PRISM Mentors

The goal of our laboratory is to develop molecular technologies for mapping cells and functional circuits. At the sub-cellular scale, maps document the spatial organization of proteins, RNA, DNA, and metabolites with nanometer precision and temporal acuity on the order of seconds. Maps also chart the connectivity between these molecules, elucidating the circuits and signaling processes that give rise to function. Beyond the single cell, we also strive to map cellular ensembles, such as brain tissue. Can we create tools that contribute to the construction of cell and tissue atlases, and can we map the cellular circuits that give rise to function and behavior? To achieve these goals, our laboratory employs a wide variety of approaches, including directed evolution, protein engineering, organic synthesis, computational design, mass spec proteomics, and single-cell RNA seq. Our work lies at the interface between chemical biology, genetics, biophysics, cell biology, and neuroscience.

Our group in Stanford's Department of Earth System Science, led by Prof. Alexandra Konings, studies how ecosystems and the carbon cycle respond to variations in water availability at large scales, and how ecosystems will change under future climate. Our research questions principally focus on plant hydraulics, water-carbon coupling in the tropics, and the role of spatial variability in plant traits. In order to answers these questions, we primarily use remote sensing data analysis and model development. In particular, we often use new microwave measurements of vegetation water content. We believe that a deep understanding of remote sensing techniques helps us do better science and therefore also work on developing new remote sensing datasets and their validation.

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

Our translational research laboratory endeavors to bring breakthroughs in stem cell biology and tissue engineering to clinical ophthalmology and reconstructive surgery. Over 6 million people worldwide are afflicted with corneal blindness, usually caused by chemical and thermal burns, ocular cicatricial pemphigoid, Stevens-Johnson syndrome, microbial infections, or chronic inflammation. These injuries often result in corneal vascularization, conjunctivalization, scarring, and opacification from limbal epithelial stem cell (LSC) deficiency (LSCD), for which there is currently no durable treatment.

The most promising cure for bilateral LSCD is finding an autologous source of limbal epithelial cells for transplantation. Utilizing recent advances in the field of induced pluripotent stem cells (iPSC), our research aims to create a reliable and renewable source of limbal epithelial cells for potential use in treating human eye diseases. These cells will be grown on resorbable biomatrices to generate stable transplantable corneal tissue. These studies will serve as the basis for human clinical trials and make regenerative medicine a reality for those with sight-threatening disease. On a broader level, this experimental approach could serve as a paradigm for the creation of other transplantable tissue for use throughout the body. Stem cell biology has the potential to influence every field of medicine and will revolutionize the way we perform surgery.

Our group combines computational and experimental techniques to study the cellular organization of complex tissues, with a focus on determining the phenotypic diversity and clinical significance of tumor cell subsets. We have a particular interest in developing innovative data science tools that illuminate the cellular hierarchies and stromal elements that underlie tumor initiation, progression, and response to therapy. As part of this focus, we develop new algorithms to resolve cellular states and multicellular communities, tumor developmental hierarchies, and single-cell spatial relationships from genomic profiles of clinical biospecimens. Key results are further explored experimentally, both in our lab and through collaboration, with the goal of translating promising findings into the clinic.

As a member of the Department of Biomedical Data Science and the Institute for Stem Cell Biology and Regenerative Medicine, and as an affiliate of graduate programs in Biomedical Informatics, Cancer Biology, and Immunology, we are also interested in the development of impactful biomedical data science tools in areas beyond our immediate research focus, including developmental biology, regenerative medicine, and systems immunology.

