PRISM Mentors

I am a clinical pathologist and assistant professor in the Departments of Medicine, Pathology, and Genetics (by courtesy) at Stanford. I completed my MD-PhD training at Yale University and my residency training and a post-doctoral fellowship in the Department of Genetics at Stanford University. My experiences as a clinical pathologist and genome scientist have made me passionate about applying cutting-edge technologies to primary patient specimens in order to characterize disease pathologies at the molecular level. The core focus of my lab is to study the mechanisms by which genetic variants influence the risk of disease through effects on intermediate molecular phenotypes.

Our laboratory is developing tools to study genetic variants commonly found in Asians within the basic science laboratory including CRISPR mouse models, drug development/design, and protein chemistry. Most of our laboratory uses basic science techniques to study the cardiovascular system and we are funded through the NIH from NIGMS and NHLBI. Our NIGMS funded project focuses on genetic variants in Asians and developing precision medicine strategies for reducing perioperative organ injury and precision medicine strategies for delivering anesthesia and pain relievers such as opioids. Our NHLBI funded project is to study the cardiopulmonary effects of e-cigarettes in rodents and to further determine how a common genetic variant in East Asians may impact the cellular toxicity of e-cigarettes.

Our laboratory develops and applies state of the art genetic, genomic and stem cell technologies to 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. Over 25 genetic factors affecting susceptibility to drug addiction, chronic pain, infectious diseases, and others have already been identified. We recently developed a novel AI for mosue genetic discovery and have received two NIH grants for advancing AI-based genetic discovery. 

Chronic pain affects 1 in 3 Americans at a huge cost to society. A more thorough understanding of the basic mechanisms contributing to chronic pain is crucial to the development of therapies that target the likely unique underlying causes of diverse pain conditions. Projects in the Tawfik Lab use clinically-informed basic science approaches to further understand the crosstalk between the nervous system and the immune system in several mouse models of perioperative injury. In particular, we have an interest in CNS glial cells (astrocytes and microglia) which, after injury, can contribute to central sensitization and persistence of pain. Preclinical use of glial modulators has been successful at reversing existing pain, however, translational efforts have thus far failed. We strive to further understand glial subtypes and functional phenotypes in order to better tailor glial-directed therapies. Our projects involve collaborations with several other labs in Neurology, Radiology and Anesthesiology in a collegial environment focused on rigorous science and close mentorship.

To understand biology, we need chemistry and physics as the physical and chemical properties of biomolecules enable and constrain what biology can do and how it has evolved. We are particularly interested in questions of: (i) how enzymes work; (ii) how RNA folds; (iii) how proteins recognize RNA; (iv) RNA/protein interactions in regulation and control; and (v) the evolution of molecules and molecular interactions. Our interdisciplinary approaches span and integrate physics, chemistry and biology, employ a wide range of techniques, and are question driven. We have new projects in each of the above areas as we:
• Pioneer high-throughput quantitative approaches to study enzymes—to address how an entire protein contributes to its function, how allosteric signals are propagated, how different human alleles affect function and/or stability, and ultimately how to design new enzymes (with Polly Fordyce);
• Work to understand the evolution of enzyme function and stability via functional, genome-scale analyses, and experimental evolutionary studies;
• Pioneer the determination of enzyme conformational ensembles—and linking these to function via novel “ensemble¬–function” studies;
• Develop a quantitative and predictive model for RNA tertiary folding thermodynamics and kinetics, building from the “RNA Reconstitution Model”;
• Provide the first quantitative and complete descriptions of the affinity and specificity of RNA binding proteins for all possible RNA sequences and structures (with Will Greenleaf);
• Pioneer Quantitative Cellular Biochemistry (QCB) to bring together the power of biochemistry and genomics to the study molecular interactions and function in cells, with the goal of providing quantitative and predictive models for molecular function and regulation in cells.

