Welcome to the Department of Systems Biology (DSB) Graduate Program! This document describes the basic requirements of students pursuing a PhD through DSB. The DSB Graduate Program is part of the Integrated Program for Molecular, Cellular, and Biomedical Studies (“Integrated Program” or CMBS), and so the majority of our requirements originate from this larger program. However, there are some crucial exceptions described below.

Course Curriculum

As students within the Integrated Program for Molecular, Cellular, and Biomedical Studies at Columbia University, students in the Systems Biology specialization must fulfill the general requirements of the program. However, given the varied interests and concentrations of our students, we make an effort to tailor specific degree requirements to the individual. DSB students should take a total of six courses including two systems biology courses, two biology courses, and two statistical or computational courses. Examples of courses in each category are listed below. This list is non-exhaustive and curricula can be customized to the research interests of each student. 

In addition, all students are required to take Responsible Conduct of Research and Related Policy Issues (CMBS 4011), the student seminar series Seminars in CMBS (CMBS G9201), and attend the Topics in Systems Biology seminar series given by DSB faculty. DSB also invites faculty from around the world to speak in our Columbia Systems Biology Distinguished Seminar Series, which typically occurs on Wednesdays at 3:00 PM.  Attendance at this departmental seminar is strongly recommended for all DSB students. Finally, although six courses are required as described above, students are welcome to take additional courses to fill gaps in their knowledge as needed.

Systems Biology Courses

BINF G4015 (Dennis Vitkup) – Computational Systems Biology: Proteins, Networks, Function
BINF G4017 (Peter Sims, Yufeng Shen, Chaolin Zhang) – Deep Sequencing
TBD (Raul Rabadan) – Topological Data Analysis for Genomics and Evolution
BIOL W4510 (Harmen Bussemaker) – Genomics of Gene Regulation
COMS W4761 (Itsik Pe’er) – Computational Genomics

Biology Courses

BCHM G4250 (Arthur Palmer) – Molecular Biophysics
BCHM G6300 (Stavros Lomvardas) – Biochemistry, Cell and Molecular Biology I
BCHM 6301 (Gregg Gunderson) – Biochemistry, Cell And Molecular Biology II
BIOL G6560 (Molly Przeworski, Guy Sella, Joseph Pickrell) – Human Evolutionary Genetics
GEND G4050 (Tim Bestor) – Advanced Eukaryotic Molecular Genetics
GEND G4501 (Virginia Papaioannou) – Methods in Genetics and Development
GEND G6210 (Rodney Rothstein) – Genetic Approaches to Biological Problems
GEND G4027 (Andrew Tomlinson) – Principles of Developmental Biology
CMBS G4150 (Jonathan Dworkin) –Molecular Genetics
MICR G4020 (Christian Schindler) – Graduate Immunology
MICR G6055 (Christian Schindler) – Advanced Topics in Microbiology I
MICR G6056 (Lorraine Symington) – Advanced Topics in Microbiology II
NBHV G4900 (Darcy Kelley) – Experimental Approaches in the Neural Sciences
NBHV G4920 (Kenneth Miller) – Quantitative Approaches for Experimental Neuroscience
NBHV G6010 (Gary Escola) – Topics in Systems Neuroscience
NBHV G6020 (Michael Goldberg) – Systems Neuroscience
PATH G4500 (Ben Tyco, Richard Baer) – Cancer Biology I
PATH G6003 (Ronald Liem) – Mechanisms in Human Disease I
PATH G6004 (Ronald Liem) – Mechanisms in Human Disease II

Statistical and Computational Courses

STAT W4240/5242 (Lauren Hannah) – Data Mining
STAT W4400/5241 (John Cunningham) – Statistical Machine Learning
STAT G6701 (David Blei) – Foundations of Graphical Models
COMS E6998 (David Blei) – Probabilistic Models of Discrete Data
BINF G4006 (Nick Tatonetti) – Translational Bioinformatics
BINF G4002 (Noemie Elhadad) – Methods II: Computational Methods}
STAT W4105 (Abolfazal Safikhani) – Probability
STAT W4107 (Ronald Neath) –Statistical Inference
COMS W4771 (Daniel Hsu) – Machine Learning
COMS W4772 (Daniel Hsu) – Advanced Machine Learning

