PRISM Mentors

The Mai Research Group engineers biopolymers, which are the building materials of life. We seek to develop functional biomaterials and to enhance understanding in the physics of soft materials. Molecular-scale biopolymer design presents a unique opportunity to rationally design materials based on biomolecular templates. Moreover, biopolymer engineering incorporates the rich functional landscape of biological systems into responsive biomaterials. We are especially interested in connecting properties across multiple length scales (molecular, microscopic, macroscopic) using experimental methods. We integrate rational biomolecular design, biological and chemical synthesis, and multi-scale characterization techniques to engineer biopolymers with tunable mechanics, stimuli-responsive behavior, and self-healing properties. Initial research efforts address biological systems where deformation is significant, with specific project areas including: (i) muscle-mimetic materials from polypeptides, (ii) biolubricants from bottlebrush polymers, and (iii) selective filters from programmable hydrogels.

The QIAI lab focuses on cutting‐edge research at the intersection of imaging science and biomedical informatics, developing and applying AI methods to large amounts of medical data for biomedical discovery, precision medicine, and precision health (early detection and prediction of future disease). The lab develops novel methods in text and image analysis and AI, including multi-modal and multi-task learning, weak supervision, knowledge representation, natural language processing, and decision theory to tackle the challenges of leveraging medical Big Data. Our exciting work is bridging a spectrum of biomedical domains with multidisciplinary collaborations with top scientists at Stanford as well as with other institutions internationally. The QIAI lab provides a unique multidisciplinary environment for conducing innovative AI-based healthcare research with a strong record of scholarly publication and achievement. Core research topics in the laboratory include: (1) automated image annotation using unsupervised methods of processing associated radiology reports using word embeddings and related methods; (2) developing methods of analyzing longitudinal EMR data to predict clinical outcomes and best treatments, (3) creating multi-modal deep learning models integrating multi-dimensional EMR and other data to discover electronic phenotypes of disease, (4) developing AI models with noisy or sparse labels (weak supervision), and cross-modal, multi-task learning, and observational AI approaches, and (5) developing and implementing algorithms for distributed computation for training deep learning models that leverage multi-institutional data while avoiding the barriers to data sharing.

Daniel Ennis (Ph.D.) is an Associate Professor in the Department of Radiology. As an MRI scientist for nearly twenty years, he has worked to develop advanced translational cardiovascular MRI methods for quantitatively assessing structure, function, flow, and remodeling in both adult and pediatric populations. He began his research career as a Ph.D. student in the Department of Biomedical Engineering at Johns Hopkins University during which time he formed an active collaboration with investigators in the Laboratory of Cardiac Energetics at the National Heart, Lung, and Blood Institute (NIH/NHLBI). Thereafter, he joined the Departments of Radiological Sciences and Cardiothoracic Surgery at Stanford University as a post doc and began to establish an independent research program with an NIH K99/R00 award focused on “Myocardial Structure, Function, and Remodeling in Mitral Regurgitation.” For ten years he led a group of clinicians and scientists at UCLA working to develop and evaluate advanced cardiovascular MRI exams as PI of several NIH funded studies. In 2018 he returned to Stanford Radiology and the Radiological Sciences Lab to bolster programs in cardiovascular MRI. He is also the Director of Radiology Research for the Veterans Administration Palo Alto Health Care System where he oversees a growing radiology research program.

The Bernstein Lab has several major foci:
 

1. Using iPSC-derived cardiomyocytes to develop a better understanding of hypertrophic cardiomyopathy and congenital heart disease.
2. The role of alterations in mitochondrial structure and function in normal physiology and in diseases such as dilated and hypertrophic cardiomyopathy.
3. Single cell analysis of mitochondrial function reveals significant heterogeneity.

Specific projects underway in our lab include:

1. Using CRISPR-edited iPSC-cardiomyocytes to understand the mechanisms of cardiomyopathies and to solve the genotype-phenotype conundrum in hypertrophic cardiomyopathy.

2. The role of altered metabolism and mitochondrial function in hypertrophic cardiomyopathy.

3. Alterations of mitochondrial structure and function, including processes of mitofusion, mitofission, autophagy and mitophagy, in normal physiology and disease.

4. Development of high-throughput single cell imaging technologies to measure single cell mitochondrial function, and to measure single mitochondrial function to determine the role of heterogeneity in cell life-death decision-making.

