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An Introduction to Columbia's Graduate Courses

Whichever program you choose for your thesis research, you should have reliable preparation. If you know something about other areas of biomedical science, you will be more likely to make connections that would otherwise not occur. Our courses are designed to help fortune meet the prepared mind. We hope that we can develop reason and knowledge, as well as a fondness for teaching.

Each of our individual PhD programs offers a unique combination of required and elective courses, and the details can be found on their individual web sites. In addition our biomedical sciences PhD students have access to the full range of courses offered by all the schools of Columbia University. The Directory of Classes is available on-line.

Below we list the major core courses within the biomedical sciences taken by students enrolled in multiple programs. They are required by some programs, and are popular electives for students in other programs. In addition to providing a common foundation of basic knowledge, these courses help foster a sense of community and offer increased opportunity for interaction among students from the different programs. Also listed is a representative sampling of advanced and elective courses offered by the individual programs. These courses offer either advanced training for students within a specific discipline, or provide an opportunity for students in other disciplines to broaden their perspective and knowledge by taking one or more of these courses as an elective.

Typically, our students take didactic courses during their first two years, while also participating in laboratory research. By the third year most students are engaged in full time research, although they continue to have the opportunity of elective courses to further their expertise in their chosen field of research.

Core courses

Biochemistry, Cell and Molecular Biology. This two semester sequence is required for all first year Ph.D. students in the Integrated Program in Cellular, Molecular and Biomedical Studies, the Programs in Basic Cell and Molecular Biology, and the Programs in Molecular Basis of Health and Disease, and provides students in these programs with a unified curriculum that covers many of the topics they need to know to successfully carry out research in biological sciences. Students in the other programs often also take one or both semesters of this course

The first semester course covers basic biochemical and experimental principles, such as protein and nucleic acid structure and chemistry, thermodynamics and enzyme kinetics, and bioinformatics. Also included are biochemical processes common to all cells such as genome replication and repair, regulation of gene expression, cell cycle control, and cell membrane and receptor biochemistry. Course Directors: Eric Greene and Larry Shapiro.

The second semester course is an Introduction to eukaryotic cell biology and covers such topics as membrane trafficking, the mitochondria, the nucleus, viral biology, apoptosis as well as the cytoskeleton and its role in various cellular processes, including mitosis, cell migration, cell polarity and cell adhesion. Course Directors: Gilbert DiPaolo and Gregg Gundersen.

Mechanisms of Human Disease. This course is required for students in the Programs in Molecular Basis of Health and Disease. It provides an in-depth analysis of several organ systems and diseases associated with each organ system. The course has four modules; each module describes the basic physiology, nutritional status and anatomy of the organ system, the genetics, cell and biochemical mechanisms and pathologies associated with the disease, as well as basic pharmacology and therapeutics to treat the disease. Course Directors: Ronald Liem and Steven Spitalnik

Molecular Genetics. This course is required for the students in the Programs in Basic Cell and Molecular Biology and the Integrated Program in Cellular, Molecular and Biomedical Studies. The course covers aspects of molecular biology and genetics from prokaryotes to mammals; regulation of gene expression, molecular genetics of bacterial viruses, plasmids and transposable elements, as well as modern molecular genetic approaches to complex biological phenomena. Course Director: Fred Chang.

Responsible Conduct of Research and Related Policy Issues. This course explores a variety of ethical and policy issues that arise during the conduct of basic and clinical scientific research. It is required of all biomedical PhD students, unless their program provides an equivalent course. Course sessions include lectures, discussion periods, and analyses of case studies. Columbia requires that all graduate students share in the discussions of this course. You will hear from your faculty speaking honestly about problems that you may face. You will find the discussions interesting. Course Directors: Arthur Palmer and Jaime Rubin.

Statisics for the Basic Sciences. This course provides an introduction to the basic statistics commonly used in biomedical research laboratories. It is required by many of the programs of students who do not have equivalent prior experience or do not plan to take a more extensive biostatistics course. Students are provided with a statistical software package for use during the course. Exercises based on relevant experimental datasets use the software to reinforce the lecture material. Topics covered include the role of statistics in biomedical research, principles of statistical analysis, and selecting and applying the appropriate statistical tests. Course Director: Jonathan Shaffer.

Survey of Neuroscience. This two-semester course is required for students in the Neurobiology and Behavior Program. The goal of the course is to provide a foundation in cellular and molecular neuroscience. The topics include excitability of neurons, synaptic transmission and plasticity, neurodevelopment, neural circuits, neural systems, memory and learning, and cognitive neuroscience. The topics are both general and specific so that the material covered will challenge those who majored in neuroscience but also be accessible to those with little neuroscience background. Each topic will include a lecture by a member of the faculty who works in the area of neuroscience covered by the topic followed by a journal club-like discussion of relevant papers that is led by specific students and the lecturer. Other course requirements include class participation,short written responses to questions posed for each topic, and research review papers on topics discussed. Course Director: Sam Schacher.

