Description of project: I'm an electrical engineer by training, but I got interested in how cells solve engineering problems, which I view as fundamentally interesting but also potentially as the key to learning how to harness cells for engineering purposes. My main focus is on how geometry arises within cells, as well as how cells perform computations and behaviors. Ask me about: Weird unicellular organisms, Quantitative Cell Biology
When I'm not doing science, I enjoy: Reading, trying to play the piano, machining, electronics and robotics
For more, follow me on Twitter @WallaceUCSF
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Description of project: My general interests are in understanding how cells control the size of their organelles. As a model system for size control, I study cilia/flagella of both cultured mammalian cells and the unicellular green alga, Chlamydomonas using quantitative live-cell imaging and analysis. Ask me about: Cilia and flagella. Chlamydomonas. Most of general molecular biology, biochemistry and cell biology experiments.
When I'm not doing science, I enjoy: Reading, cooking, walking, taking photos, and playing with my son.
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Mary Mirvis, Postdoctoral Fellow Description of project: How is the cellular interior organized? I want to understand how the spatial and mechanical interactions between organelles contribute to cytoplasmic patterning in yeast using image-based modeling and biophysical simulations. Ask me about: (your scientific expertise/interests) - organelles, cytoskeleton, confocal microscopy, live cell imaging, image analysis, cell biology/systems biology When I'm not doing science I enjoy: reading all kinds of things, yoga, trail running & hanging out in the woods, learning astronomy & stargazing, trying and failing to teach my cat tricks, bullet journaling and calligraphy |
Ben Larson, Postdoctoral Fellow
Description of project: How do cells control shape and movement to properly execute complex behaviors? To answer this and related questions, I am investigating the coordination of locomotor activity in various ciliates (primarily the unicellular walker Euplotes) and amoebae.
Ask me about: protists, microscopy, image analysis, quantitative and exploratory data analysis, biophysics, evolution, cellular biomechanics, cellular behavior, morphogenesis
When I'm not doing science, I enjoy: Fishing, playing and listening to music, cooking, and being outside in general
For more, visit: https://twitter.com/BEuplotes or www.benlarson.org
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Ambika Nadkarni, postdoc (joint with Sindy Tang Lab, Dept. Mechanical Engineering, Stanford) Description of project: mechanism of wound healing in Stentor
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Description of project: ... Stentor
i like weird cells and i cannot lie postdoc
@WallaceUcsf | @SF_IRACDA scholar | PhD @BerkeleyMCB @mbeisen | #FirstGen | UG @UNC_Biology | she/her
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Projects:
1) Illuminating mitochondrial network-shape space: Mitochondria (The Power House of The Cell) are typically presented as floating kidney beans in biology textbooks. However, most of the time, mitochondria form intricate interconnected networks that move around the surface of the cell and change their structure on the sub-minute timescale. We know that mitochondrial networks change shape and structure in response to metabolic shifts, environmental perturbations, and aging. How does mitochondrial network shape and structure reflect the underlying "state" of a cell? Using a combination of theory (graph theory, topology, stat mech) and experiment (3D fluorescence microscopy) hand in hand, I am constructing mitochondrial network shape-space, deriving its associated dynamics, and linking metabolic states to shifts in the sampling and dynamics of this space for living budding yeast.
2) Computational characterization of an evolutionary model for cyclical within-host viral infection: When a person gets a viral infection, they are very rarely infected by many viral particles with identical genomes. Usually, a person is infected by a viral quasispecies: a collection of genetically-close (but not identical) viruses exhibiting a range of infectiousness and virulence. If a person is infected by such a population, how does the viral population adapt to the host's immune system over time? In collaboration with Dr. Barbara Jones at IBM Almaden, I am extending a previously published model to better understand the space of possible host-quasispecies interactions by analyzing the dynamics of hundreds of thousands of infection cycles in silico.
