Bio-X


Showing 21-40 of 42 Results

  • Andrew Fire

    Andrew Fire

    George D. Smith Professor of Molecular and Genetic Medicine and Professor of Pathology and of Genetics

    Current Research and Scholarly InterestsWe study natural cellular mechanisms for adapting to genetic change. These include systems activated during normal development and those for detecting and responding to foreign or unwanted genetic activity. Underlying these studies are questions of how a cells can distinguish information as "self" versus "nonself" or "wanted" versus "unwanted".

  • Michael Fischbach

    Michael Fischbach

    Associate Professor of Bioengineering and of Medicine (Microbiology and Immunology)

    Current Research and Scholarly InterestsThe human microbiome is linked to a range of phenotypes in the host, but it remains difficult to test causality and explore the mechanisms of these interactions. Our lab focuses on two research areas that share a common goal of studying host-microbiota interactions at the level of molecular mechanism:

    1) Technology development. Much of what we know about biology has been learned by deleting individual genes from mice, worms, flies and yeast. The ability to do single-strain and single-gene deletion in the microbiome would be transformative but does not yet exist. We are developing technology in three areas to make this possible:

    Synthetic ecology: There is a pressing need for model systems for the microbiome that are defined, but of an order of complexity that approaches the native state. Key experiments in the field often show that a host phenotype can be transferred to a germ-free mouse via fecal transplant. If these phenomena could be recapitulated with a defined, high-complexity community, then reductionist experiments to probe mechanism would be possible. We are developing the technology required to build highly complex defined communities (100-200 bacterial species), make them stable upon transplantation into mice, and probe their function in vitro and in vivo.

    Genetics: It is difficult to probe mechanism without genetics, and genetic tools exist for only ~10% of the bacterial species in the gut and skin microbiome. We are developing technologies that will make it possible to delete and insert genes, and build mutant libraries, in many of the most common bacterial strains in the gut and skin microbiome.

    Computation: In previous work from the lab, we have developed computational algorithms that identify small-molecule-producing genes in bacterial genomes. In current work, we are devising algorithms for genome mining that are specific to the microbiome, and new tools for predicting the chemical structures of small molecules from untargeted metabolomics data.

    2) Molecular mechanisms. Many of the early findings in microbiome research are correlative or associative. We are applying the tools described above to explore the mechanisms underlying these phenomena:

    Small molecules: Our lab has had a long-standing interest in small molecules from the microbiota. These include: 1) host-derived molecules metabolized by the microbiome, like bile acids; 2) characteristic components of the bacterial membrane and cell wall, including LPS and capsular polysaccharides; and 3) hundreds of other diffusible small molecules (e.g., the products of polysaccharide and amino acid metabolism) that are present in the bloodstream at high concentrations. Our work in this area seeks to establish the mechanisms by which these molecules modulate host biology, especially by deleting them one at a time in the background of a complex community; and to discover new microbiome-derived metabolites present in the bloodstream and host tissues.

    Ecology of complex communities: Synthetic ecology at the 100+ strain scale is entirely unexplored, and the emergent properties of complex communities are not well understood. Our work in this area seeks to understand basic principles outlined by the following questions: How many meaningful interactions exist in a community of hundreds of strains? What constitutes a niche, molecularly and spatially, and how do strains map to niches? What are the molecular correlates of stability, and how does a community reconfigure in response to a perturbation? How rare or common are stable states, and how predictable is the process by which a consortium will evolve toward a stable state? To what extent do priority effects (early colonists and events) determine the outcome of ecosystem development? Can the results of ecosystem competition be predicted or engineered?

  • Daniel Fisher

    Daniel Fisher

    David Starr Jordan Professor
    On Leave from 10/01/2022 To 06/30/2023

    Current Research and Scholarly InterestsEvolutionary & ecological dynamics & diversity, microbial, expt'l, & cancer

  • Dominik Fleischmann

    Dominik Fleischmann

    Professor of Radiology (Cardiovascular Imaging)

    Current Research and Scholarly InterestsNon-invasive Cardiovascular Imaging
    Image Post-processing
    Contrast Medium Dynamics

  • Sean Follmer

    Sean Follmer

    Assistant Professor of Mechanical Engineering and, by courtesy, of Computer Science

    Current Research and Scholarly InterestsHuman Computer Interaction, Haptics, Robotics, Human Centered Design

  • James Ford

    James Ford

    Professor of Medicine (Oncology) and of Genetics and, by courtesy, of Pediatrics

    Current Research and Scholarly InterestsMammalian DNA repair and DNA damage inducible responses; p53 tumor suppressor gene; transcription in nucleotide excision repair and mutagenesis; genetic determinants of cancer cell sensitivity to DNA damage; genetics of inherited cancer susceptibility syndromes and human GI malignancies; clinical cancer genetics of BRCA1 and BRCA2 breast cancer and mismatch repair deficient colon cancer.

