PRISM Mentors

The Kay lab is interested in Gene Transfer, Genome Editing and Non-coding RNA biology.  The current research is studying: 1) rAAV vectors specifically:   developing capsid libraries, chemical modification of  vectors and screening approaches that will provide improved vectors for human application;  molecular mechanism of discordance in vector transduction between species;  molecular mechanisms involved in AAV transduction;  and chromatin formation of gene transfer vector genomes in primary tissues. 2) Approaches to achieve therapeutic levels of  non-nuclease mediated genome editing using rAAV vectors.  3)  Non coding RNAs: association between long-non coding RNAs and miRNA biogenesis in whole tissues;  tRNA derived small RNAs and their role in regulating ribosome biogenesis in cancer; and role of Line1 structural RNAs in controlling gene expression.

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.

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.

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.

Our research is concerned with the computational modeling and the experimental investigation of fluids in complex environments, including chemical reactions, phase transition, and heterogeneous flow environment. We addressing fundamental scientific questions, problems pertaining to energy-conversion and propulsion, as well as environmental issues related to wildfire predictions, carbon-capture and sequestration, and water desalination. We are developing advanced numerical algorithms, detailed physical models, and physics-informed and data-driven methods. Experimentally, our research employs X-ray absorption and scattering techniques  that involve X-ray Computed Tomography at laboratory and synchrotron sources, X-ray spectroscopy, and ultrafast X-ray techniques at the Linac Coherent Light Source to observe processes at sub-picosecond timescales. Department URL: https://me.stanford.edu

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.

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.

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.

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.

Maya Mathur is an Assistant Professor at the Stanford University Quantitative Sciences Unit and the Associate Director of the Stanford Center for Open and Reproducible Science. She is a statistician whose methodological research focuses on advancing methods for meta-analysis, replication studies, and sensitivity analysis. She has received early-career and young investigator awards from the Society for Epidemiologic Research, the Society for Research Synthesis Methods, and American Statistical Association.

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.).

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.).

We seek greater understanding of the genetic and epigenetic mechanisms driving tumorigenesis and disease progression in malignant brain tumors. We currently study the capacity of cellular and cell-free nucleic acids to inform treatment choices in patients with brain tumors, mechanisms of brain tumor cell migration, and identify potentially targetable genes and pathways. Our laboratory space lies at the heart of the Stanford campus between the core campus and the medical facilities, emblematic of the translational aspects of our work.

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.

The Maduke laboratory at Stanford University is seeking a postdoctoral scholar to study the molecular mechanisms of chloride-selective channels and transporters. Chloride channels and transporters are expressed ubiquitously, with defects giving rise to human diseases of kidney and bone, disorders of blood-pressure regulation, and epilepsy.  Projects in the lab seek to understand the molecular basis for these functions using a combination of electrophysiology, biochemistry, and a variety of structural and spectroscopic techniques, tightly integrated with results from computational collaborations. Experience in electrophysiology, structural biology, or membrane protein biochemistry is helpful but is not necessary.  More important is a strong personal motivation and willingness to learn.



Relevant publications include:



• Khantwal, C.M., et al. (2016) Revealing an outward-facing open conformational state in a CLC Cl-/H+ exchange transporter. Elife Jan 22;5. pii: e11189. doi: 10.7554/eLife.11189.


• Abraham, S.J., Cheng, R.C., Chew, T.A., Khantwal, C.M., Liu, C.W., Gong, S. Nakamoto, R.K., and Maduke, M. (2015). 13C NMR detects conformational change in the 100-kD membrane transporter ClC-ec1. J Biomol NMR, 61(3-4), 209-26.


• Han, W., Cheng, R.C., Maduke, M.* and Tajkhorshid, E.* (2014). Water Access Points and Hydration Pathways in ClC H+/Cl− Transporters. PNAS, 111: 1819–1824. PMCID: PMC3918786

The @wormsenseLab at Stanford University seeks postdoctoral scholars with an interest in the genetics, biophysics, and cell biology of sensation. Experience with in vivo and in vitro live imaging as well as gene-editing techniques in a genetic model organism such as C. elegans is preferred, but not essential. In appointing postdocs, we look for curiosity, excellence in the practice of reproducible research, and the ability to lead and work in teams — learning from and teaching others. You may launch research into the molecular and physical events responsible for touch and its degradation by persistent mechanical stress and chemotherapeutics. The latter project involves a collaboration with Katie Wilkinson (Prof. Biology, SJSU), an expert in rodent proprioception. You may also propose to join NeuroPlant, an interdisciplinary, team-based discovery platform for discovering novel ligand-receptor pairs that modulate nervous system function and for deciphering the neural codes responsible for chemical attraction and repulsion. As a NeuroPlant postdoc, you will be encouraged to select a co-advisor from the project faculty team. The @wormsenseLab believes that interdisciplinary scientists are needed in diverse careers and have helped to launch former postdocs into tenure-track academic positions, research and business development in industry, start-ups, and venture capital firms.

I design, build, and study social computing systems: the computational systems that mediate our social interactions with one another. My research sits in an area known as human-computer interaction (HCI).

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 research is focused on structural characterization of materials used for energy conversion and storage and for desalination. We use X-ray techniques at SSRL to establish structure-function relationships in complex materials.

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.

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

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/

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

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

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 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.