Chemical and Systems Biology
Contact Information
Faculty and their Research Interests
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Faculty and students in the Chemical and Systems Biology training program share an interest in the molecular aspects of cellular and organismal regulation, the quantitative analysis of cellular regulatory systems, and the development and application of comprehensive chemical and genetic tools for perturbing and probing regulatory networks. The department and its associated faculty are committed to leading Stanford's research efforts at the chemistry/biology interface. These activities include quantitative descriptions of signaling pathways and networks, cell cycleregulation, and other biological processes as well as the use of chemical approaches inbiomedical research.
Understanding biology at the molecular and systems levels requires new approaches to biomedical research, including the integration of quantitative, chemical, and biological methods. The next generation of scientists must be capable of bridging these diverse disciplines. Stanford faculty who share this vision have created this training program as an interschool initiative that provides graduate students with interdisciplinary research opportunities in the biological sciences.
The Chemical and Systems Biology Ph.D. program emphasizes individualized training and provides students with diverse research opportunities in areas such as signal transduction, cell cycle regulation, human disease, and embryonic development. This multidisciplinary and interactive environment encourages students to investigate the frontiers of biological science using a variety of modern scientific techniques, ranging from recent advances in molecular biology and protein biochemistry to synthetic organic chemistry. Concurrent with their independent research, students may take classes in cell biology, genetics, biochemistry, chemical biology, signal transduction, and drug discovery. An annual program-wide retreat allows all researchers to share their results, and regular presentations throughout the year by students, postdoctoral fellows, faculty, and outside speakers foster an interactive, interdisciplinary scientific environment.
For more information contact:
Margaret Tuggle
Department of Chemical and Systems Biology
CCSR Room 3155
Stanford, CA 94305-5174
(650) 725-5091
(650) 723-6834 (fax)
mtuggle@stanford.edu
http://casb.stanford.edu
Faculty and their Research Interests
Matthew Bogyo. Chemical biological studies of protease function in pathogenesis of human parasitic diseases; cancer imaging, chemical synthesis and inhibitor design.
http://bogyolab.stanford.edu
Steve Boxer. Physical biology. Protein electrostatics and dynamics; membrane biotechnology; light driven processes in photosynthesis and GFP.
http://www.stanford.edu/group/boxer/
James Chen. Molecular mechanisms of embryonic development and oncogenesis using zebrafish as a model system; development of chemical and genetic technologies for zebrafish studies.
http://chen.stanford.edu/
Gilbert Chu. Biochemical and genetic aspects of DNA repair. Use of microarrays to study transcriptional responses to DNA damage.
http://cmgm.stanford.edu/~chu/
Karlene Cimprich. Cell biology, biochemistry and chemical biology of cell cycle regulation and DNA damage checkpoints; genomic stability and cancer biology.
http://cimprich.stanford.edu/
Jennifer Cochran. Designer protein therapeutics and diagnostic agents. Clinical applications involve bone and wound healing, biomimetic corneas, neural cell regeneration, and cancer imaging and therapy.
http://med.stanford.edu/profiles/Jennifer_Cochran/
Markus Covert. The Covert Lab focuses on developing computational models of cellular processes and testing these models experimentally to speed up the discovery process. We have found that this model-driven approach to biological discovery leads to substantially accelerated identification of new biological functions, interactions and pathways. Currently, the two major projects in the lab are, building the first computational model of an entire cell; Understanding the complex interactions between bacterial or viral pathogens and host cells.
http://www.stanford.edu/group/covert/
Ricardo Dolmetsch. Mechanisms of calcium channel signaling in the nervous and cardiovascular systems. Development of new technologies to investigate signaling cascades in intact animals and the functions of neuronal circuits in the brain.
http://www.stanford.edu/group/dolmetschlab/
Joshua Elias. Large-scale proteomics studies of dynamic cellular systems. Developing
novel methods and computational approaches for applying mass spectrometry to
the analysis of cancer, stem cells and aging.
http://med.stanford.edu/profiles/Joshua_Elias/
James E. Ferrell, Jr. Cell cycle regulation in Xenopus oocytes and eggs. Systems-level properties of signal transduction cascades, loops, and networks.
http://www.stanford.edu/group/ferrelllab/
Amato Giaccia. Identification and characterization of the molecular and physiological changes induced by the tumor microenvironment that influence the malignant progression of transformed cells.
