The Meyer laboratory seeks to understand how human cells sense hormones, growth factors and stress and how they integrate and transduce these signals to make decisions to polarize, move or divide. They investigate these cellular regulatory systems by identifying the key signaling components and measuring when and where signaling occurs as we watch cells decide to move forward or enter the cell cycle. They have been intrigued by the near universal importance of locally acting Ca2+ and phosphoinositide lipid second messenger signals, Rho and Ras family small GTPases and protein kinases in controlling these decision processes. Their projects are focused on understanding the general principles of how signal transduction systems work which often requires the development of new experimental and analysis tools involving fluorescent microscopy, small molecule and light perturbations, systematic siRNA screens, bioinformatics, genomics and quantitative modeling of signaling pathways.
Dr. Moore's laboratory studies neural mechanisms of visual-motor integration and the neurophysiological basis of cognition (e.g. visual attention, visual awareness, and working memory). This research involves the study of the activity of single neurons in visual and motor structures within the primate brain and tests of how perturbing that activity affects neurons in other brain structures as well as how it affects the perceptual and motor performance of behaving animals. His laboratory is also driven to develop more powerful and more causal approaches to systems-level neurobiology.
Dr. Napel's primary interests are in developing diagnostic and therapy-planning applications and strategies for the acquisition and visualization of multi-dimensional medical imaging data. Examples are: creation of three-dimensional images of blood vessels using CT, visualization of complex flow within blood vessels using MR, computer-aided detection and characterization of lesions (e.g., colonic polyps, pulmonary nodules) from cross-sectional image data, visualization and automated assessment of 4D ultrasound data, and fusion of images acquired using different modalities (e.g., CT and MR). He has also been involved in developing and evaluating techniques for exploring cross-sectional imaging data from an internal perspective, i.e., virtual endoscopy (including colonoscopy, angioscopy, and bronchoscopy), and in the quantitation of structure parameters, e.g., volumes, lengths, medial axes, and curvatures. Finally, he is also interested in creating workable solutions to the problem of "data explosion," i.e., how to look at the thousands of images generated per examination using modern CT and MR scanners.
He is co-director of the Radiology 3D and Quantitative Imaging Lab, providing clinical service to the Stanford and local community, and and co-Director of IBIIS (Integrative Biomedical Imaging Informatics at Stanford), whose mission is to advance the clinical and basic sciences in radiology, while improving our understanding of biology and the manifestations of disease, by pioneering methods in the information sciences that integrate imaging, clinical and molecular data.
The long-term goal of the Schnitzer lab's research is to advance experimental paradigms for understanding normal cognitive and disease processes at the level of neural circuits, with emphasis on learning and memory processes. By contrast, much current research on learning and memory concentrates on levels of organization in the nervous system that are either more macroscopic (e.g. in cognitive psychology) or more microscopic (e.g. in synaptic physiology).
The lab's approach combines behavioral, electrophysiological, and computational methodologies with high-resolution fluorescence optical imaging that is capable of resolving individual neurons and dendrites. By necessity, they aim to advance imaging methods so that we can examine dynamics of neuronal populations or of dendritic compartments in behaving animals. En route, they are also performing experiments on circuit properties in anesthetized animals, such as the studies that use our newly invented fluorescence endoscopes for examining hippocampal cells and dendrites in vivo.
They seek explanations that span different levels of organization, from cells to entire circuits. They work with both genetic model organisms, mice and fruit flies, and human subjects. Their research emphasizes understanding the control and learning of motor behaviors, as well as the potential application of our newly developed imaging techniques to clinical use in humans.
Dr. Shenoy's group (Neural Prosthetic Systems Laboratory, NPSL) conducts neuroscience, neuroengineering, and translational research to better understand how the brain controls movement, and to design medical systems to assist people with movement disabilities. Their neuroscience research investigates the neural basis of movement preparation and generation using a combination of electro-/opto-physiological, behavioral, computational and theoretical techniques. The lab's neuroengineering research investigates the design of high-performance and robust neural prostheses. Neural prostheses are also known as brain-computer interfaces (BCIs) and brain-machine interfaces (BMIs). These systems translate neural activity from the brain into control signals for prosthetic devices, which can assist people with paralysis by restoring lost motor functions. The lab's translational research, including an FDA pilot clinical trial termed BrainGate2, are conducted as part of the our Neural Prosthetic Translational Laboratory (NPTL; co-directed by Profs. Shenoy & Henderson).
