PRISM Mentors

The Sakamoto lab studies normal and aberrant blood cell development. Her research team is interested in the pathogenesis of acute and chronic leukemia, including acute myeloid leukemia and chronic myeloid leukemia. The overall goal of her research is to understand the signaling pathways that lead to leukemia or bone marrow failure. She is also interested in developing new drugs to treat these diseases. Her group experience works with mammalian cells and mouse models of cancer and bone marrow failure syndromes, such as Diamond Blackfan Anemia. There are opportunities to work with physicians, translational researchers, medicinal chemists, and advisors from drug companies with experience in drug development.

Experiments utilize leukemia cell lines, primary mouse and human hematopoietic cells, and mouse models will be used.   Technologies in the lab include standard biochemical techniques (Western blot analysis, real-time PCR, immunoprecipitations), FACs/sorting, colony assays, lentiviral and retroviral transductions, transplantation experiments, xenograft models and bioluminescence, CyTOF, RNA-seq ,ChIP-seq, small molecule and  shRNA/CRISPR library screening. Knowledge in bioinformatics would be helpful for single cell RNA-seq experiments. The intent of these early translational studies is to develop small molecules or peptides into drugs to treat acute leukemia.  Assays to assess toxicity, metabolism, optimization, and mechanism of action of compounds are performed.

Dr. Sakamoto is committed to diversity and has trained many underrepresented high school, undergraduate, medical, graduate students and postdoctoral/MD fellows. She has served on the American Society of Hematology Minority Medical Student Program and was Chair of the Diversity Special Interest Group. She is currently working with SMASH Rising to recruit underrepresented high school graduates and community college students to Stanford to study clinical, translational, and basic hematology. 

The Davis laboratory is looking for post-doctoral scholars interested in the study of cancer. We use single-cell, high-dimensional approaches in primary patient materials to identify cells associated with poor clinical outcomes. We have a focus on childhood leukemia, neuroblastoma and Ewing sarcoma. Once identified, we can further interrogate mechanisms of resistance in candidate cell populations and develop new approaches for treatment. 

We are looking for motivated and talented computational biologists and cancer biologists with interest in joining our active group. In particular, opportunties for data scientists/computational biologists are available. 

Katherine Whittaker Ferrara is a Professor of Radiology and the Division Chief for the Molecular Imaging Program at Stanford. She is a member of the National Academy of Engineering and a fellow of the IEEE, American Association for the Advancement of Science, the Biomedical Engineering Society, the World Molecular Imaging Society, the Acoustical Society of America and the American Institute of Medical and Biological Engineering. Dr. Ferrara received her Ph.D. in 1989 from the University of California, Davis. Prior to her PhD, Dr. Ferrara was a project engineer for General Electric Medical Systems, involved in the development of early magnetic resonance imaging and ultrasound systems. Following an appointment as an Associate Professor in the Department of Biomedical Engineering at the University of Virginia, Charlottesville, Dr. Ferrara served as the founding chair of the Department of Biomedical Engineering at UC Davis. Her laboratory is known for work in molecular imaging and drug delivery.

The Poston Lab seeks to understand the biological underpinnings of non-motor symptoms in patients with Lewy Body diseases, such as Parkinson's disease and Lewy Body Dementia. While our primary focus is understanding cognition and dementia, we also study other prominent non-motor symptoms such as psychosis/hallucinations, sleep disruption, orthostatic dysregulation, and others.  A major focus is on the role of co-pathologies, such as Alzheimer's and vascular co-pathologies, and the role of neuro-inflammation, in the development of Lewy Body disease associated non-motor symptoms.  We collect clinical, motor, neuropsychological, biological, genetic, and imaging data on patients and healthy older adults to perform our studies. 

The Poston Lab seeks to understand the biological underpinnings of non-motor symptoms in patients with Lewy Body diseases, such as Parkinson's disease and Lewy Body Dementia. While our primary focus is understanding cognition and dementia, we also study other prominent non-motor symptoms such as psychosis/hallucinations, sleep disruption, orthostatic dysregulation, and others.  A major focus is on the role of co-pathologies, such as Alzheimer's and vascular co-pathologies, and the role of neuro-inflammation, in the development of Lewy Body disease associated non-motor symptoms.  We collect clinical, motor, neuropsychological, biological, genetic, and imaging data on patients and healthy older adults to perform our studies. 

The Svensson Laboratory is dedicated to the discovery of new fundamental pathways that regulates cellular and organismal metabolism. The main focus is to identify novel functions for new molecules controlling the regulation of glucose and lipid homeostasis using a combination of genomic, proteomic and physiology approaches.

