Weizhong Li

Summary

Affiliation: The Burnham Institute
Country: USA

Publications

  1. 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
  2. pmc MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data
    Zhengwei Zhu
    Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093, USA
    Bioinformatics 29:122-3. 2013
  3. pmc CD-HIT: accelerated for clustering the next-generation sequencing data
    Limin Fu
    Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093, USA
    Bioinformatics 28:3150-2. 2012
  4. pmc Artificial and natural duplicates in pyrosequencing reads of metagenomic data
    Beifang Niu
    California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, California 92093, USA
    BMC Bioinformatics 11:187. 2010
  5. 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
  6. 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
  7. 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
  8. pmc WebMGA: a customizable web server for fast metagenomic sequence analysis
    Sitao Wu
    Center for Research in Biological Systems, University of California San Diego, La Jolla, California 92093, USA
    BMC Genomics 12:444. 2011
  9. 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
  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

Publications25

  1. 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...
  2. pmc MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data
    Zhengwei Zhu
    Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093, USA
    Bioinformatics 29:122-3. 2013
    ..This viewer is easy to use on all computer systems with modern web browsers and requires no software installation...
  3. pmc CD-HIT: accelerated for clustering the next-generation sequencing data
    Limin Fu
    Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093, USA
    Bioinformatics 28:3150-2. 2012
    ..The enhanced CD-HIT is capable of handling very large datasets in much shorter time than previous versions...
  4. pmc Artificial and natural duplicates in pyrosequencing reads of metagenomic data
    Beifang Niu
    California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, California 92093, USA
    BMC Bioinformatics 11:187. 2010
    ..However, since the duplicated reads observed in a pyrosequencing run also include natural (non-artificial) duplicates, simply removing all duplicates may also cause underestimation of abundance associated with natural duplicates...
  5. 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...
  6. 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...
  7. 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...
  8. pmc WebMGA: a customizable web server for fast metagenomic sequence analysis
    Sitao Wu
    Center for Research in Biological Systems, University of California San Diego, La Jolla, California 92093, USA
    BMC Genomics 12:444. 2011
    ..The tools provided by the few available web servers are also limited and have various constraints such as login requirement, long waiting time, inability to configure pipelines etc...
  9. 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...
  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. pmc CD-HIT Suite: a web server for clustering and comparing biological sequences
    Ying Huang
    California Institute for Telecommunications and Information Technology, University of California San Diego, La Jolla, CA, USA
    Bioinformatics 26:680-2. 2010
    ..Users can now interactively explore the clusters within web browsers. We also provide downloadable clusters for several public databases (NCBI NR, Swissprot and PDB) at different identity levels...
  12. pmc FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes
    Beifang Niu
    Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA
    Bioinformatics 27:1704-5. 2011
    ..FR-HIT is slower than the fastest SOAP2, BWA and BWA-SW, but it recruited 1-5 times more reads...
  13. pmc Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families
    Kyle Ellrott
    Joint Center for Structural Genomics, Bioinformatics Core, University of California San Diego, La Jolla, California, USA
    PLoS Comput Biol 6:e1000798. 2010
    ..The identification and analysis of these families could provide us with new information about an environment critical to our health and well being...
  14. 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...
  15. pmc Analysis and comparison of very large metagenomes with fast clustering and functional annotation
    Weizhong Li
    California Institute for Telecommunications and Information Technology, University of California, San Diego, La Jolla, California 92093, USA
    BMC Bioinformatics 10:359. 2009
    ..The number of available metagenomes is rapidly increasing, so fast and efficient metagenome comparison methods are in great demand...
  16. ncbi request reprint Homotypic secretory vesicle fusion induced by the protein tyrosine phosphatase MEG2 depends on polyphosphoinositides in T cells
    Huong Huynh
    Program of Signal Transduction, Cancer Research Center, The Burnham Institute, La Jolla, CA 92037, USA
    J Immunol 171:6661-71. 2003
    ..We suggest that PTP-MEG2 through its Sec14p homology domain couples inositide phosphorylation to tyrosine dephosphorylation and the regulation of intracellular traffic of the secretory pathway in T cells...
  17. pmc Ultrafast clustering algorithms for metagenomic sequence analysis
    Weizhong Li
    Center for Research in Biological Systems, University of California San Diego, USA
    Brief Bioinform 13:656-68. 2012
    ..Artifacts can be rapidly detected through clustering. Errors can be identified, filtered or corrected by using consensus from sequences within clusters...
  18. 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...
  19. pmc Identification of ribosomal RNA genes in metagenomic fragments
    Ying Huang
    California Institute for Telecommunications and Information Technology, University of California, La Jolla, San Diego, California, USA
    Bioinformatics 25:1338-40. 2009
    ..This program provides rRNA gene predictions with high sensitivity and specificity on artificially fragmented genomic DNAs...
  20. ncbi request reprint A fast clustering algorithm for analyzing highly similar compounds of very large libraries
    Weizhong Li
    Burnham Institute for Medical Research, 10901 N Torrey Pines Rd, La Jolla, California 92037, USA
    J Chem Inf Model 46:1919-23. 2006
    ..This method can cluster a very large data set with millions of compounds in hours on a single computer. A program implemented with this method, called cd-hit-fp, is available from http://chemspace.org...
  21. ncbi request reprint A residue in the S2 subsite controls substrate selectivity of matrix metalloproteinase-2 and matrix metalloproteinase-9
    Emily I Chen
    Cancer Research Center, The Burnham Institute, La Jolla, CA 92037, USA
    J Biol Chem 278:17158-63. 2003
    ..The residues that occupy this position in other MMPs are highly variable, providing a potential structural basis for substrate recognition across the MMP family...
  22. ncbi request reprint Cysteine regulation of protein function--as exemplified by NMDA-receptor modulation
    Stuart A Lipton
    Center for Neuroscience and Aging, The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
    Trends Neurosci 25:474-80. 2002
    ..This article reviews the basis for these molecular cysteine switches, drawing on the NMDA receptor as an exemplary protein, and proposes a molecular model for the action of S-nitrosylation based on recently derived crystal structures...
  23. 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...
  24. 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...
  25. 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...