The course descriptions listed on the following pages are provided as a guide to the types of courses offered over the last several years. An official listing of courses and descriptions are made available to students prior to registration. The following information is current as of July 2010.
Basic & Biomedical Sciences Division
• Biochemistry & Molecular Pharmacology
• Bioinformatics & Computational Biology
• Cancer Biology
• Cell Biology
• Cellular & Molecular Physiology
• Immunology & Virology
• Interdisciplinary Graduate Program
• MD/PhD
• Millennium PhD
• Molecular Genetics & Microbiology
• Neuroscience
Clinical & Translational Sciences Division
• Clinical & Population Health Research
• Master of Science in Clinical Investigation
Qualifying Exam
Following completion of the Graduate Core Class, at least two semesters of laboratory rotations and two of the required Advanced Topics courses, students are eligible to take their qualifying exam. The exam consists of an oral presentation and defense of an original research proposal based on the student’s own potential thesis work or any topic of the student’s choosing. A student’s plan for rotation projects, coursework and qualifying exam can be done in consultation with the graduate director.
Courses in Biochemistry &
Molecular Pharmacology Chemical Biology
This 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.
Molecular Biophysics
The goal of this course is to give students a strong foundation in physical principles
Topics 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.
Structural Biology
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, but alternative approaches will also be discussed. Emphasis will be placed on both structural determination and analysis of dynamics, which can be crucial for macromolecular function.
RNA Biology
This Advanced Topics course covers 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
Tutorial in Biochemistry &
Molecular Pharmacology
Individual instruction on selected topics is arranged by student and instructor.
Seminar in Biochemistry
This course provides students with the opportunity to develop skills in public speaking necessary for scientific presentations. This experience will facilitate both formal and informal presentations of students’ individual research.
Biochemistry & Molecular Pharmacology Graduate Program Faculty
Program Director
William R. Kobertz, PhD (Associate Professor, Biochemistry & Molecular Pharmacology) – Structure, function and modulation of ion channels
Professors
Alexei Bogdanov, Jr., PhD (Radiology and Cell Biology) – Molecular imaging in cancer models and models of inflammatory vascular disease;
development of imaging probes for detecting enzymatic activity in vivo
Sumner H. Burstein, PhD (Biochemistry &
Molecular Pharmacology) – Regulation of anandamide biosynthesis; signal transduction events involved in cannabinoid-induced arachidonate release
Anthony Carruthers, PhD (Dean, Graduate School of Biomedical Sciences; Biochemistry
& Molecular Pharmacology) – Mechanisms of glucose transport and glucose transport regulation
Michael P. Czech, PhD (Chair, Molecular Medicine) – Transmembrane signaling elicited by the insulin receptor tyrosine kinase and its dysfunction in obesity and type 2 diabetes Biochemistry & Molecular Pharmacology’s notable achievements include:
• students awarded predoctoral training grants from the National Institutes of Health (NIH), the Department of Defense and the prestigious Harold Weintraub Graduate Student Award;
• NIH program project grant focused on HIV drug resistance and protease inhibitor design;
• faculty members named Howard Hughes Medical Institute Investigators, W. M.
Keck Foundation Distinguished Young Scholars, Burroughs Wellcome Fellows, Worcester Foundation for Biomedical Research Scholars and a Pew Scholar; and
• a faculty member who patented discoveries in RNAi.
Stephen J. Doxsey, PhD (Molecular Medicine) – Mitotic and meiotic spindle assembly with an emphasis on centrosome structure, functions and regulation
Harvey M. Florman, PhD (Cell Biology) – Cell and molecular biology of fertilization and of ion channel function
Terence R. Flotte, MD (Dean, School of Medicine; Celia and Isaac Haidak Professor of Medicine; Pediatrics, Molecular Genetics &
Microbiology) – Gene therapy for cystic fibrosis, alpha-1 antitrypsine deficiency and other single gene defects
Reid Gilmore, PhD (Vice Chair, Biochemistry
& Molecular Pharmacology) – Molecular mechanism of protein translocation across the endoplasmic reticulum; analysis of asparagine-linked glycosylation in the endoplasmic reticulum Michael R. Green, MD, PhD (Lambi and Sarah Adams Chair in Genetic Research, Howard Hughes Medical Institute Investigator; Director, Program in Gene Function & Expression;
Molecular Medicine) – Eukaryotic gene regulation and cancer molecular biology
Mitsuo Ikebe, PhD (Physiology)
– Function and regulation of motor proteins in cellular processes
Kendall L. Knight, PhD (Associate Dean, Graduate School of Biomedical Sciences;
Biochemistry & Molecular Pharmacology) – Homologous genetic recombination and DNA repair in prokaryotes and eukaryotes
David G. Lambright, PhD (Molecular Medicine) – Structural determination of key intermediates in cellular signaling and vesicle trafficking pathways
José R. Lémos, PhD (Physiology)
– Molecular mechanisms of stimulus-secretion coupling in mammalian nerve terminals Shan Lu, PhD (Medicine) – Immunogenicity of protein antigens