  • Polly Fordyce

    Polly Fordyce

    Assistant Professor of Bioengineering and of Genetics

    Current Research and Scholarly InterestsThe Fordyce Lab is focused on developing new instrumentation and assays for making quantitative, systems-scale biophysical measurements of molecular interactions. Current research in the lab is focused on three main platforms: (1) arrays of valved reaction chambers for high-throughput protein expression and characterization, (2) spectrally encoded beads for multiplexed bioassays, and (3) sortable droplets and microwells for single-cell assays.

  • Michael B. Fowler, MBBS, FRCP

    Michael B. Fowler, MBBS, FRCP

    Professor of Medicine (Cardiovascular), Emeritus

    Current Research and Scholarly InterestsAdrenergic nervous system; beta-adrenergic function in, heart failure; drugs in heart failure.

  • Emily Fox

    Emily Fox

    Professor of Statistics and, by courtesy, of Computer Science

    BioEmily Fox is a Professor in the Department of Statistics and, by courtesy, Computer Science at Stanford University. Prior to Stanford, she was the Amazon Professor of Machine Learning in the Paul G. Allen School of Computer Science & Engineering and Department of Statistics at the University of Washington. From 2018-2021, Emily led the Health AI team at Apple, where she was a Distinguished Engineer. Before joining UW, Emily was an Assistant Professor at the Wharton School Department of Statistics at the University of Pennsylvania. She earned her doctorate from Electrical Engineering and Computer Science (EECS) at MIT where her thesis was recognized with EECS' Jin-Au Kong Outstanding Doctoral Thesis Prize and the Leonard J. Savage Award for Best Thesis in Applied Methodology.

    Emily has been awarded a CZ Biohub Investigator Award, Presidential Early Career Award for Scientists and Engineers (PECASE), a Sloan Research Fellowship, ONR Young Investigator Award, and NSF CAREER Award. Her research interests are in large-scale Bayesian dynamic modeling, interpretability and computations, with applications in health and computational neuroscience.

  • Paige Fox, MD, PhD, FACS

    Paige Fox, MD, PhD, FACS

    Associate Professor of Surgery (Plastic and Reconstructive Surgery)

    BioDr. Paige Fox is Board Certified Plastic Surgeon who specialized in hand surgery, reconstructive microsurgery, as well as peripheral nerve and brachial plexus surgery. She is an Associate Professor in the Division of Plastic and Reconstructive surgery in the Department of Surgery. She works with adult and pediatric patients. Her research focuses on wound healing, disorders of the upper extremity, and surgical biosensors. Dr. Fox has a passion for sustainability and health care's effect on the environment. She is involved in efforts to green the OR and the clinics at Stanford.

  • Christopher Francis

    Christopher Francis

    Professor of Earth System Science, of Oceans and Senior Fellow at the Woods Institute for the Environment

    Current Research and Scholarly InterestsMicrobial cycling of carbon, nitrogen, and metals in the environment; molecular geomicrobiology; marine microbiology; microbial diversity; meta-omics

  • Curtis Frank

    Curtis Frank

    W. M. Keck, Sr. Professor in Engineering, Emeritus

    BioThe properties of ultrathin polymer films are often different from their bulk counterparts. We use spin casting, Langmuir-Blodgett deposition, and surface grafting to fabricate ultrathin films in the range of 100 to 1000 Angstroms thick. Macromolecular amphiphiles are examined at the air-water interface by surface pressure, Brewster angle microscopy, and interfacial shear measurements and on solid substrates by atomic force microscopy, FTIR, and ellipsometry. A vapor-deposition-polymerization process has been developed for covalent grafting of poly(amino acids) from solid substrates. FTIR measurements permit study of secondary structures (right and left-handed alpha helices, parallel and anti-parallel beta sheets) as a function of temperature and environment.

    A broadly interdisciplinary collaboration has been established with the Department of Ophthalmology in the Stanford School of Medicine. We have designed and synthesized a fully interpenetrating network of two different hydrogel materials that have properties consistent with application as a substitute for the human cornea: high water swellability up to 85%,tensile strength comparable to the cornea, high glucose permeability comparable to the cornea, and sufficient tear strength to permit suturing. We have developed a technique for surface modification with adhesion peptides that allows binding of collagen and subsequent growth of epithelial cells. Broad questions on the relationships among molecular structure, processing protocol, and biomedical device application are being pursued.

  • Michael Frank

    Michael Frank

    David and Lucile Packard Foundation Professor of Human Biology and Professor, by courtesy, of Linguistics

    Current Research and Scholarly InterestsHow do we learn to communicate using language? I study children's language learning and how it interacts with their developing understanding of the social world. I use behavioral experiments, computational tools, and novel measurement methods like large-scale web-based studies, eye-tracking, and head-mounted cameras.

  • Hunter Fraser

    Hunter Fraser

    Professor of Biology

    Current Research and Scholarly InterestsWe study the evolution of complex traits by developing new experimental and computational methods.

