Molecular Biophysics and Biochemistry

336 Bass Center, 203.432.5662
http://medicine.yale.edu/mbb
M.S., M.Phil., Ph.D.

Chair
Mark Hochstrasser

Acting Chair [F]
Karla Neugebauer

Director of Graduate Studies
Yong Xiong (336 Bass, 203.432.5662, nessie.stewart@yale.edu)

Professors Karen Anderson (Pharmacology), Susan Baserga, Ronald Breaker (Molecular, Cellular & Developmental Biology), Gary Brudvig (Chemistry), Sandy Chang (Laboratory Medicine), Enrique De La Cruz, Daniel DiMaio (Genetics; Therapeutic Radiology), Donald Engelman, Alan Garen, Mark Gerstein, Nigel Grindley (Emeritus), Mark Hochstrasser, Jonathon Howard, Michael Koelle, Anthony Koleske, William Konigsberg, Peter Lengyel (Emeritus), J. Patrick Loria (Chemistry), I. George Miller (Pediatric Infectious Diseases; Public Health), Andrew Miranker, Peter Moore (Emeritus, Chemistry), Karla Neugebauer, Thomas Pollard (Molecular, Cellular & Developmental Biology), Karin Reinisch (Cell Biology), David Schatz (Immunobiology), Robert Shulman (Emeritus), Fred Sigworth (Cellular & Molecular Physiology; Biomedical Engineering), Dieter Söll, Mark Solomon, Joan Steitz, Thomas Steitz, Scott Strobel, William Summers (Emeritus), Kenneth Williams (Adjunct; Research)

Associate Professors Titus Boggon (Pharmacology), Erdem Karatekin (Cellular & Molecular Physiology), Christian Schlieker, Charles Sindelar, Yong Xiong

Assistant Professors Julien Berro, Wendy Gilbert, Nikhil Malvankar, Candice Paulsen, Matthew Simon, Sarah Slavoff (Chemistry), Seyedtaghi Takyar (Internal Medicine/Pulmonary)

Fields of Study

The principal objective of members of the department is to understand living systems at the molecular level. Laboratories in MB&B focus on a diverse collection of problems in biology. Some specialize in the study of DNA dynamics, including replication, recombination, transposition, and/or functional genomics. Others focus on transcriptional regulation, from individual transcription factors to the control of lymphocyte activation, the interferon response, and organismal development. Other groups study RNA catalysis, RNA-protein interactions, and ribonucleoproteins including spliceosomes and the ribosome. Additionally there are those that emphasize protein folding and design, transmembrane signaling, and control of the cell cycle. Structural and computational biology is a strong component of many of these research efforts.

Special Admissions Requirements

Courses in introductory biology, general chemistry, organic chemistry, physical chemistry, mathematics through differential equations, and one year of physics with calculus are required for admission. Biochemistry is strongly recommended. Applicants must take the GRE General Test, which is preferred, or the MCAT.

To enter the Ph.D. program, students apply to an interest-based track within the interdepartmental graduate program in Biological and Biomedical Sciences (BBS), http://bbs.yale.edu.

Integrated Graduate Program in Physical and Engineering Biology (PEB)

Students applying to one of four tracks of the Biological and Biomedical Sciences program may simultaneously apply to be part of the PEB program. See the description under Non-Degree-Granting Programs, Councils, and Research Institutes for course requirements, and http://peb.yale.edu for more information about the benefits of this program and application instructions.

