School of Medicine
Showing 1-73 of 73 Results
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Bryce Allen Bagley
Ph.D. Student in Biophysics, admitted Autumn 2018
Current Research and Scholarly InterestsMy research interests are broadly in the development of theoretical and applied solutions to problems at the intersection of machine learning and medicine, with a particular eye towards data fusion and problems in cancer diagnosis and treatment.
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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 Research Fellow, 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 effect 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
On Leave from 09/10/2020 To 09/09/2021Current 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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Joao Pedro Garcia Lopes Maia Rodrigues
Postdoctoral Research Fellow, Structural Biology
Current Research and Scholarly InterestsI am interested in the structure of protein complexes and understanding how it relates to their biological function. Throughout my career, I have developed and applied computational methods to integrate crystallography, NMR, FRET, Cryo-EM, and mutagenesis data to build high-resolution (atomic) models of proteins and protein interactions. I am also interested in education and outreach, and in how computational tools can help the public understand science better.
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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 in 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
Postdoctoral Research Fellow, 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 in Cancer Research in the School of Medicine 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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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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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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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 2021
Ph.D. Student in Biophysics, admitted Autumn 2018
MSTP StudentBioI apply our lab's cutting-edge RNA structure determination methods to decipher RNA transport specificity in oligodendrocytes. More generally, I am interested in how structure modulates mRNA localization, stability, and translation in eukaryotic cells.
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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. -
Katherine Walwyn-Brown
Postdoctoral Research Fellow, Structural Biology
BioDr. Walwyn-Brown is a post-doctoral scholar in the Parham lab, where she investigates how genetic diversity impacts on the function of Natural Killer cells during pregnancy and immune responses to infection.
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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.
