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Education / Medical Scientist Training Program / Current Students / Student Handbook / Curriculum / Graduate Training & Longitudinal Clinical Experience


Graduate Training & Longitudinal Clinical Experience

Year Three (Graduate School)

The transition from medical school to graduate school is aided by familiarity with graduate training and graduate faculty gained during the first two years of the program and by rotation experience(s).  The late spring and summer following the second year provides an outstanding opportunity for students to finalize their choices for graduate degree program and thesis mentor.  The extra time afforded by the relatively late start of the graduate school calendar (September) allows students the option of completing two rotations, if desired.  Alternatively, students who establish their mentor early can initiate studies leading to their thesis.  Advising efforts are directed at helping students make program and mentor choices in order to efficiently take advantage of graduate courses starting in the fall.  Indeed, MD/PhD students are required to declare a graduate program by the beginning of the Fall Semester, and a thesis advisor by January of that year (students can elect to do an additional rotation during the Fall Semester to help in this decision), although most declare earlier. Early planning, seeking advice, and multiple meetings with graduate program directors and potential thesis advisors are critical to this process.  A list of graduate program information and website links is included in the “Contacts” section of this handbook. 

The third year is typified by graduate program coursework and initiation of thesis research.  Specific course requirements and other guidelines established for each degree program are provided in the Appendix. Program declaration and graduate course registration are handled through the office of Graduate Education and individual graduate program administrators (see contact information on pages 28 and 29).  Note that these offices differ for students in River Campus programs (Chemistry, Biology, Optics and Brain & Cognitive Science).  Components common to all guidelines include granting MSTP students 30 hours of credit toward coursework accomplished in the Double Helix Curriculum, core and advanced graduate courses specific to each program, and required participation in graduate student seminar series, journal clubs, and departmental/program seminar series. Students must complete IND 501, “Ethics and Professional Integrity” by fall of the third year in the program. Teaching requirements for many, but not all, graduate programs are waived for MD/PhD students, though students may elect to participate, and outstanding opportunities for teaching exist in most programs.  Indeed, students are strongly encouraged to gain experience with teaching through graduate programs and the Medical Education Pathway.

Participation in all graduate student activities and required steps for obtaining the PhD degree, including qualifying examinations, ensures that MD/PhD students have regular opportunities for presentation of their work and evaluation of their progress. In addition to graduate student seminars and presentations at national scientific meetings, our students present their work at MD/PhD specific events, including poster or oral presentations at our Annual Retreat, Revisit Day, Medical Scientist Research Symposium, the Tri-Institutional MD/PhD Student Conference, the National MD/PhD Student Conference in Colorado, and the American Physician Scientists Association Annual meeting in Chicago.

Students in their first two years of graduate training are encouraged to participate in a series of sessions, led by Dr. O’Banion and other graduate faculty in the Fall Semester that focuses on grant writing for MD/PhD Fellowships (e.g. F30s).  The emphasis is on understanding the nuts and bolts of grant applications, generating a specific aims page, and discussing issues specific to fellowship training. Many of our trainees have gone on to submit these fellowships and obtain individual funding.

The Longitudinal Clinical Experience


The MD-PhD program has a required Longitudinal Clerkship Experience (LCE) that is completed during the PhD portion of the training program.  The two primary purposes of the LCE are to provide MSTP students with 1) clinical experience in direct patient care to further develop their communication, physical examination and clinical reasoning skills and 2) an opportunity to work in clinical settings with physician-scientists.  For each LCE completed (see details below), students will be awarded two (2) medical school elective credits which apply to the graduation requirements for the M.D. degree.

Longitudinal Clerkships are clerkships generally conducted in the ambulatory/outpatient setting on a weekly or biweekly basis. These clerkships are completed by MSTP students during the graduate phase of training. Students, in consultation with a faculty preceptor, will identify 2-3 clinical knowledge areas and/or clinical skills in which the student will gain proficiency by the end of the LCE.

LCE Learning Objectives

  1. Improve patient interviewing, physical examination and clinical reasoning skills.
  2. Gain understanding of and experience in continuity of care relationships.
  3. Gain exposure to career options by preferentially working with faculty preceptors who have direct experience and insight into the life of the physician-scientist.
  4. Experience mentorship with the preceptor on balancing clinical and research activities. 
  5. Receive general career guidance from the faculty preceptor that complements other MSTP career counseling programs and opportunities.


  1. All students are encouraged to complete a minimum of two (2) Longitudinal Clerkship Experiences -before the end- of their third year of graduate training (G3).
  2. At least one of the LCEs must involve direct patient care and must be completed in an ambulatory, patient care-oriented setting.
  3. LCEs must consist of either half-day or full-day clinics on a weekly or biweekly basis.
  4. Students must complete a cumulative minimum of ten (10) full days of clinic time for credit.
  5. LCEs must be completed in a longitudinal fashion and must each be completed over a period of no longer than twenty-four (24) weeks.
  6. Attend at least three (3) Longitudinal Rounds Sessions (see below) during each LCE.

