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The Computational Genomics Research group at NCI CBIIT participated in the HPN-DREAM breast cancer network inference challenge for the first time in 2013. The challenge comprises network inference, time-course prediction, and visualization of time-course data derived from proteomic experiments in cancer cell lines and in silico simulation. The group developed a novel approach to construct consensus networks and predict phosphoprotein trajectories under the influence of each inhibitor. The time-series data were visualized with in-house R package OmicCircos which is available at bioconductor.org. This novel diagram not only maintains the network structure but also displays the time-course change, biological annotations, and topological features. We submitted results to Synapse.org, a site that Sage Bionetworks has developed for data sharing and live scoring. Our prediction result of 20 phosphoproteins and 10 time points for the sub-challenge 2B "In silico time-course prediction" has been ranked as the best predictor. |
BIO:
Chunhua Yan, Ph.D., is the bioinformatics project manager of Computational Genomics Research (CGR) at the NCI Center for Biomedical Informatics and Information Technology. The CGR group carries out the integrated analysis of cancer mutation, copy number, expression, and methylation data through collaborations with investigators both inside and outside of NCI as well as participation in NCI supported projects such as Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and The Cancer Genome Atlas (TCGA). Dr. Yan has published many articles in peer-reviewed journals covering the topics of bioinformatics software and next generation sequencing data analysis. He also has been awarded multiple U.S. patents related to the discovery of novel kinases and receptors. Dr. Yan obtained his B.S. in pharmacy from Shanghai Medical School and his Ph.D. in structural biology from University of Maryland at Baltimore.
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