In the Spormann lab's research, they investigate molecular microbial metabolism and its linkage to ecological and evolutionary processes. They explore the distinguishing features of novel microbial metabolism and how molecular and biochemical differences in metabolism shape microbial fitness. They study novel microbial metabolism with relevance to bioremediation, bioenergy, and intestinal microbiology.
The general research interest of Dr. Spudich's laboratory is the molecular basis of cell motility. They have 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.
They work on two experimental systems: contraction of mammalian muscle and chemotaxis of Dictyostelium discoideum cells. Each of these systems has its special advantages. Skeletal muscle has the most highly organized contractile apparatus of any cell type, and the chemistry and biochemistry of muscle actin and myosin are most advanced.
Dictyostelium discoideum, the cell that commands most of our attention, exhibits all of the behavior of nonmuscle mammalian cells and, unlike other eukaryotic cells, can be grown in large amounts for biochemical work. Furthermore, DNA-mediated transformation is being applied to this organism, and they have demonstrated efficient gene targeting by homologous recombination in the myosin gene, which they have cloned and sequenced.
Their approaches include biochemical and structural studies of actin, myosin, and associated regulatory proteins. In addition, they have designed and developed in vitro assays for ATP-dependent movement of purified myosin on filaments reconstituted from purified actin. These assays allow them to analyze mutant myosin molecules for altered function. The site-directed mutagenized forms of myosin are obtained by gene cloning and expression in an appropriate host. Their demonstration that the Dictyostelium discoideum myosin gene can undergo homologous recombination allows us to also probe the effects of the altered myosin forms on the phenotype of the cell.
Dr. Wandless's lab employs an interdisciplinary approach to studies of biological systems, combining a bit of synthetic chemistry with biochemistry, cell biology, and structural biology. More specifically, the lab concentrates on the invention of molecules and techniques that enable better studies of biological processes. In short, the Wandless lab invents tools for biology. These new techniques may provide insights into mechanisms involved in maintaining cellular homeostasis, and protein quality control is a particular interest at present.
Dr. Wong's lab develops methods in multivariate analysis, machine learning, Monte Carlo, differential equations and high performance computing, and apply them to problems in computational biology and personalized medicine.
They developed the software dChip for the analysis microarray data and the programs CisGenome, SeqMap and SpliceMap for the analysis of next generation sequencing data. Their methodological work is motivated by close collaborations with biology groups on problems arising from cancer and developmental biology. Of particular interest is the combined use of experimental and computational analysis to clarify the cis-regulatory mechanisms underlying several developmental processes. More generally, they employ and develop tools from exploratory data analysis, multivariate analysis, information theory, machine learning, Monte Carlo, graph theory, linear and nonlinear differential equations, and applied them to problems in computational biology and system biology.
A pioneer in the use of lasers to study chemical reactions at the molecular level, Dr. Zare pursues diverse theoretical and experimental interests in physical chemistry and nanoscale chemical analysis. The Zarelab has made a broad impact in analytic chemistry with development of laser-induced fluorescence to study reaction dynamics, and seminal contributions to understanding of molecular collision processes. The group continues to invent tools and measurement techniques to study phenomena from reaction in microdroplets to drug delivery.
Dr. Plevritis's research program focuses on computational modeling of cancer biology and cancer outcomes. Her laboratory develops stochastic models of the natural history of cancer based on clinical research data. They estimate population-level outcomes under differing screening and treatment interventions. They also analyze genomic and proteomic cancer data in order to identify molecular networks that are perturbed in cancer initiation and progression and relate these perturbations to patient outcomes.
The Spakowitz lab is engaged in projects that address fundamental chemical and physical processes that underlie a range of key biological mysteries and cutting-edge materials applications. Current research in the lab focuses on three main research themes: DNA Biophysics, Protein Self Assembly, and Charge Transport in Conjugated Polymers. These broad research areas offer complementary perspectives on chemical and physical processes, and they leverage this complementarity throughout our research. Their approach draws from a diverse range of theoretical and computational methods, including analytical theory of semiflexible polymers, polymer field theory, continuum elastic mechanics, Brownian dynamics simulation, equilibrium and dynamic Monte Carlo simulations, and analytical theory and numerical simulations of reaction-diffusion phenomena. A common thread in their work is the need to capture phenomena over many length and time scales, and their flexibility in research methodologies allows us to address these problems at an unprecedented level of precision.
