Genetics
Contact Information
Faculty and their Research Interests
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Genetics informs the study of many biological systems from basic cellular processes in yeast (upper left), to host/pathogen interactions in worms (upper right), to coat color in dogs (lower right), to transcriptional regulation in human cells (lower left).
The Department of Genetics at Stanford University School of Medicine provides opportunities for Ph.D. study in a broad array of areas overlying a consistent intellectual framework. All major areas of modern genetics are represented in the department, including identification and analysis of human disease genes; molecular evolution; host-pathogen/symbiont interactions; gene therapy; statistical genetics; application of model organisms to problems in biology, medicine, and environmental conservation; and computational and experimental approaches to genome biology. The department also includes the Stanford Genome & Technology Center, the Saccharomyces Genome Database (SGD), the Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB), the Tetrahymena Genome Database (TGD), the Candida Genome Database (CGD), and the Stanford Microarray Database (SMD); together, these provide resources and opportunities for large-scale and/or high-throughput approaches to biomedical research.
An underlying theme in our department is that Genetics is not merely a set of tools but a coherent and fruitful way of thinking about biology and medicine. To this end, we emphasize a spectrum of approaches based on molecules, organisms, populations, and genomes. We provide training through laboratory rotations, dissertation research, seminar series, didactic and interactive coursework, and an annual three-day retreat of nearly 200 students, faculty, postdoctoral fellows, and research staff. The mission of the department includes education and teaching as well as research; graduates from our program pursue careers in many different venues including research in academic or industrial settings, health care, health policy, and education. The department is committed to increasing diversity, and also plays a leading role in local community educational outreach programs.
For more information contact:
Graduate Program
Administrative Associate
Department of Genetics
300 Pasteur Drive
Lane Building Rm. 329
Stanford, CA 94305-5120
(650) 723-3335
(650) 725-7016 (fax)
genetics-info@genome.stanford.edu
http://genetics.stanford.edu
Faculty and their Research Interests
Russ Altman. The Helix Group (http://helix-web.stanford.edu/) applies techniques from bioinformatics and computational biology to problems in pharmacogenomics, protein structure/function annotation, RNA folding and dynamics, and physics-based simulation of biological structure. A major thrust is informatics resources to help understand the link between genotypes and phenotype, in order to accelerate personalized medicine. Methods include machine learning, data mining, natural language (text) processing, nonlinear optimization, and simulation methods.
Laura Attardi. Our laboratory uses the mouse as a model system to dissect the function of the p53 tumor suppressor gene. Our interests include studying target genes involved in p53-mediated apoptosis by cell biological and genetic methods. Our studies of one such p53 apoptosis-associated gene, Perp, have revealed important roles in both apoptosis and epithelial function. In addition, through the generation and analysis of p53 knock-in mutant mice, we are dissecting p53 function in tumor suppression in vivo.
Julie C. Baker. Molecular basis for cellular differentiation and patterning during mammalian gastrulation; mesoderm induction; neural induction; anterior/posterior patterning; TGFb signal transduction Xenopus embryology; expression cloning; functional genomics
Anne Brunet. Our lab studies the molecular basis of aging and age-related diseases. We use a combination of genetic, genomics, and proteomics approaches to investigate the genes involved in longevity in a range of model organisms. We are particularly interested in the role of FOXO transcription factors and SIRT deacetylases in aging and age-related disorders. We are also exploring the importance of the nervous system in controlling aging and longevity.
