Ph.D. Degree Program

The doctoral program of the Department of Biochemistry and Molecular Biology is designed to help students become qualified to teach and do research in the broad field of biochemistry and molecular biology. In addition, graduate students should draw from additional educational offerings and the cultural life of the University, not only for their own enjoyment but for their lifelong professional, social, and political responsibilities.

REQUIREMENTS FOR ADMISSION

  • Bachelor’s degree from an accredited institution with an overall grade point average of (B) or above
  • Official transcripts/credential and certified translations (Int’l.) from all undergraduate and graduate institutions attended are required (Colorado State University transcripts are not required)
  • One year each of biology, organic chemistry, physics, and calculus will have been completed.
  • A full-year course in biochemistry (equivalent to BC 401 and 403) with grades of B or better is required, but can be taken during the first year of graduate school
  • Three letters of recommendation preferably using the format recommended by the department. See Applying to the BMB Graduate Program
  • The Graduate Record Examination (GRE) (verbal, quantitative and analytical sections are required, subject section is optional)
  • A written “statement of purpose” that contains 1) a summary of professional/personal goals, 2) statement regarding educational goals, 3) statement explaining how this program will contribute to the applicant’s long-term goals, and 4) factors explaining your choice of Colorado State for graduate study
  • A completed resume that contains 1) collegiate work (institutions, dates attended, degrees earned); 2) professional employment with dates of service (including military); 3) special skills or competencies (including certifications or licensures); 4) publications, exhibitions, prizes, awards, or other recognition; and 5) service activities (including community and charitable)

GENERAL REQUIREMENTS  

Registration policies

Departmental policy requires all students to register for 18 credits per semester to complete their degree in a timely manner. After 72 credits (4 semesters), all graduate students will register for 1-5 credits dependent on health insurance needs. College regulations require that students who are being supported by a graduate assistantship may not register for CR (continuous registration), but must be registered for at least 1 credit.

Performance in Required courses

A grade of B (not B-) or better must be obtained in all required courses. At the close of each semester, the Graduate Affairs Committee (GAC) will evaluate the performance of each new student. A student with a grade point average below 3.0 in formal course work will be placed on academic probation or may be dismissed. In the event the student must repeat a course to improve their academic standing, the cost of registering for the repeated course will be the responsibility of the student. At the end of the first year of residence, the GAC will review the student’s entire record at CSU and then make recommendations to the faculty on the status of the student in the graduate program of the department. Courses in which an incomplete grade was received must be made up within one year, and a grade of at least B obtained.

University and Departmental Course Requirements

Total number of credits required.  

The Ph.D. degree requires a total of 72 academic credits in addition to extensive laboratory research training and is usually completed in about five years. Most of the required credits are earned during a student’s first two years in the program with a combination of course work and teaching duties, and the remaining years are devoted to full time research. The departmental requirements are built on three core courses in molecular genetics, cellular biology, and molecular structure that are taken by all students, followed by advanced elective courses that the students can tailor to their particular scientific interests.

Students who have recently earned grades of B or better in courses that are essentially equivalent to our core graduate curriculum (i.e. BC512, BC563, or BC565) may be exempted from taking those courses, but will then generally be required to take the advanced graduate level course in those areas (i.e. BC611, BC663, or BC665). Similarly, students who have not had a full semester of biochemistry or physical biochemistry may be required to take a fundamental course in these areas during the first year (i.e. BC401 & BC403 – Biochemistry I & II or BC411 – Physical Biochemistry).

11 credits of required core courses:

BC 512 – Principles of Macromolecular Structure (1) offered fall semester

BC 563 – Molecular Genetics (4 cr) offered fall semester

BC 565 – Molecular Regulation of Cell Function (4 cr) offered spring semester

BC 601 – Resp. Conduct in Biochemistry (1 cr) offered spring semester

BC 701 – Grant Writing and Reviewing (1 cr) offered fall semester

2 credits selected from 600-level Biochemistry Department courses:

BC 663 – Gene Expression (2 cr) offered spring semester

Electives.   A student must also complete a minimum of three additional advanced elective credits at the 500-level or above, bringing the total required didactic coursework to 16 credits. Courses will be selected in consultation with the student’s Graduate Advisor and student’s Student Advisory Committee (SAC) and are often chosen from the following list of suggested courses that span a wide range of departments and scientific fields.  Additional courses may be acceptable, but must be approved by the first year advisor or the SAC.

