Yuzhen Ye

Summary

Affiliation: The Burnham Institute
Country: USA

Publications

  1. pmc Integrated web service for improving alignment quality based on segments comparison
    Dariusz Plewczynski
    Bioinformatics Laboratory, BioInfoBank Institute, Poznan, Poland
    BMC Bioinformatics 5:98. 2004
  2. ncbi request reprint Multiple flexible structure alignment using partial order graphs
    Yuzhen Ye
    Program in Bioinformatics and Systems Biology, The Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
    Bioinformatics 21:2362-9. 2005
  3. ncbi request reprint Automatic detection of subsystem/pathway variants in genome analysis
    Yuzhen Ye
    Program in Bioinformatics and Systems Biology, The Burnham Institute 10901 N Torrey Pines Road, La Jolla CA 92037, USA
    Bioinformatics 21:i478-86. 2005
  4. pmc Database searching by flexible protein structure alignment
    Yuzhen Ye
    Program in Bioinformatics and Systems Biology, The Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
    Protein Sci 13:1841-50. 2004
  5. pmc FATCAT: a web server for flexible structure comparison and structure similarity searching
    Yuzhen Ye
    The Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
    Nucleic Acids Res 32:W582-5. 2004
  6. pmc Novel genes dramatically alter regulatory network topology in amphioxus
    Qing Zhang
    Burnham Institute for Medical Research, North Torrey Pines Road, La Jolla, CA 92037, USA
    Genome Biol 9:R123. 2008
  7. pmc TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model
    Mallika Veeramalai
    Joint Center for Molecular Modeling, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
    BMC Bioinformatics 9:358. 2008
  8. pmc Flexible Structural Neighborhood--a database of protein structural similarities and alignments
    Zhanwen Li
    The Burnham Institute, La Jolla, CA, USA
    Nucleic Acids Res 34:D277-80. 2006
  9. ncbi request reprint Flexible structure alignment by chaining aligned fragment pairs allowing twists
    Yuzhen Ye
    Program in Bioinformatics and Systems Biology, The Burnham Institute, La Jolla, CA 92037, USA
    Bioinformatics 19:ii246-55. 2003
  10. ncbi request reprint A segment alignment approach to protein comparison
    Yuzhen Ye
    The Burnham Institute, La Jolla, CA 92037, USA
    Bioinformatics 19:742-9. 2003