Carlos Bustamante. The Bustamante group works on developing statistical methods for inference in population and comparative genomics. We are particularly interested in approaches for testing evolutionary hypothesis regarding the importance of natural selection and demographic history in patterning genetic variation. Much of our work deals with development of population genetic theory as well as application of our tools to make inference from genome-wide data sets. We have recently become very interested in methods for association mapping in natural and domesticated populations
Michele Calos. Our laboratory is developing novel gene therapy and cell therapy approaches for genetic diseases. Our gene therapy work involves integration of the Factor VIII and IX genes in the liver for treatment of hemophilia. Our cell therapy work utilizes mesenchymal stem cells for the treatment of muscular dystrophy. We use phage integrase phiC31 as a tool to insert therapeutic genes into cells. We are also using integrase to make induced pluripotent stem cells and apply them as therapeutics.
http://www.stanford.edu/~calos/
J. Michael Cherry. Bioinfomatics and computational biology applied to genomic information describe the efforts in the group. We specialize in exploring the volumes of information that have been elucidated for the budding yeast, Saccharomyces cerevisiae. Our focus is in two areas of research using computers and databases as tools: designing databases and software tools to effectively provide biological information to the biomolecular research community, and development of ontologies and controlled vocabularies used in biological annotation.
Stanley N. Cohen. Regulation of gene expression in prokaryotes and eukaryotes. This work includes investigation of the Tsg101 tumor susceptibility gene, replicative senescence, RNA decay, and aspects of plasmid biology. A small bioinformatics group has developed a computer-based expert system for analyzing genetic data.
Ronald W. Davis. Our laboratory is focused on the development and application of molecular biology, manipulative genetics to a variety of problems. As model organisms, we generally use Saccharomyces cerevisiae and Arabidopsis thaliana. We are studying the replication of artificial yeast chromosomes and are investigating the effect of spacing of the origins of replication on chromosomal stability.
Andrew Fire. We study a variety of natural mechanisms that are utilized by cells adapting to genetic change. These include mechanisms activated during normal development and systems for detecting and responding to foreign or unwanted genetic activity. At the root of these studies are questions of how a cell can distinguish “self” versus “nonself” and “wanted” versus “unwanted” gene expression.
James M. Ford. Mammalian DNA repair and DNA damage inducible responses; P53 tumor suppressor gene; transcription in nucleotide excision repair and mutagenesis; genetic determinants of cancer cell sensitivity to DNA damage; genetics of inherited cancer susceptibility syndromes and human GI malignancies; clinical cancer genetics of BRCA1 and BRCA2 breast cancer and mismatch repair deficient colon cancer.
Uta Francke. Human genetic and developmental disorders, genotype-phenotype correlations; identification of gene variants that predispose to common diseases and sensitivity to environmental agents.
Margaret T. Fuller. Regulation of stem cell division and self-renewal; Cell type specific transcription machinery and the regulation of cell differentiation; Developmeantal regulation of cell cycle progression during male meiosis; Molecular dissection of the mechanism of cytokinesis.
Aaron Gitler. We investigate the mechanisms of human neurodegenerative diseases, including Alzheimer disease, Parkinson disease, and ALS. We don't limit ourselves to one model system or experimental approach. We start with yeast, perform genetic and chemical screens, and then move to other model systems (e.g. mammalian tissue culture, mouse, fly) and even work with human patient samples (tissue sections, patient-derived cells, including iPS cells) and next generation sequencing approaches.
Hank Greely. Since 1992 my work has concentrated on ethical, legal, and social issues in the biosciences. I am particularly active on issues arising from neuroscience, human genetics, and stem cell research, with cross-cutting interests in human research protections, human biological enhancement, and the future of human reproduction.
William Greenleaf. Our lab develops methods to probe the genome and epigenome at the single-cell and single-molecule levels. Our efforts are split between building new tools to leverage the power of high-throughput sequencing and cutting-edge optical microscopies, and bringing these new technologies to bear against basic biological questions of genetic and epigenetic inheritance and variation within populations.
http://greenleaf.stanford.edu/
Leonard A. Herzenberg. Gene Regulation; Molecular Immunology; Lymphocyte subsets; Fluorescence-Activated Cell Sorter (FACS) development; AIDS; Apoptosis; Redox Regulation; Gene Arrays; and the therapy of AIDS using the anti-oxidant N’ acetylcysteine (NAC)
Leonore A. Herzenberg. B-cell development; 1g rearrangement and repertoire analysis; T cell regulation of antibody responses; T cell subsets; glutathione regulation of HIV disease progression; Fluorescence-Activated Cell Sorting (FACS) related software development and gene arrays.
