All PhD candidates are required to intern in a biomedical laboratory, as a way to gain a deeper understanding of the research process. Here are some of the potential collaborating labs. Nearly all leaders of these laboratories have named chairs at Stanford.
Pat Brown, MD, PhD (Department of Biochemistry). A principal interest of this laboratory is investigating expression patterns of the human genome in diseased and normal states, including organization, physiological logic, and molecular mechanisms of control. Previous studies have given detailed molecular insights into how these processes are disrupted in cancer and other diseases, and new ways to diagnose, classify, and predict behavior of human cancers. Collaborations between core faculty members of our program and Dr. Brown's laboratory have motivated the development of a number of statistical techniques, including nearest shrunken centroids and supervised harvesting of expression trees.
Mark Davis, PhD (Department of Immunology). Dr. M. Davis' laboratory is interested in the molecular basis of T and B lymphocyte recognition, as well as the control of differentiation and functional responses in these cells. They have particularly focused on characterizing the types of protein-protein interactions that are involved when T-cell receptors recognize antigenic peptide/histocampatibility molecule complexes.
Ronald W. Davis, PhD (Department of Biochemistry). Dr. R. Davis is a senior leader in genetics and genomics. He was a co-author, with Botstein, Skolnick, and White, of the landmark 1980 paper on the mapping of heritable disease genes. He has been a pioneer in the development and uses of microarray and sequencing technologies. Currently he is the director of the Stanford Genome Technology Center. The Center is engaged in numerous studies in functional genomics and clinical genomics, which represent a rich source of possible collaborative projects for our trainees.
Andrew Fire, PhD (Departments of Genetic and Pathology). Dr. Fire and members of his laboratory study the molecular basis and consequences of genetic change, using both nematodes and human lymphocytes. Fire shared the 2006 Nobel Prize in Medicine for discovery of and work on RNAi. He has been collaborated with Professor Tibshirani and his students in the analysis of high throughput sequencing data, for both miRNA sequences and B-cell receptors. He has also worked with Professor Olshen and others on matters of clonality that arise in understanding human T cells and B cells.
John P.A. Ioannidis, MD (Department of Medicine). Dr. Ioannidis is the C.F. Rehnborg Professor in Disease Prevention, Professor of Medicine and Director of the Stanford’s Prevention Research Center. He studies the scientific process and reproducibility in general. He has a strong interest in large-scale evidence and in appraisal and control of diverse biases in research. Ioannidis's 2005 paper in PLoS Medicine on "Why Most Published Research Findings Are False" is the most frequently downloaded technical paper in the peer-reviewed scientific open-access journal literature and has been described by the Boston Globe as "an instant cult classic." He is currently the Editor-in-Chief of the European Journal of Clinical Investigation and has served on the editorial board of 26 international peer-reviewed journals related to medicine, epidemiology, and research methodology.
Douglas Levinson, MD (Department of Psychiatry and Behavior Science). Dr. Levinson directs the Program on the Genetics of Brain Function in the Department of Psychiatry and Behavioral Sciences. The program investigates the genetic basis of psychiatric disorders (schizophrenia and major depressive disorder), using genetic association, linkage and resequencing methodologies. In collaboration with Dr. Alice Whittemore, he is also actively engaged in statistical methods of testing and development for genetic research.
Beverly S. Mitchell, MD (Department of Medicine/Oncology). Dr. Mitchell is the Director of the Stanford Cancer Institute, and is the George E. Becker Professor of Medicine at Stanford. Dr. Mitchell's research relates to the development of new therapies for hematologic malignancies. She has a long-standing interest in IMPDH as a therapeutic target and has published extensively on the regulation of this enzyme and the potential role of inhibitors in the treatment of leukemia in pre-clinical and clinical investigations.
Thomas Quertermous, MD (Department of Medicine/Cardiovascular Medicine). Dr. Quertermous is Chief (Research) of Cardiovascular Medicine at Stanford. His laboratory employs two basic approaches of study to better understand the genetic basis of atherosclerotic heart disease. One approach uses basic molecular biology methodology, primarily working with cellular and genetic mouse models, and is focused on the recently identified apelin-APJ pathway. A second approach employs the power of modern human genetics. Initial studies have employed the candidate gene approach, and more recently whole genome association studies, to identify allelic variation that is associated with risk factor and disease susceptibility. This work has required the careful use of supervised and unsupervised learning techniques, and has inspired statistical method development (collaborators include W. Wong, R. Olshen, B. Efron, and R. Tibshirani).
