PRISM Mentors

The overall theme of our research has been the genetic basis of cardiovascular disease across the continuum from Discovery to the development of Model Systems to the Translation of these findings to the clinic and most recently to the Public Health aspect of genetics. Currently our Discovery and basic translational efforts center on understanding the genetic basis of insulin resistance using genome wide association studies coupled advanced genetic analyses such as colocalization with exploration using in vitro and in vivo model systems including induced pluripotent stem cells and and gene editing screens. 

Our lab works on biological mechanisms of patient-specific and disease-specific induced pluripotent stem cells (iPSCs). The main goals are to (i) understand basic cardiovascular disease mechanisms, (ii) accelerate drug discovery and screening, (iii) develop “clinical trial in a dish” concept, and (iv) implement precision cardiovascular medicine for prevention and treatment of patients. Our lab uses a combination of genomics, stem cells, cellular & molecular biology, physiological testing, and molecular imaging technologies to better understand molecular and pathophysiological processes.

The overall theme of our research has been the genetic basis of cardiovascular disease across the continuum from Discovery to the development of Model Systems to the Translation of these findings to the clinic and most recently to the Public Health aspect of genetics. Currently our Discovery and basic translational efforts center on understanding the genetic basis of insulin resistance using genome wide association studies coupled advanced genetic analyses such as colocalization with exploration using in vitro and in vivo model systems including induced pluripotent stem cells and and gene editing screens. 

Our interdisciplinary lab pursues research centered around advanced polymer 3D fabrication methods and their applications in human health. Focus areas include (1) creating new digital polymer 3D printing capabilities, such as single-micron resolution printing and novel multi-materials printing methods; (2) synthesizing new polymers for 3D printing, with interests in composites, bioabsorbable materials, and recyclable materials; and (3) employing our 3D printing materials and process advances for clinical applications in areas including: new medical device opportunities; vaccine platform development via the advancement of novel microneedle designs; precision delivery of therapies (molecular and cellular) and vaccines; molecular monitoring; and device-assisted, targeted drug delivery, including for cancer treatment. We also pursue novel digital treatment planning approaches using 3D printed medical devices, with our current focus on pediatric therapeutic devices. In this area, we are working with partners at Stanford to design devices and treatment planning solutions for babies with conditions including cleft palate and Pierre Robin Sequence. Complementing these research areas, our lab also emphasizes entrepreneurship; diversity, equity, and inclusion; implications of the digital revolution in the manufacturing sector; and strategies toward achieving a circular economy.ch

Our interdisciplinary lab pursues research centered around advanced polymer 3D fabrication methods and their applications in human health. Focus areas include (1) creating new digital polymer 3D printing capabilities, such as single-micron resolution printing and novel multi-materials printing methods; (2) synthesizing new polymers for 3D printing, with interests in composites, bioabsorbable materials, and recyclable materials; and (3) employing our 3D printing materials and process advances for clinical applications in areas including: new medical device opportunities; vaccine platform development via the advancement of novel microneedle designs; precision delivery of therapies (molecular and cellular) and vaccines; molecular monitoring; and device-assisted, targeted drug delivery, including for cancer treatment. We also pursue novel digital treatment planning approaches using 3D printed medical devices, with our current focus on pediatric therapeutic devices. In this area, we are working with partners at Stanford to design devices and treatment planning solutions for babies with conditions including cleft palate and Pierre Robin Sequence. Complementing these research areas, our lab also emphasizes entrepreneurship; diversity, equity, and inclusion; implications of the digital revolution in the manufacturing sector; and strategies toward achieving a circular economy.ch

Our research aims to fill a fundamental gap of knowledge about the timing, location, and causal importance of specific neuronal populations in the brain that work together in the millisecond scale to subserve a given brain function.

We record directly from inside the brain in neurosurgical patients that are implanted with multiple electrodes across different anatomical and functional systems. We also apply direct electrical current to specific populations of neurons to alter their function while testing the effect of such perturbation on the human participant subjective feelings or task performance.

Our research is beneficial to each individual patient who volunteers to participate in our cognitive and behavioral experiments because we map the location of functional units within each patient’s brain and share this information with clinicians to make more precise and safer surgical plans and prevent major cognitive deficits after surgery.  We also map the location of pathological activity  and use the data to locate the source of seizures and the pathways for their propagation in each individual patient’s brain.

Our work is also relevant to public health and has societal impact. We strive to collect novel information about the functional architecture of the human brain, and improve our understanding of how the brain works. This will be vital for our understanding of the pathophysiology of neurological and psychiatric disorders that affect higher level cognitive functions and cause major problems for afflicted individuals and their families and the society.

