2022-2023 Academic Catalog 
    Feb 07, 2023  
2022-2023 Academic Catalog

Biochemistry and Molecular Biology, PhD

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Graduate Program
The PhD program in Biochemistry and Molecular Biology (BCMB) at Clark University is offered jointly by the Biology and Chemistry Departments. The BCMB Program offers research opportunities in a wide variety of areas, including: molecular modeling, protein chemistry, chemical biology, enzymology, cell division, signal transduction, molecular evolution, and gene expression. Applicants are encouraged to contact directly those faculty members whose research interests appeal to them. 

Graduate Requirements


The Graduate School requires a minimum of 16 semester courses in residence for the Ph.D. Courses must be completed with a grade of B- or better to earn graduate credit. The time necessary for completion of the degree will depend on the student’s research and is usually in excess of this minimum. Part-time graduate work is discouraged as it is impractical for a research degree. Stipends are not available for part-time students. 

Teaching Requirements 

Students conducting doctoral research are required to complete two semesters as a teaching assistant. 

Preliminary Qualifying Exam 

If the applicant has completed two semesters of undergraduate Biochemistry with grades of B- or better, or has completed the GRE subject exam in Biochemistry, Cell and Molecular Biology with a score in at least the 50th percentile, then no Preliminary Qualifying Exam is required (please note, the GRE Biochemistry, Cell and Molecular Biology Test was discontinued in December 2016. If you took the exam prior to 2016, please contact the program director to determine if the score will be accepted.). Otherwise, the student must achieve a score in at least the 50th percentile on the American Chemical Society (ACS) standardized Biochemistry exam, which may be taken three times. The BCMB program has compiled a guide to help study for the ACS exams. Alternatively, a grade of B- or better in Clark’s Biochemistry I and II (BCMB 271 or 272) will suffice. The preliminary Qualifying Exam must be completed no later than one year after admission.  

Advisory Committee 

Early in their first semester, new students should meet with their advisor to discuss possible course requirements and recommendations for Advisory Committee members. The responsibilities of the Advisory Committee are: (1) to determine what courses must be taken; (2) to meet at least once a year to assess the student’s progress; and (3) to administer the qualifying examinations and dissertation defense, and to inform the Chair of the BCMB Graduate Studies Committee regarding their outcome. The Advisory Committee must include the student’s advisor, who serves as Chair of the committee, and at least two full-time members of the BCMB program. The advisor may invite additional scholars from within or outside the University to join the Advisory Committee. The advisor submits the proposed Advisory Committee to the BCMB Program Director, who appoints the committee. The Advisory Committee should be chosen, and a full committee meeting should be held by the end of the first year of study. 


All graduate students are required to participate in their home department’s seminar series and periodically present seminars. 

Course Requirements 

As part of the 16 credit university residency requirement (grade of B- or better), a minimum of three 300-level core courses are required as follows: one classified as Group A by the BCMB major (300 level biochemistry-related), one classified as Group B by the BCMB major (300 level molecular-biology related), and one research methods course. The Advisory Committee will determine which particular courses must be taken, based on the student’s research interests and prior training. More than the 3 core courses may be required. Grades lower than B- will not be counted towards the degree, and students who accumulate more than two grades lower than B- will not be allowed to continue in the Ph.D. program. In addition to formal courses stipulated by the committee, graduate students are required to enroll in their home department’s research seminar (BIOL 350 or CHEM 380) and attend all departmental seminars. 

Comprehensive Examination 

Ph.D candidates must take a comprehensive examination prior to being advanced to candidacy. It is expected that this examination will be completed by the end of the second year in residence. The comprehensive examination consists of a series of written exams on pre-determined subject areas, related to the student’s area of research, and administered by each Advisory Committee member. At the discretion of the Advisory Committee, there may also be an oral examination on the same material, as well as general subjects in Biochemistry and Molecular Biology. The Advisory Committee will decide whether the student passes or fails. Students who fail the comprehensive examination may, at the discretion of the Advisory Committee, be given one additional opportunity to pass the examination. Students who fail the comprehensive examination twice will be required to leave the Ph.D. program. It may be possible for some students to write and defend a master’s thesis at this point, with the approval of the Advisory Committee. 

Research Proposal Defense and Admission to Candidacy 

Each Ph.D. candidate must pass a proposal defense. It is expected the proposal defense will normally take place by the end of the third year, and no less than six months after the comprehensive examination has been passed. The proposal defense is administered by the Advisory Committee, plus any additional scholars from within or outside the University who may be invited by the Chair of the Advisory Committee to participate. The proposal defense is an oral examination that is based on a written research proposal. The proposal must be delivered to the committee at least two weeks prior to examination. The proposal may either be based on topics unrelated to the student’s research, prepared in the format of a grant proposal (see guidelines), or a detailed plan for the student’s research, at the discretion of the Advisory Committee. Passing this examination constitutes official acceptance into the PhD candidacy. 

Master’s Degree 

Candidates who do not pass either the Comprehensive Examination or the Research Proposal Defense, but who submit an acceptable research-based thesis, and pass a final oral examination, may, at the discretion of the Advisory Committee, be awarded the M.S. degree. A paper based on original research and accepted by a refereed journal may be submitted in lieu of a thesis with the approval of the Advisory Committee. Candidates who pass the Research Proposal Defense but do not write and defend a Master’s thesis are eligible for a M.A. in BCMB degree. 