Special Requirements for the Ph.D. Degree

All first-year students (except M.D./Ph.D.) perform three laboratory rotations (encompassed by MB&B 650 and MB&B 651, Lab Rotation for First-Year Students). All students are required to take, for credit, seven one-term science courses. To obtain the desired breadth and depth of education, students are required to take two courses in molecular biophysics (one of which must be MB&B 720), one course in critical thinking (MB&B 730), and one course in molecular biology (MB&B 743 is recommended but not required). The second credit in molecular biophysics and the molecular biology credit may be satisfied by taking appropriate courses from an approved list available each fall. Additional courses, chosen from within MB&B or from related graduate programs, should form a coherent background for the general area in which the student expects to do dissertation research. All students also attend MB&B 676, Responsible Conduct of Research. In their fourth year of study, all students must successfully complete B&BS 503, RCR Refresher for Senior BBS Students. Students with an extensive background in biochemistry or biophysics are permitted to substitute advanced courses for the introductory courses. There is no foreign language requirement. The student’s research committee (see below) makes the final decision concerning the number and selection of courses required of each student. All students are required to assist in teaching two terms at the TF-10 level during their graduate careers, usually during the second and third years. The student selects a research adviser by the end of the second term of residence. At that time two additional faculty members are chosen to form a research committee, with the total committee including at least two members of MB&B. Students are required to meet with this committee in the spring of years two and three, and in both the fall and spring of subsequent years. The qualifying examination, usually taken in the fall of the second year, is an oral defense of a research proposal consisting of (1) thesis aims and (2) extended goals on the same topic. The extended goals should include approaches beyond those in the thesis aims, typically beyond those generally employed by the host lab. Thus, a predominantly molecular biological set of thesis aims should be accompanied by biophysical approaches in the extended goals section, and vice versa. The three-member oral examination committee usually includes at least one of the two members of the research committee excluding the thesis adviser. Requirements for admission to candidacy, which usually takes place after four terms of residence, include (1) completion of course requirements; (2) completion of the qualifying examination; (3) certification of the student’s research abilities by vote of the faculty upon recommendation from the student’s research committee; and (4) submission of a brief prospectus of the proposed thesis research. Completion of the teaching requirement is not required for admission to candidacy. Once final drafts of the thesis chapters have been approved by the research committee, the student presents a dissertation seminar to the entire department, and only afterward may the thesis be submitted. Students must have written at least one first-author paper that is submitted, in press, or published by the time of the thesis seminar.

Honors Requirement

Students must meet the Graduate School’s Honors requirement by the end of the fourth term of full-time study; see Degree Requirements under Policies and Regulations. Students must also maintain an overall High Pass average. Student progress toward these goals is reviewed at the ends of the first and second terms.

M.D./Ph.D. Students

M.D./Ph.D. students must satisfy the requirements listed above for the Ph.D. with the following modifications: Laboratory rotations are not required but are available. Assisting in teaching of one lecture course is required. Students are required to take MB&B 800 as part of their medical curriculum in addition to the two courses in molecular biophysics described above. Students with weak backgrounds in molecular biology will need to take MB&B 743.

Master’s Degrees

M.Phil. See Degree Requirements under Policies and Regulations. Awarded only to students admitted to candidacy who are continuing for the Ph.D. Students need not have completed their teaching requirement to receive the M.Phil. Students are not admitted for this degree.

M.S. Students are not admitted for this degree. It may only be awarded to a student in the Ph.D. program who is in good standing upon completion of at least two terms of graduate study and who will not continue in the Ph.D. program. A student must receive grades of Pass or higher in at least five courses approved by the DGS as counting toward a graduate degree, exclusive of seminars or research. Students must have taken at least ten courses. A typical schedule would consist of six traditional courses, two terms of MB&B 650 and MB&B 651, and one term each of MB&B 675 and MB&B 676. A student must also meet the Graduate School’s Honors requirement for the Ph.D. program and maintain a High Pass average. Students who are eligible for or who have already received the M.Phil. will not be awarded the M.S.


More detailed program materials are available upon request to the Director of Graduate Admissions, Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven CT 06520-8114.

Courses

MB&B 500a / MCDB 500a, BiochemistryRonald Breaker and Donald Engelman

An introduction to the biochemistry of animals, plants, and microorganisms, emphasizing the relations of chemical principles and structure to the evolution and regulation of living systems.
MWF 9:25am-10:15am

MB&B 520a, Boot Camp BiologyCorey O'Hern

An intensive introduction to biological nomenclature, systems, processes, and techniques for graduate students with previous backgrounds in non-biological fields including physics, engineering, and computer science who wish to perform graduate research in the biological sciences. Counts as 0.5 credit toward MB&B graduate course requirements.  ½ Course cr
F 1:30pm-3:20pm

MB&B 523b / CB&B 523b / ENAS 541b / PHYS 523b, Biological PhysicsSimon Mochrie

The course has two aims: (1) to introduce students to the physics of biological systems and (2) to introduce students to the basics of scientific computing. The course focuses on studies of a broad range of biophysical phenomena including diffusion, polymer statistics, protein folding, macromolecular crowding, cell motion, and tissue development using computational tools and methods. Intensive tutorials are provided for MATLAB including basic syntax, arrays, for-loops, conditional statements, functions, plotting, and importing and exporting data.
TTh 1pm-2:15pm

MB&B 545b, Methods and Logic in Molecular BiologyWendy Gilbert, Mark Hochstrasser, and Christian Schlieker

