Immunology
Contact Information
Faculty and their Research Interest
The 2B4T cell receptor in complex with Moth Cytochrome c peptide bound to I-Ek (mouse MHC class II).
The Ph.D. Program in Immunology is an interdepartmental program offering training in immunology and related basic and clinical biomedical sciences. The program includes 58 faculty members in 19 different departments in the Medical School and in the Department of Biology, in the School of Humanities and Sciences.
The research interests of our faculty cover the major areas of modern immunology, including cellular immunology, molecular immunology, clinical immunology, structural immunology, and systems immunology. Research includes studies of the development and function of T- and B-lymphocytes, natural killer cells, regulatory T-cells, dendritic cells and the specific tissues and organs that contribute to host defenses. The program has a strong molecular component, and many of the laboratories have focused on key molecules in the induction and expression of immune responsiveness. These include the molecules encoded by the major histocompatability complex, T cell receptors, immunoglobulins, costimulatory and accessory molecules, adhesion molecules, (including selectins and integrins), chemokines and chemoattractant receptors, and cytokines and their receptors. Studies in progress include analysis of gene expression using microarrays and robotic sequencers and studies of the 3-dimensional structure of important immune system molecules by protein crystallography. A number of faculty are focusing on the cellular interactions involving cells of the immune system during their development and activation, from the architecture of the “immunological synapses” to the specific receptors, molecular interactions, signaling cascades, and transcription factors involved in activation. Another major strength of the program is the development and application of new tools and technologies available to immunologists that are well supported by key laboratories and core facilities available to the Immunology Program. These include the CyTOF, Mass Cytometer, confocal microscopy for cell imaging, cDNA microarrays of both mouse and human genes for expression profiling, large scale antibody arrays for detection proteins, lipids and carbohydrates, MHC-peptide tetramers for identification of antigen specific T cells, and a large reservoir of transgenic and knock-out mice strains. Important core facilities include the FACS Facility, the Protein and Nucleic Acid Facility, the Cell Imaging Facility, and the Human Immune Monitoring Core for state-of-the-art immune monitoring in clinical and translational studies.
Leveraging Stanford’s strength in basic immunology, many Stanford Immunology faculty apply basic findings to clinical diseases, including autoimmune diseases such as type I diabetes mellitus, multiple sclerosis, lupus, and rheumatoid arthritis, infectious diseases, allergy, graft rejection, and cancer. Array methodologies for autoantibody detection in autoimmune patients and functional T-cell profiling in vaccine studies have also been pioneered at Stanford. Finally, Stanford Immunology faculty have demonstrated unanticipated roles for immune-derived cells and factors fields ranging from metabolism to neuroscience to aging, thereby opening new areas of investigation.
To enhance communication, cooperation, and interaction between students, post-doctoral fellows and faculty within the Stanford Immunology community the Program sponsors the weekly Stanford Immunology Seminar Series, journal clubs in several areas of immunology, and an annual 3-day retreat.
For more information contact:
Maureen Panganiban
Immunology Program Administrator
1215 Welch Road, Modular B, Rm. 55
Stanford, CA 94305-5422
(650) 725-5076
(650) 725-2682 (fax)
immunology@stanford.edu
http://immunol.stanford.edu
Faculty and their Research Interests
Cellular, Molecular and Translational (CMT)
Participating Faculty Members
Ash Alizadeh. Systematic investigation of genome-wide programs regulating gene expression in human cancers with a focus on hematopoietic tumors, especially their relationship to developmental hierarchies including stem cells and to tumor micro-environments. Identifying gene expression patterns useful for detection and classification of human cancers, and prediction of tendency for progression or response to specific therapies; Developing new strategies and technologies for diagnosis, early detection, and surveillance of cancer.
Ann Arvin. Varicella-zoster virus (VZV): molecular mechanisms of replication and pathogenesis-identification of functional domains of viral genes/promoters, roles of viral and host cell proteins in pathogenesis of VZV infection of T-cells, skin, neurons in SCIDhu model; CD4/CD8 T cell immunity to VZV; viral mechansisms of immune evasion.
Catherine Blish. Prevention and control of HIV by studying the interplay between the virus and the host immune response. We investigate the role of various arms of the immune response, including antibodies, T cells, and NK cells in protection from HIV in the real world. We hope to gain additional insights into control of infectious diseases by studying how co-infections and human conditions (including pregnancy and aging) modulate immune responses.
John Boothroyd. Intracellular parasitism, protein trafficking, developmental biology, host pathogen interaction, and pathogenesis.
Eugene Butcher. Molecular and cellular biology of lymphocyte and neutrophil homing; cell adhesion and chemotaxis in immune responses; reproductive immunology; systems biology of the immune system.