Laboratory Rotations

Students are required to do at least two rotations, but generally do three rotations during the first year in the program. The first rotation will run from September to the end of December. The second and third rotations are each three months in length: January through March, and April through June. Students will then enter their thesis lab in July. The training faculty submits written evaluations of student’s progress in each rotation and indicates their willingness to take a student. These evaluations are part of the student’s permanent record. If after two rotations, the student has not identified a laboratory where he or she can do thesis work, we ask the student to discuss their final rotation in more detail with the director or the co-director of the program to make sure that this final rotation is a likely potential home for the student. Occasionally, it is necessary for a student to do a fourth rotation, but we strongly discourage this. 

Students are encouraged to investigate the research interests of potential rotation laboratories by meeting with faculty in person. Although there is a significant amount of information available on laboratory websites, interacting with both faculty and researchers in their laboratories is essential. Laboratory rotations require advanced planning, and we require that students commit to their first rotation by September 15, their second rotation by January 5, and their third rotation by April 1 and inform the DSB Graduate Program Coordinator of their rotation laboratory by these dates. Students in the Integrated Program have the opportunity to attend one of the departmental retreats that are held in the beginning of the year. Students in DSB also have the opportunity to attend the departmental retreat that is held annually in mid-September. The 2016 DSB retreat will take place on September 15 at the Tappan Hill Mansion in Tarrytown, NY. Transportation will be provided by the department. First year students are also required to attend the Topics in Systems Biology seminar series in which DSB faculty will present an overview of the research conducted in their laboratories. (See Events here.) This will be held Monday evenings from 5:00 PM to 6:00 PM in Fall 2016.

Guidelines for Qualifying Examination

The purpose of the qualifying examination is to determine whether the student can formulate a research proposal to investigate a scientific problem based on an in-depth understanding of the scientific literature in that field. The proposal should be based on the student’s proposed thesis project. The student should conceive and write the proposal, but is allowed to receive input from their advisor. The proposal is then defended in an oral examination before an examination committee, consisting of three faculty members associated with the Integrated Program.  The committee members (not including the advisor) who are familiar with the research topic can be chosen by the student and the student’s advisor, but should be approved by the program directors. Note that DSB students are required to have at least one DSB faculty member on their qualifying examination committee. (In the event that the student’s advisor is not a DSB faculty member, the student must have at least two faculty members.) The program directors will assign the chair of the committee. Students pass, conditionally pass and are assigned a remedial exercise or are asked to repeat all or part of the examination, or fail (see further details below). Mentors are required to attend the exam as silent observers.

The Written Proposal

Subject

The research proposal should be based on the student's proposed dissertation topic. The proposal defines an important problem, critically reviews the relevant literature, devises a hypothesis-based research plan to address that problem in a logical and direct manner, and explains how the data from such a study might be interpreted.

Copies and Submission

Student must complete and submit a copy of the written proposal to each of the examining committee members and the thesis advisor one week before the oral examination.

Length

The written proposal should be prepared in the NIH NRSA format (http://grants.nih.gov/grants/guide/pa-files/PA-14-147.html). This consists of Specific Aims (1 page maximum) followed by the Research Strategy (Significance, Approach, Preliminary Studies). The proposal should be 6 single-spaced typewritten pages (including figures), plus additional pages of references. Use at least one-half inch margins (top, bottom, left, and right) for all pages, Use an Arial typeface, a black font color, and a font size of 11 points or larger.  The proposal should be converted to a PDF before submitting to the committee.

Format

The proposal should adhere to the following format:

