An Introduction to Columbia's Graduate Courses
More than many graduate programs, we believe that education should begin with well-planned courses. When you begin your thesis work in genetics, biochemistry, nutrition, neurobiology, or informatics, you should have a reliable preparation. We do not think it is a good idea for you join a laboratory and then try to pick up everything you need to know. If you know other areas of biology or computer 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. There are too many combinations for us to write a core curriculum for all students. Pharmacology students will take a series of courses that are different from those planned for Integrated Program students. Medical Informatics follows yet another path, but often students from the various programs take a common course and so get to know each other. These courses are taught by knowledgeable people and feature the latest theory and experimental results. There is always extensive reading of primary research articles and there is a lot of discussion, some led by students, some led by faculty.

That is a beginning. After you have settled into a lab, you may want to take electives. There are many. Electives take on the character of collegial discussions, rather than the formal courses one takes as an undergraduate. In this list, we have left out the details of meeting times, prerequisites, and credits. You can find all of this information in the requirements for each department or program. These are available on-line at: http://www.columbia.edu/cu/gsas/bulletin/bulletin.html. The list that follows is probably not complete. New courses are always being developed and others dropped. You will have resources available to you outside the immediate campus - we have had students learn phylogenetics at The Museum of Natural History. Once you get beyond the basics, you can, to a large extent, define your own intellectual life.

Among the eleven basic science departments at the Columbia Medical Center Campus, there are various core sequences. The following courses are those taken by students in the Integrated Program and in some other basic science departments. Consult other departments - for example Pharmacology, Neurobiology and Behavior, or Medical Informatics - for their core sequences.

I. Microbial Molecular Genetics. Basic aspects of prokaryotic molecular biology and genetics. Regulation of gene expression, molecular genetics of bacterial viruses, plasmids and transposable elements. Modern molecular genetic approaches to complex biological phenomena. Format: four to five hours of lecture and discussion per week. F. Chang and C. Waldberger
II and III. Biochemistry and Molecular Biology of Eukaryotes I, II. This full year course is for all first year Ph.D. students and provides them with a unified curriculum that cover many of the topics that students need to know to successfully carry out research in biological sciences. The topics include basic biochemical principles, processes common to all eukaryotic cells such as transcription, translation and the cell cycle, and mechanisms of cell-cell signaling. R. Mann, Lloyd Greene, D. Thanos, P.R. Srinivasan and staff.
IV. Cellular Membranes and Organelles. Introduction to eukaryotic cell biology; discussion of modern research approaches and current literature. Format: 3 hours of lecture and 1 hour of student presentation per week. G. Gundersen, Bret Lauring, and staff.
V. Molecular biophysics. G4250. Methods and principles involved in studying the structure and function of proteins, nucleic acids, membranes and their macromolecular assemblies. Non-covalent forces and conformational analysis; ultracentrifugation, viscometry, circular dichroism, fluorescence, magnetic resonance, conformational changes in proteins and nucleic acids, topological properties of macromolecules. B. Honig and staff.
VI. Genomics: Biological Sequence Analysis G4020. Unix, web-site usage,sequence comparison, database searching, multiple sequence alignment, profile methods, secondary structure prediction, mapping, primer design, and genomic analysis. Student instruction in the various programs in a supervised lab. Richard Friedman. For other Columbia offerings in Genomics see: http://www.ccc.columbia.edu/~friedman/course-work.html.
VII. 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. 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 find the discussions interesting. R. H. Kessin and staff.

Basic and Advanced Courses
Anatomy and Cell Biology

Human development (M5103)
Lectures and demonstrations concerning the cellular biology of histogenesis and organogenesis.
T. R. Rothman. Begins October 1 and runs through mid-December

Principles of Neural Science (M6106)
Lecture and Laboratory Course An introduction to basic neurobiology and neuroanatomy, of the human nervous system, with selected aspects of clinical neurology and psychiatry. Lectures, demonstrations, conferences and neuroanatomy laboratory.
Goldberg, Martin and staff.

