PRISM Mentors

The FUNR Lab, lead by Flora Rutaganira uses choanoflagellates—the closest living single-celled relatives to animals—to study the origin of animal cell communication. We apply chemical, genetic, and cell biological tools to probe choanoflagellate cell-cell communication. We hope that our research has implications for understanding not only animal cell signaling, but also the origin of multicellularity in animals.

The Peltz laboratory develops and uses state of the art genetic, genomic and stem cell technologies in its research programs. These methodologies are used to discover the mechanisms mediating disease susceptibility and drug response, and to develop new therapies. As one example, we developed a novel computational genetic analysis method, which has identified genetic factors affecting disease susceptibility and biomedical responses in mouse models. One of the genetic findings is the basis for an ongoing clinical trial that tests a new therapy for preventing opiate withdrawal from occuring in babies born to mothers that take opiates. Over 25 genetic factors affecting susceptibility to drug addiction, chronic pain, infectious diseases, and others have been identified. An ongoing effort is now analyzing 10000 biomedical responses in panels of inbred mouse strains. Single-cell RNA sequencing and metabolic analysis are used to identify developmental and disease-causing pathways. Stem cell-based methods for liver engineering are also used. As examples of this, the Peltz lab has produced mice with humanized livers that are used to improve drug safety; developed methods to engineer human liver from adipocyte stem cells; and to produce human liver organoids from stem cells, which are used for studying the pathogenesis of human genetic liver diseases.

The Sherlock lab uses experimental approaches to understand the evolutionary process, specifically interested in i) the beneficial mutation rate, ii) the distribution of fitness effects (DFE) of beneficial mutations, iii) the identities of beneficial mutations (are they gain or loss of function, are they recessive, dominant or overdominant, are the genic or regulatory?) and iv) how do each of these change as a function of genotype, ploidy and environment. We are also interested in how mutations that are beneficial in one environment fare in others (pleiotropy), and we are interested in exploring at what level experimental evolution can be deterministic, and at what level it is stochastic. We typically use serial batch culture experiments in conjunction with lineage tracking and high throughput sequencing to understand the adaptive changes that occur in yeast in response to selective pressures as they evolve in vitro.

Department URL:
https://med.stanford.edu/genetics.html

Our lab's research lies at the interface of biology, engineering, nanotechnology, and medicine. We develop and apply translational micro/nanotechnologies to study cellular heterogeneity and complex biological systems for single cell analysis and precision medicine.  At this unique nexus, we apply key biological principles to design engineering platforms. Our research philosophy is to apply these platforms to fundamentally understand and address the mechanisms of disease (i.e., cancer, infections). 
We, for the first time, have demonstrated magnetic levitation of living cells and its application to detect minute differences in densities at the single-cell level.  We apply this unique tool to perform ultra-sensitive density measurements, magnetic blueprinting, imaging, sorting and profiling of millions of cells and rare biological materials in seconds in real-time at a single-cell resolution.  For instance, magnetic levitation technology can sort rare circulating tumor markers and cells from patient whole blood  without relying on any markers, tags or antibodies, which cut cross multiple disciplines of magnetics, microfluidics and molecular biology.
Our lab's mission is to bridge the gap between biology, engineering and nanotechnology; to develop simple, inexpensive, easy-to-use, yet, broadly applicable platforms that will change the way in which medicine is practiced as well as how patients are monitored, diagnosed and treated for precision medicine. We apply key biological principles to engineering designs.  Interfacing our unique bioengineering platforms with next-generation sequencing technologies, we aim to understand and answer fundamental questions mainly in cancer biology, antibiotic resistance, and regenerative medicine.
Our focus is to develop new tools and technologies to investigate and fundamentally understand disease and wellness. Our research efforts are summarized as follows:

• Creating new tools and technologies to detect and isolate circulating biological signatures, materials and markers from biological fluids (i.e., circulating tumor cells, circulating tumor emboli, exosomes in blood, urine, and saliva).
• Enabling investigations of these rare biological materials to “decode” the molecular, genetic and proteomics characteristics to better understand the biology of disease, with a special focus on cancer biology and metastasis.
• Detecting antibiotic susceptibility using magnetic levitation. 
• Evolving these technologies into the next generation of applications in antibiotic resistance to eradicate biofilms and resistant microorganisms.
• Exploring self-assembly of single cells under microgravity conditions for bioprinting, tissue engineering and regenerative medicine. 

We are seeking open and honest, creative, dedicated, and team-oriented individuals to join our research team. Our lab prioritizes inclusion and diversity to achieve excellence in research and to foster an intellectual climate that is welcoming and nurturing. Two positions are available for energetic, self-driven and passionate postdoctoral fellow candidates.  Applicants are expected to be technically competent in a discipline relevant to our mission and vision.  

