Ph.D. Molecular Biology

CHM 542 Principles of Macromolecular Structure: Protein Folding, Structure and Design (also

MOL 542

) Structures and properties of biological macromolecules. The forces and interactions that direct biological polymers to adapt particular 3-dimensional structures are discussed from both a structural and a thermodynamic perspective. Special emphasis is placed on recent experimental work probing the folding and stability of proteins as well as on the design of novel proteins.

COS 551 Introduction to Genomics and Computational Molecular Biology (also

MOL 551

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QCB 551

) Introduction to basic computational and genomic methods for analysis of biological systems. Topics include: sequence similarity and alignment, phylogenic inference, gene recognition, gene expression analysis, transcriptional networks, structure prediction, functional genomics and proteomics. This is primarily a graduate-level course; interested undergraduates will require permission from instructors.

COS 557 Analysis & Visualization of Large-Scale Genomic Data Sets (also

MOL 557

) Introduces students to computational issues involved in analysis and display of large-scale biological data sets. Algorithms covered will include clustering and machine learning techniques for gene expression and proteomics data analysis, biological networks, joint learning from multiple data sources, and visualization issues for large-scale biological data sets. No prior knowledge of biology or bioinformatics is required; an introduction to bioinformatics and the nature of biological data will be provided. In depth knowledge of computer science is not required, but students should have some understanding of programming and computation.

MAT 586 Computational Methods in Cryo-Electron Microscopy (also

APC 511

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MOL 511

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QCB 513

) This course focuses on computational methods in cryo-EM, including three-dimensional ab-initio modelling, structure refinement, resolving structural variability of heterogeneous populations, particle picking, model validation, and resolution determination. Special emphasis is given to methods that play a significant role in many other data science applications. These comprise of key elements of statistical inference, image processing, and linear and non-linear dimensionality reduction. The software packages RELION and ASPIRE are routinely used for class demonstration on both simulated and publicly available experimental datasets.

MOL 504 Cellular Biochemistry Couse focusses on the molecules and molecular assemblies that underlie cellular structure and function. Topics include: protein structure and folding; ligand binding and enzyme catalysis; membranes, ion channels and translocation; intracellular trafficking; signal transduction and cellular communication; and cytoskeleton assembly, regulation, and function. A major goal of the course is to increase students' proficiency in parsing and critically discussing papers from the primary literature.

MOL 505 Molecular Biology of Prokaryotes Advanced-level discussions of the genetics and molecular biology of prokaryotic organisms and their associated bacteriophages are studied. Emphasis is placed on original research papers, and extensive reading is required. Topics include the genetic code, mutagenesis, mechanisms of DNA replication, recombination, repair and transposition, gene structure and function and mechanisms of gene regulation, and protein synthesis and export.

MOL 506 Cell Biology and Development A continuation of MOL 504, with two modules, Cell Biology II and Development. Cell Biology II concerns how cells assemble into functional tissues, covering the molecular components and fundamental concepts in cell communication, adhesion, shape, division, and differentiation. Development covers the basics of developmental biology, focusing on important concepts and model systems. Primary literature is used to introduce seminal works and classic approaches, modern experimental techniques, and outstanding questions in the field. Students learn the basis of a good paper, to read critically, and to think beyond the reading.

MOL 510 Introduction to Biological Dynamics Course focuses on the application of mathematical methods to biological problems and is intended to provide a basic grounding in mathematical modeling and data analysis for students who might not have pursued further study in mathematics. Topics include differential equations, linear algebra, difference equations, and probability. Each topic has a lecture component and computer laboratory component. Lectures are in common with MOL 410. Students work extensively with the computing package Matlab. No previous computing experience necessary. Two 90-minute lectures, one laboratory.

MOL 514 Molecular Biology Advanced-level discussions of selected topics in prokaryotic and eukaryotic molecular biology. Emphasis is placed on original research papers and extensive reading together with critical thinking is required. Topics include the genetic code, mutagenesis, chromosome and chromatin structures, mechanisms of DNA replication, recombination, repair, and transposition, gene structure and function and mechanisms of gene regulation. Examples from bacteriophage, bacteria, lower and higher eukaryotes will be used to illustrate these different areas of molecular biology.

MOL 516 Genetics of Eukaryotic Organisms Course presents the genetic tools and logical framework currently used research in developmental biology, neurobiology and quantitative biology of multicellular organisms. Lecture topics and reading material focus on primary literature describing genetic approaches used in model organisms such as Drosophila, C. elegans, mouse and zebrafish. Techniques are presented in a context emphasizing basic biological phenomena and include mutagenesis, production and analysis of genetic mosaics, production of transgenics, ES cells, knock-in technologies and cell type specific expression gene expression.

MOL 518 Quantitative Methods in Cell and Molecular Biology Modern biology increasingly relies on quantitative tools to precisely measure cellular states. This course aims to provide an introduction to the experimental techniques and computational methods that enable the quantitative study of biological systems. It focuses on generating and analyzing sequencing data for studying gene networks within/across species, modeling chemical reactions to study the dynamics of gene and protein networks, and extracting information about the spatial organization of biological systems using image processing. It also introduces Python programming, a versatile and powerful platform for scientific computing.

MOL 523 Molecular Basis of Cancer Course explores the molecular events that contribute to the onset and progression of human cancer. Reviews the central elements that make up the cell cycle, then surveys the signal transduction and checkpoint pathways that regulate and coordinate the cell cycle with other cellular events. Oncogenes, tumor suppressor genes and mutator genes will be discussed. Course then explores specific clinical case studies in light of the molecular events underlying different forms of cancer.

