Stanford ChEM-H


Showing 101-120 of 127 Results

  • Julia Salzman

    Julia Salzman

    Assistant Professor of Biochemistry and of Biomedical Data Science

    Current Research and Scholarly InterestsCircular RNA regulation and function; computational and experimental approaches

  • Juan G. Santiago

    Juan G. Santiago

    Charles Lee Powell Foundation Professor

    Current Research and Scholarly Interestshttp://microfluidics.stanford.edu/Projects/Projects.html

  • Ansuman Satpathy

    Ansuman Satpathy

    Assistant Professor of Pathology

    Current Research and Scholarly InterestsOur lab works at the interface of immunology, cancer biology, and genomics to study cellular and molecular mechanisms of the immune response to cancer. In particular, we are leveraging high-throughput genomic technologies to understand the dynamics of the tumor-specific T cell response to cancer antigens and immunotherapies (checkpoint blockade, CAR-T cells, and others). We are also interested in understanding the impact of immuno-editing on the heterogeneity and clonal evolution of cancer.

    We previously developed genome sequencing technologies that enable epigenetic studies in primary human immune cells from patients: 1) 3D enhancer-promoter interaction profiling (Nat Genet, 2017), 2) paired epigenome and T cell receptor (TCR) profiling in single cells (Nat Med, 2018), 3) paired epigenome and CRISPR profiling in single cells (Cell, 2019), and high-throughput single-cell ATAC-seq in droplets (Nature Biotech, 2019). We used these tools to study fundamental principles of the T cell response to cancer immunotherapy (PD-1 blockade) directly in cancer patient samples (Nature Biotech, 2019; Nat Med, 2019).

  • Elizabeth Sattely

    Elizabeth Sattely

    Associate Professor of Chemical Engineering

    BioPlants have an extraordinary capacity to harvest atmospheric CO2 and sunlight for the production of energy-rich biopolymers, clinically used drugs, and other biologically active small molecules. The metabolic pathways that produce these compounds are key to developing sustainable biofuel feedstocks, protecting crops from pathogens, and discovering new natural-product based therapeutics for human disease. These applications motivate us to find new ways to elucidate and engineer plant metabolism. We use a multidisciplinary approach combining chemistry, enzymology, genetics, and metabolomics to tackle problems that include new methods for delignification of lignocellulosic biomass and the engineering of plant antibiotic biosynthesis.

  • Nirao Shah

    Nirao Shah

    Professor of Psychiatry and Behavioral Sciences (Major Laboratories and Clinical Translational Neurosciences Incubator) and of Neurobiology

    Current Research and Scholarly InterestsWe study how our brains generate social interactions that differ between the sexes. Such gender differences in behavior are regulated by sex hormones, experience, and social cues. Accordingly, we are characterizing how these internal and external factors control gene expression and neuronal physiology in the two sexes to generate behavior. We are also interested in understanding how such sex differences in the healthy brain translate to sex differences in many neuro-psychiatric illnesses.

  • Lucy Shapiro

    Lucy Shapiro

    Virginia and D. K. Ludwig Professor

    Current Research and Scholarly InterestsA basic question in developmental biology involves the mechanisms used to generate the three-dimensional organization of a cell from a one-dimensional genetic code. Our goal is to define these mechanisms using both molecular genetics and biochemistry.

  • Carla Shatz

    Carla Shatz

    Sapp Family Provostial Professor, The Catherine Holman Johnson Director of Stanford Bio-X and Professor of Biology and of Neurobiology

    Current Research and Scholarly InterestsThe goal of research in the Shatz Laboratory is to discover how brain circuits are tuned up by experience during critical periods of development both before and after birth by elucidating cellular and molecular mechanisms that transform early fetal and neonatal brain circuits into mature connections. To discover mechanistic underpinnings of circuit tuning, the lab has conducted functional screens for genes regulated by neural activity and studied their function for vision, learning and memory.