5. Development of micro-engineered platforms for assessment of biomechanics of single iPSC-derived cardiomyocytes.

We also are interested in clinical heart failure and cardiac transplantation in children, specifically:

1. Understanding alterations in immune system function in patients with after implantation of a left ventricular assist device, Immune system biomarkers that predict adverse outcomes after pediatric VAD implantation.

2. Understanding alterations in immune system function in children with heart failure before and after heart transplant.

3. Development of biomarkers for the detection and monitoring of post-transplant lymphoproliferative disorder in pediatric solid organ transplant patients.
 

Possible T-32 Options Include:
Training in Myocardial Biology at Stanford (TIMBS)

Our lab has several major interests: 1. Using CRISPR-edited hiPSC-derived cardiomyocytes to develop a better understanding of hypertrophic cardiomyopathy and congenital heart disease. 2. The role of alterations in mitochondrial structure and function in dilated and hypertrophic cardiomyopathy. 3. Single cell analysis of mitochondrial function and the effect of mitochondrial heterogeneity on cellular function. 4. Differences between right and left ventricular responses to stress and in their modes of failure, including gene expression and miR regulation of angiogenesis and mitochondrial function. 5. Use of iPSC-CMs in pharmacogenomics, specifically determining the role of gene variants in anthracycline cardiotoxicity.

Together with Tom Shutt, Dan works on the LUX and LZ dark matter experiments to search for dark matter in the form of Weakly Interacting Massive Particles, or WIMPs. The detectors use liquid xenon as a target medium in a time projection chamber, or TPC. The Large Underground Xenon (LUX) experiment is currently operating a 250-kg target in the former Homestake gold mine in the Black Hills of South Dakota. Preparations are underway at SLAC to design and build the 7-ton successor, known as LUX-ZEPLIN (LZ). The group is involved in many aspects of data analysis, detector design, xenon purification, control andreadout systems, and detector performance studies.

Protein self-assembly in evolution, disease, and development; Systems biology of aging;  Mutational robustness in cancer and pathogens; Quantitative analysis of evolving genotype-to-phenotoype maps. Epigenetic control of interspecies interactions.

To understand biology, we need chemistry and physics as the physical and chemical properties of biomolecules enable and constrain what biology can do and how it has evolved. We are particularly interested in questions of: (i) how enzymes work; (ii) how RNA folds; (iii) how proteins recognize RNA; (iv) RNA/protein interactions in regulation and control; and (v) the evolution of molecules and molecular interactions. Our interdisciplinary approaches span and integrate physics, chemistry and biology, employ a wide range of techniques, and are question driven. We have new projects in each of the above areas as we:
• Pioneer high-throughput quantitative approaches to study enzymes—to address how an entire protein contributes to its function, how allosteric signals are propagated, how different human alleles affect function and/or stability, and ultimately how to design new enzymes (with Polly Fordyce);
• Work to understand the evolution of enzyme function and stability via functional, genome-scale analyses, and experimental evolutionary studies;
• Pioneer the determination of enzyme conformational ensembles—and linking these to function via novel “ensemble¬–function” studies;
• Develop a quantitative and predictive model for RNA tertiary folding thermodynamics and kinetics, building from the “RNA Reconstitution Model”;
• Provide the first quantitative and complete descriptions of the affinity and specificity of RNA binding proteins for all possible RNA sequences and structures (with Will Greenleaf);
• Pioneer Quantitative Cellular Biochemistry (QCB) to bring together the power of biochemistry and genomics to the study molecular interactions and function in cells, with the goal of providing quantitative and predictive models for molecular function and regulation in cells.

I am a Theoretical Physicist by training and have been working on mathematical and computational modeling of biological systems since my PhD. My lab studies hearing and balance systems and is interested in how sensory signals are filtered, transduced, amplified, and transmitted to the brain. We have worked on the ear's mechanics, synaptic dynamics, and otoacoustic emissions and use experimental data to motivate and test our mathematical models. In collaborations with several experimental labs, we have helped explain their data and tested our mathematical models. Our work is highly interdisciplinary and sits at the intersection of many fields including physics, biology, mathematics, neuroscience, and engineering. At present, we are focusing on the sensory cells in hearing and balance systems and on auditory evoked potentials.

The research interests of the molecular imaging instrumentation lab are to create novel instrumentation and software algorithms for in vivo imaging of molecular signatures of disease in humans and small laboratory animals. These new cameras efficiently image radiation emissions in the form of positrons, annihilation photons, gamma rays, and/or light emitted from molecular contrast agents that were introduced into the body and distributed in the subject tissues. These contrast agents are designed to target molecular pathways of disease biology and enable imaging of these biological signatures in tissues residing deep within the body using measurements made from outside the body.