Atul Butte. Dr. Butte's laboratory focuses on solving problems relevant to genomic medicine by developing new methodologies in translational bioinformatics. The Butte Lab has developed bioinformatics methods to take genomic, genetic, phenotypic, and RNAi data from multiple sources and phenotypes and reason over these data.
Manish Butte. The goal of my lab is to address fundamental and therapeutic questions in immunology using innovative biophysical and bioengineering approaches to visualize and manipulate cells. Our primary focus is on understanding at a molecular level the signals that balance T cell activation versus tolerance. We are using soft lithography, microfluidics, TIRF/confocal microscopy, and biological scanning probe/atomic force microscopy to image and control the molecules that mediate T cell activation. The ultimate aim of our work is to manipulate T cell signaling pathways to control immunologically-mediated diseases.
Chang-Zheng Chen. The genetic networks controlled by regulatory RNAs, such as microRNAs and small interfering RNAs, and the roles of these RNAs in modulating the development, function and pathogenesis of vertebrate immune systems.
Yueh-Hsiu Chien. Molecular nature of gamma-delta T-cell recognition and function. Molecular mechanisms of bacterial infection and host immune responses. Contribution factors to immunocompetence and autoimmunity.
Gilbert Chu. Recognition and response to DNA damage; role of proteins in biochemical pathways for DNA repair.
Michael Cleary. Molecular and cellular biology of hematologic malignancies; role of leukemia oncogenes in mammalian development.
Christopher H. Contag. Revealing immune cell trafficking patterns in vivo through whole body imaging to understand immune function, cell-cell and cell-tissue relationships through development and in response to insult.
Gerald R. Crabtree. Genetic regulatory mechanisms in T-lymphocyte activation; lymphoid development.
Mark M. Davis. Molecular mechanisms of lymphocyte recognition and differentiation; molecular genetics and expression of T-cell receptor genes.
Firdaus Dhabhar. I am interested in identifying biological mechanisms that mediate and differentiate the recently appreciated immunoenhancing effects of short-term stress from the long-known immunosuppressive effects of chronic stress. We examine stress effects on leukocyte trafficking, innate/adaptive immunity, and cytokine gene/protein expression using models of skin immunity, surgery, and cancer.
Edgar Engleman. Human dendritic cells and T-cells; genes that regulate the functions of these cells; ontogeny of dendritic cells; immunotherapeutic approaches to cancer, AIDS, and autoimmune diseases.
C. Garrison Fathman. Mechanisms of disease pathogenesis and autoimmunity; preclinical models of immunotherapy in animal models; T-cell signalling.
Dean Felsher. Role of oncogenes in the initiation and maintenance of hematopoietic tumorigenesis, including analysis of the effects of oncogenes on lymphocyte proliferation and differentiation.
Stephen J. Galli. Regulation of mast cell and basophil development, heterogeneity and function, and roles as effector or immunoregulatory cells in health, host defense (in acquired and innate immunity) and disease; asthma and inflammation, especially allergic inflammation.
K. Christopher Garcia. Molecular immunology. Biochemical and structural studies of cell-surface receptor/ligand interactions with relevance to human health and disease. Applying biophysical and protein engineering approches to molecular problems in T-cell recognition, B-cell differentiation, innate immunity, and emerging molecules at the interface of immune and nervous systems.
Jorg J. Goronzy. Immune mechanisms in rheumatoid arthritis. Influence of age on T cell homeostasis and function. Vaccine responses. T cell signaling.
Aida Habtezion. Our lab is interested in studying mechanisms of leukocyte recruitment in inflammatory disease affecting the digestive organs. Our lab focuses on the area of mucosal immunology, particularly epithelial cell biology, T cell trafficking in inflammatory bowel disease, and role of hemeoxygenase-1 and monocyte recruitment in pancreatitis.
May Han. Autoimmune Neuroinflammation, Multiple Sclerosis (MS) and Neuromyelitis Optica (NMO): Systems Biology Approach (Proteomics) of autoimmune demyelination; Translational research, MS and NMO biomarkers; CNS protection and repair.
Leonard A. Herzenberg. Gene regulation; lymphocyte subsets; molecular immunology; fluorescence-activated cell sorter development (FACS); AIDS; apoptosis; redox regulation.
Leonore A. Herzenberg. B-cell development; Ig rearrangement and repertoire analysis; signaling processes; impact of glutathione deficiency in HIV and other diseases; High-Definition Fluorescence-Activated Cell Sorting (Hi-D FACS); knowledge-based software to support FACS and other biomedical experimentation.
Michael Hsieh. Stem cell (dys)function, carcinogenesis, and inflammation; in vivo imaging; host-microbial interactions; biomarkers of innate and adaptive immunity.
