BIOL W4004. Neurobiology I: Cellular and Molecular Neurobiology. 4 pts. Prerequisites: one year of biology; a course in physics is highly recommended.

Lecture and recitation. This is an advanced course intended for majors providing an in depth survey of the cellular and molecular aspects of nerve cell function. Topics include the cell biology and biochemistry of neurons, ionic and molecular basis of electrical signals, synaptic transmission and its modulation, function of sensory receptors. Although not required, it is intended to be followed by Neurobiology II (see below). The recitation meets once per week in smaller groups and emphasizes readings from the primary literature.

BIOL W4005. Neurobiology II: Development and Systems. 3 pts. Prerequisites: Biology W3004, one year of biology or instructor's permission.

This course is the "capstone" course for the Neurobiology and Behavior undergraduate major at Columbia University and will be taught by the faculty of the Kavli Institute of Brain Science (http://www.kavli.columbia.edu/). It is designed for advanced undergraduate and graduate students. Knowledge of Cellular Neuroscience (how an action potential is generated and how a synapse works) will be assumed. It is strongly recommended that students take w3004 Neurobiology 1: Molecular and Cellular Neuroscience, or a similar course, before enrolling in w3005. Students unsure about their backgrounds should check a representative syllabus of w3004 in http://www.columbia.edu/cu/biology/courses/w3004/index.html

BIOL G4008. Advanced Seminar In Neurobiology: Developmental wiring of neural systems. 3 pts. Prerequisites: one year of introductory biology and W3004/W4004 "Cellular and Molecular Neurobiology" (or equivalent).

Emphasizing sensory systems, where the input and output are known, we will investigate how the development of sensory system neural circuitry determines function. We will read and discuss articles in the primary literature and recent reviews. Students will write short summaries and may present some material in our discussion. Topics will include the interaction of genetics and environmental input, encoding of sensory stimuli, similarities and differences in the strategies employed by different sensory systems, regeneration and repair of sensory systems. Emphasis will be on the visual, olfactory and proprioceptive systems. Permission of instructor is required. Interested students should email Professor Firestein and include a list of the neurobiology and other relevant courses they have taken and a short statement about why they are interested in this course. (20 students maximum)

BIOL W4008. The Cellular Physiology of Disease. 3 pts. Prerequisites: One 3000 level course in Cell Biology or Biochemistry or the instructor's permission.

This course will present a quantitative description of the cellular physiology of excitable cells (mostly nerve and muscle). While the course will focus on examining basic mechanisms in cell physiology, there will be a thread of discussion of disease mechanisms throughout. The end of each lecture will include a discussion of the molecular mechanisms of selected diseases that relate to the topics covered in the lecture. The course will consist of two lectures per week. This course will be of interest to advanced (3000-4000 level) undergraduates that aim to pursue careers in medicine as well as those that will pursue careers in biomedical research. This course will also be of interest to graduate students desiring an introduction to the cellular physiology of nerve and muscle.

BIOL W4011. Neural Systems: Circuits in the Brain. 3 pts.

This course is an advanced seminar that will review current knowledge about the computations carried out by circuits present in the CNS. The class will run as a seminar discussion, where it is assumed that every student will have studied the reading material ahead of time and will be knowledgeable enough to explain it. W3004 and W3005 are ideal background for the course. To maintain a small class size and ensure the participation of all students in all the discussions, only 10 students will be admitted. Graduate students are welcome but undergraduate students in their final year majoring in Neuroscience and Behavior will have preference. Auditors will not be accepted. Instructor permission is necessary for registration. For grading, a short (maximum 5 page) essay on any of the topics discussed in the course is due on the last day of class and will be used for the final grade, together with evaluation of class participation.

BIOL W4022. Developmental Biology. 3 pts. Prerequisites:BIOL C2005-C2006 or equivalent

Come discover how the union of egg and sperm triggers the complex cellular interactions that specify the diverse variety of cells present in multicellular organisms. Cellular and molecular aspects of sex determination, gametogenesis, genomic imprinting, X-chromosome inactivation, telomerase as the biological clock, stem cells, cloning, the pill and cell interactions will be explored, with an emphasis on humans. Original research articles will be discussed to further examine current research in developmental biology.

BIOL W4031. Genetics. 3 pts. OPEN TO BIOTECH M.A. STUDENTS & OTHER GRADUATE STUDENTS Prerequisites:BIOL C2005-C2006 or the equivalent Corequisites: Recommended co-requisite: one term of organic chemistry

Students may receive credit for W3031 or C3032, but not both due to overlap in course content. General course in genetics dealing with principles of gene structure, function, and transmission. Historical development and experimental basis of current knowledge are stressed.

