FACULTY DIRECTORY


Phil Beachy
Professor of Biochemistry and of Developmental Biology
Ph.D. in Biochemistry (Stanford University)
Joint with Department of Developmental Biology

Phil Beachy's laboratory studies the function of Hedgehog proteins and other extracellular signals in morphogenesis, and in repair and regeneration of tissue injury. The group studies how the distribution of such signals in tissues is regulated, how cells perceive and respond to distinct concentrations of signals, and how such signaling pathways arose in evolution. The lab also studies the normal roles of such signals in the physiology of stem and progenitor cells and the abnormal roles of such signaling pathways in the formation and expansion of cancer stem cells.

Lab Website         Lab Summary        CAP Profile

The role of ciliary trafficking in Hedgehog receptor signaling

Cellular origin of bladder neoplasia and tissue dynamics of its progression to invasive carcinoma

Hedgehog/Wnt feedback supports regenerative proliferation of epithelial stem cells in bladder


Onn Brandman
Assistant Professor of Biochemistry
Ph.D. in Chemical and Systems Biology (Stanford University)

The Brandman Lab studies how cells ensure protein quality and how they signal stress. To achieve this, we employ an integrated set of techniques including single cell anaysis of proteotoxic stress pathways, structural studies, in vitro translation, and full genome screens in yeast and mammalian cells.

Lab Website          Lab Summary        CAP Profile

A Ribosome-Bound Quality Control Complex Triggers Degradation of Nascent Peptides and Signals Translation Stress

Ribosome-associated protein quality control

Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains


Rhiju Das
Assistant Professor of Biochemistry
Ph.D. in Physics (Stanford University) 

Rhiju Das's research group strives to predict how sequence codes for structure in proteins, nucleic acids, and heteropolymers whose folds have yet to be explored. The Das lab uses new computational and experimental tools to tackle the de novo modeling of protein and RNA folds, the high-throughput structure mapping of riboswitches and random RNAs, and the design of self-knotting and self-crystallizing nucleic acids.

Lab Website          Lab Summary        CAP Profile

Blind tests of RNA nearest-neighbor energy prediction

Principles of Predicting RNA Secondary Structure Design Difficulty

Consistent global structures of complex RNA states through multidimensional chemical mapping


Ron Davis
Professor of Biochemistry and of Genetics
Ph.D. in Chemistry (California Institute of Technology) 

Ron Davis' research group is using Saccharomyces cerevisiae and Human to conduct whole genome analysis projects. The yeast genome sequence has approximately 6,000 genes. The Davis group has made a set of haploid and diploid strains (21,000) containing a complete deletion of each gene. In order to facilitate whole genome analysis each deletion is molecularly tagged with a unique 20-mer DNA sequence. This sequence acts as a molecular bar code and makes it easy to identify the presence of each deletion.

Lab Website          Lab Summary        CAP Profile

Mapping the Cellular Response to Small Molecules Using Chemogenomic Fitness Signatures

A Novel Low Energy Electron Microscope for DNA Sequencing and Surface Analysis

Genomic responses in mouse models poorly mimic human inflammatory diseases


Pehr Harbury
Associate Professor of Biochemistry
Ph.D. in Biological Chemistry (Harvard University)


The Harbury lab aims to measure and understand dynamic structural changes in proteins, and their role in the functional biology of macromolecular machines. We are developing tools to determine 3D protein structures and to detect structural fluctuationsin situ: directly inside cells and in complex reconstituted systems. A second objective is to genetically map chemical space and exploit it for the discovery of tailored small molecules. We have created a technology that reenacts billions of years of natural product evolution in a test tube. More generally, we explore innovative experimental approaches to problems in molecular biochemistry, focusing on technologies with the potential for broad impact.

Lab Website         Lab Summary         CAP Profile

Design of Protein-Ligand Binding Based on the Molecular-Mechanics Energy Model

Remeasuring the Double Helix

Synthetic Ligands Discovered by In Vitro Selection


Dan Herschlag
Professor of Biochemistry and, by courtesy, of Chemistry and of Chemical Engineering

Ph.D. in Biochemistry (Brandeis University) 
 

The Herschlag group's research is aimed at understanding the chemical and physical behavior underlying biological macromolecules and systems, behaviors that define the capabilities and limitations of biology. Toward this end we use multidisciplinary approaches to understand how RNA and protein enzymes assemble active sites and achieve their enormous catalytic power and exquisite specificity; we are developing a quantitative and predictive understanding of RNA folding; and we are uncovering the rules that determine RNA/protein interactions in vitro and in vivo. Our research has broad implications for evolution and function of RNA and proteins and for how RNA/protein interactions regulate gene expression. 