My research focuses on advanced MRI and PET/MRI techniques and their application to alleviate neurological disease.  I lead an inter-disciplinary team of physicians, graduate and post-doctoral students, and research associates with technical expertise in all the required realms to perform successful advanced imaging studies.  As an active clinical neuroradiologist, I have a strong track record of integrating advanced imaging methods to clinical patients and have published extensively on its value in a wide range of diseases.  During the past several years, I have become convinced that AI generally and deep learning in particular will transform medicine.  Radiology will be fundamentally affected.  In the area of deep learning, I have demonstrated its use to improve MR reconstruction, reduce MR contrast dose and radiation dose, segmentation of brain metastases, and to predict the future.

Our lab’s research portfolio crosses multiple disciplines including computational neuropsychiatry, multimodal neuroimaging, cognitive neuroscience and neurocognitive rehabilitation. Our computational neuropsychiatry research mainly involves investigating alterations in the organization of connectome in various neurodevelopmental and neurocognitive disorders using state of the art neuroimaging techniques (fMRI, sMRI, DWI, functional NIRS) combined with novel computational methods (graph theoretical and multivariate pattern analyses). The ultimate research goal is to translate the findings from computational neuropsychiatry research toward developing personalized interventions. We have been developing personalized interventions that integrate computerized cognitive rehabilitation, real-time functional brain imaging and neurofeedback, as well as virtual reality (VR) tailored toward targeted rehabilitation of the affected brain networks in patients with neurocognitive disorders.

Ongoing studies in Dr. Hosseini’s lab include: .

• Multimodal data integration using multilayer networks for early detection of Alzheimer's disease   
• Real-time fNIRS neuromonitoring and neurofeedback for targeted enhancement of working memory in children with ADHD.
• Multimodal neuroimaging study to examine the effect of long-term, cognitive intervention on brain networks in older adults at risk of developing Alzheimer’s disease.
• Developing a low-cost, wireless, wearable, optical imaging system for personal and population-based functional neuroimaging and neuro-intervention.
• Noninvasive optical imaging for monitoring of functional stroke recovery and to direct and optimize stroke therapies.

Our lab is dedicated to discovering the underpinnings of immune-related diseases in the heart. Many cancer drugs may cause immune-related toxicity in the heart, including severe myocarditis, making it difficult for patients with cancer to get the life-saving treatments they need. We have previously discovered that several key types of immune cells may be involved in potentiating disease. We are currently performing experiments to pin down the underlying mechanisms of how immune cells may cause various inflammatory heart diseases. We use a combination of precision medicine-oriented techniques including single-cell RNA-seq, TCR-seq, and CyTOF as well as classical molecular biology, cell modeling and animal modeling to answer mechanistic questions about the pathogenesis of cardiac inflammatory diseases, with the goals of discovering therapeutic targets which can be brought to the patient bedside. 

My research focuses on the neurobiological basis of language, reading, and cognition in children.  Functional imaging studies demonstrate that language and reading skills require the integrated activity of a network of distributed brain regions.  Diffusion magnetic resonance imaging (dMRI) documents that variations in the properties of long-range white matter pathways connecting these brain regions within the cerebrum and between the cerebrum and cerebellum are associated with variations in language and reading skills.  These white matter pathways may be disturbed in childhood illnesses, such as brain tumors. We have been collecting dMRI scans on children born preterm and full term at different ages, including infancy.  We also have been collecting clinical scans on children with brain tumors in the cerebellum and posterior fossa. We seek students who want to learn techniques for analyzing dMRI and related imaging methods in children and to link the neurobiological findings to clinical outcomes.  Selected studies include: (1) analyzing white matter pathways in preterm infants at near term age in relation to medical and environmental variables; (2) applying spherical deconvolution to scans of children age 6 to 8 years who are learning to read; (3) evaluating longitudinal change in children with mutism after resection of a posterior fossa brain tumor.

Cancer Imaging, Nanoparticles, MRI, PET/MR, Cancer Immunotherapy Imaging, Tumor Associated Macrophages, Stem Cell Tracking

Our focus is on the basic molecular mechanisms of stem cells and muscle and their application to aging, regenerative medicine, and disease. The Blau lab brings together biologists, bioinformatics experts, and bioengineers who are interested in everything from the basic mechanisms of disease, to technology development, to clinical translation. We capitalize on an interdisciplinary approach to science because 'Where we look and how we look determines what we see’. The laboratory collaborates extensively with other researchers. Our overall objective is to understand and apply biology to improve quality of life.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.