An examination of fundamental concepts in molecular biology through analysis of landmark papers. Development of skills in reading the primary scientific literature and in critical thinking. Open only to MB&B students pursuing the B.S./M.S. degree.
Th 2:30pm-4:20pm

MB&B 561a / CB&B 561a / MBIO 561a / MCDB 561a / PHYS 561a, Introduction to Dynamical Systems in BiologyDamon Clark, Kathryn Miller-Jensen, and Jonathon Howard

Study of the analytic and computational skills needed to model genetic networks and protein signaling pathways. Review of basic biochemical concepts including chemical reactions, ligand binding to receptors, cooperativity, and Michaelis-Menten enzyme kinetics. Deep exploration of biological systems including: kinetics of RNA and protein synthesis and degradation; transcription activators and repressors; lyosogeny/lysis switch of lambda phage and the roles of cooperativity and feedback; network motifs such as feed-forward networks and how they shape response dynamics; cell signaling, MAP kinase networks and cell fate decisions; bacterial chemotaxis; and noise in gene expression and phenotypic variability. Students learn to model using MATLAB in a series of in-class hackathons that illustrate biological examples discussed in lectures.
TTh 2:30pm-3:45pm

MB&B 562b / AMTH 765b / CB&B 562b / INP 562b / MCDB 562b / PHYS 562b, Dynamical Systems in BiologyThierry Emonet and Jonathon Howard

This course covers advanced topics in computational biology. How do cells compute, how do they count and tell time, how do they oscillate and generate spatial patterns? Topics include time-dependent dynamics in regulatory, signal-transduction, and neuronal networks; fluctuations, growth, and form; mechanics of cell shape and motion; spatially heterogeneous processes; diffusion. This year, the course spends roughly half its time on mechanical systems at the cellular and tissue level, and half on models of neurons and neural systems in computational neuroscience. Prerequisite: MCDB 561 or equivalent, or a 200-level biology course, or permission of the instructor.
TTh 2:30pm-3:45pm

MB&B 570a and MB&B 571b, Intensive Research for B.S./M.S. CandidatesMichael Koelle

Required of students in the joint B.S./M.S. program with Yale College.  2 Course cr per term
HTBA

MB&B 591a / ENAS 991a / MCDB 591a / PHYS 991a, Integrated WorkshopCorey O'Hern, Mark Gerstein, Scott Holley, Marcus Bosenberg, Madhusudhan Venkadesan, Michael Murrell, and Nikhil Malvankar

This required course for students in the PEB graduate program involves a series of modules, co-taught by faculty, in which students from different academic backgrounds and research skills collaborate on projects at the interface of physics, engineering, and biology. The modules cover a broad range of PEB research areas and skills. The course starts with an introduction to Matlab, since Matlab is used throughout the course for analysis, simulations, and modeling.  ½ Course cr
MW 9am-10:15am

MB&B 600a, Principles of Biochemistry IMichael Koelle, Matthew Simon, Enrique De La Cruz, and Candice Paulsen

Discussion of the physical, structural, and functional properties of proteins, lipids, and carbohydrates, three major classes of molecules in living organisms. Energy metabolism, hormone signaling, and muscle contraction as examples of complex biological processes whose underlying mechanisms can be understood by identifying and analyzing the molecules responsible for these phenomena.
TTh 11:35am-12:50pm

MB&B 601b, Principles of Biochemistry IIChristian Schlieker and Karla Neugebauer

A continuation of MB&B 600a that considers the chemistry and metabolism of nucleic acids, the mechanism and regulation of protein and nucleic acid synthesis, and selected topics in macromolecular biochemistry.
TTh 11:35am-12:50pm

MB&B 602a / CBIO 602a / MCDB 602a, Molecular Cell BiologyCharles Lusk, David Breslow, Christopher Burd, Michael Caplan, Nadya Dimitrova, Valerie Horsley, Megan King, Thomas Melia, Thomas Pollard, James Rothman, Martin Schwartz, and Josephina van Wolfswinkel

A comprehensive introduction to the molecular and mechanistic aspects of cell biology for graduate students in all programs. Emphasizes fundamental issues of cellular organization, regulation, biogenesis, and function at the molecular level. Prerequisites: none, but some knowledge of basic cell biology and biochemistry is assumed. Students who have not taken courses in these areas can prepare by reading relevant sections in basic molecular cell biology texts. We recommend Pollard et al., Cell Biology (3rd ed., 2016), Alberts et al., Molecular Biology of the Cell (6th ed., 2014), or Lodish et al., Molecular Cell Biology (8th edition, 2016).
MW 1:45pm-3pm

