PRISM Mentors

The Skylar-Scott Lab specializes in cardiovascular tissue biomanufacturing, seeking to push the complexity and scale at which tissue can be designed and manufactured on demand. By integrating high-throughput culture of designer organoids with new machines and methods for advanced 3D bioprinting, our laboratory seeks to enhance the maturation and function of vascularized cardiac tissues in vitro and in vivo.

Our lab is embedded at the intersection of synthetic biology, tissue engineering, and 3D printing. We are always seeking new students and postdocs with a demonstrated passion for rethinking how we make things, with relevant expertise in bioengineering, mechanical engineering, or materials science.

By studying calcineurin, the conserved Ca2+/calmodulin-regulated protein phosphatase, we aim to discover and elucidate new Ca2+-regulated signaling pathways in humans. The calcineurin phosphatase dephosphorylates proteins only when Ca2+ signaling is triggered, for example by a hormone, growth factor, neurotransmitter etc. Previous work from the Cyert lab discovered how calcineurin allows yeast cells to survive environmental stress (Goldman et al, 2014, Molecular Cell). Currently, we are studying human calcineurin which is ubiquitously expressed and plays critical roles throughout the body, but especially in the nervous, cardiac and immune systems. Calcineurin is best known for activating the adaptive immune response by dephosphorylating the NFAT transcription factors, and is the target of widely prescribed immunosuppressant drugs, FK506 (tacrolimus) and Cyclosporin A. However, these drugs cause many adverse effects due to inhibition of calcineurin in non-immune tissues, where the majority of calcineurin substrates and functions remain to be discovered. We are using a variety of experimental and computational strategies to systematically map human calcineurin signaling pathways in healthy and diseased cells. We have uncovered surprising roles for calcineurin in Notch signaling, regulation of transport though nuclear pores, and at centrosomes. See our recent paper (Wigington, Roy et al, 2020, Molecular Cell) to learn more about our studies.

I am a physician scientist with interests in cardiomyopathies, rare and undiagnosed diseases, therapeutics and genomics. I have research training in myocardial and skeletal muscle biology and genetics, genomics, and multi-scale networks. In addition to my research training, I am a physician with interest and experience treating patients with hypertrophic cardiomyopathy, neuromuscular disease associated cardiomyopathies, and inherited dilated cardiomyopathies. I have clinical training in medicine, cardiology, cardiovascular genetics, and advanced heart failure and transplant cardiology. I have extensive translational science efforts, as site PI for ongoing clinical trials for hypertrophic cardiomyopathy and dilated cardiomyopathy and for cardiomyopathy consortia including NONCOMPACT, PPCM and the Precision Medicine Study/DCM Consortium. I am Co-PI of Stanford’s NIH-funded Center for Undiagnosed Diseases, a clinical site of the Undiagnosed Diseases Network. I am also Co-PI of the NIH-funded Bioinformatics Center of the Molecular Transducers of Physical Activity Consortium. I pursue projects and collaborations at the intersection of striated muscle genetics, genomics, therapeutics and clinical investigation.

Department URL:
https://med.stanford.edu/cvmedicine.html

With a creative, collaborative, biophysical mindset, we aim to understand the ability of parasites to interface with their host-cell to a point at which we can exploit the mechanisms not only for finding cures against the disease the parasites cause but also to make parasite mechanisms a tool that we can use to engineer the host’s cells. By developing approaches that allow a quantitative understanding and manipulation of molecular transport our research transforms parasites from agents of disease to tools for health.

Specifically, we are studying how the malaria parasite takes control over red blood cells. By learning the biophysical principles of transport in between the host and the parasite we can design ways to kill the parasite or exploit it to reengineer red blood cells. The transport we study is broadly encompassing everything from ions to lipids and proteins. We use variations of quantitative microscopy and electrophysiology to gain insight into the unique strategies the parasite evolved to survive.