    Our work brings together quantitative genetics, genomics, epigenetics, and evolutionary biology to achieve a deeper understanding of how genetic variation shapes the phenotypic diversity of life. Our main focus is on the evolution of gene expression, which is the primary fuel for natural selection. Our long-term goal is to be able to introduce complex traits into new species via genome editing.

  • Richard Frock

    Richard Frock

    Assistant Professor of Radiation Oncology (Radiation and Cancer Biology)

    Current Research and Scholarly InterestsWe are a functional genomics laboratory interested in elucidating mechanisms of DNA repair pathway choice and genome instability. We employ a powerful discovery platform, High-Throughput Genome-wide Translocation Sequencing (HTGTS), which maps DNA junctions at single nucleotide resolution. Our expertise overlaps many different fields including: genome editing, ionizing radiation and cancer therapeutics, V(D)J and IgH class switch recombination, and meiosis.

  • Victor Froelicher, MD

    Victor Froelicher, MD

    Professor of Medicine (Cardiovascular) at the Veterans Affairs Palo Alto Health Care System, Emeritus

    Current Research and Scholarly InterestsScreening of athletes for sudden cardiac death, Computerized ECG and clinical data management; exercise Physiology including expired gas analysis; the effect of chronic and acute exercise on the heart; digital recording of biological signals; diagnostic use of exercise testing; development of Expert Medical System software and educational tools.

  • Wolf B. Frommer

    Wolf B. Frommer

    Member, Bio-X

    Current Research and Scholarly InterestsWatching cells at work
    Focus: Transport / signaling across the plasma membrane (sugars, amino acids).
    Tools: FRET-based nanosensors for metabolite imaging (with subcellular resolution) in living organisms using confocal fluorescence microscopy and HTS; Sensor optimization by computational design; RNAi to modify cellular functions.
    Goals: Identify unknown sugar effluxers from liver/plant cells; study regulatory networks.
    Model systems: liver, neuronal, plant cell cultures, Arabidopsis, yeast

  • Judith Frydman

    Judith Frydman

    Donald Kennedy Chair in the School of Humanities and Sciences and Professor of Genetics

    Current Research and Scholarly InterestsThe long term goal of our research is to understand how proteins fold in living cells. My lab uses a multidisciplinary approach to address fundamental questions about molecular chaperones, protein folding and degradation. In addition to basic mechanistic principles, we aim to define how impairment of cellular folding and quality control are linked to disease, including cancer and neurodegenerative diseases and examine whether reengineering chaperone networks can provide therapeutic strategies.

  • Takako Fujioka

    Takako Fujioka

    Associate Professor of Music

    BioResearch topics include neural oscillations for auditory perception, auditory-motor coupling, brain plasticity in development and aging, and recovery from stroke with music-supported therapy.

    Her post-doctoral and research-associate work at Rotman Research Institute in Toronto was supported by awards from the Canadian Institutes of Health Research. Her research continues to explore the biological nature of human musical ability by examining brain activities with non-invasive human neurophysiological measures such as magnetoencephalography (MEG) and electroencephalography (EEG).

  • Gerald Fuller

    Gerald Fuller

    Fletcher Jones Professor in the School of Engineering

    BioThe processing of complex liquids (polymers, suspensions, emulsions, biological fluids) alters their microstructure through orientation and deformation of their constitutive elements. In the case of polymeric liquids, it is of interest to obtain in situ measurements of segmental orientation and optical methods have proven to be an excellent means of acquiring this information. Research in our laboratory has resulted in a number of techniques in optical rheometry such as high-speed polarimetry (birefringence and dichroism) and various microscopy methods (fluorescence, phase contrast, and atomic force microscopy).

    The microstructure of polymeric and other complex materials also cause them to have interesting physical properties and respond to different flow conditions in unusual manners. In our laboratory, we are equipped with instruments that are able to characterize these materials such as shear rheometer, capillary break up extensional rheometer, and 2D extensional rheometer. Then, the response of these materials to different flow conditions can be visualized and analyzed in detail using high speed imaging devices at up to 2,000 frames per second.

    There are numerous processes encountered in nature and industry where the deformation of fluid-fluid interfaces is of central importance. Examples from nature include deformation of the red blood cell in small capillaries, cell division and structure and composition of the tear film. Industrial applications include the processing of emulsions and foams, and the atomization of droplets in ink-jet printing. In our laboratory, fundamental research is in progress to understand the orientation and deformation of monolayers at the molecular level. These experiments employ state of the art optical methods such as polarization modulated dichroism, fluorescence microscopy, and Brewster angle microscopy to obtain in situ measurements of polymer films and small molecule amphiphile monolayers subject to flow. Langmuir troughs are used as the experimental platform so that the thermodynamic state of the monolayers can be systematically controlled. For the first time, well characterized, homogeneous surface flows have been developed, and real time measurements of molecular and microdomain orientation have been obtained. These microstructural experiments are complemented by measurements of the macroscopic, mechanical properties of the films.