The goals of the instrumentation projects are to advance the sensitivity and spatial, spectral, and/or temporal resolutions, and to create new camera geometries for special biomedical applications. The computational modeling and 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 designing and building instrumentation, including arrays of position sensitive sensors, readout electronics, and data acquisition electronics, signal processing research, including creation of computer models, and image reconstruction, 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.

The research interests of the molecular imaging instrumentation lab are to create novel instrumentation and software algorithms for in vivo imaging of molecular signatures of disease in humans and small laboratory animals. These new cameras efficiently image radiation emissions in the form of positrons, annihilation photons, gamma rays, and/or light emitted from molecular contrast agents that were introduced into the body and distributed in the subject tissues. These contrast agents are designed to target molecular pathways of disease biology and enable imaging of these biological signatures in tissues residing deep within the body using measurements made from outside the body.

The goals of the instrumentation projects are to advance the sensitivity and spatial, spectral, and/or temporal resolutions, and to create new camera geometries for special biomedical applications. The computational modeling and 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 designing and building instrumentation, including arrays of position sensitive sensors, readout electronics, and data acquisition electronics, signal processing research, including creation of computer models, and image reconstruction, 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.

The research interests of the molecular imaging instrumentation lab are to create novel instrumentation and software algorithms for in vivo imaging of molecular signatures of disease in humans and small laboratory animals. These new cameras efficiently image radiation emissions in the form of positrons, annihilation photons, gamma rays, and/or light emitted from molecular contrast agents that were introduced into the body and distributed in the subject tissues. These contrast agents are designed to target molecular pathways of disease biology and enable imaging of these biological signatures in tissues residing deep within the body using measurements made from outside the body.

The goals of the instrumentation projects are to advance the sensitivity and spatial, spectral, and/or temporal resolutions, and to create new camera geometries for special biomedical applications. The computational modeling and 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 designing and building instrumentation, including arrays of position sensitive sensors, readout electronics, and data acquisition electronics, signal processing research, including creation of computer models, and image reconstruction, 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.

The research interests of the molecular imaging instrumentation lab are to create novel instrumentation and software algorithms for in vivo imaging of molecular signatures of disease in humans and small laboratory animals. These new cameras efficiently image radiation emissions in the form of positrons, annihilation photons, gamma rays, and/or light emitted from molecular contrast agents that were introduced into the body and distributed in the subject tissues. These contrast agents are designed to target molecular pathways of disease biology and enable imaging of these biological signatures in tissues residing deep within the body using measurements made from outside the body.

The goals of the instrumentation projects are to advance the sensitivity and spatial, spectral, and/or temporal resolutions, and to create new camera geometries for special biomedical applications. The computational modeling and 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 designing and building instrumentation, including arrays of position sensitive sensors, readout electronics, and data acquisition electronics, signal processing research, including creation of computer models, and image reconstruction, 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.

THE PETRITSCH BRAIN TUMOR STEM CELL AND MODELS RESEARCH LAB

The Petritsch lab broadly investigates underlying causes for the intra-tumoral heterogeneity and immune suppression in brain tumors from a developmental neurobiology point of view. Defects in cell fate control could explain many key defects present in brain tumors and an understanding of how brain cells control the fate of their progeny may identify novel points of vulnerabilities to target with therapeutics. Of special emphasis, we study the establishment of cell fates within normal hierarchical brain lineages for comparison to the dysregulated cell-fate hierarchies seen in brain tumors. Our lab was the first to demonstrate that normal adult oligodendrocyte progenitor cells (OPCs) undergo asymmetric divisions to make cell fate decisions, i.e. to generate OPCs as well as differentiating cells each time they divide. Drawing from these data, we investigate whether brain tumors divide along hierarchical lineages and how oncogenic mutations might affect cell fate decisions within these hierarchies. A major line of investigation in our lab focuses on whether defects in the asymmetric division lead to aberrant cell fate decisions that cause the paradigm mixed-lineage phenotypes and the intra-tumoral heterogeneity present across tumors.

To study the interactions between tumor cells and the immune system, we have developed and utilized transplantable mouse glioma models. We are tasked to facilitate and coordinate the distribution of fresh tissue from the neurosurgery operating room and have access to fresh brain tissue from patient surgeries, from which we prepare cell culture models for brain tumors and normal progenitors. We complement our work with human cells with studies in genetically engineered mouse models of gliomagenesis to conduct molecular, cellular, and bioinformatic analyses.

