Biophysical, Chemical, and Computational Biology Pathway Courses

This is a required course for all third year Basic Sciences students and all MD/PhD students entering doctoral study but who are not on the CPHR track. The PARC course helps to center our students in areas that are foundational to success in research: responsible data management; management of intellectual property; the ethical use of research subjects; recognizing and resolving conflicts of interest, professionalism in peer review and publishing; engaging mentors; and career exploration and planning. The PARC course comprises faculty-led presentations and small group discussions with case studies and workshop material. An online learning module (CITI training program comprising many case studies) is also included and must be completed before the end of the fall semester. 

Credits: 1

Prerequisite(s): None

Fulfills an elective requirement: No

Course Directors: Anthony Imbalzano, Cynthia Fuhrmann

Semester Offered: Fall 

Last Taught: Fall 2023

This course will help prospective scientists in the biological and medical sciences communicate their work effectively, in writing, graphics, and oral presentations. The course teaches how to prepare a research paper using words, statistics, and figures; how to present science to a lay audience; how to write a grant proposal; and how to present orally to scientific peers.

Credits: 2

Prerequisite(s): None

Fulfills an elective requirement: No

Course Directors: Jill Zitzewitz, Daryl Bosco, and Nese Kurt Yilmaz

Semester Offered: Fall 

Last Taught: Fall 2023

This is an inter-disciplinary course focused on the use of quantitative, physical techniques in biological problem solving. Students will become familiar with contemporary methodologies and their applications in different biological and disease contexts. Topic areas will include structural biology and molecular biophysics, optical microscopy, bioinformatics and computational biology, chemical biology, and biomedical imaging. Students will gain exposure to a variety of different biological fields through the lens of cutting-edge quantitative tools and techniques. The course is required for all first-year students in the Biophysics, Chemistry, and Computational Biology (BCCB) Pathway.

Credits: 3

Prerequisite(s): None

Fulfills an elective requirement: No

Course Directors: James Munro, Francesca Massi

Semester Offered: Fall 

Last Taught: New course fall 2024

This is an inter-disciplinary course focused on the use of quantitative, physical techniques in biological problem solving. Students will become familiar with contemporary methodologies and their applications in different biological and disease contexts. Topic areas will include structural biology and molecular biophysics, optical microscopy, bioinformatics and computational biology, chemical biology, and biomedical imaging. Students will gain exposure to a variety of different biological fields through the lens of cutting-edge quantitative tools and techniques. The course is required for all first-year students in the Biophysics, Chemistry, and Computational Biology (BCCB) Pathway.

Credits: 3

Prerequisite(s): None

Fulfills an elective requirement: No

Course Directors: James Munro, Francesca Massi

Semester Offered: Spring

Last Taught: New course spring 2025

Chemical biology uses the power of chemistry to ask and answer questions of biological significance, typically using molecular tools designed to inhibit, activate, or report on the function of biomolecules. In this class we will cover a wide range of chemical biology topics. We will start with a basic chemistry review, then cover peptide and nucleic acid chemistry and synthesis, post-translational modification of proteins, optical imaging, chemoselective chemistry in water, and approaches to lead discovery for drug development. In the second half of the course, we will cover chemical genetics, orthogonal ligands and receptors, DNA recognition and modification, unnatural amino acids, enzyme inhibitors, rational drug design, nanoparticles, and synthetic biopolymers.

Credits: 3

Prerequisite(s): None

Fulfills an elective requirement: Yes

Course Director: Stephen Miller

Semester Offered: Fall, odd years

Last Taught: Fall 2023

The goal of this course is to give students a strong foundation in physical principles that underlie the thermodynamic and mechanistic properties of biological macromolecules and macromolecular complexes. In addition to providing theoretical background, lectures and discussion groups will focus on the application of physical chemical principles in contemporary biomedical research. Topics will include spectroscopic and computational approaches to studying protein and nucleic acid structures, thermodynamics and kinetics of protein folding, the solution behavior of macromolecules and principles that govern molecular recognition.

Credits: 3

Prerequisite(s): Strongly recommended, but not required: undergraduate Physical Chemistry

Fulfills an elective requirement: Yes

Course Director: Francesca Massi, Sy Redding

Semester Offered: Fall, even years

Last Taught: Fall 2022

The goal of this course is to provide students with a theoretical and practical understanding of techniques used to determine the three-dimensional structures of biological macromolecules. The primary methods explored will be X-ray crystallography and Nuclear Magnetic Resonance (NMR), but also including discussions of computational methods and cryo electron microscopy (cryo-EM).  Emphasis will be placed on both structural determination and analysis of dynamics, which can be crucial for macromolecular function.

Credits: 2

Prerequisite(s): None

Fulfills an elective requirement: Yes

Course Directors: Brian Kelch

Semester Offered: Spring

Last Taught: Spring 2024

Cellular Biochemistry takes an inside-out approach to teaching the molecular biological underpinnings of DNA replication, gene transcription, translation, metabolism, secretion and cell signaling.