Our lab seeks to understand the molecular basis of inherited Parkinson's Disease.  Activating mutations in the LRRK2 kinase cause Parkinson's , and the major substrates of LRRK2 kinase are a subset of proteins called Rab GTPases.  Together with our collaborators, we have discovered that phosphorylation of Rab proteins completely changes the partner proteins with which they interact and leads to a blockade in the formation of critical signaling structures called primary cilia.  We are using biochemical, cell biological and genome-wide approaches to study the molecular cell biology of Parkinson's Disease by focusing on the consequences of Rab GTPase phosphorylation.  Our work includes single molecule biochemical experiments to undertstand the kinase and its corresponding phosphatase--how they are recruited to membranes and activated.  We also study LRRK2-mediated loss of cilia in specific neuronal cell types and astrocytes in both mouse and human brains.  We are using state of the art microscopic tools to understand why cilia are lost and how this leads to Parkinson's disease.

Our lab uses cellular, biochemical, and genetic approaches to understand the mechanism by which developmental signaling pathways, such as the WNT and Hedgehog pathways, function and how they are damaged in disease states. We use a broad range of approaches in our work: genome-wide CRISPR screens, proteomics, imaging, and both protein and lipid biochemistry.

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

The Yeh Lab studies the apicoplast, a unique plastid organelle in Plasmodium falciparum parasites that cause malaria. We are particularly focused on unbiased chemical and genetic screens to discover new cell biology and therapeutic targets for this important global health disease. Our work highlights the untapped opportunities in exploring divergent biology in non-model organisms, a theme we plan to expand in the lab by studying ocean algae (malaria's cousins!) and their role in the global ecosystem.

In our laboratory, we are at the forefront of cutting-edge research focused on the integration of cryogenic electron microscopy and tomography with state-of-the-art artificial intelligence-driven image analysis techniques. Our primary objective is to uncover distinctive and common cellular structural patterns associated with various human diseases. With access to mulitple state-of-the-art electron cryomicroscopes and cutting-edge detectors, our laboratory is well-equipped to advance the field. Our methodological innovations are motivated by the imperative to gain deeper insights into disease pathologies and to pinpoint potential therapeutic targets within cells.

We are active engaging extensive collaborations with biomedical researchers spanning diverse domains including neurodegeneration, visual impairments, viral infections, cancer and cardiovascular disorders. This collaborative approach enables us to look for possible subcellular structure patterns common to these diseases, tackle complex disease-related questions from multiple angles, enriching our understanding of these conditions and opening new avenues for potential interventions.

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

Heilshorn's interests include biomaterials in regenerative medicine, engineered proteins with novel assembly properties, microfluidics and photolithography of proteins, and synthesis of materials to influence stem cell differentiation. Current projects include tissue engineering for spinal cord and blood vessel regeneration, designing injectable materials for use in stem cell therapies, and the design of biomaterials for culture of patient-derived biopsies and organoids. Postdoctoral candidates with expertise (or an interest in learning) preclinical animal models of injury and disease are particularly encouraged.

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

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.

We work on technology development for genome engineering, discovery-focused synthetic biology, and epigenetic gene therapy. We aim to develop new technologies for studying the mammalian genome and treating complex diseases.

For technology development, we are interested in novel technologies that reprogram the mammalian genome and epigenome. We developed the first nuclease-dead dCas9 from the natural CRISPR-Cas9 nuclease. We developed a series of CRISPR tools that greatly enriched the CRISPR toolbox and expanded genome engineering beyond editing. These tools include CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) for targeted gene activation and repression, LiveFISH for live imaging of DNA and RNA, CRISPR-GO for manipulating the 3D genome organization, and miniature Cas (CasMINI) and hyper-efficient Cas12a (hyperCas12a) for in vivo applications. We harness natural molecules for molecular engineering and evolve novel functions. These tools are broadly used by the community for research and and translational applications.

For discovery-focused synthetic biology, we apply synthetic biology to design and engineer molecules and molecular circuits in mammalian cells. We use synthetic systems to study how cells can be rationally designed as an 'engineering' entity and be harnesses for disease treatment. For example, we engineer T cells to detect new antigens to kill cancer cells or stem cells to integrate environment cues to determine cell fate. By engineering at the scale from molecular to cellular to organismal level, we hope to make synthetic biology a better discovery tool.

