Institute of Molecular Biology
Molecular Biology and Biophysics Training Program
The Molecular Biology and Biophysics Training Program (MBBTP) brings together scientists from the Departments of Biology
, Chemistry and Biochemistry
, and Physics
, as well as from the new Knight Campus for Accelerating Scientific Impact
. Originally founded within the Institute of Molecular Biology (IMB), the program now spans three institutes: IMB
, the Institute of Neuroscience (ION
) and the Institute of Ecology and Evolution (IE2
Students and faculty in the MBBTP share a common interest in understanding the molecular underpinnings of biological processes, yet they approach these problems from a diverse range of disciplines, including biochemistry, structural biology, quantitative cellular biology, molecular evolution, biophysics, and molecular biology. The main objective of the training program is to provide excellent training in technical, operational and professional skills for PhD students in molecular biology and biophysics. This is accomplished through interdisciplinary training combining quantitative and modern coursework together with individual mentored research experiences that give trainees the skills to make rigorous and impactful contributions to their field. Student-hosted seminars, an annual retreat, journal clubs, career development opportunities, and cohort-building activities are also important parts of the training program, and these activities help create an interactive and supportive environment that fosters cooperation amongst MBBTP laboratories.
A PhD from the MBBTP opens up a broad array of potential career options, and while most MBBTP graduates go on to establish careers in scientific research, our graduates find success in many different science-related positions (see career outcomes below). The MBBTP provides training that helps students identify STEM-related fields that interest them and gives them the skills needed for entry into those fields.
Cohort Graduating in 2006-2011
Cohort Graduating in 2012-2017
Cohort Graduating in 2018-2022
The MBBTP seeks to create an inclusive training environment that supports a diverse group of students, including students with disabilities and underrepresented minorities. Information and links about the resources available to promote a diverse community at UO and within the training program can be found here
Training Activities Summary
- Students are required to take CH 662: Advanced Biochemistry, plus one course in each of three categories: quantitative biophysics/biochemistry, computational methods, and biological statistics.
- BI 610: Ethics in the Life Sciences is taken in the fall of the second year of training.
- Inviting and hosting academic researchers for seminar visits.
- Regular attendance at the Institute of Molecular Biology Seminar Series.
- Regular attendance at the Molecular Biosciences Trainee Talks. Students in the training program are present on an annual basis beginning in their third year.
- Participation in one of the journal clubs (Biophysics JC, Chemical Biology JC, Gene Regulation/Epigenetics JC, Development JC . . . etc).
- Inviting and meeting with speakers from the Career Exploration Speaker Series. These speakers are STEM PhDs who have successful careers in industry, government or “non-traditional” academic sectors.
- Students are required to take CH/BI: 610 Career Exploration in the Life Sciences, and most students take this course in either their third or fourth year of training.
- Many students complete an internship during their training through our Life Sciences PhD internship program.
I. Core Molecular Biology and Biophysics Course
- CH 662 Advanced Biochemistry (Winter term)
This course teaches students the fundamental principles, terminology, and experimental approaches used in the fields of biochemistry and biophysics. Emphasis is placed on defining the relationship between biomolecular structure and function. The curriculum includes structural organization of proteins, thermodynamics of protein folding, mutation stability analysis, energetics of macromolecules, enzymes kinetics, protein purification, and methods for measuring biochemical interactions. Students gain practical knowledge, such as methods in protein purification, molecular visualization tools using UCSF Chimera/PyMol, and kinetic modeling using MATLAB/Python. This course improves the ability of students to read, interpret, discuss, and solve problems related to primary literature in the fields of biochemistry, molecular biology and biophysics.
II. Graduate Course in Quantitative Biophysics/Biochemistry
- CH 565 Physical Biochemistry
This course focuses on the use of thermodynamics, kinetics, and biomolecular structure to understand the molecular basis of biological processes. Students typically have a background in biochemistry, molecular biology, and/or genetics with a minimal or no background in statistical physics.
- CH 566 Structural Biochemistry
This course covers the theory and practice behind techniques used to solve macromolecular structures, including x-ray crystallography, biomolecular NMR and cryo-electron microscopy. In addition to structure solution, a major portion of the course is dedicated to using macromolecular structures to understand function. Students also read, discuss, and critique papers from the scientific literature that use structural biology techniques.
- CH 568 Cellular Biochemistry
This course covers the major technological advances that contributed to scientific discovery at the interface between cell biology and biochemistry. Students learn modern experimental approaches that incorporate concepts from chemistry, statistical mechanics, biophysics, and cell biology. Methods used to visualize, quantify, and interpret how biochemical reactions are executed in living cells are discussed using primary literature.
- PHYS 610 Introduction to Biological Physics
This course explores how physical properties guide and constrain life, whether it be the mechanical properties of biomaterials or the dynamical properties of information processing networks. It requires more advanced mathematics and a deeper understanding of physics than CH 565.