BC 566 – Advanced Mitotic Processes (1 cr) offered fall & spring semesters

BC 571 – Quantitative Biochemistry (1 cr) offered spring semester

BC 663 – Gene Expression (2 cr) offered spring semester

BC 711C – Advanced Topics in Structural Biology (1 cr) offered spring semester

BIOM 581B7 – Advanced Optical Imaging (3 cr) offered fall semester

CHEM 521 – Principles of Chemical Biology (3 cr) offered fall semester

CHEM 522 – Methods in Chemical Biology (2 cr) offered spring semester

CHEM 567 – Crystallographic Computation (1cr) offered spring semester

CHEM 571 – Quantum Chemistry (3 cr) offered fall semester

ERHS 510 – Cancer Biology (3 cr) offered spring semester

ERHS 611 – Cancer Genetics (2 cr) offered fall semester

MIP 530 – Adv. Molecular Virology (4 cr) -offered every other spring during even numbered years, so it will be offered in spring 2016

MIP 540 – Biosafety in Research Laboratories (2 cr) offered fall semester

MIP 555 – Principles & Mechanisms-Disease (3 cr) offered fall semester

MIP 636 – Mechanisms of Viral Infection/Disease (4 cr) only offered odd numbered years spring semester

MIP 651 – Immunobiology (3 cr) offered fall semester

NB 501 – Cellular and Molecular Neurophysiology (2 cr) offered fall semester

NB 502 – Techniques in Neuroscience (2 cr) offered fall semester

NB 503 – Developmental Neurobiology (3 cr) offered spring semester

NB 505 – Neuronal Circuits, Systems and Behavior (3 cr) offered spring semester

NB 750 – Physiology of Ion Channels (2 cr) – (temporarily not offered)

NSCI 580A3 – RNA Sequencing Data Analysis (1 cr)  offered fall semester

NSCI 580A4 – Linux as a Computational Platform (1 cr) offered fall semester

NSCI 580A5 – Genomics Data Analysis in Python (2 cr) offered fall semester

Transfer Credits and Waiving of Core Courses:

Per university requirements, a minimum of 32 credits toward the Ph.D. must be earned at Colorado State University and at least 21 credits must be in courses numbered 500 or above. A master’s degree from an accredited college or university may be accepted for a maximum of 30 credits.

The First Year Advisor will review requests for waivers of the core course requirements based on prior coursework. Requests must be accompanied by a transcript and course description and may require an oral and/or written exam to demonstrate proficiency. The student will be responsible for the material in the waived course as part of the Comprehensive Oral Examination given at the end of the first year. Note that the prior course credits need not be transferred to CSU as the waiver is merely an exemption from having to take the core courses, allowing the student the opportunity to take alternative courses to fulfill their credit requirements.

BC 793 Seminar.   Participation in BC 793 is required each semester a student is in residence. Students who have not completed 72 credits must register for BC 793. Students who have completed 72 credits do not register for BC 793, but are still required to participate fully in the course. The Fall semester seminar course will consist of research progress reports from all students in their second year and beyond, except for those who will defend their dissertation during the semester. The Spring semester seminar course will consist of journal article presentations by students in their third and fourth year.

Grading Policy.   In courses such as BC 793, 795, and 798, for which there are no formal evaluative procedures, grades will be assigned by the faculty member responsible on the following basis: a satisfactory level performance will be graded as S and performance that is unsatisfactory will be graded as U.

Teaching Experience.   As part of a student’s overall training, every student in the Ph.D. degree program in the Department of Biochemistry and Molecular Biology is obliged to teach the equivalent of two semesters at a half-time level in the field of biochemistry and molecular biology. Usually this obligation is fulfilled in the student’s second year in residence by assisting in the teaching of undergraduate courses. For each semester the student teaches he/she must register for an appropriate number of credits in BC 784, Supervised College Teaching.

First Year Sample Curriculum:

FALL

SPRING

BC 793 Seminar
1
BC 793 Seminar
1
BC 563 Molecular Genetics
4
BC 565 Molecular Regulation of Cell Function
4
BC 512 Principles of Macromolecular Structure
1
BC 600-level courses
2-6
Fundamental Courses if needed   (BC401, BC411)
0-7
BC 795 Lab Rotation to total 18 credits
5-12
Fundamental Courses if needed (BC403)
0-3

BC 795 Lab Rotation to total 18 credits

3-10

 

Second Year Sample Curriculum

FALL

SPRING

BC 701   Grant Writing & Reviewing
1
 BC 601 Responsible Conduct in Biochemistry 1
Advanced Electives
1-3
Advanced Electives  1-3
BC 784 Supervised College Teaching
1-2
BC 784 Supervised College Teaching
BC 793 SeminarBC 798 Research to total 18 credits
1-2
1
12-15
BC 793 Seminar
1
BC 798 Research to total 18 credits
11-14

 

ADDITIONAL INFORMATION FOR FIRST YEAR STUDENTS

Financial Support

Specific information about the current level of available support is provided to each student when he/she begins graduate work in the department. The current financial support (2017-18) is $27,000/yr.   First year students may receive additional financial support. The student is expected to devote all of his/her time to the pursuit of a degree and outside jobs are discouraged. Support by University funds may be limited to six years.