BIOL W4032. Genetics. 3 pts. Not offered in 2009-2010. Prerequisites:EEEB W2001 or BIOL C2005, and C2006 or the equivalent. Corequisites: one term of organic chemistry.

General course in genetics dealing with principles of gene structure, function, and transmission. Both classical (transmission) and molecular genetics are discussed. Historical development and experimental basis of current knowledge are stressed to familiarize the student with the methods and logical bases of genetic research. Students may receive credit for W3031 or W3032, but not both due to overlap in course content.

BIOL W4034. Biotechnology. 3 pts. Prerequisites: genetics or molecular biology.

The course covers techniques currently used to explore and manipulate gene function and their applications in medicine and the environment. Part I covers key laboratory manipulations, including DNA cloning, gene characterization, association of genes with disease, and methods for studying gene regulation and activities of gene products. Part II covers commercial application, including animal cell culture, production of recombinant proteins, novel diagnostics, high throughput screening, and environmental biosensors.

BIOL G4035. Seminar in Epigenetics. 3 pts. Prerequisites: Genetics (3032/4032) or Molecular Biology (3512/4512), and the permission of the instructor.

This is a combined lecture/seminar course designed for advanced undergraduates and graduate students. The focus is on understanding the mechanisms underlying epigenetic phenomena: the heritable inheritance of genetic states without change in DNA sequence. Epigenetic mechanisms play important roles during normal animal development and oncogenesis. It is an area under intensive scientific investigation and the course will focus on recent advances in understanding these phenomena. In each class, students will present and discuss in detail recent papers and background material concerning each individual topic, followed by an introductory lecture on the following week's topic. This course will emphasize critical analysis of the scientific literature and help students understand how to identify important biological problems and how to address them experimentally.

BIOL W4037. BIOINFORMATCS OF GENE EXPRESSION. 3 pts. Not offered in 2009-2010.

Treats a number of topics in the emerging fields of genomics and bioinformatics, such as sequence alignment, genome annotation, and DNA microarray analysis, with an emphasis on the proper use of statistics. Provides a practical introduction to the Perl programming language and utilizes a computer lab.

BIOL G4044. Advanced Topics in Cell Biology. 3 pts. Prerequisites: Enrollment in the Biological Sciences Ph.D. Program, one of the other biomedical Ph.D. programs, or permission of the instructor. Generally students with a solid background in biology (four or more courses) are accepted.

Advanced Topics in Cell Biology is a graduate course, primarily enrolling Ph.D. students, but also enrolling advanced M.A. students and undergraduates with consent of one of the instructors. This year's offering will concentrate on the basic cell biology of signal transduction and its readouts within the cytoskeleton and its activities inside the cell. Students will read the literature and give presentations. Topics include the pathways by which cells respond to extracellular signals such as growth factors and cell-cell contact, and the mechanisms by which extracellular signals are translated into alterations in the cell cycle, morphology, differentiation state, and motility of the responding cells.

BIOL W4070. The Biology and Physics of Single Molecules. 3 pts. Not offered in 2009-2010. Prerequisites: calculus, chemistry, physics, 1 year biology, or instructors' permission

This course will examine the fundamental mechanisms underlying the behavior of biological molecules, at the single molecule level. The course will cover the methods used to track single molecules: optical tweezers, single molecule AFM, Magnetic tweezers, Optical techniques and Fluorescence energy transfer (FRET) probes. The course will cover the mechanism of action of mechanical motors such as myosin dyneyin, kinesin. It will cover the action of DNA binding enzymes such as topoisomerases, helicases, etc. We will also discuss the function of large motors such as the ATP Synthase and the bacterial AAA ATPases. We will discuss the mechanical properties of DNA, RNA, and proteins. The course will consist mainly of reviewing classical experiments in each category, and developing the background physical theories to promote a deep understanding of biological mechanisms at the mesoscopic level.

BIOL W4073. Immunology. 3 pts. Prerequisites: Two semesters of a rigorous, molecularly-oriented introductory biology course (such as C2005) and at least one advanced biology course, or the instructor's permission.

This course will cover the basic concepts underlying the mechanisms of innate and adaptive immunity, as well as key experimental methods currently used in the field. To keep it real, the course will include clinical correlates in such areas as infectious diseases, autoimmune diseases, cancer and transplantation. Taking this course won't turn you into an immunologist, but it may make you want to become one, as was the case for several students last year. After taking the course, you should be able to read the literature intelligently in this rapidly advancing field.

