Investigator Program

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U |V | W | X | Y | Z

Adam Abate, PhD.

UCSF
Abate builds new technologies to enable complex biological systems to be understood quantitatively and comprehensively, as illustrated by his development of the picoinjector to inject very small volumes of reagents into droplets at high rates. He is now developing ways of printing organ-like structures by the precise placement of different cell types at defined positions.

"The CZ Biohub has chosen some of Berkeley’s best and most innovative researchers, who offer an amazing breadth of expertise. This first cohort of Investigators illustrates the potential and promise of the CZ Biohub to push the boundaries of biomedical research, and to accelerate the development of breakthrough scientific and medical advancements, applications and therapeutics for the public’s benefit.” Nicholas Dirks Chancellor, UC Berkeley 

Jillian Banfield, PhD.

UC Berkeley
Banfield is uncovering the vast diversity of microorganisms that depend on co-existing microbial community members for most core metabolic resources and has discovered two major evolutionary radiations, one in bacteria and the other in archaea. She is exploring the medical, industrial, and ecological significance of these newly found microorganisms.

Catherine Blish, MD, PhD.

Stanford
Blish aims to build an atlas of host-pathogen interactions to serve as a template to elicit immune responses that will promote pathogen eradication. She seeks to understand how to control the innate immune response mediated by NK and other cells to eliminate infections and develop more potent methods of protection.

Abigail Buchwalter, PhD.

UCSF
Buchwalter studies the mechanisms that govern the maintenance, remodeling, and specialization of nuclear organization across cell types. Her work is uncovering relationships between nuclear bodies such as the nuclear lamina and the nucleolus and defining how nuclear organization is disrupted by aging and disease.

Carlos Bustamante, PhD.

Stanford
Bustamante is making the transition from population genetics to a new area, the integration and analysis of massive data coming from consumer, health care, and financial sources. He is especially interested in bringing together direct-to-consumer genetics and phenotype data in a secure space that can be explored by academic, industry, and citizen scientists.

“The extraordinary promise of the CZ Biohub is being realized today with the announcement of a remarkably talented group of researchers from our three campuses. These Investigators are each working at the leading edge of science. Support from the CZ Biohub will drive exciting new collaborations across biomedical science, engineering, and computational science to attack some of the biggest unsolved problems in biology and human health.” Sam Hawgood Chancellor, UCSF

Seemay Chou, PhD.

UCSF
Chou studies the mechanisms driving tick-borne transmission of bacterial pathogens, such as Borrelia burgdorferi, the causative agent of Lyme disease. She would like to understand why only certain tick species are capable of transmitting these bacteria, with the goal of identifying new strategies for blocking the cycle of infection.

Michael Clarke, MD.

Stanford
Clarke investigates the molecular regulation of stem cell regeneration (self-renewal) in normal and diseased tissue. His laboratory has generated novel tools to define epigenetic regulators of stem cell self-renewal. He is using these tools to elucidate how self-renewal pathways are modified in cancer and degenerative diseases such as Alzheimer’s disease, Down’s syndrome, osteoporosis and diabetes mellitus.

Adam de la Zerda, PhD.

Stanford
De la Zerda’s goal is to image 100 million cells in living tissues at single-cell resolution by using optical coherence tomography. One of the potential uses of his technique will be to visualize cancer markers to delineate the margins of tumors.

Hana El-Samad, PhD.

UCSF
El-Samad analyzes the control of feedback loops, a fundamental underpinning of life, to understand their interconnected architecture and predict their failure modes in disease. She is embarking on a major effort to build de novo synthetic circuits consisting of biomolecules that can implement feedback control on demand.

Michael Fischbach, PhD.

Stanford CZ Biohub Microbiome Initiative Investigator
Fischbach is identifying and characterizing small molecules produced by the microbiome. Fischbach also seeks to design and build highly complex synthetic communities with a defined metabolite output, which includes efforts to map strain-strain and strain-metabolite interactions within communities, and to 'backfill' communities in vitro and in vivo with strains that contribute to increased community stability

Daniel Fletcher, PhD.

