Graduate Training Curriculum

Crystal Colon-Ortiz_3rd Year Grad Student 2019

Crystal Colon-Ortiz - 3rd Year Graduate Student 2019

The Pathobiology and Mechanisms of Disease program is designed to give the students a strong background in the basic sciences, as well as an appreciation on how to study mechanisms of disease. To accomplish this, our students take courses in basic cell and molecular biology, genetics, statistics, as well as a course in histopathology, and our signature one-year course, called “Mechanisms of Human Disease.” Students in the Pathobiology and Mechanisms of Disease also have a wide variety of research possibilities in the mechanism of human disease, as well as basic cell and molecular biology. The faculty trainers are from the Department of Pathology and Cell Biology, as well as from clinical departments with strong research components, such as the Departments of Dermatology, Ophthalmology, and Medicine. Students are also eligible to participate in the Med into Grad program, which gives graduate students the opportunity to shadow a clinician in their area of research. The goal is to give students a better understanding of how their research can impact patients.

The Program Director (PD) is responsible for most of the direct advising of the students, especially during the first year regarding coursework, rotations and any other issues that arise. The PD has formal meetings with the first year students at least three times a year, at the beginning of the year and at the end of each semester. The PD is always available to advise the students, and keeps close track of the students’ performance throughout their course of study, especially during the first year. The students take their qualifying examinations during the second year and formal advising is then taken over by the student's thesis committee.

First-Year Students

New graduate students 2018 - Pathobiology and Molecular Medicine Program

New graduate students 2018 - Pathobiology and Molecular Medicine Program

The Pathobiology and Mechanisms of Disease Program and the Office of Graduate Affairs are in frequent contact with the students during the summer prior to matriculation to make sure that they are able to obtain housing, and make any special arrangements that may be required. In addition to Columbia sponsored housing, off-campus housing is available and realtors with good working relations with the housing office are available to assist. Orientation events (usually held the last week of August) include an overnight camping and hiking trip, an orientation lunch, as well as other events that are sponsored by the Office of Graduate Affairs or the Graduate Student Organization. The Program Director has an orientation lunch with the new students to discuss their future graduate career, course requirements, laboratory rotations, qualifying examinations etc.


To select a rotation, the incoming students should study the website to determine with which faculty members they may be interested in doing a laboratory rotation. The PD meets with each student individually to discuss his/her rotation choices and provides extensive input on the selection of the rotation. At the end of the rotation, the PD receives written evaluation from faculty mentors, and discusses the evaluation with the student to examine problems that may have arisen and how they can be addressed.


During orientation, all the first year graduate students in all the different program attend 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. 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. Students also get a lecture on Responsible Conduct of Research (RCR), where they will also receive the publication "On Being a Scientist," as well as Columbia University's institutional RCR policy.


During the first year, students have the following basic curriculum:

Fall semester

  • Biochemistry, Cell and Molecular Biology I
  • Mechanisms of Human Disease I
  • Student Seminar

Spring semester

  • Biochemistry, Cell and Molecular Biology II
  • Mechanisms of Human Disease II
  • Statistics for Basic Scientists
  • Student Seminar

Second-Year Students

In the second year, students take their qualifying examination, Molecular Genetics and Histopathology (Cellular Tissue and Architecture). In addition, they take the Responsible Conduct of Research course.

The schedule for second year is as follows:

Fall Semester

  • Molecular Genetics
  • Student Seminar

Spring Semester

  • Cellular Tissue and Architecture
  • Student Seminar
  • Responsible Conduct of Research

Students can take additional electives during their second year or later, but are not required to do so. Since Columbia also offers many non-science courses to all the students, any student wishing to take such a course must receive permission from their mentor as well as the Program Director. Students are required to maintain a B average.

Qualifying Examination

During the second year, students prepare for their qualifying examination. This examination is used as a formal evaluation of the student's potential as a candidate for the PhD degree. It is designed to assess the student's ability to develop a sophisticated, in-depth understanding of their thesis project and it also serves as a tool for identifying deficiencies in the students' background that could be remedied by further coursework or additional reading.

In addition to course work, all students take part in the Pathobiology Program Seminar. Other journal and data clubs are topic-related and available to all students.

Thesis Committees

During the fall of the third year, the students have their first meeting with their Thesis Committee. The Thesis Committee is typically the same as the qualifying examination committee, although occasionally one of the members might be replaced, especially if the student's research is going in a different direction. This Committee provides scientific expertise related to the student's projects and monitors thesis research. For the first Committee meeting that is held either in the spring or summer of the second year, the student presents a short written report that contains the Specific Aims of their proposal and any progress they have made since the qualifying examination. The Committee discusses with the student the progress to date and 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 the experimental design or priorities. The Committee also decides when to have the next meeting, which can be either in 3, 6 or 9 months, but no longer than one year. For these subsequent meetings, the student prepares a 1-2 page report outlining their progress on the previous aims and presents 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.

Dissertation and Thesis Defense

After the thesis committee gives its approval for the student to finish writing the thesis, the defense is scheduled. The final thesis committee consists of the mentor, three existing thesis committee members, and one additional examiner. If the additional examiner is outside the University, they have to be approved by the Program and the Dissertation Office as a competent examiner. The thesis should be submitted to the committee two weeks before the scheduled defense. A public presentation is given immediately before the closed defense. At the time of the closed defense, the student may be asked to make additional revisions that will then need to be approved by the mentor and one other member of the committee (assigned at the time of the defense.) On rare occasions, the student may be required to do additional experimental work, extensive thesis revisions or a second dissertation defense. Students are required to submit a first author paper before their defense.