PRISM Mentors

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.

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 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.

My overarching goal is to understand how cell growth triggers cell division. Linking growth to division is important because it allows cells to maintain a specific size range to best perform their physiological functions. For example, red blood cells must be small enough to flow through small capillaries, whereas macrophages must be large enough to engulf pathogens. In addition to being important for normal cell and tissue physiology, the link between growth and division is misregulated in cancer.

Today, thanks to decades of research into the question of how cells control division, we have an extensive, likely nearly complete parts-list of key regulatory proteins. Deletion, inhibition, or over-expression of these proteins often results in changes to cell size. However, the underlying molecular mechanisms for how growth triggers division are not understood.  How do the regulatory proteins work together to produce a biochemical activity reflecting cell size or growth? Since we now have most of the parts, the next step to solving this fundamental question is to better understand how they work together.

We are a highly interdisciplinary research team, joined in our desire to derive a more mechanistic understanding of prokaryotic life.

To elucidate how bacterial cells accumulate biomass and grow,  we study the model organism Escherichia coli. Our approaches tightly combine quantitative experimentation with mathematical modeling to consider the coordination of major physiological processes across scales; from metabolism and protein synthesis, via cell-size control, to swimming.

We further focus on gut bacteria and their interactions with each other and the human host. Our analyses include considerations of intestinal physiology and diet habits on the host side, as well as metabolism,  growth-physiology, ecology, and evolution on the bacterial side.

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.

We are a diverse and dynamic group of researchers working to solve clinically important problems using AI. We integrate deep clinical domain expertise with machine learning to develop innovative, AI-driven tools for enhanced patient care. Our areas of focus include the development and validation of digital pathologic and multi-modal deep learning models for: (1) Greater diagnostic accuracy and efficiency, (2) Improved outcome prognostication and prediction of treatment response in cancer patient populations, and (3) Discovery of novel image-based biomarkers for precision medicine across various oncologic and non-oncologic diseases. 

Our laboratory uses chemical and genetic approaches to study the signaling pathways that control mammalian energy homeostasis. We focus on blood-borne metabolic hormones and other hormone-like molecules. Ultimately, we seek to translate our discoveries into therapeutic opportunities that matter for obesity and other age-associated metabolic diseases.

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.

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

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.

My laboratory develops and implements ultrasonic beamforming methods, ultrasonic imaging modalities, and ultrasonic systems and devices. Our current focus is on beamforming methods that are capable of generating high-quality images in the difficult-to-image patient population. These methods include coherence beamforming techniques and neural network beamformers for general B-mode and Doppler imaging, sound speed estimation for quantification of liver steatosis and image correction, and molecular imaging techniques for early cancer detection. We attempt to build these imaging methods into real-time imaging systems in order to apply them to clinical applications for the difficult-to-image patient population. Other projects in our laboratory include the development of novel ultrasonic imaging devices, such as small, intravascular ultrasound arrays that are capable of generating high acoustic output to elucidate the mechanical properties and structure of vascular plaques, and the development of ultrasound-guided drug delivery and therapy systems for cancer and diabetes applications.

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.

The Engreitz Lab is mapping the regulatory wiring of the genome to understand the genetic basis of heart diseases.  This wiring includes millions of enhancers that tune gene expression in the thousands of cell types in the body. Yet, it has been unclear which enhancers regulate which genes — a massive and complex network that rewires in each cell type. To understand this network, we invent new genomics tools combining CRISPR and single-cell approaches; dissect molecular mechanisms of enhancer-gene communication; build computational models to map genome regulation; and apply these tools to connect human genetic variants to biological mechanisms of disease.

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.

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.

Dr. Prochaska’s research program leverages technology to study and treat tobacco, alcohol, and other risk behaviors in populations at high risk. Her research spans community-based epidemiologic studies, randomized controlled clinical trials, and health policy analysis. Dr. Prochaska has conducted and collaborated on over 25 randomized controlled behavioral intervention trials, targeting tobacco and other risk behaviors with adolescents and adults.

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). 

I direct the NIH supported T32 Epilepsy postdoctoral training program, with faculty broadly interested in the cellular/circuit basis of normal brain excitability and how it is disrupted in the disease of epilepsy.  My particular interest is in large scale brain rhythms occuring during childhood absence epilepsy as studied in animal models.