Our group at SLAC National Accelerator Laboratory is leading R&D of machine learning applications for in the area of experimental neutrino physics and a wider community of High Energy Physics.  Modern neutrino experiments employ a big (100 to 10,000 tonnes), high-resolution (~mm/pixel) particle imaging detectors that records meters-long particle trajectories produced from a neutrino interaction. We address fundamental challenges in modeling these detectors, analyzing particle images, and inferring physics from big data using machine learning and advanced computing techniques. Our research has potential to accelerate physics discovery process by orders of magnitude and to maximize physics information extracted from the big, high-recision particle imaging detectors. 

Areas of technical R&D include:

• Development and optimization of end-to-end deep-learning based data analysis chain
• Scaling applications at massively parallel computing infrastructure
• Quantification of uncertainty/confidence-interval for deep-learning models
• Mitigation and quantification of domain shift (e.g. discrepancies between data and simulation)
• Differentiable software for modeling physics and solving the inverse problems

Areas of physics research include:

• Neutrino oscillation analysis and cross-section measurements at the Short Baseline Neutrino program and Deep Underground Neutrino Experiment
• Physics of neutrino-nucleus interaction including modeling of many-body interactions inside a large (~40 nucleons) nucleus
• Modeling of detector physics processes using machine learning and differentiable simulation softwares

For details, feel free to contact Kazuhiro Terao.

Professor Gaffney leads a research team focused on femtosecond resolution measurements of chemical dynamics in complex condensed phase systems. This research takes advantage of recent advances in ultrafast x-ray lasers, like the LCLS at SLAC National Accelerator Laboratory, to directly observe chemical reactions on the natural time and length scales of the chemical bond – femtoseconds and Ångströms. This research focuses on the discovery of design principles for controlling the non-equilibrium dynamics of electronic excited states and using these principles to spark new approaches to light-driven catalysis in chemical synthesis.

This research builds on Professor Gaffney’s extensive experience with ultrafast optical laser science and technology. This work began with time- and angle- resolved two photon photoemission studies of electron solvation and localization at interfaces as a graduate student working with Professor Charles Harris at the University of California at Berkeley and extended to multidimensional vibrational spectroscopy studies of hydrogen bonding and ion solvation dynamics in solution during postdoctoral studies with Professor Michael Fayer at Stanford and as an Assistant Professor. The transition to ultrafast x-ray science began in 2004 at SLAC, where he helped establish the first chemical dynamics research program at SLAC.

The primary goal of the Plasma Dynamics Modeling Laboratory (PDML), directed by Professor Ken Hara, is to develop numerical methods and theoretical models in order to understand the physical phenomena in various plasma discharge and flows. Current applications include electric propulsion (EP) and fundamental plasma physics phenomena including plasma-material interactions, plasma-wave interactions, and plasma-beam interactions.

Our laboratory studies the mechanisms by which highly complex behaviors are mediated at the neuronal level, mainly focusing on the example of dynamic social interactions and the neural circuits that drive them. From dyadic interactions to group dynamics and collective decision making, the lab seeks a mechanistic understanding for the fundamental building blocks of societies, such as cooperation, empathy, fairness and reciprocity. The computations underlying social interactions are highly distributed across many brain areas. Our lab is interested in which specific areas are involved in a particular function, why such an architecture arises and how activity in multiple networks is coordinated. Our goal is to develop a roadmap of the social brain and use it for guiding restorative treatments for conditions in which social behavior is impaired, such as Autism Spectrum Disorders and Schizophrenia.

The Wang Lab takes an interdisciplinary approach to studying fundamental mechanisms controlling gene expression in mammalian cells. Our work shows how epigenetic mechanisms such as DNA methylation, chromatin modifications, and RNA influence chromatin dynamics to affect gene regulation. OUR LAB IS CURRENTLY FOCUSED ON: How various dynamic epigenetic changes in chromatin structure impact gene expression during stem cell pluripotency/self-renewal, cellular differentiation, and reprogramming; How three-dimensional chromosomal structure and dysregulation contribute to development of diseases such as aging and cancer; and How to create novel genome engineering tools to interrogate the noncoding genome and the epigenome.   The long-term goal of The Wang Lab is to translate our understanding of these complex mechanisms to studies of human diseases.

