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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 most are actively recruiting. As you look for potential postdoc mentors, consider how faculty research interests align with your own.

For an overview of how the Faculty Nomination/Selection process works, please view our Stanford PRISM Faculty Guide.

As a rule of thumb, we recommend starting with the faculty listed on this page and then expanding your search to other faculty across the university. This is not intended to be a comprehensive list of all faculty eligible to appoint postdocs through PRISM.

For School of Medicine faculty, browse SoM Departments or find details about individual faculty members in the School of Medicine via Community Academic Profiles (CAP).

For faculty outside of the School of Medicine, browse departments in the Natural SciencesEarth Sciences, or Engineering and find details about individual faculty members in these areas via Stanford Profiles.

Please check back often -- Faculty/Lab profiles may be added or edited throughout the application period. 

 

PRISM Faculty Opt-In   Displaying 1 - 50 of 415
Department:
PRISM mentor Research Interests

Utkan Demirci


Professor, Department of Radiology , Canary Interim Chief and Director, Electrical Engineering (by courtesy)
View in Stanford Profiles


Last Updated: June 24, 2022

Maya Kasowski


Assistant Professor
View in Stanford Profiles


Last Updated: June 23, 2022

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.

Department: Anesthes, Periop & Pain Med
PRISM mentor Research Interests

Nima Aghaee Pour

Anesthes, Periop & Pain Med
Assistant Professor
View in Stanford Profiles


Last Updated: August 11, 2020

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
View in Stanford Profiles


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
View in Stanford Profiles


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

Vivianne Tawfik

Anesthes, Periop & Pain Med
Assistant Professor
View in Stanford Profiles


Last Updated: September 18, 2020

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.

Department: Biochemistry
PRISM mentor Research Interests

Rhiju Das

Biochemistry
Associate Professor
View in Stanford Profiles


Last Updated: August 11, 2020

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
View in Stanford Profiles


Last Updated: September 02, 2020

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.

Suzanne Pfeffer

Biochemistry
Professor
View in Stanford Profiles


Last Updated: August 28, 2020

Activating mutations in the LRRK2 kinase cause Parkinson's disease, 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.  We are also studying  cholesterol transport out of lysosomes and lysosome dysfunction in neurodegenerative disease.

Rajat Rohatgi

Biochemistry, Med: Oncology
Associate Professor
View in Stanford Profiles


Last Updated: November 29, 2021

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, Med: Oncology
Associate Professor
View in Stanford Profiles


Last Updated: August 06, 2020

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.

Rajat Rohatgi

Biochemistry, Med: Oncology
Associate Professor
View in Stanford Profiles


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.

Julia Salzman

Biochemistry, Biomedical Data Sciences
Assistant Professor
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Last Updated: August 06, 2020

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

Aaron Straight

Biochemistry
Associate Professor
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Last Updated: September 18, 2020

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, Pathology, Microbiology and Immunology
Associate Professor
View in Stanford Profiles


Last Updated: August 06, 2020

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
Department: Bioengineering
PRISM mentor Research Interests

Michael Fischbach

Bioengineering
Associate Professor
View in Stanford Profiles


Last Updated: September 18, 2020

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, Genetics
Assistant Professor
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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

Sarah Heilshorn

Materials Sci & Engineering, Bioengineering, Chemical Engineering
Professor, Director, Geballe Laboratory for Advanced Materials (GLAM)
View in Stanford Profiles


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

Craig Levin

Radiology, Physics, Electrical Engineering, Bioengineering, Radiology-MIPS, Stanford Cancer Center, Cardiovascular Med Institute, Neuroscience Institute
Professor
View in Stanford Profiles


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

Pediatrics, Bioengineering, Mechanical Engineering, Institute for Computational and Mathematical Engineering, Cardiovascular Med Institute
Associate Professor
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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

Mark Skylar-Scott

Bioengineering
Assistant Professor
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Last Updated: March 03, 2021

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.

Bo Wang

Bioengineering
Assistant Professor
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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
View in Stanford Profiles


Last Updated: September 18, 2020

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

Orthopedic Surgery, Materials Sci & Engineering, Bioengineering
Associate Professor
View in Stanford Profiles


Last Updated: August 06, 2020

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

Department: Biology
PRISM mentor Research Interests

Christopher Barnes

Biology, Structural Biology
Assistant Professor
View in Stanford Profiles


Last Updated: August 24, 2021

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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Last Updated: December 02, 2021

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.

Dominique Bergmann

Biology
Professor
View in Stanford Profiles


Last Updated: September 18, 2020

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.

Xiaoke Chen

Biology
Associate Professor
View in Stanford Profiles


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


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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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).

  • Other

Martha Cyert

Biology
Professor
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Last Updated: August 06, 2020

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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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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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.

Christine Jacobs-Wagner

Biology
Professor
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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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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


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
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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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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, Woods Institute
Associate Professor
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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. 

