Development of Computational Methods

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 into the biological processes and […]

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 reference annotations to define a

Project Summary A complex disease often affects the functions of multiple organs of the human body. In intensive care, the recovery of major organ functions is essential to patient’s overall recovery averting death. As part of the Glue Grant Consortium, the Inflammation and the Host Response to Injury, we have collected functional trajectories of six

Project Summary  The evolution of a cancer system consisting of cancer clones and normal cells is a complex and dynamic process with multiple interacting factors including clonal expansion, somatic mutation, and sequential selection. As a typical example, in patients with chronic lymphocytic leukemia (CLL), a monoclonal population of transformed B cells expands to dominate the

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 splicing using junction-specific peptide information

Description JETTA is an integrated software tool for gene and exon expression calculation and alternative splicing analyses. It can be applied to the analysis and visualization of both exon-junction array and RNA-Seq data.See more about JETTA Updates 05/18/11: version 1.0.0— Interfaces for RNA-Seq data was added.10/07/10: version 0.6.0— GUI was built, plotting asa output was