Lab Website           Lab Summary         CAP Profile

A Kinetic and Thermodynamic Framework for P4-P6 RNA Reveals Tertiary Motif Modularity and Modulation of the Folding Preferred Pathway

Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and their mRNA Targets

Extensive Site-directed Mutagenesis Reveals Interconnected Functional Units in the Alkaline Phosphatase Active Site


Peter Kim
Professor of Biochemistry
Ph.D. in Biochemistry (Stanford University)

We are studying the mechanism of viral membrane fusion and its inhibition by drugs and antibodies. We use the HIV envelope protein (gp120/gp41) as a model system. Some of our studies are aimed at creating an HIV vaccine that elicits antibodies against a transient, but vulnerable, intermediate in the membrane-fusion process, called the pre-hairpin intermediate. We are also interested in protein surfaces that are referred to as “non-druggable”. These surfaces are defined empirically based on failure to identify small, drug-like molecules that bind to them with high affinity and specificity. Some of our efforts are aimed at characterizing select non-druggable targets. We are also interested in developing methods to identify ligands for non-druggable protein surfaces.

Lab Website         Lab Summary        CAP Profile

Vaccination with peptide mimetics of the gp41 prehairpin fusion intermediate yields neutralizing antisera against HIV-1 isolates

Protein design of an HIV-1 entry inhibitor

Inhibiting HIV-1 entry: discovery of D-peptide inhibitors that target the gp41 coiled-coil pocket


Mark Krasnow
Professor of Biochemistry
M.D. and Ph.D. in Biochemsistry (University of Chicago)

Genetic and molecular basis of respiratory system development, maintenance, and disease in Drosophila, mouse, and human.

Lab Website          Lab Summary         CAP Profile

Alveolar progenitor and stem cells in lung development, renewal and cancer

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

Oxygen regulation of breathing through an olfactory receptor activated by lactate


Lingyin Li
Assistant Professor of Biochemistry
Fellow of ChEM-H Institute
Ph. D., Chemistry, University of Wisconsin-Madison

We use chemical biology to uncover biochemical mechanisms in innate immunity and, in parallel, develop therapeutic hypotheses and lead compounds. Innate immune pathways as the first line of defense against pathogens present many exciting opportunities for chemical biologists. These pathways are a rich source of novel chemistry: they involve diverse molecular patterns in pathogens, little-explored second messengers, and drugs with poorly understood mechanism. Activation of innate immunity is a proven therapeutic strategy for vaccination, viral infection, and cancer, while inhibition is a strategy for treating autoimmune diseases and sterile inflammation. To date, however, most modulators of innate immunity are broad, non-specific, and poorly characterized, such as killed bacteria, alum crystals, and steroids. The Li lab seeks to improve understanding of these pathways and facilitate the development of more precise drugs for preventing or treating specific diseases. 

Lab Website          Lab Summar         CAP Profile

Anticancer Flavonoids are Mouse-Selective STING Agonists

Hydrolysis of 2’3’-cGAMP by ENPP1 and design of nonhydrolyzable analogs


Suzanne Pfeffer
Professor and Chairman of Biochemistry
Ph.D. in Biochemistry (U.C. San Francisco) 

The goal of research in the Pfeffer Lab is to elucidate the molecular mechanisms by which proteins are targeted to specific membrane compartments. How do transport vesicles select their contents, bud, translocate through the cytoplasm, and then fuse with their targets? The Pfeffer Lab studies the Ras-like Rab GTPases--how they are localized to distinct intracellular compartments in human cells, and how they serve as master regulators of all receptor trafficking events.

Lab Website          Lab Summary        CAP Profile

Protein flexibility is required for vesicle tethering at the Golgi

Lysosomal membrane glycoproteins bind cholesterol and contribute to lysosomal cholesterol export

The Rab6-regulated KIF1C kinesin motor domain contributes to Golgi organization


Rajat Rohatgi
Assistant Professor of Biochemistry and of Medicine (Oncology)
M.D. and Ph.D. in Cell Biology (Harvard University)
Joint with Department of Medicine

The Rohatgi Lab is working to elucidate the biochemical and cell biological principles that govern signaling pathways that sit at the intersection between developmental biology and cancer. Their toolkit combines bulk biochemical techniques, such as cell-free reconstitution, with microscopy using novel optical probes to study the dynamics of signal propagation in cells. The group strives to develop novel strategies for the manipulation of these pathways for cancer therapies and applications in regenerative medicine.

