Systems Biology

  • FMM

    A web server for metabolic pathway reconstruction and comparative analysis. (Nucl Acids Res, 2009)

  • MoNetFamily

    A web server to infer homologous modules and module-module interaction networks in vertebrates. (Nucleic Acids Res, 2012)

  • GeNOSA

    Inferring and experimentally supporting quantitative gene regulatory networks in prokaryotes (Bioinformatics, 2015)

MicroRNA and small RNA Regulation

  • miRTar

    An integrated web server for identifying miRNA-target interactions. (BMC Bioinformatics, 2011)

  • RegRNA

    An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. (Nucl Acids Res, 2006 and BMC bioinformatics, 2013)

Next Generation Sequencing Analysis

  • miRExpress

    Analyzing high-throughput sequencing data for profiling microRNA expression. (BMC Bioinformatics, 2009)

  • miRTarCLIP

    A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. (BMC Genomics, 2013)

Protein Function, Interaction, and Modification

  • KinasePhos

    A web tool for identifying protein kinase-specific phosphorylation site. (Nucl Acids Res, 2005 and Nucl Acids Res, 2007)


    Prediction and characterization of photosynthetic proteins based on a scoring card method.


    Prediction and analysis of heme binding proteins using propensity scores of dipeptides.

Structure Biology


    Prediction of protein subcellular localization. (Proteins: Structure, Function and Bioinformatics, 2006)

  • (PS)2

    Protein structure prediction server. (Nucleic Acids Res 2006 and BMC Bioinformatics 2009)

  • pKNOT

    The protein KNOT web server. (Nucleic Acids Res, 2007 and Nucleic Acids Res, 2012


    A generic evolutionary method for molecular docking. (Proteins: Structure, Function and Bioinformatics, 2004)

  • 3D-BLAST

    A a very fast and accurate method for discovering the homologous proteins and evolutionary classifications of a newly determined protein structure. (Genome Biology, 2007)

Bioimage informatics

  • NeurphologyJ

    An automatic neuronal morphology quantification method and its application in pharmacological discovery. (BMC Bioinformatics, 2011)