PRISM Mentors

Nanoscale Materials to Solve Next Generation Challenges
The challenges facing us today are immense, and nanomaterials have shown great promise to aid in their solutions. Yet individual material systems often have significant drawbacks that prevent successful adaptation. We seek to unite material systems to build nanoscale systems where we control the flow of light, energy, and spin. By combining and understanding these material systems, we aim to uncover unique strengths and physics that are unachievable by individual systems alone, finding solutions to the challenging problems facing us.

See congrevelab.stanford.edu for more information!

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

Dr. Spielman’s research is in the field of MRI, spectroscopy (MRS), and PET, with a focus on the development of new methods of imaging in vivo metabolism. Current projects include 13C MRS of hyperpolarized substrates for the assessment of glycolysis and oxidative phosphorylation in cancer, 1H MRS measurements brain oxidative stress and neurotransmission, and combined PET/MRS studies.  He has focused on a novel array of both acquisition and analysis techniques for use in preclinical and clinical studies.

Associated T32s: Stanford Center for Imaging Training (SCIT), Stanford Molecular Imaging Scholars (SMIS), Stanford Training in Biomedical Imaging Instrumentation (TBI2)

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

Our lab has several major foci:

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

Specific projects underway in our lab include:

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

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

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

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

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

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

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

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

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

Our lab has several major focuses:
1. Using iPSC-derived cardiomyocytes to develop a better understanding of hypertrophic cardiomyopathy and congenital heart disease.
2. The role of alterations in mitochondrial structure and function in normal physiology (such as exercise) and in disease such as dilated and hypertrophic cardiomyopathy.
3. Single cell analysis of mitochondrial function reveals significant heterogeneity.
4. Differences between right and left ventricular responses to stress and in their modes of failure, including gene expression and miR regulation.
5. Use of iPSC-CMs in pharmacogenomics, specifically determining the role of gene variants in doxorubicin cardiotoxicity.

Specific projects underway in our lab include:

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

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

3. Differences between the right and left ventricles in their responses to stresses such as increased afterload and increased preload, including gene expression and gene regulation by micro-RNAs. The use of plasma miRs as biomakers for RV failure.

4. Using patient-derived iPSC-cardiomyocytes to understand the mechanisms of cardiomyopathies common in children and to solve the genotype-phenotype conundrum in hypertrophic cardiomyopathy. The role of altered metabolism and mitochondrial function in hypertrophic cardiomyopathy.

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

6. Developing tools to further mature hiPSC-CMs to more accurately recapitulate the mechanobiology of adult human CMS.

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

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

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

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

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

The Stanford Center for Biomedical Ethics (SCBE) is an interdisciplinary hub for faculty who do research, teaching, and service on topics in bioethics and medical humanities. SCBE researchers have pioneered new approaches to studying the ethical issues presented by new technologies in biomedicine, including Artificial Intelligence, CRISPR and Gene Therapy, Stem Cell Research, Synthetic Biology, and the Human Brain Initiative. To benefit patients, SCBE has undertaken novel, ground-breaking research to improve clinical care, including end of life care, communication between patients and physicians, care for disabled patients, and organ transplantation processes. SCBE offers postdoctoral fellowships in Ethical, Legal, and Social Implications (ELSI) Research and Clinical Ethics. We currently have an opening for a postdoctoral fellow in Clinical Ethics. View more information here. 

