Cell Analysis and Modeling Graduate Program
The Cell Analysis and Modeling graduate program at the
University of Connecticut Health Center offers training leading
to a Ph.D. in biomedical sciences. The curriculum for the first
year includes a choice of core courses in the basic biomedical
sciences that have been specially formulated to acquaint the
student with the principles and practice of modern biomedical
research. These core courses include Immunology, Genetics,
Biochemistry, Cell Biology and Developmental Biology. In
addition to these core courses students also participate in the
Computational Analysis and Modeling Journal Club and Laboratory
Rotations during the first year. During the second year students
can choose from advanced courses in a number of topics. In
consultation with their advisory committee, students work out a
supplementary program of advanced courses, laboratory and
computer experiences and independent study based on their
previous experiences and interests that is designed to prepare
them for general examinations near the end of their second year. All courses are described in the
Catalogue found on the
Registration page. Thesis research begins in the second or third
year, and research and thesis writing normally occupy the third
and fourth years.
Guide for Graduate Students
Course work requirements are consistent with the current
Graduate Program in Biomedical Sciences requirements. The PhD
degree requires at least 44 credits beyond the baccalaureate or
its equivalent. These credits will be composed of a set of core
courses and a number of electives, as outlined below.
At least 15 credits of GRAD 6950 (Dissertation Research) must
be included in the Plan of Study, representing the research
effort the student devotes to the dissertation.
The Ph.D. course work will be consistent with the standard
Graduate School credit requirement for students. The credits
required for the Ph.D. may be earned through regular courses
which include BMS required and elective courses, journal clubs
and lab rotations/independent studies. This includes all courses
numbered in the 5300 or 6400 series. Special topics courses may
account for 9 credit hours and at least 8 credit hours will
typically be from the Cell Analysis and Modeling journal clubs.
Additional credit hours should be taken as lab
Strongly recommended courses:
MEDS 5380. Cell Biology
4 credits. Lecture. Prerequisite: MEDS 350.
Basic eucaryotic cell biology. Major topics include: Methods in
Cell Biology; Cell Growth and Proliferation; Cytoskeleton;
Transport: Hormone Response; Cytoplasmic Organelles and Membrane
Structure, Function, Biogenesis, Transport and Sorting; Cell
Motility; Chromatin Structure and Organization; and
Extracellular Matrix and Cell Adhesion.
MEDS 5382. From Microscope to Model: Quantitative
Approaches in Cell Biology
2 credits. Lecture (Currently listed as Molecular Mechanisms of
Modern cell biology builds upon a combination of sophisticated
methods of high resolution microscopy and computational
approaches to modeling of cell physiological processes in the
context of the actual three dimensional structure of individual
cells. The objective of this course is to develop a general view
on the basic cell biology problems from a multidisciplinary
perspective. The participating faculty members will give
lectures, advise students on modeling exercises and supervise
the microscopy laboratory in the key areas of cell biology and
modeling. The following topics will be covered: Dynamics of
cytoskeleton; growth control; organelle biogenesis;
intracellular trafficking; nuclear transport; regulation of ion
channels; cell locomotion; signal transduction. Labs will
include hands-on experience in the following microscopy
techniques: Fluorescence microscopy of living cells;
microinjection; fluorescence recovery after photobleaching
(FRAP); fluorescence correlation spectroscopy (FCS); 4D imaging;
time-lapse microscopy. Co- or prerequisite: This course is
designed to be a companion course with Cell Biology I.
MEDS 6450. Optical Microscopy and Bioimaging
3 credits. 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 6460. Advanced Optical Microscopy and Bio-imaging
3 credits. Lecture/Laboratory y. Prerequisite: BME 341.
This course will cover several aspects of state of the art
biological and biophysical imaging. We will focus on advanced
techniques including nonlinear optical processes (multi-photon
excitation, second harmonic generation, and stimulated Raman
processes), as well as optical coherence tomography. Three lab
projects will supplement the lectures, providing hands-on
experience with nonlinear optical methods. Special emphasis will
be given to current imaging literature and experimental design.
BME 6150. Computational Cell Biology for Biomedical
3 credits. Lecture.
In the last decade, interdisciplinary science has established
itself as a leading area of scientific investigation. The use of
physics and mathematics to help understand biological systems
hints at being one of the major scientific frontiers of this
coming century. This course looks at biology at three separate
length scales: molecular, cellular, and organismal/population.