Credits: 3

Prerequisite(s): None

Fulfills an elective requirement: Yes

Course Director: William Kobertz

Semester Offered: Spring

Last Taught: Spring 2024

This course covers several important areas of modern bioinformatics and computational biology. The course is aimed not only at students specializing in bioinformatics, but also general biology students who would like to utilize bioinformatics tools in their daily research. The course will begin with an overview of modern sources of bioinformatics data, especially high-throughput sequencing data (RNA-seq, ChIP-seq, DNase-seq, ATAC-seq, Whole genome bisulfite sequencing, etc.), followed by a thorough presentation of an extensive set of statistical learning and machine learning algorithms and their application to analyzing biological data. The course will include 10 lectures each with a homework set, followed by individual or group projects, presented in lieu of the final exam. 

Credits: 2

Prerequisite(s): Familiarity with at least one programming language (e.g. Python, MatLab, R, etc.)

Fulfills an elective requirement: Yes

Course Director: Zhiping Weng, Jill Moore

Semester Offered: Fall, Even Years

Last Taught: Fall 2022

This course examines topics across four short modules within the broader scope of systems biology. These modules are Gene Regulation, Network Biology, Genome Organization, and Mathematical and Quantitative Methods. In addition, this course has a hands-on component that teaches programming in the MatLab coding environment to analyze data and generate insights through computational approaches. No prior knowledge of computation is assumed, and beginners are encouraged to enroll.

Credits: 3

Prerequisite(s): BBS 614 or BBS 748 (non-degree students) or course equivalent or coordinator's approval.

Fulfills an elective requirement: Yes

Course Director: Hyun Youk, Manuel Garber

Semester Offered: Spring

Last Taught: Spring 2024

Research rotations are defined periods of research experience under the direction of a faculty member. They are intended to familiarize the student with concepts and techniques in several areas of research and to assist the student in evaluating research laboratories and projects that might be developed into a dissertation project. The student will participate in an ongoing research project; gain familiarity with concepts underlying the research; acquire a working knowledge of techniques used in the research; and write a report and present an oral summary of the results of the research.

In the summer term, only MD/PhD students may register.

Credits: 2-5

Fulfills an elective requirement: No

Course Director: Varies

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every Fall, Spring, and Summer

Students are required to register for this course in the fall semester of the academic year in which they are to pass their Qualifying Examination.

Credits: 1

Fulfills an elective requirement: No

Course Director: Mary Ellen Lane

Semester Offered: Fall

Last Taught: Taught every year 

All graduate students are required to have at least one Thesis Research Advisory Committee (TRAC) meeting each academic year. After passing their Qualifying Examination and selection of their TRAC, students are required to register for this course each fall semester until their Dissertation Advisory Committee is formed.

MD/PhD Goals: 1) To periodically review progress along thesis research project advised by content experts 2) To provide guidance for establishing a thesis research project consistent with the MD/PhD Program goals

MD/PhD Curricular Expectations: Two Thesis Research Advisory Committee (TRAC) meeting each academic year as define by the Professionalism Benchmark Checklist

Credits: 1

Fulfills an elective requirement: No

Course Director: Mary Ellen Lane

Semester Offered: Fall

Last Taught: Taught every year

This course is for students who have selected a program and thesis advisor but who have not yet passed the Qualifying Examination. 

Credits: 9

Fulfills an elective requirement: No

Course Director: Student's thesis advisor

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every semester

Students register for Thesis Research fall term of year three of the program (MD/PhD Students: Fall term of year four in the program), after passing the Qualifying Exam.

Credits: 12

Fulfills an elective requirement: No

Course Director: Student's thesis advisor

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every semester

Students register for Graduate Research fall term of year four (MD/PhD Students: Fall term of year five+) in the PhD Program and will continue to register each semester until they complete all remaining requirements.

Credits: 0

Fulfills an elective requirement: No

Course Director: Student's thesis advisor

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every semester

This course provides an overview of multivariable analysis and advanced analytical strategies for clinical and population health research. Emphasis is on developing an understanding of multivariable modeling in the context of linear, logistic and Poisson regression. Computational lab assignments and two exams will be completed.

Credits: 4

Prerequisite(s): CTS605A, Introduction to Statistics or permission from course coordinator 

Course Director: JungAe Lee

Semester Offered: Spring

Last Taught: Spring 2024

This course teaches students how to develop a peer reviewed scientific manuscript, through the review of elements of style, authorship and extent of information that needs to be incorporated into a scientific research paper. Students will learn how to develop the elements that go into a successful scientific manuscript, submit an article for peer review and respond to reviewers' concerns. During each session, students will critique the work of others enrolled in the course to obtain hands on experience in the write-up of the introduction, methods, results and discussion sections of a manuscript. This course will also teach students how to put together a successful oral, as well as poster, scientific presentation.

Credits: 3

Prerequisite(s): None

Course Director: Robert Goldberg

Semester Offered: Fall, Spring

Last Taught: Spring 2024