My research focuses on the influence of the external environment on entrepreneurship. Specifically, I have sought to be a leader in investigating the types of environments that encourage the founding of high growth, technology-based firms. Although I build on previous work that focuses on individual characteristics, network ties, and strategy, my major contribution is to demonstrate that institutions matter. I have broken new ground in showing that effective institutional change influences who starts firms, not just how many firms are started. I have repeatedly studied entrepreneurship in a single country (China, Chile, Japan, and the U.S.) before and after a major institutional change. My work is divided into three streams: (1) formal institutions (policies and regulations), (2) university and industry environments, and (3) informal institutions (social movements).
STREAM 1: My research in this stream advances theory by introducing novel mechanisms (e.g. barriers to growth and failure, institutional inconsistency), introducing new concepts (e.g. skill adequacy and context relevance) and in theorizing that institutional changes that lower barriers to growth and to failure alter who becomes an entrepreneur, the type of firms, and performance.
STREAM 2: My work in this stream changes the way we think about team composition as well as what characteristics lead to venture performance by linking their impacts to industry environments.
STREAM 3: In this stream, I explored how social movement organizations can change firms.
My research changes the way we think about how the environment – formal institutions, informal institutions, and industry contexts – influences entrepreneurship. I am a leader in situating ventures within environments and showing that interactions between environments and entrepreneurs matter. I am among the first to argue and show that policies that foster high-growth entrepreneurship are different than those that spawn small businesses. If policy leaders wish to foster technology-based start-ups, then we must consider how institutions operate. My research shows that institutional changes can significantly influence the types of firms that are created, who creates them, and how they perform. My research challenges widely accepted ideas about entrepreneurship by highlighting taken-for-granted notions that are incomplete or misleading. My studies call into question the assumption that institutions that make it easier to start firms are unambiguously beneficial, and that experienced, diverse founding teams are always superior. My theoretical contributions include introducing such concepts as institutional barriers to growth, skill adequacy and context relevance. I lead the way in broadening our conception of entrepreneurship beyond the developed North American economies. I have contributed methodologically by (A) showing how to measure talent, (B) collecting data internationally, (C) using randomized field experiments, and (D) analyzing multi-industry databases with state-of-the-art statistics (instrumental variables, differences-in-differences). I have been a pioneer in overcoming the challenges of inferring causality, by finding changes that altered the landscape for entrepreneurship, along with collecting novel data in international settings. In future work, I plan to do more studies incorporating software development for data collection and digital platforms for randomized experiments focusing on issues related to strategic change and entrepreneurship training. 

We combine biophysical methods with in vivo approaches to understand how viruses such as HIV and SARS-CoV-2 infect host cells and elicit specific humoral immune responses. Our research will translate knowledge of the structural correlates of antibody-mediated neutralization of viruses into the rational development of highly protective antibodies. A related goal is the structure-based design of potent and stable immunogens for vaccination.

The Jacobs-Wagner lab has two main research interests:

1. They examine the general principles and spatiotemporal mechanisms by which bacterial cells replicate. Bacteria are infamous for their remarkable ability to proliferate. Yet, despite their medical and agricultural importance, little is known about how bacteria control and integrate their growth, cell morphogenesis and cell cycle functions. The Jacobs-Wagner lab addresses this fundamental question at all levels, from a systems-level perspective down to the physical mechanisms, using genetics and cutting-edge quantitative microscopy techniques. The primary model bacterial systems are Escherichia coli and Caulobacter crescentus. Microbiologists, physicists and individuals with expertise in quantitative biology are encouraged to contact us.
2. Recently, the Jacobs-Wagner lab expanded their interests to the Lyme disease agent Borrelia burgdorferi, revealing unsuspected ways by which this pathogen grows and causes disease. Lyme disease is tick-born disease whose incidence and geographic distribution have rapidly increased over the years, in part due to climate change. The Jacobs-Wagner lab has developed genetic and cell biological tools as well as mass spectrometry and microscopy protocols to study this important human pathogen, from its unique cell biology to its pathogenesis. Individuals with expertise in microbial pathogenesis or immunology are encouraged to contact us.
    

Department URL:
https://biology.stanford.edu/

Our lab is interested in the capability of robots and other agents to develop broadly intelligent behavior through learning and interaction. We work on robotics and machine learning, and we are affiliated with SAIL, the ML Group, the Stanford Robotics Center, and CRFM.

