Knowledge-based network analysis of genomic data

Introduction Extracting new biological insight from high throughput genomic studies of human diseases is a daunting challenge, limited by difficulties in recognizing and evaluating relevant biological processes from the immense quantities of experimental data. Cluster and principal component analyses describe overall changes in apparent gene expression, but provide few insights…

Continue reading

Knowledge-based Reconstruction of mRNA Transcripts with Short Sequencing Reads for Transcriptome Research

Introduction The knowledge-based transcript reconstruction algorithm was developed to aid the design and analysis of next-generation transcriptome arrays, using RNA-Seq data in NCBI SRA (1) and annotation databases of RNA transcripts, such as RefSeq, Ensembl and UCSC known genes. The algorithm combines information in the RNA-Seq data and in the…

Continue reading

Junction-specific peptide detection and alternative splicing

We are developing a computational method to analyze proteomics data for the detection of junction-specific peptide and alternative splicing. In details, we will Identify the human junction-specific peptides using information from the exon database we created; Assign confidence for junction-specific peptides using the fragment ions in MS/MS spectra; Modeling alternative…

Continue reading

Time course multifactor analysis

Description Time-course microarray experiment is capable of capturing the dynamic profile of genomic response to treatment factors. The profile contains valuable information for researchers to identify possible genetic factors that lead to different clinical outcomes, which can help directing future investigation. We developed a general statistical method to extract gene-specific…

Continue reading