PRISM Mentors

My laboratory seeks to identify mechanisms responsible for human congenital heart disease, the most common cause of still-births in the U.S. and one of the major contributors to morbidity and mortality in infants and toddlers. We believe that by understanding the mechanisms regulating growth and differentiation of heart precursor stem/progenitor cells during early embryonic development we can then apply these principles to understand the pathogenesis heart malformation during fetal development and to leverage them for treating adult onset heart diseases such as heart failure and arrhythmia. We currently use both genetically-modified mice as our in vivo model to understand the biology of heart development as well as induced pluripotent stem cells (iPSCs) as a in vitro model to study the process of heart cell formation. Our major areas of interests include cardiovascular developmental biology, disease modeling, tissue engineering, and regenerative biology. Within each of these areas we are particularly focused on understand the major genes that regulate the proper formation of heart chambers and the consequesnces of disrupting the normal expression of these genes and how that may lead to the development of congenital heart diseases. While mouse models are useful for studying the process of heart formation, they are not exactly like the human hearts in various ways. Since human heart fetal tissue are diffulty to obtain, we have chosen to use iPSCs derived from patients with particular congenital heart diseases to study steps involved in human heart malformation. Furthermore, to bring our work closer to treating heart disease patients, we have combined our expertise in stem cell biology with 3D biopring to make engineered functional heart tissue for screening drugs and to serve as replacement tissues for damaged heart muscles.

Prof. Wang and his group are engaged in the research of magnetic nanotechnologies and information storage in general, including magnetic biochips, in vitro diagnostics, cell sorting, magnetic nanoparticles, nano-patterning, spin electronic materials and sensors, magnetic inductive heads, as well as magnetic integrated inductors and transformers. He uses modern thin-film growth techniques, lithography, and nanofabrication to engineer new electromagnetic materials and devices and to study their behavior at nanoscale and at very high frequencies. His group is investigating magnetic nanoparticles, high saturation soft magnetic materials, giant magnetoresistance spin valves, magnetic tunnel junctions, and spin electronic materials, with applications in cancer nanotechnology, in vitro diagnostics, spin-based information processing, efficient energy conversion and storage, and extremely high-density magnetic recording. His group conducts research in the Geballe Laboratory for Advanced Materials (GLAM), Stanford Nanofabrication Facility (SNF) and Stanford Nano Shared Facilities (SNSF), Center for Cancer Nanotechnology Excellence (CCNE) hosted at Stanford, and Stanford Cancer Institute. The Center for Magnetic Nanotechnology (formerly CRISM) he directs has close ties with the Information Storage Industry and co-sponsors The Magnetic Recording Conference (TMRC).

Prof. Wang directs the Center for Magnetic Nanotechnology and is a leading expert in biosensors, information storage and spintronics. His research and inventions span across a variety of areas including magnetic biochips, in vitro diagnostics, cancer biomarkers, magnetic nanoparticles, magnetic sensors, magnetoresistive random access memory, and magnetic integrated inductors. 

Prof. Wang directs the Center for Magnetic Nanotechnology and is a leading expert in biosensors, information storage and spintronics. His research and inventions span across a variety of areas including magnetic biochips, in vitro diagnostics, cancer biomarkers, magnetic nanoparticles, magnetic sensors, magnetoresistive random access memory, and magnetic integrated inductors. 

Current Research Projects

• Pediatric Research Immune Network on SARS-CoV-2 and MIS-C (PRISM)
• Work with our team to consent subjects, obtain and process samples for immune assays to determine the immune responses in children with COVID.

• Identification and Therapeutic Targeting of a Novel Cell Population in Rejection of Vascularized Composite Allotransplantation
• Work with our microsurgeon to establish the cell populations, using CyTOF, important in the initiation of T cell‒mediated rejection of vascularized composite allotransplantation.

• Exosomes as a Reliable Noninvasive Method for Monitoring VCA Graft Rejection
• Work with our microsurgeon to assess the importance of exosomes and their cargo in graft rejection in a novel experimental model of vascularized composite allotransplantation

• Exosomes and the Immune Response in Allograft Outcomes in Pediatric Transplant
Recipients
• Work with a senior postdoctoral fellow to determine the impact of an allograft on the early post-transplant immune response.