Biochemistry and Molecular Biophysics

General biochemistry (G4021)
An integration, from a dynamic point of view, of cellular constituents with the chemical processes of living systems: chemistry and function, mode of synthesis and degradation by the cell, the characterization and role of particular enzymes and coenzymes in these reactions, and the mechanisms of oxidation and energy production. Nucleic acids, replication, and the genetic code. (Given at the Morningside campus.)
A. I. Krasna.

Biochemistry of nucleic acid and protein synthesis (G4026)
Structure and organization of chromatin, nucleic acid hybridization and sequence complexity of DNA, DNA and RNA sequencing methods, current views of replication and repair, transcription and translation, regulation of nucleic acid and protein syntheses, recombinant DNA techniques, gene transfer, and gene duplication. Discussion of original papers and evaluation of experimental procedures and conclusions.. (Given at the Morningside campus.)
P. R. Srinivasan.

Special methods of biochemistry (G6011-G6012)
Practical experience in the use of biochemical methods, with the aim of preparing the student for research.

Membrane receptors and transport proteins (G6045)
Molecular structure and function of membrane proteins; general principles and common threads.
A. Karlin.

NMR spectroscopy of macromolecules (G6270)
Theoretical principles and applications of NMR spectroscopy for the study of biological macromolecules, including proteins, nucleic acids and carbohydrates, in solution.
A.G. Palmer

Diffraction analysis of macromolecules (G6275)
Diffraction theory and applications to protein, nucleic acid, and membrane structures. Topics include electron microscopy, x-ray diffraction, protein crystallography, electron and neutron diffraction and electron microscopy.
W. Hendrickson.

Genetics and Development

Introduction to mathematical genetics (G4005)
Introductory courses in probability are recommended but are not required. Basic concepts of genetics and population genetics. Genetic linkage. Models of disease transmission. While general genetic principles are covered, emphasis is on human genetics and on human genetic linkage.
J. Ott.

Principles of developmental biology (G4027)
Required for first-year Genetics and Development students. Open to students from all departments. The course emphasizes the molecular control of vertebrate embryogenesis. Divided into three main areas: early embryogenesis, developmental neurobiology, and the development and differentiation of specialized organs or lineages. A combination of faculty lectures and presentations by participating students.
D. Wolgemuth and staff.

Advanced eukaryotic molecular genetics (G4050)
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. Students participate in discussions of problem sets on the current literature.
Staff.

Genetic approaches to biological problems (G6210)
Designed to illustrate how genetic systems have played a fundamental role in our understanding of basic biological problems. The course 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 analysis, and the genetic analysis of development in Drosophila.
R. Rothstein and staff.

Genetic approaches to biological problems (G6211)
Basic principles and current areas of interest in mouse and human genetics. 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.
A continuation of the course given by Prof. Rothstein.

Medical Informatics

Introduction to Computer Applications in Health Care and Biomedicine (G4001)
An overview of the field of medical informatics. Use of computers and information in health care, specific applications and general methods, current issues, capabilities and limitations of medical informatics.
E. Shortliffe.

Methods in Medical Informatics (G4002)
A survey of the methods underlying the field of medical informatics. Explores techniques in mathematics, logic, decision science, computer science, engineering, cognitive science, management science and epidemiology, and demonstrates the application to health care and biomedicine.
S. Johnson

Survey of Clinical Science (G4010)
Overview of the practice of clinical care. Examination of issues and approaches in treating the major disease processes.
J. Starren.

Acculturation to Medicine for Information Specialists (G4011)
An overview of the field of medicine for informaticians. Topics include: medical language and terminology, introduction to pathology and pathophysiology, the process of medical decision making, and an understanding of how information flows in the practice of medicine.
R. Barrows.

Introduction to Genomics (G4012)
Survey of the major problems in the present-day eclectic field called “Genomics” or “Bioinformatics.” Exploration of computational methods for gene discovery.
A. Rzhetsky

Representation and Coding of Medical Data (G4020)
Methods for representing information in medical systems including clinical data about patients, indexing information for medical knowledge resources, and expert systems. Analysis of existing national and international standards. Exploration of knowledge-based approaches to medical terminology representation, maintenance and use.
J. Cimino.

