National Centers of Systems Biology
Graduate
Information is grouped by Center and the Centers are listed in chronological order with the oldest Center first
Center for Modular Biology (Harvard University)
Marine Biological Laboratory Physiology Course
The Center for Modular Biology provides support for students from outside biology to attend The MBL Physiology Course. The course, founded by Jacques Loeb and one of the oldest continually running biology courses in the world, has a distinguished history that includes the discovery of cyclin B, which led to a Nobel prize for Tim Hunt. Despite its name (which is unalterable since the course has been in existence since 1892), this course has been revamped by Ron Vale and Tim Mitchison into a systems biology course in which half the students come from biological backgrounds and half come from engineering, mathematics, physics or other quantitative sciences. This course is providing exactly the kind of meeting place, graduate training and cutting edge research for biologists and quantitative scientists that the National Centers of Systems Biology try to foster.
Harvard University Systems Biology PhD program
Together with the Harvard Medical School Department of Systems Biology the Center runs the Harvard cross-school PhD program in Systems Biology. Through coursework and collaborative research, the Program enables students to combine experimental and theoretical approaches to develop physical and quantitative models of biological processes. The Program aims to introduce students to the tools that are now available, and to help them select important unsolved problems in biology that may now be possible to address using quantitative and theoretical approaches.
Center for Quantitative Biology (Princeton University)
QCB at Princeton Ph.D. Program
The Program in Quantitative and Computational Biology (QCB) is intended to facilitate graduate education at Princeton at the interface of biology and the more quantitative sciences and computation. Administered from The Lewis-Sigler Institute for Integrative Genomics, QCB is a collaboration in multidisciplinary graduate education among faculty in the Institute and the Departments of Chemistry, Computer Science, Ecology and Evolutionary Biology, Molecular Biology, and Physics. The program covers the fields of genomics, computational biology, systems biology, biophysics, quantitative genetics, molecular evolution, and microbial interactions.
Center for Systems Biology (Institute for Systems Biology, Seattle)
Since 2006, the Institute for Systems Biology has had 32 graduate students, 70 postdoctoral fellows, and has been acknowledged by The Scientist as a “Best Place to Work: Postdocs”, in the top ten in 2009 (7) and top fifteen in 2008 (13). In 2008, a Postdoctoral Association was formed to provide a formal forum for scientific exchange, professional development and mentoring. The Association hosts postdoctoral speakers and Faculty, as well as specialized ‘topic’ guest speakers, addressing such challenges as work-life balance, academic career path options and alternatives, and effective grant writing. In 2009 a Graduate student group was formed to provide peer-to-peer mentoring and foster a Graduate student support network. The Association and Group share ‘topic’ guest lecturers with ISB-at-large.
Center for Complex Biological Systems (UC Irvine)
Ph.D. training program in Mathematical, Computational and Systems Biology
The Center for Complex Biological Systems (CCBS) at the University of California Irvine administers a Ph.D. training program in Mathematical, Computational and Systems Biology that was developed with the assistance of a grant from the Howard Hughes Medical Institute to create new interdisciplinary Ph.D. programs. Currently, this program is supported by two NIH training grants.
The goal of UCI’s program in Mathematical, Computational and Systems Biology (MCSB) is to provide students from a variety of educational backgrounds with Ph.D. training suitable for research careers in the nascent field of Systems Biology. The program emphasizes in-depth classroom study, interdisciplinary research rotations, and individualized advising. Currently, the program begins with an initial “gateway” year, known as the Mathematical and Computational Biology (MCB) program, during which students receive basic training in principles of biology, as well as in mathematics, engineering and computer science. Students also participate in research rotations, workshops, and directed reading of the Systems Biology literature. Upon successful completion of the MCB year, students select a thesis advisor from among the participating faculty, who represent departments throughout the biological, physical and information sciences and engineering. Students fulfill the remainder of their degree requirements according to the guidelines of the departmental programs to which their thesis advisors belong, at the same time continuing to participate in workshops, retreats, journal clubs and other activities of the MCSB program. At some point in the future, it is expected that MCSB students will also have the option of receiving an interdisciplinary degree independent from departmental program requirements.