MOL 540 Research Projects in Molecular Biology (Laboratory Rotations) Students perform research in the laboratories of two faculty advisers.

MOL 541 Research Projects in Molecular Biology (Laboratory Rotations) Students perform research in the laboratories of two faculty advisers.

MOL 548 Special Topics in Molecular Biology Selected topics in the areas of molecular biology, cell biology, genetics, and molecular genetics, with the subject matter changing yearly. Seminars are given by graduate students on topics related to their interests and/or thesis research areas

MOL 558 Psychopharmacology Medicinal chemistry, mechanisms of action, uses and abuses of drugs and botanical extracts that affect the central nervous system are examined. Relevant issues of mental health are addressed as well as implications for public health. The history and current public policies toward psychotropic drugs and natural products are discussed. Topics include pain management and opiate addiction, schizophrenia hallucinogens and anti-psychotics, anti-depressants and anxiolytics, mechanisms of addiction and withdrawal.

MOL 559 Viruses: Strategy and Tactics Viruses are unique parasites of living cells and may be the most abundant, highest evolved life forms on the planet. The general strategies encoded by all known viral genomes are discussed using selected viruses as examples. The first half of the course covers the molecular biology (the tactics) inherent in these strategies. The second half introduces the biology of engagement of viruses with host defenses, what happens when viral infection leads to disease, vaccines and antiviral drugs, and the evolution of infectious agents and emergence of new viruses.

MOL 561 Scientific Integrity in the Practice of Molecular Biology Through case studies and class discussion, this course will examine the social framework for the public support of basic biomedical research, the rights and responsibilities of students and mentors in the conduct of research, and the significance of intellectual property. Course will also review regulations concerning research with human subjects and animals. The nature of, and response to, personal misconduct will be a principal focus. Course satisfies the mandate of the National Institutes of Health for training molecular biologists in the ethical practice of science.

NEU 501A Neuroscience: From Molecules to Systems to Behavior (also

MOL 501A

) A survey of modern neuroscience in lecture format combining theoretical and computational/quantitative approaches. Topics include cellular neurophysiology, neuroanatomy, neural circuits and dynamics, neural development and plasticity, sensory systems, genetic model systems, and molecular neuroscience. This is one-half of a double-credit core course required of all Neuroscience Ph.D. students.

NEU 501B Neuroscience: From Molecules to Systems to Behavior (also

MOL 501B

) This lab course complements NEU 501A and introduces students to the variety of techniques and concepts used in modern neuroscience, from the point of view of experimental and computational/quantitative approaches. Topics will include synaptic transmission, fluorescent and viral tracers, patch clamp recording in brain slices, optogenetic methods to control neural activity, and computational modeling approaches. In-lab lectures give students the background necessary to understand the scientific content of the labs, but the emphasis is on the labs themselves. Second half of a double-credit core course required of all NEU Ph.D. students.

NEU 502A From Molecules to Systems to Behavior (also

MOL 502A

) A survey of modern neuroscience in lecture format combining theoretical and computational/quantitative approaches. Topics include systems and cognitive neuroscience, perception and attention, learning and behavior, memory, executive function/decision-making, motor control and sequential actions. Diseases of the nervous system are considered. This is one-half of a double-credit core course required of all Neuroscience Ph.D. students.

NEU 502B From Molecules to Systems to Behavior (also

MOL 502B

) This lab course complements NEU 502A and introduces students to the variety of techniques and concepts used in modern neuroscience, from the point of view of experimental and computational/quantitative approaches. Topics include electrophysiological recording, functional magnetic resonance imaging, psychophysics, and computational modeling. In-lab lectures give students the background necessary to understand the scientific content of the labs, but the emphasis is on the labs themselves. Second half of a double-credit core course required of all Neuroscience Ph.D. students.

NEU 503 Neurogenetics of Behavior (also

MOL 503

) How do seemingly simple organisms generate complex behaviors? Course will explore our current understanding of the genetic and neural basis for animal behavior, with an emphasis on cutting-edge research and model systems that are amenable to genetic manipulation. Each week students will discuss a new behavior with a focus on the underlying mechanisms; students will also lead discussions of primary literature. The goal of this course is to provide required background knowledge and critical thinking skills to move beyond the published literature to proposing original experiments. This effort will culminate in a final paper from each student.

NEU 537 Computational Neuroscience and Computing Networks (also

MOL 537

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PSY 517

) An Introduction to the biophysics of nerve cells and synapses, the mathematical description of neural networks, and how neurons represent information. Course will survey computational modeling and data analysis methods for neuroscience and will parallel some topics from 549, but from a computational perspective. Topics will include representation of visual informaion, spatial navigation, short-term memory, and decision-making. Two 90 minute lectures, one laboratory. Lectures in common with MOL 437. Graduate students will carry out and write up an in-depth semester-long project. Prerequisite: 410, or elementary knowledge of linear algebra, di

QCB 515 Method and Logic in Quantitative Biology (also

PHY 570

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EEB 517

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CHM 517

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MOL 515

) Close reading of published papers illustrating the principles, achievements and difficulties that lie at the interface of theory and experiment in biology. Two important papers, read in advance by all students, will be considered each week; emphasis will be on student discussion, not formal lectures. Topics include: cooperativity, robust adaptation, kinetic proofreading, sequence analysis, clustering, phylogenetics, analysis of fluctuations, maximum likelihood methods.

WWS 585A Topics in Science, Technology, and Environmental Policy (also

MOL 586

) These are courses intended to help students develop and apply skills in the application of scientific, technological, and environmental analyses to problems of policy interest. Fall courses are numbered 585, Spring courses are numbered 586.