III. Graduate Course in Computational Methods
- CH 510 Introduction to Programming for Molecular Biologists (Spring term)
This course is intended for students with little or no previous programming experience and aims to provide them with the foundational knowledge to use programming tools in diverse research areas. Students will gain proficiency in the Python programming language while using it to solve modern problems in molecular biology, including examples from high-throughput sequencing analyses, biological database mining, quantitative image analyses, model fitting, and simulation of experiments to facilitate experimental design.
- CH 547 Computational Chemistry
This course is an introduction to modern computational methods used to understand the properties of molecular liquids. Statistical mechanics fundamentals necessary to perform molecular simulations are presented, along with a survey of molecular dynamics, Monte Carlo, and Brownian dynamics simulation methods. Students learn to run computational chemistry software packages and to analyze, visualize, and interpret computational results.
IV. Graduate Course in Biological Statistics
- BI 610 Foundational Statistics
This course in an introduction to data management, data visualization, and statistical inference. It is intended for early-stage graduate students and no prior coursework in statistics or programming is assumed. Students learn to organize, manipulate, visualize, and analyze data sets using the R statistical language.
- BI 610 Advanced Biological Statistics
This is the first of a two-quarter graduate course that aims to provide students with practical understanding of and experience with concepts and methods in modern data analysis. Trainees with research projects that require a more extensive understanding of the principles and practice of statistical analysis take this course, and typically go on to take Advanced Biological Statistics II. Students become familiar with major topics in univariate and multivariate statistics, analysis of large data sets, and Bayesian analysis.
Career Development Activities
Trainees complete an Individual Development Plans (IDP) annually in year 2 and beyond. The purpose of the IDP is to encourage introspection concerning career goals, and concrete action to tailor training to those goals. The IDP procedures are outlined in the IDP Year 2
and IDP Years 3-5
The Careers in Bioscience course is typically taken in the third or fourth year of training. This course teaches self-assessment skills and provides students with information about the types of careers available to them. The course features multiple panel discussions with STEM PhD scientists with diverse careers and gives students the opportunity to research two careers of interest in detail. In addition to the course, the Career Development Team offers workshops that help students develop professional skills needed to land positions, including CV and cover letter preparation, internship and job search strategies, informational interviewing skills, and elevator pitches. One-on-one career counseling is also available.
Students also have the option of completing an internship during their training as part of the Life Sciences PhD Internship Program. Career Develop Team members help graduate trainees land internships and navigate the logistics of completing an internship during their graduate education.
Additional Professional Development and Career Resources can be found here
Criteria and Application Procedure for Molecular Biology and Biophysics Training Program Support
Training grant appointments are made on an annual basis, starting on July 1. Applications for training grant support are emailed to all eligible students in mid-May, and appointment decisions are made by the MBBTP Executive Committee by ~June 20. Trainees may be reappointed for a maximum of two years of support, assuming satisfactory progress and availability of funds. Initial appointments are limited to students who are starting their second or third year of graduate study.
Students who are potentially interested in joining the Molecular Biology and Biophysics Training Program are strongly encouraged to take CH662/663 Advanced Biochemistry in the Winter of their first year. Students who have not taken this course at the time of applying for training grant support should address their decision not to take it in their application.
The following criteria are considered in choosing students for MBBTP support:
- Students should provide evidence of a strong interest in the core disciplines relevant to the Molecular Biology and Biophysics Training Program, as displayed by the research summary in their application, and by their course, journal club, seminar and host lab choices.
- Instructor and rotation evaluations are considered, or thesis committee reports, as appropriate.
- We aim to support students for whom the course requirements and other training activities would be beneficial rather than burdensome.
- The distribution of training grant support among training labs, and track records of senior faculty in mentoring trainees (as reflected by publications and post-graduation outcomes) are also considered.
Criteria for selection of Molecular Biology and Biophysics Training Faculty and application procedure
Faculty join the Molecular Biology and Biophysics Training Program at the invitation of the MBBTP Advisory Committee based on three primary criteria: (i) the degree to which their research program matches the mission of this training program, (ii) current funding and recent productivity and (iii) their track record of successful mentoring.
The objective of the MBBTP is to prepare scientists to work on biological and biophysical problems at the molecular level. This means training biology students to think in terms of models based on the structures and properties of macromolecules and, conversely, to train chemistry, physics, and bioengineering students to understand the biological context of problems and to couple in vivo approaches with detailed biochemical/biophysical studies.
Faculty who study biological mechanisms at the molecular level are central to our training mission. In addition, the Advisory Committee will consider faculty whose primary research area is peripheral to the MBBTP focus, but who accept a student whose thesis topic matches the core goals of our program. It must be clear that such students would benefit from the required coursework and training activities of the MBBTP. Sufficient laboratory funding must be available to support trainee research and the trainer must have a consistent record of productivity.
Procedure: Faculty may apply at any time to join the MBBTP faculty by emailing the MBBTP Director. In addition, the MBBTP Executive Committee extends invitations annually to new faculty members whose research programs match our focus.
Brad Nolen (Director)
Parisa Hosseinzadeh (Executive Committee Member)
Raghu Parthasarathy (Executive Committee Member)
David Garcia (Executive Committee Member)