Although the genomes of many organisms have now been sequenced, we still know relatively little about the specific DNA sequence changes that underlie important traits and diseases. My laboratory has developed an innovative combination of genetic and genomic approaches to identify the detailed molecular mechanisms that control key vertebrate traits. We use genetic crosses in mice, stickleback fish, and pluripotent stem cells to identify key chromosome regions controlling phenotypic traits. We use comparative genomics and  gene expression analysis in different populations, species, and hybrids to identify particular genomic changes with these key regions.  And we use transgenic and genome editing approaches to test the phenotypic effect of specific genomic changes, thus providing a direct functional link  between DNA sequence changes and classic phenotypes.  By combining genetics and genomics we have been able to identify the detailed molecular basis of major changes in skeletal structures, limb development, pigmentation, and neural functions across a range of populations and species.  We are currently extending these approaches to genetic and genomic mapping of human traits and diseases using experiments with chimp and human stem cells.    We are still a long way from knowing the genomic mechanisms that have made us human. However, we believe that molecular mechanisms contributing to human  traits can now be studied, and that progress in this area will lead to important new insights into both human health and human disease.

The primary research focus of the Relman Lab is the human indigenous microbiota (microbiome), and in particular, the nature and mechanisms of variation in patterns of microbial diversity within the human body as a function of time (microbial succession), space (biogeography within the host landscape), and in response to perturbation, e.g., antibiotics (community robustness and resilience). One of the goals of this work is to define the role of the human microbiome in health and disease. We are particularly interested in measuring and understanding resilience in the human microbial ecosystem. Our work includes the human oral cavity, gut, and female reproductive tract, as well as an analysis of microbial diversity in marine mammals. This research integrates theory and methods from ecology, population biology, environmental microbiology, genomics and clinical medicine.

I am a Professor of Medicine-Oncology and Pathology and the Director of TRAM, ARTS and CTNT Programs.

My laboratory studies how oncogenes such as MYC initiate and maintain cancer.  In partic ular we have shown that shutting down oncogenes even for a brief time can revese cancer or elicit "Oncogene Addiction"  For a recent review of our work please see:

The MYC oncogene - the grand orchestrator of cancer growth and immune evasion Nature Reviews Clinical Oncology, 2022

Members of my laboratory are studying basic mechanisms of Oncogene Addiction, the role of Self-renewal/Stemness, Metabolism, Host Immune System, Protein 
Biogenesis, Microbiome, Extracellular Vesicles.  

We are developing novel therapuetics using small molecules, nanoparticles, proteins/peptides that can be used to target oncogenes and/or restore the immune response against cancer.

We are developing new diagnostic and imaging agents using PET, Mass Spec, Nanoproteomics, MIcrofluidics.

For recent examples of our work please see: Casey et al, Science, 2016; Gouw et al, Cell Metabolism, 2019; Dhanasekaran et al eLife, 2020; Swaminathan et al, Nat Comm 2020.

The overall goal of my research program is to understand how stem cell-like populations are created and maintained in the context of an intact and environmental responsive tissue.  We use the Arabidopsis stomatal lineage for these studies as this epidermal cell lineage distills many of the features common to all tissue development: stomatal precursor cells are chosen from an initially equivalent field, they undergo asymmetric and self-renewing divisions, they communicate among themselves to establish pattern and they terminally differentiate into stable, physiologically important cell-types.  In the past decade, we have developed the stomatal lineage into a conceptual and technical framework for the study of cell fate, stem-cell self-renewal and cell polarity. Currently, we are especially interested in: (1) using new single-cell technologies to capture transcriptomic and chromatin state information about cells as they transit through various identities (stem cell-like, committed, differentiated, and reprogrammed); (2) using new ‘in vivo biochemical’ approaches to identify plant-specific cell polarity complexes and how these guide changes in cell shape, size and fate; (3) computational modeling of pattern formation in the epidermis, and (4) testing how environmental information impacts developmental choices and robustness.

One of the key ways that the gut microbiome impacts human health is through the production of bioactive metabolites. By understanding how microbes produce these molecules, we aim to develop new approaches to promote human health and treat disease. Our laboratory employs bacterial genetics, metabolomics, and gnotobiotic mouse colonization to uncover the chemistry that underlies host-microbe interactions in the gut.