Lab Website         Lab Summary         

In Vivo Formation of Vacuolated Multi-phase Compartments Lacking Membranes

Chromatin-Remodeling Complex SWI/SNF Controls Multidrug Resistance by Transcriptionally Regulating the Drug Efflux Pump ABCB1

Structural basis of Smoothened regulation by its extracellular domains


Julia Salzman
Assistant Professor of Biochemistry
Ph.D. in Statistics (Stanford University) 
Joint with Stanford Cancer Institute 

Our goal is to develop statistical and experimental tools to construct a high dimensional picture of gene regulation, including cis and trans control of the full repertoire of RNAs expressed by cells.  Currently, we are studying the function and biogenesis of circular RNA, which we recently discovered to be a ubiquitous and uncharacterized component of eukaryotic gene expression.  A second major goal is to study gene expression variation in human cancer.  Using massive public datasets and primary tumors, we develop new bioinformatic and statistical tools and test models.  We use the cancer genome as window into functional roles played by RNA, and are attempting to characterize potential biomarkers.

Lab Website         Lab Summary        CAP Profile

Detecting Circular RNAs: bioinformatic and experimental challenges

Circular RNA biogenesis can proceed through an exon-containing lariat precursor

Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during fetal development


James Spudich
Professor of Biochemistry
Ph.D. in Biochemistry (Stanford University) 

The general research interest of The Spudich Group is the molecular basis of cell motility. the lab has three specific research interests, the molecular basis of energy transduction that leads to ATP-driven myosin movement on actin, the biochemical basis of the regulation of actin and myosin interaction and their assembly states, and the roles these proteins play in vivo, in cell movement and changes in cell shape.

Lab Website          Lab Summary         CAP Profile

Contractility parameters of human β-cardiac myosin with the hypertrophic cardiomyopathy mutation R403Q show loss of motor function

The myosin mesa and a possible unifying hypothesis for the molecular basis of human hypertrophic cardiomyopathy

Beyond the myosin mesa: a potential unifying hypothesis on the underlying molecular basis of hyper-contractility caused by a majority of hypertrophic cardiomyopathy mutations


Aaron Straight
Associate Professor of Biochemistry
Ph.D. in Biochemistry (U.C. San Francisco) 

The Straight Group studies the process of cell division in eukaryotes focusing on the mechanisms of chromosome segregation. Their research utilizes biophysical, biochemical, microscopic and cell biological approaches in systems ranging from yeasts and flies to frogs and humans. Their goal is to understand, at a molecular level, the principles of chromosome organization and segregation that ensure genome stability during cell division and differentiation.

Lab Website          Lab Summary        CAP Profile

A cell-free CENP-A assembly system defines the chromatin requirements for centromere maintenance

A Conserved Mechanism for Centromeric Nucleosome Recognition by Centromere Protein CENP-C

In vitro centromere and kinetochore assembly on defined chromatin templates


Julie Theriot
Professor of Biochemistry and of Microbiology and Immunology
Ph.D. in Cell Biology (U.C. San Francisco) 

The Theriot group studies the interactions between infectious bacteria and the human host cell actin cytoskeleton. Listeria monocytogenes and Shigella flexneri are unrelated food-borne bacterial pathogens that share a common mechanism of invasion and actin-dependent intercellular spread in epithelial cells. The lab's studies fall into three broad areas: the biochemical basis of actin-based motility by these bacteria; the biophysical mechanism of force generation; and the evolutionary origin of pathogenesis.

Lab Website         Lab Summary         CAP Profile

Bipedal Locomotion in Crawling Cells

Myosin II contributes to cell-scale actin network treadmilling via network disassembly

Bacterial Chromosomal Loci Move Subdiffusively through a Viscoelastic Cytoplasm


Ellen Yeh
Assistant Professor of Biochemistry, of Pathology and of Microbiology and Immunology
M.D. and Ph.D. in Biophysics (Harvard University) 
Joint with Department of Pathology

My research focuses on the apicoplast, a prokaryotically-derived plastid organelle unique to Plasmodium (and other pathogenic Apicomplexa parasites) and a key anti-malarial drug target. My laboratory's goal is to elucidate apicoplast biology, function, and role in pathogenesis with the ultimate goal of realizing the potential of the apicoplast as a therapeutic target.

