Daniel Fisher's group webpage

Current Members

Daniel S. Fisher

My primary research focus in recent years has been the statistical dynamics of evolutionary processes. This includes theoretical work on general issues and models in evolutionary dynamics, especially quantitative aspects, collaborations with experimental groups on laboratory evolution of microbes and on field studies of microbial diversity, and now exploring the interplay of microbial evolution and ecology. For humans, active collaborations are on the repertoire and dynamics of the immune system, and on the evolution of cancers, and I am starting to actively pursue a long-standing interest in neuroscience.

My biological research also includes projects on the dynamics of cellular processes. Before diving into biology, I worked in various areas of condensed matter and statistical physics including ultralow temperature phases of helium, superconductivity, physics of disordered materials, fracture mechanics, and earthquakes.

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Alana Papula

I am a PhD student in Applied Physics investigating evolution of bacterial populations using the model organism marine Prochlorococcus, the most abundant photosynthetic organism on Earth responsible for 10% of global carbon fixation. Prochlorococcus is a very diverse species exhibiting many levels of population structure, which is puzzling in the context of its well-mixed marine environment. I am interested in how this diversity is generated and maintained, with a particular focus on homologous recombination throughout the species. I work with hundreds of single cell genomes, from the most closely-related Prochlorococcus cells sequenced to date, to the most distantly-related, to address these questions.

Past projects include modeling the dynamics of pre-cancerous mutants in the blood and quantifying the aggressiveness of the most common hematopoietic driver mutations.

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Aditya Mahadevan

I am a physics PhD student interested in statistical physics and the evolution of biodiversity. How do ecological dynamics, from resource competition to host-pathogen interactions, influence the trajectory of evolution? What evolutionary forces, from drift to selection to recombination, lead to the immense biodiversity we see across vast spatiotemporal scales in nature? What are mechanisms for the coexistence of fine-scale diversity and how can we understand these theoretically? Email: adityam2[at]stanford.edu

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Alex Heyde

I am a postdoctoral scholar working on the evolutionary dynamics of human health and disease. I develop and investigate theoretical models for the stochastic biological processes that underlie clonal evolution, aging, heart disease, cancer progression, and metastasis. Using computational, statistical, and analytic methods, I work to infer pathways of mutation, selection, and drift from patient data, often genetic or phylogenetic, with the goal to better understand and predict treatment response. Previously, I did my PhD with L. Mahadevan and Martin Nowak at Harvard University, where I worked on similar topics, as well as on modeling eco-evolutionary dynamics, niche construction, and malleable fitness landscapes.

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Avaneesh Narla

I am a postdoctoral fellow interested in how biological collectives dynamically adapt to environmental changes. My research interests include feedback between ecology, evolution, and physiology in microbial ecosystems, and collective behavior and information processing in social insects. I wish to understand how living systems can operate outside of equilibrium to actively extract information from the environment, dynamically self-organize, and seemingly coordinate actions. My Ph.D. thesis was on phenomenological modeling of spatial and temporal dynamics in microbial ecosystems and was supervised by Prof. Terry Hwa at UC San Diego.

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Federico Ghimenti

I am a postdoctoral fellow interested in the behavior of high dimensional systems evolving far from equilibrium, from ecological communities to neural networks. During my PhD I explored how some clever irreversible dynamics can be exploited to accelerate sampling in amorphous systems, from spin glasses to supercooled liquids.

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