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Computational Biology

ArborTron, Arbor Harbor, and Beyond: An Arbor-centric framework for identifying species and their geographic origin to counter illegal logging

Illegal logging and timber trade, valued at $50-$150B annually, is estimated to account for 30-50% of all internationally traded timber, cost $5B in lost revenue to governments, and negatively impact biodiversity, climate, and local communities. The Lacey Act fosters forest legality by restricting importation of unlawfully harvested goods into the US. This act requires declaring the harvested species and its country of origin.

Computational modeling of emergent spatiotemporal cell population dynamics: A survey of our successes, challenges, and best practices.

Computational models are essential tools that can be used to simultaneously explain and guide biological intuition. My lab employs agent-based modeling, machine learning, and dynamical systems to explain biological observations and to uncover design principles that drive individual cellular decisions as well as cell population dynamics. We are interested in the inherent multiscale nature of biology, with a specific focus on system-level dynamics that emerge from interactions of simpler individual-level modules.

Mechanistic insights into actin force generation during vesicle formation from cryo-electron tomography

Serwas D, Akamatsu M, Moayed A, Vegesna K, Vasan R, Hill JM, Schöneberg J, Davies KM, Rangamani P, Drubin DG.  2022.  Mechanistic insights into actin force generation during vesicle formation from cryo-electron tomography. Developmental Cell.

Agile movement and embodied intelligence: Computational and comparative considerations

Our ability to study brain and behavior has long proceeded in lock-step with advances in technology. At the same time, understanding of neurobiological principles has continuously driven technological innovations, including serving as the inspiration for most of the major advances in artificial intelligence. Even so, engineered systems still struggle to achieve flexible behaviors that require interaction with the physics of the world. All animals excel at such sensorimotor behaviors within their natural contexts.

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