Martin G. Marinus, PhD (Biochemistry &
Molecular Pharmacology) – Mechanism and specificity of DNA mismatch repair; drug resistance and DNA mismatch repair; function of methylated bases in nucleic acids
C. Robert Matthews, PhD (Arthur F. and Helen P. Koskinas Professor of Biochemistry &
Molecular Pharmacology; Chair, Biochemistry
& Molecular Pharmacology) – Investigation of structures and the dynamics of structural changes in biological molecules in solution, i.e., the mechanisms by which proteins fold to unique conformations; studies on the effects of single amino acid substitutions on the folding process;
folding mechanisms of multi-subunit peptides and proteins; protein engineering
Melissa J. Moore, PhD (Howard Hughes Medical Institute Investigator; Biochemistry & Molecular Pharmacology) – Pre-mRNA splicing and its connections to intracellular mRNA localization, translation and degradation
Thoru Pederson, PhD (Vitold Arnett Professor of Cell Biology; Biochemistry & Molecular Pharmacology) – Eukaryotic gene expression at the level of RNA processing; RNA protein interactions and RNA traffic in the nucleus Craig L. Peterson, PhD (Vice Chair, Molecular Medicine) – Roles of the SWI/SNF complex and chromatin in regulation of eukaryotic gene expression
Alonzo H. Ross, PhD (Biochemistry & Molecular Pharmacology) – PTEN phosphatase and tumor suppressor; CNS stem cells and neural tumors
William E. Royer Jr., PhD (Biochemistry &
Molecular Pharmacology) – X-ray crystallographic imaging of macromolecular structures; structural basis for inter-subunit communication and macromolecular interactions
Celia A. Schiffer, PhD (Biochemistry & Molecular Pharmacology) – How conformational adaptability affects molecular recognition in drug resistant variants of HIV protease using phage display, X-ray crystallography and molecular dynamics calculations
Lawrence J. Stern, PhD (Pathology) – Molecular recognition in the immune system
William E. Theurkauf, PhD (Molecular Medicine) – Regulation of mitotic chromosome segregation M. David Ullman, PhD (Shriver Center) – Glycoconjugates in neuropathology and neuroprotection
Zhiping Weng, PhD (Director, Program in Bioinformatics & Integrative Biology) – To explore and understand biological data through the application and development of computational tools
Zuoshang Xu, MD, PhD (Biochemistry &
Molecular Pharmacology) – Structure, transport and function of neuronal cytoskeleton;
neurodegenerative disease
Phillip D. Zamore, PhD (Gretchen Stone Cook Chair in Biomedical Sciences; Howard Hughes Medical Institute Investigator) – Control of mRNA stability and translation in development;
molecular mechanisms of RNAi (post-transcriptional gene silencing)
Associate Professors
Ingolf Bach, PhD (Molecular Medicine) – Neuronal cell fate specification
Job Dekker, PhD (Biochemistry & Molecular Pharmacology, Program in Gene Function) – Spatial organization of genomes
Lawrence J. Hayward, MD, PhD (Neurology) – Mechanisms of motor neuron diseases and ion channel disorders using mouse and zebrafish models
Haley E. Melikian, PhD (Psychiatry) –
Regulation and membrane trafficking of cocaine and antidepressant-sensitive monoamine transporters
Mary Munson, PhD (Biochemistry & Molecular Pharmacology) – Regulation of vesicle targeting and fusion
Nick Rhind, PhD (Biochemistry & Molecular Pharmacology) – DNA replication and replication checkpoints; cell size control; fission yeast comparative genomics
Charles G. Sagerström, PhD (Biochemistry &
Molecular Pharmacology) – Transcriptional regulation in embryogenesis
Scot A. Wolfe, PhD (Biochemistry & Molecular Pharmacology, Program in Gene Function) – Protein-DNA recognition; targeted genome modification; transcriptional regulatory networks in metazoans
Assistant Professors
Daniel Bolon, PhD (Biochemistry & Molecular Pharmacology) – Role of molecular chaperones in biology and disease
Hong-Sheng Li, PhD (Neurobiology) – Neuronal regulation of membrane receptor signaling Francesca Massi, PhD (Biochemistry &
Molecular Pharmacology) – Protein dynamics, function and stability using NMR and computer simulation
Zdenka Matijasevic, PhD (Cell Biology) – Cellular responses to hypothermia Stephen C. Miller, PhD (Biochemistry &
Molecular Pharmacology) – Chemical approaches to study and control of cell biology
Oliver Rando, MD, PhD (Biochemistry &
Molecular Pharmacology) – Role of chromatin structure in transcriptional control and mechanism of inheritance of chromatin states;
role of epigenetically inherited information in evolution, development and disease
Sean Ryder, PhD (Biochemistry & Molecular Pharmacology) – RNA regulation in development and disease regulatory networks, mechanisms of specificity and ribonucleoprotein complex assembly
Konstantin Zeldovich, PhD (Bioinformatics &
Integrative Biology, Biochemistry & Molecular Pharmacology) – Molecular evolution and protein folding using computer simulations and theory
Research Assistant Professors
Osman Bilsel, PhD (Biochemistry & Molecular Pharmacology) – Use of time-resolved fluorescence, excitation energy transfer and rapid mixing techniques to obtain structural information on protein folding intermediates in the microsecond-to-seconds time regime Jill A. Zitzewitz, PhD (Biochemistry & Molecular Pharmacology) – Folding and assembly of multi-meric proteins and peptides using stopped-flow circular dichroism and fluorescence spectroscopies