PRISM Mentors

We study how genetic and environmental factors contribute to biological diversity and adaptation. We are particularly interested in understanding (1) how behavior evolves through changes in brain function and (2) how animal physiology evolves through repurposing existing cellular components.
Our mission is to perform rigorous, ethical, and ecologically relevant science across many areas of organismal biology. We aspire to maintain an environment that fosters creativity, diversity, and inclusion as well as engagement with communities in the areas where we work.
We stand in solidarity with the BlackLivesMatter Movement. Scientists and the institutions we work in are complicit in centuries of racism and we will hold ourselves and our institutions accountable by using lab meetings to reflect on our own privileges and by demanding action from Stanford University. We will continue supporting the careers of our Black colleagues by inviting them to seminars, reading their papers, and promoting their work through collaboration and our social media spaces. We are committed to including classrooms in predominantly Black neighborhoods to our Froggers School Program.

Proteins embedded in the cell envelope of bacteria perform multiple important functions, including signaling, nutrient acquisition, and export of virulence factors. Understanding the structure and functions of these proteins is critical for the development of new anti-bacterial therapies. Currently, the lab focuses on both ABC transporters and lipoproteins of Gram-negative bacteria. The ultimate goal of the research to translate basic lipoprotein research into novel therapuetics.

My goal as a mentor is to contribute to my mentees’ scientific and professional development by leveraging their strengths and providing them with the tools and resources they need to pursue their desired careers. My mentoring philosophy relies on (1) maintaining honest and open communication, (2) providing feedback and guidance, (3) setting clear expectations, and (4) creating a supportive and inclusive learning environment.

We are a chemical biology laboratory focused on the development of technologies to map molecules, cells, and functional circuits. We apply the technologies to understand signaling in the mitochondria and in the mammalian brain.

Our technologies probe molecules and functional networks at both the sub-cellular and multi-cellular level, leveraging our laboratory’s unique strengths in chemical synthesis, protein engineering, directed evolution, proteomics, and microscopy. While we strive to develop technologies that are broadly applicable across biology, we also pursue applications of our methods to neuroscience and mitochondrial biology in our own laboratory and through collaborations.

Our research program is broadly divided into three areas: (1) molecular recorders for scalable, single-cell recording of past cellular events; (2) molecular editors for the precise manipulation of cellular biomolecules, pathways, and organelles; and (3) proximity labeling for unbiased discovery of functional molecules.

Dr. Huang's laboratory aims to understand the chemical and mechanical interactions between extracellular matrix (ECM) proteins and pluripotent stem cells that regulate vascular and myogenic function. The fundamental insights of cell-matrix interactions are applied towards stem cell-based therapies with respect to improving cell survival and regenerative capacity, as well as engineered vascularized tissues for therapeutic transplantation. Current projects focus on various aspects of mechanical and physical factors on tissue regeneration. Examples include:

1) Cellular Biomechanics for in High Through Chemical Screening: To develop new technology for high-throughput quantitative assessment of vascular endothelial cell biomechanics for cardiovascular drug screening. We hypothesize that cellular biomechanics can be a predictive biomarker of endothelial health.

2) Engineered Matrix Microarrays to Enhance the Regenerative Potential of iPSC-Derived Endothelial Cells: We propose to develop a combinatorial family of engineered ECMs (eECMs) with independently tunable biochemical and biomechanical cues, including stiffness and stress relaxation rate for high-throughput, matrix array studies of induced pluripotent stem cell-derived endothelial cell (iPSC-EC) survival and angiogenic potential. The optimally designed eECMs will then be coinjected with iPSC-EC for treatment of peripheral arterial disease in a mouse model of hindlimb ischemia (Sponsor: NIH).

3) iPSC-Derived Smooth Muscle Progenitors for Treatment of Abdominal Aortic Aneurysm: We propose to deliver human induced pluripotent stem cell-derived smooth muscle progenitors to the site of abdominal aortic aneurysm will replenish smooth muscle cells, enhance elastin production, and abrogate wall dilatation in a murine model (Sponsor: CIRM).

