The overarching goal of the Lopez lab is to develop and apply numerical, modeling, and statistical methods to understand cellular processes and their dysregulation. My group efforts comprise a tri-partite approach to study cellular biology: (1) Develop modeling and simulation tools necessary to study signaling events across multiple spatiotemporal time-scales. To this end we use techniques from statistical mechanics, molecular simulation, mesoscale modeling, reaction kinetics, and cell-population modeling to develop a systems-level description of cellular environments. (2) Use developed tools to study signaling processes relevant to cancer phenotypes. (3) Collaborate with experimental and theoretical groups to test and expand our hypotheses to develop a fundamental understanding of the rules that govern functional genomics and systems biology. My group currently co-develops and contributes to the PySB (www.pysb.org) modeling platform, which uses a novel modeling-with-programs paradigm to biological signaling pathway simulations. With this approach, the biological knowledge is encoded into executable programs that enhance our capabilities to express, share, and revise our understanding of complex interactions at a large signaling network scale. Given the complexity of biological systems, we have recently developed and implemented novel simulation and calibration tools in parallel computing environments to accelerate progress toward understanding of biological systems. My lab is located in the department of Biochemistry at Vanderbilt University and with strong ties to the Vanderbilt-Ingram Cancer Center. My work provides a theoretical perspective to experimental and clinical efforts in the department and university with the goal of developing a better understanding of cancer development and treatment.
- Our projects on GitHub: https://github.com/lolab-vu
- Our PySB project: http://pysb.org/
- PI Page on ORCID: http://orcid.org/0000-0003-3668-7468