We study human brain function at multiple levels of cognitive and behavioral processing. We study brain activity from the very early sensory input to very late decision making in even social or emotional domains. We do not focus on a specific area of the brain or on a narrow field of cognitive neuroscience. As documented by our published work, every level of human cognition, every stage of human brain function, and every regions of the human brain - are of interest to us – as we want to understand how different areas of the brain work together across different experimental tasks. For instance, we have studied the prefrontal cortex (PFC) as we have recorded directly from the human periaqueductal gray (PAG) and we have electrically stimulated the human default network as we have stimulated the human hypothalamus.  Our goal is to acquire a universal understanding of the functional architecture of the human brain with millisecond and millimeter precision.

In the next 50 years, one of the greatest advances we can make for global human health is the realization of a society that is fully sustainable. My research aims to improve agricultural sustainability by using a holistic approach that integrates across genetic, cellular and organismal scales to understand how plants survive stressful environments (Dinneny, 2015a; 2019). Prior research has explored water-stress responses at unparalleled spatial and temporal resolution, and identified the endodermal tissue layer as a critical signaling center for controlling growth and tissue differentiation in roots (Duan et al., 2013; Geng et al., 2013; Dinneny et al., 2008). The discovery of novel adaptive mechanisms used by roots to capture water established potential targets for breeding to improve water use efficiency (Bao et al., 2014; Sebastian et al., 2016). The invention of imaging methods enabled multidimensional studies of plant acclimation and illuminated our understanding of organ system growth from germination to senescence (Rellán-Álvarez et al., 2015; Sebastian et al., 2016). Physiological and molecular insight has been gained in understanding how plants sense water availability through computational modeling of tissue hydraulics (Robbins and Dinneny, 2015, 2018). Additionally, fine-scale biomechanical measurements identified a novel mechanism by which salinity damages cells through its effects on cell-wall integrity (Feng et al., 2018). I have paired my research with a personal passion for improving the education of young plant scientists, engaging lawmakers through science policy, and by being a vocal advocate for the broad deployment of agricultural biotechnology (Fahlgren et al., 2016, Friesner et al., 2021).

Department URL:
https://biology.stanford.edu/people/jose-r-dinneny

Underlying the complexity of the human body is the ability of our cells to adopt diverse forms and functions. This process of cell differentiation requires cells to polarize, translating developmental information into cell-type specific arrangements of intracellular structures. The major goal of the research in my laboratory is to understand how cells build these functional intracellular patterns during development. In particular, we are currently focused on understanding the molecules and mechanisms that build microtubules at cell-type specific locations and the polarity cues that guide this patterning, both of which are essential for normal development and cell function. We study these processes in living animals because the chemical, mechanical, and ever-changing environments experienced by cells in intact organisms are not readily replicated ex vivo. Thus, we take innovative approaches in the model organism C. elegans using novel genetic and proteomic tools, high resolution live imaging, and embryological manipulations.

We study the evolution of complex traits by developing new experimental and computational methods.

Although genetics is often taught in terms of simple Mendelian traits, most traits are far more complex. They evolve via a multitude of genetic changes, each having a small effect by itself, which in sum give rise to the spectacular adaptation of every organism to its environment.

Our work brings together quantitative genetics, genomics, epigenetics, and evolutionary biology to achieve a deeper understanding of how genetic variation shapes the phenotypic diversity of life. Our main focus is on the evolution of gene expression, since this is the primary fuel for natural selection. Our long-term goal is to understand the genetic basis of complex traits well enough to introduce them into new species via genome editing.

Research in the Pollack lab centers on translational genomics, with a current focus on diseases of the prostate. The lab employs next-generation sequencing, single-cell genomics, genome editing, and cell/tissue-based modeling to uncover disease mechanisms, biomarkers and therapeutic targets. Current areas of emphasis include: (1) Defining molecular features of prostate cancer that distinguish indolent from aggressive disease; (2) Determining disease mechanisms and new therapeutic targets in benign prostatic hyperplasia (BPH); and (3) Defining disease drivers in rare neoplasms (e.g., ameloblastoma).