User Interfaces in Medicine (G4030)
Overview of the special challenges in developing interfaces between humans and computers for medical applications. Data presentation, data entry, and usability testing, as they apply to the medical domain.
J. Starren.

Medical Language Processing (G4031)
Methods for the analysis of medical language for processing by computer. Sublanguage methodology, formal grammars, corpus-based techniques, representation of medical semantics.
S. Johnson.

Medical Image Processing (G4032)
A survey of the various imaging modalities used in medicine, and the computational methods used in processing them.
C. Imelinska.

Health Information Systems Architecture (G4040)
Design of computer systems for health care. Distributed system architectures, management of heterogeneity, layers of communication, data exchange standards.
S. Sengupta.

Quantitative Models for Medical Decision Making (G4050)
Survey of a number of techniques for quantitative reasoning, including probabilistic reasoning, decision analysis, ROC analysis, and meta-analysis.
S. Henry.

Clinical Decision Support (G4051)
An overview of the various techniques used in providing computerized clinical decision support, both from the perspective of the underlying theory and the applications designed using the theory.
R. Jenders.

Medical Knowledge Structures (G4052)
Methods of structuring knowledge in medicine from multiple perspectives. Knowledge structures in traditional information environments such as libraries. Cognitive theories of learning and methods of instruction. Principles of visual displays for presenting knowledge. Computational issues for representing and manipulating knowledge.
P. Molholt.

Evaluation Methods in Medical Informatics (G4060)
Methods for evaluating the use of information systems in health care. Analysis of user needs, system design, effectiveness, utility, and costs in information systems.
G. Hripcsak.

Economics of Informatics: Cost and Investment Issues in Healthcare Information Technology (G4061)
Cost models of information technology in health care settings, including total cost of ownership, value chain analysis and return on investment.
L. Vogel.

Microbiology

Introduction to immunology (G4020)
Required Course. This course is a survey of the major topics in basic immunology with an emphasis on the molecular basis for immune recognition and regulation. Specific topics include Clonal Selection, Ig and TCR gene organization and rearrangement, VDJ recombination, MHC Biology, T cell function and development, cytokines, innate immunity and pathogen recognition, and mucosal immunity. Course Directors: P.B. Rothman, K. Calame.

Advanced Topics in Immunology (G4021)
Elective Course. This discussion course provides a survey of recent developments in Immunology from the literature, including dendritic cell function, gamma-delta T cell activation, Toll-like receptors, and relevant signal transduction pathways. Course Director: K. Calame.

Introduction to Computational Biology (G4120)
Required Course. This course introduces the fundamental concepts and methods of computational biology, bioinformatics and genomics. It presents the databases, web sites, software, hardware, algorithms, and programming languages currently used to analyze biological data and explains how these tools are best used. The course focuses on Macintosh OS X and computational biology applications that run under that operating system. (Microbiology Ph.D. students are provided with an iBook laptop for the duration of the course.) Course Director: O. S. Jovanovic.

Chromosome dynamics and genome stability (G4900)
Elective Course. This seminar course focuses on recent advances in chromosome replication, segregation and DNA repair, processes essential for the stable inheritance of the genome. Guest lecturers present a Microbiology Departmental Seminar and meet with the students to discuss their work. Papers to be discussed focus on the use of several model systems and emphasize the use of genetic approaches to understand these processes. Course Director: L. Symington.

Virology (G6021)
Elective Course. A principle-based discussion of virology, emphasizing the common reactions that must be completed by all viruses for successful reproduction within a host cell and survival and spread within a host population. The molecular basis of alternative reproductive cycles, the interactions of viruses with host organisms, and how these lead to disease are presented with examples drawn from a set of representative animal viruses. Course Director: V. Racaniello.