Patricia P. Jones. Genetic, cellular, and molecular mechanisms that regulate adaptive immune responses (the antigen-specific responses carried out by B and T lymphocyte, unique to vertebrates), and innate immune responses (responses present in both invertebrates and vertebrates triggered by microbial components).
Sheri Krams. Apoptosis in transplantation; activation of NK cells; mechanisms of tissue damage in liver disease.
Calvin Kuo. Characterization of novel chemokine receptors through knockout strategies in mouse and zebrafish; study of inflammatory effects on angiogenesis; and effects of Wnt, Hh and Notch pathways on the immune response.
Ronald Levy. Immunology and molecular biology of lymphoid malignancy; molecular vaccines.
Shoshana Levy. Study of tetraspanins; the immunoregulatory role of the CD81 (TAPA-1), characterization of the new tretraspanins. Vaccine development; polarizing immune responses by antigen-cytokinefusion proteins and DNA constructs.
David B. Lewis. Cellular and molecular mechanisms limiting T-cell effector function during postnatal life; Th2 cytokine-mediated diseases involving the lung.
Richard S. Lewis. Biophysical mechanisms and cellular functions of calcium signaling during T cell activation and development. Imaging T-cell development in vivo with two-photon microscopy, and the role of calcium dynamics in controlling the specificity of gene expression.
Holden Maecker. My research focuses on cellular immune responses to pathogens, and the correlation of those responses with protection from clinical disease. Most of my work and collaborations involve systems-level assays for immune monitoring of diseases like cytomegalovirus (CMV), HIV, and cancer. I'm interested in determining immune correlates of protection for such diseases, where cellular immunity is important.
Ravindra Majeti. Pathogenesis of human AML stem cells, targeting leukemia stem cells with therapeutic monoclonal antibodies.
Olivia Martinez. Pathogenesis of EBV B cell lymphomas; cellular and molecular mechanisms of graft selection and tolerance induction.
Elizabeth Mellins. Antigen processing/presentation; structure/function of MHC class II molecules, including HLA-antibodiesDM; mechanisms of pathogen evasion of the class II pathway, with a focus on B. pertussis and human CMV; development of antigen presentation function in the human infant.
Sara Michie. Lymphocyte/endothelial adhesion and activation mechanisms involved in lymphohocyte migration into lymphoid tissues and sites of inflammation.
Emmanuel Mignot, Study of sleep disorder narcolepsy, indentification of HLA-DQB1*0602 as the main HLA susceptibility factor in human narcolepsy, positionally cloned the canine narcolepsy gene.
David Miklos. Investigates the targets of immune responses after human allogeneic stem cell transplantation. BMT patients develop antibodies against minor histocompatibility antigens (mHA) that are associated with chronic graft-v-host disease (cGVHD) and disease remission. Current projects: investigate Ab anti-tumor mechanism, high-throughput serologic identification of novel mHA in the development of GVHD and prevention of disease relapse, and clinical trials of B cell therapeutics for cGVHD.
Denise Monack. Genetic and molecular mechanisms of intracellular bacterial pathogenesis. Using Salmonella and Francisella tularensis as models to study complex host-pathogen interactions; ultimate goal is understanding how Salmonella persists within certain hosts for years in the face of a robust immune response and how F. tularensis, a stealth invader, can cause a rapid, lethal infection.
Robert Negrin. NK-T cells, gamma-delta T-cells, in vivo imaging and tumor models, hematopoietic cell transplantation.
Mark Nicolls. Contribution of the immune response to lung disease. We are specifically examining the contribution of inflammation to the development of pulmonary hypertension. We also study how airway remodeling occurs in transplantation with specific respect to the microvascular circulation and to the initiation of fibroproliferation.
Garry Nolan. The Nolan Laboratory’s areas of research include hematopoiesis, cancer and leukemia, autoimmunity and inflammation, and computational approaches for network and systems immunology. Our most recent efforts are focused on a single cell analysis advance using a mass spectrometry-flow cytometry hybrid device. The approach uses an advanced ion plasma source to determine the levels of tagged reagents bound to cells—enabling a vast increase in the number of parameters that can be measured per cell. His laboratory has already begun a large scale mapping of the hematopoietic hierarchy in healthy human bone marrow at an unprecedented level of detail. Our efforts are to enable a deeper understanding not only of normal immune function, but also detailed substructures of leukemias and solid cancers—which will enable wholly new understandings that will enable better management of disease and clinical outcomes.
Theo Palmer. For most areas of the mammalian brain, neurogenesis concludes at birth but there are exceptions to the rule. In rodents and humans, some areas of the brain continue to make new neurons throughout life. This process is mediated by neural stem cells and our research goals are to understand how stem cell activity is regulated and whether the nascent potential of resident stem cells can be harnessed for brain repair.
Peter Parham. Role of MHC Class I molecules in presenting antigens to cytotoxic T lymphocytes and regulating natural killer cell; evolution of the immune system.