Detail Information

Publications20

  1. pmc Integrated web service for improving alignment quality based on segments comparison
    Dariusz Plewczynski
    Bioinformatics Laboratory, BioInfoBank Institute, Poznan, Poland
    BMC Bioinformatics 5:98. 2004
    ..Structural comparison is able to detect approximately twice as many distant relationships as sequence comparison at the same error rate...
  2. ncbi request reprint Multiple flexible structure alignment using partial order graphs
    Yuzhen Ye
    Program in Bioinformatics and Systems Biology, The Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
    Bioinformatics 21:2362-9. 2005
    ..Understanding the structural divergence and flexibility is critical for studying the evolution of functions and specificities of proteins...
  3. ncbi request reprint Automatic detection of subsystem/pathway variants in genome analysis
    Yuzhen Ye
    Program in Bioinformatics and Systems Biology, The Burnham Institute 10901 N Torrey Pines Road, La Jolla CA 92037, USA
    Bioinformatics 21:i478-86. 2005
    ..However, no computational techniques are presently available for an automated detection and analysis of subsystem variants...
  4. pmc Database searching by flexible protein structure alignment
    Yuzhen Ye
    Program in Bioinformatics and Systems Biology, The Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
    Protein Sci 13:1841-50. 2004
    ....
  5. pmc FATCAT: a web server for flexible structure comparison and structure similarity searching
    Yuzhen Ye
    The Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
    Nucleic Acids Res 32:W582-5. 2004
    ..In addition, FATCAT server can report the conformational changes of the query structure as compared to other proteins in the structure database. FATCAT server is available at http://fatcat.burnham.org...
  6. pmc Novel genes dramatically alter regulatory network topology in amphioxus
    Qing Zhang
    Burnham Institute for Medical Research, North Torrey Pines Road, La Jolla, CA 92037, USA
    Genome Biol 9:R123. 2008
    ....
  7. pmc TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model
    Mallika Veeramalai
    Joint Center for Molecular Modeling, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
    BMC Bioinformatics 9:358. 2008
    ..Such intuitions could help speed up similarity searches and make it easier to understand the results of such analyses...
  8. pmc Flexible Structural Neighborhood--a database of protein structural similarities and alignments
    Zhanwen Li
    The Burnham Institute, La Jolla, CA, USA
    Nucleic Acids Res 34:D277-80. 2006
    ..FSN is available from a server http://fatcat.burnham.org/fatcat/struct_neighbor and by direct links from the PDB database...
  9. ncbi request reprint Flexible structure alignment by chaining aligned fragment pairs allowing twists
    Yuzhen Ye
    Program in Bioinformatics and Systems Biology, The Burnham Institute, La Jolla, CA 92037, USA
    Bioinformatics 19:ii246-55. 2003
    ....
  10. ncbi request reprint A segment alignment approach to protein comparison
    Yuzhen Ye
    The Burnham Institute, La Jolla, CA 92037, USA
    Bioinformatics 19:742-9. 2003
    ..However, predicted or real LSSs are rarely exploited by protein sequence comparison programs that are based on position-by-position alignments...
  11. pmc Comparative analysis of protein domain organization
    Yuzhen Ye
    Program in Bioinformatics and Systems Biology, The Burnham Institute, La Jolla, California 92037, USA
    Genome Res 14:343-53. 2004
    ..Finally, we report on the specific domain combinations characterizing the three kingdoms of life, and the kingdom "signature" domain organizations derived from those specific domain combinations...
  12. pmc Surprising complexity of the ancestral apoptosis network
    Christian M Zmasek
    Burnham Institute for Medical Research, North Torrey Pines Road, La Jolla, CA 92037, USA
    Genome Biol 8:R226. 2007
    ....
  13. pmc Homology modeling provides insights into the binding mode of the PAAD/DAPIN/pyrin domain, a fourth member of the CARD/DD/DED domain family
    Tong Liu
    The Burnham Institute, La Jolla, California 92037, USA
    Protein Sci 12:1872-81. 2003
    ..Multiple alignment analysis and modeling suggest that it may be partly disordered, following a new paradigm for interaction proteins that are stabilized by protein-protein interactions...
  14. ncbi request reprint The interplay of fold recognition and experimental structure determination in structural genomics
    Iddo Friedberg
    The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
    Curr Opin Struct Biol 14:307-12. 2004
    ..However, problems that surfaced during the first few years of active work have put many of the early estimates in doubt and new ones are still slow in coming...
  15. ncbi request reprint POSA: a user-driven, interactive multiple protein structure alignment server
    Zhanwen Li
    Bioinformatics and Systems Biology, Sanford Burnham Medical Research Institute, La Jolla, CA 92037, USA
    Nucleic Acids Res 42:W240-5. 2014
    ..The user can rotate structure(s) in any of the windows and study similarities or differences between structures clearly visible in individual windows. ..
  16. ncbi request reprint Subunit-specific roles of glycine-binding domains in activation of NR1/NR3 N-methyl-D-aspartate receptors
    Marc Awobuluyi
    Burnham Institute for Medical Research, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
    Mol Pharmacol 71:112-22. 2007
    ..NR3 subunits thus induce plasticity in NR1 with respect to subunit assembly and ligand binding/channel coupling that is unique among ligand-gated ion channel subunits...
  17. pmc The amphioxus genome illuminates vertebrate origins and cephalochordate biology
    Linda Z Holland
    Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California 92093 0202, USA
    Genome Res 18:1100-11. 2008
    ..Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates...
  18. pmc The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
    Ross Overbeek
    Fellowship for Interpretation of Genomes, 15W155 81st Street, Burr Ridge, IL 60527, USA
    Nucleic Acids Res 33:5691-702. 2005
    ..The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms...
  19. ncbi request reprint Genetic variation analysis within and among six varieties of common carp (Cyprinus carpio L.) in China using microsatellite markers
    Jianfeng Zhou
    State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
    Genetika 40:1389-93. 2004
    ..However, among six populations Japanese decorative carp displayed the highest level of variability in terms of heterozygosity...
  20. ncbi request reprint Geographic distribution of Pelteobagrus fulvidraco and Pelteobagrus vachelli in the Yangtze River based on mitochondrial DNA markers
    Zhongwei Wang
    Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P R China
    Biochem Genet 42:391-400. 2004
    ..Genetic diversity of P. fulvidraco was low and only five haplotyes were detected from all 60 samples. Phylogenic relationships also indicated that the fishes from upstream and mid-downstream were apparently divided into two populations...