  • Mark Smith

    Mark Smith

    Senior Research Scientist-Basic Life

    BioDr. Mark Smith joined Stanford ChEM-H in May 2013 as the Head of the Medicinal Chemistry Knowledge Center. He graduated with a Ph.D. from the laboratory of Prof. Richard Stoodley at the University of Manchester Institute for Science and Technology (UMIST), where his research focused on the application of Lewis acid catalyzed hetero Diels-Alder reactions to the synthesis of novel disaccharide structures. In 2000, Dr. Smith joined the research laboratory of Prof. David Crich at the University of Illinois at Chicago. Here his research focused on the generation of new reagents for the synthesis of beta-mannosides from thioglycosides. From 2002 to 2013, Dr. Smith worked as a medicinal chemist in Roche’s research facilities both in Palo Alto, CA and then Nutley, NJ, where he specialized in antiviral research.

  • Hyongsok Tom  Soh

    Hyongsok Tom Soh

    Professor of Radiology (Early Detection), of Electrical Engineering and, by courtesy, of Chemical Engineering and of Bioengineering

    BioDr. Soh received his B.S. with a double major in Mechanical Engineering and Materials Science with Distinction from Cornell University and his Ph.D. in Electrical Engineering from Stanford University. From 1999 to 2003, Dr. Soh served as the technical manager of MEMS Device Research Group at Bell Laboratories and Agere Systems. He was a faculty member at UCSB before joining Stanford in 2015. His current research interests are in analytical biotechnology, especially in high-throughput screening, directed evolution, and integrated biosensors.

  • Edward I. Solomon

    Edward I. Solomon

    Monroe E. Spaght Professor in the School of Humanities and Sciences and Professor of Photon Science

    Current Research and Scholarly InterestsProf. Solomon's work spans physical-inorganic, bioinorganic, and theoretical-inorganic chemistry, focusing on spectroscopic elucidation of the electronic structure of transition metal complexes and its contribution to reactivity. He has advanced our understanding of metal sites involved in electron transfer, copper sites involved in O2 binding, activation and reduction to water, structure/function correlations over non-heme iron enzymes, and correlation of biological to heterogeneous catalysis.

  • Aaron F. Straight

    Aaron F. Straight

    Professor of Biochemistry and, by courtesy, of Chemical and Systems Biology

    Current Research and Scholarly InterestsWe study the biology of chromosomes. Our research is focused on understanding how chromosomal domains are specialized for unique functions in chromosome segregation, cell division and cell differentiation. We are particularly interested in the genetic and epigenetic processes that govern vertebrate centromere function, in the organization of the genome in the eukaryotic nucleus and in the roles of RNAs in the regulation of chromosome structure.

  • James Swartz

    James Swartz

    James H. Clark Professor in the School of Engineering and Professor of Chemical Engineering and of Bioengineering

    BioUsing and Understanding Cell-Free Biology

    Swartz Lab General Research Focus:

    The current and projected research in the Swartz lab balances basic research in microbial metabolism, protein expression, and protein folding with a strong emphasis on compelling applications. The power and versatility of cell-free methods coupled with careful evaluation and engineering of these new systems enables a whole new range of applications and scientific investigation. Fundamental research on: the mechanisms and kinetics of ribosomal function, fundamental bioenergetics, basic mechanisms of protein folding, functional genomics, and metabolic pathway analysis is motivated by a variety of near- and medium term applications spanning medicine, energy, and environmental needs.

    Swartz Lab Application Focus:

    In the medical area , current research addresses the need for patient-specific vaccines to treat cancer. Particularly for lymphomas, there is a strong need to be able to make a new cancer vaccine for each patient. Current technologies are not practical for this demanding task, but cell-free approaches are rapid and inexpensive. We have already demonstrated feasibility in mouse tumor challenge studies and are now expanding the range of applications and working to improve the relevant technologies. Experience with these vaccines has also suggested a new and exciting format for making inexpensive and very potent vaccines for general use.

    To address pressing needs for a new and cleaner energy source, we are working towards an organism that can efficiently capture solar energy and convert it into hydrogen. The first task is to develop an oxygen tolerant hydrogenase using cell-free technology to express libraries of mutated enzymes that can be rapidly screened for improved function. Even though these are very complex enzymes, we have produced active hydrogenases with our cell-free methods. We are now perfecting the screening methods for rapid and accurate identification of improved enzymes. After these new enzymes are identified, the project will progress toward metabolic engineering and bioreactor design research to achieve the scales and economies required.

