School of Medicine
Showing 1-100 of 101 Results
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Vivek Bajpai
Postdoctoral Research Fellow, Chemical and Systems Biology
Current Research and Scholarly Interests Molecular regulation of stem cell plasticity in development and disease
Tissue Engineering and Regenerative Medicine -
Philip Beachy
The Ernest and Amelia Gallo Professor in the School of Medicine, Professor of Developmental Biology and, by courtesy, of Chemical and Systems Biology
Current Research and Scholarly Interests Function of Hedgehog proteins and other extracellular signals in morphogenesis (pattern formation), in injury repair and regeneration (pattern maintenance). We study how the distribution of such signals is regulated in tissues, how cells perceive and respond to distinct concentrations of signals, and how such signaling pathways arose in evolution. We also study the normal roles of such signals in stem-cell physiology and their abnormal roles in the formation and expansion of cancer stem cells.
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Carolyn Bertozzi
Anne T. and Robert M. Bass Professor in the School of Humanities and Sciences and Professor, by courtesy, of Radiology and of Chemical and Systems Biology
Bio Professor Carolyn Bertozzi's research interests span the disciplines of chemistry and biology with an emphasis on studies of cell surface sugars important to human health and disease. Her research group profiles changes in cell surface glycosylation associated with cancer, inflammation and bacterial infection, and uses this information to develop new diagnostic and therapeutic approaches, most recently in the area of immuno-oncology.
Dr. Bertozzi completed her undergraduate degree in Chemistry at Harvard University and her Ph.D. at UC Berkeley, focusing on the chemical synthesis of oligosaccharide analogs. During postdoctoral work at UC San Francisco, she studied the activity of endothelial oligosaccharides in promoting cell adhesion at sites of inflammation. She joined the UC Berkeley faculty in 1996. A Howard Hughes Medical Institute Investigator since 2000, she came to Stanford University in June 2015, among the first faculty to join the interdisciplinary institute ChEM-H (Chemistry, Engineering & Medicine for Human Health). Named a MacArthur Fellow in 1999, Dr. Bertozzi has received many awards for her dedication to chemistry, and to training a new generation of scientists fluent in both chemistry and biology. She has been elected to the Institute of Medicine, National Academy of Sciences, and American Academy of Arts and Sciences; and received the Lemelson-MIT Prize, the Heinrich Wieland Prize, and the ACS Award in Pure Chemistry, among many others. Her efforts in undergraduate education have earned the UC Berkeley Distinguished Teaching Award and the Donald Sterling Noyce Prize for Excellence in Undergraduate Teaching.
Today, the Bertozzi Group at Stanford studies the glycobiology underlying diseases such as cancer, inflammatory disorders such as arthritis, and infectious diseases such as tuberculosis. The work has advanced understanding of cell surface oligosaccharides involved in cell recognition and inter-cellular communication.
Dr. Bertozzi's lab also develops new methods to perform controlled chemical reactions within living systems. The group has developed new tools for studying glycans in living systems, and more recently nanotechnologies for probing biological systems. Such "bioorthoganol" chemistries enable manipulation of biomolecules in their living environment.
Several of the technologies developed in the Bertozzi lab have been adapted for commercial use. Actively engaged with several biotechnology start-ups, Dr. Bertozzi founded Redwood Bioscience of Emeryville, California, and has served on the research advisory board of GlaxoSmithKline. -
Ewa Bielczyk Maczynska
Postdoctoral Research Fellow, Chemical and Systems Biology
Current Research and Scholarly Interests adipocyte dedifferentiation, TGF-beta signaling in adipogenesis
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Matthew Bogyo
Professor of Pathology and of Microbiology and Immunology and, by courtesy, of Chemical and Systems Biology
Current Research and Scholarly Interests Our lab uses chemical, biochemical, and cell biological methods to study protease function in human disease. Projects include:
1) Design and synthesis of novel chemical probes for serine and cysteine hydrolases.
2) Understanding the role of hydrolases in bacterial pathogenesis and the human parasites, Plasmodium falciparum and Toxoplasma gondii.
3) Defining the specific functional roles of proteases during the process of tumorogenesis.