Research activities in our group focus on the computational modeling and experimental analysis of turbulent and chemically reacting flows. Applications include propulsion systems, renewable energy, carbon sequestration, and high-speed and multiphase flows. Particular emphasis is directed towards improving the fundamental understanding of underlying physical processes involving the coupling between turbulence, reaction chemistry, pollutant formation and noise emission. Our research approach combines classical theoretical analysis tools (including linear stability analysis, rapid distortion theory, and stochastic models), numerical models, and the utilization of direct numerical simulation (DNS) results for the development, analysis, and validation of computational models. Current research interests include:

• Fundamental analysis of non-equilibrium and supercritical flows
• Heat-transfer and boundary layers
• High-order numerical techniques for chemically reacting flows
• Development of models for application to kinetics-controlled combustion, including auto-ignition, low-temperature combustion, and combustion-dynamic processes
• Particle-laden flows and atmospheric entry
• Heterogeneous flows in micro-, meso-, and nano-porous flows
• CO2 capture and sequestration

Another active area of research involves the experimental analysis of ultrafast non-equilibrium processes using X-ray diffraction and spectroscopy, specfically focusing on sub-picosecond physico-chemical processes in complex fluids and chemical systems. For this, we're closely working with the SLAC National Accelerator Laboratory, the Advanced Light Source at LBNL and other facility to perform X-ray experiments.

The overarching research goal of the Diehn lab is to develop and translate novel diagnostic assays and therapies to improve personalized treatment of cancer patients. We have a major focus on the development and application of liquid biopsy technologies for human cancers, with a particular emphasis on lung cancers and circulating tumor DNA (ctDNA). We also investigate mechanisms of treatment resistance to radiotherapy, immunotherapy, and targeted agents. Most of our research projects start by identifying an unmet need in the clinical management of cancer patients that we then try to solve via development or application of novel technologies. We use genomics, bioinformatics, stem cell biology, genome editing, mouse genetics, and preclinical cancer models in our work. Discoveries from our group are currently being tested in multiple clinical trials at Stanford and elsewhere in order to translate them into the clinic.

I am a clinical pathologist and assistant professor in the Departments of Medicine, Pathology, and Genetics (by courtesy) at Stanford. I completed my MD-PhD training at Yale University and my residency training and a post-doctoral fellowship in the Department of Genetics at Stanford University. My experiences as a clinical pathologist and genome scientist have made me passionate about applying cutting-edge technologies to primary patient specimens in order to characterize disease pathologies at the molecular level. The core focus of my lab is to study the mechanisms by which genetic variants influence the risk of disease through effects on intermediate molecular phenotypes.

The mission of the Water & Energy Efficiency for the Environment Lab (WE3Lab) is to reduce the cost and carbon intensity of water desalination and reuse. Ongoing research efforts include:

1) developing automated, precise, robust, intensified, modular, and electrified (A-PRIME) water desalination technologies to support a circular water economy;

2) optimizing the coordinated operation of decarbonized water and energy systems; and

3) supporting the design and enforcement of water-energy-food policies (e.g., Effluent Limitation Guidelines, the Clean Power Plan, CA Sustainable Groundwater Management Act, etc.).

The mission of the Water & Energy Efficiency for the Environment Lab (WE3Lab) is to reduce the cost and carbon intensity of water desalination and reuse. Ongoing research efforts include:

1) developing automated, precise, robust, intensified, modular, and electrified (A-PRIME) water desalination technologies to support a circular water economy;

2) optimizing the coordinated operation of decarbonized water and energy systems; and

3) supporting the design and enforcement of water-energy-food policies (e.g., Effluent Limitation Guidelines, the Clean Power Plan, CA Sustainable Groundwater Management Act, etc.).

Our lab focuses on the biology of chimeric antigen receptor (CAR) T cells in order to improve the efficacy and safety of this therapy (1) by investigating donor and third-party CAR T cells in an immunocompetent mouse model of allogeneic hematopoietic cell transplant (allo-HCT) and (2) by assessing the impact of the intestinal microbiome on CAR T cell response. We will seek to enhance the development, administration, and mechanistic understanding of how to safely administer donor and third-party CAR T cells with the aim to potentially translate our work to the clinic. We will investigate the regulatory mechanism of the impact of bacterial taxa and the metabolites that they produce on CAR T cell outcomes.

Our research lab focuses on studying the molecular mechanisms of ion channels and transporters. We use a combination of biophysical methods to probe membrane protein structure and dynamics, together with functional assays and electrophysiological analysis. Ongoing projects in our lab include:
• Examining the molecular mechanisms of chloride/proton transporters
• Developing new small-molecule probes to studying mammalian chloride channels
• Exploring the biophysics and physiology of the mammalian chloride channels
• Using electrophysiology techniques to study the molecular effects of ultrasound neuromodulation on ion channels in brain tissue

Department URL:

https://med.stanford.edu/mcp.html

Small molecules from the human microbiota. Many of the most widely used human medicines come from soil and marine bacteria, including treatments for cancer, infectious disease, diabetes, and organ transplant. We have recently found that bacteria from a surprisingly underexplored niche -- the human body -- are prolific producers of drug-like small molecules. We are identifying small molecules from gut- and skin-associated bacteria, studying their biosynthetic genes, and characterizing the roles they play in human biology and disease. 
 
