Research

  • Network Inference and Analysis

    Complex dynamical biomolecular systems govern virtually all biological processes, on time scales ranging from development to physiology. A paramount problem is to understand the structural and dynamical properties of such systems and their role in cellular function and dysfunction. Our group is developing model inference approaches by integrating the information from multiple types of measurement data in a variety of modeling formalisms, including differential equations, nonlinear discrete dynamical systems, such…

    Read More
  • Image Analysis

    High-throughput cellular imaging and microfluidic technologies are enabling phenotypic measurements on single-cell and population-wide scales. The extraction of information from such imaging data is necessary for establishing the relationships between the behavior of molecular networks in cells and quantitative phenotypic features under a variety of conditions. We are developing image processing and analysis methods to detect and count objects (including subcellular and multicellular structures), statistically describe their shape (both in…

    Read More
  • Computational Biology Tools and Methods

    Large-scale high-throughput measurement technologies have allowed system-wide modeling and analysis of cells in health and disease. Each type of measurement data, be it transcript enumeration data, protein lysate array data, flow cytometry data, or microarray data from heterogeneous cell populations, requires appropriate statistical and computational methods. Publications:

    Read More
  • Complex Systems

    We are studying complex dynamical systems for gaining insights into fundamental principles governing living systems at various scales of organization. We have focused on: the relationships between the structure of such systems and their dynamics; the ability to balance robustness with adaptability in an uncertain and variable environment while making decisions in response to information in the environment; and the coordination of complex behaviors and memory. We are exploring information-theoretic…

    Read More
  • Cancer Studies

    Cancer is a complex genetic disease that results from a combination of genetic and environmental perturbations to biomolecular networks that typically maintain a homeostatic balance between normal cellular functional states, such as proliferation, apoptosis, and differentiation. Using genome-wide genomic and proteomic measurements of cancer cells (primary tumors, distant metastases, cell lines treated with chemotherapeutic drugs, etc.), coupled with computational approaches, we can gain insights into cellular dysfunction underlying cancer onset,…

    Read More