For epigenetic gene therapy, we combine epigenome engineering, synthetic biology, and disease models to develop novel therapy to treat cancer, neurodegeneration, and complex genetic diseases. We aim to reveal the importance of noncoding elements including enhancers in the regulation of genome and disease. We harness safe and powerful tools to precisely rewrite the epigenome marks to reverse or cure diseases. We developed PAC-MAN as a treatment to influenza and broad variants of SARS-CoV-2. We aim to greatly expand genome and epigenome engineering towards neurodegenerative diseases and complex diseases.

Postdoctoral Research Fellow – Cell biology & microfluidics, UCSF & Stanford

A joint postdoc position between the labs of Wallace Marshall (UCSF) and Sindy Tang (Stanford) is immediately available in the area of single-cell wound healing. The broad question we aim to answer is how the single-celled ciliate Stentor can heal drastic wounds. We are looking for a candidate with a background in cell biology or related fields. This position will allow ample opportunities to learn new techniques including microfluidics for single-cell manipulation and mathematical modeling.

Application
For questions or applications (see below), please feel free to reach out to Prof. Wallace Marshall (wallace.ucsf@gmail.com) or Prof. Sindy Tang (sindy@stanford.edu). To apply, please include a CV (with a publication list) and some detail about your background and interest in the project.

Project description:
Biomechanical mechanisms conferring wound resilience in single-celled organisms
Stentor coeruleus is a large, single-celled ciliate that has remarkable wound healing and regenerative capacity (see Slabodnick et al., Current Bio, 2014 https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.10...). It is found in environments that can be subject to high mechanical stresses due to natural flows or predation. The overall goal of this project is to investigate how this organism employs both mechanical and biochemical mechanisms upstream of wounding for wound prevention, as well as downstream of wounding for robust healing from wounds (https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-00970-0).

We have sequenced the Stentor genome, and developed tools for molecular manipulation of Stentor gene expression to pave the way to a molecular understanding of Stentor wound response.   This project involves conceptualization of a novel chemical screen to test the role of the cytoskeleton in conferring wound resistance to the cell, and the role of large-scale mechanical force generation in complementing biochemical healing modes to close wounds of increasing severity.

Some questions we ask are: how does Stentor cell mechanics give rise to wound resistance? How do cells respond to shear or other types of stresses? What molecular pathways are important in Stentor wound healing, and are they the same as in other eukaryotes?
The project combines cell biology, microfluidics for precise wounding (see Blauch et al., PNAS 2017 https://www.pnas.org/doi/abs/10.1073/pnas.1705059114), and mechanobiology modeling.

Required Qualifications:
Desired skills for this project include:
• Cell biology
• Chemical screen
• RNAi and genetic transformation
• Past experience with Stentor, other ciliates, or manipulation (e.g., microinjection) of large cells or embryos such as Drosophila
• Mathematical modelling of cellular processes
Candidates proficient in certain skills outlined above will have opportunities to receive training in complementary skill sets.

Required Application Materials:
Your CV with a publication list, and some detail about your background and interest in the project.

We integrate single-cell multiomics, advanced microscopy, and quantitative models to understand organismal regeneration using a variety of organisms. We invite postdoctoral colleagues to build on our current systems or establish new models to understand foundamental principles controlling regeneration.  

We combine biophysical methods with in vivo approaches to understand how viruses such as HIV and SARS-CoV-2 infect host cells and elicit specific humoral immune responses. Our research will translate knowledge of the structural correlates of antibody-mediated neutralization of viruses into the rational development of highly protective antibodies. A related goal is the structure-based design of potent and stable immunogens for vaccination.

Our lab is interested in how stem cell-like populations are created and maintained in developing, environmental responsive tissues.  We primarily use the Arabidopsis stomatal lineage for these studies because this epidermal cell lineage distills features common to all tissue development: stomatal precursor cells are chosen from an initially equivalent field, they undergo asymmetric and self-renewing divisions, they communicate among themselves to establish pattern and they terminally differentiate into stable, physiologically important cell-types.  In the past decade, we have developed the stomatal lineage into a conceptual and technical framework for the study of cell fate, stem-cell self-renewal and cell polarity. Currently, we are especially interested in: (1) using single-cell technologies to capture transcriptomic and chromatin state information about cells as they transit through various identities (stem cell-like, committed, differentiated, and reprogrammed); (2) using new ‘in vivo biochemical’ approaches to identify transcription factor modules in the nuclear and cell polarity complexes at the plasma membrane, and to determine how these complexes guide changes in cell shape, size and fate; (3) computational modeling of pattern formation in the epidermis, and (4) testing how environmental information impacts developmental choices and robustness.