We will find that the math/physics of elasticity, hydrodynamics,
statistical mechanics and reaction/diffusion can explain a broad
range of phenomena throughout these size ranges. This course
stresses the physical intuition of how to apply quantitative
methods to the study of biology through the use of dimensional
analysis, analytic calculation and computer modeling
MEDS 5351. Biochemistry II
3 credits. Lecture.
This course covers fundamentals of biomolecular interactions and
protein structure. Additionally, the course covers the
structure/function of select proteins and enzymes essential to
the following: metabolic pathways, DNA/RNA transactions, gene
expression, cell cycle and signal transduction, and the
In addition to the 15 credit hours of Doctoral Dissertation
research, students are required to take the Cell Analysis and
Modeling journal club associated with CCAM.
MEDS 6497 Journal Club in Cell Analysis and Modeling.
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.
Trainees in the Cell Analysis and Modeling AoC will also
participate in CCAM Group meeting. The weekly CCAM Group Meeting
features research updates from all CCAM-associated laboratories.
Because this meeting is attended by all scientific personnel
associated with the Center, it provides not only scientific
continuity but also the social continuity that helps to maintain
the unique interdisciplinary focus of the AoC as a whole. Talks
at this meeting encompass all research areas, including cell and
molecular biology, mathematical modeling, optical engineering,
organic chemistry and computational techniques. The diversity of
topics makes this a unique learning environment for both
trainees and faculty.
Students will have access to a diverse set of seminar
programs and research meetings. The Center for Cell Analysis and
Modeling (CCAM) Seminar Series features invited speakers of
international renown. In addition to the main seminar program
there is also a “Physics in Biology Seminars” series, and often
a single invited speaker will present a seminar in each of these
series, the former designed for a cell biology audience and the
latter for a more theoretical audience.
Courses available to trainees during the first and second
years include all courses in the Biomedical Sciences and
Graduate School curricula. As well, the independent study
mechanism will be used to alleviate specific deficiencies in a
cross-disciplinary area primarily through short, modular study
rotations with an identified set of CCAM faculty members. These
may be pursued in the first year, for example for students who
lack sufficient biology background to successfully complete
traditional first year courses, or may be pursued in the second
year, for example for students lacking sufficient training in
mathematics, physics, or optical engineering.
The electives related to the degree contain computational
and/or biophysical methods developed by faculty associated with
CCAM and may be also listed in other programs, specifically
Biomedical Engineering (BME). These courses are:
MEDS 5327 The Biochemical and Genetic Language of
4 credits. Lecture
This course covers the fundamental biochemical and genetic
principles that underlie all areas of modern biology. The
biochemistry and genetics of both prokaryotes and eukaryotes and
addressed. Reading and discussion of papers in the literature is
an important element of the course. Instructor consent required.
BME 5100 Physiological Modeling
3 credits. Lecture. Recommended preparation: BME 3100 and BM
3400 (or equivalent).
Unified study of engineering techniques and basic principles in
modeling physiological systems. Focuses on membrane biophysics,
biological modeling, and systems control theory. Significant
engineering and software design is incorporated in homework
assignments using MATLAB and SIMULINK.
MEDS 5378 Computational Neuroscience
3 – 4 credits
Students study the function of single neurons and neural systems
by the use of simulations on a computer. The course will combine
lectures and classroom discussions with conducting computer
simulations. The simulations will include exercises and a term
project. Each student will complete a term project of neural
simulation to be developed during the second half of the
semester. The topic of the term project should be approved by
the instructor by the middle of the semester. The grade will be
based on the exercise and the term project.
BME 5800. Bioinformatics
3 credits. Lecture. Recommended preparation: BME 4800 (or
Advanced mathematical models and computational techniques in
bioinformatics. Topics covered include genome mapping and
sequencing, sequence alignment, database search, gene
prediction, genome rearrangements, phylogenetic trees, and
BME 6140. Cellular Systems Modeling
3 credits. Lecture. Prerequisite: BME 5600.
Cellular response to drugs and toxins, as well as normal cell
processes such as proliferation, growth and motility often
involve receptor-ligand binding and subsequent intracellular
processes. Focuses on mathematical formulation of equations for
key cellular events including binding of ligands with receptors
on the cell surface, trafficking of the receptor-ligand complex
within the cell and cell signaling by second messengers.
Background material in molecular biology, cell physiology,
estimation of parameters needed for the model equations from
published literature and solution of the equations using
available computer programs are included. Examples from the
current literature of cell processes such as response to drugs
and proliferation will be simulated with the model equations.
