School of Medicine
Showing 1-100 of 110 Results
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Christopher O. Barnes
Assistant Professor of Biology and, by courtesy, of Structural Biology
Current Research and Scholarly InterestsResearch in our lab is aimed at defining the structural correlates of broad and potent antibody-mediated neutralization of viruses. We combine biophysical and structural methods (e.g., cryo-EM), protein engineering, and in vivo approaches to understand how enveloped viruses infect host cells and elicit antigen-specific immune responses. We are particularly interested in the co-evolution of HIV-1 and broadly-neutralizing IgG antibodies (bNAbs), which may hold the key to the development of an effective HIV-1 vaccine. In addition, we are investigating antibody responses to SARS-CoV-2 and related zoonotic coronaviruses (CoV), with the related goal of developing broadly-protective immunotherapies and vaccines against variants of concern and emerging CoV threats.
HIV-1; SARS-CoV-2; coronaviruses; cryo-EM; crystallography; vaccines; directed evolution -
Andrew Beel
Instructor, Structural Biology
BioAndrew Beel received an M.D. and a Ph.D. in Biophysics from Stanford, where he studied the structure and condensation of the eukaryotic chromosome under the supervision of Roger Kornberg. He started his independent research program in late 2022 after receiving an Early Independence Award from the Office of the Director of the National Institutes of Health. His group is broadly interested in mesoscale biological organization and the physical underpinnings thereof, with a current emphasis on the axial core of the metaphase chromosome. The Beel lab is actively recruiting new members at all stages of training; interested parties are encouraged to apply (please direct inquiries to beelaj@stanford.edu).
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Axel Brunger
Professor of Molecular and Cellular Physiology, of Neurology, of Photon Science and, by courtesy, of Structural Biology
Current Research and Scholarly InterestsOne of Axel Brunger's major goals is to decipher the molecular mechanisms of synaptic neurotransmitter release by conducting imaging and single-molecule/particle reconstitution experiments, combined with near-atomic resolution structural studies of the synaptic vesicle fusion machinery.
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Zev Bryant
Associate Professor of Bioengineering and, by courtesy, of Structural Biology
Current Research and Scholarly InterestsMolecular motors lie at the heart of biological processes from DNA replication to vesicle transport. My laboratory seeks to understand the physical mechanisms by which these nanoscale machines convert chemical energy into mechanical work.
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Alexander Cocker
Postdoctoral Scholar, Structural Biology
BioFollowing two years working in clinical trials Dr Cocker started his PhD under the supervision of Professor Mark Johnson and Dr Nesrina Imami, studying the impact of HIV-1 infection on pregnancy related immunological changes using fluorescent cytometry and functional assays to explore natural killer, dendritic and T cell populations longitudinally.
Dr Cocker is continuing his work in HIV and other infectious diseases, and is especially focussed on how chronic infection can affect natural killer cell education, development and function. -
Patricia Cross
Professor (Teaching) of Structural Biology, Emerita
Current Research and Scholarly InterestsI am not now actively involved in research, but my past endeavors remain central to my position in guiding medical students in their scholarship pursuits.
The cited publications represent three areas of interest:
(1) medical student research (Jacobs and Cross)
(2) women in medicine (Cross and Steward)
(3) the reproductive physiology of early development (Cross and Brinster)
Only one publication is listed in this area since the research is not current, but others (in e.g. Nature, DevBiol, ExpCellRes) give a broader picture of my pursuit when at the University of Pennsylvania. -
Adam de la Zerda
Associate Professor of Structural Biology and, by courtesy, of Electrical Engineering
Current Research and Scholarly InterestsMolecular imaging technologies for studying cancer biology in vivo
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Ron Dror
Associate Professor of Computer Science and, by courtesy, of Molecular and Cellular Physiology and of Structural Biology
Current Research and Scholarly InterestsMy lab’s research focuses on computational biology, with an emphasis on 3D molecular structure. We combine two approaches: (1) Bottom-up: given the basic physics governing atomic interactions, use simulations to predict molecular behavior; (2) Top-down: given experimental data, use machine learning to predict molecular structures and properties. We collaborate closely with experimentalists and apply our methods to the discovery of safer, more effective drugs.
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Chris Garcia
Younger Family Professor and Professor of Structural Biology
Current Research and Scholarly InterestsStructural and functional studies of transmembrane receptor interactions with their ligands in systems relevant to human health and disease - primarily in immunity, infection, and neurobiology. We study these problems using protein engineering, structural, biochemical, and combinatorial biology approaches.