UC Berkeley
Fletcher studies how cells assemble molecular-scale parts into micron-scale structures necessary for cell motility, cell-cell signaling, and host-pathogen interactions. He plans to launch a new effort to map the topography and spatial organization of cell-cell surfaces, starting with macrophages in their interactions with tumor cells.

“The research by these extraordinary scientists receiving CZ Biohub awards exemplifies the exciting opportunities that lie in collaborative research at the intersection of biology and engineering. We look forward to the new discoveries benefiting human health that will be made possible by their collaborations.” Marc Tessier-Lavigne President, Stanford University

Polly Fordyce, PhD.

Stanford
Fordyce will develop new biochip technologies for high-throughput functional characterization of proteins to enhance our ability to predict the function of a protein given its amino acid sequence. Her aim is to characterize the properties of more than a thousand proteins, such as enzymes and transcription factors, in a single experiment.

Adam Frost, MD, PhD.

UCSF
Frost uses atomic-resolution cryo-electron microscopy in concert with biochemistry, genetics and live imaging to advance our understanding of how cellular machines function normally, how they are corrupted by disease, and how they are hijacked by infectious pathogens. His studies of protein quality control may lead to new targets for the therapy of infectious diseases.

Judith Frydman, PhD.

Stanford
Frydman uses multidisciplinary approaches to gain a comprehensive understanding of the complex networks mediating protein homeostasis, the maintenance of protein quality. She plans to map the proteostasis network involving more than a thousand proteins, and use this information to develop a new class of therapeutic agents for dengue, Zika, and other viral diseases.

Zev Gartner, PhD.

UCSF
Gartner aims to define the rules used by cells to self-organize into structurally ordered tissues, and to reveal how tissue structure guides the flow of information between cells to coordinate decisions and behaviors. He is developing a system to quantitatively measure how the local density of mesenchymal cells and their tractions affects the curvature of overlying tissue.

Bryan Greenhouse, MD.

UCSF
Greenhouse addresses fundamental questions about the transmission of malaria to better target and evaluate interventions for controlling the disease, combining field studies in infected areas with advanced molecular genetic studies in the laboratory. He is using more sensitive parasite detection and genotyping methods to track infections and screening for malaria-specific antibodies as a record of past exposure.

William Greenleaf, PhD.

Stanford
Greenleaf studies the physical and spatial organization of the human genome at multiple scales and across different biological states. His aim is to unravel the quantitative relations between regulatory elements and gene expression in a massive parallel way to generate a quantitative model of the regulatory wiring of cells.

Lisa Gunaydin, PhD.

UCSF
Gunaydin seeks to elucidate the cellular and circuit mechanisms underlying major psychiatric diseases. She will carry out optogenetic studies of a genetic mouse model of obsessive-compulsive disorder to elucidate the patterns of abnormal neural activity as a first step in intervening to restore normal behavior.

Amy Herr, PhD.

UC Berkeley
Herr is designing, developing, and disseminating tools to quantify biological complexity, from the level of biomolecules to tissues, using novel engineering approaches. She is focusing on protein cytometry, as exemplified by single-cell electrophoresis followed by antibody probing to simultaneously achieve high specificity and high sensitivity.

Bo Huang, PhD.

UCSF
Huang has visualized the dynamics of chromosomal organization by multicolor imaging and has developed super-resolution microscopic methods for mapping proteins in key cellular structures. He plans to develop a fluorescence-microscopy-based approach for the discovery and characterization of cell signaling networks, particularly those involving G-protein coupled receptors.

KC Huang, PhD.

Stanford
CZ Biohub Microbiome Initiative Investigator Huang is mapping the spatial structure of microbial communities surrounding the host epithelium in the gut. He is developing biomarkers for imaging-based approaches to diagnosis and also devising strategies (e.g., adding or subtracting community members) to inhibit pathogens by diverting their adhesive interactions.

Alexander (Sandy) Johnson, PhD.

