Genetics and Development

This fall-semester course is required for all first-year students and covers basic biochemical and experimental principles, such as protein and nucleic acid structure and chemistry, thermodynamics and enzyme kinetics, and bioinformatics. Also discussed 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 Director: Stavros Lomvardas.

This course is designed to illustrate how genetic systems have played a fundamental role in our understanding of basic biological problems. Topics include 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.

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Basic principles and current areas of interest in mouse and human genetics. Topics include 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, human linkage analysis, somatic cell genetics, physical mapping of the human genome, cytogenetics, mitochondrial genetics, and disease. Course Directors: Michael Shen and Wayne Frankel.

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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 problems set on the current literature. Course Director: Tim Bestor.

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This spring-semester course explores a variety of ethical and policy issues that may arise during 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. Course Directors: Arthur Palmer and Jaime Rubin.

This spring-semester course provides an introduction to the basic statistics commonly used in biomedical research laboratories. Students are provided with a statistical software package for use during the course. Exercises based on relevant experimental data sets 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: Arthur Palmer.

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This spring-semester course explores a variety of ethical and policy issues that may arise during 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. Course Directors: Arthur Palmer and Jaime Rubin.

The wealth of opportunities available to trainees can be explored during the first year through a series of three research rotations. These involve carrying out a research project in the chosen lab and usually giving a lab presentation. Rotations occur from September-December, January-March, and April-June. First-year trainees choose their rotations following faculty presentations and talks at the annual retreat.

Rotations may be in the laboratories of Training Faculty members or can be done in any lab outside the training faculty. If a student wishes to do more than one outside rotation, or to do their doctoral research in a lab other than that of training faculty, consultation with the Training Committee is required. Following the third rotation, trainees will enter a lab by mutual agreement with the mentor to begin their thesis research at the end of June or early July.

The qualifying examination in the Department of Genetics and Development is a two-part process involving a presentation to a committee of the student's research activities in the laboratory: Part I should be completed by December 31st of year two. Part II must be completed by June 30th of year three. The qualifying exam has as its major goal determining whether a student is capable of PhD thesis research. The qualifying committee is concerned with two questions in this regard: 1) Is the student expert enough in his/her field of research interest to pursue thesis research? and 2) Is the student qualified to do the laboratory bench research required for a PhD project?

The exam itself is an oral presentation (usually PowerPoint) to the committee with questions and discussion. Following the presentation of Part II, the student will receive a grade of pass, contingent pass, contingent upon satisfying prescribed conditions, or fail. In the event of a failing grade, the training committee, in consultation with the qualifying exam committee and mentor, will determine whether the student leaves the program or is allowed a reexamination. There is no requirement for completion of a specific research project to pass the qualifying examination. The qualifying committee must simply be convinced that the student is capable of undertaking thesis research by virtue of their evaluation of the student's research plan, laboratory work, and understanding of the thesis research area. The program director may solicit information from the student’s mentor prior to Part II of the qualifying exam.

The qualifying committee should consist of three members of the Genetics and Development training faculty, excluding the mentor. In exceptional circumstances, one faculty member may be chosen from outside the training faculty, subject to prior approval by the training committee. The qualifying committee should include members who will afford the broadest service to the student as well as enough expertise in the area of the student's research to adequately evaluate the student's knowledge and laboratory progress. The qualifying committee is chosen by the student and their mentor.

After completion of the qualifying examination, the student will meet at least once per year with a monitoring committee, the Thesis Research Advisory Committee (TRAC), that will advise on the thesis work and monitor progress. The committee will include the mentor/adviser and two other members. One member may be chosen from outside the training faculty, subject to prior approval by the training committee. The compositions of the qualifying committee and the TRAC need not be identical.

The annual TRAC meeting should be held between September 1st and November 30th. For this meeting, the student will submit, at least 3 days in advance, a one-page summary of the previous year’s work and a one-page outline of proposed work for the following year. Notebooks with supporting data can be brought to the meeting and other materials (papers, recent posters, etc.) may be presented, at the discretion of TRAC. The student will usually present an oral progress report with slides (PowerPoint or similar). Additional meetings may be scheduled at the request of either the student or the TRAC, and should be scheduled more frequently (i.e. every 4-6 months) once the student enters their 6th year.

Five to seven months prior to the anticipated thesis defense, there must be a meeting of the TRAC to approve the thesis outline. One of the annual TRAC meetings may serve this purpose if the timing is appropriate. Each member of the committee should be provided with an outline of chapters one week in advance.  Any disagreement between student and advisor on thesis content will be mediated by the TRAC.

The Thesis Defense Committee is composed of 5 members. Three must be from the Training Faculty or TRAC. These will usually include: the committee chair, the mentor/sponsor (who is the first reader), and a second reader, who reads the thesis prior to its distribution to the Thesis Defense Committee. In addition, there should be two outside examiners from other GSAS departments and/or other universities. It is usually advantageous to have TRAC members serve on the Thesis Defense Committee.

Information about submitting and defending a dissertation can be found at the GSAS Dissertation Office by following 10 steps. The Application of Dissertation Defense form should be submitted at least eight weeks in advance of the anticipated date of defense. No defense will be scheduled until the dissertation sponsor and second reader have signified that the dissertation is acceptable enough to warrant a defense and final exam. The dissertation should include an introductory chapter, chapters of original data, and a discussion chapter. Copies of the dissertation should be distributed to the committee members at least four weeks before the anticipated defense date.  As a courtesy, these should be printed, bound copies (e.g. in a pressure binder).

Seminars in Genetics and Development is organized and run by the students and postdocs in the department and features their work. It provides a forum to meet with peers and gain experience presenting and critiquing ongoing research. Faculty members are generally excluded from these sessions without special invitation. Thesis defense seminars, which are open to faculty and students, are scheduled as part of this seminar series. Attendance is mandatory for registered students, although 2 unexcused absences per term are allowed. The department has an active weekly seminar series with speakers from around the world. As part of this series, first and second year Genetics and Development students, as well as advanced students have the opportunity to select and host speakers.