Tuition

Tuition charges for graduate students vary from year to year, and there is considerable differential between tuition charges to Colorado residents and nonresidents. In most instances, tuition is paid for all Ph.D. students. Domestic students who are not Colorado residents are obligated to follow guidelines for obtaining in-state residency status by the beginning of their 3rd semester in residence. Failure to do so will result in the student paying the considerable differential between in- and out-of-state tuition themselves in their second year and beyond.

Advising of New Students

New graduate students will be advised by the First Year Advisor until their dissertation advisor is selected.

Laboratory Rotation Program

All students are required to carry out rotations in a minimum of three different laboratories.  Students should register for sufficient credits of BC 795 each semester to reach 18 total credits. Graduate education is a fulltime activity and involves a high degree of experiential practical learning. It is expected that students will devote at least 40 hours per week, minus the hours spent in class, to their laboratory rotations and will participate fully in the efforts of the laboratory to which they are assigned. The student’s motivation and research aptitude are critical factors in the performance evaluations conducted at the end of the Fall and Spring semesters of the first year, and student participation in research is a major criterion faculty use in this evaluation.

The approximate schedule for the three rotations for Fall entry students is as follows: 1st rotation – beginning of fall semester through mid November; 2nd rotation – mid November through the middle of February; 3rd rotation – mid February through the middle of May. Spring entry students will complete their first rotation during the Spring semester and two rotations during the summer session.

Fall entry students will select a laboratory for the first rotation following the departmental retreat, which occurs during the week preceding start of classes in the Fall term. In September/October, members of the faculty will give presentations to the new students on research opportunities in their laboratory to aid students in selecting the second and third rotations. Spring entry students will select their rotations based upon information available on the departmental web site, faculty publications, and discussions with individual faculty members.

Rotation placements are arranged by each student presenting a prioritized list of choices for each rotation to the First Year Advisor. The Advisor will assign the rotation based upon this list and consultation with faculty mentors and students. By mid to late October, following faculty research presentations, Fall entry students will submit to the First Year Advisor a prioritized list of laboratories for the second rotation. The students’ list of choices for the third rotation must be submitted to the First Year Advisor by the end of January.

Performance Evaluations

All first-year students will be evaluated using the criteria described in this section.

Comprehensive Oral Examination.   All students in the Ph.D. program are required to take a comprehensive oral examination at the end of their second semester. The purpose of the exam is to test each student’s general knowledge of biochemistry and molecular biology as well as his/her ability to utilize this information to solve problems. This approximately one-hour exam will be conducted by three faculty members who will examine all students in a given semester.

Material tested is based on two scientific papers that are chosen by the exam committee approximately one week prior to the exam. Questions pertaining to research of departmental faculty members may also be included. All three sections must receive a passing evaluation to remain in good standing in the program. If the student fails one section, this must be retaken within 3 months. If 2 or 3 sections are failed, the student is eligible to retake the exam but will not receive financial support during the interim. If a student does not pass all three sections of the exam by August 15th (just prior to their second year), they will be dismissed from the program.

Faculty Evaluation.   The overall performance of each first-year student is evaluated by the entire faculty at the end of the Fall and Spring semesters. This evaluation will include a review of the student’s academic record, participation in seminars, progress in laboratory rotations, and performance on the comprehensive oral examination. Possible outcomes are: a) clear or conditional approval to continue in the Ph.D. program, b) transfer to the M.S. program, c) academic probation (less than a 3.0 GPA), which is accompanied by loss of GTA or GRA support, or d) dismissal from the graduate program if it is determined that the student is making unsatisfactory progress toward the degree and that satisfactory progress cannot reasonably be anticipated (per graduate school policies).

A student who is placed on academic probation must be re-evaluated by the entire faculty at the end of the following semester for a decision as to his/her continuation in the program. Students transferred to the M.S. program may reapply to the Ph.D. program upon satisfactory completion of the M.S. degree but acceptance is likely only with a strong recommendation from their M.S. advisory committee.