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Kathleen Guan
Student Services Officer, Structural Biology
Current Role at StanfordStudent Services Officer
Biophysics Program
Department of Structural Biology -
Ted Jardetzky
Professor of Structural Biology
Current Research and Scholarly InterestsThe Jardetzky laboratory is studying the structures and mechanisms of macromolecular complexes important in viral pathogenesis, allergic hypersensitivities and the regulation of cellular growth and differentiation, with an interest in uncovering novel conceptual approaches to intervening in disease processes. Ongoing research projects include studies of paramyxovirus and herpesvirus entry mechanisms, IgE-receptor structure and function and TGF-beta ligand signaling pathways.
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Roger Kornberg
Mrs. George A. Winzer Professor of Medicine
Current Research and Scholarly InterestsWe study the regulation of transcription, the first step in gene expression. The main lines of our work are 1) reconstitution of the process with more than 50 pure proteins and mechanistic analysis, 2) structure determination of the 50 protein complex at atomic resolution, and 3) studies of chromatin remodelling, required for transcription of the DNA template in living cells
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Miri Krupkin
Basic Life Research Scientist, Structural Biology
BioMy background is deeply rooted in structural biology and biochemistry of proteins and RNA. My current research focuses on understanding the regulatory role of RNA structures in HIV infection. To this end, I am focusing on revealing the conformational landscape of viral RNA during reverse transcription. I am also devoted to promoting science education and outreach.
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Michael Levitt
Robert W. and Vivian K. Cahill Professor of Cancer Research and Professor, by courtesy, of Computer Science
Current Research and Scholarly InterestsStanford Professor of Biophysics and Computational Biology, Cambridge PhD and DSc, 2013 Chemistry Nobel Laureate (complex systems), FRS & US National Academy member, I code well for my age.
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David B. McKay
Professor of Structural Biology, Emeritus
Current Research and Scholarly InterestsThree-dimensional structure determination and biophysical studies of macromolecules.
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Hesam N. Motlagh
Adjunct Professor, Structural Biology
BioHesam is passionate about translating basic science discoveries into products that have a significant impact on society. He is Chief of Staff at Khosla Ventures where he works with Vinod Khosla on strategic projects for the firm and advises portfolio companies on fundraising, product, business development, marketing, and general strategy.
Currently, Hesam is an Adjunct Professor in the Department of Structural Biology at Stanford Medicine and a Fellow in The Johns Hopkins Institute for Applied Economics, Global Health, and the Study of Business Enterprise where he is editor of the Studies in Applied Finance. Previously, he worked on financial and corporate strategy at Seer Biosciences and was a Pear Fellow at Pear VC. Before Seer, he was a quant at an investment management firm after being a molecular and computational biophysicist for almost a decade.
Hesam has many peer-reviewed publications including a review article that was highlighted on the cover of Nature. He completed his MBA at Stanford Graduate School of Business, obtained his PhD from the Program in Molecular Biophysics at The Johns Hopkins University under the supervision of Vincent Hilser, and obtained his undergraduate degrees from Miami University in Oxford, Ohio. -
Vijay Pande
Adjunct Professor, Structural Biology
BioVijay Pande, Henry Dreyfus Professor of Chemistry and, by courtesy, of Structural Biology and Computer Science, also currently directs of the Stanford Program in Biophysics and the Folding@home Distribtued Computing project. His research centers on novel cloud computing simulation techniques to address problems in chemical biology. In particular, he has pioneered distributed computing methodology to break fundamental barriers in the simulation of protein and nucleic acid kinetics and thermodynamics. As director of the Folding@home project (http://folding.stanford.edu), Prof. Pande has, for the first time, directly simulated protein folding dynamics, making quantitative comparisons with experimental results, often considered a “holy grail” of computational biology. His current research also includes novel computational methods for drug design, especially in the area of protein misfolding and associated diseases such as Alzheimer’s and Huntington’s Disease.
Professor Pande studied physics at Princeton University (B.A. 1992), where he was first introduced to biophysical questions, especially in undergraduate research with Nobel Laureate P. Anderson. His doctoral research in physics under Profs. T. Tanaka and A. Grosberg at MIT (Ph.D. 1995) centered on statistical mechanical models of protein folding, suggesting new ways to design protein sequences for stability and folding properties. As a Miller Fellow under Prof. D. Rokhsar at UC Berkeley, Prof. Pande extended this methodology to examine atomistic protein models, laying the foundations for his work at Stanford University. Among numerous awards, Prof. Pande has received the Biophysical Society’s Bárány Award for Young Investigators and Protein Society’s Irving Sigal Young Investigator Award, and was named to MIT’s TR100 and elected a Fellow of the American Physical Society.
