Affiliation: University of Wisconsin
- Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4.1 and its use for whole-genome shotgun sequence assemblyShiguo 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...
- Validation of rice genome sequence by optical mappingShiguo 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...
- An improved genome release (version Mt4.0) for the model legume Medicago truncatulaHaibao Tang
J, Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD, USA
BMC Genomics 15:312. 2014..The initial sequencing approach was based on a BAC tiling path, culminating in a BAC-based assembly (Mt3.5) as well as an in-depth analysis of the genome published in 2011...
- AGORA: Assembly Guided by Optical Restriction AlignmentHenry C Lin
Center for Bioinformatics and Computational Biology, University of Maryland College Park, College Park, MD, USA
BMC Bioinformatics 13:189. 2012....
- Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host associationJohn 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...
- Whole-genome shotgun optical mapping of Rhodospirillum rubrumSusan 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...
- A single molecule scaffold for the maize genomeShiguo 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....
- Single-molecule approach to bacterial genomic comparisons via optical mappingShiguo 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...
- Shotgun optical mapping of the entire Leishmania major Friedlin genomeShiguo 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...
- Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysisMohana 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...
- Optical mapping discerns genome wide DNA methylation profilesGene 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...
- High-resolution human genome structure by single-molecule analysisBrian 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...
- Optical mapping of the Mycobacterium avium subspecies paratuberculosis genomeChia 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)...
- Genome sequence of Yersinia pestis KIMWen 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...
- A whole-genome shotgun optical map of Yersinia pestis strain KIMShiguo 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...
- The genome of the kinetoplastid parasite, Leishmania majorAlasdair 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...
- The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolismE Virginia Armbrust
School of Oceanography, University of Washington, Seattle, WA 98195, USA
Science 306:79-86. 2004....
- The sequence and analysis of Trypanosoma brucei chromosome IINajib M A El-Sayed
The Institute for Genomic Research, Rockville, MD 20850, USA
Nucleic Acids Res 31:4856-63. 2003....
- An algorithm for assembly of ordered restriction maps from single DNA moleculesAnton 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....