MB&B 625a / GENE 625a / MCDB 625a, Basic Concepts of Genetic AnalysisJun Lu

The universal principles of genetic analysis in eukaryotes are discussed in lectures. Students also read a small selection of primary papers illustrating the very best of genetic analysis and dissect them in detail in the discussion sections. While other Yale graduate molecular genetics courses emphasize molecular biology, this course focuses on the concepts and logic underlying modern genetic analysis.
MW 11:35am-12:50pm

MB&B 630b / MCDB 630b, Biochemical and Biophysical Approaches in Molecular and Cellular BiologyThomas Pollard, Karen Anderson, and Titus Boggon

This course introduces the theory and application of biochemical and biophysical methods to study the structure and function of biological macromolecules. The course considers the basic physical chemistry required in cellular and molecular biology but does not require a previous course in physical chemistry. One class per week is a lecture introducing a topic. The second class is a discussion of one or two research papers utilizing those methods. Does not count for graduate course credit for BQBS graduate students.
TTh 2:30pm-3:45pm

MB&B 635a / ENAS 518a, Quantitative Approaches in Biophysics and BiochemistryJulien Berro, Yong Xiong, and Jonathon Howard

The course offers an introduction to quantitative methods relevant to analysis and interpretation of biophysical and biochemical data. Topics covered include statistical testing, data presentation, and error analysis; introduction to dynamical systems; analysis of large datasets; and Fourier analysis in signal/image processing and macromolecular structural studies. The course also includes an introduction to basic programming skills and data analysis using MATLAB. Real data from research groups in MB&B are used for practice. Prerequisites: MATH 120 and MB&B 600 or equivalents, or permission of the instructors.
TTh 11:35am-12:50pm

MB&B 650a and MB&B 651b, Lab Rotation for First-Year StudentsYong Xiong

Required of all first-year BQBS graduate students. Credit for full year only.
HTBA

MB&B 675a, Seminar for First-Year StudentsYong Xiong and Karen Anderson

Required of all first-year BQBS graduate students.
HTBA

MB&B 676b, Responsible Conduct of ResearchSusan Baserga, Dieter Söll, Mark Gerstein, Christian Schlieker, Jonathon Howard, Karla Neugebauer, Julien Berro, and Wendy Gilbert

Designed for students who are beginning to do scientific research. The course seeks to describe some of the basic features of life in contemporary research and some of the personal and professional issues that researchers encounter in their work. Approximately six sessions, run in a seminar/discussion format. Required of all first-year BBSB graduate students.
HTBA

MB&B 710b / C&MP 710b, Electron Cryo-Microscopy for Protein Structure DeterminationFrederick Sigworth and Charles Sindelar

Understanding cellular function requires structural and biochemical studies at an ever-increasing level of complexity. The course is an introduction to the concepts and applications of high-resolution electron cryo-microscopy. This rapidly emerging new technique is the only method that allows biological macromolecules to be studied at all levels of resolution from cellular organization to near atomic detail.  ½ Course cr
TTh 9am-10:15am

MB&B 720a, Macromolecular Structure and Biophysical AnalysisAndrew Miranker and Yong Xiong

An in-depth analysis of macromolecular structure and its elucidation using modern methods of structural biology and biochemistry. Topics include architectural arrangements of proteins, RNA, and DNA; practical methods in structural analysis; and an introduction to diffraction and NMR. Prerequisites: physical chemistry (may be taken concurrently) and biochemistry.
TTh 9am-10:15am

MB&B 730a, Methods and Logic in Molecular BiologyMark Solomon, Anthony Koleske, Scott Holley, Patrick Sung, Christian Schlieker, and Candice Paulsen

The course examines fundamental concepts in molecular biology through intense critical analysis of the primary literature. The objective is to develop primary literature reading and critical thinking skills. Required of and open only to first-year graduate students in BQBS.
HTBA

MB&B 743b / GENE 743b / MCDB 743b, Advanced Eukaryotic Molecular BiologyMark Hochstrasser and Wendy Gilbert

Selected topics in transcriptional control, regulation of chromatin structure, mRNA processing, mRNA stability, RNA interference, translation, protein degradation, DNA replication, DNA repair, site-specific DNA recombination, somatic hypermutation. Prerequisite: biochemistry or permission of the instructor.
TTh 11:35am-12:50pm

