Curriculum

The Microbiology and Immunology program and the Office of Graduate Affairs (OGA) interact with trainees in the summer prior to matriculation to facilitate acquisition of Columbia sponsored housing. Off campus housing is available and facilitated by realtors who have long-standing working relations with Columbia housing administration. Upon arrival at Columbia, OGA holds a series of orientation events to acclimatize the students to the campus and the city. The program also holds an orientation meeting to discuss with incoming students what their time in the graduate program will be like, including course requirements, laboratory rotations, qualifying examinations, student seminars and any other requirements that they might have during their tenure as graduate students. The Program Director subsequently meets individually with each student to discuss her/his rotation choices.

During the orientation, OGA holds a number of important events that are important for the students. We start with a mini-course that explains how to establish the framework for an experimental project, how to set up a system, design experiments within that system, and how to determine and use the correct set of controls. This course also covers an introduction to rigor and reproducibility in experimentation that is necessary for all the students.

The students also get mandatory training in Laboratory Safety, an orientation on sexual violence and response, as well as discrimination, harassment and gender-based misconduct policy. Finally, as part of their orientation session, the students will be given a lecture on Responsible Conduct of Research (RCR). They also receive the booklet “On Being a Scientist”, as well as Columbia University’s regulation on RCR."

In the first year, students are expected to complete three laboratory rotations of three months duration each. Rotations will occur from September-December, January-March, and April-June. In summer, students begin their doctoral research, or in exceptional circumstances, complete a fourth rotation. The function of the rotation is not only to enable the student to select a laboratory, but also to experience a diversity of experimental approaches and systems. We require that the first rotation be in the home department. To facilitate the selection of rotations, students attend faculty presentations, including the department retreat, where ongoing research is described.

• First year fall semester: Biochemistry, Cell and Molecular Biology I, Molecular Genetics, Introduction to Computational & Quantitative Biology
• First year spring semester: Biochemistry, Cell and Molecular Biology II, Statistics for the Basic Sciences, Graduate Immunology
• Second year fall semester: Advanced Topics in Microbiology & Immunology I
• Second year spring semester: Responsible Conduct of Research and Related Policy Issues, Advanced Topics in Microbiology & Immunology II
• Third year fall semester: Small Group Discussion - Responsible Conduct of Research

The Qualifying Examination tests the ability of each student to formulate and present a research project. These exams are given in the spring of the second year. The student prepares a concise, single-spaced 6-page report written in the style of an F31 fellowship application that describes their dissertation research progress and future plans. The proposal is distributed to the Qualifying Examination Committee one week before the scheduled Exam date. The committee will consist of two faculty members of the department who will serve on each committee and a third member selected by the student and mentor. At the Qualifying Exam, the student explains and defends the proposal to the Qualifying Examination Committee before answering questions.

At the beginning of the second year, the student must choose a laboratory for his or her thesis research. The student and the thesis advisor then select a Thesis Research Advisory Committee (TRAC) consisting of at least three faculty members, not including the advisor. One of the faculty members, who is a Professor or Associate Professor in the department, should be designated a Chair; other faculty members may be from the department or from outside departments. The purpose of the TRAC is to monitor the student's progress throughout the period of dissertation research. To accomplish this goal, the student must meet at least once a year with the committee, unless the committee recommends a more frequent schedule After 5 years, the committee must meet twice a year.

The students must hold a TRAC meeting within a year of successful completion of the qualifying examination, and preferably within 6-8 months. The student presents a complete description or the proposed research project at the first meeting, and any data gathered. For subsequent meetings, the student must prepare a written summary of progress and of future objectives and distribute it to the committee prior to the meeting. Please note that students are welcome at any point to request a meeting with the Program Director or their designated TRAC Chair (see above) to discuss any concerns that may arise along the way.

Members of the Thesis Advisory Committee are usually part of the Thesis Defense Committee. The advisor, department chair, and Director of Graduate studies nominate the Dissertation Defense Committee, and students are not permitted to be involved in asking faculty members to sit their committee. The committee must consist of two members from inside the department, including the advisor, and two members from outside the department. At least three of the five members must hold a seat on the GSAS Faculty.

The Department of Microbiology & Immunology expects that all graduate students will complete their thesis research within 5–5.5 years of entering the dissertation laboratory. When the student, thesis advisor, and Thesis Research Advisory Committee agree that the student has completed work of sufficient novelty and quality to merit the PhD, the student prepares a dissertation. Students must distribute copies of their dissertation to defense committee members at least two weeks prior to the defense date to ensure the committee members have time to read the dissertation thoroughly before the defense.

The thesis defense consists of a one-hour public lecture followed by a closed-door thesis exam with members of your thesis committee. The thesis exam typically takes about 2 hours, during which time the committee will probe your fund of knowledge about your research and its broader context. At the completion of the exam, the committee will vote for a pass with minor revisions, a conditional pass that requires major revisions, or a fail. A conditional pass may require another examination, although that is rare. At the completion of the exam, the student is expected to generate a document that lists the revisions that were requested. The student then will make the changes and needs to present these changes along with a completed summary of revisions to both the research advisor and the graduate director. Once you have passed your defense, you must submit the Approval deposit the final thesis copy (with any pertinent revisions) to the Dissertation Office.

The Microbiology and Immunology Department hosts an outside speaker each Wednesday and a student or postdoctoral speaker each Friday of the week. We believe these seminars are crucial to the training program, and therefore all students are required to attend in the form of a two-credit course entitled Seminars in Microbiology & Immunology.

Students also serve as hosts for the Richard C. Parker Memorial Lecture, which is held once each year in memory of a former faculty member of the Microbiology & Immunology Department. Third year students select the speaker and arrange a schedule that provides the opportunity for all students and postdoctoral fellows to meet with him or her. In connection with this lecture, an outstanding student near completion of the PhD thesis is selected each year to receive the Richard C. Parker Memorial Award.

The development of speaking skills is crucial for the ultimate success of scientists. The Department recognizes this need and provides many meaningful opportunities for trainees to speak about their research in a seminar format. After completing their PhD qualifying examination, students are asked to present a seminar at least once a year in the Department's Friday seminar series.

A department happy hour follows the Research in Progress on Fridays from 4:30-5:30 PM, in the 12th floor lobby or 13th floor conference room. This is a great occasion for students, postdocs and faculty to socialize in a more causal environment and we encourage all to attend.

Students are encouraged to participate in one of several departmental journal/data clubs, preferably one related to the student’s area of research. We encourage each student to attend at least one club regularly and make at least one presentation each year. These clubs include:

DNA Dynamics – Alberto Ciccia (attended by Basu, Symington and Zha labs from Micro and Immuno). 2nd Mon of every month 1:30 PM ICRC auditorium.

Immunology and Microbiology Journal Club – contact Nicholas Arpaia for meeting times.

In the fall of each year, the Microbiology & Immunology Department holds a departmental retreat away from the campus. All departmental faculty, students and postdoctoral fellows are invited to attend. The retreat begins on Friday afternoon and lasts until Sunday afternoon. There are three sessions of 10-15 minute research talks, and a poster session. The level of participation is extraordinary, the scientific discussions, both formal and informal, are excellent, and the ability to spend leisure time with colleagues has enhanced the collegiality of the department.