4) Vascularized Cardiac Patch with Physiological Orientation for Myocardial Repair: The aims are to engineer a vascularized aligned iPSC-derived CM (cardiomyocyte) patch and elucidating the molecular mechanisms of ECM-mediated nitric oxide signaling in enhancing iPSC-CM survival and phenotype; and to determine the therapeutic effect of a vascularized aligned iPSC-derived CM patch for treatment of myocardial infarction (Sponsor: Dept of Veteran Affairs).

5) Other ongoing research areas: mRNA-based therapeutics, exosome biologics, microgravity effects on tissue regeneration and dysfunction, 3D bioprinting of engineered skeletal muscle, viscoelasticity effects on endothelial-to-mesenchymal transition, electro-osmosis for treatment of lymphedema, tissue chips for stem cell manufacturing

Dr. Huang's laboratory research is funded by the National Institues of Health, Department of Defense, California Institute for Regenerative Medicine, National Science Foundation, and the Department of Veteran Affairs.

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.

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.

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.

We are interested in identifying novel pathways that enable cellular and organismal adaptation to metabolic stress and changes in environmental conditions. We also study how these pathways go awry in human diseases such as cancer, neurodegeneration and metabolic syndrome, in order to engineer new therapeutic modalities.

To address these questions, our lab uses a multidisciplinary approach to study the biochemical functions of the lysosome in vitro and in vivo. Lysosomes are membrane-bound compartments that degrade macromolecules and clear damaged organelles to enable cellular adaptation to various metabolic states. Lysosomal function is critical for organismal homeostasis—mutations in genes encoding lysosomal proteins cause severe human disorders known as lysosomal storage diseases, and lysosome dysfunction is implicated in age-associated diseases including cancer, neurodegeneration and metabolic syndrome.

By developing novel tools and harnessing the power of metabolomics, proteomics and functional genomics, our lab will define 1) how the lysosome communicates with other cellular compartments to fulfill the metabolic demands of the cell under various metabolic states, 2) and how its dysfunction leads to rare and common human diseases. Using insights from our research, we will engineer novel therapies to modulate the pathways that govern human disease.

Bao’s research focuses on fundamental understanding of molecular design rules for organic electronic materials. She pioneered a number of molecular design concepts for efficient charge transport in organic electronic materials. Her work has enabled flexible electronic circuits and displays. In the decade, she pioneered the field of skin-inspired organic electronic materials, which resulted in unprecedented performance or functions in wearable and implantable medical devices and energy storage applications.

The major research directions of Bao Group currently include developing materials and devices for understanding brain-gut axis, large-area high resolution soft electronic electrophysiology from brain, heart, intestine and muscle, wearable for mental health monitoring and genetically-targeted chemical assemblies in brain and peripheral nerve for brain-machine interface.

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

The research in our laboratory is focused on understanding and controlling surface and interfacial chemistry and applying this knowledge to a range of problems in semiconductor processing, micro- and nanoelectronics, nanotechnology, and sustainable and renewable energy. Much of our research aims to develop a molecular-level understanding in these technologically important systems. Our group uses a variety of atomic and molecular spectroscopies combined with atomically-precise materials synthesis. Systems currently under study in our group include organic functionalization of semiconductor surfaces, mechanisms and control of atomic layer deposition, molecular layer deposition, area selective deposition processes, nanoscale materials for light absorption, interface engineering in photovoltaics and batteries, and catalyst and electrocatalyst synthesis and characterization.