Microbial pathogenesis (G6048)
Elective Course. This literature-based course focuses on principles and problems in the study of bacterial and fungal pathogens. Specific topics are chosen each year based on the current literature and availability of visiting speakers, and have included Innate Immunity, Toll-like receptors, TB, Pseudomonas, Enteric Pathogens, Type III Secretion Systems, Fungal Cell Wall Biogenesis, C. albicans, H. capsulatum, C. neoformans, and Antimicrobial Agents and Resistance. About 10 visiting speakers present a Microbiology Departmental Seminar and meet with students afterwards for a 2-hour discussion period. The course also includes lectures and discussions of research articles. Course Directors: A. Mitchell and H. Shuman.

Prokaryotic Transcription (G6080)
Elective Course. This seminar course presents advanced topics in bacterial transcription and its regulation chosen from the current literature, including antitermination, PhoP-Q, iron regulation, transcriptional control of motility, RpoS and stationary phase regulation, and B. subtilis competence and sporulation. Course Directors: M Gottesman and C. Waldburger.

Neurobiology and Behavior

Cellular and Molecular Neurobiology (W3004/W4004)
Survey course with a basic science emphasis. Introduction to cellular neurobiology, neural development, and to the organization of the human brain at a systems and anatomical level. Lectures and recitation sessions in which original papers and problem sets are discussed.
Yang and Kelley/Firestein and Yuste (Dept. of Biological Sciences, Morningside Heights)

Principles of Neural Science: Section on Neuroanatomy (M6106)
Human neuroanatomy laboratory from a basic science perspective. Student presentations of relevant original literature.
Shacher

-or-

Principles of Neural Science: Lecture and Laboratory Course (M6106)
An introduction to basic neurobiology and neuroanatomy, of the human nervous system, with selected aspects of clinical neurology and psychiatry. Lectures, demonstrations, conferences and neuroanatomy laboratory. Goldberg, Martin and staff.

Structure and Function of Membrane Channels (G4600)
Seminar course on the biophysical properties and the structure-function relationships of ion channels in neuronal and muscle membranes. Emphasis on biophysical, molecular, and structural approaches. Lectures and student presentations of original papers in the field.
Siegelbaum, Yang and Koester

Advanced Seminar in Neuroscience: G-protein Coupled Receptors (G4008)
A seminar that concentrates on the importance of G- protein coupled receptors in the nervous system, with in depth readings from the recent literature. Particular attention will be paid to the application of molecular and pharmacological techniques that have added significantly to our current view of the structure and function of these ubiquitous receptors.
Firestein (Dept. of Biological Sciences, Morningside Heights)

Advanced Seminar in Neuroscience: Dendrites (G4008)
A seminar-style discussion on the function of mammalian dendrites. Students read and present papers from the literature.
Yuste (Dept. of Biological Sciences, Morningside Heights)

Molecular Mechanisms in Synaptic Transmission and the Control of Transmitter Release (G4007)
A seminar on the cellular and molecular processes influencing synaptic transmission. Lectures and student presentations of original papers in the field.
Goldberg, Bailey, MacDermott, and Role.

Neural Systems: Circuits in the Brain (G4011)
A seminar that uses RollÕs Neural Networks and Brain Function and selected papers to review current knowledge about the computation carried out by different microcircuits present in the mammalian CNS. The material covered by the course concentrates on synaptic physiology, neuro-anatomy, and circuit analysis. Student presentations and discussion.
Yuste. (Dept. of Biological Sciences, Morningside Heights)

Introduction to Neural Development (G9002)
Seminar on the development of vertebrate and invertebrate nervous systems with emphasis on experimental approaches. Lectures and student presentations.
Mason, Kelley, Hobert, and Jessell.

Neuroethology (G9010)
An examination of how the nervous system controls behavior in a variety of animal model systems, both vertebrate and invertebrate (owls to crickets). Topics include: navigation, social communication, aggression, courtship, feeding, fear, and dreaming. Lectures and student presentations.
Kelley and Kupferman

Neuroscience of Neurological and Psychiatric Disorders (G4100)
Advanced seminar course on basic science approaches to schizophrenia, Alzheimer's, Parkinson's, and Huntington's disease, anxiety disorders, epilepsy, etc. Hen, Kriegstein, Rayport, and staff.