Lab Website          Lab Summary          CAP Profile

Chemical Rescue of Malaria Parasites Lacking an Apicoplast Defines Organelle Function in Blood-Stage Plasmodium falciparum

A Chemical Rescue Screen Identifies a Plasmodium falciparum Apicoplast Inhibitor Targeting MEP Isoprenoid Precursor Biosynthesis

The prenylated proteome of Plasmodium falciparum reveals pathogen-specific prenylation activity and drug mechanism-of-action


ASSOCIATE FACULTY

Steve Artandi
Professor of Medicine (Hematology) and of Biochemistry
M.D. and Ph.D. in Microbiology (Columbia University)
Joint with Department of Medicine

In the Artandi lab, we are interested in unraveling the molecular and cellular mechanisms according to which telomeres and telomerase modulate stem cell function and carcinogenesis. Telomeres, the nucleotide repeats that cap the ends of eukaryotic chromosomes, which serve critical roles in promoting cell viability and in maintaining chromosomal stability. In humans, telomeres shorten progressively with cell division in primary human culture because DNA polymerase cannot fully replicate the extreme ends of chromosomes. Critical telomere shortening and loss of the protective telomere capping function in cell culture initiates senescence and crisis responses that profoundly alter chromosome stability, cell cycle progression and survival.

Lab Website          Lab Summary          

High telomerase is a hallmark of undifferentiated spermatogonia and is required for maintenance of male germline stem cells

A Human Telomerase Holoenzyme Protein Required for Cajal Body Localization and Telomere Synthesis

TPP1 OB-Fold Domain Controls Telomere Maintenance by Recruiting Telomerase to Chromosome Ends


chu.jpg

Gil Chu
Professor of Medicine (Oncology) and of Biochemistry
M.D. (Harvard University) and Ph.D. in Physics (MIT) 
Joint with Department of Medicine

Gil Chu's laboratory studies how cells respond to damaged DNA. The group focuses on pathways for the repair of UV-damaged DNA and the repair of DNA double-strand breaks induced by ionizing radiation and V(D)J recombination, the mechanism that generates immunological diversity. In the hope of improving cancer treatment and prevention, the lab uses microarrays to study transcriptional responses to DNA damage in cancer patients.

Lab Website         Lab Summary         CAP Profile

Local false discovery rate facilitates comparison of different microarray experiments

Cooperative Assembly of a Protein-DNA Filament for Nonhomologous End Joining

Double-Strand Break Repair


James Ferrell
Professor of Chemical and Systems Biology and of Biochemistry
M.D. and Ph.D. in Chemistry (Stanford University) 
Joint with Department of Chemical and Systems Biology


The Ferrell Lab has been studying the system of regulatory proteins that drives the cell cycle, through a combination of quantitative experimental approaches, computational modeling, and the theory of nonlinear dynamics. The goal is to understand the design principles of this system, and perhaps to gain insight into the systems that drive other biological oscillations (e.g. heart beats, calcium oscillations, circadian rhythms) as well.

Lab Website           Lab Summary         CAP Profile

Mitotic trigger waves and the spatial coordination of the Xenopus cell cycle

Changes in Oscillatory Dynamics in the Cell Cycle of Early Xenopus laevis Embryos

Thresholds and ultrasensitivity from negative cooperativity


COURTESY FACULTY

Chaitan Khosla
Professor of Chemical Engineering and of Chemistry and, by Courtesy, of Biochemistry
Ph.D. (California Institute of Technology)
Joint with Department of Chemical Engineering

Research interests in the Khosla Laboratory lie at the interface of chemistry and medicine. For the past several years, the lab has investigated the catalytic mechanisms of modular megasynthases such as polyketides synthases, with the concomitant of harnessing their programmable chemistry for preparing new antibiotics. More recently, the group has investigated the pathogenesis of celiac sprue, an HLA-DQ2 associated autoimmune disease of the small intestine.

Lab Website          Lab Summary         

A Turnstile Mechanism for the Controlled Growth of Biosynthetic Intermediates on Assembly Line Polyketide Synthases

Partial In Vitro Reconstitution of an Orphan Polyketide Synthase Associated with Clinical Cases of Nocardiosis

Parallel shRNA and CRISPR-Cas9 screens enable antiviral drug target identification


Sharon Long
Professor in Biological Sciences and, by courtesy, of Biochemistry
Ph.D. in Cell and Developmental Biology (Yale University)
Joint with Department of Biology


The Long Laboratory studies the early stages of symbiosis between Rhizobium (also Sinorhizobium) meliloti and and its host plants in the genus Medicago. The symbiosis is uniquely approachable by experiment because each partner can be genetically manipulated, and transgenic organs can be constructed, allowing highly specific genetic tests of various components of signal and response. The lab uses genetics, biochemistry and cell biological approaches to study how cell division, growth, and gene expression arise in each partner due to stimulation from the other.

Lab Website         Lab Summary        CAP Profile


Founding Faculty
June 1959

 

Robert Lehman

Robert Lehman

Lab Website

Dale Kaiser

Dale Kaiser

Lab Summary      Lab Website

David Hogness

David Hogness

Lab Website



Emeritus Faculty

shapeimage_5.jpg

Pat Brown

Lab Website

 
Doug Brutlag

  Doug Brutlag

Lab Website