Our group's research interests center around entrepreneurship. We are particularly interested in policy and the institutional environment, entrepreneurs in emerging economies and entrepreneurship among historically under-represented populations. We also do some work on technology platforms to facilitate startups and refugee entrepreneurship.

Chao-Lin’s group use the most ancient light, the Cosmic Microwave Background (CMB) radiation, emitted when the universe was in its infancy to shed light on the question of how the universe began. Currently Chao-Lin's group are involved in a number of experiments such as BICEP/BICEP2/Keck Array and have been working hard on detecting primordial B-mode polarization. His group are involved in both he design and construction of instruments as well as the data analysis and theoretical interpretation.

My research interests lie at the interface between chemistry and biology. While ongoing research in my lab focuses on multiple problems, all of these efforts are motivated by the twin goals of shining light on fundamentally new molecular mechanisms in biology and leveraging these insights to address unmet challenges in human health. Two examples of ongoing research themes in my lab are outlined below:

I] Assembly-line biosynthesis of polyketide antibiotics: The primary objective of this longstanding research project in my lab is to understand the enzymatic mechanisms of assembly-line polyketide synthases (PKSs). Having defined the physical boundaries and chemical reactivity of individual domains and modules, our goal now is to understand these assembly lines as integrated metabolic systems. We also seek to understand the genetic mechanisms for extraordinary evolutionary diversification of this family of multifunctional enzymes.

II] Chemical approaches to understanding celiac disease pathogenesis: Over the past two decades, we have made significant contributions to an understanding of celiac disease (CeD) pathogenesis. Furthermore, at each step along the way, we have sought to translate these emerging molecular insights into enhanced disease management tools for CeD patients and their doctors, as illustrated by the translation of two experimental therapeutics from our lab into advanced preclinical/early clinical studies, and the translation of a biomarker discovered in our lab into CeD patients.
 

Research in this laboratory focuses on problems where deep insights into enzymology and metabolism can be harnessed to improve human health.
For the past two decades, we have studied and engineered enzymatic assembly lines called polyketide synthases that catalyze the biosynthesis of structurally complex and medicinally fascinating antibiotics in bacteria. An example of such an assembly line is found in the erythromycin biosynthetic pathway. Our current focus is on understanding the structure and mechanism of this polyketide synthase. At the same time, we are developing methods to decode the vast and growing number of orphan polyketide assembly lines in the sequence databases.

For more than a decade, we have also investigated the pathogenesis of celiac disease, an autoimmune disorder of the small intestine, with the goal of discovering therapies and related management tools for this widespread but overlooked disease. Ongoing efforts focus on understanding the pivotal role of transglutaminase 2 in triggering the inflammatory response to dietary gluten in the celiac intestine.

The Gifford lab is focused on defining the complex genetic and molecular mechanisms that are necessary for faithful cardiovascular development and how perturbation of these mechanisms can lead to disease. We use both stem cell and rodent experimental models to:

• characterize the cellular interactions involved in cardiovascular development
• define the oligogenic mechanisms underlying congenital heart diseases, such as hypoplastic left heart syndrome and left ventricular noncompaction
• explore the link between congenital heart disease and neurodevelopmental delay

We also collaborate closely with clinicians, for example on a project integrating cardiac imaging and genetic data to predict adverse cardiac outcomes. Ultimately, we hope to make personalized medicine a reality for those that suffer from CHD and associated comorbidities, such as autism.

Chromatin regulators are highly altered in diseases. Of interest, these proteins are easily targetable by drugs. Furthermore, the plasticity of epigenetic events makes them a powerful target for new therapeutic strategies and reversion of disease phenotype. Histone and DNA modifications influence many processes including transcription, replication, genomic stability and cell division, which are altered in diseases. Therefore, understanding the molecular basis of chromatin modifiers in both normal and pathological cells could help us frame new potential biomarkers and targeted therapies. My long-term interest lies in understanding the impact chromatin modifiers have on disease development and progression so that more optimal therapeutic opportunities can be achieved. My laboratory explores the direct molecular impact of chromatin-modifying enzymes during cell cycle progression, and characterizes the unappreciated and unconventional roles that these chromatin factors have on cytoplasmic function such as protein synthesis. By gaining molecular understanding into the mechanism of action of chromatin modifiers in normal and pathological cells, we will improve our basic knowledge and provide needed insights into new potential targeted therapies in diseases.

Department URL:
https://www.google.com/search?client=safari&rls=en&q=stanford+department+of+pathology&ie=UTF-8&oe=UTF-8