http://med.stanford.edu/profiles/faculty/Amato_Giaccia
Dan Herschlag. Chemical and physical principles that underlie biological function. Fundamental principles of catalysis by RNA and protein enzymes; mechanisms of RNA folding; and global analysis of cellular RNA processing.
http://cmgm.stanford.edu/biochem/herschlag/
Stuart Kim. Global discovery of conserved genetic modules; Functional genomics of human aging; Functional genomics of C. elegans aging; Global profiles of gene expression during development.
http://cmgm.stanford.edu/~kimlab/
Karla Kirkegaard. Genetics, biochemistry and cell biology of infection with positive-strand RNA viruses such as poliovirus, rhinovirus, and hepatitis C virus.
http://cmgm.stanford.edu/micro/kirkegaard_lab/
Brian Kobilka. Signal transduction by adrenergic receptors, with a focus on receptor structure, drug-induced conformational changes, and the physiologic implications of receptor subtype diversity.
http://med.stanford.edu/kobilkalab/research.html
Calvin Kuo. Research in the Kuo laboratory is focused on the biologic characterization of novel molecules regulating angiogenesis and assessment of their use for anti-angiogenic therapy of cancer.
http://med.stanford.edu/profiles/cancer/researcher/Calvin_Kuo/
Richard Lewis. Molecular mechanisms of calcium signaling underlying T lymphocyte activation and development. Regulation of store-operated calcium channels, signaling networks, and the specificity of gene expression.
http://med.stanford.edu/profiles/faculty/Richard_Lewis
Tobias Meyer. Understanding the fundamental principles of signal transduction networks that regulate synaptic plasticity, secretion, and chemotaxis.
http://www.stanford.edu/group/meyerlab/
Beverly Mitchell. Development of new therapies for hematologic malignancies with a long-standing interest in inosine monophosphate dehydrogenase as a therapeutic target.
http://med.stanford.edu/profiles/Beverly_Mitchell/
Daria Mochly-Rosen. Mechanisms underlying the specificity of protein kinase C isozymes in normal heart function and in cancer; role of protein-protein interactions in signal transduction.
http://www.stanford.edu/group/mochly-rosen/
Vijay Pande. Computational biophysics, structural biology, and chemical biology: simulations of protein folding in vitro and vivo, protein dynamics, and protein-ligand binding.
http://www.stanford.edu/group/pandegroup/
Joseph D. Puglisi. Role of RNAs in various biological processes with a focus on the ribosome, the mechanism of translation, and how antibiotics disrupt ribosome function; nuclear magnetic resonance spectroscopy.
http://puglisi.stanford.edu/
Richard A. Roth. Molecular biology, biochemistry, and cell biology of insulin and insulin-like growth factor action.
http://molepharm.stanford.edu/faculty/homepages/roth.html
Jan Skotheim. 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. A systematic understanding of biological control circuits should allow us to more readily discern the function of natural systems and aid us in engineering synthetic systems.
http://www.stanford.edu/group/skotheim/Site/Welcome.html
Aaron Straight. Optical microscopy, biochemical and cell biological techniques to study cell division, focusing on how chromosomes are segregated in mitosis and how the cell cleaves during cytokinesis.
http://straightlab.stanford.edu/
Mary Teruel. Understanding how timing, crosstalk, and feedback in the PI3K-insulin
signaling network controls fat cell function. Our laboratory makes use of high-throughput screening, targeted mass spectrometry, bioinformatics, and live-cell imaging to identify new regulators and characterize how new and known regulators contribute to insulin signaling.
http://med.stanford.edu/labs/mary-teruel/
Tom Wandless. Development of new technologies to rapidly and reversibly regulate the function of specific proteins in living cells and animals using organic chemistry, protein engineering, and cell biology.
http://wandless.stanford.edu/
Paul Wender. Drug design, drug delivery, biological barriers, novel therapeutic modes of action, kinase regulation, medicinal and synthetic chemistry.
http://www.stanford.edu/group/pawender/
Joanna Wysocka. Epigenetic regulation of differentiation and development, chromatin in embryonic stem cells, molecular basis of pluripotency, histone modifications in the regulation of gene expression, and the mechanisms of writing and reading histone-methylation patterns.
http://casb.stanford.edu/faculty/primary/wysocka.html