Energy metabolism encompasses the fundamental homeostatic processes by which we regulate our energy storage and energy expenditure. Energy metabolism is highly dynamic and changes according to availability of nutrients, physical activity, or environmental conditions. Dysregulation of energy metabolism is a hallmark of many age-associated chronic diseases, including obesity, type 2 diabetes, dyslipidemias, neurodegeneration, and cancer. Therefore a complete understanding of the molecular pathways of energy metabolism represents an important basic scientific goal with implications for many of the most pressing biomedical problems of our generation. Metabolic tissues including adipose, liver, and muscle play critical roles in energy homeostasis. We are interested in understanding the dynamic endocrine signals that control metabolic tissue function. What are the identities of these signals? How do their levels change in response to physiologic energy stressors? Where are they made? What cell types or tissues do they act on? To answer these questions, we use chemical and mass spectrometry-based technologies as discovery tools. We combine these tools with classical biochemical and genetic techniques in cellular and animal models. Our goal is to discover new molecules and signaling pathways that regulate organismal energy metabolism. Recent studies from our laboratory have identified a family of cold-regulated lipid hormones that stimulate mitochondrial respiration as well as a thermogenic polypeptide hormone regulated by exercise. We suspect that many more remain to be discovered. We anticipate that our approach will uncover fundamental homeostatic mechanisms that control mammalian energy metabolism. In the long term, we hope to translate our discoveries into therapeutic opportunities that matter for metabolic and other age-associated chronic diseases.

Evolution, extinction, Earth system history.

My group does medical imaging research.  Particular areas of interest are image guided interventions, image reconstruction, and fast imaging methods. We are particularly interested in the application of machine learning methods for

The Weker Research Group is at the Stanford Synchrotron Radiation Lightsource (SSRL), a Directorate of the SLAC National Accelerator Laboratory. SLAC is a Department of Energy National Lab managed by Stanford Univeristy. Our research is focused on X-ray microscopy and X-ray characterization of materials far from equilibrium. Using X-rays we study a broad range of systems including energy storage materials such as Li-ion batteries, catalysts, and 3D metal printing (additive manufacturing). 

Li Lab studies RNA editing mediated by ADAR enzymes. The laboratory currently focuses on two fascinating aspects of ADAR. One is the major biological function that is to evade MDA5-mediated dsRNA sensing to suppress autoimmunity. This has led to therapeutic applications in cancer, autoimmune diseases and viral infection. The other is to harness the endogenous ADAR enzyme for transcriptome engineering that holds great potential for RNA-based therapeutics. This approach overcomes challenges faced by CRISPR-based genome engineering technologies.

I am a Professor in the Department of Surgery at Stanford University. I trained as a dentist and have a certificate in Periodontics and a PhD. My lab works in the field of Regenerative Medicine and Dental Medicine, with a focus on the biological and mechanical regulation of tissue repair and regeneration. Our objective has remained unchanged for the last two decades: to make new discoveries that improve patient outcomes.

While conducting clinically relevant research has been my main objective, it has always gone hand-in-hand with another goal: I believe that education is one of the most important tools to improving human health, and I am committed to diversifying our profession for the good of our communities and society. I use every avenue available to transform the way people think about science and medicine and emphasize its contribution to their daily lives. I also invest my time in supporting initiatives that promote inclusion, equity, and diversity. I am the Vice Chair of Diversity and Inclusion in our Department of Surgery at Stanford, and in this role I oversee diversity/equity/inclusion initiatives that impact students ranging from high school and college, through to trainees and junior faculty. In my lab I have assembled a team of individuals from different racial, ethnic, gender, age, and socioeconomic backgrounds, and I believe our science is stronger because of this diversity.

An emerging hallmark of cancer is the modulation of metabolic pathways by malignant cells to promote cancer development. Dr. Jiangbin Ye’s professional interest is to investigate the causes and consequences of the abnormal metabolic phenotypes of tumor cells, with the prospect that therapeutic approaches might be developed to target these metabolic pathways to improve cancer treatment. The lab’s current goal is to explore the complex role of metabolic reprogramming in epigenetic regulations, and how cell fate and differentiation process are controlled by these epigenetic regulations. Ye’s lab is located in the Stanford University School of Medicine, with state-of-art research facilities. The multidiscipline research environment provides unique and outstanding training and collaborating opportunities. The candidate will have direct access to modern metabolomics research tools, including YSI biochemical analyzer, Seahorse XF Analyzer, hypoxia chamber and Agilent Q-TOF LC-MS. The lab is specialized in both untargeted and targeted metabolomics analysis, particularly isotope tracing technique for metabolic flux analysis. Dr. Ye is committed to mentoring and training for the candidate, providing all the support the candidate needs to reach the career goal.

Dr. Jeremy Heit is a neurointerventional surgeon (neurointerventional radiologist) who specializes in treating stroke, brain aneurysms, brain arteriovenous malformations, brain and spinal dural arteriovenous fistulae, carotid artery stenosis, vertebral body compression fractures, and congenital vascular malformations. Dr. Heit treats all of these conditions using minimally-invasive, image-guided procedures and state-of-the-art technology.

