PRISM Mentors

The Stanford Screenomics Lab is a multidisciplinary group that uses newly available data streams to understand what people actually do on their smartphones, and how the content of their screen experiences relate to health and well-being. We use a variety of computer vision and text analysis tools to extract information from long sequences of screenshots, develop new descriptors of smartphone behavior and smartphone content, and examine how those behavior and content are related to users' emotions, sleep, and mental health. Our lab is committed to global diversity and fostering minority representation in social science, and we collaborate widely with schools and departments across Stanford and other universities.

We analyze multiple types of health data (EHR, Claims, Wearables, Weblogs, and Patient blogs), to answer clinical questions, generate insights, and build predictive models for the learning health system. Our group runs the country's only bedside consult service to enable better medical decisions using aggregate EHR and Claims data at the point of care. Our team leads the Stanford Medicine Program for Artificial Intelligence in Healthcare, which makes predictions that allow taking mitigating actions, and studies the ethical implications of using machine learning in clinical care. We have built models for predicting future increases in cost, identifying slow healing wounds, missed diagnoses of depression and for improving palliative care.

The Martinez lab studies RNA regulatory mechanisms that control gene expression. We focus on mRNA processing, RNA modifications and their roles in development and disease.

Dr. Huang's laboratory aims to understand the chemical and mechanical interactions between extracellular matrix (ECM) proteins and pluripotent stem cells that regulate vascular and myogenic function. The fundamental insights of cell-matrix interactions are applied towards stem cell-based therapies with respect to improving cell survival and regenerative capacity, as well as engineered vascularized tissues for therapeutic transplantation. Current projects focus on various aspects of mechanical and physical factors on tissue regeneration. Examples include:

1) Cellular Biomechanics for in High Through Chemical Screening: To develop new technology for high-throughput quantitative assessment of vascular endothelial cell biomechanics for cardiovascular drug screening. We hypothesize that cellular biomechanics can be a predictive biomarker of endothelial health.

2) Engineered Matrix Microarrays to Enhance the Regenerative Potential of iPSC-Derived Endothelial Cells: We propose to develop a combinatorial family of engineered ECMs (eECMs) with independently tunable biochemical and biomechanical cues, including stiffness and stress relaxation rate for high-throughput, matrix array studies of induced pluripotent stem cell-derived endothelial cell (iPSC-EC) survival and angiogenic potential. The optimally designed eECMs will then be coinjected with iPSC-EC for treatment of peripheral arterial disease in a mouse model of hindlimb ischemia (Sponsor: NIH).

3) iPSC-Derived Smooth Muscle Progenitors for Treatment of Abdominal Aortic Aneurysm: We propose to deliver human induced pluripotent stem cell-derived smooth muscle progenitors to the site of abdominal aortic aneurysm will replenish smooth muscle cells, enhance elastin production, and abrogate wall dilatation in a murine model (Sponsor: CIRM).

4) Vascularized Cardiac Patch with Physiological Orientation for Myocardial Repair: The aims are to engineer a vascularized aligned iPSC-derived CM (cardiomyocyte) patch and elucidating the molecular mechanisms of ECM-mediated nitric oxide signaling in enhancing iPSC-CM survival and phenotype; and to determine the therapeutic effect of a vascularized aligned iPSC-derived CM patch for treatment of myocardial infarction (Sponsor: Dept of Veteran Affairs).

5) Other ongoing research areas: mRNA-based therapeutics, exosome biologics, microgravity effects on tissue regeneration and dysfunction, 3D bioprinting of engineered skeletal muscle, viscoelasticity effects on endothelial-to-mesenchymal transition, electro-osmosis for treatment of lymphedema, tissue chips for stem cell manufacturing

Dr. Huang's laboratory research is funded by the National Institues of Health, Department of Defense, California Institute for Regenerative Medicine, National Science Foundation, and the Department of Veteran Affairs.