Systems Neurophysiology and Modeling (G4300)
Advanced seminar course that examines discuss classic as well as recent papers in systems neurophysiology and modeling. The emphasis will be on visual perception and eye movement systems. Lectures and student presentations.
Ferrera, Qian and staff.

Human Brain Mapping with fMRI (Course number not yet available)
This course focuses on the development of creative approaches to the study of human brain functions using fMRI. Lecture topics provide a working knowledge of image acquisition techniques and data analysis strategies, and the reading list will be aimed at a comprehensive selection of recent developments in neuroscience based on fMRI studies. Students select a research question and design an fMRI experiment which will be presented for class discussion and a short paper. Students will also have an opportunity to participate in on-going fMRI studies.
Hirsch

Visual Cognition (G4210)
The nature and function of visual/spatial representations in selected areas of perception and cognition. Lectures and student presentations.
Cooper (Psychology, Morningside Heights Campus)

Information processing (G4270)
The systems approach to the study of human memory. Lesion studies, psychological dissociations, the relation of human to animal memory, and current computational models of human memory.
Metcalfe (Psychology, Morningside Heights Campus)

In addition, these courses may be of interest:
Psychophysics, sensory processes, and perception. Psychology (G4005)
Production and perception of language. Psychology (G4232)
Special topics in vision. Psychology (G4235)
Computational Neural Modeling and Neuroengineering. Biomedical Engineering (E6480)
Psychology and Neuropsychology of Language (G4470)

Nutrition

Growth and development (M8200)
General aspects of normal human growth and development from viewpoints of physical growth, cellular growth and maturation, and adjustments made at birth; the impact of altered nutrition on these processes. Prenatal and postnatal malnutrition, the role of hormones in growth; relationships between nutrition and disease in such areas as anemia, obesity, infection, and carbohydrate absorption.
Sharon Akkabas and Staff.

Biochemical and physiological basis of nutrition (M8205)
Aspects of carbohydrate, lipid, protein, and energy metabolism relevant to the understanding of nutrition at cellular and organism levels. Biochemical and physiological aspects of vitamin and mineral metabolism and action during both normal conditions and deficiency toxicity states.
Fall semester: Dave Talmage and Staff.
Spring Semester: William Blaner and Staff

Food and nutrition: a public health perspective (M8220)
An introduction to the problem of food and nutritional diseases from a public health perspective, and the relationship between the determinants and the program designed to solve these problems. Various types of interventions are discussed, with emphasis on the health sector role.
Audry Cross

Clinical nutrition (M8207)
Discussion of pathology, symptomatology, and clinical manifestations with case presentations when possible. Laboratory assessments of each condition. Principles of nutritional intervention for therapy and prevention.
Maudene Nelson and Staff.

Molecular nutrition (M8210)
The molecular principles that underlie the regulation of gene expression in response to the nutritional status of the organism.
Steve Sturley and Staff

Human Nutrition (G4020)
Molecular and Cell Biology of Nutrients. Second Term. This course explores molecular and cellular mechanisms of nutrient action. Six major foci of modern nutritional science are presented. These include the actions of nutrients in transcriptional regulation, in signaling pathways, on intra- and extracellular trafficking, in assuring normal development, in the maintenance of antioxidant defences and nutrient/gene interactions. The course consists of lectures by faculty and student presentations and discussions of recent literature.
Li-Shin Huang and Neil Shachter.

Pathology

Introduction to pathobiology (G4001)
Instructor to be announced.

Molecular and cellular mechanics in human disease (G6003)
The molecular and cellular basis for human disease, with an emphasis on modern research in characterization and treatment. Lectures, conferences, assigned readings, written and oral presentations.
R. Liem and members of the staff.