Our laboratory is an ultrasound engineering laboratory, located within in a clinical departement.  We are interesed in the development and implementation of ultrasonic beamforming methods, ultrasonic imaging modalities, and real-time ultrasound imaging devices. Our current focus is on beamforming methods that are capable of generating high-quality images in the difficult-to-image patient population, and include projects in reverberation noise reduction, sound speed estimation & phase aberration correction, and novel beamforming techniques for anatomica and functional imaging. We attempt to build these imaging methods into real-time imaging systems in order to apply them to clinical scenarios including cardiac, liver, and placental imaging, as well as cancer imaging in the kidney and breast.  Other collaborative projects in our laboratory include molecular imaging of cancer, microbubble-mediated drug delivery in hepatocellular carcinoma, passive cavitation imaging, and pulsed focused ultrasound for the stimulation of cells for therapetuic treatment of the pancreas.

The goal of our research is to understand the algorithms the brain uses to learn. A fundamental feature of our neural circuits is their plasticity, or ability to change. How does the brain use this plasticity to tune its own performance? What are the learning rules that determine whether a neural circuit changes in response to a given experience, and which specific neurons or synapses are altered?  Our research integrates molecular, cellular, systems and computational neuroscience approaches in mice to uncover the logic of how the cerebellum implements learning.

Synthetic biology in plants and their associated microbes with the goal of driving innovation in agriculture for a sustainable future.

We work on the cellular and molecular basis of neuronal survival and axon growth relevant to neuroprotection and regeneration, and on differentiation and transplant relevant to neural development and cell replacement therapies. Using retinal ganglion cells, a type of CNS neuron, as our primary model system in vitro and in rodent models in vivo, we use diverse "omics" and discovery research, combined with hypothesis-driven experiments and novel techniques, to unveil the basis for neuronal development, integration, and regeneration in the visual system.

Mission: Our mission is to both use neuroscience as a tool for improving education, and use education as a tool for furthering our understanding of the brain. On the one hand, advances in non-invasive, quantitative brain imaging technologies are opening a new window into the mechanisms that underlie learning. For children with learning disabilities such as dyslexia, we hope to develop personalized intervention programs that are tailored to a child’s unique pattern of brain maturation. On the other hand, interventions provide a powerful tool for understanding how environmental factors shape brain development. Combining neuroimaging with educational interventions we hope to further our understanding of plasticity in the human brain.

The Lab: The Brain Development & Education Lab is located in the Graduate School of Education at Stanford University and represents a collaboration between the Division of Developmental and Behavioral Pediatrics within the School of Medicine, the Graduate School of Education and the Wu Tsai Neuroscience Institute (we recently moved from The University of Washington’s Institute for Learning & Brain Sciences). The focus of the lab is understanding the interplay between brain maturation and cognitive development.  The lab is interdisciplinary, drawing on the fields of neuroscience, psychology, education, pediatrics and engineering to answer basic scientific and applied questions.  Current projects focus on understanding how the brain’s reading circuitry develops in response to education and how targeted behavioral interventions prompt changes in the brain’s of children with dyslexia. A major component of this work is the development of software to measure properties of human brain tissue, localize differences and quantify changes over development.

Mission: Our mission is to both use neuroscience as a tool for improving education, and use education as a tool for furthering our understanding of the brain. On the one hand, advances in non-invasive, quantitative brain imaging technologies are opening a new window into the mechanisms that underlie learning. For children with learning disabilities such as dyslexia, we hope to develop personalized intervention programs that are tailored to a child’s unique pattern of brain maturation. On the other hand, interventions provide a powerful tool for understanding how environmental factors shape brain development. Combining neuroimaging with educational interventions we hope to further our understanding of plasticity in the human brain.

The Lab: The Brain Development & Education Lab is located in the Graduate School of Education at Stanford University and represents a collaboration between the Division of Developmental and Behavioral Pediatrics within the School of Medicine, the Graduate School of Education and the Wu Tsai Neuroscience Institute (we recently moved from The University of Washington’s Institute for Learning & Brain Sciences). The focus of the lab is understanding the interplay between brain maturation and cognitive development.  The lab is interdisciplinary, drawing on the fields of neuroscience, psychology, education, pediatrics and engineering to answer basic scientific and applied questions.  Current projects focus on understanding how the brain’s reading circuitry develops in response to education and how targeted behavioral interventions prompt changes in the brain’s of children with dyslexia. A major component of this work is the development of software to measure properties of human brain tissue, localize differences and quantify changes over development.