How the richly varied cell-types in the human body arise from one embryonic cell is a biological marvel and mystery. We have mapped how human pluripotent stem cells develop into over thirty different human cell-types. This roadmap allowed us to efficiently and rapidly generate human liver, bone, heart and blood vessel progenitors in a Petri dish from pluripotent stem cells. Each of these tissue precursors could regenerate their cognate tissue upon injection into respective mouse models, with relevance to regenerative medicine. In addition to our interests in developmental and stem cell biology, we also harbor an emerging interest in deadly biosafety level 4 viruses, such as Ebola and Nipah viruses.

We study the genetic and molecular mechanisms that regulate proliferation and differentiation in adult stem cell lineages, using the Drosophila male germ line as a model.  Our current work is focused on the switch from mitosis to meiosis and how the new gene expression program for cell type specific terminal differentiation is turned on.  One emerging surprise is the potential role of alternative processing of nascent mRNAs in setting up the dramatic change in cell state

How the richly varied cell-types in the human body arise from one embryonic cell is a biological marvel and mystery. We have mapped how human pluripotent stem cells develop into over thirty different human cell-types. This roadmap allowed us to efficiently and rapidly generate human liver, bone, heart and blood vessel progenitors in a Petri dish from pluripotent stem cells. Each of these tissue precursors could regenerate their cognate tissue upon injection into respective mouse models, with relevance to regenerative medicine. In addition to our interests in developmental and stem cell biology, we also harbor an emerging interest in deadly biosafety level 4 viruses, such as Ebola and Nipah viruses.

We study the genetic and molecular mechanisms that regulate proliferation and differentiation in adult stem cell lineages, using the Drosophila male germ line as a model.  Our current work is focused on the switch from mitosis to meiosis and how the new gene expression program for cell type specific terminal differentiation is turned on.  One emerging surprise is the potential role of alternative processing of nascent mRNAs in setting up the dramatic change in cell state

The Steinmetz group develops experimental approaches to read, edit and write entire genomes across scales. By applying these technologies, members of the lab aim at understanding the genetic basis of complex phenotypes, the mechanisms of transcription, and the molecular systems underpinning disease. One of the most daunting obstacles in biomedicine is the complex nature of most phenotypes (including cancer, diabetes, heart disease and several rare diseases) due to epistatic interactions between multiple genetic variants and environmental influences. Our aim is to transform the way we approach biomedical research, eventually by assigning a function to every nucleotide in the human genome. Along the way, we continually innovate and improve novel genomics technologies, enabling us to achieve our goals faster and more efficiently. For example, we will develop novel tools for precision genome editing, increase the scale and complexity of functional genomics screens, learn how to write genomes with unique traits from scratch, and apply long-read sequencing methods to understand disease mechanisms. Ultimately, we are working towards an era in which we can predict phenotypic traits from genetic and environmental information. Achieving this ambitious goal would have far-reaching implications, from facilitating precision medicine for everyone, and to predicting how natural populations will respond to changing environments.

Dr. Cong's group is developing novel technology for genome editing and single-cell genomics, leveraging scalable methods inspired by data science and machine learning and artificial intelligence.

His group has a focus on using these gene-editing tools to study immunological and neurological diseases. His work has led to one of the first FDA-approved clinical trials using CRISPR/Cas9 gene-editing for in vivo gene therapy. More recently, his group invented tools for cleavage-free large gene insertion via mining microbial recombination protein (Wang et al. 2022), and developed single-cell perturbating - tracking approach for studying cancer immunology and neuro-immunology (Hughes et al. 2022). We have also strong interest in using deep learning for predicting and designing gene-editing system and protein function (Hughes et al. 2022 and Yuan et al. 2023). Dr. Cong is a recipient of the NIH/NHGRI Genomic Innovator Award, a Baxter Foundation Faculty Scholar, and has been selected by Clarivate Web of Science as a Highly Cited Researcher.

The gene encoding the p53 transcription factor is the most commonly mutated gene in human cancer, yet we lack a complete understanding of how its loss promotes cancer and how to target this pathway therapeutically. My lab studies p53 in the context of two very deadly and common cancer, pancreatic cancer and lung cancer, to understand how p53 loss promotes tumor initiation and progression. We are investigating not only how p53 mutation changes tumor cells themselves but also how these changes in tumor cells alter the cells of the tumor microenvironment to promote cancer development. We strive to understand p53 function using varied approaches, including mass spectrometry, CRISPR screening, ATAC-sequencing, spatial transcriptomics and in vivo mouse analyses. Using these combined approaches, we are gaining key new insights into the fundamental functions of p53 in vivo, which will ultimately inform us on how to target this critical pathway therapeutically.