UCSF CZ Biohub Microbiome Initiative Investigator
Johnson is initiating a comprehensive study of how mixed species microbiome communities form and thrive. He is interested in the sociobiology of the human microbiome and in elucidating how communities from the three domains of life interact. Johnson is also reconstructing the evolutionary changes that enabled the yeast Candida albicans to become a component of the microbiome as well as a pathogen in humans.

Martin Kampmann, PhD.

UCSF
Kampmann’s goal is to understand the molecular mechanisms driving neurodegenerative diseases such as Alzheimer’s and Parkinson’s. He is developing cell-based models of neurodegenerative disease processes in human induced pluripotent stem cells and is carrying out CRISPRi screens to identify underlying neuron-specific processes.

Brian Kobilka, MD.

Stanford
Kobilka’s pioneering x-ray crystallographic studies have revealed how the binding of a hormone to the extracellular pocket on a G-protein coupled receptor is transmitted across the cell membrane to trigger a signaling cascade. He is now carrying out structural studies of opioid receptors to identify more effective painkillers with fewer side effects.

Tanja Kortemme, PhD.

UCSF
Kortemme is developing a platform technology to computationally engineer novel biological components that convert the sensing of diverse and currently undetectable small molecule signals into cellular responses. She is devising ways of making CRISPR-based gene editing switchable by small molecules.

Markita Landry, PhD.

UC Berkeley
Landry is developing new nanosensor technology and near infrared imaging platforms to visualize neurotransmitters in the living brain at high spatial and temporal resolution. She will focus on deep brain imaging of dopamine as an initial step in furthering our understanding of psychiatric disorders.

Jure Leskovec, PhD.

Stanford
Leskovec studies massive complex networks at a very wide range of scales, from interactions of proteins in a cell to interactions between humans in a society. He is devising new computational network tools to enhance patient care through social support, facilitate the diagnosis of disease by wearable sensors, and promote positive behaviors conveyed by social networks.

Jennifer Listgarten, PhD.

UC Berkeley
Listgarten works at the intersection of machine learning, statistics and molecular biology. Problem domains of interest to her include genetics, epigenetics, immunology, proteomics, gene editing and rational protein engineering. She develops new computational and machine learning methods to uncover data-driven insights from complex systems, along with corresponding tools for others to use.

Hiten Madhani, MD, PhD.

UCSF
Madhani is exploring whether cells maintain epigenetic memory, mediated for example by the methylation of cytosine residues in DNA, over evolutionary timescales. He is characterizing extant DNA methyltransferases, particularly those involved in fungal virulence, to trace their evolution and to engineer cellular memory devices.

Michel Maharbiz, PhD.

UC Berkeley
Maharbiz explores the ways that miniaturized technology and biology can be threaded together to create novel clinical devices that interface with the human body and provide real-time information about molecular and physiological states. He invented neural dust as a general platform for reading and writing data to tiny (~100 micrometer) implants that are activated by ultrasound.

Susan Marqusee, MD, PhD.

UC Berkeley
Marqusee uses biophysical approaches to understand the information encoded in a protein sequence that governs protein dynamics and folding. She plans to develop new high-throughput methods to characterize the effect of changes in sequence and environment on protein function with the aim of enabling more precise predictions of the biological effects of genetic mutations and other sequence variants.

Alex Marson, MD, PhD.

UCSF
Marson is developing genome editing technologies to understand how sequence variation in the human genome alters and controls T cell immune function. He aims to engineer a new generation of targeted therapies for autoimmune disorders, immunodeficiencies, and infectious diseases.

Rikky Muller, PhD.

UC Berkeley
Muller is developing new wireless microsystems that directly interface with the brain for long-term, minimally-invasive neurological recording. Her broad goal is to engineer novel implants that can simultaneously sense and alter physiological responses to enable drug delivery and the treatment of neuropsychiatric disorders.

Katherine Pollard, PhD.

Gladstone Institutes/UCSF
Pollard studies the microbiome of humans, the microorganisms and viruses harbored by us, to determine its role in shaping the health of people and their responses to therapeutic agents. Her laboratory has just released prototype open source software that quantifies microbial population genetic variation using metagenomics data and will scale it for use by hospitals.

Ada Poon, PhD.

