PRISM Mentors

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

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.

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 Climate and Earth System Dynamics Group is led by Prof. Noah S. Diffenbaugh. Our research takes an integrated approach to understanding climate dynamics and climate impacts by probing the interface between physical processes and natural and human vulnerabilities. This interface spans a range of spatial and temporal scales, and a number of climate system processes. Much of the group's work has focused on the role of fine-scale processes in shaping climate change impacts, including studies of extreme weather, water resources, agriculture, human health, and poverty vulnerability.

Food security; Agriculture; Data science; Remote Sensing

Earth’s history is marked by atmospheric and climatic fluctuations that have shaped life and its evolution. Floral and faunal fossils have revealed that these ancient events profoundly changed the abundance and diversity of macroscopic organisms, yet much less is known about how microbial communities responded to these dramatic environmental changes. This is one of the challenges in geomicrobiology - how do we study microorganisms in the context of Earth’s distant past?

While microbes do not readily leave diagnostic morphological fossils, subtle microbial signatures are preserved in sedimentary rocks for billions of years. One such group of biosignatures are well-preserved lipid compounds with specific biological origins, which can be used as biomarkers or "molecular fossils" for the presence of certain microbes or environmental conditions at the time of deposition.

Despite the significant implications biomarker studies have on our interpretation of microbial evolution and Earth’s ancient environment, our understanding of the phylogenetic distribution and physiological function of these molecules in modern bacteria is quite limited. In our lab, we combine techniques from bioinformatics, genetics, physiology and biochemistry to address three general questions that can be applied to any biomarker:

• What is its phylogenetic distribution in modern bacteria?
• What are its physiological roles in modern bacteria?
• What is the evolutionary history of its biosynthetic pathway?

-education of Youth of Color, particularly focusing on processes of pushout, criminalization, and resistance, and racial and/or disability justice;

-experience with qualitative research in the humanistic social science tradition;

-commitment to the academic mentoring of undergraduate and graduate students as well as students from other groups underrepresented in education research;

-interdisciplinary and transdisciplinary work welcome including Black Studies, Ethnic Studies, Disability Studies, Women and Gender Studies, law, criminology, sociology, and Queer Studies.

The Stanford BAD Lab is dedicated to centering the lives of Black academics and to the study of liberatory linguistics. We are invested in research that provides insight on factors that affect the academic and professional retention and the quality of life of Black people throughout the teaching and learning lifespan. Our current research projects focus on increasing racial diversity in the STEM fields, including the linguistic sciences; supporting teachers in building their knowledge of linguistic variation and its role in student outcomes across subject areas; and survivorship care of Black cancer patients.

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.

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

See congrevelab.stanford.edu for more information!

The research interests of the molecular imaging instrumentation lab are to create novel instrumentation and software algorithms for in vivo imaging of molecular signatures of disease in humans and small laboratory animals. These new cameras efficiently image radiation emissions in the form of positrons, annihilation photons, gamma rays, and/or light emitted from molecular contrast agents that were introduced into the body and distributed in the subject tissues. These contrast agents are designed to target molecular pathways of disease biology and enable imaging of these biological signatures in tissues residing deep within the body using measurements made from outside the body.

The goals of the instrumentation projects are to advance the sensitivity and spatial, spectral, and/or temporal resolutions, and to create new camera geometries for special biomedical applications. The computational modeling and algorithm goals are to understand the physical system comprising the subject tissues, radiation transport, and imaging system, and to provide the best available image quality and quantitative accuracy.

The work involves designing and building instrumentation, including arrays of position sensitive sensors, readout electronics, and data acquisition electronics, signal processing research, including creation of computer models, and image reconstruction, image processing, and data/image analysis algorithms, and incorporating these innovations into practical imaging devices.

The ultimate goal is to introduce these new imaging tools into studies of molecular mechanisms and treatments of disease within living subjects.

I am interested in how we could use electronics to treat diseases. I am particularly interested in diseases where currently, there is no drug to cure it (Alzheimer's disease), drug has side effects (obesity), and drug is too expensive (diabetes). For the obesity project, I have a hypothesis on the plasticity of white adipose tissue. I am looking for postdoc students to validate the hypothesis and then build the device making use of the hypothesis to treat obesity.

My research interests revolve around the following areas: - Novel systems and methods for x-ray and CT imaging - Applications of x-ray/CT to image-guided interventions and therapy and diagnostic imaging - Dual energy / spectral imaging, including photon counting detectors - Applications of artificial intelligence / machine learning / deep learning to medical imaging - Monte Carlo and Deterministic methods for x-ray imaging and radiation dose - Model-based image reconstruction

Prof. Wang directs the Center for Magnetic Nanotechnology and is a leading expert in biosensors, information storage and spintronics. His research and inventions span across a variety of areas including magnetic biochips, in vitro diagnostics, cancer biomarkers, magnetic nanoparticles, magnetic sensors, magnetoresistive random access memory, and magnetic integrated inductors. 

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.

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.

The central focus of our laboratory is to develop novel microfluidic technologies that for high-throughput and quantitative biophysics, biochemistry, and single-cell biology.

The Gifford lab is focused on defining the complex genetic and molecular mechanisms that are necessary for faithful cardiovascular development and how perturbation of these mechanisms can lead to disease. We use both stem cell and rodent experimental models to:

• characterize the cellular interactions involved in cardiovascular development
• define the oligogenic mechanisms underlying congenital heart diseases, such as hypoplastic left heart syndrome and left ventricular noncompaction
• explore the link between congenital heart disease and neurodevelopmental delay

We also collaborate closely with clinicians, for example on a project integrating cardiac imaging and genetic data to predict adverse cardiac outcomes. Ultimately, we hope to make personalized medicine a reality for those that suffer from CHD and associated comorbidities, such as autism.