Our research focuses on the control of immune responses to alloantigen and viruses (EBV, SARS-CoV-2) using both experimental models and human immunology. Current studies ongoing in the lab are:

Insight into Development and Progression of Multi-System Inflammatory Syndrome and  COVID in Children.
Exosomes and microRNAs in the regulation of  Immune Responses
NK Cell Diversity and Responses to viral and allo antigens
Novel T regulatory populations

Molecular and Cellular Immunobiology/CyTOF/bioinformatics

The research at Stanford's Health Policy Data Science Lab is centered on developing and integrating innovative statistical machine learning approaches to improve human health and health equity. This includes ethical algorithms in health care, risk adjustment, comparative effectiveness research, and health program evaluation. 

My health services research lab focuses on how novel risk predictors can be used to guide improvements in patient centered outcomes and healthcare value. I study improvement of healthcare outcomes for vulnerable populations such as frail and older adults and disparities in care for vascular patients. My accumulated research points to frailty as a versatile tool that can guide surgical decision making, inform patient consent and design quality improvement initiatives at the patient and hospital level. My previous work includes the development and validation of the Risk Analysis Index (RAI), a surgical frailty calculator that can be used prospectively with a clinical questionnaire or retrospectively. The RAI is easily applied, and when used in widespread preoperative screening, was associated with reduced mortality. The next step is to incorporate frialty screening into clinical workflow and develop interventions to mitigate postoperative adverse events for these high-risk patients. Using mixed methods (quantitative and qualitative) research and implementation science, we are now developing interventions to improve outcomes for this high risk population.

Our basic research program focuses on understanding the roles of virus-host interactions in viral infection and disease pathogenesis via both molecular and systems virology/immunology single cell approaches. This program is combined with translational efforts to apply this knowledge for the development of broad-spectrum host-centered antiviral approaches to combat emerging viral infections, including dengue, encephalitic alphaviruses, SARS-CoV-2 and Ebola, and means to predict disease progression.

Our studies focus on the following emerging concepts that are transforming our understanding of virus-host interactions:

1. Understanding the pathogenesis of flaviviral infections via an integrative systems immunology single cell approach. The goal of this project is to elucidate the cellular and molecular factors contributing to increased severity of dengue and Zika disease in distinct patient populations (children, adults, pregnant women). To achieve this goal, we are advancing and utilizing various single-cell immunological approaches (virus-inclusive single cell RNA-seq, CyTOF etc) and samples from our large Colombia dengue cohort (>500 patients) and Zika cohort. We are mapping an atlas of viral immune cellular targets and studying critical protective and pathogenic elements of the host response to these viruses in multiple distinct infected and bystander cell subtypes with an unprecedented resolution. The translational goals of this project are to identify candidate biomarkers associated with infection outcome and candidate targets for antiviral therapy, as well as improve vaccine strategies.

2. Deciphering the intracellular membrane trafficking pathways essential for viral pathogens. We have used proteomic and genetic approaches to identify proteins that are critical for the replication of multiple globally relevant RNA viruses including dengue virus, Zika virus, encephalitis alphaviruses, SARS-CoV-2, hepatitis C virus, and Ebola virus. We are studying the molecular mechanisms by which these viruses hijack intracellular membrane trafficking pathways for mediating key steps in their viral life cycle and are characterizing the roles these factors play in cellular biology using viruses as complexed probes. Ongoing work focuses on the roles of cellular kinases and adaptor protein complexes in viral trafficking during viral entry, assembly, release, and direct cell-to-cell spread, the role of the ESCRT machinery in intracellular viral budding, and the roles of ubiquitin signaling pathways in the regulation of trafficking during viral assembly and release.

3. Advancing the development of small molecules targeting host functions as broad-spectrum antivirals. Most direct antiviral strategies targeting viral enzymes provide a “one drug, one bug” approach and are associated with the emergence of viral resistance. We have discovered several host functions exploited by multiple viruses as targets for broad-spectrum antivirals. We have demonstrated the utility of a repurposed approach that inhibits these factors in suppressing replication of multiple RNA viruses both in vitro and in mouse models and are advancing this approach into the clinic and studying its mechanism of action. In parallel, we are developing chemically distinct small molecules targeting various cellular functions as pharmacological tools to study cell biology and viral infection and as broad-spectrum antivirals to combat SARS-CoV-2, dengue virus, encephalitic alphaviruses and Ebola virus.

The Clarke Lab uses genomics, epidemiology, and data science to understand cardiovascular disease risk. Key areas of focus include:

1. Equitable development and applications of polygenic risk scores

2. Novel phenotyping using electronic health records, wearables, and/or medical imaging

3.  Artificial intelligence applications to medical imaging

4. Studying nataionl biobanks (Million Veteran Program, UK Biobank, All of Us)

X-ray laser physics; matter at extreme conditions and fusion research

Two postdoc positions in the lab of Prof. Sindy Tang are immediately available in the areas of microfluidics, nanofabrication, and spatial proteomics.