Mark A. Kay. The laboratory focus is to: (1) develop the scientific principles required for developing novel non-viral and viral-vector based gene transfer technologies, (2) study the molecular process of vector transduction in vivo, (3) develop RNAi based therapeutics, (4) define the mechanisms of RNAi/microRNA induced gene silencing in mammals, and (5) establish the molecular process of RNA-directed RNA transcription in mammals. Our major disease targets are viral hepatitis, hemophilia, and diabetes mellitus.
Jin Billy Li. We are primarily interested in identifying and understanding sequence variations in the RNA and DNA. In particular, we focus on RNA editing where genomically encoded information is changed in the RNA. We aim to identify RNA editing events in the entire transcriptomes, and understand their functions. Our approaches include molecular genetics, genomics, computational biology, and technology development.
Joseph Lipsick. Our laboratory utilizes genetics, biochemistry, and cell biology to understand the function and evolution of chromosomes in animals. Our wedge into this problem is the Myb gene family, first identified because altered forms of c-Myb cause leukemias and lymphomas in vertebrate animals. Three closely related Myb genes are present in vertebrates, whereas invertebrate animals including the sea urchin and the fruit fly have a single Myb gene. The Myb proteins are nuclear and bind to specific DNA sequences. We have shown that in the absence of Myb, Drosophila display abnormalities of chromosome condensation, chromosome segregation, and mitotic spindle assembly. The Myb protein localizes to euchromatin, not pericentric heterochromatin. Myb is part of a larger complex that includes the protein products of the RB tumor suppressor gene, the E2F-DP DNA binding proteins, and various other proteins that modify and/or bind to histones.
Stephen B. Montgomery. We focus on understanding the effects of genome variation on cellular phenotypes and cellular modeling of disease through genomic approaches such as next generation RNA sequencing in combination with developing and utilizing state-of-the-art bioinformatics and statistical genetics approaches. See our website at:
http://montgomerylab.stanford.edu/
Kelly Ormond. While my primary role is to direct the MS in Human Genetics and Genetic Counseling program, my research focuses on the intersection between genetics and ethics, particularly around informed consent and patient decision making. I am also very interested in how genetic counseling and disability interface.
John Pringle. My laboratory works in two major areas. In one set of projects, we continue to exploit the awesome power of yeast as an experimentally tractable model eukaryote to investigate fundamental problems in cell and developmental biology such as the mechanisms of cell polarization and of cytokinesis. In a second set of projects, we are developing the small sea anemone Aiptasia pallida as a model system for study of the almost totally unexplored molecular and cell biology of the dinoflagellate-cnidarian symbiosis, which is critical for the survival of the reef-building corals and hence for the health of a major world ecosystem.
Julien Sage. The retinoblastoma tumor suppressor gene (RB) is mutated in a broad range of pediatric and adult tumors. Our goal is to take advantage of the central role of RB in cell cycle control, development, and tumorigenesis in order to address basic issues in cancer. To this end, we generate and study genetically engineered mice modeling human cancers associated with loss of RB function. Using these models, we aim to identify the cell of origin of cancer, the order of mutations involved in cancer progression, and the molecular mechanisms of tumorigenesis. In particular, we have found that RB plays a critical role in adult and embryonic stem cells and we investigate how loss of RB function affects the proliferation, the self-renewal, and the fate of stem cells.
http://www.stanford.edu/group/sage/
Matthew P. Scott. We study the genetic regulation of development and disease. Our research is focused on evolutionarily conserved regulators of development and their links to birth defects, cancer, and degenerative disease. We employ genetics and genomics approaches, along with molecular cell biology, to study fly and mouse development. Specific areas include Hedgehog/ patched signaling and its links to brain cancer, genetic control of body size, development of the neural tube and cerebellum, intracellular organelle trafficking and Niemann-Pick neurodegenerative disease, and effects of neural activity on neural development.
