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PRISM Mentors

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PRISM supports all faculty in recruiting postdocs. The faculty listed on this page have expressed special interest in the PRISM program and may be actively recruiting. This is one of many ways to identify potential postdoc mentors; also review the guidance and links in the PRISM Application Guide for other ways to explore Stanford faculty. As you look for potential postdoc mentors, consider how faculty research interests align with your own.

Faculty: to create a profile, click "Log In" at the top right corner, then the "PRISM Faculty Opt In" button below. To edit an existing profile, click "Log In" at the top right corner, then the "Edit" button under your name/department/URL.

 

Aeronautics and Astronautics
PRISM mentor Research Interests

Ken Hara

Aeronautics and Astronautics
Assistant Professor
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Aeronautics and Astronautics

Last Updated: August 16, 2023
Anesthes, Periop & Pain Med
PRISM mentor Research Interests

Nima Aghaee Pour

Anesthes, Periop & Pain Med
Assistant Professor
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Anesthes, Periop & Pain Med

Last Updated: February 23, 2024

We are a machine learning lab with a primary focus on predictive modeling of clinical outcomes using multiomics biological assays. Our research covers a wide range of unconventional yet high-impact topics ranging from space medicine to the integration of mental health, physical health, immune fitness, and nutrition in various clinical settings. We are primarily a computational immunology research group but depending on the problem at hand, our datasets include clinical measurements, readouts from advanced wearable technologies, and various genomics and proteomics assays.
 
Our group has a strong commitment to translating research findings into actionable products. We encourage (and financially support) our postdoctoral fellows to receive extensive training in entrepreneurship and business management from Stanford’s School of Business. This provides an excellent opportunity for a candidate who is not only interested in participating in state-of-the-art academic research, but is also interested in exploring industrial and entrepreneurial career trajectories.

Eric Gross

Anesthes, Periop & Pain Med
Assistant Professor
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Anesthes, Periop & Pain Med

Last Updated: August 11, 2020

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.

  • Anesthesia Training Grant in Biomedical Research

Sean Mackey

Anesthes, Periop & Pain Med
Professor
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Anesthes, Periop & Pain Med

Last Updated: August 06, 2020

Mission of our group is to “Predict, prevent and alleviate pain”. Broad range of human pain research topics including neuroimaging, transcranial magnetic stimulation, EEG, psychophysics, patient outcomes, learning healthcare systems across many NIH funded projects. Projects include mechanistic characterization of pain to novel treatment developments.

  • Anesthesia Training Grant in Biomedical Research
  • Interdisciplinary Research Training in Pain and Substance Use Disorders

Gary Peltz

Anesthes, Periop & Pain Med
Professor
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Anesthes, Periop & Pain Med

Last Updated: August 15, 2023

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. 

  • Anesthesia Training Grant in Biomedical Research

Laura Simons

Anesthes, Periop & Pain Med
Professor
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Anesthes, Periop & Pain Med

Last Updated: August 24, 2023

The primary goal of this laboratory is to promote the health and well being of children and adolescents with chronic pain and their families. In line with this goal, research projects focus on biological, neurological, cognitive, affective, and social risk and resiliency factors of the pain experience. Projects include brain imaging, longitudinal clinical cohort, and treatment intervention studies.

  • Anesthesia Training Grant in Biomedical Research

Vivianne Tawfik

Anesthes, Periop & Pain Med
Assistant Professor
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Anesthes, Periop & Pain Med

Last Updated: February 23, 2024

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.

Biochemistry
PRISM mentor Research Interests

Rhiju Das

Biochemistry
Associate Professor
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Biochemistry

Last Updated: February 23, 2024

We develop algorithms to predict and design the structures and energetics of RNAs and RNA/protein complexes. We test these ideas through community-wide blind trials; by enhancing NMR, crystallographic, and cryoelectron microscopy methods; and by designing new complexes. Upcoming projects involve directly visualizing how natural RNA machines work inside human cells and designing molecules that might enable RNA-based optogenetics, self-replication, and sequence-controlled synthesis of novel polymers.