Ashby Morrison

Biology
Associate Professor
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Last Updated: August 06, 2020

The regulation of chromatin structure is essential for all eukaryotic organisms. Our research interests are to determine the contribution of chromatin to mechanisms that maintain genomic integrity and metabolic homeostasis in the context of disease and development. We utilize a varied experimental approach that includes computational, biochemical, molecular and cellular assays in both yeast and mammalian systems to ascertain the contribution of chromatin remodelers and histone modifiers to carcinogen susceptibility and metabolic gene expression. We hope to contribute to the formulation of epigenetic therapies that treat genomic and metabolic dysfunction, which influence cancer, heart disease, and diabetes to name a few.

  • Cancer Etiology, Prevention, Detection and Diagnosis
  • Cardiovascular Disease Prevention Training Program
  • Diabetes, Endocrinology and Metabolism
  • Institutional Training Grant in Genome Science
  • Postdoctoral Training in the Radiation Sciences
  • Stanford Training Program in Aging Research
  • Stanford Training Program in Lung Biology

Lauren O'Connell

Biology, Neuroscience Institute
Assistant Professor


Last Updated: August 10, 2020

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

Kabir Peay

Biology
Associate Professor
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Last Updated: August 10, 2020

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.

Naima Sharaf

Biology
Assistant Professor
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Last Updated: August 25, 2021

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

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

Jan Skotheim

Biology
Professor
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Last Updated: August 10, 2020

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.

Alice Ting

Biology, Genetics, Chemistry
Professor
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Last Updated: January 12, 2022

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

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

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

 

Zhiyong Wang

Biology
Associate Professor
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Last Updated: October 02, 2020

The goal of our research is to illucidate the signaling mechanisms that regulate plant growth and environmental responses. Plants have remarkable ability to alter growth and development in response to environmental signals. In fact, this ability is essential for their survival in nature as sessile organisms and is also a major target for breeding high-yield crops. My lab has dissected the signaling networks that integrate hormonal (brassinosteroid, auxin, gibberellin), environmental (light, temperature, pathogens), and nutritional (sugar) signals in regulating plant growth. We use a wide range of approaches including proteomic, genomic, and genetic approaches in Arabidopsis and algae. Our research has focused on the brassinosteroid (BR) signaling pathway, which is the best understood receptor kinase signaling pathway in plants. We have elucidated how this steroid signal is transduced from the receptor kinase BRI1 to the transcription factor BZR1, and how BR crosstalks with other growth hormones, light, temperature, pathogen, and sugar signals in optimizing shoot and root growth. Current focuses of our lab include: (1) How does nutrient signaling through O-linked glycosylation (O-GlcNAc and O-fucose modifications) regulate plant growth? (2) How does sugar-dependent O-glycosylation crosstalk with BR-dependent phosphorylation in regulating transcription, RNA splicing, and translation? (3) How do GSK3 kinase and BSU phosphatase regulate cell division and membrane trafficking? (4) How do receptor kinases maintain cell wall integrity during cell growth and under stress?

Department: Cardiothoracic Surgery
PRISM mentor Research Interests

Ngan Huang

Cardiothoracic Surgery
Assistant Professor
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Last Updated: August 11, 2020

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 differentiation. 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 implantation. Current projects focus on the role of naturally-derived ECMs to enhance endothelial differentiation of induced pluripotent stem cells on two-dimensional ECM microarrays of varying substrate rigidity. The knowledge gained from understanding cell-ECM interactions are applied towards engineering prevascularized skeletal or cardiac muscle constructs using nanotopographical cues derived from nanofibrillar ECMs. We have an opening currently for a postdoctoral fellow to develop vascularized skeletal muscle tissues for treatment of traumatic muscle injury.

  • Mechanisms in Innovation in Vascular Disease
  • Training in Myocardial Biology at Stanford (TIMBS)

Ioannis Karakikes

Cardiothoracic Surgery
Assistant Professor
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Last Updated: December 02, 2021

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.

Department: Chemical and Systems Biology
PRISM mentor Research Interests

James Chen

Chemical and Systems Biology
Professor
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Last Updated: September 18, 2020

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.

Gary Peltz

Chemical and Systems Biology
Professor
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Last Updated: January 12, 2022

The Peltz laboratory develops and uses state of the art genetic, genomic and stem cell technologies in its research programs. These methodologies are used to discover the mechanisms mediating disease susceptibility and drug response, and to develop new therapies. As one example, we developed a novel computational genetic analysis method, which has identified genetic factors affecting disease susceptibility and biomedical responses in mouse models. One of the genetic findings is the basis for an ongoing clinical trial that tests a new therapy for preventing opiate withdrawal from occuring in babies born to mothers that take opiates. Over 25 genetic factors affecting susceptibility to drug addiction, chronic pain, infectious diseases, and others have been identified. An ongoing effort is now analyzing 10000 biomedical responses in panels of inbred mouse strains. Single-cell RNA sequencing and metabolic analysis are used to identify developmental and disease-causing pathways. Stem cell-based methods for liver engineering are also used. As examples of this, the Peltz lab has produced mice with humanized livers that are used to improve drug safety; developed methods to engineer human liver from adipocyte stem cells; and to produce human liver organoids from stem cells, which are used for studying the pathogenesis of human genetic liver diseases.

  • Anesthesia Training Grant in Biomedical Research

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