Computational Analysis Core

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Core 2 – Project Summary The Computational Analysis Core (Core 2) will support Projects 1 & 2 by bringing necessary bioinformatics and computational methods to bear on the questions addressed by each project. More specifically, we will apply established computational pipelines to perform quality control on, and extract maximal information (cell types, states, circuits, and drivers) from, our rich data sets. We will help our CSBC team identify the cell types, states, and circuits active in the Leukemia and Colon and Pancreatic tumor models of Core 1 from the single- cell RNA-Seq data collected in Projects 1 & 2, as well as the molecular drivers of interesting behaviors. We will deploy numerical algorithms to uncover the predictive power of phenotypic measurements, alone or in combination, made via our Nanowell (NW) and Suspended Microchannel Resonator (SMR) platforms to explain cancer cell drug responses. When necessary, we will identify and/or develop new algorithms, enhancing our CSBC's quantitative and multivariate capabilities. Finally, we will work closely with our CSBC team members to help with experimental design, ensuring that an appropriate number of cells/samples are processed to test hypotheses of interest and that appropriate statistical testing is performed. By providing comprehensive analysis (QC, power, gene set enrichment) and modeling capabilities, we will dramatically enhance our ability to draw crucial insights from our data. This will lead to new hypotheses that can be tested by designing new experiments.