Dr. Krummel's current research interests are in the surgical Innovation, simulation and virtual reality in surgical education, and fetal healing - cellular and biochemical mechanisms.
Dr. Krummel has served in leadership positions in many of the important surgical societies including the American College of Surgeons, the American Pediatric Surgical Association, the American Surgical Association, the American Board of Surgery, the American Board of Pediatric Surgery, the American Board of Plastic Surgery and is currently President of the Halsted Society. He has mentored over 100 students, residents and post docs during their research training. Tom has been a pioneer and a consistent innovator in the following important areas throughout his career:
The Lee lab uses interdisciplinary approaches from biology and engineering to analyze, debug, and manipulate systems-level brain circuits. They seek to understand the connectivity and function of these large-scale networks in order to drive the development of new therapies for neurological diseases. This research finds its basic building blocks in areas ranging from medical imaging and signal processing to genetics and molecular biology.
Dr. Levin's research interests involve the development of novel instrumentation and software algorithms for in vivo imaging of cellular and molecular signatures of disease in humans and small laboratory animal subjects. These new cameras efficiently image radiation emissions in the form of positrons, annihilation photons, gamma rays, and light from molecular probes developed to target molecular signals from deep within tissue of live subjects. The goals of the instrumentation projects are to push the sensitivity and spatial, spectral, and/or temporal resolutions as far as physically possible. The algorithm goals are to understand the physical system comprising the subject tissues, radiation transport, and imaging system, and to provide the best available image quality and quantitative accuracy. The work involves computer modeling, position sensitive sensors, readout electronics, data acquisition, image formation, image processing, and data/image analysis algorithms, and incorporating these innovations into practical imaging devices. The ultimate goal is to introduce these new imaging tools into studies of molecular mechanisms and treatments of disease within living subjects.
Dr. Henderson is director of the Stereotactic and Functional Neurosurgery program at Stanford and thre co-director of the Stanford Neural Prosthetics Translational Laboratory (NPTL). Dr. Henderson is an expert in the surgical treatment of movement disorders and chronic pain, and is active in research to improve stereotactic navigation and the efficacy of neuromodulatory therapies for movement disorders, pain, and other neurological diseases.
His research interests encompass several areas of stereotactic and functional neurosurgery, including frameless stereotactic approaches for therapy delivery to deep brain nuclei; deformable patient-specific atlases for targeting brain structures; cortical physiology and its relationship to normal and pathological movement; neural prostheses; and the development of novel neuromodulatory techniques for the treatment of movement disorders, pain, and other neurological diseases.
Dr. Dror is an Associate Professor of Computer Science and (by courtesy) Molecular and Cellular Physiology, and a faculty member in the Institute for Computational and Mathematical Engineering, ChEM-H, and the Biophysics Program.
Professor Dror's research focuses on computational biology, with an emphasis on the spatial organization and dynamics of biomolecules and cells. His work, usually carried out in close collaboration with experimentalists, spans fields ranging from biochemistry and cell biology to parallel computing, image processing, and machine learning.
Dr. Wakatsuki's research interests include structural biology of post-translational modification and vesicle transport, structural biology of polyubiquitin recognition, synchrotron radiation and XFEL instrumentation, protein crystallography and small angle X-ray scattering, integrative multi-scale bioimaging.
Dr. Pritchard's lab is interested in a broad range of problems at the interface of genomics and evolutionary biology. One current focus of the lab is in understanding how genetic variation impacts gene regulation and complex traits. They also have long-term interests in using genetic data to learn about population structure, history and adaptation, especially in humans.
Dr. Marsden's work focuses on the development of numerical methods for cardiovascular blood flow simulation, medical device design, application of optimization to large-scale fluid mechanics simulations, and application of engineering tools to impact patient care in cardiovascular surgery and congenital heart disease.
Under Dr. Alison Marsden, the Cardiovascular Biomechanics Computation Lab at Stanford develops novel computational methods for the study of cardiovascular disease progression, surgical methods, and medical devices.
The lab's interests include: cardiovascular disease and biofluid mechanics, shape optimization for complex flows, pediatric cardiology and congenital heart disease, vascular surgery, derivative-free optimization methods, uncertainty quantification, multiscale modeling, vascular design principles, vascular growth and remodeling, thrombosis, cardiovascular device design, Kawasaki Disease, bypass graft optimization, and ventricular assist devices.