Program Description

The Systems Biology area of concentration (SB AoC) prepares students for exploring complex biological systems using the tools of computational cell biology, optical imaging and other quantitative approaches to analyze processes in living cells. Our program is designed to train students from diverse disciplinary backgrounds in the cutting-edge research techniques that comprise the interdisciplinary research of modern cell biology. Students are provided with rigorous cross training in areas of mathematical, physical, and computational sciences and biology. Systems Biology students take courses, attend seminars and work on interdisciplinary research projects to broaden and strengthen their abilities to do quantitative cell biology research.

The Systems Biology area of concentration is based within the Richard D. Berlin Center for Cell Analysis and Modeling (CCAM) at UConn Health. Established in 1994, CCAM has emerged as a Center that promotes the application of physics, chemistry and computation to cell biology. The environment of CCAM is designed to promote interdisciplinary interactions and its cadre of physical scientists are supported and valued in a way that is unique for a medical school.  CCAM is also the home of the Virtual Cell modeling and simulation software project (http://vcell.org) and COPASI software application for simulation and analysis of biochemical networks and their dynamics (http://copasi.org).

Note: Any questions not answered by this web page should be directed to the Systems Biology AoC Director or pursued via the UConn Health Graduate School Registrar’s Office or the Associate Dean of the Graduate School.

Major Steps in attaining the Ph.D. in the Systems Biology AoC

First Year

Second Year

Third and later Year(s)

  • Continuation of thesis research
  • Additional course work per Plan of Study
  • Dissertation prospectus: Doctoral Dissertation Proposal of the student’s proposed research project should be completed within 12 months of passing the preliminary exam and at least six months before the expected graduate date. It is filed on a specific form obtained at The Graduate School website (under Forms for Enrolled Doctoral Students).
  • Systems Biology Journal Club & Research in Progress seminar

      Final Year

          Systems Biology Research in Progress and Journal Club

          The SB AoC is unique in having a combined Research in Progress and Journal Club, every Friday at noon. This way all faculty and students equally attend and present all seminars. Each student in the AoC will be scheduled for one journal club and one research in progress presentation per year (for the first year, it’s only Journal Club).

          • MEDS 6497 Journal Club in Cell Analysis and Modeling (Fall and Spring; 1 credit)
            Reading and discussion of research at the interface of physical and cell biological research with emphasis on molecular aspects. Students and postdoctoral fellows present and discuss with faculty a recent paper from the literature.

          Systems Biology Seminar Series

          The Center for Cell Analysis and Modeling (CCAM) conducts an invited seminar series, meeting on Thursdays at 4pm during the academic year (https://health.uconn.edu/cell-analysis-modeling/ccam-events/) . Each SB AoC student is required to attend the seminars. Often, students and PostDocs (no faculty) will host the speaker for lunch, with time for informal discussions. Students may also be invited for a dinner with the speaker and other hosting faculty.

          Systems Biology Courses Strongly Recommended

            • MEDS 6455 Introduction to Systems Biology (Fall; 3 credits)
              Faculty: Blinov/Moraru
              Lecture/Seminars.
              The course will guide students into a biology world as seen by engineers, physicists, mathematicians and computer scientists. We will discuss topics such as: What is a predictive mathematical model? Which kinds of models describe biological reality? What are the dynamical behavior, stability, switching and stochasticity of a biological system? What resources do you need to start building a model? How models are stored, simulated and visualized? What are public databases and software tools available for a modeler?  The ultimate goal of the course is to provide students with necessary background to read modeling papers, choose Systems Biology resources that will help them in biological projects, and be able to select an appropriate modeling technique to be used with a biological project.

           

            • MEDS 5420. Molecular Genomics Practicum (Spring; 3 credits)
              Faculty: Michael Guertin
              Lecture/Seminars
              The course will teach students to comfortably navigate the command line; use scripting to automate processing and analysis of genomics data; align sequencing reads to reference genome; retrieve and analyze publicly available genomic data sets; visualize genomics data on a browser; perform alignment, peak calling, and motif analysis starting of raw ChIP-seq data; perform alignment, differential expression, and gene set enrichment analysis of raw RNA-seq data.

           

            • MEDS 6450. Optical Microscopy and Bioimaging (Fall; 2 credits)
              Faculty: Yu
              Lecture/Laboratory.
              The course presents the current state of the art of optical imaging techniques and their applications in biomedical research. The course materials cover both traditional microscopies (DIC, fluorescence etc.) that have been an integrated part of biologists’ tool-box, as well as more advance topics, such as single-molecule imaging and laser tweezers. Four lab sessions are incorporated in the classes to help students to gain some hand-on experiences. Strong emphasis will be given on current research and experimental design.

           

          • MEDS 5382. Practical Microscopy and Modeling for Cell Biologists (Spring; 2 credits)
            Faculty: Rodionov
            Modern cell biology builds upon sophisticated methods of high resolution microscopy. The objective of this course is to get students familiar with modern microscopy techniques and computational approaches that help to interpret results of microscopical observations.  The participating faculty members will give lectures, supervise the microscopy laboratory, and advise students on modeling exercises in the key areas of cell biology. Labs will include hands-on experience in the following microscopy techniques: fluorescence microscopy of living cells; fluorescence recovery after photobleaching (FRAP); foster resonance energy transfer (FRET); fluorescence correlation spectroscopy (FCS); 4D imaging; time-lapse microscopy; microinjection. The following topics will be covered: dynamics of the cytoskeleton; growth control; organelle biogenesis; intracellular trafficking; nuclear transport; regulation of ion channels; cell locomotion; signal transduction. Co- or prerequisite: none.
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