Dan Herschlag

Biochemistry
Professor
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Biochemistry

Last Updated: May 31, 2024

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.

Flora Novotny Rutaganira

Biochemistry
Assistant Professor
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Biochemistry

Last Updated: August 15, 2023

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.

Suzanne Pfeffer

Biochemistry
Professor
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Biochemistry

Last Updated: August 15, 2023

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.

Rajat Rohatgi

Biochemistry
Associate Professor
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Biochemistry

Last Updated: July 14, 2022

A central focus of our laboratory is to uncover new regulatory mechanisms in cell-cell communication system, understand how these mechanisms are damaged in disease states and devise strategies to repair their function. We are actively recruiting post-doctoral fellows to join projects in the following areas:
--Signaling pathways implicated in birth defects, cancer and regeneration.
--Regulation of signaling and development by primary cilia.
--Genetic and biochemical dissection of lipid pathways that regulate signaling, development and cancer.
--The role of biomolecular condensates in cancer and cancer therapeutics.
We strive to provide a supportive, inclusive, organized and collaborative lab environment that maximizes the ability to tackle important biomedical problems. Career development is a priority. Nearly all prior lab members have obtained multiple publications and top-level competitive positions in academics or in the biotech industry.


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

Rajat Rohatgi

Biochemistry
Associate Professor
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Biochemistry

Last Updated: January 12, 2022

The overall goal of our laboratory is to uncover new regulatory mechanisms in signaling systems, to understand how these mechanisms are damaged in disease states and how to devise new new strategies to repair their function.  Specific areas are highlighted below:

1. The Hedgehog and WNT pathways, two cell-cell communication systems that regulate the formation of most tissues during development. These same pathways play central roles in tissue stem-cell function and organ regeneration in adults. Defects in these systems are associated with degenerative conditions and cancer.

2. Signal transduction at the primary cilium and the mechanism of cilia-associated human diseases. Primary cilia are solitary hair-like projections found on most cells in our bodies that function as critical hubs for signal transduction pathways (such as Hedgehog). Over fifty human genetic diseases, called “ciliopathies,” are caused by defects in cilia. Patients with ciliopathies can show phenotypes in nearly all organ systems, suffering from abnormalities ranging from birth defects to obesity.

3. Regulation of signaling pathways by endogenous lipids. The landscape of endogenous small-molecules and their biological functions remains a terra incognita, one that provides many opportunities to discover new regulatory layers in signaling pathways and other membrane dependent processes.

4. Biomolecular condensates in cancer and cancer therapeutics. The formation of reversible, membrane-less compartments in cells by the segregation of proteins into liquid phases, hydrogels or amyloid-like assemblies is an emerging principle of cellular organization. Emerging evidence shows that some cytotoxic drugs used in oncology can accumulate in and disrupt the biophysical properties of these condensates. A future challenge is to develop strategies to target such membraneless compartments (such as the nucleolus) for effective and safe cancer therapies.

5. Cellular adaptation to extreme tissue environments. Many cells in our bodies can be considered “extremophiles,” charged with maintaining homeostasis in the face of an environment containing markedly non-physiological concentrations of ions, small molecules and toxins. For instance, cells in the kidney medulla face tissue concentrations of ions, urea and other small molecules that are several-fold higher than blood.

Rajat Rohatgi

Biochemistry
Associate Professor
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Biochemistry

Last Updated: July 14, 2022

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.