MB&B 749a, Medical Impact of Basic ScienceJoan Steitz, Peter Moore, Scott Strobel, I. George Miller, David Schatz, Daniel DiMaio, Sandy Chang, Karla Neugebauer, and Wendy Gilbert

Consideration of examples of recent discoveries in basic science that have elucidated the molecular origins of disease or that have suggested new therapies for disease. Emphasis is placed on the fundamental principles on which these advances rely. Reading is from the primary scientific and medical literature, with emphasis on developing the ability to read this literature critically. Aimed primarily at undergraduates. May not be taken by MB&B B.S./MS. students for graduate course credit. Prerequisite: biochemistry or permission of the instructor.
MW 1pm-2:15pm

MB&B 750b, Biological MembranesDonald Engelman

Biological membranes and their resident proteins are essential for cellular function; yet comparatively little is known about their structure and dynamics. This class provides an introduction to the biochemistry and biophysics of lipids, lipid bilayers, and lipid-derived second messengers. In addition, structural as well as functional aspects of the different classes of membrane proteins are discussed along with an outline of experimental approaches used to achieve an understanding of membrane protein structure and function at a molecular level. Counts as 0.5 credit toward MB&B graduate course requirements. Prerequisite: biochemistry.
MW 11:35am-12:50pm

MB&B 752b / CB&B 752b / CPSC 752b / MCDB 752b, Biomedical Data Science: Mining and ModelingMark Gerstein

Biomedical data science encompasses the analysis of gene sequences, macromolecular structures, and functional genomics data on a large scale. It represents a major practical application for modern techniques in data mining and simulation. Specific topics to be covered include sequence alignment, large-scale processing, next-generation sequencing data, comparative genomics, phylogenetics, biological database design, geometric analysis of protein structure, molecular-dynamics simulation, biological networks, normalization of microarray data, mining of functional genomics data sets, and machine-learning approaches to data integration. Prerequisites: biochemistry and calculus, or permission of the instructor.
MW 1pm-2:15pm

MB&B 753b, Biomedical Data Science: MiningMark Gerstein

Biomedical data science encompasses the analysis of gene sequences, macromolecular structures, and functional genomics data on a large scale. It represents a major practical application for modern techniques in data mining and simulation. This module of the full-term course MB&B 752 focuses on the first of these techniques, data mining. Specific topics include sequence alignment, comparative genomics and phylogenetics, biological databases, microarray normalization, and machine-learning approaches to data integration. Counts as 0.5 credit toward MB&B graduate course requirements. Prerequisites: biochemistry and calculus, or permission of the instructor.
MW 1pm-2:15pm

MB&B 754b, Biomedical Data Science: ModelingMark Gerstein

Biomedical data science encompasses the analysis of gene sequences, macromolecular structures, and functional genomics data on a large scale. It represents a major practical application for modern techniques in data mining and simulation. This module of the full-term course MB&B 752 focuses on the second of these techniques, simulation. Specific topics to be covered include geometric analysis of protein structure, molecular-dynamics simulation, and biological networks. Counts as 0.5 credit toward MB&B graduate course requirements. Prerequisites: biochemistry and calculus, or permission of the instructor.
MW 1pm-2:15pm

MB&B 800a, Advanced Topics in Molecular MedicineSusan Baserga and William Konigsberg

The seminar, which covers topics in the molecular mechanisms of disease, illustrates timely issues in areas such as protein chemistry and enzymology, intermediary metabolism, nucleic acid biochemistry, gene expression, and virology. M.D. and M.D./Ph.D. students only. Prerequisite: biochemistry (may be taken concurrently).
HTBA

MB&B 900a and MB&B 901b, Reading Course in BiophysicsYong Xiong

Directed reading course in biophysics. Term paper required. By arrangement with faculty. Open only to graduate students in MB&B. Please see syllabus for additional requirements.
HTBA

MB&B 902a and MB&B 903b, Reading Course in Molecular GeneticsYong Xiong

Directed reading course in molecular genetics. Term paper required. By arrangement with faculty. Open only to graduate students in MB&B. Please see syllabus for additional requirements.
HTBA

MB&B 905b, Reading Course in BiochemistryYong Xiong

Directed reading course in biochemistry. Term paper required. By arrangement with faculty. Open only to graduate students in MB&B. Please see syllabus for additional requirements.
HTBA