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 […]
Analysis of Alternative Splicing Read More »
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 RNA-seq can simultaneously discover new
Transcriptome Analysis of Clinical FFPE Samples Read More »
Project Summary In clinical medicine and in most research on physiology and patho-physiology, it has been a traditional concept to use the total amount or the concentration of certain substances (proteins or substrates) in a special compartment of the body of a living organism to represent the metabolism or health condition of the host. With
Measuring in vivo Protein Synthesis Read More »
Project Summary We propose and test a method for the absolute quantitation of RNA molecules in RNA-Seq gene expression studies. Prior to any PCR amplification, cDNA fragments are generated and randomly labeled with a diverse set of “stochastic labels” comprising of nucleic acid barcodes. After amplification and sequencing, the number of stochastic labels observed for
Improving RNA-Sequencing by Stochastic Labels Read More »
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
Systems Analysis of Multiple Organ Recovery after Injury Read More »
Project Summary Murine models have been extensively used in recent decades to identify and test drug candidates for subsequent human trials. However, few of these human trials have shown success. To date, there have been nearly 150 clinical trials testing candidate agents intended to block the inflammatory response in critically ill patients, and every one
Translation of Murine Models to Human Inflammatory Diseases Read More »
Project Summary RNA-Seq has been recently developed for transcriptome studies, including the discovery and quantification of genes, exons and isoforms, alternative splicing and differential expression. We participated in the MAQC-III/SEQC consortium led by FDA (Leming Shi, PI), to conduct a dedicated multi-site multi-platform experiment with several built-in ground truths to evaluate the performance of this technology. The consortium systematically analyzed the data to establish best
Evaluation of the Performance of RNA-Seq and Microarray Read More »
Summary A comprehensive understanding of a disease requires a systems view in the context of the whole human body, covering from the molecular level, cell level, to the organ and system level. Recent developments of technologies enable direct assay of patient’s genomic, proteomic and metabolomic profiles from multiple tissues. These datasets, together with physiological and
Multi-scale Modeling of Inflammatory Diseases Read More »
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
Sequencing the Immune Repertoire Read More »
INTRODUCTION Trauma injury remains a major human disease, causing >2 million hospitalizations and >120,000 deathsv every year in the US. The resulting toll on humanity and the cost to the society is staggering (estimated >$200 billion per year). To date, all the clinical trials to block the inflammatory response in critically ill patients failed. The
Genomics of Human Inflammatory Response to Injury Read More »