Cellular and molecular biology of cancer (G4500)
An integrated and critical review of cancer biology, emphasizing recent research. Topics discussed include: natural history and epidemiology of cancer; morphology and behavior of cancer cells; DNA and RNA tumor viruses; oncogenes; tumor suppressor genes; signal transduction; the genetics of cancer; cancer and cellular differentiation; cancer causation: physical and chemical agents; multistage carcinogenesis; hormones, nutrients, and growth factors in cancer. Readings are largely original research papers and review articles. One 2-hour seminar per week.
R. Dalla-Favera, B. Tycko and staff.

Neuropathology (G6004)
Open only to graduate students in the basic medical science departments. Gross and microscopic study of lesions of the nervous system, with attention to functional derangement associated with them. Lectures, laboratory, conferences, and assigned readings.
J. Goldman and members of the staff.

Pharmacology

Molecular pharmacology: from membrane to nucleus (G9600)
Required for all graduate students in pharmacology. Introduction to molecular approaches to target identification and drug development and delivery for cellular and subcellular processes that contribute to human disease. 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; neuro-psychopharmacology; the pharmacology of inflammation; and novel approaches to gene-targeted pharmacology. Integration of molecular processes and human disease including cancer, neuro degenerative disease; cardiovascular disease, and psychiatric disorders is stressed.
R. S. Kass and staff.

Backgrounds in Pharmacology (G8003-G8004)
This course provides each student with an opportunity to identify and critically analyze relevant papers in a circumscribed topic in pharmacology, and to develop the ability to give a well organized oral report of that analysis. The student works with two faculty members, assigned by the Program Director, to select a suitable topic. The topic generally involves a question which has not yet been fully resolved by the scientific community. The student researches the topic and selects 2-5 representative papers to form the focus of the presentation. He/she provides copies to the two faculty members and the Program Director. Drawing on both the selected papers and additional material, the student summarizes and evaluates research in the chosen area and discusses any unresolved issues. Usually one hour is allotted for the presentation and questions by the faculty. The presentation is evaluated in terms of organization, manner of presentation, understanding and adequacy of critical evaluation, and ability to answer questions related to the selected topic. Students are required to take two sessions of this course, presenting a different topic each time.

Scientific Communication (G8015)
A report on the topic considered in the Mini-Oral, prepared as a short review, is submitted for evaluation by selected members of the faculty. The report is evaluated in terms of clarity and style as well as content and organization. The faculty members work with the student to improve writing skills.

Structure and Function of Membrane Channels (G4600)
This course provides a detailed analysis of the biophysical and structural properties of ionic channels in biological membranes. In addition, the physiological role of such channels in regulating neuronal excitability is covered. The course begins with the classical Hodgkin-Huxley voltage clamp analysis of the squid action potential. Key topics in channel function are then discussed, including ion permeation and selectivity, models of channel gating, studies of single ion channels with the patch clamp technique, transmitter-activated channels, and channel blockade by drugs and ions. Ion channel function is related to the structure of channels as revealed by biomedical and molecular-biological techniques. Finally the role of channels in controlling the integrative and repetitive firing patterns observed in nerve cell bodies is discussed. The course consists of an initial series of lectures to provide students with an adequat background in the basic principles of membrane biophysics. Subsequently, original papers are assigned, with one student in charge of leading a discussion during each class.
Course Director: Dr. S. Siegelbaum.

Physiology and Cellular Biophysics

Principles of physiology (G6001)
Prerequisites: instructor’s permission. Biophysics of solutions and membranes; membrane transport, ion channels, action potentials; synaptic transmission, muscle contraction, secretion; selected topics in cardiovascular, renal, endocrine, and gastrointestinal physiology. Lectures integrate basic material with in-depth discussions of particular topics. Emphasis on experimental approaches and recent advances.
M. Low and staff.

Structure and function of membrane channels (G4600)
A detailed analysis of the biophysical and structural properties of ionic channels in biological membranes.
S. Siegelbaum, J. Koester.

Scientific communication (G8015)
R.S. Kass and members of the staff.

Molecular mechanisms in synaptic transmission and the control of transmitter release (G4007)
A detailed examination of the cellular and molecular processes influencing synaptic transmission.
C. Bailey, D. Goldberg, A. MacDermott and L. Role.