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.

We discover and elucidate new Ca2+-regulated signaling pathways in humans by studying calcineurin, the conserved Ca2+/calmodulin-regulated protein phosphatase. The calcineurin phosphatase dephosphorylates proteins only when Ca2+ signaling is triggered, for example by a hormone, growth factor, neurotransmitter etc. Previous work from the Cyert lab showed how calcineurin allows yeast cells to survive environmental stress (Goldman et al, 2014, Molecular Cell). Currently, we are studying human calcineurin which is ubiquitously expressed and plays critical roles throughout the body, but especially in the nervous, cardiac and immune systems. Calcineurin is best known for activating the adaptive immune response by dephosphorylating the NFAT transcription factors, and is the target of widely prescribed immunosuppressant drugs, FK506 (tacrolimus) and Cyclosporin A. However, these drugs cause many adverse effects due to inhibition of calcineurin in non-immune tissues, where the majority of calcineurin substrates and functions remain to be discovered. We are using a variety of experimental and computational strategies to systematically map human calcineurin signaling pathways in healthy and diseased cells. These rely on identifying Short Linear peptide Motif (SLiMs), i.e. highly variable sequences that reside in regions of intrinsic disorder and mediate specific interactions of substrates and regulators with calcineurin. These approaches have revealed surprising roles for calcineurin  that we are currently studying: in Notch signaling, trafficking though nuclear pores, at centrosomes/cilia, and in regulating phosphoinositide signaling at membranes. A new project is studying calcineurin's role in pancreatitis, where we are identifying calcineurin substrates that mediate the major pathophysiological events that occur during pancreatitis.  We are also interested in understanding how reversible protein lipidation (palmitoylation) is regulated and how palmitoylation impacts calcineurin signaling at membranes by modifying calcineurin itself and some of its regulators.

To learn more about our studies, see our recent papers: Wigington, Roy et al, 2020, Molecular Cell (https://pubmed.ncbi.nlm.nih.gov/32645368/) and Ulengin-Talkish et al, Nature Communications (https://www.nature.com/articles/s41467-021-26326-4).

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.

The Jacobs-Wagner lab has two main research interests:

1. They examine the general principles and spatiotemporal mechanisms by which bacterial cells replicate. Bacteria are infamous for their remarkable ability to proliferate. Yet, despite their medical and agricultural importance, little is known about how bacteria control and integrate their growth, cell morphogenesis and cell cycle functions. The Jacobs-Wagner lab addresses this fundamental question at all levels, from a systems-level perspective down to the physical mechanisms, using genetics and cutting-edge quantitative microscopy techniques. The primary model bacterial systems are Escherichia coli and Caulobacter crescentus. Microbiologists, physicists and individuals with expertise in quantitative biology are encouraged to contact us.
2. Recently, the Jacobs-Wagner lab expanded their interests to the Lyme disease agent Borrelia burgdorferi, revealing unsuspected ways by which this pathogen grows and causes disease. Lyme disease is tick-born disease whose incidence and geographic distribution have rapidly increased over the years, in part due to climate change. The Jacobs-Wagner lab has developed genetic and cell biological tools as well as mass spectrometry and microscopy protocols to study this important human pathogen, from its unique cell biology to its pathogenesis. Individuals with expertise in microbial pathogenesis or immunology are encouraged to contact us.
    

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

The Kopito laboratory seeks a molecular understanding of how cells maintain the fidelity of their proteomes. Unlike DNA, which can be repaired if damaged or incorrectly made, proteins cannot be mended. Instead, damaged or incorrectly synthesized proteins must be rapidly and efficiently destroyed lest they form toxic aggregates. Our laboratory use state-of-the-art cell biological, genetic and systems-level approaches to understand how proteins are correctly synthesized, folded and assembled in the mammalian secretory pathway, how errors in this process are detected and how abnormal proteins are destroyed by the ubiquitin-proteasome system.