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

Evolution, extinction, Earth system history.

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

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. 

As a physician scientist with a clinical focus on osteoporosis, my laboratory focuses on stem cell sources for bone-forming osteoblasts, and osteoblast support of hematopoiesis in the bone marrow. In particular we are interested in the pathways that promote osteoblast differentiation, using genetically modified mice and lineage tracing techniques in vivo. We are also studying the role of the osteoblast niche in normal hematopoiesis and bone metastases from breast cancer.

Department URL:
https://medicine.stanford.edu/

We invent and develop systems which couple fluid flow, chemical reactions, mass transport, heat transfer, and/or electric fields and apply these to chemical and biological assays.  We design, build, and test microfluidic devices that couple electrokinetics with chemical reactions for on-chip analyses of DNA and high-throughput flow systems for cell assays.  We have two funded projects for which we seek a motivated postdoctoral researcher:

1. We are developing a microfluidic device for fully automated detection of the RNA of SARS-CoV-2 RNA (the virus which causes Covid-19) in less than 60 min.  The device will feature electric field control and enhancement of four processes: RNA extraction, reverse transcription, LAMP amplification, and highly specific detection using CRISPR/Cas enzymes.  See a preliminary version of this assay here:  Ramachandran et al., PNAS, 117, 47 (2020).

2. We are conducting a fundamental study of CRISPR/Cas enzymes with the goal of exploring the ultimate sensitivity of CRISPR-based diagnostic systems.  This work includes developing experimentally validated models of enzyme kinetics and detailed models for the signal-to-noise ratio associated with CRISPR diagnostics.  See Ramachandran & Santiago, Analytical Chem., 93, 20 (2021).

Department URL:
https://me.stanford.edu

Statistical algorithms for genomics, RNA biology, splicing, cancer genomics, spatial transcriptomics

Statistical algorithms for genomics, RNA biology, splicing, cancer genomics, spatial transcriptomics

Dr. Parsonnet is an Infectious Diseases epidemiologist and clinician.  The Parsonnet lab works to understand how infectious agents influence the development of chronic diseases.  During the COVID crisis, the lab has also been actively involved in a wide range of investigations of this disease ranging from large seroepidemiologic studies to novel treatment trials to collaborative studies on COVID immunology.  Studies that could potentially take a fellow include:

• Large seroepidemiologic, longitudinal studies of COVID in the counties throughout California both before and after the initiation of vaccines.   We have collected data sets that allow us to understand risk factors for breakthrough infections,  how vaccination and other interventions change behavior,  and the role of natural infection in building immunity.
• Studies on COVID infection, immunity and vaccination in patients receiving dialysis
• A clinical trial of camostat, a TMPPRS2 blocker, that prevents SARS-CoV2 from entering cells.
• Studies that define the normal human body temperature in children and adults
• Research on how skin care in babies varies across populations and how this influences skin integrity and development of allergic diseases later in life (with Kari Nadeau).
• Studies on the development of the pediatric virome, microbiome and immunome in the first three years of life.

Dr. Parsonnet is an Infectious Diseases epidemiologist and clinician.  The Parsonnet lab works to understand how infectious agents influence the development of chronic diseases.  During the COVID crisis, the lab has also been actively involved in a wide range of investigations of this disease ranging from large seroepidemiologic studies to novel treatment trials to collaborative studies on COVID immunology.  Studies that could potentially take a fellow include:

• Large seroepidemiologic, longitudinal studies of COVID in the counties throughout California both before and after the initiation of vaccines.   We have collected data sets that allow us to understand risk factors for breakthrough infections,  how vaccination and other interventions change behavior,  and the role of natural infection in building immunity.
• Studies on COVID infection, immunity and vaccination in patients receiving dialysis
• A clinical trial of camostat, a TMPPRS2 blocker, that prevents SARS-CoV2 from entering cells.
• Studies that define the normal human body temperature in children and adults
• Research on how skin care in babies varies across populations and how this influences skin integrity and development of allergic diseases later in life (with Kari Nadeau).
• Studies on the development of the pediatric virome, microbiome and immunome in the first three years of life.