Welcome to the Data Center of Species Inspired Research for Innovative Treatments (SPIRIT) Most tissue damage from infectious disease is caused by secondary inflammation elicited in the host. Furthermore, identical pro-inflammatory stimuli from the same pathogen load causes markedly different amounts of inflammation in different species, different hosts, and even within a single individual. Given […]
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
Knowledge-Based Network Analysis of Genomic Data Read More »
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
Multiple Variant Survival Analysis 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
Modeling of Immune Repertoire Read More »
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
Junction-specific peptide detection and alternative splicing Read More »
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 »
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 »
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 »