Graduate

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.

A Short Course in Systems Biology: Morphogenesis & Spatial Dynamics

January 7-12, 2013 (Preparatory Workshops)
January 14-25, 2013 (Core Course)

We welcome scientists from all disciplines (biological, physical, mathematical, computational and engineering) with an interest in developing Systems Biology skills. This high-level introductory course is geared towards senior graduate students, postdocs, faculty and industry researchers with a long term interest in pursuing Systems Biology research but who have little or no prior experience in this emerging discipline.

The course design will provide a mix of strategies to help participants:

identify and pose scientific questions from a Systems Biology perspective,
provide biological methodologies for gathering the appropriate kinds of data
and apply mathematical tools for analyses and modeling.

The subject emphasis of the first course will be on cellular controls of cell differentiation, with a central theme of morphogenesis and spatial dynamics. Research models that are dependent on complex spatial information will be the primary focus since this builds on the extensive research expertise of participating faculty, departments and existing centers of excellence at UCI. The course consists of both didactic lectures and hands-on “wet/dry” laboratories and tutorials.

Center for Genome Dynamics (The Jackson Laboratory)

Short Course on Systems Genetics
The one-week Short Course on Systems Genetics covers computational and experimental approaches to genetic studies that utilize whole genome approaches. The course is led by Gary Churchill of the Center for Genome Dynamics and lectures and computer workshops are designed to accommodate students with a wide variety of backgrounds.

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 and Synthetic Biology (UC San Francisco)

IPQB Ph.D. Program
UCSF has an umbrella graduate program that brings together three programs focused on applying physical, mathematical, and systems approaches to biological problems. The Integrative Program in Quantitative Biology (IPQB) establishes an innovative common core curriculum drawn from the PhD curricula in Biophysics, Bioinformatics, and Complex Biological Systems. This program fits very well with the systems and quantitative biology themes of our Center. Thus, we’ve been contributing Center resources to course development in this UCSF-generated graduate program. In the fall semesters, we participate in the development and execution of the Systems Biology Course organized by IPQB for first year graduate students. This course is co-taught by center co-investigator Hana El-Samad and teaching assistance is provided by several Center-associated postdoctoral fellows and graduate students, as well as the Center’s Education & Outreach Coordinator, Veronica Zepeda. Furthermore, an emphasis on Complex Biological Systems was recently created in the IPQB program and its development is greatly benefitting from associations with our Center.

Minicourses within IPQB: Two of our Systems Biology Fellows, Matt Thomson and David Soloveichik, developed a Center-generated Minicourse for the 2012 spring semester of the IPQB program, entitled ‘How do organisms, cells, and molecules organize themselves: distributed computation in biology.’ Biological systems often solve problems through distributed computations, where individual agents (proteins, cells, organisms) collect information and dynamically interact to accomplish a task. Examples of distributed computation exist across scales of biological organization: the computation of cell morphology by the actin cytoskeleton; the selection of high affinity B-cell clones by the immune system; sensory integration in the brain; choice of flight direction in bird flocks. Even regulatory networks can be thought of as multi-agent systems, in which a set of molecules has to make a concerted decision. Computer science and statistical physics have developed rich theoretical tools for studying multi-agent systems and collective behaviors. This course drew on this rich history, combining it with an analysis of specific biological examples, to discuss the development of a theory for distributed computation in biology. Topics included chemical reaction networks, cell polarity, immune system dynamics, Hopfield neural networks, and flocking. Theoretical investigation into distributed algorithms in biology could uncover common principles used across systems and common implementation challenges like the aggregation of noisy signals and decision making in groups. For the spring 2013 Minicourse series, Matt Thomson and seed grant recipient Zev Gartner are developing the Minicourse ‘Multicellular systems biology’.

Tetrad Program
The UCSF joint Tetrad Program includes the biochemistry and molecular biology, cell biology, genetics and developmental biology programs. Several graduate students who are members of Center labs are also part of this graduate program.