We aim to understand the genetic basis of diabetes and related metabolic conditions and to use this to leverage a better understanding of what causes diabetes and how we can improve treatment options for patients. Our work is predominantly focused on understanding what causes pancreatic islets to release insufficient insulin to control blood glucose levels after a meal in patients with type 2 diabetes, but often extends to efforts to relate this to metabolic dysfunction in other relevant tissues such as fat and liver.

We are an inter-disciplinary team of basic and clinical scientists with shared interests in using molecular genetics as a tool to uncover novel biology. We use a variety of different approaches to address important challenges in the field, which range from studies that work genome wide to those which are focused on specific genes and even precise nucleotide changes to understand their impact on pancreatic islet biology.

We have developed a series of pipelines that use primary human islets and authentic beta-cell models which allow us to generate and then integrate complex genomic, transcriptomic and cellular datasets. We use state-of-the art genome engineering approaches combined with induced pluripotent stem-cells to study the impact of T2D-associated genetic variants on islet cell development and function. We are also funded to investigate the impact of T2D risk variants on pancreatic beta-cell function in vivo.

We are a highly collaborative team and work with multiple national and international consortia involved in efforts to understand the genetic basis of type 2 diabetes (eg DIAGRAM, NIDDK Funded Accelerated Medicines Partnership) and related glycaemic traits (MAGIC). We are also part of several Innovative Medicines Initiatives (IMIs) efforts including STEMBANCC and RHAPSODY and Horizon 2020 initiatives (eg T2DSYSTEMS), which are working to develop tools and frameworks to capitalize on genetic and genomic data.

We are also part of the NIDDK funded Human Islet Research Network (HIRN) where we play a role in two of their initiatives. The Human Pancreas Atlas Program- T2 (HPAP-T2D) and the Integrated Islet Phenotype Program (IIPP). Our role is to support the genetic and genomic characterization of islets which are distributed for research and to support the genomic characterization of the pancreas’ phenotyped within the HPAP-T2D program.

Our work extends to playing a role in the interpretation of genetic variants identified in genes with known roles in monogenic forms of diabetes. We are part of the Clin Gen Expert Review Panel for Monogenic Diabetes where are expertise contributes to interpretation of coding alleles in glucokinase (GCK) and Hepatocyte Nuclear Factor 1 alpha (HNF1A). We are a number of on-going projects which are supporting efforts to better understand how to use exome-sequencing data in a diagnostic setting.

The Horns Lab creates and uses new technologies to understand and manipulate cells. We aim to discover the fundamental principles governing how cells and tissues operate, and to harness these insights to improve human health. Our work unites molecular engineering, synthetic biology, and genomics to answer questions and solve problems in immunology, neuroscience, cancer, and aging.

We are looking for postdoctoral researchers interested in understanding the impact of rare variants on human diseases. Projects in the lab are either computational and experimental (or both!). We are particularly interested in establishing new research directions for using genomics data to interpret undiagnosed rare diseases. We are also interested in helping to improve the use of genetic data in diverse populations. Great opportunities for networking also as many of the projects in our lab are often part of major genomics research consortium like the UDN, Mendelian Genomics Research Centres, MoTrPAC, GTEx, TOPMED, ENCODE and more!

Please check out our website and our recent list of papers on Google Scholar https://scholar.google.com/citations?user=117h3CAAAAAJ&hl=en

We study the organizing principles of the genome and how these principles regulate cell identity and developmental switches. We combine Biochemistry and Biophysical methods such as NMR and Hydrogen-Deuterium Exchange-MS with Cell Biology, and Genetics to explore genome organization across length and time scales and understand how cells leverage the diverse biophysical properties of chromatin to regulate genome function.

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

The goal of our laboratory is to develop molecular technologies for mapping cells and functional circuits. At the sub-cellular scale, maps document the spatial organization of proteins, RNA, DNA, and metabolites with nanometer precision and temporal acuity on the order of seconds. Maps also chart the connectivity between these molecules, elucidating the circuits and signaling processes that give rise to function. Beyond the single cell, we also strive to map cellular ensembles, such as brain tissue. Can we create tools that contribute to the construction of cell and tissue atlases, and can we map the cellular circuits that give rise to function and behavior? To achieve these goals, our laboratory employs a wide variety of approaches, including directed evolution, protein engineering, organic synthesis, computational design, mass spec proteomics, and single-cell RNA seq. Our work lies at the interface between chemical biology, genetics, biophysics, cell biology, and neuroscience.

Anne Villeneuve’s laboratory investigates the molecular and cellular events underlying the faithful inheritance of chromosomes during meiosis, the specialized cell division program by which diploid organisms generate haploid gametes. These events are crucial for reproduction, since failure to execute them correctly leads to aneuploidy, one of the leading causes of miscarriages and birth defects in humans. One major goal is to understand the mechanisms and regulation of genetic recombination, which is responsible both for reassortment of genetic traits and for promoting segregation of homologous chromosomes during meiosis. An inter-related goal is to understand how meiosis-specific chromosome organization is established, maintained, and remodeled to bring about successful genome inheritance. Dr. Villeneuve approaches these issues using the nematode C. elegans, a simple organism that is especially amenable to combining sophisticated microscopic, genetic and genomic approaches in a single experimental system. Dr. Villeneuve’s research interrogates the process of meiosis at multiple different scales: 1) at the level of the DNA repair complexes that assemble at the sites of meiotic recombination; 2) at the level of the meiosis-specific chromosome structures that promote, regulate and respond to meiotic recombination events and 3) at the level of DNA organization at the whole-chromosome scale.