Molecular Biophysics and Biochemistry
334A Bass Center, 203.432.5662
https://mbb.yale.edu
M.S., M.Phil., Ph.D.
Chair
Ronald Breaker
Director of Graduate Studies
Wendy Gilbert (SHM C-127, 203.785.7580, wendy.gilbert@yale.edu)
Professors Karen Anderson (Pharmacology), Susan Baserga, Ronald Breaker (Molecular, Cellular, and Developmental Biology), Gary Brudvig (Chemistry), Sandy Chang (Laboratory Medicine), Enrique De La Cruz, Daniel DiMaio (Genetics; Therapeutic Radiology), Donald Engelman, Mark Gerstein, Wendy Gilbert, Nigel Grindley (Emeritus), Mark Hochstrasser, Jonathon Howard, Michael Koelle, Anthony Koleske, William Konigsberg (Emeritus), Mark Lemmon (Pharmacology), J. Patrick Loria (Chemistry), I. George Miller (Pediatric Infectious Diseases; Public Health), Andrew Miranker, Peter Moore (Emeritus; Chemistry), Karla Neugebauer, Lynne Regan (Emerita), Karin Reinisch (Cell Biology), David Schatz (Immunobiology), Christian Schlieker, Robert Shulman (Emeritus), Fred Sigworth (Cellular and Molecular Physiology; Biomedical Engineering), Dieter Söll (Emeritus), Mark Solomon, Joan Steitz, Scott Strobel, Kenneth Williams (Adjunct; Research), Yong Xiong, Carl Zimmer (Adjunct)
Associate Professors Julien Berro, Titus Boggon (Pharmacology), Erdem Karatekin (Cellular and Molecular Physiology), Nikhil Malvankar, Matthew Simon, Sarah Slavoff (Chemistry), Seyedtaghi Takyar (Internal Medicine/Pulmonary), Yongli Zhang (Cell Biology)
Assistant Professors Franziska Bleichert, Allison Didychuk, Luisa Escobar-Hoyos (Therapeutic Radiology), Lilian Kabeche, Wei Mi (Pharmacology), Candice Paulsen, Shaogeng (Steven) Tang, Kai (Jack) Zhang
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, cell cycle control, cytoskeletal dynamics, and neuroscience. Structural and computational biology is a strong component of many of these research efforts.
To enter the Ph.D. program, students apply to an interest-based track within the interdepartmental graduate program in Biological and Biomedical Sciences (BBS), https://medicine.yale.edu/bbs.
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 BQBS First-Year Students). All students from the BQBS track who affiliate with MB&B are required to take, for credit, six one-term science courses. To obtain the desired breadth and depth of education, students coming from the BQBS track are required to take MB&B 720, MB&B 730, one course in molecular biophysics or quantitative biology, and one course in molecular biology (MB&B 743 is strongly recommended but not required). The credit in molecular biophysics or quantitative biology and the credit in molecular biology may be satisfied by taking appropriate courses from an approved list available each fall and listed in the MB&B graduate handbook. Students originating from a BBS track other than BQBS must discuss their curriculum with the MB&B DGS prior to joining the department to ensure equivalent foundational course work in MB&B topic areas; these students are strongly encouraged to take or audit MB&B 720. 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 complete MB&B 677, RCR Refresher for Senior MB&B 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 during their graduate careers, usually during the second and third years. Students who require additional support from the Graduate School must teach additional terms, if needed, after they have fulfilled the academic teaching requirement.
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 MB&B faculty members. The chair of the committee will be an MB&B faculty member who is not the research adviser. 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 or b / MCDB 500a or b, Biochemistry Staff
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.
HTBA
MB&B 517b / ENAS 517b / MCDB 517b / PHYS 517b, Methods and Logic in Interdisciplinary Research Corey O'Hern and Emma Carley
This full PEB class is intended to introduce students to integrated approaches to research. Each week, the first of two sessions is student-led, while the second session is led by faculty with complementary expertise and discusses papers that use different approaches to the same topic (for example, physical and biological or experiment and theory).
TTh 4pm-5:30pm
MB&B 520a, Boot Camp Biology Corey O'Hern and Emma Carley
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 2pm-4pm
MB&B 523a / CB&B 523a / ENAS 541a / PHYS 523a, Biological Physics Yimin Luo
This course has three aims: (1) to introduce students to the physics of biological systems, (2) to introduce students to the basics of scientific computing, and (3) to familiarize students with characterization methods and analysis tools. We focus on studies of a broad range of biophysical phenomena including diffusion, polymer statistics, entropic forces, membranes, and cell motion using computational tools and methods. We provide intensive tutorials for Matlab including basic syntax, arrays, functions, plotting, and importing and exporting data.
