Computational Methods in Cell Biology

- Principles of model building: an experimentation-aided approach to development of models for signaling networks - Integrated Inference and Analysis of Regulatory Networks From Multi-Level Measurements - Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets - A framework for modeling the relationship between cellular steady-state and stimulus-responsiveness - Stochastic Modeling of Cellular Networks - Quantifying Traction Stresses in Adherent Cells - CellOrganizer: Image-derived Models of Subcellular Organization and Protein Distribution - Spatial Modeling of Cell Signaling Networks - Stochastic models of cell protrusion arising from spatiotemporal signaling and adhesion dynamics - Nonparametric Variable Selection and Modeling for Spatial and Temporal Regulatory Networks - Quantitative Models of the Mechanisms that Control Genome-Wide Patterns of Animal Transcription Factor Binding - Computational Analysis of Live Cell Images of the Arabidopsis thaliana Plant - Multi-scale modeling of tissues using CompuCell3D - Multiscale Model of Fibrin Accumulation on the Blood Clot Surface and Platelet Dynamics