Stanford
Poon aims to find new ways of miniaturizing bioelectronic devices, targeting specific neural circuits in vivo, and supporting closed-loop monitoring and manipulation of neural circuits. Her bioelectronics platform integrates electrical stimulation and recording with optogenetic stimulation and will be used to study neural circuits in a mouse model of Alzheimer’s disease.

Matthew Porteus, MD, PhD.

Stanford
Porteus uses genome editing as curative therapy for genetic diseases, as exemplified by his correction of the mutation in sickle cell disease in hematopoietic stem and progenitor cells. He is now combining genome editing with synthetic biology to engineer cells having new phenotypic properties, such as engineering resistance to HIV and enhancing wound healing.

Manu Prakash, PhD.

Stanford
Prakash develops measurement tools, such as ultra-low cost microscopy platforms for field diagnostics of infectious diseases, for use in extreme resource-poor areas of the world. His aim is to devise new frugal platforms for the diagnosis and surveillance of schistosomiasis, leishmaniasis, and malaria.

David Relman, MD.

Stanford CZ Biohub Microbiome Initiative Investigator
Relman is exploring the assembly, composition, interactions, stability and resilience of the human microbiome in health and disease. He will design and test strategies for monitoring, measuring and manipulating the human microbiome to promote health and accelerate recovery from disease.

Oren Rosenberg, MD, PhD.

UCSF
Rosenberg uses structural biology and microbial genetics to discover and exploit molecular vulnerabilities in bacteria for the development of next-generation therapeutics. He focuses on bacterial virulence systems that mediate interactions with the mammalian host in his search for new targets.

Kole Roybal, PhD.

UCSF
Roybal explores how T cells orchestrate a vast signaling network during their activation in the immune response. He will focus on the dynamics of synthetic notch receptors and other signaling domains to devise new ways of controlling immune function in cancer therapy.

Kim Seed, PhD.

UC Berkeley
Seed carries out epidemiologic studies of the interactions between bacteriophages and Vibrio cholera in samples obtained from cholera outbreaks to enhance our understanding of how these viruses shape the communities of these pathogens and affect infectivity. She will also determine how microclimates impact phage-host interactions.

Lucy Shapiro, PhD.

Stanford
Shapiro has established the bacterium Caulobacter crescentus as a powerful model organism for understanding self-organization and spatially controlled differentiation leading to daughter cells with different cell fates. She is developing a reaction-diffusion model that includes all essential cellular process to gain a deeper understanding of asymmetric cell division and cell polarity.

Christina Smolke, PhD.

Stanford
Smolke is engineering yeast to produce complex, valuable plant-inspired medicinal compounds like those widely used as antihypertensives and anticancer agents. She interacts with experts in plant-specialized metabolism to identify gene clusters that can be inserted into her optimized yeast platform to accelerate the discovery of new therapeutic agents.

Tom Soh, PhD.

Stanford
Soh has devised sensors capable of continuously monitoring specific biomolecules in vivo and a control system for achieving real-time closed-loop controlled drug delivery in live animals. He plans to generate detection systems for hitherto untargetable biomolecules and to develop real time sensors that can be implanted in vivo to detect multiple biomolecules that are medically important.

Yun Song, PhD.

UC Berkeley
Song has derived novel mathematical formulas and new analytical techniques for inferring demographic history from population genetic data and for increasing the power of genome-wide natural selection scans. He is using new probabilistic models to elucidate the dynamics of protein initiation and elongation on ribosomes, and has recently moved into computational immunology.

Justin Sonnenburg, PhD.

Stanford CZ Biohub Microbiome Initiative Investigator
Sonnenburg is analyzing the microbiome of the gut from a mechanistic, ecological, and systems perspective. He focuses on how the microbiome is altered by dietary interventions in human subjects. Sonnenburg's goal is to empirically determine the diet-microbiota-immune interplay by bringing together genomic, transcriptomic, mass cytometric, and machine learning approaches.

Matthew Spitzer, PhD.