TTh 4pm-5:15pm
MB&B 529b / PHAR 529b, Structural Biology and Drug Discovery Titus Boggon and Ya Ha
A comprehensive introduction to the concepts and practical uses of structural biology and structural biology-related techniques in drug discovery. The first half of the course focuses on techniques used to discover and optimize small and macromolecule drugs. Students are introduced to topics such as small molecule lead discovery, X-ray crystallography, cryo-electron microscopy, and biophysical techniques. The first half of the course also includes a practical component where students conduct hands-on structural biology experiments and learn about biophysical techniques in a laboratory setting. The second half of the course focuses on drug discovery, particularly for protein kinases. It includes a field trip to the Yale Center for Drug Discovery, where the students are introduced to the in-house Yale screening facilities for small molecule drug discovery. Two half-credit courses—PHAR 530 and PHAR 531—are also offered for the two halves of PHAR 529.
MW 9:25am-10:40am
MB&B 545b, Methods and Logic in Molecular Biology Julien Berro and Andrew Miranker
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.
TTh 2:30pm-3:45pm
MB&B 561a / MCDB 561a / PHYS 561a, Modeling Biological Systems I Thierry Emonet and Kathryn Miller-Jensen
Biological systems make sophisticated decisions at many levels. This course explores the molecular and computational underpinnings of how these decisions are made, with a focus on modeling static and dynamic processes in example biological systems. This course is aimed at biology students and teaches the analytic and computational methods needed to model genetic networks and protein signaling pathways. Students present and discuss original papers in class. They learn to model using MatLab in a series of in-class hackathons that illustrate the biological examples discussed in the lectures. Biological systems and processes that are modeled include: (1) gene expression, including the kinetics of RNA and protein synthesis and degradation; (2) activators and repressors; (3) the lysogeny/lysis switch of lambda phage; (4) network motifs and how they shape response dynamics; (5) cell signaling, MAP kinase networks and cell fate decisions; and (6) noise in gene expression. Prerequisites: MATH 115 or 116, BIOL 101–104, or with permission of instructors. This course also benefits students who have taken more advanced biology courses (e.g. MCDB 200, MCDB 310, MB&B 300/301).
TTh 2:30pm-3:45pm
MB&B 562b / AMTH 765b / CB&B 562b / ENAS 561b / INP 562b / MCDB 562b / PHYS 562b, Modeling Biological Systems II Thierry Emonet
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: a 200-level biology course or permission of the instructor.
TTh 2:30pm-3:45pm
MB&B 565b, Biochemistry and Our Changing Climate Karla Neugebauer
Climate change is impacting how cells and organisms grow and reproduce. Imagine the ocean spiking a fever: cold-blooded organisms of all shapes, sizes, and complexities struggle to survive when water temperatures go up two–four degrees. Some organisms adapt to extremes, while others cannot. Predicted and observed changes in temperature, pH, and salt concentration do and will affect many parameters of the living world, from the kinetics of chemical reactions and cellular signaling pathways to the accumulation of unforeseen chemicals in the environment, the appearance and dispersal of new diseases, and the development of new foods. In this course, we approach climate change from the molecular point of view, identifying how cells and organisms―from microbes to plants and animals―respond to changing environmental conditions. To embrace the concept of “one health” for all life on the planet, this course leverages biochemistry, cell biology, molecular biophysics, and genetics to develop an understanding of the impact of climate change on the living world. We consider the foundational knowledge that biochemistry can bring to the table as we meet the challenge of climate change. Prerequisites: MB&B 500, MB&B 600, and MB&B 601, or permission of the instructor.
TTh 4pm-5:15pm
MB&B 570a and MB&B 571b, Intensive Research for B.S./M.S. Candidates Staff
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 Workshop Yimin Luo
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, which is used throughout the course for analysis, simulations, and modeling.
TTh 9am-10:15am
MB&B 600a, Principles of Biochemistry I Matthew Simon, Michael Koelle, and Candie 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. 0 Course cr
TTh 11:35am-12:50pm
MB&B 601b, Principles of Biochemistry II Christian Schlieker, Karla Neugebauer, and Franziska Bleichert
A continuation of MB&B 600 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 / MBIO TBD-2 / MCDB 602a, Molecular Cell Biology Thomas Melia and Patrick Lusk
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. Graduate Prerequisites: 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). Undergraduate Prerequisites: This is a graduate-level cell biology class. Any undergraduates wishing to enroll must have already taken MCDB 205. In addition, undergraduates are strongly encouraged to reach out to the course directors prior to enrollment.