Julia Salzman

Biochemistry
Assistant Professor
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Biochemistry

Last Updated: July 13, 2022

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

Aaron Straight

Biochemistry
Associate Professor
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Biochemistry

Last Updated: February 23, 2024

Our laboratory studies the dynamics and organization of eukaryotic genomes. Every eukaryotic cell must compact its DNA into the nucleus while maintaining the accessibility of the DNA to the replication, repair, expression and segregation machinery. Eukaryotes accomplish this feat by assembling their genomes into chromatin and folding that chromatin into functional compartments. We are studying four key processes in the eukaryotic nucleus: 1) the genetic and epigenetic basis for centromere formation that enables chromosome segregation, 2) the role of noncoding RNAs in structuring the genome and regulating gene expression, 3) the formation of silent heterochromatin and its role in genome organization and 4) the activation of the embryonic genome at the maternal to zygotic transition. We rely on biochemistry, quantitative microscopy and genomics to probe genome dynamics in vitro and in living systems. Our goal is to uncover the core principles that organize eukaryotic genomes and to understand how genome organization controls organismal function.

Ellen Yeh

Biochemistry
Associate Professor
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Biochemistry

Last Updated: July 14, 2022

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.

  • Molecular Basis of Host Parasite Interaction
Bioengineering
PRISM mentor Research Interests

Jennifer Brophy

Bioengineering
Assistant Professor
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Bioengineering

Last Updated: August 15, 2023

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

Wah Chiu

Bioengineering
Wallenberg-Bienenstock Professor
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Bioengineering

Last Updated: August 18, 2023

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.

  • Multi-Disciplinary Training Program in Cardiovascular Imaging at Stanford

Michael Fischbach

Bioengineering
Associate Professor
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Bioengineering

Last Updated: February 23, 2024

Small molecules from the human microbiota. Many of the most widely used human medicines come from soil and marine bacteria, including treatments for cancer, infectious disease, diabetes, and organ transplant. We have recently found that bacteria from a surprisingly underexplored niche -- the human body -- are prolific producers of drug-like small molecules. We are identifying small molecules from gut- and skin-associated bacteria, studying their biosynthetic genes, and characterizing the roles they play in human biology and disease. 
 
Using synthetic ecology to control microbiome metabolism. One of the most concrete contributions the microbiome makes to human biology is to synthesize dozens of metabolites, many of which accumulate in human tissues at concentrations similar to what is achieved by a drug. We are engineering gut and skin bacterial species to produce new molecules, and constructing synthetic communities whose molecular output is completely specified.

Polly Fordyce

Bioengineering
Assistant Professor
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Bioengineering

Last Updated: November 11, 2021

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

  • Institutional Training Grant in Genome Science

Matthias Garten

Bioengineering
Assistant Professor
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Bioengineering

Last Updated: August 31, 2023

With a creative, collaborative, biophysical mindset, we aim to understand the ability of parasites to interface with their host-cell to a point at which we can exploit the mechanisms not only for finding cures against the disease the parasites cause but also to make parasite mechanisms a tool that we can use to engineer the host’s cells. By developing approaches that allow a quantitative understanding and manipulation of molecular transport our research transforms parasites from agents of disease to tools for health.

Specifically, we are studying how the malaria parasite takes control over red blood cells. By learning the biophysical principles of transport in between the host and the parasite we can design ways to kill the parasite or exploit it to reengineer red blood cells. The transport we study is broadly encompassing everything from ions to lipids and proteins. We use variations of quantitative microscopy and electrophysiology to gain insight into the unique strategies the parasite evolved to survive.

  • Molecular Basis of Host Parasite Interaction

Sarah Heilshorn

Bioengineering
Professor, Director, Geballe Laboratory for Advanced Materials (GLAM)
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Bioengineering

Last Updated: December 01, 2021

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

  • Mechanisms in Innovation in Vascular Disease

Rogelio Hernandez-Lopez

Bioengineering
Assistant Professor
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Bioengineering

Last Updated: July 08, 2022

The Hernandez-Lopez Lab works at the interface of mechanistic, synthetic, and systems biology to understand and program cellular recognition, communication, and organization. We are currently interested in engineering biomedical relevant cellular behaviors for cancer immunotherapy. We are also launching new multidisciplinary projects.

We are looking for outstanding, motivated graduate students and physician-scientists from diverse fields who are interested in joining our interdisciplinary research program. Postdoctoral candidates with expertise (or an interest in learning) preclinical animal models of disease or structural biology (cryo-EM) are particularly encouraged.