BIOL G4095. Chemical Genomics. 2 pts. Prerequisites: One year of college-level biology and one year of organic chemistry, or the instructor's permission. Advanced undergraduate students are encouraged to enroll, and they will be given extra assistance in preparing the research proposal (no prior experience in writing proposals is needed).

In this course, we will cover subject matter in chemical biology and genomics. We will discuss approaches for discovering and optimizing chemical tools for measuring and perturbing biological systems. Topics covered will include high-throughput assay development, chemical and genomic screening, chemical library creation, high-throughput chemistry, affinity purification of target proteins and target validation, protein microarrays and the druggable genome.

The course is intended to provide a foundation needed for advanced chemical biology and genomic research, i.e. the creation and use of chemical and genomic probes of biological processes. The course will be of interest to students at the interface between chemistry and biology, and students interested in medicine, academic chemical biology and drug discovery efforts.

BIOL W4150. The Cell As a Machine: Cell Biophysics and Biosystems Engineering. 3 pts. Not offered in 2009-2010.

Prerequisite: calculus, cell biology or biochemistry, and physics. Cells are complex micron-sized machines that rely upon basic physical aspects of the cell components (diffusion, mechanics, electrostatics, and hydrophobicity) and energy transduction (by motors, transporters, chaperones, and synthesis complexes) to perform basic cell functions. The biophysical principles involved are described.

BIOT W4200. Biopharmaceutical Development & Regulation. 3 pts.

The program aims to provide current life sciences students with an understanding of what drives the regulatory strategies that surround the development decision making process, and how the regulatory professional may best contribute to the goals of product development and approval. To effect this we will examine operational, strategic and commercial aspects of the regulatory approval process for new drug, biologic and biotechnology products both in the United States and worldwide. The topics are designed to provide a chronological review of the requirements needed to obtain marketing approval. Regulatory strategic, operational, and marketing considerations will be addressed throughout the course. We will examine and analyze the regulatory process as a product candidates are advanced from Research and Development, through pre-clinical and clinical testing, to marketing approval, product launch and the post-marketing phase. The goal of this course is to introduce and familiarize students with the terminology, timelines and actual steps followed by Regulatory Affairs professionals employed in the pharmaceutical or biotechnology industry. Worked examples will be explored to illustrate complex topics and illustrate interpretation of regulations.

BIOL G4260. Proteomics Laboratory. 3 pts. Prerequisites: Instructor's permission

Starting with fall 2009, this course will now be offered only in the fall semester.

Open to students in M.A. in Biotechnology Program (points can be counted against laboratory requirement for that program), Ph.D. and advanced undergraduate students with background in genetics or molecular biology. Students should be comfortable with basic biotechnology laboratory techniques as well as being interested in doing computational work in a Windows environment. This course deals with the proteome: the expressed protein complement of a cell, matrix, tissue, organ or organism. The study of the proteome (proteomics) is broadly applicable to life sciences research, and is increasing important in academic, government and industrial research through extension of the impact of advances in genomics. These techniques are being applied to basic research, exploratory studies of cancer and other diseases, drug discovery and many other topics. Techniques of protein extraction, two-dimensional gel electrophoresis and mass spectrometry will be covered. Emphasis will be on mastery of practical techniques of MALDI-TOF mass spectrometry and database searching for identification of proteins separated by gel electrophoresis as well as background tutorials and exercises covering other techniques used in descriptive and comparative proteomics. Lab Fee: $150.

BIOL W4300. Drugs and Disease. 3 pts. Prerequisites: Four semesters of biology with a firm foundation in molecular and cellular biology.

Introduces students to the current understanding of human diseases, novel therapeutic approaches and drug development process. Selected topics will be covered in order to give students a feeling of the field of biotechnology in health science. This course also aims to strengthen students' skills in literature comprehension and critical thinking. Website: http://www.columbia.edu/cu/biology/courses/w4300/

BIOL G4305. Seminar in Biotechnology. 3 pts. Prerequisites:W4300 or instructor's permission.

A weekly seminar and discussion course focusing on the most recent development in biotechnology. Professionals of the pharmaceutical, biotechnology and related industries will be invited to present and lead discussions.

BIOL G4310. Intensive Lab in Biotechnology. 6 pts.

Intense laboratory exercise where students meet 4 days a week for eight weeks in the summer term participating in experimental design, bench work, and data analysis. Grades depend on participation in the laboratory, reports, and practical exams. Class starts immediately following Spring final exams. Open to MA and Postbac Biotechnology students. This course is offered in the summer. Students from other schools or programs may enroll if space is available.

BIOL W4400. Biological Networks. 4 pts.