Longitudinal Rounds (LR): Longitudinal Rounds are interactive seminars during which MSTP students synthesize LCE clinical encounters into succinct patient presentations and discuss a variety of relevant diagnostic and therapeutic modalities. LR sessions will be held monthly and students must attend a minimum of three (3) LR sessions and present at least one (1) patient encounter during the course of each LCE.

LR Learning Objectives

  1. Refine oral presentation skills and synthesis of patient histories and physical examinations.
  2. Gain exposure to a broad range of medical sub-specialties via sharing of LCE experiences among students.
  3. Improve differential diagnosis, assessment/plan, and team-based medical decision making skills in a wide variety of clinical disciplines.
  4. Develop skills in the incorporation of relevant technology (e.g. eRecord review of lab values) into patient presentations, and review HIPPA regulations of patient privacy with respect to electronic patient information.



No more than one (1) Longitudinal Clerkship Experience may be completed per semester, and no more than two (2) Longitudinal Clerkships may be completed per academic year.  No more than eight (8) total weeks of clinical elective credit may be earned for Longitudinal Clerkship Experiences.  Students must register for the LCE before beginning as retroactive credit will not be given per medical school policy. Students who begin a longitudinal clerkship but fail to complete it within the allotted time (24 weeks as noted above) will be assigned a grade of “Withdraw” or “Withdraw Fail” by their preceptor.  The grade will be noted on the student’s medical school transcript in accordance with medical school policy and no credit, including partial credit will be given. Students are expected to complete all appropriate evaluations of the LCE.

Accepted Longitudinal Clerkship Experiences include:

  • Ambulatory, clinical specialties (e.g., medicine, medicine subspecialties, neurology, psychiatry)
  • Ambulatory, clinical component of a procedural or surgical specialty (e.g., OB/GYN, radiation oncology)
  • Diagnostic specialties (e.g., pathology, radiology)


Graduate-phase MSTP students can enroll in LCs in MedSIS via the following link:

Within the “Academics” tab, select “Add/Drop Requests”

Indicate the appropriate academic year, and select “New Request”

Request Action: “Add”

Course title: PHDCLK

Select the appropriate institution, dates, and preceptor from the drop down menus.

Note: All clinical electives completed in graduate school, regardless of format, must be approved by the student’s Advisory Dean. Deviations from the policy stated above require advanced approval by both the student’s advisory dean and graduate advisor.


To receive credit for the clerkship, students must complete evaluations for both the medical school and for the MSTP. While the medical school evaluation provides valuable feedback to the preceptor, the MSTP evaluation will be used exclusively for internal purposes, for the benefit of the program and other MSTP students.

Years 4, 5, (and 6) (Graduate School)

For most programs these years are filled with ongoing research towards the student’s thesis and engagement in laboratory and departmental activities.  Because MD/PhD trainees typically enter their graduate training phase with a thesis mentor already selected, MD/PhD students are expected to complete their thesis qualifying examination by October of the second year in graduate training for most graduate programs.  Exceptions to this rule include programs such as Biostatistics and those affiliated with Health and Population Sciences, which have substantial course requirements and cumulative examinations.  Once a student has passed their thesis qualifying examination, they are required to meet with their thesis committee every six months.  Because of the nature of the research, students earning a degree in Epidemiology may complete the 3rd and 4th year of medical school while their data “matures”, returning in the last year to write up results.  Details are found in the Graduate Curricular Guidelines section. 


Attending and presenting results at scientific conferences is another important part of training, and MD/PhD students are encouraged to attend the American Physician Scientists Association (APSA) regional and annual meetings, as well as the National MD/PhD Student Conference sponsored by the University of Colorado MSTP.  The program helps cover costs associated with these two meetings.  MD/PhD students continue to participate in MD/PhD seminars, MSRS, social events, MD/PhD Student Council service, and program retreats. Indeed, interaction between students at all phases in the program is a critical aspect of the training process.  Students are also called upon to help with admissions and recruiting efforts, including conducting applicant interviews for the program.

As thesis research nears completion, students are encouraged to work closely with their thesis committee to ensure that the goals of graduate training have been reached.  Submission and publication of manuscripts in peer-reviewed journals, presentation of work at national meetings, and completion of the thesis document represent important milestones in this process.  Indeed, MD/PhD students are required to have a minimum of one first-author paper submitted at the time they defend their thesis.  Students should consult with the graduate office regarding proper thesis formatting and the timing of thesis submission and scheduling the final thesis defense.  This should be done well in advance since there are University imposed blackout dates for conducting the thesis examination.