  • Institutional Training Grant in Genome Science

Michael Jewett

Bioengineering
Professor
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Bioengineering

Last Updated: January 23, 2024

We develop data-driven, multiplexed methods to elucidate fundamental principles about how the living world works. We use the knowledge from these insights to develop cell-free biotechnologies for decentralized biomanufacturing, portable diagnostics, and educational kits to serve human needs. A key feature of our work is an emphasis on advancing and applying our capacity to partner with biology to make what is needed, where and when it is needed, on a sustainable and renewable basis. Our work holds promise to transform bioengineering applications in health, manufacturing, sustainability, and education, anywhere on earth and even beyond.

Craig Levin

Bioengineering
Professor
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Bioengineering

Last Updated: March 16, 2022

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.

  • Cancer-Translational Nanotechnology Training Program (Cancer-TNT)
  • Multi-Disciplinary Training Program in Cardiovascular Imaging at Stanford
  • Stanford Cancer Imaging Training (SCIT) Program
  • Stanford Molecular Imaging Scholars (SMIS)

Alison Marsden

Bioengineering
Associate Professor
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Bioengineering

Last Updated: August 09, 2020

The Cardiovascular Biomechanics Computation Lab  develops fundamental computational methods for the study of cardiovascular disease progression, surgical methods, treatment planning and medical devices.  We focus on patient-specific modeling in pediatric and congenital heart disease, as well as adult cardiovascular disease.  Our lab bridges engineering and medicine through the departments of Pediatrics, Bioengineering, and the Institute for Computational and Mathematical Engineering. We develop the SimVascular open source project.

  • Mechanisms in Innovation in Vascular Disease
  • Multi-Disciplinary Training Program in Cardiovascular Imaging at Stanford

Lei Stanley Qi

Bioengineering
Associate Professor
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Bioengineering

Last Updated: January 27, 2023

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.

Mark Skylar-Scott

Bioengineering
Assistant Professor
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Bioengineering

Last Updated: May 31, 2024

The Skylar-Scott Lab specializes in cardiovascular tissue biomanufacturing, seeking to push the complexity and scale at which tissue can be designed and manufactured on demand. By integrating high-throughput culture of designer organoids with new machines and methods for advanced 3D bioprinting, our laboratory seeks to enhance the maturation and function of vascularized cardiac tissues in vitro and in vivo.

Our lab is embedded at the intersection of synthetic biology, tissue engineering, and 3D printing. We are always seeking new students and postdocs with a demonstrated passion for rethinking how we make things, with relevant expertise in bioengineering, mechanical engineering, or materials science.

Sindy Tang

Bioengineering
Associate Professor
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Bioengineering

Last Updated: January 27, 2024

From finger prick tests for blood glucose monitoring to industrial-scale drug screening in pharmaceutical companies, the ability to extract information from scarce volumes of samples quickly and cheaply is key to effective disease management and drug discovery. To this end, microfluidics offers major advantages over conventional liquid handling due to drastic reduction in reagent volume and the precise control of single cells, microtissues, and their microenvironments. The micro-nano-bio lab under the direction of Dr. Sindy Tang aims to develop innovative micro and nanoscale devices that harness mass transport phenomena to enable precise manipulation, measurement, and recapitulation of biological systems, in order to understand the "rules of life" and accelerate precision medicine and material design for a future with better health and environmental sustainability. Our approach involves building new tools to probe biological systems (from single cells to microtissues), and engineering smart materials, synthetic cells & tissues with properties that mimic some of the amazing properties biological systems have. Current research projects include:

 

  • Understanding and accelerating the diagnosis of allergic diseases
  • Biomechanics of single cell wound resilience
  • Tools for advancing cancer research
  • Bottom-up construction of biological systems

Sindy Tang

Bioengineering
Associate Professor
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Bioengineering

Last Updated: August 24, 2023

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.

