Degui Zhi

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi Identifying repeat domains in large genomes
    Degui Zhi
    Bioinformatics Program, University of California, San Diego, CA 92093 0419, USA
    Genome Biol 7:R7. 2006
  2. ncbi Correcting base-assignment errors in repeat regions of shotgun assembly
    Degui Zhi
    Bioinformatics Program, University of California, San Diego, La Jolla 92093, USA
    IEEE/ACM Trans Comput Biol Bioinform 4:54-64. 2007
  3. ncbi A novel method for multiple alignment of sequences with repeated and shuffled elements
    Benjamin Raphael
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093 0114, USA
    Genome Res 14:2336-46. 2004
  4. ncbi Representing and comparing protein structures as paths in three-dimensional space
    Degui Zhi
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 3102, USA
    BMC Bioinformatics 7:460. 2006
  5. ncbi Recombination-associated sequence homogenization of neighboring Alu elements: signature of nonallelic gene conversion
    Alexey Aleshin
    Department of Medicine, Division of Hematology, Oncology, David Geffen School of Medicine, University of California, Los Angeles, USA
    Mol Biol Evol 27:2300-11. 2010
  6. ncbi Sequence correlation between neighboring Alu instances suggests post-retrotransposition sequence exchange due to Alu gene conversion
    Degui Zhi
    Department of Plant and Microbial Biology, 461 Koshland Hall, University of California, Berkeley, CA 94720 3102, USA
    Gene 390:117-21. 2007
  7. ncbi AliWABA: alignment on the web through an A-Bruijn approach
    Neil C Jones
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
    Nucleic Acids Res 34:W613-6. 2006
  8. ncbi Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters
    Stefan Roepcke
    Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany
    Gene 365:48-56. 2006

Detail Information

Publications8

  1. ncbi Identifying repeat domains in large genomes
    Degui Zhi
    Bioinformatics Program, University of California, San Diego, CA 92093 0419, USA
    Genome Biol 7:R7. 2006
    ..Our method recovers documented mosaic repeat structures and suggests additional putative ones. Our method is useful for elucidating the evolutionary history of repeats and annotating de novo generated repeat libraries...
  2. ncbi Correcting base-assignment errors in repeat regions of shotgun assembly
    Degui Zhi
    Bioinformatics Program, University of California, San Diego, La Jolla 92093, USA
    IEEE/ACM Trans Comput Biol Bioinform 4:54-64. 2007
    ..We demonstrate that EULER-AIR is a software tool that can be used to find and correct base-assignment errors in a genome assembly project...
  3. ncbi A novel method for multiple alignment of sequences with repeated and shuffled elements
    Benjamin Raphael
    Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093 0114, USA
    Genome Res 14:2336-46. 2004
    ..In addition, ABA is useful in the alignment of genomic sequences that contain duplications and inversions. We provide several examples illustrating the applications of ABA...
  4. ncbi Representing and comparing protein structures as paths in three-dimensional space
    Degui Zhi
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 3102, USA
    BMC Bioinformatics 7:460. 2006
    ..Most existing formulations of protein structure comparison are based on detailed atomic level descriptions of protein structures and bypass potential insights that arise from a higher-level abstraction...
  5. ncbi Recombination-associated sequence homogenization of neighboring Alu elements: signature of nonallelic gene conversion
    Alexey Aleshin
    Department of Medicine, Division of Hematology, Oncology, David Geffen School of Medicine, University of California, Los Angeles, USA
    Mol Biol Evol 27:2300-11. 2010
    ..We believe that these observations help to illuminate the nature and impact of the enigmatic phenomenon of gene conversion...
  6. ncbi Sequence correlation between neighboring Alu instances suggests post-retrotransposition sequence exchange due to Alu gene conversion
    Degui Zhi
    Department of Plant and Microbial Biology, 461 Koshland Hall, University of California, Berkeley, CA 94720 3102, USA
    Gene 390:117-21. 2007
    ..Our results suggest that this effect reflects post-retrotransposition sequence exchanges between Alu instances, mainly due to Alu gene conversions...
  7. ncbi AliWABA: alignment on the web through an A-Bruijn approach
    Neil C Jones
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
    Nucleic Acids Res 34:W613-6. 2006
    ..To facilitate the analysis of protein domains, AliWABA provides direct querying of the Conserved Domain Database. Availability: http://aba.nbcr.net/..
  8. ncbi Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters
    Stefan Roepcke
    Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany
    Gene 365:48-56. 2006
    ..Such a factor binds the target DNA at a fixed location relative to the TSS, and possibly interacts directly with the basal transcription machinery...