Representative Advanced and Elective Courses

Advanced Eukaryotic Molecular Genetics. Advanced treatment of the principles and methods of the molecular biology of eukaryotes, emphasizing the organization, expression, and evolution of eukaryotic genes. Topics include reassociation and hybridization kinetics, gene numbers, genomic organization at the DNA level, mechanisms of recombination, transposable elements, DNA rearrangements, gene amplification, oncogenes, recombinant DNA techniques, transcription and RNA splicing. Course Director: Tim Bestor.

Cellular & Molecular Biology of Cancer. An integrated and critical review of cancer biology, emphasizing recent research. Topics discussed include: a brief introduction to the natural history and epidemiology of cancer; morphology and behavior of cancer cells; DNA and RNA tumor viruses; oncogenes; tumor suppressor genes; signal transduction; genetics and epigenetics of cancer; cancer and cellular differentiation: physical and chemical carcinogens and DNA repair; multistage carcinogenesis; angiogenesis, growth factors; and targeted therapies in cancer. Special lectures devoted to mouse models and specific tumor types are also included. Readings are largely original research papers and review articles. Course Directors: Benjamin Tycko and Richard Baer.

Computational Systems Biology: Proteins, Networks, Function. This course presents computational approaches of reconstruction, analysis, and simulation of cellular networks. Metabolic, signaling, and protein-interaction networks are covered. The networks are discussed at several levels of structural organization: overall network, functional and structural modules, network motifs. The course emphasizes how specific biophysical and biochemical properties of different networks lead to conceptual simplifications for analysis and simulation. Network evolution and similarities between cellular and non-biological networks are discussed. Course Director: Dennis Vitkup.

Genetic Approaches to Biological Problems. This two semester sequence is designed to illustrate how genetic systems have played a fundamental role in our understanding of basic biological problems. The first semester discusses mitosis and meiosis, chromosomal linkage and mapping, consequences of chromosomal rearrangements, mechanisms of recombination and gene conversion, the use of mutants to study gene structure, regulation and the cell cycle, uses of recombinant DNA in genetic. The second semester covers basic principles and current areas of interest in mouse and human genetics including an introduction to mouse genetics; X-chromosome inactivation and genomic imprinting; genetic manipulation of the mouse; genetics of mouse coat color; genetics of sex determination; the mouse T-complex; human linkage analysis; somatic cell genetics; physical mapping of the human genome; cytogenetics; Huntington's disease; muscular dystrophy and Alzheimer's disease; and gene therapy. Course Director: Rodney Rothstein.

Introduction to Computer Applications in Health Care and Biomedicine. An overview of the field of biomedical informatics, combining perspectives from medicine, computer science and social science. Use of computers and information in health care and the biomedical sciences, covering specific applications and general methods, current issues, capabilities and limitations of biomedical informatics. Biomedical Informatics studies the organization of medical information, the effective management of information using computer technology, and the impact of such technology on medical research, education, and patient care. The field explores techniques for assessing current information practices, determining the information needs of health care providers and patients, developing interventions using computer technology, and evaluating the impact of those interventions. Course Director: Michael Chiang.

Introduction to Neural Development. This course combines lectures by invited faculty on historical and current findings in the field of neural development, including their own research, with student presentations. Topics include: 1) Neural induction, neuro- and gliogenesis, migration and cell specification; cell death; 2) axon and dendritic growth and guidance in invertebrate and vertebrate models; 3) synapse formation in CNS and neuromuscular junction; 4) circuit formation and plasticity; activity-dependent remodeling; 5) behaviors and development, including development of sex-specific song behaviors and circuits, and role of adult neurogenesis in psychiatric perturbations. Course Directors: Carol Mason, Wes Grueber and Brian McCabe.

Introduction to Theoretical Neuroscience. This introductory course roughly follows the text Theoretical Neuroscience by Abbott and Dayan, with updates and excursions covering recent advances. Problem sets involve Matlab, C or C++ programming and also analytic calculation. The topics covered include: biophysics of neurons and synapses; reduced spiking and rate models of neurons and circuits and mean field descriptions; neural coding (encoding and decoding); models of sensory and motor cortical network dynamics; models of circuits underlying memory and decision-making; models of synaptic plasticity, learning and development; Bayesian models of sensory and motor function and optimization; and dimensional reduction. This course is aimed at a general neuroscience audience, including both experimentalists and theory students. Course Directors: Larry Abbott, Stefano Fusi and Ken Miller.