Our team’s research spans the fields of dermatology, technology and public health. One of our main projects is centered on developing innovative skin cancer prevention interventions using social media. Another project area is the use of shared decision-making, mobile app technology for monitoring and optimal care of low risk skin cancers. We collaborate closely with colleagues in bioinformatics and computer science on use of visual Artificial intelligence methods to skin image monitoring. Additionally, we advocate for diversity and gender equity in medicine by writing both original data articles and perspective pieces on these topics. We collaborate with epidemiologists, clinicians, biostatisticians, basic, computer and social scientists at Stanford University as well as other institutions.

Malaria is one of the leading causes of childhood morbidity and mortality in the world. The etiologic agent of severe malaria, Plasmodium falciparum, exclusively infects red blood cells during the blood stage of its life cycle, when all of the symptoms of malaria occur. P. falciparum is an obligate intracellular parasite, suggesting that it critically depends on host factors for its biology and pathogenesis. This concept is also supported by population genetic studies, which indicate that humans have evolved certain red cell traits, such as hemoglobinopathies, to protect against malaria. The importance of these host-pathogen interactions raises the possibility that critical red cell factors could serve as targets for new, host-directed therapeutics for malaria. However, our understanding of host determinants for malaria is limited because red cells are enucleated and lack DNA, hindering genetic manipulation. In the Egan laboratory we have surmounted this hurdle by adapting advances from stem cell biology to the study of malaria host factors. Specifically, we have developed approaches to differentiate primary human CD34+ hematopoietic stem/progenitor cells down the erythroid lineage to enucleated red blood cells that can be infected by P. falciparum. This thus gives us access to the nucleated progenitor cells for genetic modification using RNAi and CRISPR-Cas9 genome editing. We are using these methods to develop forward genetic screens to identify novel host factors for malaria, as well as to perform mechanistic studies to understand the specific functions of critical host factors during the developmental cycle of malaria parasites. In addition, the lab has projects focused on understanding human adaptation to malaria using clinical samples. Our long term goal is to explore the possibility of host-directed therapeutics for malaria.

Alzheimer's disease pathology begins decades before clinical symptoms of dementia are present, providing an important opportunity to understand early disease and the impact of this disease on cognitive aging.  We combine multimodal neuroimaging and genetics to determine how AD changes and risk factors influence subtle cognitive decline in older individuals. We have a particular focus on PET imaging of Amyloid and Tau proteins, but also work with structural and functional MRI data. The ultimate goals of our work are to improve our ability to predict who is most at risk for dementia, and to understand the time course of brain changes that occur decades before clinical symptoms are present.  We are specifically recruiting trainees with expertise in genetics, neuroimaging, or neuropsychology, to work on large scale multimodal imaging-genetic studies.

Environmental microbiology (e.g. diatoms, algae) and synthetic biology

Topics: Nitrogen fixation, lipid biosynthesis and transprot, cellular endosymbiosis, nonmodel organisms

Application areas: Fertilizers, Biofuels

The Yeh Lab studies the apicoplast, a unique plastid organelle in Plasmodium falciparum parasites that cause malaria. We are particularly focused on unbiased chemical and genetic screens to discover new cell biology and therapeutic targets for this important global health disease. Our work highlights the untapped opportunities in exploring divergent biology in non-model organisms, a theme we plan to expand in the lab by studying ocean algae (malaria's cousins!) and their role in the global ecosystem.

The Yeh Lab studies the apicoplast, a unique plastid organelle in Plasmodium falciparum parasites that cause malaria. We are particularly focused on unbiased chemical and genetic screens to discover new cell biology and therapeutic targets for this important global health disease. Our work highlights the untapped opportunities in exploring divergent biology in non-model organisms, a theme we plan to expand in the lab by studying ocean algae (malaria's cousins!) and their role in the global ecosystem.

We are an interdisciplinary team focusing on generating new biomaterials to tackle healthcare challenges of critical importance to society. We are using these new biomaterials as sustained delivery technologies that can act as tools to better understand fundamental biological processes and to engineer next-generation healthcare solutions.