Biochemistry & Molecular Pharmacology Program 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. 

Course Directors: Anthony Imbalzano, Cynthia Fuhrmann

Semester Offered: Fall 

Last Taught: Fall 2020

This course seeks to 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.

Course Directors: Jill Zitzewitz, Darryl Conte

Semester Offered: Fall 

Last Taught: Fall 2020

This problem-based course provides learning opportunities through exploration of multidisciplinary areas of contemporary biomedical research, and creates a forum for practice in the skills required for research.

Course Directors: Jill Zitzewitz, Sean Ryder, Neal Silverman

Semester Offered: Fall 

Last Taught: Fall 2020

The course focuses on the use of chemical approaches to answer fundamental questions in biology. Topics include post-translational modifications; chemical synthesis and modification of biopolymers; combinatorial chemistry; chemical genetics; rational drug design; ligand-receptor interactions; and the fundamentals of fluorescence. 

Course Director: Stephen Miller

Semester Offered: Fall, odd years

Last Taught: Fall 2019

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.

Course Director: Francesca Massi

Semester Offered: Fall, even years

Last Taught: Fall 2020

Structural Biology has revolutionized biology.  The purpose of this course is to provide graduate students with a detailed introduction to approaches for structural determination of macromolecules including protein crystallography, cryo electron microscopy (CryoEM), nuclear magnetic resonance (NMR) spectroscopy and small angle X-ray scattering (SAXS).  Emphasis will be placed on both structural determination and analysis of dynamics, which can be crucial for macromolecular function.   Normally, each week will include a 90 minute lecture that is supplemented with either a practical laboratory exercise, paper discussion or problem set, whose time and venue will depend upon the activity.

Course Directors: Brian Kelch

Semester Offered: Spring, odd years

Last Taught: Spring 2021

This advanced topics course will cover current research in the general area of RNA biology. Topics envisioned may include RNA synthesis; modification and processing pathways; RNA structure; RNA transport and subcellular localization; translational regulation; RNAi and microRNAs; RNA decay; RNA aptamers; RNA catalysts; RNA and early evolution; and RNA as a drug and/or drug target. The format of this course will center around group discussion of papers from the primary literature. Grading will be based on student attendance, performance in presentations and participation in group discussions. 

Course Director: Sean Ryder

Semester Offered: Spring, even years

Last Taught: Spring 2020

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

Course Director: Paul Thompson

Semester Offered: Spring

Last Taught: Spring 2021

The Advanced Topics in Bioinformatics 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. 

Course Director: Zhiping Weng

Semester Offered: Fall, Even Years

Last Taught: Fall 2020

The objective of this course is to introduce GSBS graduate students to approaches used to understand the molecular causes of representative diseases and application of such knowledge toward the design and implementation of rational therapies. The course is divided into five-week sections covering neurodegenerative, cardiovascular, and metabolic diseases. Interspersed among these topics will be guest speakers who will discuss specific aspects of the drug design process and novel approaches to therapy, including gene-, RNA-, and cell-based interventions. Class discussions will also help prepare students to participate effectively in team-oriented translational science. Pairs of students will each write a research proposal addressing a disease mechanism or therapy development of interest and defend the proposal during the last two weeks of class.

Course Directors: Pranoti Mandrekar, Chinmay Trivedi

Semester Offered: Spring

Last Taught: Spring 2021

This course provides students with the opportunity to develop public speaking skills necessary for scientific presentations. This experience will facilitate both formal and informal presentation of a student’s own research. All Biochemistry & Molecular Pharmacology students will be registered in this course to satisfy the annual presentation requirement.

Course Director: Nick Rhind

Semester Offered: Fall, Spring

Last Taught: Spring 2021

Individual instruction on selected topics is arranged by student and instructor.

Course Director: William Kobertz

Semester Offered: Fall, Spring, Summer

Last Taught: Has not been taught within last two years

Laboratory 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. 

Course Director: Faculty member in whose lab student is working

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every Fall and Spring semester

Laboratory 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. 

Course Director: Faculty member in whose lab student is working

Semester Offered: Summer

Last Taught: Taught every 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.

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. 

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. 

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, after passing the Qualifying Exam.

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 in the PhD Program and will continue to register each semester until they complete all remaining requirements.

Course Director: Student's thesis advisor

Semester Offered: Fall, Spring, Summer

Last Taught: Taught every semester