The Pande research group develops and applies new theoretical methods to understand the physical properties of biological molecules such as proteins, nucleic acids and lipid membranes, using this understanding to design synthetic systems including small-molecule therapeutics. In particular, the group examines the self-assembly properties of biomolecules. For example, how do protein and RNA molecules fold? How do proteins misfold and aggregate? How can we use this understanding to tackle misfolding related degeneration and develop small molecules to inhibit disease processes?
As these phenomena are complex, spanning molecular to mesoscopic lengths and nanosecond to millisecond timescales, the lab employs a variety of methods, including statistical mechanical analytic models, Markov State Models, and statistical and informatic methods. Other tools include Monte Carlo, Langevin dynamics, and molecular dynamics computer simulations on workstations and massively parallel supercomputers, superclusters, and worldwide distributed computing. The group has also done extensive work in the application of machine learning, pioneering traditional and deep learning approaches to cheminformatics, biophysics and drug design.
For example, simulations in all-atom detail on experimentally relevant timescales (milliseconds to seconds) have produced specific predictions of the structural and physical chemical nature of protein aggregation involved in Alzheimer’s and Huntington’s diseases. These results have fed into computational small molecule drug design methods, yielding interesting new chemical entities.
Since such problems are extremely computationally demanding, the group developed a distributed computing project for protein folding dynamics. Since its launch in October 2000, Folding@Home has attracted more than 4,000,000 PCs, and today is recognized as the most powerful supercluster in the world. Such enormous computational resources have allowed simulations of unprecedented folding timescales and statistical precision and accuracy. For more details, please visit http://pande.stanford.edu. -
Peter Parham
Professor of Structural Biology and of Microbiology and Immunology
Current Research and Scholarly InterestsThe Parham laboratory investigates the biology, genetics, and evolution of MHC class I molecules and NK cell receptors.
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Elisabetta Viani Puglisi
Associate Professor (Research) of Structural Biology
Current Research and Scholarly InterestsViral infections and subsequent host response depend on multiple RNA-protein interaction. My research focuses on the structural and functional characterization of RNA-protein complexes involved in viral infection. Current research aims to understand how the Human Immunodeficiency Virus (HIV) initiates its replication upon host infection. We use NMR spectroscopy and x-ray crystallography to study the structure of the initiation complex, formed by a host tRNA and HIV genomic RNA, coupled with biochemical and biophysical methods to understand functional properties. The goal of this research is to gain a molecular view of HIV replication initiation, and use this information to develop new therapeutic approaches to combat HIV.
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Joseph (Jody) Puglisi
Jauch Professor and Professor of Structural Biology
Current Research and Scholarly InterestsThe Puglisi group investigates the role of RNA in cellular processes and disease. We investigate dynamics using single-molecule approaches. Our goal is a unified picture of structure, dynamics and function. We are currently focused on the mechanism and regulation of translation, and the role of RNA in viral infections. A long-term goal is to target processes involving RNA with novel therapeutic strategies.
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Ramya Rangan
Ph.D. Student in Biophysics, admitted Autumn 2017
BioI am interested studying complex RNA processes like pre-mRNA splicing using 2D and 3D computational structural modeling along with experimental structural probing techniques.
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Kacper Rogala
Assistant Professor of Structural Biology and of Chemical and Systems Biology
Current Research and Scholarly InterestsOur team is fascinated by how cells make growth decisions — to grow or not to grow. In order to grow, cells require nutrients, and we are unraveling how cells use specialized protein sensors and transporters to sense and traffic nutrients in between various compartments. We use approaches from structural biology, chemical biology, biophysics, biochemistry, and cell biology — to reveal the mechanisms of basic biological processes, and we develop chemical probes that modulate them.
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Naima G. Sharaf
Assistant Professor of Biology and, by courtesy, of Structural Biology
Current Research and Scholarly InterestsResearch in the lab bridges biology, microbiology, and immunology to translate lipoprotein research into therapeutics
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Georgios Skiniotis
Professor of Molecular and Cellular Physiology, of Structural Biology and of Photon Science
BioThe Skiniotis laboratory seeks to resolve structural and mechanistic questions underlying biological processes that are central to cellular physiology. Our investigations employ primarily cryo-electron microscopy (cryoEM) and 3D reconstruction techniques complemented by biochemistry, biophysics and simulation methods to obtain a dynamic view into the macromolecular complexes carrying out these processes. The main theme in the lab is the structural biology of cell surface receptors that mediate intracellular signaling and communication. Our current main focus is the exploration of the mechanisms responsible for transmembrane signal instigation in cytokine receptors and G protein coupled receptor (GPCR) complexes.