UCSF
Spitzer investigates how immune responses are coordinated across cell types, time and space. His lab uses single-cell analysis and computational biology to build models of the immune system and its dynamics during challenges, including cancer and infection.

Aaron Streets, PhD.

UC Berkeley
Streets will develop optical and microfluidic methods to carry out chemical and transcriptional profiling of single-cells in whole tissues with preservation of positional information. He will use stimulated Raman scattering microscopy for determining chemical composition and laser-assisted microfluidics for transcriptional profiling.

Alice Ting, PhD.

Stanford
Ting develops, scales up, and broadly disseminates molecular technologies for mapping cells and functional circuits, as illustrated by her biotin-based method for protein mapping in living cells. She is devising methods for identifying the ensemble of neurons that encode or control a specific memory, behavior or emotional state by using a light- and calcium-gated transcription factor.

Peter Turnbaugh, PhD.

UCSF CZ Biohub Microbiome Initiative Investigator
Turnbaugh focuses on discovering and characterizing human gut microbial enzymes involved in the metabolism of drugs and dietary compounds. Together with members of the CZ Biohub Microbiome Initiative, he plans to scale-up these discovery efforts and to develop strategies for the precise manipulation of gut microbial structure and function.

Laura Waller, PhD.

UC Berkeley
Waller’s goal is to develop simple and inexpensive microscopes that can image previously inaccessible information using computational microscopy, the joint design of imaging system hardware and software. She is now working on the challenging problem of 3D imaging in scattering media, such as deep structures of the brain, essential for unraveling neural activity.

Taia Wang, MD, PhD.

Stanford
Wang studies human immunity and susceptibility to viral pathogens such as dengue virus. Her research is driven by the finding that humans have diverse immunoglobulin Fc domains that affect the severity of viral diseases and the effectiveness of vaccines.

James Wells, PhD.

UCSF
Wells is tackling the fundamental question of how cells remodel their surface proteomes, encoded by about 3000 genes, in response to changes in state, disease, and therapeutic intervention. He is developing robust quantitative proteomics methods for profiling cell surfaces and generating recombinant antibodies to membrane proteins on an industrialized scale to address this challenge.

Ke Xu, PhD.

UC Berkeley
Xu is developing novel super-resolution microscopy methods with a resolution below 10 nm that are revealing new ordered structures, such as a periodic cytoskeleton in nerve axons. His next step is to obtain functional information from super-resolution microscopy by combining it with multi-color fluorescence spectroscopy.

Ellen Yeh, MD, PhD.

Stanford

Yeh studies the apicoplast, a unique organelle in Plasmodium falciparum parasites, to identify new targets for the prevention and therapy of malaria. She aims to comprehensively identify the apicoplast proteome and to understand the novel biogenesis pathways of this unusual plastid in her search for novel therapeutic targets.

Nir Yosef, PhD.

UC Berkeley
Yosef uses computational tools to understand how transcription is regulated in mammalian cells and to learn how changes in transcription are associated with different cell-states or diseases. He seeks to develop data-driven approaches for defining the key factors that contribute to cell-to-cell variability with a focus on the cellular diversity of the immune system.

Wenjun Zhang, PhD.

UC Berkeley
Zhang is engineering the biosynthesis of natural products by exploiting novel enzymatic machinery for synthesizing many unique pharmacophores and molecular scaffolds. She is developing a general platform for the in situ tagging of natural product mixtures to enable subsequent visualization by fluorescence imaging or stimulated Raman scattering microscopy.

James Zou, PhD.

Stanford
Zou develops novel machine learning tools that enable researchers to make complex predictions and quantify disease mechanisms using population genomics and epigenomics data. He is devising new deep learning models to increase the accuracy of predicting genetic risk from genotypes and of identifying distinct cell populations based on single cell transcriptional profiles.

Investigator Program Alumni

Elizabeth Sattely, PhD.

Stanford
Sattely plans to merge engineering and detailed knowledge of plant biochemical pathways to enhance human health. Her specific goal is to engineer strains of the most widely consumed dietary plants, such as maize and wheat, to improve their nutrient content and to then test the effect of a diet rich in these strains on the health of rodents.