Selection of Dissertation Advisor

The selection of a dissertation advisor should be made at the end of the third laboratory rotation. Students are required to familiarize themselves with the research programs of the faculty throughout their first year.   Before substantial discussions between potential mentors and students takes place, students will submit a prioritized list of no fewer than three mentors to the First Year Advisor. The First Year Advisor will mediate the distribution of students to the laboratories.

Student’s Advisory Committee (hereafter SAC)

Composition.   The SAC will be composed of at least four members; the student’s advisor, who will serve as chair; at least two additional departmental faculty members, and at least one faculty member from outside the department.

Appointment.   The student, after consultation with his/her advisor, will present to the department chair a list of possible candidates for their SAC by the Friday before the first day of classes in August. Formal appointments will then be made by the department chair after consultation with the student’s advisor. The SAC must be formed within three months after selection of the advisor. If circumstances so warrant, later changes in the composition of the SAC can be made.

Responsibilities of the SAC.   The SAC shall be responsible throughout the remainder of the student’s graduate career for advice on the student’s course work program and evaluation of progress therein. The committee will advise, counsel, and guide the student in the planning and execution of a research program. The first meeting of the student with the members of his/her SAC should be held promptly after the SAC is formed, and a GS-6 form listing a recommended course of study should be filed with the Graduate School no later than registration for the fourth semester in graduate school.

Annual Performance Evaluation by SAC. To assist the SAC in its evaluation of the student’s progress in research, each student will meet annually with his/her SAC. This annual evaluation will consist of three elements:

1.   A written progress report . The report should briefly summarize the goals of the research as described in the “Guidelines for the Progress Report.” Progress report guidelines will be distributed in the fall semester. The progress report must be in the hands of the SAC members at least one week before the student’s research seminar (BC 793). An announcement of the date, time and title of the research seminar should be included with this report, and the student should deliver a copy of the seminar notice to the external members of the SAC. Students failing to provide their SAC members with a written progress report 7 days prior to their seminar and failing to meet with their SAC within two weeks following their seminar each Fall semester will receive an unsatisfactory evaluation of their research. Exceptions to this policy will be given only in unusual circumstances and must be approved in writing by the GAC.

2.   A research seminar in BC 793 followed by a meeting with the student’s SAC. As described above, a copy of the written progress report must be given to members of the SAC a week prior to the student’s research seminar. A meeting must be scheduled within two weeks after the seminar to clarify the questions raised by the progress report and the seminar, and for soliciting guidance and suggestions from the SAC concerning the goals, methods, and evaluation of the research. The SAC members and the chairman of the GAC will sign an evaluation form for the student’s file.

3.   Evaluation of performance in course work and research (BC798V) . The SAC and dissertation advisor will determine the appropriate grade for BC 798V. The results of such evaluations, as well as the committee’s recommendations for furthering the student’s progress, will be submitted by the SAC in written form to the GAC to be included in the student’s file. Submission of such reports no later than one week after each meeting is a firm departmental requirement.

Unsatisfactory progress. Persistent lack of progress is grounds for dismissal from the Ph.D. program. Students who receive an unsatisfactory evaluation on their progress from their SAC must meet again with their SAC within 6 months and receive a satisfactory evaluation or they will be dismissed from the program. Should the SAC decide to recommend dismissal from the Ph.D. program, the student will be notified in writing. The student will then have the opportunity to appeal this decision with their SAC and the Provost/Academic Vice President (see CRS 24-19-104) before a final decision is made and implemented. The student will be notified in writing by their SAC of this final decision.

University Preliminary Examination for Admission to Candidacy for the Ph.D.  

Examining Committee. All aspects of the Preliminary Examination are overseen by the Graduate Affairs Committee (GAC). A member of the GAC will substitute for the dissertation advisor. The Preliminary Examination is administered by the full committee, and the GAC member will write a report to the student and the major advisor to review the strengths and weaknesses of the written proposal and the student’s performance on the oral examination.

Coverage . This examination consists of two parts: 1) a written proposal describing the student’s dissertation research and 2) an oral examination. The written research proposal must follow the guidelines for the “Research Plan” format contained in the instructions available from the GAC or graduate program administrative assistant. It must be completed and submitted in final form to the GAC during the second semester of the second year. The due date for the proposal will be announced no later than January 1st. The proposal will be reviewed for format by the GAC before distributing it to the Examining Committee. The oral examination focuses on a defense of the student’s research proposal and related areas, and will include general questions related to biochemical and molecular areas of the life sciences. Successful completion of this examination qualifies the student as a candidate for the Ph.D. degree, and the student submits a GS-16 form to the Graduate School.