In the Planetary Modeling Group, we use a variety of modeling techniques to study planets near and far. We focus on the interaction between the interiors and atmospheres of rocky planets both in the Solar System and around other stars. We study the birth and differentiation of planets, the exotic lava worlds of the exoplanet population, but also questions about the environment of the early Earth and other potentially habitable planets and how those planets evolve due to geology, stellar influences, and life.

The primary goal of this laboratory is to promote the health and well being of children and adolescents with chronic pain and their families. In line with this goal, research projects focus on biological, neurological, cognitive, affective, and social risk and resiliency factors of the pain experience. Projects include brain imaging, longitudinal clinical cohort, and treatment intervention studies.

We study how genetic and environmental factors contribute to biological diversity and adaptation. We are particularly interested in understanding (1) how behavior evolves through changes in brain function and (2) how animal physiology evolves through repurposing existing cellular components.

Our mission is to perform rigorous, ethical, and ecologically relevant science across many areas of organismal biology. We aspire to maintain an environment that fosters creativity, diversity, and inclusion as well as engagement with communities in the areas where we work.

We stand in solidarity with the BlackLivesMatter Movement. Scientists and the institutions we work in are complicit in centuries of racism and we will hold ourselves and our institutions accountable by using lab meetings to reflect on our own privileges and by demanding action from Stanford University. We will continue supporting the careers of our Black colleagues by inviting them to seminars, reading their papers, and promoting their work through collaboration and our social media spaces. We are committed to including classrooms in predominantly Black neighborhoods to our Froggers School Program.

We study how genetic and environmental factors contribute to biological diversity and adaptation. We are particularly interested in understanding (1) how behavior evolves through changes in brain function and (2) how animal physiology evolves through repurposing existing cellular components.

Our mission is to perform rigorous, ethical, and ecologically relevant science across many areas of organismal biology. We aspire to maintain an environment that fosters creativity, diversity, and inclusion as well as engagement with communities in the areas where we work.

We stand in solidarity with the BlackLivesMatter Movement. Scientists and the institutions we work in are complicit in centuries of racism and we will hold ourselves and our institutions accountable by using lab meetings to reflect on our own privileges and by demanding action from Stanford University. We will continue supporting the careers of our Black colleagues by inviting them to seminars, reading their papers, and promoting their work through collaboration and our social media spaces. We are committed to including classrooms in predominantly Black neighborhoods to our Froggers School Program.

We work on technology development for genome engineering, discovery-focused synthetic biology, and epigenetic gene therapy. We aim to develop new technologies for studying the mammalian genome and treating complex diseases.

For technology development, we are interested in novel technologies that reprogram the mammalian genome and epigenome. We developed the first nuclease-dead dCas9 from the natural CRISPR-Cas9 nuclease. We developed a series of CRISPR tools that greatly enriched the CRISPR toolbox and expanded genome engineering beyond editing. These tools include CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) for targeted gene activation and repression, LiveFISH for live imaging of DNA and RNA, CRISPR-GO for manipulating the 3D genome organization, and miniature Cas (CasMINI) and hyper-efficient Cas12a (hyperCas12a) for in vivo applications. We harness natural molecules for molecular engineering and evolve novel functions. These tools are broadly used by the community for research and and translational applications.

For discovery-focused synthetic biology, we apply synthetic biology to design and engineer molecules and molecular circuits in mammalian cells. We use synthetic systems to study how cells can be rationally designed as an 'engineering' entity and be harnesses for disease treatment. For example, we engineer T cells to detect new antigens to kill cancer cells or stem cells to integrate environment cues to determine cell fate. By engineering at the scale from molecular to cellular to organismal level, we hope to make synthetic biology a better discovery tool.

For epigenetic gene therapy, we combine epigenome engineering, synthetic biology, and disease models to develop novel therapy to treat cancer, neurodegeneration, and complex genetic diseases. We aim to reveal the importance of noncoding elements including enhancers in the regulation of genome and disease. We harness safe and powerful tools to precisely rewrite the epigenome marks to reverse or cure diseases. We developed PAC-MAN as a treatment to influenza and broad variants of SARS-CoV-2. We aim to greatly expand genome and epigenome engineering towards neurodegenerative diseases and complex diseases.

At the Feng Lab we are interested in the structure, dynamics and function of eukaryotic transport proteins mediating ions and major nutrients crossing the membrane, the kinetics and regulation of transport processes, the catalytic mechanism of membrane embedded enzymes and the development of small molecule modulators based on the structure and function of membrane proteins.

