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…

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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…

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High-throughput Proteomics for Biomarker Discovery

Description The ability to reliably, robustly, and reproducibly detect quantitative protein abundance from biofluids and tissues of patients would have many applications in both research and clinical medicine. SGTC enjoys a long-standing collaboration with the laboratory of Richard Smith (Pacific Northwest National Laboratory), one of the leading groups developing the…

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Transcriptome Analysis of Clinical FFPE Samples

Introduction Clinical genomic studies often require profiling of the human transcriptome from a large number of patients. These RNA samples are typically from small amount of tissues or blood and often partially degraded from clinical archives of formalin-fixed, paraffin-embedded (FFPE) specimens, which present challenges for transcriptome analysis. For example, while…

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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…

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