3) Creating an automatic classifier to determine B-cell maturity in vivo: In collaboration with Dr. Hsin Chu in Jason Cyster's lab at UCSF, I have created an end-to-end pipeline for predicting the maturity level of B cells in high throughput. I adapted a standard convolutional neural network to process full-field microscopy data of nuclear reporters and track the maturity of individual cells over time.
Ask me about:
Math! Machine learning! How to think critically about models! How to use mathematical modeling in cell biology!
When I'm not doing science, I'm: cooking, reading, or hiking.
For more, visit: www.greyson.xyz
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Description of project: I use imaging and micromanipulation techniques to study dynamics of the cytoskeleton and cytoplasm. I'm interested in mixing driven by amoeboid motility as well as turnover and re-use of cytoskeletal proteins during Stentor growth and regeneration. |
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Description of project: I study the molecular basis of pattern formation and regeneration in Stentor, with a focus on the role of SFI1 proteins and the E2F pathway in controlling the spatial and temporal process of rebuilding cellular structure |
Description of project: How can we improve our mental models of biology with the aid of computer graphics? I am interested in applying the latest 3D modeling softwares developed by the video game and film industries to simulate the structure and dynamics of organelles. Perhaps hidden in the geometry and movements of organelles lies the information that ultimately generates the emergent properties of cells and tissues! Ask me about: animation science, mitochondrial networks, complex-systems theory, energetic scaling laws, and all the ways art can help us do better science. When I’m not doing science I enjoy: rollerblading, meditating, and ruminating about climate change. |
Deepa Rajan, MD/PhD student Description of project: exploring the basis of cognition in cells using Stentor |
Jamarc Allen-Henderson, Masters student Description of project: role of microtubule motor proteins and mitochondria in Stentor regeneration |
Raphael Mostov, Undergrad student Description of project: using graph theory and abstract algebra to understand mitochondrial network geometry |
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Lab Alumni
Former Postdoctoral Fellows
Shigenori Nonaka
Associate Professor, National Institute for Basic Biology, Okazaki Japan
Susanne Rafelski
Deputy Director, Allen Institute for Cell Science (formerly, Assistant Professor of Developmental and Cell Biology, UC Irvine)
Juliette Azimzadeh
Group Leader, Institute Jacques Monod, Paris, France
Nan Tang
Associate Professor, National Institute of Biological Science (NIBS), Beijing, China
Prachee Avasthi
Cofounder and CSO, Arcadia Science (formerly, Associate Professor of Biology, Dartmouth University)
Mark Chan
Assistant Professor, San Francisco State University, San Francisco, CA
Guillermina Ramirez-San Juan
Assistant Professor, EPFL (formerly assistant professor, Dept. Biology, Brandeis University)
Sarah Reiff
Data curator, 4D Nucleome Data Coordination and Integration Center, Harvard Medical School
Pranidhi Sood
Computational Biologist, Calico
Tatyana Makushok
Computatinal scientist - Altos Labs
Former Graduate Students
Jessica Feldman
Associate Professor, Dept. Biology, Stanford University
Benjamin Engel
Assistant Professor, University of Basel, Switzerland
Will Ludington
Assistant Professor, Dept. Embryology, Carnegie Institution for Science, Baltimore MD
Mark Slabodnick
Assistant Professor, Dept. Biology, Knox College
Lani Keller
Wu Tsai Endowed Chair of Science, Bishops School, La Jolla,CA
Zachary Apte
Founder and CSO of uBiome
Kim Wemmer
Senior Scientist, Zymogen
Elisa Kannegaard
Former Grad Student
Jacob Kimmel
Founder and Head of Research, NewLimit
Amy Chang
Computational Biologist, UC Laboratory for Genomics Research, San Francisco, CA
Athena Lin
Staff Scientist, Lucira
David Bauer
Software Developer, Image Analysis, BioRad
Nathan Hendel
Software engineer, Bio-rad
Rebecca McGillivary
Postdoc, UC Davis, Starr/Luxton group
Karina Perlaza
Staff Scientist, Chan Zuckerberg Biohub
Erik Navarro
Computational Biologist, Altos Labs
Former post-bac students