Issues in Neural Circuity. Reading and discussion of papers on cerebral cortical, hippocampal, and cerebellar circuitry, dendritic processing, and other topics in neural circuits. Course Directors: Randy Bruno, Attila Losonczy, Ken Miller and Nate Sawtell.

Molecular and Cell Biology of Nutrients. This course is directed at Ph.D. students in the biological sciences who wish to broaden their familiarity with current knowledge of molecular and cellular mechanisms of nutrient action. The areas represented vary from year to year and represent the major foci of nutrition research at Columbia. Topics covered in recent years include: micronutrient metabolism; retinoid signaling and differentiation; sphingolipids - major regulators of lipid metabolism; molecular biology of adipose tissue and obesity; sterol regulatory element binding proteins - key nutrient responsive transcription factors; Toll-like receptors - role in inflammation and wound healing of the liver and cardiovascular system; genetics and complex trait analysis of atherosclerosis; molecular controls of tissue fatty acid uptake; effects of dietary factors on cell proliferation and apoptosis; VLDL metabolism and diabetes; substrate metabolism in cardiac stress. The importance of technology in determining the direction of scientific progress is highlighted, facilitating the transition of students as participants and leaders in research efforts. Course Director: Li-Shin Huang.

Molecular Biophysics. This course covers methods and principles involved in studying the structure and function of proteins, nucleic acids, membranes and their macromolecular assemblies. Noncovalent forces and conformational analysis; ultracentrifugation, viscometry, circular dichroism, fluorescence, magnetic resonance, conformational changes in proteins and nucleic acids, topological properties of macromolecules. Course Director: Barry Honig.

Molecular Pathophysiology of the Cardiovascular System. This course presents a translational molecular focus on advanced topics related to cardiac physiology and vascular biology as it impacts health and disease processes. Topics include lipoprotein physiology, angiogenesis, athogenesis of atherosclerosis, mechanisms of heart arrhythmias, cardiac/circulatory physiology, and the role of inflammation in atherosclerosis and heart disease. A good background in physiology is required. Course directors: John Loike and Alan Tall.

Molecular Pharmacology: from Membrane to Nucleus. The purpose of this course is to provide students with an introduction to molecular approaches to target identification and drug development and delivery for cellular and subcellular processes that contribute to human disease. Material covered includes the principles of drug-receptor interactions; ion channels as molecular targets of neurohormones and drugs; structure and function of G-protein coupled receptors; cytoplasmic signaling molecules including receptor and non-receptor tyrosine kinases and serine-threonine kinases; neuropsychopharmacology; the pharmacology of inflammation; and novel approaches to gene-targeted pharmacology. Integration of molecular processes and human disease including cancer, neurodegenerative disease; cardiovascular disease, and psychiatric disorders is stressed. Course Director: Susan Steinberg.

Neuroethology. Seminar course in the neural bases for natural animal behaviors, using an evolutionary approach. The focus is on the neurobiology and behavior of animal communication and other natural behaviors and the relation between sensory processing and motor output. Course Directors: Darcy Kelley and Sarah Woolley.

Neuropsychopharmacology. This course explores selected topics in the area of brain and behavior, especially as related to the molecular, cellular, physiological and psychological properties of agents acting within the central nervous system, with a focus on the pathophysiology and treatment of neuropsychiatric disorders. Course Director: Jonathan Javitch.

Stem Cells and Cell Lineage Specification. This course comprises general lectures, analyses and discussions of primary literature on stem cell and lineage biology as well as student seminars. The themes that are presented include basic cell and molecular biological characterization of stem cells, regulation of self-replication versus lineage restriction and differentiation of cells, model systems used in studies of stem cells, and the relevance of tissue formation, regeneration and disease states. Course Director: Lori Sussel.

Structure and Function of Membrane Channels. This course provides a detailed analysis of the biophysical and structural properties of ion channels, as well as their physiological contributions to various aspects of membrane excitability. Particular emphasis is placed on channels found in nerve and skeletal muscle. Ion channel function is related to the structure of channels as revealed by biophysical and molecular-biological techniques. Key topics in channel structure-function relationships that are covered include ion permeation and channel selectivity, control of channel-gating, channel-blockade by drugs and ions, and modification of channel function by disease. Finally, the roles of various channels in controlling the spontaneous activity patterns and input-output relations of nerve and muscle is discussed. Course Directors: Steven Siegelbaum and John Koester.

Systems Neuroscience. Seminar on current research topics in the neural basis of perception, cognition and sensorimotor integration, using the macaque monkey visual system as the primary experimental model. Topics covered include visual and oculomotor systems, attention, learning and plasticity, decision-making and executive function. Course Directors: Mickey Goldberg and Jackie Gottlieb.

 

 
 
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