Branimir Sikic, MD (Department of Medicine/Oncology). Dr. Sikic is the Professof of Medicine of Oncology. He is Co-Director of the Stanford Center for Clinical and Translational Education and Research (Spectrum) and Director of the Stanford Clinical and Translational Research Unit (CTRU). His lab's goals are to understand mechanisms of drug resistance in cancer cells and to develop more effective therapies. Current research ranges from biochemical and molecular studies in cellular models to Phase I, II, and III clinical trials, and translational studies of molecular determinants of therapeutic response and toxicity to anticancer drugs, particularly multidrug resistance (MDR1/P-glycoprotein), resistance to taxanes, and pharmacogenetics and pharmacogenomics.
Michael Snyder, PhD (Department of Genetics Operations). Dr. Snyder is the Stanford W. Ascherman Professor and Chair of Genetics, and the Director of the Center of Genomics and Personalized Medicine. Dr. Snyder received his PhD training at the California Institute of Technology and carried out postdoctoral training at Stanford. He is a leader in the field of functional genomics and proteomics. His laboratory conducted pioneering large-scale functional genomics studies, and currently carries out a variety of projects in the areas of genomics and proteomics both in yeast and humans.
Stanford Cancer Institute. This NCI-designated Comprehensive Cancer Center has multiple goals: understanding the origins of cancer and how to treat patients with particular diagnoses, including research in cancer stem cells, radiation biology, cancer biology, cancer imaging, molecular therapeutics, lymphoma and Hodgkin disease, immunology and immunotherapy, hematopoietic stem cell transplantation, cancer epidemiology, and cancer prevention and control. Students involved in this area will be required not only to participate in particular laboratory meetings, but also to attend weekly Friday morning seminars at which statistical aspects of research, including the design of clinical experimentation is discussed. The first life-saving treatment of Hodgkin’s disease originated at Stanford with the late Henry Kaplan and senior investigator Saul Rosenberg, and Rituximab comes from the laboratory of Ronald Levy, former Chief of the Division of Oncology at Stanford. Dr. Levy is a close colleague of many of those who make this proposal. These efforts continue to involve substantial statistical input.
Stanford Cardiovascular Institute. Stanford has a long history of excellence in cardiovascular medicine and related surgical transplantation. Specialties include but are not limited to bioengineering, biomarkers, imaging, ion channels as they relate to arrhythmias, metabolic disease, pulmonary medicine, vascular surgery, and women’s health. These and other areas have been and will continue to be fertile areas for collaboration of biostatistical sicentists and cardiovascular scientists. Nearly all makers of the proposal have been involved in one or several of these collaborations.
Institute for Immunity, Transplantation and Infection (ITI). This interdisciplinary institute is headed by colleague Mark Davis, whose research achievements include cloning the T-cell receptor. Goals include developing more powerful vaccines for old and new threats. Stanford colleagues have done cutting edge work on the design of vaccine clinical trials. Much ITI research involves immune monitoring as individuals age, with special interest in the decline of the immune system. These concerns are above and beyond thymic decline. Other ITI interests involve many autoimmune diseases, including but not limited to arthritis, lupus, and multiple sclerosis. A further topic of ITI interest concerns organ transplantation. Stanford's place in the history of cardiothoracic surgery is well known, not least in the field of heart transplantation. Now, of course, transplantation of other organs is also wide-spread. Organ rejection is not entirely understood. Here future steps will involve using donor stem cells to induce tolerance. These somewhat combinatorial problems are non-trivial mathematically and statistically. Recent attention has focused on assessing low but predictive levels of circulating proteins on different phenotypes. Assessing low levels of luminescence has been of interest. Robust regression has been adapted to that goal.
Center for Innovative Study Design (CISD). Through the CISD Spectrum provides assistance to investigators for designing clinical trials, including the biostatistical aspects such as sample size and data collection and analysis plans. The CISD has also facilitated contacts between trainees in the Department of Statistics and investigators, in projects involving design and analysis of clinical trials with biomarkers.