4) In vivo imaging of protease activity -
James K. Chen
Professor of Chemical and Systems Biology and of Developmental Biology and, by courtesy, of Chemistry
Current Research and Scholarly Interests Our laboratory combines synthetic chemistry and developmental biology to investigate the molecular events that regulate embryonic patterning, tissue regeneration, and tumorigenesis. We are currently using genetic and small-molecule approaches to study the molecular mechanisms of Hedgehog signaling, and we are developing chemical technologies to perturb and observe the genetic programs that underlie vertebrate development.
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Karlene Cimprich
Professor of Chemical and Systems Biology
Current Research and Scholarly Interests Genomic instability contributes to many diseases, but it also underlies many natural processes. The Cimprich lab is focused on understanding how mammalian cells maintain genomic stability in the context of DNA replication stress and DNA damage. We are interested in the molecular mechanisms underlying the cellular response to replication stress and DNA damage as well as the links between DNA damage and replication stress to human disease.
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Markus Covert
Associate Professor of Bioengineering and, by courtesy, of Chemical and Systems Biology
Current Research and Scholarly Interests Our focus is on building computational models of complex biological processes, and using them to guide an experimental program. Such an approach leads to a relatively rapid identification and validation of previously unknown components and interactions. Biological systems of interest include metabolic, regulatory and signaling networks as well as cell-cell interactions. Current research involves the dynamic behavior of NF-kappaB, an important family of transcription factors.
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Madzia Crossley
Postdoctoral Research Fellow, Chemical and Systems Biology
Current Research and Scholarly Interests Investigating the role of R-loops in genome stability and human disease
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Justin Du Bois
Associate Professor of Chemistry and, by courtesy, of Chemical and Systems Biology
Bio Research and Scholarship
Research in the Du Bois laboratory spans reaction methods development, natural product synthesis, and chemical biology, and draws on expertise in molecular design, molecular recognition, and physical organic chemistry. An outstanding goal of our program has been to develop C–H bond functionalization processes as general methods for organic chemistry, and to demonstrate how such tools can impact the logic of chemical synthesis. A second area of interest focuses on the role of ion channels in electrical conduction and the specific involvement of channel subtypes in the sensation of pain. This work is enabled in part through the advent of small molecule modulators of channel function.
The Du Bois group has described new tactics for the selective conversion of saturated C–H to C–N and C–O bonds. These methods have general utility in synthesis, making possible the single-step incorporation of nitrogen and oxygen functional groups and thus simplifying the process of assembling complex molecules. To date, lab members have employed these versatile oxidation technologies to prepare natural products that include manzacidin A and C, agelastatin, tetrodotoxin, and saxitoxin. Detailed mechanistic studies of metal-catalyzed C–H functionalization reactions are performed in parallel with process development and chemical synthesis. These efforts ultimately give way to advances in catalyst design. A long-standing goal of this program is to identify robust catalyst systems that afford absolute control of reaction selectivity.
In a second program area, the Du Bois group is exploring voltage-gated ion channel structure and function using the tools of chemistry in combination with those of molecular biology, electrophysiology, microscopy and mass spectrometry. Much of this work has focused on studies of eukaryotic Na and Cl ion channels. The Du Bois lab is interested in understanding the biochemical mechanisms that underlie channel subtype regulation and how such processes may be altered following nerve injury. Small molecule toxins serve as lead compounds for the design of isoform-selective channel modulators, affinity reagents, and fluorescence imaging probes. Access to toxins and modified forms thereof (including saxitoxin, gonyautoxin, batrachotoxin, and veratridine) through de novo synthesis drives studies to elucidate toxin-receptor interactions and to develop new pharmacologic tools to study ion channel function in primary cells and murine pain models. -
Joshua Eric Elias-Merriman
Assistant Professor of Chemical and Systems Biology
Current Research and Scholarly Interests Developing new mass spectrometry-based experimental and computational tools that advance the field of proteomics, and applying them to a variety of important biomedical paradigms, including antigen presentation in cancer, and monitoring host responses to the gut microbiome.
