People



Daniel S. Fisher

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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Atish Agarwala

Atish Agarwala

I’m a PhD student in the physics department. My primary interest is in studying models of epistasis, and understanding how the statistics of “fitness landscapes” contribute to the dynamics of evolution. I’m particularly interested in questions about the speed and predictability of long term evolution.

I’ve also worked on designing fitness assays using DNA barcoding technology in yeast, in collaboration with the Sherlock and Petrov labs at Stanford. We can use these fitness measurements to quantitatively understand the of evolution, and to try to tease out the reasons why some variants succeed while others fail.

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Lily Blair

Lily Blair

I’m a graduate student in the department of Biology, and I’m interested in the dynamics of evolution and adaptation of biological systems. Currently I am studying the response of the human antibody repertoire to seasonal influenza vaccine and dengue infection.

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Jamie Blundell

Jamie Blundell

I read Natural Sciences at Cambridge focusing on theoretical physics. I remained at the Cavendish for my PhD where I modeled the physical properties of the cellular cytoskeleton, using methods from statistical physics. In 2012 I joined Stanford as a postdoc and began studying evolutionary dynamics with Daniel Fisher, Dmitri Petrov and Sasha Levy. At Stanford I also began training as an experimentalist. Since 2015 I spend about a third of my time at SUNY, Stony Brook, NY, where my experimental mentor, Sasha, set up his new lab.

My work combines experimental evolution, analyses of “big data” sets obtained from genetic lineage-tracking tools, and theory to understand how quickly clonal populations evolve. The central idea is to develop a quantitative understanding of clonal evolution in order to (i) predict how cellular populations evolve in the lab (ii) make more informed treatment decisions of evolutionary diseases in the clinic.

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Sam Ocko

Sam Ocko

I’m a postdoc co-advised by Profs. Daniel Fisher and Surya Ganguli studying grid cells and animal navigation in collaboration with the Giocomo lab. I work on a combination of theory and data analysis developing neural models of how an animal navigates and learns about its environment from a combination of step-counting and landmarks. I’m also interested in the statistics of ensembles of trained neural networks. During my Ph.D., I studied the physics of termite mound ventilation. Find out more on my website.

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Michael Pearce

Michael Pearce

I am a physics PhD student studying models of evolution and ecology. I’m broadly interested in how the interplay of various factors–from mutation and recombination to epistasis and spatial structure–determine the pace of evolution and the diversity observable in sequencing data.

Some species are capable of both sexual and asexual reproduction and my work has focused on how the asexual evolutionary dynamics are altered by very low frequencies of sexual mating. In ecology, I am interested in how microbial interactions lead to high levels of coexistence and am exploring models with spatial structure and environmental feedback.

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Alumni

Oguzhan Atay

Oguzhan Atay

Former PhD student in Biology, co-founder/CEO at Billion To One.

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Michael Rosen

Michael Rosen

Former PhD student in Applied Physics, scientist at Karius.

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Ben Callahan

Ben Callahan

Former postdoc, currently Assistant Professor of Microbiomes and Complex Microbial Communities at NC State University.

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Daniel Weissman

Daniel Weissman

Former PhD student in Physics, currently Assistant Professor of Physics at Emory.

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Josh Weinstein

Josh Weinstein

Former PhD student in Biophysics, currently a postdoc at the Broad Institute/MIT.

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Kendra Burbank

Kendra Burbank

Former PhD student in Physics (at Harvard), currently lecturer in the Department of Statistics at University of Chicago.

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Michael Desai

Michael Desai

Former PhD student in Physics (Harvard), currently Professor of Physics and Organismic and Evolutionary Biology at Harvard.

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