The course will start with an introduction to types of biological networks and many of the new high throughput and quantitative technologies now available. We will start with the mathematical and computational analysis of small networks in order to understand some of the basic principles in biological networks including network motifs, modularity, robustness and stochasticity. The course will then scale up to much larger networks teaching the computation techniques needed to address these including Hidden Markov Models, Bayesian networks, FDR, Bootstrapping, Expectation Maximization, Inference, Gibbs Sampling, Monte Carlo and Belief Propagation. We cover many of the pitfalls of high throughput data and how to over come these, proper modeling choices when building large scale models of molecular networks and how to apply the techniques learned to real data. We will learn how to reconstruct regulatory networks from such data and understand how these networks compute, dynamically change and the connections between genetic sequence and these molecular regulatory networks. Finally will demonstrate how the Bayesian techniques learned in the course can be applied to other biological networks such as a network of interacting neurons.

For students currently enrolled in MA Biotechnology only.

BIOL G4500. Supervised Research in Biotechnology. 2-6 pts. Point total is based on work-load in lab which is determined by discussion with course instructor prior to registration.

Students conduct research related to biotechnology under the sponsorship of a mentor within the University. The student and the mentor determine the nature and extent of this independent study. In some laboratories, the student may be assigned to work with a postdoctoral fellow, graduate student or a senior member of the laboratory, who is in turn supervised by the mentor. The mentor is responsible for mentoring and evaluating the student's progress and performance. Credits received from this course may be used to fulfill the laboratory requirement for the degree. Instructor permission required. Web site: http://www.columbia.edu/cu/biology/courses/g4500-g4503/index.html

BIOC W4501. Biochemistry: Structure and Metabolism. 4 pts. Undergraduates should register for Bioc C3501 Prerequisites:BIOL W2001 or C2005 and one year of organic chemistry.

Lecture and recitation. Students wishing to cover the full range of modern biochemistry should take both BIOC C3501 and C3512. C3501 covers subject matters in modern biochemistry, including chemical biology and structural biology, discussing the structure and function of both proteins and small molecules in biological systems. Proteins are the primary class of biological macromolecules and serve to carry out most cellular functions. Small organic molecules function in energy production and creating building blocks for the components of cells and can also be used to perturb the functions of proteins directly. The first half of the course covers protein structure, enzyme kinetics and enzyme mechanism. The second half of the course explores how small molecules are used endogenously by living systems in metabolic and catabolic pathways; this part of the course focuses on mechanistic organic chemistry involved in metabolic pathways.

For students currently enrolled in MA Biotechnology only.

BIOL G4501. Supervised Research in Biotechnology. 2-6 pts. Point total is based on work-load in lab which is determined by discussion with course instructor prior to registration.

Students conduct research related to biotechnology under the sponsorship of a mentor outside the University. The student and the mentor determine the nature and extent of this independent study. In some laboratories, the student may be assigned to work with a postdoctoral fellow, graduate student or a senior member of the laboratory, who is in turn supervised by the mentor. The mentor is responsible for mentoring and evaluating the student's progress and performance. Credits received from this course may be used to fulfill the laboratory requirement for the degree. Instructor permission required. Web site: http://www.columbia.edu/cu/biology/courses/g4500-g4503/index.html

For students currently enrolled in MA Biotechnology only.

BIOL S4502. Supervised Research in Biotechnology. 2-6 pts. Point total is based on work-load in lab which is determined by discussion with course instructor prior to registration.

Students conduct research related to biotechnology under the sponsorship of a mentor within the University in the summer term. The student and the mentor determine the nature and extent of this independent study. In some laboratories, the student may be assigned to work with a postdoctoral fellow, graduate student or a senior member of the laboratory, who is in turn supervised by the mentor. The mentor is responsible for mentoring and evaluating the student's progress and performance. Credits received from this course may be used to fulfill the laboratory requirement for the degree. Instructor permission required. Web site: http://www.columbia.edu/cu/biology/courses/g4500-g4503/index.html

For students currently enrolled in MA Biotechnology only.

BIOL S4503. Supervised Research In Biotechnology. 2-6 pts. Point total is based on work-load in lab which is determined by discussion with course instructor prior to registration.

Students conduct research related to biotechnology under the sponsorship of a mentor outside the University in the summer term. The student and the mentor determine the nature and extent of this independent study. In some laboratories, the student may be assigned to work with a postdoctoral fellow, graduate student or a senior member of the laboratory, who is in turn supervised by the mentor. The mentor is responsible for mentoring and evaluating the student's progress and performance. Credits received from this course may be used to fulfill the laboratory requirement for the degree. Instructor permission required. Website: http://www.columbia.edu/cu/biology/courses/g4500-g4503/index.html

BIOL W4510. Molecular Systems Biology I. 4 pts. Prerequisites: One year of Biology, Chemistry, and Physics. Courses taken at CU are recommended, but AP courses may be sufficient with permission from the instructors.