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Ved Topkar
MD Student, expected graduation Spring 2023
Ph.D. Student in Biophysics, admitted Autumn 2018
MSTP StudentBioI am a lover of all things RNA currently interested in studying sub-cellular localization of mRNA molecules. Using primary oligodendrocytes as a model system, I am studying the mechanisms of mRNA transport in myelin development.
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Yonatan Winetraub
Instructor, Structural Biology
Current Research and Scholarly InterestsMy interests span non-invasive imaging for early cancer diagnosis and space exploration.
I'm focusing on utilizing Optical Coherence Tomography (OCT) and machine learning to create virtual histology tools to image cancer non invasively at a single cell resolution, allowing physicians to skip biopsy (read more about the research). Prior to my PhD at Stanford, I co-founded SpaceIL, a non-profit organization that launched the first private interplanetary robotic mission to the Moon launched 2019. -
Soichi Wakatsuki
Professor of Photon Science and of Structural Biology
Current Research and Scholarly InterestsUbiquitin signaling: structure, function, and therapeutics
Ubiquitin is a small protein modifier that is ubiquitously produced in the cells and takes part in the regulation of a wide range of cellular activities such as gene transcription and protein turnover. The key to the diversity of the ubiquitin roles in cells is that it is capable of interacting with other cellular proteins either as a single molecule or as different types of chains. Ubiquitin chains are produced through polymerization of ubiquitin molecules via any of their seven internal lysine residues or the N-terminal methionine residue. Covalent interaction of ubiquitin with other proteins is known as ubiquitination which is carried out through an enzymatic cascade composed of the ubiquitin-activating (E1), ubiquitin-conjugating (E2), and ubiquitin ligase (E3) enzymes. The ubiquitin signals are decoded by the ubiquitin-binding domains (UBDs). These domains often specifically recognize and non-covalently bind to the different ubiquitin species, resulting in distinct signaling outcomes.
We apply a combination of the structural (including protein crystallography, small angle x-ray scattering, cryo-electron microscopy (Cryo-EM) etc.), biocomputational and biochemical techniques to study the ubiquitylation and deubiquitination processes, and recognition of the ubiquitin chains by the proteins harboring ubiquitin-binding domains. Current research interests including SARS-COV2 proteases and their interactions with polyubiquitin chains and ubiquitin pathways in host cell responses, with an ultimate goal of providing strategies for effective therapeutics with reduced levels of side effects.
Protein self-assembly processes and applications.
The Surface layers (S-layers) are crystalline protein coats surrounding microbial cells. S-layer proteins (SLPs) regulate their extracellular, self-assembly by crystallizing when exposed to an environmental trigger. We have demonstrated that the Caulobacter crescentus SLP readily crystallizes into sheets both in vivo and in vitro via a calcium-triggered multistep assembly pathway. Observing crystallization using a time course of Cryo-EM imaging has revealed a crystalline intermediate wherein N-terminal nucleation domains exhibit motional dynamics with respect to rigid lattice-forming crystallization domains. Rate enhancement of protein crystallization by a discrete nucleation domain may enable engineering of kinetically controllable self-assembling 2D macromolecular nanomaterials. In particular, this is inspiring designing robust novel platform for nano-scale protein scaffolds for structure-based drug design and nano-bioreactor design for the carbon-cycling enzyme pathway enzymes. Current research focuses on development of nano-scaffolds for high throughput in vitro assays and structure determination of small and flexible proteins and their interaction partners using Cryo-EM, and applying them to cancer and anti-viral therapeutics.
Multiscale imaging and technology developments.
Multimodal, multiscale imaging modalities will be developed and integrated to understand how molecular level events of key enzymes and protein network are connected to cellular and multi-cellular functions through intra-cellular organization and interactions of the key machineries in the cell. Larger scale organization of these proteins will be studied by solution X-ray scattering and Cryo-EM. Their spatio-temporal arrangements in the cell organelles, membranes, and cytosol will be further studied by X-ray fluorescence imaging and correlated with cryoEM and super-resolution optical microscopy. We apply these multiscale integrative imaging approaches to biomedical, and environmental and bioenergy research questions with Stanford, DOE national labs, and other domestic and international collaborators. -
William Weis
William M. Hume Professor in the School of Medicine, Professor of Structural Biology, of Molecular and Cellular Physiology and of Photon Science
Current Research and Scholarly InterestsOur laboratory studies molecular interactions that underlie the establishment and maintenance of cell and tissue structure. Our principal areas of interest are the architecture and dynamics of intercellular adhesion junctions, signaling pathways that govern cell fate determination, and determinants of cell polarity. Our overall approach is to reconstitute macromolecular assemblies with purified components in order to analyze them using biochemical, biophysical and structural methods.