Our lab is interested in the host pathways that determine the susceptibility of humans to viral disease. Viruses constantly evolve to exploit host machineries for their benefit whilst disarming host restriction mechanisms. Discovery of host proteins critical for viral infection illuminates basic aspects of cellular biology, reveals intricate virus host relationships, and leads to potential targets for antiviral therapeutics.

A major aim of our lab is to define metrics of immune competence in various settings, including cancer immunotherapy, organ transplantation, allergy, and chronic viral infection. We use CyTOF mass cytometry, often in combination with other technologies, to broadly survey immune features at the cellular level, then examine links between features or groups of features and clinical outcome. A long-term goal is to create an assay of global immune competence that could predict risk for various immune-related outcomes in both healthy individuals and in disease.

The focus of our research is understanding the role of genetic changes in cancer genes in the risk and development of common cancers and on manipulating DNA repair mechanisms for the prevention and treatment of cancer. Solid tumors often exhibit high levels of reactive oxygen species (ROS) resulting in oxidative damage and the generation of 8-oxoguanine (8-oxoG), a common source of mutations and DNA damage in the cell. ROS can be generated by multiple mechanisms including activating RAS mutations, exposure to chemical carcinogens and ionizing reagents, or as a by-product of metabolic processes in the cell.  ROS likely impacts the initiation of BRCA-mutated triple negative breast cancer (TNBC) through the accumulation of mutations in the cell.  Up-regulating base excision repair (BER) pathways is a potentially viable approach to inhibiting tumorigenesis in BRCA-mutated individuals by reducing mutagenesis. We have identified small-molecule activators of BER and are exploring their mechanism of action and activity in cells and tumorogenesis models in mice. We are seeking a Postdoctoral scholar to work in this area who is
well-versed in tissue culture, cellular assays, and molecular biology techniques. Experience and a willingness to work with mice is preferred.

Our laboratory integrates synthetic chemistry, genetics, and developmental biology to investigate the molecular mechanisms that control tissue formation, regeneration, and oncogenic transformation. Our research group is currently focused on three major areas: (1) small-molecule and genetic regulators of the Hedgehog signaling pathway; (2) optochemical and optogenetic tools for studying tissue patterning with spatiotemporal precision; and (3) zebrafish models of vertebrate development.

Our interest is in developing diagnostic and prognostic markers for urological diseases. Our work spans discovery, measurement methodologies, and clinical validation of candidate biomarkers. We have primarily used genomic and proteomic approaches for biomarker discovery. While our primary focus has been in prostate cancer, we have also worked in kidney cancer and other malignancies. We are also working to characterize the functional roles of several of the candidate biomarkers in cancer. In the past several years our work has expanded into benign urologic diseases including benign prostatic hyperplasia, obstructive nephropathy, and androgen insensitivity syndrome. In collaboration with bioengineers and radiologists, we have active research in molecular imaging, and protein and nucleotide detection on biological samples. We also participate in several large clinical trials for development, validation and implementation of clinical biomarkers in prostate cancer.

Our research aims to improve population health by creating high quality evidence about what health interventions work in whom and where, when, and how to implement them. Most of our research is focused on infectious diseases, including malaria, diarrhea, soil-transmitted helminths, and influenza. Our focus is on improving the health of vulnerable populations from low-resource settings, both domestically and internationally. We use a variety of epidemiologic, computational, and statistical methods, including causal inference and machine learning methods.

The Karakikes Lab investigates the molecular mechanisms of rare cardiac diseases, such as dilated cardiomyopathy (DCM). We employ an interdisciplinary approach, integrating functional genomics approaches in human pluripotent stem cell (hPSC) derived cardiovascular cells with single-cell transcriptomics and epigenetics to study cardiomyopathies in a genetically controlled and systematic manner.

We know far more than what we can directly experience. We learn about the world by drawing rich, abstract inductive inferences that go beyond what we can observe, and much of these observations come from behaviors of others around us. By engaging in social learning in diverse contexts, humans learn from others, share their knowledge with others, and even accumulate a body of cultural knowledge over generations. 

The Social Learning Lab (SLL) aims to understand the cognitive mechanisms that underlie the communicative interactions we experience in our lives. In particular, the ways in which young children learn from others provide a unique window to the interface between our ability to draw powerful inferences and to our understanding of others’ thoughts and actions (Theory of Mind). To better understand this process, we design and conduct behavioral experiments with young children and adults, often combined with computational models that help predict and explain behavioral results.