    To address environmental needs, we are developing an improved water filters using an amazing membrane protein, Aquaporin Z. It has the ability to reject all other chemicals and ions except water. We have efficiently expressed the protein into lipid bilayer vesicles and are now working to cast these membranes on porous supports to complete the development of a new and powerful water purification technology. The same lessons will be applied toward the development of a new class of biosensors that brings high sensitivity and selectivity.

  • Sindy Tang

    Sindy Tang

    Associate Professor of Mechanical Engineering, Senior Fellow at the Woods Institute for the Environment and Professor, by courtesy, of Radiology (Precision Health and Integrated Diagnostics)

    Current Research and Scholarly InterestsThe long-term goal of Dr. Tang's research program is to harness mass transport in microfluidic systems to accelerate precision medicine and material design for a future with better health and environmental sustainability.

    Current research areas include: (I) Physics of droplets in microfluidic systems, (II) Interfacial mass transport and self-assembly, and (III) Applications in food allergy, single-cell wound repair, and the bottom-up construction of synthetic cell and tissues in close collaboration with clinicians and biochemists at the Stanford School of Medicine, UCSF, and University of Michigan.

    For details see https://web.stanford.edu/group/tanglab/

  • Alice Ting

    Alice Ting

    Professor of Genetics, of Biology and, by courtesy, of Chemistry

    Current Research and Scholarly InterestsWe develop chemogenetic and optogenetic technologies for probing and manipulating protein networks, cellular RNA, and the function of mitochondria and the mammalian brain. Our technologies draw from enzyme engineering, directed evolution, chemical biology, organic synthesis, high-resolution microscopy, genetics, and computational analysis.

  • Soichi Wakatsuki

    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.

  • Robert Waymouth

    Robert Waymouth

    Robert Eckles Swain Professor in Chemistry and Professor, by courtesy, of Chemical Engineering

    BioRobert Eckles Swain Professor in Chemistry Robert Waymouth investigates new catalytic strategies to create useful new molecules, including bioactive polymers, synthetic fuels, and sustainable plastics. In one such breakthrough, Professor Waymouth and Professor Wender developed a new class of gene delivery agents.

    Born in 1960 in Warner Robins, Georgia, Robert Waymouth studied chemistry and mathematics at Washington and Lee University in Lexington, Virginia (B.S. and B.A., respectively, both summa cum laude, 1982). He developed an interest in synthetic and mechanistic organometallic chemistry during his doctoral studies in chemistry at the California Institute of Technology under Professor R.H. Grubbs (Ph.D., 1987). His postdoctoral research with Professor Piero Pino at the Institut fur Polymere, ETH Zurich, Switzerland, focused on catalytic hydrogenation with chiral metallocene catalysts. He joined the Stanford University faculty as assistant professor in 1988, becoming full professor in 1997 and in 2000 the Robert Eckles Swain Professor of Chemistry.

    Today, the Waymouth Group applies mechanistic principles to develop new concepts in catalysis, with particular focus on the development of organometallic and organic catalysts for the synthesis of complex macromolecular architectures. In organometallic catalysis, the group devised a highly selective alcohol oxidation catalyst that selectively oxidizes unprotected polyols and carbohydrates to alpha-hyroxyketones. In collaboration with Dr. James Hedrick of IBM, we have developed a platform of highly active organic catalysts and continuous flow reactors that provide access to polymer architectures that are difficult to access by conventional approaches.

    The Waymouth group has devised selective organocatalytic strategies for the synthesis of functional degradable polymers and oligomers that function as "molecular transporters" to deliver genes, drugs and probes into cells and live animals. These advances led to the joint discovery with the Wender group of a general, safe, and remarkably effective concept for RNA delivery based on a new class of synthetic cationic materials, Charge-Altering Releasable Transporters (CARTs). This technology has been shown to be effective for mRNA based cancer vaccines.

  • William Weis

    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.