‘What can you be with a PhD’ Workshop
In November 2012, the Center Education Coordinator co-organized a workshop at Prairie View A&M University, a historically black university in Prairie View, Texas. The workshop was titled “What can you be with a PhD: Navigating Interdisciplinary Research in Engineering and Life Sciences” and focused on the varied reasons for pursuing a graduate degree and determining which university/graduate program would be the best fit for a student. Over 100 undergraduate students registered and attended the workshop which included speakers from MIT, UC Berkeley, Texas A&M, Rice University, and UCSF. The workshop was co-organized by our UCSF Center, the SynBERC Center at UC Berkeley, and Prairie View A&M University.

Center for Systems Biology (Institute for Systems Biology)

Graduate students. Since 2006, 25 graduate students have been supervised by ISB Faculty through affiliate appointments with the University of Washington Departments of Bioengineering, Immunology, Computer science, Biology, Biochemistry, Microbiology, and Genome sciences, as well as with the interdisciplinary programs in Molecular and Cellular Biology, and Biomolecular Structure and Design. In 2009, the Center formed a graduate student group to provide career development training. A monthly lunch for the student group is managed by a Center senior scientist, and topics have included ‘op-ed’ discussions relating to current research, laboratory practice, and choosing a postdoctoral position.

Postdoctoral fellows. In 2008, a “Postdoc Association” was formed in response to an ISB survey which indicated postdoctoral fellows needed additional career resources and a formal forum for increased social networking, both within and outside ISB. The Association developed the first annual “ISB Postdoc Retreat”, an all day meeting which also included graduate students as presenters. Agenda items included: “Grant writing at ISB”, discussions on specific research, “Postdoc issues forum”, “All you need to know about IP”, and a workshop “How to pitch to a biotech”. Additionally the Association is a member of the “Postdoc Administrative Leaders”, a cross-organizational group which includes the University of Washington, Fred Hutchinson Cancer Research Center, Seattle BioMed, and Seattle Children’s Hospital. The group was formed to identify and address institutional postdoctoral challenges, and is brainstorming a “Careers in Industry” workshop with the Washington Biotechnology and Biomedical Association (WBBA) early in 2011.

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.

Duke Center for Systems Biology

The DCSB supports the PhD program in Computational Biology and Bioinformatics. CBB is an integrative, multi-disciplinary training program that encompasses the study of biology using computational and quantitative methods. In and out of the classroom, students learn to apply the tools of statistics, mathematics, computer science and informatics to biological problems. The vibrant and innovative Duke research in these fields provides exciting interactions between biological and computational scientists.

Systems Biology Center New York (SBCNY)

PhD Training Program: Systems Biology of Disease and Therapeutics
The Graduate School of Biomedical Sciences at the Icahn School of Medicine at Mount Sinai offers a PhD in Biomedical Sciences in several training areas, including Systems Biology of Disease and Therapeutics (SBDT). The SBDT program trains graduate students in research that aims to understand the complex interactions underlying human disease, and how drugs can be used to treat these diseases. Knowledge of the healthy and diseased states of a cell, tissue, or organism, requires an understanding of networks of molecular interactions within and between cells. The SBDT curriculum emphasizes the integration of concepts from multiple disciplines: genomics, molecular biology and biochemistry, physiology, and pharmacology. Important approaches for this integration are quantitative reasoning and computational biology. This program, set within a tightly knit medical school and hospital environment, provides unique opportunities to study systems from genomes and proteins to cells to animal models to humans at both the bench and the bedside.

Systems Biology Courses on Coursera
Systems Biology Center New York investigators will begin offering three courses that focus on training students to use computation to convert the information in large and small data-sets in biomedical sciences to understand disease progression, adverse events in individual patients, and to predict efficacy of drug therapy. The three courses – Introduction to Systems Biology, Network Analysis in Systems Biology, and Dynamical Modeling Methods for Systems Biology – will be offered in 2013. The courses provide a solid basis for understanding the new era of personalized and precision medicine that is being made possible by advanced gene sequencing technologies.