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James Ferrell
Professor of Chemical and Systems Biology and of Biochemistry
Current Research and Scholarly Interests My lab has two main goals: to understand mitotic regulation and to understand the systems-level logic of simple signaling circuits. We often make use of Xenopus laevis oocytes, eggs, and cell-free extracts for both sorts of study. We also carry out single-cell fluorescence imaging studies on mammalian cell lines. Our experimental work is complemented by computational and theoretical studies aimed at identifying the design principles of regulatory circuits.
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David M Garcia
Postdoctoral Research Fellow, Chemical and Systems Biology
Bio I received a B.S. in Biochemistry and Molecular Biology from UC Santa Cruz, with one year of my bachelor's spent at the Pontifical Catholic University of Chile. Returning to the Bay Area where I grew up, I worked briefly at the VA Medical Center, San Francisco. I then did my Ph.D. studies at MIT, in David Bartel’s lab at the Whitehead Institute. I discovered new features of microRNA recognition sequences that were so predictive of mRNA repression that they were integrated into a major update of TargetScan.org, a microRNA target prediction program that receives ~20,000 visitors per month. I became interested in the link between protein homeostasis and RNA regulation, and joined Dan Jarosz’s lab at Stanford to study novel prion-like states of RNA binding proteins. My interest in prions also led me to a collaboration with Jon Clardy of Harvard, in which we identified for the first time an example of a bacterially secreted molecule that potently induces a prion. I continue to be fascinated with the biologically beneficial roles of prions, how they are induced in nature and the resulting physiological consequences, as well as their characteristic molecular features. Once I complete my training at Stanford I look forward to leading my own research group. In addition to research, I have longstanding interests in science communication for the public (see publications) and celebrating diversity in the academy through outreach opportunities.
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Daniel Jarosz
Assistant Professor of Chemical and Systems Biology and of Developmental Biology
Current Research and Scholarly Interests My laboratory studies conformational switches in evolution, disease, and development. We focus on how molecular chaperones, proteins that help other biomolecules to fold, affect the phenotypic output of genetic variation. To do so we combine classical biochemistry and genetics with systems-level approaches. Ultimately we seek to understand how homeostatic mechanisms influence the acquisition of biological novelty and identify means of manipulating them for therapeutic and biosynthetic benefit.
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Opher Kornfeld
Ph.D. Student in Chemical and Systems Biology, admitted Autumn 2013
Current Research and Scholarly Interests I am interested in the molecular mechanisms that regulate mitochondrial dynamics. I am using rationally-designed peptide inhibitors to target mitochondrial fission/fusion factors in order to understand the interplay between these factors under normal and stressed cellular conditions.
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Michael Lin
Associate Professor of Neurobiology, of Bioengineering and, by courtesy, of Chemical and Systems Biology
Current Research and Scholarly Interests Our lab applies biochemical and engineering principles to the development of protein-based tools for molecular imaging and gene therapy. Topics of investigation include fluorescent proteins structure and biophysics, fluorescent protein-based biosensors, spatiotemporal analysis of protein translation pathways, chemical control of protein translation, and light-responsive proteins.
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Tobias Meyer
Mrs. George A. Winzer Professor in Cell Biology
Current Research and Scholarly Interests CELLULAR INFORMATION PROCESSING The main problem in signal transduction is to understand how different receptor-stimuli specifically control diverse cell functions. We are using automated microscopy, live-cell fluorescent biosensors and perturbations of predicted signaling proteins to systematically dissect signaling networks. This allows us to identify signaling modules and to elucidate and ultimately model the flow of cellular information.
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Beverly S. Mitchell, M.D.
George E. Becker Professor in Medicine and Professor, by courtesy, of Chemical and Systems Biology
Current Research and Scholarly Interests Beverly Mitchell's research relates to the development of new therapies for hematologic malignancies, including leukemias and myelodsyplastic syndromes. She is interested in preclinical proof of principle studies on mechanisms inducing cell death and on metabolic targets involving nucleic acid biosynthesis in malignant cells. She is also interested in the translation of these studies into clinical trials.
