Systems Biology Laboratory

Welcome to Systems Biology Laboratory!  We are part of Institute of Genomics and Bioinformatics at National Chung Hsing University  (中興大學 基因體暨生物資訊學研究所).  Lab homepage: http://syslab.nchu.edu.tw/  https://sites.google.com/site/sysbiolab1/  Research topics:   Construction of RNA-seq databases (2016) Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells. Nucleic Acids Research 44: D944-51. [Abstract] [http://syslab4.nchu.edu.tw/CRN/] (2016) CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Research 44: D209-15. [Abstract] [http://syslab5.nchu.edu.tw/CircNet/] Gene expression data analysis for drug repositioning (ppt) (2016) Integrated Drug Expression Analysis for leukemia: an integrated in silico and in vivo approach to drug discovery. Pharmacogenomics J. in press. [Abstract] [http://syslab5.nchu.edu.tw/IDEAL/] (2014) DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. Nucleic Acids Research 42: W137-146. [Abstract] [http://disease-connect.org/]  Integration of gene expression and phenotype data (2014) High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance-based label propagation method. Nucleic Acids Research 42: e39. (2011) Integrative Analysis of Many Weighted Coexpression Networks Using Tensor Computation. PLoS Computational Biology 7: e1001106.  (2010) Bayesian Approach to Transforming Public Gene Expression Repositories into Disease Diagnosis Databases. Proc. Natl. Acad. Sci. USA. 107: 6823-8.  Integration of gene expression and ChIP-seq data. (2014) DPRP: A database of phenotype-specific regulatory programs derived from transcription factor binding data. Nucleic Acids Research 42: D178-183.  (2013) REACTIN: Regulatory activity inference of transcription factors underlying human diseases with application to breast cancer. BMC Genomics 14:504.  (2011) Polycomb-Repressed Genes Have Permissive Enhancers that Initiate Reprogramming. Cell 147: 1283-1294.  Integration of gene expression and miRNA expression data. (2014) miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Research 42: D78-85. Integration of gene expression, miRNA expression and DNA methylation data. (2012) Discovery of multi-dimensional modules by integrative analysis of cancer genomic data. Nucleic Acids Research 40: 9379-9391. (2012) Identifying multi-layer gene regulatory modules from multi-dimensional genomic data. Bioinformatics 28: 2458-66. Discovering chromatin motifs (2013) Discovering chromatin motifs using FAIRE sequencing and the human diploid genome. BMC Genomics 14:310.