Our group is an eclectic mixture of physicists, biologists and engineers who are all passionately interested in the problem of how living cells self-assemble into structures of often dazzling complexity. Unlike human-engineered systems, for example a car or computer chip, every aspect of cell and tissue function must arise from bottom-up self-assembly. The physical mechanisms that govern this self-assembly process are largely unknown, making this one of the most interesting problems in biological research today. Understanding how biological self-assembly occurs is also of critical practical importance. At present, tissue engineering is largely driven by empirical, trial-and-error approaches. A deeper understanding of the processes that underlie cell and tissue organization will, over the longer term, help drive the transformation of tissue engineering into a discipline with understood and predictable design principles, as is the case, for example, in mechanical or electrical engineering. To tackle this general problem we use techniques drawn from molecular biophysics, cell and developmental biology, and increasingly, computer science. Please check out our web page for details on specific problems, and email Alex for more details. 

My research interests lie at the interface between chemistry and biology. While ongoing research in my lab focuses on multiple problems, all of these efforts are motivated by the twin goals of shining light on fundamentally new molecular mechanisms in biology and leveraging these insights to address unmet challenges in human health. Two examples of ongoing research themes in my lab are outlined below:

I] Assembly-line biosynthesis of polyketide antibiotics: The primary objective of this longstanding research project in my lab is to understand the enzymatic mechanisms of assembly-line polyketide synthases (PKSs). Having defined the physical boundaries and chemical reactivity of individual domains and modules, our goal now is to understand these assembly lines as integrated metabolic systems. We also seek to understand the genetic mechanisms for extraordinary evolutionary diversification of this family of multifunctional enzymes.

II] Chemical approaches to understanding celiac disease pathogenesis: Over the past two decades, we have made significant contributions to an understanding of celiac disease (CeD) pathogenesis. Furthermore, at each step along the way, we have sought to translate these emerging molecular insights into enhanced disease management tools for CeD patients and their doctors, as illustrated by the translation of two experimental therapeutics from our lab into advanced preclinical/early clinical studies, and the translation of a biomarker discovered in our lab into CeD patients.
 

The Mai Research Group engineers biopolymers, which are the building materials of life. We seek to develop functional biomaterials and to enhance understanding in the physics of soft materials. Molecular-scale biopolymer design presents a unique opportunity to rationally design materials based on biomolecular templates. Moreover, biopolymer engineering incorporates the rich functional landscape of biological systems into responsive biomaterials. We are especially interested in connecting properties across multiple length scales (molecular, microscopic, macroscopic) using experimental methods. We integrate rational biomolecular design, biological and chemical synthesis, and multi-scale characterization techniques to engineer biopolymers with tunable mechanics, stimuli-responsive behavior, and self-healing properties. Initial research efforts address biological systems where deformation is significant, with specific project areas including: (i) muscle-mimetic materials from polypeptides, (ii) biolubricants from bottlebrush polymers, and (iii) selective filters from programmable hydrogels.

The mission of the Water & Energy Efficiency for the Environment Lab (WE3Lab) is to reduce the cost and carbon intensity of water desalination and reuse. Ongoing research efforts include:

1) developing automated, precise, robust, intensified, modular, and electrified (A-PRIME) water desalination technologies to support a circular water economy;

2) optimizing the coordinated operation of decarbonized water and energy systems; and

3) supporting the design and enforcement of water-energy-food policies (e.g., Effluent Limitation Guidelines, the Clean Power Plan, CA Sustainable Groundwater Management Act, etc.).

My research objective is to develop new biophysical methods to advance current understandings of cellular machinery in the complicated environment of living cells. We bring together state-of-the-art nanotechnology, physical science, engineering and molecular and cell biology, to advance current understandings of biological processes.  Currently, there are two major research directions: (1) Developing nanoscale tools to probe electric activities and cellular processes at the cell-material interface. In this area, we have developed nanoscale electric probes, structural probes and optical probes with high sensitivity and subcellular localization. We identify membrane curvature as one of the crucial biochemical signals that translate nanoscale surface topography into intracellular signaling. (2) Employing optical, magnetic, and optogenetic tools to understand nerve growth factor (NGF) signaling in neurons.  By adapting a variety of microscopy, optogenetic, nanotechnology and biochemical tools, we aim for a deeper understanding of NGF signaling in normal neurons and neurodegenerative diseases.