Bo Wang

Bioengineering
Assistant Professor
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Bioengineering

Last Updated: January 26, 2022

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.  

  • Other

Bo Wang

Bioengineering
Assistant Professor
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Bioengineering

Last Updated: July 14, 2022

Flatworms include more than 44,000 parasites, many of which are pathogenic to humans or livestock, with flukes, tapeworms, and hookworms as notorious representative species. They typically transmit through multiple hosts using several drastically different body plans specialized for infecting and reproducing within each host. Although flatworms’ complex life cycles were established over a century ago, little is known about the cells and genes they use to optimize their transmission potential, thereby limiting our ability to develop effective therapeutic and preventive strategies. We aim to develop a comprehensive cellular and molecular understanding of the stereotypical life cycle of a blood fluke, Schistosoma mansoni, and identify novel targets to block it. Schistosomes cause one of the most prevalent but neglected infectious diseases, schistosomiasis. With over 250 million people infected and a further 800 million at risk of infection, schistosomiasis imposes a global socioeconomic burden comparable to that of tuberculosis, HIV/AIDS, and malaria. This project will use novel single-cell technologies to build a schistosome "cell atlas", and map the developmental states of their stem cells as they produce all other cell types in the schistosome body plans.

Peter Yang

Bioengineering
Associate Professor
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Bioengineering

Last Updated: February 23, 2024

Biomaterials, medical devices, drug delivery, stem cells and 3D bioprinting for musculoskeletal tissue engineering

Biology
PRISM mentor Research Interests

Christopher Barnes

Biology
Assistant Professor
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Biology

Last Updated: July 22, 2022

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.

Dominique Bergmann

Biology
Professor
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Biology

Last Updated: February 23, 2024

The overall goal of my research program is to understand how stem cell-like populations are created and maintained in the context of an intact and environmental responsive tissue.  We use the Arabidopsis stomatal lineage for these studies as this epidermal cell lineage distills many of the 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 new 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 plant-specific cell polarity complexes and how these 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.

Dominique Bergmann

Biology
Professor
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Biology

Last Updated: February 23, 2024

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.

Xiaoke Chen

Biology
Associate Professor
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Biology

Last Updated: January 12, 2022

Our lab study neural circuits underlying motivated behaviors and how maladaptive change in these circuits causing neuropsychiatric disorders. We currently focuse on pain and addiction. Both conditions trigger highly motivated behaviors, and the transition to chronic pain and to compulsive drug use involves maladaptive changes of the underlying neuronal circuitry. 

Neuroal circuits mediating opioid addiction:

We established the paraventricular nucleus of the thalamus (PVT) to nucleus accumbens (NAc) pathway as a promising target for treating opioid addiction (Zhu et al., 2016), and revealed the PVT’s role in tracking the dynamics of behavioral relevance and gating associative learning (Zhu et al., 2018).  Using brainwide activity mapping, we identifed a distributed neuronetwork including 23 brain regions that might involve in storing drug-associated memory (Keyes et al, 2020). Ongoing work in the lab is to examining how   

Neuroal circuits underlying descending pain modulation:

We developed a battery of viral, genetic and imaging tools and gained robust access of the mu-opioid receptor expressing spinal cord projecting neurons in the rostromiddel medulla (RVM). We found that these neurons has limited contirbution to nociception in normal mice but is essential for the initiation and maintenance of nerve injury induced chronic pain. We are profiling nerve injury caused gene expression changes in these neurons with the goal to identify key molecular plays that engages these neurons in chronic pain. Based on our finding, we will develop gene therapy reagents and small molecues to treat chronic pain.     

  • Interdisciplinary Research Training in Pain and Substance Use Disorders

Jonas Cremer

Biology
Assistant Professor

Biology

Last Updated: June 23, 2022

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.

Martha Cyert

Biology
Professor
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Biology

Last Updated: January 26, 2022

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).

