discerns genome wide DNA methylation profiles
    Gene E Ananiev
    Department of Chemistry, Laboratory for Molecular and Computational Genomics, University of Wisconsin Biotechnology Center, University of Wisconsin Madison, Madison, WI 53706, USA
    BMC Mol Biol 9:68. 2008
    ..In this regard, a single molecule approach to methylation profiling offers several unique advantages that include elimination of chemical DNA modification steps and PCR amplification...
  11. pmc High-resolution human genome structure by single-molecule analysis
    Brian Teague
    The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706 1580, USA
    Proc Natl Acad Sci U S A 107:10848-53. 2010
    ..We also describe thousands of new variants with sizes ranging from kb to Mb...
  12. pmc Optical mapping of the Mycobacterium avium subspecies paratuberculosis genome
    Chia Wei Wu
    The Laboratory of Bacterial Genomics, Department of Pathobiological Sciences, University of Wisconsin Madison, WI, USA
    BMC Genomics 10:25. 2009
    ..In an effort to better examine diversity among M. ap strains, we used optical mapping to profile genomic variations between strains of M. ap K-10 (sequenced strain) and M. ap ATCC 19698 (type strain)...
  13. pmc Genome sequence of Yersinia pestis KIM
    Wen Deng
    Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
    J Bacteriol 184:4601-11. 2002
    ..In KIM-specific islands, new genes encode candidate pathogenicity proteins, including iron transport systems, putative adhesins, toxins, and fimbriae...
  14. pmc A whole-genome shotgun optical map of Yersinia pestis strain KIM
    Shiguo Zhou
    Laboratory for Molecular and Computational Genomics, University of Wisconsin Madison, 53706, USA
    Appl Environ Microbiol 68:6321-31. 2002
    ..Given the recent advancements to the optical mapping system, increased resolution and throughput are enabling such maps to guide sequence assembly at a very early stage of a microbial sequencing project...
  15. pmc The genome of the kinetoplastid parasite, Leishmania major
    Alasdair C Ivens
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Science 309:436-42. 2005
    ..Abundant RNA-binding proteins are encoded in the Tritryp genomes, consistent with active posttranscriptional regulation of gene expression...
  16. ncbi request reprint The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism
    E Virginia Armbrust
    School of Oceanography, University of Washington, Seattle, WA 98195, USA
    Science 306:79-86. 2004
    ....
  17. pmc The sequence and analysis of Trypanosoma brucei chromosome II
    Najib M A El-Sayed
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Nucleic Acids Res 31:4856-63. 2003
    ....
  18. pmc An algorithm for assembly of ordered restriction maps from single DNA molecules
    Anton Valouev
    Department of Mathematics, University of Southern California, 3620 South Vermont Avenue, KAP 108, Los Angeles, CA 90089 2532, USA
    Proc Natl Acad Sci U S A 103:15770-5. 2006
    ....