I am a surgeon-scientist with a clinical interest in caring for patients with hearing loss and deafness, and research interests in inner ear development and regeneration. For almost 20 years, I have been studying hair cell biology. Since 2007, my research has focused on defining the role of Wnt signaling in regulating hair cell progenitors in the developing and damaged inner ear using a combination of genetic, molecular biological, pharmacological, and imaging techniques. In particular, our work has led to the discovery of Wnt-responsive hair cell progenitors in the neonatal mouse cochlea and utricle, and more recently, functional recovery during vestibular regeneration. Department URL: https://med.stanford.edu/ohns.html

The lab's current research is aimed primarily at understanding how hematopoietic stem cells interact with their microenvironment in order to subsequently modulate these interactions to ultimately improve bone marrow transplantation and unlock biological secrets that further enable regenerative medicine broadly. We are primarily focused on studying the cell surface receptors on hematopoietic stem/progenitor cells and bone marrow stromal cells, and are actively learning how manipulating these can alter cell state and cell fate.  We have also pioneered several antibody-based conditioning methods that are at various stages of clinical development to enable safer stem cell transplantation.

There are many exciting opportunities that stem from this work across a variety of disease states ranging from rare genetic diseases, autoimmune diseases, solid organ transplantation, microbiome and cancer. While we are primarily focused on blood and immune diseases, the expanded potential of this work is much broader and can be applied to other organ systems as well and we are very eager to develop collaborations across disease areas. The Czechowicz lab hopes to further add in the field of translation research.

Goals We aim to increase our understanding of the basic science principles that govern these cells and then exploit these findings to develop improved therapies for patients We are particularly focused on pediatric non-malignant bone marrow transplantation with a strong interest in genetic blood/immune diseases and bone marrow failure, but do complementry work on solid tumors with marrow disease, solid organ tolerance induction, autoimmune diseases and gene therapy/gene editing.

My research interests revolve around the following areas: - Novel systems and methods for x-ray and CT imaging - Applications of x-ray/CT to image-guided interventions and therapy and diagnostic imaging - Dual energy / spectral imaging, including photon counting detectors - Applications of artificial intelligence / machine learning / deep learning to medical imaging - Monte Carlo and Deterministic methods for x-ray imaging and radiation dose - Model-based image reconstruction

My research interests revolve around the following areas: - Novel systems and methods for x-ray and CT imaging - Applications of x-ray/CT to image-guided interventions and therapy and diagnostic imaging - Dual energy / spectral imaging, including photon counting detectors - Applications of artificial intelligence / machine learning / deep learning to medical imaging - Monte Carlo and Deterministic methods for x-ray imaging and radiation dose - Model-based image reconstruction

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.

Aaron's current research focus is the study of dark energy using images from the ongoing Dark Energy Survey (DES) and the  future Large Synoptic Survey Telescope (LSST). He is interested in studying dark energy using both galaxy clusters and weak gravitational lensing. His research group connects instrumental work, in particular active optics and wavefront measurements at DES and a program of camera-wide testing at LSST,  with cosmology measurements. For example, they are developing a new method to characterize the telescope+camera point spread function using optical data, to be part of the weak lensing data analysis at both DES and LSST.

Aaron's current research focus is the study of dark energy using images from the ongoing Dark Energy Survey (DES) and the  future Large Synoptic Survey Telescope (LSST). He is interested in studying dark energy using both galaxy clusters and weak gravitational lensing. His research group connects instrumental work, in particular active optics and wavefront measurements at DES and a program of camera-wide testing at LSST,  with cosmology measurements. For example, they are developing a new method to characterize the telescope+camera point spread function using optical data, to be part of the weak lensing data analysis at both DES and LSST.

Our group combines computational and experimental techniques to study the cellular organization of complex tissues, with a focus on determining the phenotypic diversity and clinical significance of tumor cell subsets. We have a particular interest in developing innovative data science tools that illuminate the cellular hierarchies and stromal elements that underlie tumor initiation, progression, and response to therapy. As part of this focus, we develop new algorithms to resolve cellular states and multicellular communities, tumor developmental hierarchies, and single-cell spatial relationships from genomic profiles of clinical biospecimens. Key results are further explored experimentally, both in our lab and through collaboration, with the goal of translating promising findings into the clinic.

As a member of the Department of Biomedical Data Science and the Institute for Stem Cell Biology and Regenerative Medicine, and as an affiliate of graduate programs in Biomedical Informatics, Cancer Biology, and Immunology, we are also interested in the development of impactful biomedical data science tools in areas beyond our immediate research focus, including developmental biology, regenerative medicine, and systems immunology.