The spatial organization of proteins within biological tissues plays a critical role in the normal functioning of the tissue and disease development. The goal of this NIH-funded project is to develop a high throughput and scalable technology to perform tissue microdissection that preserves tissue spatial information and couples directly to established LC-MS/MS workflow for deep and unbiased spatial mapping of the proteome. Our approach integrates a novel tissue micro-dicing device, a nanodroplet sample preparation platform for LC-MS/MS analysis with single-cell sensitivity, and novel microfluidic device to transfer the diced tissue pixels while preserving their spatial order. This position will allow exciting opportunities to collaborate with the Pacific Northwest National Lab and the Stanford School of Medicine. 

The project is expected to accelerate MS-based spatial proteomics for deep and unbiased mapping of tissue heterogeneity down to single-cell resolution, thereby accelerating biomedical research and clinical diagnostics towards a better understanding of the role of tissue heterogeneity in pathophysiology, such as the role of the tumor microenvironment on cancer initiation and progression. The deep and unbiased proteome coverage will enable the discovery of novel protein biomarkers and molecular pathways to identify new therapeutic targets, which would be difficult using antibody-based approaches. Our ability to quantitatively map ECM and secreted proteins will facilitate the elucidation of the role of ECM, such as their remodeling, in disease progression. Finally, while this project focuses on spatial proteomics, we expect our technology and workflow to be extended to other biomolecules that LC-MS/MS can readily measure, such as lipids and metabolites, thereby opening the opportunity for spatial multi-omic measurements in future studies.

Skills useful for this project include:
• Microfluidics design and integration, and related areas
• Micro- and nanofabrication, e.g., silicon micromachining, high resolution 3D printing
(e.g., Nanoscribe)
• Experience working with biological samples (tissues)

Postdoctoral Research Fellow – Cell biology & microfluidics, UCSF & Stanford

A joint postdoc position between the labs of Wallace Marshall (UCSF) and Sindy Tang (Stanford) is immediately available in the area of single-cell wound healing. The broad question we aim to answer is how the single-celled ciliate Stentor can heal drastic wounds. We are looking for a candidate with a background in cell biology or related fields. This position will allow ample opportunities to learn new techniques including microfluidics for single-cell manipulation and mathematical modeling.

Application
For questions or applications (see below), please feel free to reach out to Prof. Wallace Marshall (wallace.ucsf@gmail.com) or Prof. Sindy Tang (sindy@stanford.edu). To apply, please include a CV (with a publication list) and some detail about your background and interest in the project.

Project description:
Biomechanical mechanisms conferring wound resilience in single-celled organisms
Stentor coeruleus is a large, single-celled ciliate that has remarkable wound healing and regenerative capacity (see Slabodnick et al., Current Bio, 2014 https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.10...). It is found in environments that can be subject to high mechanical stresses due to natural flows or predation. The overall goal of this project is to investigate how this organism employs both mechanical and biochemical mechanisms upstream of wounding for wound prevention, as well as downstream of wounding for robust healing from wounds (https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-00970-0).

We have sequenced the Stentor genome, and developed tools for molecular manipulation of Stentor gene expression to pave the way to a molecular understanding of Stentor wound response.   This project involves conceptualization of a novel chemical screen to test the role of the cytoskeleton in conferring wound resistance to the cell, and the role of large-scale mechanical force generation in complementing biochemical healing modes to close wounds of increasing severity.

Some questions we ask are: how does Stentor cell mechanics give rise to wound resistance? How do cells respond to shear or other types of stresses? What molecular pathways are important in Stentor wound healing, and are they the same as in other eukaryotes?
The project combines cell biology, microfluidics for precise wounding (see Blauch et al., PNAS 2017 https://www.pnas.org/doi/abs/10.1073/pnas.1705059114), and mechanobiology modeling.

Required Qualifications:
Desired skills for this project include:
• Cell biology
• Chemical screen
• RNAi and genetic transformation
• Past experience with Stentor, other ciliates, or manipulation (e.g., microinjection) of large cells or embryos such as Drosophila
• Mathematical modelling of cellular processes
Candidates proficient in certain skills outlined above will have opportunities to receive training in complementary skill sets.

Required Application Materials:
Your CV with a publication list, and some detail about your background and interest in the project.

