- Core Credit Requirements
- Required Focus Areas
- Scientific Ethics
- Scientific Communication
- Proposal Writing
- Analysis of Data
- Training Group Introductory Courses
- Seminar Course
- Recommended First-Year Classes
The PULSe curriculum has been designed to provide students with the basic information they will need to succeed in the PULSe TGs during their Ph.D. work. In addition, the curriculum provides a broad and interdisciplinary program of study with the maximum possible flexibility so that students may tailor their programs to their individual needs and explore several training areas before deciding on one for their thesis program. The core requirements are a combination of general courses, TG-specific survey courses and laboratory rotations.
- 6 credits of general course work, divided into four focus areas (described below);
- 4-7 credits of TG Introductory courses (2 courses of 2 - 4 credits each); TGs may require additional, specialty coursework, beyond the core requirements.
- 1 credit of a participatory seminar course;
- 4 rotation credits of GRAD 60100, performing lab rotations in the first year. Not to be listed on the Plan of Study;
- 69900 research credits (number of 69900 hours taken are determined on an individual basis by the PULSe Office each semester; note that a total of 90 credit hours are required for the Ph.D.);
- The student's research progress will be monitored for its ability to meet demands for publication in a peer-reviewed journal. This is one component of the Advisory Committee evaluation performed each year.
Focus Area Courses: There are four required focus areas. One course must be taken to satisfy each area. The core is designed to provide breadth to otherwise very specialized training; therefore, the same course may not be counted as satisfying multiple areas.
- Scientific Ethics: One of the following courses must be taken at any time during PULSe graduate training.
- GRAD 61200 - Responsible Conduct in Research (1 credit) Lecture once per week for 50 minutes per meeting for 8 weeks. Offered: Fall, Spring.Overview of values, professional standards, and regulations that define responsible conduct in research. Students learn the values and standards of responsible research through readings and lecture/discussion and practice application of these values and standards to research situations through class discussion of case studies from life sciences research.
- HORT 60100 - Planning and Presenting Horticulture Research (1 credit) Lecture once per week for 50 minutes per meeting for 16 weeks. Typically Offered Fall. Students will be familiarized with planning and presenting plant science and horticulture research. Written and oral presentations based on the students' proposed thesis topic will be evaluated. Class trips required. Students will pay individual lodging or meal expenses where necessary. Instructor permission required.
- Scientific Communication:
- GRAD 60100 - PULSe Scientific Communications (1 credit/taken twice). Designed to develop the skills needed for effective scientific presentations. Students register for this course in the Fall and Spring semesters of Year 1 of study.
- Proposal Writing: One of the following courses must be completed before the end of Year 2 of PULSe graduate training; however, the proposal writing class should not be taken during the first year.
- HORT 60300 - Grants and Grantsmanship (1 credit). Lecture once per week for 50 minutes per meeting for 16 weeks. Offered Spring. Focuses on funding opportunities in agricultural research and techniques of writing successful scientific grant proposals. Students will write a proposal on a research topic of their choice during the course, and they will gain experience in the peer review process by preparing written reviews of proposals and participating in a panel meeting in which proposals are discussed and ranked.
- MCMP 62500 - Grant Writing (1 credit). Offered Fall. Instructions for the preparation and submission of an NIH-style RO1 grant proposal will be covered. Each student will write and submit a complete proposal. The proposals will be student reviewed in a mock study section at the end of the course.
- Analysis of Data: This requirement is designed to train students from a variety of backgrounds in methods of acquiring and/or analyzing data in any of the various disciplines within PULSe. As such, there is a menu of courses from which students (and TGs) can choose depending on individual student or TG needs. These courses and their descriptions are listed below. Students must satisfy this requirement by the end of Year 2.
- BIOL 59500 - Methods and Measurements in Physical Biochemistry (3 credits) Lecture 3 times per week for 50 minutes per meeting for 16 weeks. Offered: Fall. Introduction to physical methods in biochemistry and physical measurements of biological systems, such as UV/Visspectroscopy, circular dichroism, IR and Raman spectroscopy, fluorescence, neutron diffraction, light scattering, scattering from ordered materials, x-ray crystallography, NMR and ESR spectroscopy, electron microscopy, mass spectroscopy. Application of these techniques to studies of structure and dynamic behavior of biological macromolecules, composition and orientation of structural elements and cofactors, ligand binding and conformational change in biological interactions and detailed probes of local changes in structure, solvent accessibility and specific bonds formed in biological reactions. Interpretation of the resulting data and analysis of strengths and limitations of each technique. Examples from research articles are discussed that illustrate how these methods are used in modern biochemistry. Prerequisite: Introductory Calculus and Physics or permission of the instructor.