Using synthetic ecology to control microbiome metabolism. One of the most concrete contributions the microbiome makes to human biology is to synthesize dozens of metabolites, many of which accumulate in human tissues at concentrations similar to what is achieved by a drug. We are engineering gut and skin bacterial species to produce new molecules, and constructing synthetic communities whose molecular output is completely specified.

How 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 am interested in bringing larger datasets to bear on these questions and use a wide variety of methods including eye-tracking, tablet experiments, and computational models. Recent work in my lab has focused on data-oriented approaches to development, including the creation of large datasets like Wordbank and MetaLab. I also have a strong interest in replication, reproducibility, and open science; some of our research addresses these topics.

http://web.stanford.edu/~mcfrank

Our lab is broadly interested in how intestinal microbes shape our immune system to promote both health and disease. Recently we discovered that a type of intestinal epithelial cell, called tuft cells, act as sentinels stationed along the lining of the gut. Tuft cells respond to microbes, including parasites, to initiate type 2 immunity, remodel the epithelium, and alter gut physiology. Surprisingly, these changes to the intestine rely on the same chemosensory pathway found in oral taste cells. Currently, we aim to 1) elucidate the role of specific tuft cell receptors in microbial detection. 2) To understand how protozoa and bacteria within the microbiota impact host immunity. 3) Discover how tuft cells modulate surrounding cells and tissue.

We develop data-driven, multiplexed methods to elucidate fundamental principles about how the living world works. We use the knowledge from these insights to develop cell-free biotechnologies for decentralized biomanufacturing, portable diagnostics, and educational kits to serve human needs. A key feature of our work is an emphasis on advancing and applying our capacity to partner with biology to make what is needed, where and when it is needed, on a sustainable and renewable basis. Our work holds promise to transform bioengineering applications in health, manufacturing, sustainability, and education, anywhere on earth and even beyond.

Specificity and efficacy in intracellular signal transduction can be conferred by the anchoring and co-localization of key enzymes and their upstream activators and substrate effectors by scaffold proteins. The Kapiloff lab investigates “signalosomes” formed by scaffold proteins, asking fundamental questions such as: 1) how are signalosomes constituted; 2) how are upstream signals integrated by signalosomes to regulate in a concerted manner downstream effectors; 3) what is the physiologic relevance of these signalosomes; and 4) can signalosomes be targeted in a clinically relevant manner so as to constitute new therapeutic strategies. In particular, the Kapiloff lab studies signaling within the myocardium and retina. Using a comprehensive approach that includes biochemistry, cell biology, and in vivo physiology, ongoing projects address the regulation of pathological cardiac remodeling and the effects of disease on retinal neurons.

My lab focuses on translating advanced MRI into clinical practice. In Alzheimer’s disease, we are investigating the nature of iron deposition to understand how iron interacts with inflammation, amyloid, and tau in the progression of AD. We bring to this disease the full arsenal of imaging: ultra-high resolution MRI of human AD specimens coupled with novel histological methods including x-ray microscopy and electron microscopy. We bring this armamentarium full circle to living human imaging with 7.0T MR and multi-tracer PET-MR. In mild traumatic brain injury, we are studying the imaging signatures of brain insult that occur in high-contact sports using advanced MRI combined with mouthguard accelerometer measurements of impacts. In chronic fatigue syndrome, we are identifying microstructural changes that accompany fatigue and correlate with systemic circulating cytokines that together may form a biomarker for this disorder.

Dr. Michael Zeineh received a B.S. in Biology at Caltech in 1995 and obtained his M.D.-Ph.D. from UCLA in 2003. After internship also at UCLA, he went on to radiology residency and neuroradiology fellowship both at Stanford. He has been faculty in Stanford Neuroradiology since 2010. He spearheads many initiatives in advanced clinical imaging at Stanford, including clinical fMRI and DTI. Simultaneously, he runs a lab with the goal of discovering new imaging abnormalities in neurodegenerative disorders, with a focus on detailed microcircuitry in regions such as the hippocampal formation using advanced, multi-modal in vivo and ex vivo methods, with applications to neurodegenerative disorders such as Alzheimer’s disease and mild traumatic brain injury.