Systems Biology Center New York (SBCNY)
Systems Biomedicine: Molecules, Cells and Networks
This active-learning course will introduce core biochemical, cell biological and molecular mechanisms together with basic bioinformatic and systems biology concepts and applications in the context of human biomedical research. The emphasis is ‘topdown’, beginning with a pathophysiological condition studied from a clinical perspective and moving towards explication of the molecular and metabolic logic, regulatory circuits and cell and tissue specific properties that distinguish the disease and normal state. The goals of this course are to provide inquisitive, self-directed students with an appreciation of the complexity of biological systems across scales and to give insight into pathophysiology as a basis for scientific enquiry and development of new therapeutic strategies. Students will be guided to relevant textbook material and current reviews, and will also participate in analyses of primary journal articles to enhance their study of scientific method and to illustrate a variety of experimental and computational approaches to contemporary translational biomedicine. Problem sets and the methodologies for handling large data sets, including epidemiological and genetic data, will be introduced.
Systems Biology: Biomedical Modeling
We take a case-based approach to teach contemporary mathematical modeling techniques to graduate students. Lectures provide biological background and describe the development of both classical mathematical models and more recent representations of biological processes. Students are taught how to analyze the models and use computation to generate predictions that may be experimentally tested. The course is useful for students who plan to use experimental techniques as their primary approach but who will employ computational modeling as a tool to obtain integrative understanding of complex systems. The course should also be valuable as an introductory overview for students planning to conduct their thesis research in computational modeling of biological systems.
The course has four sections to cover different modeling approaches that are currently being used in biomedical research. These approaches can be classified as: 1) graph theory and network analysis; 2) statistical models, including principal components and regression; 3) ordinary differential equation & partial differential equation-based models; and 4) stochastic models. Matlab will be the major modeling program used for the course, but other programs are used when they are more appropriate. For each section introductory lectures are followed by one or more cases that require the students to implement and analyze mathematical models. Considerable class time is therefore devoted to “hands on” problem solving sessions in which the students can get assistance from the instructors and teaching assistant.
Recent, rapid progress in genomic and computational biology and technologies offer the potential for dramatic advances in the application of genomic sciences to medical practice. This graduate course will provide a detailed overview of the burgeoning field of genomic medicine and pharmacogenomics.
Applied Mathematics for Biologists
These lectures are from a course taught by Lawrence Sirovich at the Courant Institute for Mathematical Sciences in the Fall 2008. The purpose of this course is to present an extensive, integrated treatment of applied mathematics useful to science students who wish to include mathematical modeling and simulation in their future research.
Pharmacology and Systems Biology Multidisciplinary Training Area
The research programs within the Pharmacology and Systems Biology (PSB) multidisciplinary training area share the following common theme. Knowledge of the health or disease state of a cell, tissue, or organism, requires an understanding of networks of molecular interactions within and between cells. Thus, new and more effective therapies can be developed by considering how biological components interact with each other to produce emergent behaviors.
Accordingly the PSB curriculum emphasizes training in several disciplines and approaches ranging from molecular and cell biology to genetics and biochemistry, from physiology and pharmacology to neuroscience and computational biology, from single cell model systems to organ-level and animal studies. The PSB faculty investigate disease processes and drug actions in a variety of cell types but share the underlying philosophy that systems approaches are required for transformative advances. Because mathematics provides a common language for understanding physical and biological processes, quantitative reasoning and computational approaches are integrated into the PSB curriculum and employed by many of the PSB faculty. The core courses, journal clubs, lab rotations, and works-in-progress presentations provide our students with an understanding of how to use diverse data sets to delineate biological networks, how to translate this information into new therapeutic and preventive strategies, and how to apply this paradigm to their own research.
Chicago Center for Systems Biology
Systems Biology Ph.D. Program Overview
A new graduate training program builds on the University of Chicago’s rich tradition of organizing interdisciplinary programs and facilities to encourage collaborative learning and research. Within the Biological Sciences Division (BSD) exists the Committee on Genetics, Genomics and Systems Biology.
Post-Baccalaureate Research Education Program (PREP), The University of Chicago
The Center will fund and host two participants in PREP per year.