- MCMP 51400 - Biomolecular Interactions: Theory and Practice (Four 1-credit modules) In order to fulfill this course requirement, PULSe students are required to take Module 1 and at least two other modules for a total of three credit hours. Offered: Spring. Theory and applications of biophysical and bioanalytical methods for the identification and quantification of biological and pharmaceutical samples. Methods to be discussed include chromatography, electrophoresis, optical spectroscopy, mass spectrometry, electrochemical methods, radiochemical analysis, ultracentrifugation, calorimetry and surface phasmon resonance. Physical measurements, such as binding equilibrium, kineticsand macromolecular structure will be discussed. Fundamentals of each technique will be discussed, with a major focus on the application and integration of presented methods for the analysis of biological problems. Prequisite: MCMP 31000 or authorized equivalent courses or consent of instructor.
- STAT 50300 - Statistical Methods for Biology (3 credits) Lecture 3 times per week for 50 minutes per meeting for 16 weeks. Offered: Fall, Spring. Introductory statistical methods, with emphasis on applications in biology. Topics include descriptive statistics, binomial and normal distributions, confidence interval estimation, hypothesis testing, analysis of variance, introduction tononparametric testing, linear regression and correlation, goodness-of-fit tests, and contingency tables. Credit allowed in either 50300 or 51100 but not both. Prerequisite: Calculus.
- STAT 51100 - Statistical Methods (3 credits) Lecture 3 times per week for 50 minutes per meeting for 16 weeks. Offered: Fall, Spring. Descriptive statistics; elementary probability; sampling distributions; inference, testing hypotheses, and estimation; normal, binomial, Poisson, hypergeometric distributions; one-way analysis of variance; contingency tables; regression. Credit allowed in either 503 or 511 but not both. Prequisite: MA 16200 or authorized equivalent courses or consent of instructor.
- STAT 51200 - Applied Regression Analysis (3 credits) Lecture 3 times per week for 50 minutes per meeting for 16 weeks. Offered: Fall, Spring. Inference in simple and multiple linear regression, residual analysis, transformations, polynomial regression, model building with real data, nonlinear regression. One-way and two-way analysis of variance, multiple comparisons, fixed and random factors, analysis of covariance. Use of existing statistical computer programs. Prequisite: STAT 50300, STAT 51100, STAT 51700, or consent of instructor.
- CS 59000 Computing for Life Sciences (3 credits) Lecture 3 times per week for 50 minutes per meeting for 16 weeks. Offered: Fall. Basic bioinformatics algorithms and Python programming. Course topics include biological databases, algorithms for biological sequence (DNA, protein), sequence alignment and database search, sequence motif search (DNA, protein), sequence alignment and database search, sequence motif search, protein tertiary (3D0 structure comparison, protein-proteing interaction and comparative genomics. This course is targeted at non-CS majors who are working or interested in the bioinformatics field. No programming experience is required.
- CS 66200 - Pattern Recognition and Decision-Making Processes (3 credits) Lecture 3 times per week for 50 minutes per meeting for 16 weeks. Offered: Spring. Introduction to the basic concepts and various approaches of pattern recognition and decision-making processes. Topics include various classifier designs,evaluation of classifiability, learning machines, feature extraction, and modeling. Prerequisite: ECE 30200 or authorized equivalent courses or consent of instructor.
- CS 53000 -Introduction to Scientific Visualization (3 credits) Lecture 3 times per week for 50 minutes per meeting for 16 weeks. Offered: Spring. Teaches the fundamentals of scientific visualization and prepares students to apply these techniques in fields such as astronomy, biology, chemistry, engineering, and physics. Emphasis is on the presentation of scalar, vector, and tensor fields; data sampling and resampling; and reconstruction using multivariate finite elements (surfaces, volumes, and surfaces on surfaces). Prerequisite: CS 25100 or authorized equivalent courses or consent of instructor.