Postdoctoral Research Fellow – Cell biology & microfluidics, UCSF & Stanford

A joint postdoc position between the labs of Wallace Marshall (UCSF) and Sindy Tang (Stanford) is immediately available in the area of single-cell wound healing. The broad question we aim to answer is how the single-celled ciliate Stentor can heal drastic wounds. We are looking for a candidate with a background in cell biology or related fields. This position will allow ample opportunities to learn new techniques including microfluidics for single-cell manipulation and mathematical modeling.

Application
For questions or applications (see below), please feel free to reach out to Prof. Wallace Marshall (wallace.ucsf@gmail.com) or Prof. Sindy Tang (sindy@stanford.edu). To apply, please include a CV (with a publication list) and some detail about your background and interest in the project.

Project description:
Biomechanical mechanisms conferring wound resilience in single-celled organisms
Stentor coeruleus is a large, single-celled ciliate that has remarkable wound healing and regenerative capacity (see Slabodnick et al., Current Bio, 2014 https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.10...). It is found in environments that can be subject to high mechanical stresses due to natural flows or predation. The overall goal of this project is to investigate how this organism employs both mechanical and biochemical mechanisms upstream of wounding for wound prevention, as well as downstream of wounding for robust healing from wounds (https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-00970-0).

We have sequenced the Stentor genome, and developed tools for molecular manipulation of Stentor gene expression to pave the way to a molecular understanding of Stentor wound response.   This project involves conceptualization of a novel chemical screen to test the role of the cytoskeleton in conferring wound resistance to the cell, and the role of large-scale mechanical force generation in complementing biochemical healing modes to close wounds of increasing severity.

Some questions we ask are: how does Stentor cell mechanics give rise to wound resistance? How do cells respond to shear or other types of stresses? What molecular pathways are important in Stentor wound healing, and are they the same as in other eukaryotes?
The project combines cell biology, microfluidics for precise wounding (see Blauch et al., PNAS 2017 https://www.pnas.org/doi/abs/10.1073/pnas.1705059114), and mechanobiology modeling.

Required Qualifications:
Desired skills for this project include:
• Cell biology
• Chemical screen
• RNAi and genetic transformation
• Past experience with Stentor, other ciliates, or manipulation (e.g., microinjection) of large cells or embryos such as Drosophila
• Mathematical modelling of cellular processes
Candidates proficient in certain skills outlined above will have opportunities to receive training in complementary skill sets.

Required Application Materials:
Your CV with a publication list, and some detail about your background and interest in the project.

From finger prick tests for blood glucose monitoring to industrial-scale drug screening in pharmaceutical companies, the ability to extract information from scarce volumes of samples quickly and cheaply is key to effective disease management and drug discovery. To this end, microfluidics offers major advantages over conventional liquid handling due to drastic reduction in reagent volume and the precise control of single cells, microtissues, and their microenvironments. The micro-nano-bio lab under the direction of Dr. Sindy Tang aims to develop innovative micro and nanoscale devices that harness mass transport phenomena to enable precise manipulation, measurement, and recapitulation of biological systems, in order to understand the "rules of life" and accelerate precision medicine and material design for a future with better health and environmental sustainability. Our approach involves building new tools to probe biological systems (from single cells to microtissues), and engineering smart materials, synthetic cells & tissues with properties that mimic some of the amazing properties biological systems have. Current research projects include:

• Understanding and accelerating the diagnosis of allergic diseases
• Biomechanics of single cell wound resilience
• Tools for advancing cancer research
• Bottom-up construction of biological systems

The research in our laboratory is focused on understanding and controlling surface and interfacial chemistry and applying this knowledge to a range of problems in semiconductor processing, micro- and nanoelectronics, nanotechnology, and sustainable and renewable energy. Much of our research aims to develop a molecular-level understanding in these technologically important systems. Our group uses a variety of atomic and molecular spectroscopies combined with atomically-precise materials synthesis. Systems currently under study in our group include organic functionalization of semiconductor surfaces, mechanisms and control of atomic layer deposition, molecular layer deposition, area selective deposition processes, nanoscale materials for light absorption, interface engineering in photovoltaics and batteries, and catalyst and electrocatalyst synthesis and characterization.

Dr. Luby’s research group is engaged in several efforts to generate knowledge that will alter the way that bricks are manufactured across South Asia so that they generate less air pollution, less climate change and tens of thousands fewer deaths per year. This involves: 1) evaluating interventions to improve combustion efficiency within brick kilns and so simultaneously reduce coal costs for producers while generating less pollution 2) using remote sensing to specify the location of brick kilns and ultimately evaluate their emissions.

