Yang Zhou

Publications (4)18.96 Total impact

• Source

  Available from: Wubin Qu

  Article: MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity.

  Wubin Qu, Yang Zhou, Yanchun Zhang, Yiming Lu, Xiaolei Wang, Dongsheng Zhao, Yi Yang, Chenggang Zhang
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  ABSTRACT: Evaluating the specificity of polymerase chain reaction (PCR) primers is an essential step in PCR primer design. The MFEprimer-2.0 server allows users to check primer specificity against genomic DNA and messenger RNA/complementary DNA sequence databases quickly and easily. MFEprimer-2.0 uses a k-mer index algorithm to accelerate the search process for primer binding sites and uses thermodynamics to evaluate binding stability between each primer and its DNA template. Several important characteristics, such as the sequence, melting temperature and size of each amplicon, either specific or non-specific, are reported on the results page. Based on these characteristics and the user-friendly output, users can readily draw conclusions about the specificity of PCR primers. Analyses for degenerate primers and multiple PCR primers are also supported in MFEprimer-2.0. In addition, the databases supported by MFEprimer-2.0 are comprehensive, and custom databases can also be supported on request. The MFEprimer-2.0 server does not require a login and is freely available at http://biocompute.bmi.ac.cn/CZlab/MFEprimer-2.0. More over, the MFEprimer-2.0 command-line version and local server version are open source and can be downloaded at https://github.com/quwubin/MFEprimer/wiki/Manual/.
  Nucleic Acids Research 06/2012; 40(Web Server issue):W205-8. · 8.03 Impact Factor
• Article: VizPrimer: a web server for visualized PCR primer design based on known gene structure.

  Yang Zhou, Wubin Qu, Yiming Lu, Yanchun Zhang, Xiaolei Wang, Dongsheng Zhao, Yi Yang, Chenggang Zhang
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  ABSTRACT: The visualization of gene structure plays an important role in polymerase chain reaction (PCR) primer design, especially for eukaryotic genes with a number of splice variants that users need to distinguish between via PCR. Here, we describe a visualized web server for primer design named VizPrimer. It utilizes the new information technology (IT) tools, HTML5 to display gene structure and JavaScript to interact with the users. In VizPrimer, the users can focus their attention on the gene structure and primer design strategy, without wasting time calculating the exon positions of splice variants or manually configuring complicated parameters. In addition, VizPrimer is also suitable for the design of PCR primers for amplifying open reading frames and detecting single nucleotide polymorphisms (SNPs). VizPrimer is freely available at http://biocompute.bmi.ac.cn/CZlab/VizPrimer/. The web server supported browsers: Chrome (≥5.0), Firefox (≥3.0), Safari (≥4.0) and Opera (≥10.0). zhangcg@bmi.ac.cn; yangyi528@vip.sina.com.
  Bioinformatics 12/2011; 27(24):3432-4. · 5.47 Impact Factor
• Source

  Available from: Wubin Qu

  Article: A Lasso regression model for the construction of microRNA-target regulatory networks.

  Yiming Lu, Yang Zhou, Wubin Qu, Minghua Deng, Chenggang Zhang
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  ABSTRACT: MicroRNAs have recently emerged as a major class of regulatory molecules involved in a broad range of biological processes and complex diseases. Construction of miRNA-target regulatory networks can provide useful information for the study and diagnosis of complex diseases. Many sequence-based and evolutionary information-based methods have been developed to identify miRNA-mRNA targeting relationships. However, as the amount of available miRNA and gene expression data grows, a more statistical and systematic method combining sequence-based binding predictions and expression-based correlation data becomes necessary for the accurate identification of miRNA-mRNA pairs. We propose a Lasso regression model for the identification of miRNA-mRNA targeting relationships that combines sequence-based prediction information, miRNA co-regulation, RISC availability and miRNA/mRNA abundance data. By comparing this modelling approach with two other known methods applied to three different datasets, we found that the Lasso regression model has considerable advantages in both sensitivity and specificity. The regression coefficients in the model can be used to determine the true regulatory efficacies in tissues and was demonstrated using the miRNA target site type data. Finally, by constructing the miRNA regulatory networks in two stages of prostate cancer (PCa), we found the several significant miRNA-hubbed network modules associated with PCa metastasis. In conclusion, the Lasso regression model is a robust and informative tool for constructing the miRNA regulatory networks for diagnosis and treatment of complex diseases. The R program for predicting miRNA-mRNA targeting relationships using the Lasso regression model is freely available, along with the described datasets and resulting regulatory network, at http://biocompute.bmi.ac.cn/CZlab/alarmnet/. The source code is open for modification and application to other miRNA/mRNA expression datasets. zhangcg@bmi.ac.cn Supplementary data are available at Bioinformatics online.
  Bioinformatics 09/2011; 27(17):2406-13. · 5.47 Impact Factor
• Article: VizPrimer: a web server for visualized PCR primer design based on known gene structure.

  Yang Zhou, Wubin Qu, Yiming Lu, Yanchun Zhang, Xiaolei Wang, Dongsheng Zhao, Yi Yang, Chenggang Zhang
  Bioinformatics. 01/2011; 27:3432-3434.