Weizhong Li

Summary

Affiliation: University of California
Country: USA

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. ncbi request reprint Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology
    W Li
    San Diego Supercomputer Center, La Jolla, CA 92093, USA
    Bioinformatics 16:1105-10. 2000
  10. 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

Collaborators

Detail Information

Publications38

  1. 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...
  2. 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...
  3. 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...
  4. 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...
  5. 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...
  6. 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...
  7. 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...
  8. 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...
  9. ncbi request reprint Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology
    W Li
    San Diego Supercomputer Center, La Jolla, CA 92093, USA
    Bioinformatics 16:1105-10. 2000
    ..In its brute-force implementation, ISS is a strategy that repetitively uses the results of the previous query as new search seeds, making it time-consuming and difficult to analyze...
  10. 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...
  11. 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...
  12. ncbi request reprint Clustering of highly homologous sequences to reduce the size of large protein databases
    W Li
    San Diego Supercomputer Center, La Jolla, CA 92093, USA
    Bioinformatics 17:282-3. 2001
    ..The output database, including only the representative sequences, can be used for more efficient and sensitive database searches...
  13. 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...
  14. 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...
  15. 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...
  16. 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...
  17. 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...
  18. 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...
  19. 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...
  20. pmc Alternative splicing regulated by butyrate in bovine epithelial cells
    Sitao Wu
    Center for Research in Biological Systems, University of California San Diego, San Diego, California, United States of America
    PLoS ONE 7:e39182. 2012
    ..Our results provided a snapshot into complex transcriptome dynamics regulated by butyrate, which will facilitate our understanding of the biological effects of butyrate and other HDAC inhibitors...
  21. 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...
  22. 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...
  23. 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...
  24. 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...
  25. 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...
  26. ncbi request reprint Occurrence of phosphate acquisition genes in Prochlorococcus cells from different ocean regions
    Adam C Martiny
    Department of Earth System Science, University of California, Irvine, 92697 CA, USA
    Environ Microbiol 11:1340-7. 2009
    ..Overall, this study further demonstrates a linkage between environmental conditions in the ocean and genome content of Prochlorococcus...
  27. pmc Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource
    Shulei Sun
    The CAMERA Project, Center for Research on Biological Systems and California Institute of Telecommunication and Information Technology, University of California San Diego, 9500 Gilman Drive, Mail Code 0446, California 92093 5004, USA
    Nucleic Acids Res 39:D546-51. 2011
    ..CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data...
  28. pmc Transcriptome characterization by RNA-seq unravels the mechanisms of butyrate-induced epigenomic regulation in bovine cells
    Sitao Wu
    Center for Research in Biological Systems, University of California San Diego, San Diego, California, United States of America
    PLoS ONE 7:e36940. 2012
    ..Our results provided insight into the transcriptome alterations induced by butyrate, which will undoubtedly facilitate our understanding of the molecular mechanisms underlying butyrate-induced epigenomic regulation in bovine cells...
  29. 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...
  30. pmc Worm burden-dependent disruption of the porcine colon microbiota by Trichuris suis infection
    Sitao Wu
    Center for Research in Biological Systems, University of California San Diego, San Diego, California, United States of America
    PLoS ONE 7:e35470. 2012
    ..Our findings provided insight into the dynamics of the proximal colon microbiota in pigs in response to T. suis infection...
  31. ncbi request reprint A unique substrate binding mode discriminates membrane type-1 matrix metalloproteinase from other matrix metalloproteinases
    Steven J Kridel
    Program on Cell Adhesion, The Cancer Research Center, The Burnham Institute, La Jolla, California 92037, USA
    J Biol Chem 277:23788-93. 2002
    ..Altogether the study provides a structural basis for selective and non-selective substrate recognition by MT1-MMP. The findings in this report are likely to explain several aspects of MT1-MMP biology...
  32. 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...
  33. ncbi request reprint Defective cytochrome c-dependent caspase activation in ovarian cancer cell lines due to diminished or absent apoptotic protease activating factor-1 activity
    B B Wolf
    La Jolla Institute for Allergy and Immunology, San Diego, California 92121, USA
    J Biol Chem 276:34244-51. 2001
    ..Lack of APAF-1 activity correlated in some but not all cell lines with resistance to apoptosis. These data suggest that regulation of APAF-1 activity may be important for apoptosis regulation in some ovarian cancers...
  34. 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...
  35. ncbi request reprint Identification of a novel transcriptional repressor (HEPIS) that interacts with nsp-10 of SARS coronavirus
    Min Hong
    Institute of Medical Biology, Chinese Academy of Medicine Science, Peking Union Medical College, Kunming, China
    Viral Immunol 21:153-62. 2008
    ..Taken together, our results suggest that HEPIS may function as a potential transcriptional repressor...
  36. ncbi request reprint Cutaneous immune responses in the common carp detected using transcript analysis
    Santiago Fernandez Gonzalez
    Department of Veterinary Pathobiology, Laboratory for Fish Diseases, The Royal Veterinary and Agricultural University, Stigbøjlen 7, DK 1870 Frederiksberg C, Denmark
    Mol Immunol 44:1664-79. 2007
    ..These results confirm the active role of fish skin in the immune response against infections, acting as an important site of expression of immune-related molecules...
  37. ncbi request reprint Seasonally hibernating phenotype assessed through transcript screening
    Daryl R Williams
    School of Biological Sciences, University of Liverpool, United Kingdom
    Physiol Genomics 24:13-22. 2005
    ....
  38. pmc The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families
    Shibu Yooseph
    J Craig Venter Institute, Rockville, Maryland, United States of America
    PLoS Biol 5:e16. 2007
    ..Our analysis indicates that new families are being discovered at a rate that is linear or almost linear with the addition of new sequences, implying that we are still far from discovering all protein families in nature...

Research Grants5

  1. CD-HIT: A Fast Program to Cluster and Compare Large Sets of Biological Sequences
    Weizhong Li; Fiscal Year: 2009
    ..Continued development of CD-HIT will better serve researchers who are facing more challenges in sequence analysis by the explosive growth of public sequence databases. ..
  2. CD-HIT: A Fast Program to Cluster and Compare Large Sets of Biological Sequences
    Weizhong Li; Fiscal Year: 2010
    ..Continued development of CD-HIT will better serve researchers who are facing more challenges in sequence analysis by the explosive growth of public sequence databases. ..
  3. CD-HIT: A Fast Program to Cluster and Compare Large Sets of Biological Sequences
    Weizhong Li; Fiscal Year: 2009
    ..Continued development of CD-HIT will better serve researchers who are facing more challenges in sequence analysis by the explosive growth of public sequence databases. ..
  4. Novel Methods for Effective Analysis Assembly and Comparison of HMP Sequences
    Weizhong Li; Fiscal Year: 2010
    ..The proposed methods will help researchers in preliminary data analysis, annotation, clinical sample comparison, novel gene discovery and other analysis in a very rapid way. ..