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Daria Mochly-Rosen
The George D. Smith Professor in Translational Medicine
Current Research and Scholarly Interests Two areas: 1. Using rationally-designed peptide inhibitors to study protein-protein interactions in cell signaling. Focus: protein kinase C in heart and large GTPases regulating mitochondrial dynamics in neurodegdenration. 2. Using small molecules (identified in a high throughput screens and synthetic chemistry) as activators and inhibitors of aldehyde dehydrogenases, a family of detoxifying enzymes, and glucose-6-phoshate dehydrogenase, in normal cells and in models of human diseases.
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Lei Qi (Stanley)
Assistant Professor of Bioengineering and of Chemical and Systems Biology
Bio Dr. Lei Qi (Stanley) is Assistant Professor in the Department of Bioengineering (School of Engineering), Department of Chemical and Systems Biology (School of Medicine), and a core faculty member in Stanford ChEM-H Institute. He is one pioneer in the CRISPR technology development for genome engineering. He has developed the CRISPRi/a technologies for purposes beyond gene editing: gene regulation using CRISPR interference (CRISPRi, gene repression) and CRISPR activation (CRISPRa, gene activation), CRISPR dynamic imaging of chromatin in living cells, and CRISPRi/a high-throughput single or combinatorial genetic screens. He is also active in the field of Synthetic Biology and has developed synthetic noncoding RNAs for controlling transcription and translation. He obtained his Ph.D. in Bioengineering from the University of California Berkeley/UCSF in 2012. He joined UCSF as faculty fellow between 2012 to 2014, and joined the faculty at Stanford University since 2014. His lab currently is applying genetic engineering to rational cell design for understanding genomics and cell therapy.
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Atefeh Rabiee
Affiliate, Chemical and Systems Biology Operations
Bio • Honors & Awards
Visiting Scholar Fellowships at Stanford Bio-X | Novo Nordisk Foundation (NNF)
• Professional Education
Postdoctoral Researcher, University of Copenhagen (2014-2017)
Doctor of Philosophy, University of Southern Denmark (2010-2014)
• Stanford Advisor
Mary Teruel
• Links
https://www.linkedin.com/in/atefehrabiee/
https://teruel.stanford.edu/lab-team/ -
Richard Roth
Professor of Chemical and Systems Biology, Emeritus
Current Research and Scholarly Interests Insulin is one of the primary regulators of rapid anabolic responses in the body. Defects in the synthesis and/or ability of cells to respond to insulin results in the condition known as diabetes mellitus. To better design methods of treatment for this disorder, we have been focusing our research on how insulin elicits its various biological responses.
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Jan Skotheim
Associate Professor of Biology and, by courtesy, of Chemical and Systems Biology
Current Research and Scholarly Interests A central aim of the burgeoning field of systems biology is to understand the principles governing genetic control networks. I believe finding the principles underlying genetic circuits will occur through detailed studies and then comparisons of several natural systems. Due to its extensive development as an experimental system, our favorite model, the budding yeast cell cycle, is poised to become central to this enterprise.
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David E. Solow-Cordero
Director, HTBC, Chemical and Systems Biology Operations
Current Role at Stanford Director, High-Throughput Bioscience Center
The High-Throughput Bioscience Center's mission is to provide researchers at Stanford with the ability to run high-throughput chemical, siRNA, cDNA, and high-content screens for the purpose of drug and/or target discovery. The HTBC is a Stanford University School of Medicine core facility and was created in 2003 by the Department of Chemical and Systems Biology (formerly Molecular Pharmacology). The HTBC is a shared resource (Bioscience Screening Facility) for the Stanford Cancer Institute (more info), the Digestive Disease Center (Chemical Genomics Core), and the NIH Clinical and Translational Science Award (Spectrum).
Research approaches that were previously done exclusively in industry are now being used in academia to advance basic research. This high-throughput screening (HTS) laboratory allows Stanford researchers and others to discover novel modulators of targets that otherwise would not be practical in industry. The center incorporates instrumentation (purchased with NCRR NIH Instrumentation grant numbers S10RR019513 and S10RR026338), databases, compound libraries, and personnel whose previous sole domains were in industry. Among our instrumentation are a Molecular Devices ImageXpress Micro High-Content fluorescence microplate imager, with live cell and phase contrast/brightfield options, a Caliper Life Sciences SciClone ALH3000 and an Agilent Bravo microplate liquid handler, and the Molecular Devices Analyst GT and FlexStation II 384 and Tecan Infinite M1000 PRO fluorescence, luminescence and absorbance multimode microplate readers. We have over 135,000 small molecules for compound screens, 15,000 cDNAs for genomic screens, and the siARRAY whole human genome siRNA library from ThermoFisher Scientific (formerly Dharmacon) targeting 21,000 genes.
