Systems Biology and Bioinformatics Group

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The overall goal of the SBG is to provide several established bioinformatics tools, and develop new methods to perform integrated multi-modality, multi-tissue, and multi-center analysis of the AMP Network generated data. The goals of the SBG will be (1) to collaborate with the Network investigators that are generating primary data, (2) to provide robust bioinformatics methods for analysis of the data, (3) to serve data to the Network investigators for hypothesis testing, and (4) to publish the data for public availability in collaboration with the Data Coordination and Management Core (DCM). The SBG will work with all Network sites to address their need for robust bioinformatics techniques to identify biomarkers and pathways for understanding disease mechanisms and predicting novel drug targets. More importantly, the SBG will carry out integrated multi-cohort, multi-tissue analysis by integrating data obtained through the Network with large amounts of publicly available human profiling data. Furthermore, the SBG will work closely with the DCM to publish analysis results to the Internet. Using Galaxy and Stanford Data Miner, the SBG will establish a pipeline for integrated analysis, in close collaboration with the DCM and the Statistical Research Group (SRG), to enable state-of-the-art analysis of multiple types of genome-scale data from human, in vitro and in vivo models. This will enable participating Network sites to maximally utilize the genomic, immune monitoring, clinical, phenotypic, and other types of data to determine functional dependencies among the measured elements and to direct further biological validation of these putative dependencies.