Molecular Biophysics & Biochemistry

Courses

MB&B 500a / MCDB 500a, Biochemistry  Ronald 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 517b, Methods and Logic in Interdisciplinary Research  Corey O'Hern

This half-term 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). Counts as 0.5 credit toward graduate course requirements.  ½ Course cr
MW 5:30pm-7:30pm

MB&B 520a, Boot Camp Biology  Corey 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 Physics  Simon 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 Biology  Wendy 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 Biology  Damon 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 Biology  Thierry 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. Candidates  Michael 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 Workshop  Corey 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 I  Michael 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 II  Christian 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 Biology  Charles Lusk, Michael Caplan, Nadya Dimitrova, Thomas Pollard, James Rothman, Valerie Horsley, Thomas Melia, Megan King, Martin Schwartz, Christopher Burd, Josephina van Wolfswinkel, and David Breslow

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 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  Thomas Pollard, Karen Anderson, Karin Reinisch, 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 Biochemistry  Julien 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 Students  Yong Xiong

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

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

Required of all first-year BQBS graduate students.
HTBA

MB&B 676b, Responsible Conduct of Research  Susan 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 Determination  Frederick 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 Analysis  Andrew Miranker, Yong Xiong, and Jonathon Howard

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 Biology  Mark 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 734b / GENE 734 / MBIO 734b, Molecular Biology of Animal Viruses  Brett Lindenbach

Lecture course with emphasis on mechanisms of viral replication, oncogenic transformation, and virus-host cell interactions.
TTh 10am-11:30am

MB&B 743b / GENE 743b / MCDB 743b, Advanced Eukaryotic Molecular Biology  Mark 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 / GENE 749a, Medical Impact of Basic Science  Joan 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 Membranes  Donald 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.
TTh 9am-10:15am

MB&B 752b / CB&B 752b / CPSC 752b / MCDB 752b, Biomedical Data Science: Mining and Modeling  Mark 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: Mining  Mark 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: Modeling  Mark 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 Medicine  Susan 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 Biophysics  Yong 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 Genetics  Yong 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 Biochemistry  Yong 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