William Robinson. Mechanisms of autoimmunity; use of preclinical models to develop immunotherapeutic approaches to autoimmunity; proteomics and lipidomics; autoantibodies and B cells; translational research.
David Schneider. Using the fruit fly Drosophila as a model vector to study the cell biology and genetics of malaria transmission.
Robert Shafer. Mechanisms and consequences of HIV evolution with an emphasis on HIV drug resistance.
Judith Shizuru. Transplantation of defined populations of allogeneic hematopoeitic cells. How hematopoeitic cell grafts alter antigen specific immune responses to allo-, auto-, and viral antigens. The cellular and molecular basis of resistance to engraftment of allogeneic hematopoietic stem cells.
Raymond Sobel. Cellular and molecular mechanisms of immune reactions in the central nervous system, particularly in multipole sclerosis, EAE and other animal models.
Lawrence Steinman. Autoimmune diseases of the nervous system; inflammatory response in neuro-degenerative disease; multiple sclerosis, Parkinson’s disease, Alzheimer’s disease, and polyglutamine repeat diseases.
Samuel Strober. Induction of immune tolerance in bone marrows and organ transplantation, T-cell progenitor development in the bone marrow. Pathogenesis and treatment of systemic lupus in mice and man, regulatory NK T-cells and CD1.
John Sunwoo. The overarching goal of our laboratory is to understand how natural killer (NK) cells, in the broader context of the host immune system, protect against developing and metastasizing tumor cells, especially a rare population of tumor-initiating cells called cancer stem cells. In addition, we are very interested in understanding the transcriptional regulation of NK cell development and differentiation from stem and progenitor cells and have recently identified a novel role for a family of homeobox transcription factors in this developmental program.
Paul J. Utz. Role of stress and apoptosis signaling pathways in autoimmunity; post-translational modifications of autoantigens; auto-antibodies and autoantigens; auto-antigen microarrays and micro-fluidics; proteomics assay development; tolerizing DNA therapy for SLE and related autoimmune diseases.
Irving L. Weissman. Developmental biology of the immune system, including analysis of hematopoeitic stem cells, T-cell differentiation, lymphocyte homing receptors, and killer T-cell genes.
Cornelia M. Weyand. Innate and adaptive immune responses in vascular inflammation. Telomere function in T lymphocytes. DNA damage responses in autoimmunity.
Joy Wu. Our laboratory studies how the osteoblast lineage supports B cell development in the bone marrow.
Joseph Wu. My lab works on biological mechanisms of adult stem cells, embryonic stem cells, and induced pluripotent stem cells. We use a combination of gene profiling, tissue engineering, physiological testing, and molecular imaging technologies to better understand stem cell biology in vitro and in vivo. For adult stem cells, we are interested in monitoring stem cell survival, proliferation, and differentiation. For ESC, we are currently studying their tumorigenicity, immunogenicity, and differentiation. For iPSC, we are working on novel derivation techniques. We also work on development of novel vectors and therapeutic genes for cardiovascular gene therapy applications.
Tony Wyss-Coray. We focus on the use of genetic and molecular tools to dissect injury and inflammatory pathways in Alzheimer’s disease and neurodegeneration.
Computational and Systems Immunology (CSI)
Participating Faculty Members
Ash Alizadeh. Systems Immunology & Oncogenomics of B-cell Lymphomas.
John Boothroyd. How Toxoplasma manipulates the host's immune response and avoids
clearance.
Scott Boyd. High-throughput characterization of B cells and T cells in immune disorders.
Atul Butte. We apply computational tools to the world's data yielding diagnostics and drugs.
Mark Davis. Studies of T cell receptor and antibody ligand recognition and the related functionality.
Andrew Fire. Diversity of antibody and small RNA responses in infection and genome defense.
Karla Kirkegaard. Using SHAPE, ChIRP, other deep sequencing approaches to fathom pathogen-host interactions.
Holden Maecker. Systems-level analysis of immune responses to chronic pathogens.
Garry Nolan. Single Cell Proteomics and Genomics of Cancer, Stem Cells & Autoimmunity.
Richard Olshen. Statistics and their application to systems immunology and medicine.
Stephen Quake. Computational studies of integrated microfluidics and large scale biological automation in immunology.
Michael Snyder. Large scale functional genomics and proteomics.
Paul Utz. Multiplexed assays for studying autoimmune and inflammatory diseases.
CSI Affiliated Faculty:
Russ Altman. Computational technologies applied to molecular biology problems of medical relevance.
Ronald Davis. Large-scale studies of relationship between immune repertoire, HLA & diseases.
Daphne Koller. Novel methods for data analysis, omics, systems genetics, regulatory networks.
Robert Tibshirani. Applied statistics and biostatistics in immunological research.