Affiliation: University of California
- Transcriptome assembly and isoform expression level estimation from biased RNA-Seq readsWei 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...
- IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assemblyWei 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...
- Experimental verification of the identity of variant-specific surface proteins in Giardia lamblia trophozoitesWei 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...
- CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression modelLiguo 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...
- The profile of snoRNA-derived microRNAs that regulate expression of variant surface proteins in Giardia lambliaWei 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...
- FungiDB: an integrated functional genomics database for fungiJason 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...
- Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technologyPaul M Ruegger
Department of Plant Pathology and Microbiology, University of California, Riverside, CA, USA
J Microbiol Methods 90:235-40. 2012....
- ElliPro: a new structure-based tool for the prediction of antibody epitopesJulia 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...