MW 1:45pm-3pm
MB&B 625a / GENE 625a / MCDB 625a, Basic Concepts of Genetic Analysis Jun 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 Biology Sigrid Nachtergaele and Jing Yan
In this course, we provide an overall of various biochemical and biophysical approaches used in modern research in molecular and cellular biology, ranging from spectroscopic tools, microscopy, to X-ray crystallography. The goal of the course is to make students familiar with these techniques so that they can find relevant materials in their future research. Does not count for graduate course credit for BQBS graduate students.
TTh 2:30pm-3:45pm
MB&B 635a / CBIO 635 / ENAS 518a, Quantitative Methods in Biophysics Nikhil Malvankar, Julien Berro, and Yong Xiong
An introduction to quantitative methods relevant to analysis and interpretation of biological data. Topics include statistical testing, data presentation, and error analysis; introduction to artificial intelligence-based data analysis tools, Alpha Fold Tutorial, introduction to mathematical modeling of biological dynamics; and Fourier analysis in signal/image processing and macromolecular structural studies. Instruction in basic programming skills and data analysis using MATLAB; study of real data from MB&B research groups. Prerequisites: MATH 120 and MB&B 600 or equivalents, or permission of the instructors.
TTh 9am-10:15am
MB&B 650a and MB&B 651b, Lab Rotation for BQBS First-Year Students Christian Schlieker
Required of all first-year BQBS graduate students. Credit for full year only.
HTBA
MB&B 675a, Seminar for First-Year Students Christian Schlieker, Thierry Emonet, and Karen Anderson
Required of all first-year BQBS graduate students.
HTBA
MB&B 676b, Responsible Conduct of Research Andrew Miranker, Titus Boggon, Michael Koelle, Sandy Chang, Nikhil Malvankar, Mark Lemmon, Mark Gerstein, David Schatz, Donald Engelman, and Karin Reinisch
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 and open only to first-year graduate students in BQBS.
F 3pm-4pm
MB&B 677b, RCR Refresher for Senior MB&B students Mark Solomon, Christian Schlieker, Karen Anderson, and Mark Hochstrasser
This course meets the NIH requirement that students receive training in the responsible conduct of research at least every four years. The course consists of eight half-hour recorded lectures combined with four one-hour small-group discussions. Required of and open only to senior MB&B graduate students, typically in their fourth year. The course is graded Satisfactory/Unsatisfactory.
F 3pm-4pm
MB&B 710b / C&MP 710b, Electron Cryo-Microscopy for Protein Structure Determination Staff
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
HTBA
MB&B 711b / C&MP 711b, Practical cryo-EM Workshop Yong Xiong and Franziska Bleichert
This laboratory course provides hands-on training in the practical aspects of macromolecular structure determination by cryo-electron microscopy (cryo-EM). Topics include cryo-EM data collection, image preparation and correction, single-particle picking and 2-D classification, 3-D classification, refinement and post-processing, model building, refinement and evaluation. The course includes training in the use of computer programs used to perform these calculations. Prerequisite: MB&B 710/C&MP 710. ½ Course cr
HTBA
MB&B 720a, Macromolecular Structure and Biophysical Analysis Yong Xiong, Joe Howard, Steven Tang, and Franziska Bleichert
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 11:35am-12:50pm
MB&B 730a, Methods and Logic in Molecular Biology Wendy Gilbert, Candie Paulsen, Mark Solomon, and Matthew Simon
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.
TTh 1:45pm-3:45pm
MB&B 734b / GENE 734b / MBIO 734b, Molecular Biology of Animal Viruses Walther Mothes and Maudry Laurent-Rolle
Lecture course with emphasis on mechanisms of viral replication, oncogenic transformation, and virus-host cell interactions.
HTBA
MB&B 743b / GENE 743b / MCDB 743b, Advanced Eukaryotic Molecular Biology Mark Hochstrasser, Matthew Simon, and Franziska Bleichert
Selected topics in transcriptional control, regulation of chromatin structure, mRNA processing including spliceosomal splicing, mRNA turnover, RNA interference, translational regulation, protein modification, and protein degradation. Emphasis is placed on how these processes are regulated and the experiments that led to their discovery and understanding. Prerequisite: biochemistry or permission of the instructor.
TTh 11:35am-12:50pm
MB&B 752b and MB&B 753b and MB&B 754b / CB&B 752b / CPSC 752b / MCDB 752b, Biomedical Data Science: Mining and Modeling Mark Gerstein and Matthew Simon
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.
MWF 1pm-2:15pm
MB&B 800a, Advanced Topics in Molecular Medicine Susan Baserga and Mark Solomon
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 or b, Reading Course in Molecular Biophysics and Biochemistry Staff
Directed reading course in molecular biophysics and biochemistry. Term paper required. By arrangement with faculty. Open only to graduate students in MB&B. Please see the syllabus for additional requirements.
HTBA