The goal of the Food for Health Equity Lab is to generate evidence of the effectiveness of 'Food as Medicine' programs that can be implemented in diverse healthcare settings to address food insecurity in a way that improves patient outcomes. This work particularly focuses on improving nutrition and reducing chronic diseases within under-resourced communities and communities of color. The lab includes diverse studies including two large-scale randomized controlled trials, a large scale evaluation of a produce prescription program, and multiple pilot studies in different clinical and demographic populations. We use a community-based participatory research orientation and have a Community Advisory Board for our project. The ultimate goal of our research is to inform health policy that will support programs that address food insecurity and reduce inequities in chronic disease. 

We are a computational neuropsychiatry lab dedicated to developing computational methods to better understand brain’s overall dynamical organization in healthy and patient populations. We employ algorithms from a wide range of fields, including Applied Mathematics, Econometrics, Machine Learning, Biophysics, and Network Science.

We have immediate multiple openings for postdoc and research engineer/scientist positions. Please contact Dr. Manish Saggar (saggar@staford.edu), Assistant Professor (Research) of Psychiatry and Behavioral Sciences (Interdisciplinary Brain Science Research), for any questions and for applications.  See here for more details - https://braindynamicslab.github.io/misc/join/  

The overarching goal of Brain Dyanamics Lab is to develop computational methods that could allow for anchoring psychiatric diagnosis into biological features (e.g., neural circuits, spatiotemporal neurodynamics). The lab is funded through an NIH Director’s New Innovator Award (DP2), an NIMH R01, and a faculty scholar award from Stanford’s Maternal and Child Health Research Institute. Our lab excels in developing data-driven computational methods to generate clinically and behaviorally relevant insights from high-dimensional biological data (e.g., neuroimaging) without necessarily averaging the data at the outset. The lab also actively pursue developing novel technologies for experimental design and data collection for enhancing human cognition (e.g., creativity and collaboration). Lastly, the lab also uses large-scale biophysical network modeling approaches to study effects of neuromodulation via TMS and pharmacology (e.g., psychedelics).

If mood symptoms are identified early in life, the opportunity exists to prevent them from progressing to more disabling chronic conditions. Dr. Singh has developed a scientifically-informed comprehensive framework to accurately diagnose and treat childhood-onset depression and other mood disorders before or soon after they present. The Pediatric Emotion And Resilience Lab uses a multimodal neurobiological approach combining neuroimaging, affective neuroscience, and rigorous clinical assessment to understand the mechanisms of risk and resilience in children. We are looking for postdoctoral candidates from the fields of psychiatry, psychology, pediatrics, neurology, genetics, neuroscience, developmental biology, computer science and related fields who seek to improve or expand their ability to conduct interdisciplinary and translational research in pediatric mood disorders.

We study the genetic and molecular mechanisms that regulate proliferation and differentiation in adult stem cell lineages, using the Drosophila male germ line as a model.  Our current work is focused on the switch from mitosis to meiosis and how the new gene expression program for cell type specific terminal differentiation is turned on.  One emerging surprise is the potential role of alternative processing of nascent mRNAs in setting up the dramatic change in cell state

Roncarolo laboratory is exploring the basic biology and translational applications of human type 1 regulatory cells (Tr1). We are using engineered Tr1, ex vivo Tr1, and alloantigen-specific Tr1 to uncover the molecular frameworks that govern Tr1 identity, differentiation and function. We are also translating Tr1 into the clinic. First, Tr1 can be used as a supportive cell therapy to enhance stem cell engraftment and immune reconstitution after hematopoietic stem cell transplantation (HSCT). Alloantigen-specific Tr1, designed to prevent graft-vs-host disease (GvHD) after allogeneic HSCT, are already being tested in a phase I/II clinical trial (NCT03198234). Second, we are investigating the mechanisms of action and clinical potential of the engineered Tr1 called CD4(IL-10) or LV-10, generated by lentiviral transduction of CD4 T cells with IL10 gene. Besides their immunosuppressive and anti-GvHD properties, LV-10 lyse primary acute myeloid leukemia (AML) cells and delay myeloid leukemia progression in vivo. We are exploring LV-10 as a novel cell immunotherapy for AML. Finally, we are interested in curing inborn errors of immunity by stem cell transplantation or autologous stem cell gene correction. We are testing a gene editing strategy to correct pathogenic mutations in IL10 and IL10 receptor genes, which cause severe and debilitating VEO-IBD (very early onset inflammatory bowel disease) in infants and young children.