  • Title
  • Specific Aims: In a maximum of one page, state precisely the goals of your proposed research and summarize the expected outcome(s), including the impact that your results will exert on the research fields(s) involved. Include the questions you will address as aims (2-3 in number), and briefly state how you will address each.
  • Significance: Explain the importance of the problem or critical barrier to progress in the field that the project you are proposing addresses; how it will improve scientific knowledge, technical capability, and/or clinical practice in one or more fields; and how the concepts, methods, technologies, treatments, services, or preventative interventions that drive this field will be changed if the proposed aims are achieved.
  • Approach: Describe the overall strategy, methodology, and analyses you will use to accomplish the specific aims of the project. Include how the data will be collected, analyzed, and interpreted as well as any resource sharing plans that should be mentioned. Discuss potential problems, alternative strategies, and benchmarks for success that you anticipate in order to achieve your aims. If the project is in the early stages of development, describe any strategy to establish feasibility, and address the management of any high-risk aspects of the proposed work. Point out any procedures, situations, or materials that may be hazardous to personnel and precautions to be exercised. If you are proposing research on human embryonic stem cells (hESCs) but an approved cell line from the NIH hESC Registry cannot be identified, provide a strong justification for why an appropriate cell line cannot be chosen from the Registry at this time. 
  • Preliminary Studies: Include information on preliminary studies (including data collected by others in your lab), if any. Discuss any preliminary studies, data, and/or experience that are pertinent to your proposal.
  • References

The Oral Presentation

This should last no more 25-30 minutes. It should be a “chalk talk” with no slides or Powerpoint presentation, unless a complicated sequence (or similar data) must be presented. It is important to give a well-organized and clear presentation; students should endeavor to speak without notes.

Time Frame

Qualifying exams must take place no later than the end of October of the second year (April for MD/PhD students). Students are encouraged to take the exam late in the summer after the first year, or early fall of the second year. The proposal must be distributed to the examining committee one week before the scheduled exam. Failure to do so may result in cancellation of the exam.

Outcomes

The examination committee will decide on one of the following outcomes:

  • Pass indicates that the student demonstrated adequate preparation and reasoning ability for pursuit of thesis research.
  • Conditional Pass indicates that the student demonstrated some deficiencies in the exam. The committee may make a specific recommendation, such as specific coursework, or rewriting the paper(s) without a reexamination.
  • Failure indicates that the student had a serious deficiency in preparation or reasoning ability. In such cases, the committee recommends to the CMBS Program Directors that the student leave the program.
  • Retake the exam within three months. In some cases, the committee may not be satisfied with the student’s performance and recommends that the student rewrite his proposal and be reexamined within three months of the original examination. At the end of the reexamination, one of the three outcomes listed above would result.

Note: The written proposal should be prepared in the NIH fellowship format. Students who are eligible for NIH funding should use the proposal to apply for Individual NIH Fellowships (F31). The standard deadlines for NIH predoctoral proposals are April 13th, August 13th, and December 13th.

Example Curriculum

DSB students typically complete their PhD within five years and very rarely take longer than six years. Although there are many configurations that satisfy the PhD requirements for DSB students, here is an example of an acceptable curriculum:

Sample Curriculum

Dissertation

Either in the spring or the summer of the second year, students choose their thesis committees with the help of their research advisor. These committees will provide scientific expertise related to the students’ projects and they monitor the progress that the student makes during their research career. Note that DSB students are required to have three faculty members in addition to their PhD advisor on their thesis committee, and at least one of these three faculty members must be on the DSB faculty. (In the event that the student’s advisor is not a DSB faculty member, the student must have at least two faculty members.) 

Students must notify the DSB Graduate Program Coordinator of their thesis committee membership and meeting dates. In general, we have found that monitoring by thesis committees is crucial to make sure that the students finish their research in a timely manner.

We have set up certain rules for the student's thesis committee meetings, depending on their year in the program. For the first committee meeting, which is held either in the spring or summer of the second year, the students prepare the Specific Aims of the research they will do for the thesis. The committee discusses with the student the background of the thesis work, the priorities for the order in which the work will proceed, as well as the chosen design of experiments. It is possible that the committee may recommend changes to experimental design or priorities. Students are required to hold a thesis committee meeting every year, but a thesis committee can decide to meet with a student more frequently. In any case, another meeting will be scheduled for third year of graduate school to assess the progress the students are making in their thesis work.

For these meetings, the students prepare a short presentation of work accomplished during the year, detailing how it addresses previously proposed aims. The committee assesses the student’s progress on previous aims and apparent viability of the original plan. At the next annual meeting, the students prepare a 1-2 page report, outlining their progress on the previous aims and present their timetable for finishing their thesis work. The committee can and should recommend improvements to experimental strategies and fallback plans for difficult or risky experiments.

Format of dissertation

Students must follow the Graduate School of Arts & Sciences dissertation formatting guidelines.