My research interests lie at the interface between chemistry and biology. While ongoing research in my lab focuses on multiple problems, all of these efforts are motivated by the twin goals of shining light on fundamentally new molecular mechanisms in biology and leveraging these insights to address unmet challenges in human health. Two examples of ongoing research themes in my lab are outlined below:

I] Assembly-line biosynthesis of polyketide antibiotics: The primary objective of this longstanding research project in my lab is to understand the enzymatic mechanisms of assembly-line polyketide synthases (PKSs). Having defined the physical boundaries and chemical reactivity of individual domains and modules, our goal now is to understand these assembly lines as integrated metabolic systems. We also seek to understand the genetic mechanisms for extraordinary evolutionary diversification of this family of multifunctional enzymes.

II] Chemical approaches to understanding celiac disease pathogenesis: Over the past two decades, we have made significant contributions to an understanding of celiac disease (CeD) pathogenesis. Furthermore, at each step along the way, we have sought to translate these emerging molecular insights into enhanced disease management tools for CeD patients and their doctors, as illustrated by the translation of two experimental therapeutics from our lab into advanced preclinical/early clinical studies, and the translation of a biomarker discovered in our lab into CeD patients.
 

Our research focuses on the theory and simulation of chemical systems to address problems at the interface of quantum mechanics and statistical mechanics, with applications ranging from chemistry and biology to geology and materials science. Our research frequently explores theories of hydrogen bonding, the interplay between structure and dynamics, systems with multiple time and length-scales, and quantum mechanical effects. Particular current interests include proton and electron transfer in materials and enzymatic systems, atmospheric isotope separation, and the control of catalytic chemical reactivity in heterogeneous environments.

We work to advance water resources management to promote resilient and equitable responses to an uncertain future. We develop computational modeling approaches that bridge the natural, built, and social environments. Our approach improves understanding of the water and climate risks that threaten people and the environment, while developing systems-based engineering and policy solutions.

The Stanford Urban Informatics Lab & SLAC Grid Integration, Systems, and Mobility (GISMo) group are seeking a post-doctoral fellow to work on the Department of Energy sponsored Impact of Demand Response on short and long term building Energy Efficiency Metrics (IDREEM) project. The goal of this project is to answer the following research questions: Does developing DR capabilities within a building generally lead to more or less efficient buildings (over periods of years)? Does implementing EE strategies within a building generally lead to more or less demand response capacity from those buildings (over periods of years)? Do buildings providing grid services via load shifting consume more energy (over the day) than they would have if not providing services? If so, what are the expected long-term energy impacts? The key outcomes are the establishment of comprehensive long-term DR/efficiency trends; assessment of the system-wide cost, efficiency, and emissions associated with DR; add-ons/extensions to commercial building software models that capture the trends; and a variety of reports, papers, and software documenting our models, methods, and results.

The Stanford Media & Psychology Lab is a multidisciplinary group focused on design and data analysis techniques for study of media and human behavior, integrating established and new disciplines to accelerate research innovations that foster innovations in psychological theory and social policy. Current research directions include emotional regulation, media and technology use, lifespan development, and new methods for analysis of intensive longitudinal analysis–including analysis of ecological momentary assessment and smartphone sensor data. Our lab is committed to global diversity and fostering minority representation in social science, and we collaborate widely with schools and departments across Stanford and other universities.

Automated reasoning; satisfiability modulo theories (SMT); formal methods; formal verification; verification of smart contracts; verification of neural networks; AI safety; hardware design productivity and verification.

Our lab is interested in the capability of robots and other agents to develop broadly intelligent behavior through learning and interaction. We work on robotics and machine learning, and we are affiliated with SAIL, the ML Group, the Stanford Robotics Center, and CRFM.

Our research interests encompass cancer genomics and tumor evolution, stem cell biology and hair/skin development and regeneration, and definitive molecular and cellular therapeutics. Our basic science focus is motivated by our clinical interests that include hair biology, non-melanoma skin cancer, and stem cell-based therapies for genetic skin diseases.

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