Deadlines. The due date for the Preliminary Examination proposal is noon on Friday of the second full week in February of the second year and the deadline for completing the (1 st) Preliminary Examination is April 15.   For students who enter the program in the spring semester these deadlines are on the Friday of the second full week in September and on November 15.

Failed Preliminary Examination. Graduate School regulations stipulate that:

(a) a candidate who fails the preliminary examination may be re-examined once, provided the Examining Committee approves;

(b) the re-examination must be held no earlier than two months following the first exam;

(c) failure to pass the second exam results in dismissal from the Ph.D. program;

(d) a student who is dismissed for this reason may apply for readmission to complete the M.S. degree.

DISSERTATION REQUIREMENTS

Defense of Dissertation

Eligibility. This examination cannot be held until two or more semesters have passed after satisfactory completion of the University Preliminary Examination and must take place within the time period prescribed by the Graduate School. The student must have completed a typed draft of the dissertation and submitted a copy thereof to each committee member at least two weeks prior to the examination. The thesis advisor must agree that the dissertation is of such quality and completeness as to warrant setting a date for the defense.

Examining Committee . The SAC will be the examining committee with the student’s advisor serving as chair. The defense of dissertation, however, is open to the public and the chair has the prerogative of allowing non-SAC members to ask questions of the candidate.

Procedures . The student will present a formal seminar concerning the dissertation research.  Following the presentation, the committee will probe, in detail, the student’s comprehension of, approach to, and solution of, the dissertation research problem. The committee, in executive session, shall determine if the thesis and its defense were satisfactory. In the event of an unsatisfactory performance, the committee may allow re-examination once and may require the student to complete further work.

Leave of Absence Prior to the Defense of Dissertation . To ensure timely completion of the Ph.D. requirements, students are encouraged to complete the writing, defense, and submission of their dissertation before leaving the Department. Exceptions to this policy may be granted on an individual basis provided the student and his/her advisor have filed a written agreement outlining a schedule for completing the requirements. A letter from the Department will be sent to the student’s employer indicating that the student has not fulfilled his/her Ph.D. requirements. Failure to comply with the schedule for the completion of degree requirements is cause for dismissal from the Ph.D. program.

Submission of Dissertation  

Approval and deadlines. After passing the Defense of Dissertation, the dissertation will be prepared in final form following all of the rules of the Graduate School for its preparation. The SAC must examine and approve the dissertation in its final form prior to the submission. In order to be awarded at the end of the current semester, this must be completed no later than the end of the eleventh week for Fall or Spring semester and by the end of the fifth week of summer term. After Approval by the SAC, the dissertation must be submitted to the University Libraries within two months of completion of the oral defense. Failure to meet this deadline without a written extension signed by the Chair of the Department will result in dismissal from the Ph.D. program.

Number of Copies. In addition to electronic submission to the Graduate School and Department, two copies of the dissertation are required:  one for the Department, and one for the advisor (submitted to the Department). The advisor will pay for in-house copying and for binding of the advisor copy, as well as a student copy (3rd copy, by request) of the dissertation/thesis. The department will pay for the binding of the a departmental copy of the dissertation/thesis. All remaining expenses for any additional copies requested by the student are the responsibility of the student.

Waiver of requirements

Any exceptions to the guidelines must be requested in writing to the GAC to be evaluated and approved by the Biochemistry and Molecular Biology faculty.

Summary of the Steps to the Ph.D.

Action Normal Time of Completion
Application for admission Before arrival
Performance evaluation by GAC End of every semester
Comprehensive oral examination End of 1st academic year
Appointment of student’s advisor Completion of 1st year
Selection of the SAC One week before beginning of Fall Semester, 2nd year
File Program of Study (GS6 form) No later than October, 2nd year
Research seminar and meeting of SAC. File evaluation form with GAC Fall semester, every year
Submission of preliminary exam research proposal to GAC End of second full week in February, 2nd year
University preliminary exam (GS16 form) April 15th, 2nd year
Application for graduation (GS25 form) Beginning of semester in which student plans to graduate
Defense of dissertation (GS24 form) During the semester in which student plans to graduate
Submit electronic dissertation to Graduate School and Department, and two copies ready for binding: Department (1 copy) Advisor (1 copy) In accordance with the graduate school guidelines

The deadlines listed above apply to fall entry students.

See the Graduate School website for their complete list of required forms and procedures:  http://graduateschool.colostate.edu/current-students/forms/index.aspx