This course will present a quantitative description of the molecular networks that underlie the myriad phenotypes of living cells, from yeast to human. Topics covered include high-throughput genomics technologies (DNA sequencing, mRNA expression profiling, ChIP, proteomics), mathematical models of transcriptional and post-transcriptional regulatory networks, quantitative genetics of gene expression, synthetic biology, and the world of RNA structure, dynamics, and function. These topics will be integrated with introductory lectures on molecular and structural biology, thermodynamics, statistics, and machine learning. The course is intended for advanced undergraduates as well as beginning graduate students in Biology, Chemistry, Physics, Engineering, and Computer Science. Taught by research scientists active in various areas of systems biology, the course is highly interdisciplinary and rooted in recent research. (Same as CHBC W4510)

BIOC W4512. Molecular Biology. 3 pts. Prerequisites: One year of biology. Recommended but not required: BIOC C3501.

Nucleic acid structure and enzymology; DNA replication, DNA repair, and transcription; RNA processing and translation; biochemical approach to the study of gene expression and regulation, with emphasis on the role og gene regulatory pathways in cell growth, differentiation and disease.

BIOL G4600. Signal Transduction. 3 pts. Not offered in 2009-2010. Prerequisites: One term each of biochemistry and genetics.

Limited to 24 students. Instructor's permission required for undergraduate students. In each class, an introductory lecture provides a summary of past approaches to studying cellular communication and a summary of the current understanding of major signal transduction mechanisms. Students then present and discuss in detail recent papers and background material concerning restricted aspects of signal transduction of particular current interest.

BIOL G4700. Seminar in Stem Cell Biology. 3 pts.

Alternating weeks of high-level research seminars from guest speakers and class discussions will cover selected topics at the forefront of stem cell biology research in a course designed for PhD and advanced Masters' students. Grading based on class participation, written assignments every other week and a term paper with an original synthesis of ideas or a research proposal.

BIOL W4799. Readings In the Molecular Biology of Cancer. 3 pts.

Tracing the discovery of the role of DNA tumor viruses in cancerous transformation. Oncogenes and tumor suppressors are analyzed with respect to their function in normal cell cycle, growth control and human cancers.

BIOL G6001 (Section 1). Graduate Core, I: Genetics. 4.5 pts.

This course provides an introduction to classical and molecular genetics to first year graduate students. Topics include transmission genetics, gain and loss of function mutations, genetic redundancy, suppressors, enhancers, epistasis, expression patterns, using transposons, and introduction to genome analysis. As part of the Core Program in the Department of Biological Sciences the course is a mixture of lectures, student presentations, and readings from the original literature. Ph.D. students from other departments can take this course with the permission of the instructor. Enrollment is limited to 20 students.

BIOL G6001 (Section 2). Graduate Core, I: Genomics. 2 pts.

This course provides an introduction to genomics and bioinformatics to first year graduate students. Topics include sequence alignment, DNA microarrays, massively parallel sequencing, gene set based analysis, and transcriptional network modeling. Students will also be introduced to selected topics in statistics and PERL computer programming. As part of the Core Program in the Department of Biological Sciences the course is a mixture of lectures, readings from the original literature, and hands-on computer tutorials. Ph.D. students from other departments can take this course with the permission of the instructor. Enrollment is limited to 20 students.

BIOL G6002 (Section 2). Grad Core II: Protein Thermodynamics. 2 pts.

This course presents a rigorous introduction to solution thermodynamics and applies it to understanding the structural and functional features of proteins. After exploring the conceptual origins of thermodynamic theory, the standard equations describing solution equilibria are derived and applied to analyzing biochemical reactions, with a focus on those involved in protein folding and allosteric communication. The semester culminates with exploration of the energetic factors controlling the formation of protein secondary structures and the role of entropy-enthalpy compensation in determining the complex temperature-dependent thermodynamic properties of aqueous solutions. The course emphasizes both qualitative understanding of the thermodynamic forces controlling the evolution and function of living organisms as well as practical application of thermodynamic methods and structural insight in laboratory research. Tutorials cover the use of curve-fitting techniques to analyze biochemical equilibria as well as the use of molecular visualization software to understand protein structure and function.

BIOL G9301. Preresearch Seminars. 3 pts.

Required for all first-year PhD graduate students in the Biological Sciences program. The research of members of the faculty is presented.

BIOL G9500. Supervised Individual Research. 1-12 pts.

Students in the Biological Science PhD program only.