Weizhong Li

Summary

Publications

  1. ncbi request reprint Discovering new genes with advanced homology detection
    Weizhong Li
    Quorex Pharmaceuticals, 1890 Rutherford Road, Suite 200, Carlsbad CA 92008, USA
    Trends Biotechnol 20:315-6. 2002
  2. ncbi request reprint Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    Weizhong Li
    Burnham Institute for Medical Research La Jolla, CA 92037, USA
    Bioinformatics 22:1658-9. 2006
  3. ncbi request reprint Tolerating some redundancy significantly speeds up clustering of large protein databases
    Weizhong Li
    The Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
    Bioinformatics 18:77-82. 2002
  4. pmc Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering
    Shibu Yooseph
    J, Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    BMC Bioinformatics 9:182. 2008
  5. ncbi request reprint Crystal structure of the tetrameric inositol 1-phosphate phosphatase (TM1415) from the hyperthermophile, Thermotoga maritima
    Kimberly A Stieglitz
    Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
    FEBS J 274:2461-9. 2007
  6. ncbi request reprint VISSA: a program to visualize structural features from structure sequence alignment
    Weizhong Li
    Burnham Institute for Medical Research, La Jolla, CA 92037, USA
    Bioinformatics 22:887-8. 2006
  7. pmc FFAS03: a server for profile--profile sequence alignments
    Lukasz Jaroszewski
    Bioinformatics Program, The Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
    Nucleic Acids Res 33:W284-8. 2005
  8. pmc Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate
    Andrew Y Gracey
    School of Biological Sciences, University of Liverpool, Biosciences Building, Crown Street, Liverpool L39 7ZB, United Kindgom
    Proc Natl Acad Sci U S A 101:16970-5. 2004
  9. 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
  10. ncbi request reprint Sequence clustering strategies improve remote homology recognitions while reducing search times
    Weizhong Li
    The Burnham Institute, La Jolla, CA 92037, USA
    Protein Eng 15:643-9. 2002

Collaborators

Detail Information

Publications13

  1. ncbi request reprint Discovering new genes with advanced homology detection
    Weizhong Li
    Quorex Pharmaceuticals, 1890 Rutherford Road, Suite 200, Carlsbad CA 92008, USA
    Trends Biotechnol 20:315-6. 2002
    ..Alternative approaches involving more sensitive homology recognition methods are playing an increasingly important role in the next stage of gene discovery. The hunt for new genes is far from over...
  2. ncbi request reprint Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    Weizhong Li
    Burnham Institute for Medical Research La Jolla, CA 92037, USA
    Bioinformatics 22:1658-9. 2006
    ..All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST...
  3. ncbi request reprint Tolerating some redundancy significantly speeds up clustering of large protein databases
    Weizhong Li
    The Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
    Bioinformatics 18:77-82. 2002
    ..Bioinformatics, 17, 282, 2001); however even faster clustering speed is needed because the size of protein databases are rapidly growing and many applications desire a lower attainable thresholds...
  4. pmc Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering
    Shibu Yooseph
    J, Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
    BMC Bioinformatics 9:182. 2008
    ..and consequently gene identification is challenging. The vast amount of sequence data also requires faster protein family classification tools...
  5. ncbi request reprint Crystal structure of the tetrameric inositol 1-phosphate phosphatase (TM1415) from the hyperthermophile, Thermotoga maritima
    Kimberly A Stieglitz
    Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
    FEBS J 274:2461-9. 2007
    ..Two of the subunits have the active site loop folded into a beta-hairpin structure, whereas in the remaining two subunits the same loop adopts an alpha-helical conformation...
  6. ncbi request reprint VISSA: a program to visualize structural features from structure sequence alignment
    Weizhong Li
    Burnham Institute for Medical Research, La Jolla, CA 92037, USA
    Bioinformatics 22:887-8. 2006
    ..This program, called Visualize Structure Sequence Alignment, also has many other built-in tools that can help analyze multiple sequence alignments. AVAILABILITY: http://bioinformatics.burnham.org/liwz/vissa CONTACT: liwz@burnham.org...
  7. pmc FFAS03: a server for profile--profile sequence alignments
    Lukasz Jaroszewski
    Bioinformatics Program, The Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
    Nucleic Acids Res 33:W284-8. 2005
    ..Access to the server is open for both academic and commercial researchers. The FFAS03 server is available at http://ffas.burnham.org...
  8. pmc Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate
    Andrew Y Gracey
    School of Biological Sciences, University of Liverpool, Biosciences Building, Crown Street, Liverpool L39 7ZB, United Kindgom
    Proc Natl Acad Sci U S A 101:16970-5. 2004
    ....
  9. 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...
  10. ncbi request reprint Sequence clustering strategies improve remote homology recognitions while reducing search times
    Weizhong Li
    The Burnham Institute, La Jolla, CA 92037, USA
    Protein Eng 15:643-9. 2002
    ..All methods are evaluated with a large fold-recognition benchmark...
  11. ncbi request reprint Cloning and characterization of glucose transporter 11, a novel sugar transporter that is alternatively spliced in various tissues
    Xiaohua Wu
    The Burnham Institute, La Jolla, CA 92037, USA
    Mol Genet Metab 76:37-45. 2002
    ..Furthermore, a liposome reconstitution functional assay showed that GLUT11-L has glucose transport activity...
  12. pmc In search for more accurate alignments in the twilight zone
    Lukasz Jaroszewski
    Program in Bioinformatics and Biological Complexity, The Burnham Institute, 10901 N Torrey Pines Road, La Jolla, CA 92037, USA
    Protein Sci 11:1702-13. 2002
    ..We combined their best features and produced a hybrid method, which yielded alignments that surpassed the original alignments for about 50% of protein pairs with minimal computational effort...
  13. pmc Probing metagenomics by rapid cluster analysis of very large datasets
    Weizhong Li
    California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, California, USA
    PLoS ONE 3:e3375. 2008
    ..2007 PLoS Biol 5, e16). Such datasets, not only by their sheer size, but also by many other features, defy conventional analysis and annotation methods...