The STAAR Lab is a dynamic new neuroscience lab in Stanford’s Psychiatry Department, led by Neir Eshel, MD, PhD. We are looking to hire curious and ambitious postdocs to join our team. Lab projects focus on the neural circuitry of aggressive and compulsive behaviors, using optogenetics, in vivo imaging, electrophysiology, and sophisticated machine learning/artificial intelligence analyses of animal behavior. There are ample opportunities for career development and clinical exposure based on candidate interest. Compensation and benefits are highly competitive. The ideal postdoctoral candidate has an MD and/or PhD in neuroscience or related field and extensive experience with rodent neuroscience. Excellent analytical skills, e.g., Python & Matlab, are strongly preferred. An expert data analyst may be considered even without animal experience. We are strongly committed to diversity and inclusion.

Our laboratory has been focusing on the mechanisms of fibrosis  elucidating the links between activation of redox pathways, cell death, stellate cell activation and transdifferentiation to myofibroblasts. We have been interested in the role of NADPH oxidases and their cell-specific roles in liver injury and repair.   We are  investigating  how changes in the mechanical properties  of the extracellular matrix and architecture  elicit changes in cellular behavior, and how these predispose to cancer invasion.   While matrix stiffness in advanced fibrosis/cirrhosis and its effects on cancer progression have been extensively studied, we demonstrated how changes in viscoelasticity, independent of stiffness, impact hepatocellular carcinoma growth. This is clinically very relevant as increasing viscoelasticity could be a new risk factor foretelling more invasive features of cancer in diabetic patients.

With the  type 2 diabetes and steatotic liver disease epidemics, the ultimate goal is to translate our findings and develop novel therapeutic approaches that  improve patient outcomes.

The main focus of Dr. Gomez-Ospina’s lab is to develop therapies for patients with genetic neurodgenerative diseases. The lab uses genome editing and stem cells to produce definitive treatments for childhood neurodegenerative diseases, many of which are lysosomal storage disorders.

Current projects in the lab include developing autologous transplantation of genome-edited hematopoietic stem cells for Mucopolysaccharidosis type I, Gaucher, Krabbe disease, Frontotemporal Dementia, and Friedreich's ataxia.

Although there is a strong translational focus to the lab, we are also pursuing basic science questions to understand and enhance our therapies including: 1) increasing the efficiency of genome editing tools, 2) understanding microglia turnover in response to conditioning before hematopoietic stem transplant, and 3) stablishing brain-specific conditioning regimens to neurometabolic diseases.

We are interested in identifying novel pathways that enable cellular and organismal adaptation to metabolic stress and changes in environmental conditions. We also study how these pathways go awry in human diseases such as cancer, neurodegeneration and metabolic syndrome, in order to engineer new therapeutic modalities.

To address these questions, our lab uses a multidisciplinary approach to study the biochemical functions of the lysosome in vitro and in vivo. Lysosomes are membrane-bound compartments that degrade macromolecules and clear damaged organelles to enable cellular adaptation to various metabolic states. Lysosomal function is critical for organismal homeostasis—mutations in genes encoding lysosomal proteins cause severe human disorders known as lysosomal storage diseases, and lysosome dysfunction is implicated in age-associated diseases including cancer, neurodegeneration and metabolic syndrome.

By developing novel tools and harnessing the power of metabolomics, proteomics and functional genomics, our lab will define 1) how the lysosome communicates with other cellular compartments to fulfill the metabolic demands of the cell under various metabolic states, 2) and how its dysfunction leads to rare and common human diseases. Using insights from our research, we will engineer novel therapies to modulate the pathways that govern human disease.

The wormsenseLab seeks to decipher the genetic, molecular and physical basis of touch sensation and its disruption by mechanical and chemical stress, such as exposure to elevated glucose in diabetes and chemotherapeutic drugs. We use a combination of genetics, electrophysiology, and quantitative analysis of behavior and also develop new tools for delivering and measuring mechanical force.  We also lead an interdisciplinary project (NeuroPlant) that uses nematode behavior to identify compounds synthesized by medicinal plants that modulate neuron function.  This project also seeks to link compounds to their conserved protein receptors.

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. 

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/

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. 

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.

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. 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

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.

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.

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.

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.

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

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.

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

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.