- BIOL 59500/CS 59000 - Protein Bioinformatics (3 credits) Lecture 2 times per week for 75 minutes per meeting for 16 weeks. Offered: Spring. Algorithmic challenges in analyzing sequences (what genes encode an organism, and how are genes related across organisms), structures (what do the protein constructed for these genes look like, and what does that imply about their functions), interactions (how are proteins helping and hindering each other in complex networks), and the underlying experimental data. The computational techniques applied include dynamic programming, graph search, hidden Markov models, clustering, optimization and simulation. Computer Science Department registration approval is required.
Training Group Introductory Courses: (4-7 credits) The TG Introductory courses generally involve two classes of two to four (2-4) credits each. PULSe students must enroll in at least two of these courses in addition to the core courses. One introductory course must be within a student's TG, and the second introductory class must be taken outside of a student's TG. These courses are to be completed by the end of Year 2. Some TGS require more than one introductory course within the group.
- Biomolecular Structure and Biophysics - For students in this TG, BIOL 59500 must be taken:
- BIOL 59500 - Methods Measurement Biophysical Chemistry (3 credits) Typically Offered Fall
- MCMP 51400 Biomolecular Interactions: Theory and Practice Modules 1 and 2 (2-4 credits) Typically Offered Spring
- Biotechnology - For students in this TG, six credit hours from the courses below mujst be taken. Course availability is dependent on enrollments. For this reason, appropriate courses may be substituted. Contact the PULSe office and/or the Biotechnology TG Curriculum Committee representative for course advice and approval.
. ABE 49500/69500 Cell and Molecular Design Principles (3 credits)
. ABE 56000/BME 52100 Biosensors: Applications and Fundamentals (3 credits) Typically Offered Fall
. ABE 59100 Biotechnology and Systems Biology - (3 credits) Typically Offered Fall
. ABE 62700 Collodial Phenomena in Bioprocessing (3 credits) Typically Offered Every Other Fall
. BME 54100 Biomedical Fluid Dynamics (3 credits) Typically Offered Every Other Year
- Chemical Biology
- MCMP 57000 Basic Principles of Chemical Action on Biological Systems (3 credits) Typically Offered Fall
- Chromatin and Regulation of Gene Expression - For students in this TG, both of the following must be taken:
- BCHM 61000 Regulation of Eukaryotic Gene Expression (3 credits) Typically Offered Spring
- BCHM 61100 Chromatin Biology & Chromosome Dynamics (2 credits) Typically Offered Fall
- Immunology and Infectious Diseases
- BIOL 53700 Immunbiology
- CPB 62200 Microbial Pathogenesis
- Integrative Neuroscience
- BIOL 53800 Molecular, Cellular & Developmental Neurobiology (3 credits) Typically Offered Spring
- BIOL 56200 Neural Systems (3 credits) Typically Offered Spring
- BIOL 60200 Cellular Neurobiology (3 credits) Typically Offered Fall
- Integrative Plant Sciences
- BTNY 55300 Plant Growth and Development (3 credits) Typically Offered Spring
- Membrane Biology - For students in this TG, both of the following courses must be taken:
- BIOL 64700 Membrane Protein Structural Biology (2 credits) Typically Offered Spring
- CHM 63200 Membranes: Structure and Function (3 credits) Typically Offered Fall
- AGRY 64900 Molecular Microbial Ecology (3 credits) Typically Offered Fall
- BIOL 53300 Medical Microbiology (3 credits) Typically Offered Fall
- BIOL 54900 Microbial Ecology (2 credits) Typically Offered Every Other Spring
- Molecular Signaling and Cancer Biology - For students in this TG, both of the following courses must be taken:
- BIOL 51600 Molecular Biology of Cancer (3 credits) Typically Offered Spring
- BCHM 61501 Pathways (3 credits) Typically Offered Spring
Seminar: (1 credit) PULSe students are required to take one additional participatory seminar course offered by a department or a training group. In this course, the students are required to attend weekly seminars and to give a presentation during one of the class periods.
For Recommended Classes for First-Year PULSe Students, click here.