People

Wallace Marshall, Principal Investigator

Description of project: I am interested in how cells solve engineering problems, which I think is 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, electronics and robotics, Muay Thai
 
For more visit (eg twitter, pubmed): @WallaceUCSF

Hiroaki Ishikawa, Postdoctoral Fellow

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.
 
For more, visit: Linkedin, Google Scholar, Twitter

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

For more, visit: TwitterLinkedin, PubMed

Vincent Boudreau, Postdoctoral Fellow
 
Description of project: Photosynthetic algae are responsible for ~50% of global production of oxygen, making them critical microorganisms in our ecosystems. Despite their critical ecological role, algae and plants convert sunlight to chemical energy rather inefficiently. Having to respond to changing light conditions over either seconds during the day or seasons during the year, algae use multiple mechanisms to avoid shade, dissipate excessive sunlight and optimize their ability to do photosynthesis. Stentor pyriformis, a giant single cell, contains several hundred photosynthetic endosymbiotic algae. Remarkably, S. pyriformis is able to accomplish complex tasks as a single cell, including swimming towards light, feeding and regenerating when wounded. I am interested in the physiological contributions of the endosymbionts to their host including phototaxis and the contributions of the host to its endosymbionts including photosynthetic efficiency.
 
Ask me about: Ciliates, algae, symbiosis, photosynthesis, phototaxis, microtubule cytoskeleton, microscopy
 
When I'm not doing science, I enjoy: Exploring the diversity of the west coast from rugged deserts to alpine lakes and hydrothermal vents while building a bestiary of extreme photosynthetic microorganisms. Also an avid art consumer exploring the craftsmanship of neon sign making.
 
For more, visit: https://viboud12.github.io/
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
 

Karina Perlaza, Tetrad Graduate Student

Description of project: I am interested in how and when cells use and replenish their "reserve" resources in order to build organelles of a fixed size. I study this in Chlamydomonas reinhardtii which has two protruding organelles, called flagella, that regenerate super quickly after decapitation.

 
Ask me about: Chlamy! Genetics stuff. Dramatic transcriptional responses.
 
When I'm not doing science, I enjoy: Soccer, Watching birds, Trying to make academia a brighter place for future URMs in STEM, Reading
 
For more visit: @karina_perlaza
 

David Bauer, Biophysics Graduate Student
Description of Project: Can we learn about how cells control the size of their organelles from how Chlamydomonas regulates the length of their flagella? To address this question, I built a microfluidic device to trap live cells and image their flagella. By studying both length measurements and the noise in flagellar regeneration, we gain additional probes into the flagellar length control system.
 
Ask me about: microfluidics, microscopes, or writing code!
 
When I am not doing science, I love running, watching movies, and playing video games.
 
For more, visit me on Twitter or LinkedIn.

Nathan Hendel (Nat), Bioinformatics Graduate Student

Description of project: How do cells sense length? I am working on a mathematical model of flagellar length control in the eukaryotic algae C. reinhardtii. I am developing a theory for a mechanism of length control that harnesses the passive physics of diffusion, in which the cell uses the diffusive gradient of motor proteins as a proxy for length measurement.

Ask me about: Math, physics, programming, mathematical modeling, simulations.

When I'm not doing science, I enjoy: Playing bluegrass music on my mandolin, playing basketball and tennis, hiking.

For more, visit: LinkedIn, Twitter, PubMed

Rebecca McGillivary, Tetrad Graduate Student

Description of project: How do nuclei change shape? How does this change affect the physiology of the cell? To address these questions, I am studying a cell that undergoes a dramatic and developmentally regulated nuclear shape change: Stentor coeruleus. During regeneration, stentor’s nucleus morphs from a 1 millimeter long “string of beads” structure, to a 75 micron wide sphere, and then back to its beaded shape – all in the span of about two hours. I use microscopy and molecular biology tools to learn how nuclear transport, cytoskeletal remodeling, and the physical properties of the nucleus contribute to this remarkable shape change.

Ask me about: Ciliate biology, cell biology of the nucleus, finding really old but awesome protistology papers, immunofluorescence, live cell imaging, light microscopy, image analysis in Fiji, RNAi, and how to catch and culture stentors from your local pond


When I’m not doing science I enjoy: Drawing and painting; learning how to knit, sew, and make pottery; hiking and backpacking; and baking

For more: Visit me on Twitter or LinkedIn

Greyson Lewis, Biophysics Graduate Student
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

Ulises Diaz, Tetrad Graduate Student

Erik Navarro, Biophysics Graduate Student

Connie Yan, Tetrad Graduate Student

Peter Chudinov, Junior Specialist

 

Description of project: I study how single cells solve computational problems and navigate complex environments
 
Ask me about: Bio-inspired computing, automata, data science
 
When I'm not doing science, I enjoy: Hiking, tennis, synthesizers
 

Asa Kalish, Junior Specialist

Description of project: We're looking at how slime-mold solves problems. It turns out that this ancient single-celled organism has impressive decision-making skills, despite not having a brain. We're focused on uncovering the underlying biological mechanisms to learn more about cellular biology and cellular computation.

Ask me about: image processing, slime-mold, and organelle size control.

When I'm not doing science I enjoy: reading, baking, and biking.

For more, visit: https://twitter.com/AsaKalish

 

 

Lab Alumni

Former Postdoctoral Fellows

Shigenori Nonaka
Associate Professor, National Institute for Basic Biology, Okazaki Japan

Susanne Rafelski
Director for Assay Development, Allen Institute for Cell Science

Juliette Azimzadeh
Group Leader, Institute Jacques Monod Paris, France

Nan Tang
Assistant Professor, National Institute of Biological Science (NIBS), Beijing, China

Prachee Avasthi
Assistant Professor, University of Kansas Medical Center, Kansas City, KA

Mark Chan
Assistant Professor, San Francisco State University, San Francisco, CA

Sarah Reiff
Data curator, 4D Nucleome Data Coordination and Integration Center, Harvard Medical School

Pranidhi Sood
Calico

Guillermina Ramirez-San Juan
Brandeis University

Tatyana Makushok
Gilead

Former Graduate Students

Athena Lin
Lab Manager, Jacobs-Wagner lab, Stanford University

Jacob Kimmel
Compuational Biologist, Calico

Amy Chang
Computational Biologist

Lani Keller
Assistant Professor, Quinnipiac University

Jessica Feldman
Assistant Professor, Dept. Biology, Stanford University

Benjamin Engel
Postdoc at Max Planck Institute, Martinsried, Germany

Zachary Apte
Biotech Entrepreneur - founder of EvolveMol, SoilGen, and co-founder of uBiome

Will Ludington
Bowes Fellow at UC Berkeley

Mark Slabodnick
Postdoctoral Fellow, UNC Chapel Hill

Kim Wemmer
Senior Scientist, L'Oreal

Elisa Kannegaard
Former Grad Student