Gavin Sherlock. We use experimental laboratory and computational approaches to solve biological problems. We are high throughput sequencing technology to define transcripts from related yeast species, and to understand the changes in genome architecture and the transcriptome that occur in yeast as they evolve in vitro. We are also developing novel yeast strains for use in biofuel production, with the aim of being able to ferment five carbon sugars such as xylose, as well as 6 carbon sugars into ethanol. In addition, we developed and run the Stanford Microarray Database, the Tuberculosis Database, the Candida Genome Database and the Aspergillus Genome Database. Finally, we have also written software for the analysis and visualization of microarray data, including GO::TermFinder, Caryoscope, and GeneXplorer.
http://genetics.stanford.edu/~sherlock
Arend Sidow. We work on the systems biology of gene regulatory networks in normal development and cancer. We leverage massively parallel sequencing to elucidate (1) Interaction networks in mouse embryogenesis, (2) Chromatin function in human cell types (partly in conjunction with the Encode Project) and (3) Breast cancer progression.
Michael Snyder. Our laboratory uses large scale approaches to characterize genomes, proteomes and biological systems in yeast and humans. Our genomics research focuses the identification of transcribed regions, transcription factor binding sites, genomic variation and human disease. Proteomics activities include the identification of novel biochemical activities, protein phosphorylation, interactions with small molecules, and the diagnostics and understanding of human disease. We are particularly interested in regulatory networks, their organization, integration, and differences both within a population and between organisms.
Tim Stearns. The central question in our work is how cells accurately segregate their genome at each cell division. The work is focused on the centrosome, a unique organelle at the center of the cell that organizes the cytoskeleton and serves as a site for integration of cellular signals. We use the tools of cell biology, genetics, and biochemistry in systems ranging from yeast to human cells to understand how the centrosome duplicates once per cell cycle, and how centrosome defects are involved in the genome instability that is observed in many types of cancer.
Zijie Sun. We investigate the transcriptional processes that govern the transformation of normal mammalian cells to neoplastic state. Specifically we are interested in the molecular mechanism of the nuclear hormone receptors in the pathogenesis of human tumors.
Hua Tang. I am interested in various aspects of human genetics and genomics, including statistical and population genetics, mapping of disease-susceptibility loci, and the inference of evolutionary history of human populations. By integrating evolutionary theory into statistical modeling, my theoretical research aims at developing methods for identifying disease-susceptibility loci in stratified or admixed populations, and methods for genome-wide association studies. My applied research includes a large population-based study of the genetics of hypertension in humans. I have also collaborated on genetic studies of asthma in the Hispanic population, neurological disorders in the Romani population, and lysosomal storage diseases in the Jewish population.
Anne M. Villeneuve. Mechanisms underlying pairing and recombination between homologous chromosomes during meiosis, using the nematode Caenorhabditis elegans as an experimental system. High-resolution 3-D imaging of meiotic chromosomes. Transgene-mediated cosuppression of germline gene expression.
Douglas E. Vollrath. Work in our laboratory is focused on understanding basic processes in the eye that are relevant to human health and disease. We use a combination of human and rodent genetics, genomics, and cell biology to understand processes such as circadian regulation of photoreceptor renewal, phagocytic clearance of apoptotic cells and debris, the interdependence of photoreceptors and adjacent polarized retinal epithelial cells, age-related retinal changes, and the mechanisms by which misfolded proteins cause neurodegenerative blindness. Our studies connect with areas of investigation outside of the eye including tissue remodeling, autoimmunity, and neurodegeneration.
Monte Winslow. Our laboratory uses genome-wide methods to uncover alterations that drive cancer progression and metastasis in genetically-engineered mouse models of human cancers. We combine cell-culture based mechanistic studies with our ability to alter pathways of interest during tumor progression in vivo to better understand each step of metastatic spread and to uncover the therapeutic vulnerabilities of advanced cancer cells.