PRISM Mentors

I study how ecological communities assemble and influence ecosystem processes, focusing on the role of microbial symbioses, which are ubiquitous in plants and animals. My research is driven primarily by intellectual curiosity about the unseen organisms that shape our planet, but is also aimed to provide knowledge that can be used to better manage ecosystem responses to global change, agriculture, and human health.

My lab uses a combination of ecological theory, molecular biology techniques, and field and laboratory experiments to study microbial communities. Our lab works across a large range of systems, both geographically and ecologically. We work on a number of local projects in the SF Bay Area, across North America, and in tropical rainforests of South American and Southeast Asia. We also study a wide range of interactions, from decomposer bacteria and fungi that are key agents of elemental cycling, to pathogenic fungi  and mutualistic fungi. While I am open to working on a variety of systems, a large portion of my work has  focused on root-fungal mutualisms, known  as mycorrhizal symbiosis, because nearly all plants species, including >98% of all trees, use these partnerships to acquire the soil macronutrients that most limit plant growth and ecosystem productivity. While we now know that such microbial mutualisms are common, there has been far less ecological research on mutualisms compared with antagonistic interactions, such as competition and predation. I ask (a) what controls mycorrhizal community assembly across spatial scales, (b) how mycorrhizal symbiosis structures plant communities, and (c) how mycorrhizal symbiosis is linked to ecosystem processes. By integrating these three topics I seek to build a roots-to-biomes understanding of ecological communities and ecosystem function.

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.

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.

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 Martinez lab studies RNA regulatory mechanisms that control gene expression. We focus on mRNA processing, RNA modifications and their roles in development and disease.

How are nutrients recognized by their protein sensors? How is their transport across cellular and intracellular membranes regulated? And, how is nutrient sensing integrated with other chemical signals, such as hormones, to determine cellular decisions, especially the decision: to grow or not to grow?

We are a team of structural and chemical biologists aiming to answer these fundamental questions at the level of ångstroms, nanometers, and micrometers. Many proteins in these pathways are deregulated in cancer, and our mission is to first reveal the mechanism of action of these proteins, and then use that knowledge to develop targeted chemical probes to modulate their activity in cells and organisms.

Our lab is friendly to trainees from all walks of life, and we cherish trust, inclusiveness and intellectual curiosity, where no question is too big to study, as long as we have the right approach and a unique angle. Most importantly, our lab operates with a growth mindset for all of our trainees, and we put a heavy emphasis on training and skills development — across a wide range of experimental and computational techniques. And through collaboration, strong work ethic, seeking feedback, and trying out new strategies, we drive innovation and novel discoveries for our team.

If this is something you might be interested in, please contact Kacper directly. We are always on the lookout for driven postdocs! Especially, we want cell biologists and biochemists to join our team and to contribute your unique skillsets to a number of collaborative projects.

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 Screenomics Lab is a multidisciplinary group that uses newly available data streams to understand what people actually do on their smartphones, and how the content of their screen experiences relate to health and well-being. We use a variety of computer vision and text analysis tools to extract information from long sequences of screenshots, develop new descriptors of smartphone behavior and smartphone content, and examine how those behavior and content are related to users' emotions, sleep, and mental health. 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 team’s research spans the fields of dermatology, technology and public health. One of our main projects is centered on developing innovative skin cancer prevention interventions using social media. Another project area is the use of shared decision-making, mobile app technology for monitoring and optimal care of low risk skin cancers. We collaborate closely with colleagues in bioinformatics and computer science on use of visual Artificial intelligence methods to skin image monitoring. Additionally, we advocate for diversity and gender equity in medicine by writing both original data articles and perspective pieces on these topics. We collaborate with epidemiologists, clinicians, biostatisticians, basic, computer and social scientists at Stanford University as well as other institutions.

The Wang Lab takes an interdisciplinary approach to studying fundamental mechanisms controlling gene expression in mammalian cells. Our work shows how epigenetic mechanisms such as DNA methylation, chromatin modifications, and RNA influence chromatin dynamics to affect gene regulation. OUR LAB IS CURRENTLY FOCUSED ON: How various dynamic epigenetic changes in chromatin structure impact gene expression during stem cell pluripotency/self-renewal, cellular differentiation, and reprogramming; How three-dimensional chromosomal structure and dysregulation contribute to development of diseases such as aging and cancer; and How to create novel genome engineering tools to interrogate the noncoding genome and the epigenome.   The long-term goal of The Wang Lab is to translate our understanding of these complex mechanisms to studies of human diseases.

Our lab focuses on the role of three-dimensional genome organization in regulating gene expression and shaping cell fate specification during development. We pursue this with advanced single-molecule imaging and transgenic techniques in Drosophila and mammalian cell culture.