The HTBC is located in CCSR Room 0133-North Wing, between the Transgenic Mouse Facility, the Immune Monitoring Core, and the Stanford Functional Genomics Facility. -
Aaron Straight
Associate Professor of Biochemistry and, by courtesy, of Chemical and Systems Biology
Current Research and Scholarly Interests We study the biology of chromosomes. Our research is focused on understanding how chromosomal domains are specialized for unique functions in chromosome segregation, cell division and cell differentiation. We are particularly interested in the genetic and epigenetic processes that govern vertebrate centromere function, in the organization of the genome in the eukaryotic nucleus and in the roles of RNAs in the regulation of chromosome structure.
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Kavya Swaminathan
Postdoctoral Research Fellow, Chemical and Systems Biology
Bio Kavya received her Ph.D. from the University of Sydney in Australia. During her PhD, she developed and applied mass spectrometry-based approaches to study antiviral binding to influenza virus antigens and monitor the emergence of antiviral resistance. She joined the Elias lab to explore the host immune responses to viral infections.
Her current research focuses on identifying viral and host antigens that are differentially presented upon infection both in vitro and in vivo, in the context of the dynamic proteome. These studies will enable identifying immunologically relevant targets for the design of efficacious vaccines and therapeutics against a range of devastating infectious diseases such as Dengue, TB, Malaria, and Zika. -
Mary Frances Nunez Teruel
Assistant Professor of Chemical and Systems Biology and, by courtesy, of Bioengineering
Current Research and Scholarly Interests The Teruel Lab uses a combination of engineering and biological approaches including high-throughput screening of RNAi and DNA construct libraries, targeted mass spectrometry, live-cell fluorescence microscopy, and bioinformatics to investigate the systems biology of cell differentiation and cell signaling with particular focus on uncovering the molecular mechanisms underlying insulin resistance, diabetes, and obesity.
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Tom Wandless
Professor of Chemical and Systems Biology and, by courtesy, of Chemistry
Current Research and Scholarly Interests We employ an interdisciplinary approach to studies of biological systems, combining synthetic chemistry with biochemistry, cell biology, and structural biology. We invent tools for biology and we are motivated by approaches that enable new experiments with unprecedented control. These new techniques may also provide a window into mechanisms involved in maintaining cellular homeostasis. Protein quality control is a particular interest at present.
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Paul Wender
Francis W. Bergstrom Professor of Chemistry and Professor, by courtesy, of Chemical and Systems Biology
Current Research and Scholarly Interests Molecular imaging, therapeutics, drug delivery, drug mode of action, synthesis
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Marius Wernig
Associate Professor of Pathology and, by courtesy, of Chemical and Systems Biology
Current Research and Scholarly Interests Epigenetic Reprogramming, Direct conversion of fibroblasts into neurons, Pluripotent Stem Cells, Neural Differentiation: implications in development and regenerative medicine
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James Whitlock
Professor of Molecular Pharmacology, Emeritus
Current Research and Scholarly Interests We analyze the mechanisms by which mammalian cells adapt to environmental changes, such as exposure to foreign chemicals, hypoxia, or hormones, by altering the transcription of specific sets of genes. We use both biohchemical and genetic approaches and many techniques in molecular and cellular biology. See: http://www.stanford.edu/group/whitlock/
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Joanna Wysocka
Professor of Chemical and Systems Biology and of Developmental Biology
Current Research and Scholarly Interests The precise and robust regulation of gene expression is a cornerstone for complex biological life. Research in our laboratory is focused on understanding how regulatory information encoded by the genome is integrated with the transcriptional machinery and chromatin context to allow for emergence of form and function during human embryogenesis and evolution, and how perturbations in this process lead to disease.