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Martha Cyert

Biology
Professor
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Biology

Last Updated: July 13, 2022

By studying calcineurin, the conserved Ca2+/calmodulin-regulated protein phosphatase, we aim to discover and elucidate new Ca2+-regulated signaling pathways in humans. 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 discovered 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. We have uncovered surprising roles for calcineurin in Notch signaling, regulation of transport though nuclear pores, and at centrosomes. See our recent paper (Wigington, Roy et al, 2020, Molecular Cell) to learn more about our studies.

José Dinneny

Biology
Associate Professor
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Biology

Last Updated: December 01, 2021

In the next 50 years, one of the greatest advances we can make for global human health is the realization of a society that is fully sustainable. My research aims to improve agricultural sustainability by using a holistic approach that integrates across genetic, cellular and organismal scales to understand how plants survive stressful environments (Dinneny, 2015a; 2019). Prior research has explored water-stress responses at unparalleled spatial and temporal resolution, and identified the endodermal tissue layer as a critical signaling center for controlling growth and tissue differentiation in roots (Duan et al., 2013; Geng et al., 2013; Dinneny et al., 2008). The discovery of novel adaptive mechanisms used by roots to capture water established potential targets for breeding to improve water use efficiency (Bao et al., 2014; Sebastian et al., 2016). The invention of imaging methods enabled multidimensional studies of plant acclimation and illuminated our understanding of organ system growth from germination to senescence (Rellán-Álvarez et al., 2015; Sebastian et al., 2016). Physiological and molecular insight has been gained in understanding how plants sense water availability through computational modeling of tissue hydraulics (Robbins and Dinneny, 2015, 2018). Additionally, fine-scale biomechanical measurements identified a novel mechanism by which salinity damages cells through its effects on cell-wall integrity (Feng et al., 2018). I have paired my research with a personal passion for improving the education of young plant scientists, engaging lawmakers through science policy, and by being a vocal advocate for the broad deployment of agricultural biotechnology (Fahlgren et al., 2016, Friesner et al., 2021).

Department URL:
https://biology.stanford.edu/people/jose-r-dinneny

Jessica Feldman

Biology
Associate Professor
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Biology

Last Updated: November 11, 2021

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.

Hunter Fraser

Biology
professor
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Biology

Last Updated: January 27, 2023

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.

Christine Jacobs-Wagner

Biology
Professor
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Biology

Last Updated: December 02, 2021

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/

 

Ron Kopito

Biology
Professor
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Biology

Last Updated: July 27, 2021

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.

  • Epilepsy Training Grant
  • Other

Ron Kopito

Biology
Professor
View in Stanford Profiles

Biology

Last Updated: December 01, 2021

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.

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

  • Epilepsy Training Grant
  • Stanford Training Program in Aging Research

Ron Kopito

Biology
Professor
View in Stanford Profiles

Biology

Last Updated: August 11, 2020

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.

  • Institutional Training Grant in Genome Science
  • Stanford Training Program in Aging Research

Liqun Luo

Biology
Professor
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Biology

Last Updated: February 03, 2022

The human brain contains about 100 billion neurons, each making thousands of synaptic connections. While individual neurons can themselves perform sophisticated information processing, it is the assembly of neurons into circuits via specific patterns of synaptic connections that endows our brain with the computational capacity to sense, act, think, and remember.

How are neurons organized into specialized circuits to perform specific functions? How are these circuits assembled during development? We are investigating these questions in the brains of the fruit fly (~100 thousand neurons) and mouse (~100 million neurons). We have developed molecular-genetic and viral tools, and are combining them with transcriptomic, proteomic, physiological, and behavioral approaches to study these problems.

  • Epilepsy Training Grant

Erin Mordecai

Biology
Associate Professor
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Biology

Last Updated: January 12, 2022

Our research investigates how environmental changes like climate and land use change are affecting infectious diseases in humans and wildlife. We use tools from disease ecology, including mathematical and statistical models, health surveillance data, remotely sensed data, laboratory experiments, and field surveys to better understand the mechanisms by which changes in temperature and habitat affect vectors and disease transmission. 

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