Wei Li

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads
    Wei Li
    Department of Computer Science and Engineering, University of California, Riverside, Riverside CA 92507, USA
    Bioinformatics 28:2914-21. 2012
  2. pmc IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly
    Wei Li
    Department of Computer Science and Engineering, University of California, Riverside, Riverside, CA 92507, USA
    J Comput Biol 18:1693-707. 2011
  3. pmc Experimental verification of the identity of variant-specific surface proteins in Giardia lamblia trophozoites
    Wei Li
    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
    MBio 4:e00321-13. 2013
  4. pmc CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model
    Liguo Wang
    Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA, Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA and State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210000, China
    Nucleic Acids Res 41:e74. 2013
  5. pmc The profile of snoRNA-derived microRNAs that regulate expression of variant surface proteins in Giardia lamblia
    Wei Li
    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158 2280, USA
    Cell Microbiol 14:1455-73. 2012
  6. pmc FungiDB: an integrated functional genomics database for fungi
    Jason E Stajich
    Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
    Nucleic Acids Res 40:D675-81. 2012
  7. pmc Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technology
    Paul M Ruegger
    Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA
    J Microbiol Methods 90:235-40. 2012
  8. pmc ElliPro: a new structure-based tool for the prediction of antibody epitopes
    Julia Ponomarenko
    San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    BMC Bioinformatics 9:514. 2008

Collaborators

Detail Information

Publications8

  1. pmc Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads
    Wei Li
    Department of Computer Science and Engineering, University of California, Riverside, Riverside CA 92507, USA
    Bioinformatics 28:2914-21. 2012
    ..Much effort has been made in the literature to calibrate the expression level estimation from biased RNA-Seq data, but the effect of biases on transcriptome assembly remains largely unexplored...
  2. pmc IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly
    Wei Li
    Department of Computer Science and Engineering, University of California, Riverside, Riverside, CA 92507, USA
    J Comput Biol 18:1693-707. 2011
    ..Experiments on simulated and real RNA-Seq datasets show that IsoLasso achieves, simultaneously, higher sensitivity and precision than the state-of-art transcript assembly tools...
  3. pmc Experimental verification of the identity of variant-specific surface proteins in Giardia lamblia trophozoites
    Wei Li
    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
    MBio 4:e00321-13. 2013
    ..By these criteria, 73 genes are identified in the Giardia WB strain genome database as the putative repertoire of VSPs...
  4. pmc CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model
    Liguo Wang
    Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA, Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA and State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210000, China
    Nucleic Acids Res 41:e74. 2013
    ..The software accepts input sequences in either FASTA- or BED-formatted data files. We also developed a web interface for CPAT that allows users to submit sequences and receive the prediction results almost instantly...
  5. pmc The profile of snoRNA-derived microRNAs that regulate expression of variant surface proteins in Giardia lamblia
    Wei Li
    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158 2280, USA
    Cell Microbiol 14:1455-73. 2012
    ..Of the total 220 vsp genes in Giardia, we have now found 178 of them carrying putative binding sites for all the miRNAs that have been currently identified, suggesting that miRNAs are likely the regulators of VSP expression in Giardia...
  6. pmc FungiDB: an integrated functional genomics database for fungi
    Jason E Stajich
    Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
    Nucleic Acids Res 40:D675-81. 2012
    ..The underlying genomic sequence and annotation combined with functional data, additional data from the FungiDB standard analysis pipeline and the ability to leverage orthology provides a powerful resource for in silico experimentation...
  7. pmc Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technology
    Paul M Ruegger
    Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA
    J Microbiol Methods 90:235-40. 2012
    ....
  8. pmc ElliPro: a new structure-based tool for the prediction of antibody epitopes
    Julia Ponomarenko
    San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    BMC Bioinformatics 9:514. 2008
    ..The aim of this work was to implement that method as a web-tool and evaluate its performance on discontinuous epitopes known from the structures of antibody-protein complexes...