Another strand of his work looks at the release of lead into the environment in low and middle income countries, seeks to identify the sources of lead that is generating the greatest public health burden and develops and evaluates interventions to reduce this burden.

His research group also explores practical interventions to reduce infectious disease transmission in low and middle income countries. These activities include efforts to maximize the uptake of masks, water treatment and vaccines with careful evaluation of the impact of these interventions. His research group explores strategies to reduce the risk of pathogen transmission in healthcare facilities in lower income countries.

We are looking for postdoctoral researchers interested in understanding the impact of rare variants on human diseases. Projects in the lab are either computational and experimental (or both!). We are particularly interested in establishing new research directions for using genomics data to interpret undiagnosed rare diseases. We are also interested in helping to improve the use of genetic data in diverse populations. Great opportunities for networking also as many of the projects in our lab are often part of major genomics research consortium like the UDN, Mendelian Genomics Research Centres, MoTrPAC, GTEx, TOPMED, ENCODE and more!

Please check out our website and our recent list of papers on Google Scholar https://scholar.google.com/citations?user=117h3CAAAAAJ&hl=en

Steve is interested in the physics of the most massive objects in the Universe and how we can use them to probe how the Universe evolved. Steve and his group are currently focused on understanding the astrophysics of galaxies and of galaxy clusters using multi-wavelength observations, and on using large, statistical samples of these objects to probe the natures of dark matter, dark energy and fundamental physics. More information regarding ongoing research and a list of Steve's current group members can be found here.

Our research focuses on unraveling the molecular mechanisms underlying retinal development and diseases. We employ genetic and genomic tools to explore how various retinal cell types, including neurons, glia, and the vasculature, respond to developmental cues and disease insults at the epigenomic and transcriptional levels. In addition, we investigate their interactions and collective contributions to maintain retinal integrity.

Susan is broadly interested in astrophysical magnetism and the physics of the interstellar medium (ISM), from diffuse gas to dense, star-forming regions. Susan’s research tackles open questions like the structure of the Milky Way’s magnetic field, the nature of interstellar turbulence, and the role of magnetism in star formation. These big questions demand multiwavelength observations and new data analysis techniques. Susan is particularly interested in deciphering the magnetic ISM using sensitive measurements of synchrotron and polarized dust emission made by cosmic microwave background experiments like the Atacama Cosmology Telescope (ACT) and the Simons Observatory (SO).

Susan is broadly interested in astrophysical magnetism and the physics of the interstellar medium (ISM), from diffuse gas to dense, star-forming regions. Susan’s research tackles open questions like the structure of the Milky Way’s magnetic field, the nature of interstellar turbulence and the multi-phase ISM, and the role of magnetism in star formation. These big questions demand multiwavelength observations and new data analysis techniques. Susan and her group decipher the magnetic ISM using a combination of theory and observation. Data-wise, the group uses a wide range of tracers including gas line emission and absorption, polarized dust and synchrotron emission, starlight polarization, Zeeman splitting, and Faraday rotation. Susan is involved in a number of current and future telescope projects, and leads several efforts focused on Galactic science with sensitive measurements of millimeter-wavelength emission made by cosmic microwave background experiments like the Atacama Cosmology Telescope (ACT) and the Simons Observatory (SO).

My laboratory's overall goal is to (i) understand the mechanisms of right heart failure in children and adults with congenital heart disease and (ii) to develop biomarkers as a plasma signature of myocardial events to better understand the mechanisms of heart failure, improve monitoring of disease progression, early detection of heart failure and risk-stratification.

We have focused on tetralogy of Fallot population and single ventricle heart disease. As the survival continues to improve, so also has the incidence of heart failure. However, the underlying cellular mechanisms of heart failure are poorly understood as a result of which no targeted therapy is available. Since it is not possible to obtain heart muscle biopsies routinely on patients, we have taken a novel strategy of using Multi-Omics to better understand disease mechanisms and to follow patients over time comparing their Omics signature to themselves thereby personalizing their care. The goal is to create a targeted biomarker panel for clinical utility to be used in conjunction with imaging data to improve overall prediction of risk. Based on our work to date, we are also interested in understanding myocardial mitochondrial and vascular dysfunction as these have the potential to serve as novel therapeutic targets.

Lab website is in creation. Link will be updated when it is ready.