Specific projects:

Ex vivo MRI of iron in Alzheimer’s disease
MR-histopathology correlation (both traditional histology and clearing methods)
MR-PET of AD
7T MR in AD
Analysis of iron-changes in exosomes from AD
Multi-modal MRI (DTI, ASL, QSM, rsfMRI) in mild traumatic brain injury
7T MR in Epilepsy
Ultra-high resolution 7T MRI
X-ray imaging of iron
X-ray imaging of myelin and myelin orientation
Scattered light imaging
Hippocampal microanatomy

We are an interdisciplinary research laboratory that focuses on model-based analysis, design, and control of biological function at the molecular, cellular, and organismal levels to optimize therapeutic intervention.

Near-future research directions

• Design and implementation targeted synthetic microbe therapies
• Interorgan communication in health and disease
• Synthetic pattern formation in growing microbial populations

The Mayalu Lab is seeking bright, talented, and motivated graduate students and postdocs to fill several positions.

These are great opportunities to work on control theoretic and experimental aspects of model-based design of synthetic biological and biomedical systems. 

Postdocs with additional training in synthetic microbiology, genetic recombination technology, bioengineering or related fields are encouraged to apply to help launch the experimental research program.

Dr. Lin's active NIH-funded research portfolio includes developing a novel patient-reported outcome measure for emergency asthma care; evaluating post-acute transitions and outcomes for high-risk populations; and enhancing gender equity in the health professions workforce. Her prior funded projects have evaluated the impact of value-based care on emergency care delivery and payment; drivers of ED admission rates; and changes in the intensity of emergency care.

Stanford Training Program in Ethical, Legal, and Social Implications (ELSI) Research

• Co-Principal Investigators and Program Co-Directors:  Mildred Cho, PhD, Holly Tabor, PhD
• Funding source: NIH National Human Genome Research Institute
• Appointment:  One year, renewable for up to three years
• Qualifications: The NIH requires that candidates must have a PhD or MD (JD or Master’s degree only not accepted) prior to starting the fellowship, and be a U.S. citizen or permanent resident to be eligible for funding.  We are seeking candidates with a background in social science, ethics, philosophy, history, health services research, public policy or other related disciplines.

Job description: 

The postdoctoral fellow will conduct independent research on ethical, legal and social considerations arising from genetics and genomics.  The fellow will be part of an interdisciplinary community including faculty and fellows from this program and other affiliated programs. Fellows are expected to gain practical experience in professional activities through programs such as the Stanford Benchside Ethics Consultation Service, a research ethics consultation program to assist life sciences researchers in the resolution of ethical concerns in their research, one of the Stanford-affiliated clinical ethics consultation services, and/or teaching.

In addition to participating in SCBE and CIRGE activities, fellows will have access to a full range of courses at Stanford University, which includes genetics, social science, humanities and law courses.  It is expected that the fellow may need formal coursework in genetics, ethics, or ELSI research methods.  Mentors will assist the fellow in formulating an individualized curriculum and career strategies.  All trainees will be expected to present their research in scholarly venues.  Fellowship support includes a stipend, tuition, and health insurance. Funds will be provided by the fellowship for each fellow to travel to one meeting per year.

For more information, please see our website. 

The Laboratory for Integrative Personalized Medicine (PIMed) is directed by Dr. Mirabela Rusu, PhD,  and is part of the School of Medicine, Department of Radiology, Division of Integrative Biomedical Imaging Informatics at Stanford University.   

The PIMed Laboratory has a multi-disciplinary direction and focuses on developing analytic methods for biomedical data integration, with a particular interest in radiology-pathology fusion to facilitate radiology image labeling . Such integrative methods may be applied to create comprehensive multi-scale representations of biomedical processes and pathological conditions, thus enabling their in-depth characterization. The radiology-pathology fusion allows the creation of detailed spatial labels, that later on can be used as input for advanced machine learning, such as deep learning.

PIMed closely collaborates with the Urologic Cancer Innovation Lab at Stanford for the prostate cancer work. 

Department URL:
http://radiology.stanford.edu/

The PIMed Laboratory has a multi-disciplinary direction and focuses on developing analytic methods for biomedical data integration, with a particular interest in radiology-pathology fusion to facilitate radiology image labeling . The radiology-pathology fusion allows the creation of detailed spatial labels, that later on can be used as input for advanced machine learning, such as deep learning. The recent focus of the lab has been on applying deep learning methods to detect and differentiate aggressive from indolent prostate cancers on MRI using the pathology information (both labels and the image content). Other applications include breast cancer and brain samples.