MEDS 5325. Practical Applications of Sequence Analysis
2 credits. Lecture.
Provides an understanding of how to analyze genetic sequence
information by computer. Includes basic analyses such as
restriction mapping and detection of coding sequences, to more
advanced analyses such as sequence similarity searching,
sequence comparisons and multi-sequence alignment, prediction of
functional motifs from primary sequence information, and current
tools for mapping, assembly, and analysis of genomic sequence
information. The course emphasizes NCBI and other Web-based
tools currently available for use. Students will be exposed to
the Genetic Computer Group (GCG) series of sequence analysis
programs, but these are not emphasized. Students are required to
complete a series of computer-based exercises to demonstrate
proficiency in the application and use of the various computer
programs presented in class
BME 6110. Computational Neuroscience
3 credits. Lecture.
Explores the function of single neurons and neural systems by
the use of simulations on a computer.
Combines lectures and classroom discussions with conducting
computer simulations. The simulations
include exercises and a term project.
The following faculty will be responsible for the subsequent
list of courses: Blinov, Carson, Cowan, Huber, Loew, Mayer,
Mohler, Moraru, Rodionov, Schaff, Schiller, Slepchenko,
Wolgemuth, and Yu.
MEDS 5395. Independent Study
1-6 credits. Independent Study.
MEDS 6495. Independent Study
1-6 credits. Independent study.
A reading course for those wishing to pursue special topics in
the biomedical sciences under faculty supervision.
MEDS 6496. Laboratory Rotation
1-6 credits. Laboratory.
MEDS 6497. Graduate Seminar
1-6 credits. Seminar. May be repeated for credit with a change
of content. Reading and discussion of recent research
developments in various areas of biomedical science.
GRAD 6950. Doctoral Dissertation Research,
Variable credit. Hours by arrangement
GRAD 6998. Special Readings (Doctoral).
Noncredit. Continuing registration for doctoral students prior
to reaching candidacy.
GRAD 6999. Dissertation Preparation.
Noncredit. Continuing registration for doctoral candidates.
First year students generally enter the biomedical sciences
program uncommitted to a specific AoC and are each assigned a
first year advisory committee by the Associate Dean of the
Graduate School at the Health Center. Once a thesis research
laboratory has been chosen (typically at the start of the second
year), a thesis advisory committee is formed after consultation
between the student and the major advisor. It includes at least
two associate advisors. The major advisor and at least one
associate advisor are members of the graduate faculty appointed
to advise Ph.D. students in the student’s field of study and
AoC. One associate advisor may be chosen from outside the
University in accordance with Graduate School procedures.
The student must prepare a Plan of Study that must be
approved by the advisory committee and the Executive Committee
of the Graduate School. The plan will specify all formal courses
which are to be completed, the scheduling of the General
Examination, and the general area of the thesis research. The
Plan of Study must gain the approval of the student’s advisory
committee before the General Examination can be taken.
The general examination is taken near the end of the
student's sequence of formal courses, as contained on the Plan
of Study. There will be both a written and oral examination. No
fewer than five faculty members, including all members of the
student’s advisory committee, participate in the examination. No
fewer than five faculty shall be invited to submit questions and
to evaluate the student's answers.
For the Cell Analysis and Modeling AoC, the examination will
be set by the executive committee of the AoC with approval by
the Graduate Programs Committee at UCHC. Initially the
examination will consist of the preparation and defense of a
research proposal, following the format of the NIH National
Research Service Award (NRSA).
As the student reaches the point of undertaking the major
part of the dissertation research, he or she prepares a proposal
(10 pages in length) that is composed of several parts. These
include the background and context of the proposed topic, a
description of the work to be done, and the methodology through
which it will be accomplished. The thesis committee typically
reviews the proposal, followed by the Graduate Programs
Committee. It is finally approved by the GFC Executive
Upon approval of the Plan of Study, passing the General
Examination, and having had the Dissertation Proposal fully
approved by the Executive Committee of the Graduate Faculty
Council, the student becomes a candidate for the degree of
Doctor of Philosophy. Students are notified of their advancement
A dissertation representing a significant contribution to
ongoing research in the candidate’s field is required. The
advisory committee gives final approval of the dissertation
following the final examination.
The final examination is oral and under the jurisdiction of
the advisory committee. It deals mainly with the subject matter
of the dissertation. Invitation to participate in the
examination will be issued by the advisory committee, although
members of the faculty may attend. No fewer than five members of
the faculty, including all members of the candidate’s advisory
committee, participate in the final examination.