Ph.D. Dissertation 

The Ph.D. dissertation is written under the supervision of the student’s advisor and is based on the student’s original research. Formal guidelines are available at the Office of Graduate Studies and Research. Papers published in or accepted by the refereed journal may be submitted as part of a thesis with the approval of the Advisory Committee. A copy of the work, in final format and approved by the student’s advisor must be submitted to each member of the examining committee and made available to the department faculty as a whole at least one week before the dissertation defense, and at least six weeks prior to commencement if the degree is to be awarded at commencement. 

Dissertation Defense 

The dissertation defense consists of two part: a public seminar in which the student presents his or her research, and an oral dissertation defense before the Advisory Committee. The examination is conducted by the Advisory Committee, and any additional persons from within or outside of the University whom the Chair of the Advisory Committee may appoint. The Director of the BCMB program has final approval over the composition of the examining committee. The Chair of the Advisory Committee notifies the program director and the Dean of the Graduate School when the defense has been scheduled, and also informs them of the outcome of the dissertation defense. 

Acceptance of Dissertation 

After revisions required by the advisory committee have been made, the thesis or dissertation is submitted to the advisor for final approval and signature.  After receiving the advisor’s approval, the dissertation must be submitted to ProQuest via the ETD Administrator by the deadline online (typically by August 1st for degrees awarded in August, December 1st for degrees awarded in December, and April 1st for degrees awarded in May).


Example timetable for Ph.D. program: 

Year 1 

  • New graduate student orientation meeting (in the first few weeks of the semester) 

  • Campus-wide orientation 

  • Meeting with prospective advisor (within first two weeks of the semester) 

  • Selection of home department and Advisory Committee members 

  • Advisory Committee meeting 

  • Complete Preliminary Qualifying Exam 

Year 2 

  • Comprehensive examination 

Year 3 

  • Proposal defense (seminar and oral exam) 

Year 4 

  • Advisory Committee meeting to finalize dissertation outline 

Year 5 

  • Dissertation defense (at least five weeks before commencement, if the student is participating in commencement activities) 

  • Submission of dissertation (at least four weeks before commencement, if the student is participating in commencement activities) 


Academic Standing 

For a student to maintain satisfactory academic standing in the program, the student needs to complete four course units per semester and making satisfactory progress through the program milestones in a timely fashion based on the suggested schedule. A student also needs to be making satisfactory progress in research activity to maintain satisfactory academic standing. In cases where a student has taken one or more incompletes, the work must be completed satisfactorily by the agreed-upon date.  

Students who achieve unacceptable grades (less than B- or withdrawal from a course) in two courses before obtaining credit for the five-course minimum will be dismissed from the Ph.D. program. 

Students who fail the second stage of the Qualifying Exam may be retested once, if the student’s Research Advisor and Faculty Advisory Committee deem it appropriate. Students who fail to pass this exam will be dismissed from the Ph.D. program. 

Evaluations of Satisfactory Academic Standing 

The Faculty Advisory Committee for the student is responsible for overseeing important decisions concerning the student’s graduate program and evaluating the academic standing of the student. It will meet annually to review academic and research progress, write the student’s Secondary Qualifying Exam, and sit in review of the student’s Research Proposal and Dissertation. Should the student or faculty advisor deem it necessary to address issues regarding academic standing or progress in the graduate program, the Faculty Advisory Committee can be asked to meet.  


Students who do not make satisfactory progress in research or teaching will be placed on probation. Requirements to return to satisfactory progress in research will be determined by the research advisor and the Faculty Advisory Committee and communicated to the BCMB Program Director. Requirements to return to satisfactory progress in teaching will be determined by the BCMB Program Director and Department chair (either Biology or Chemistry, depending on the faculty advisors home department). Students who fail to meet the probation requirements over the next two academic semesters will be dismissed from the Ph.D. program. 

Change or Loss of Research Advisor 

A doctoral student is unable to continue in the program without a faculty advisor.  The period of transition between advisors is expected to last no longer than one month.  In the event that the student is unable to find a faculty advisor to work with for longer than one month, the BCMB Program Director will convene a meeting of the department faculty with the purpose of determining whether the student will be allowed to continue in the overall graduate program. 

Grievance Procedures 

Ordinarily, difficulties that may arise between students and faculty are resolved through informal discussions between the individuals involved. When a student believes that such discussions have not led to a fair outcome, the student may ask the BCMB Program Director to intervene. The Program Director will attempt to resolve the issue informally through discussions with those involved. If the student considers that these methods have failed, the student may ask the Program Director to convene a meeting of the Grievance Committee for resolution. The Grievance Committee will include two additional BCMB faculty and the Program Director. Students who believe that they have not been treated fairly through such procedures may appeal the decision to the Dean of Graduate Studies and Research.  


Those who do not fulfill the required academic standing for the program will be dismissed from the program.  The decision will be made by Faculty Advisory Committee or the BCMB Program Director, if the Faculty Advisory Committee has not been determined. Dismissal may include conferral of a terminal Master’s degree, pending satisfactory completion of work recommended by the Faculty Advisory Committee and agreed by the student. The advisor/committee are not obligated to accept work for an MS degree. Appeals against dismissal should be addressed to the Dean of Graduate Studies and Research following the procedure as stated in the academic catalog.

Program Faculty

Nathan Ahlgren, Ph.D.

Robert Drewell, Ph.D.

Sergio Granados Focil, Ph.D.

David Hibbett, Ph.D

Shuanghong Huo, Ph.D

Charles Jakobsche, Ph.D

Denis Larochelle, Ph.D

Noel Lazo, Ph.D

Neva Meyer, Ph.D

Arundhati Nag, Ph.D.

Deborah Robertson, Ph.D, Program Director

Donald Spratt, Ph.D.

Justin Thackeray, Ph.D

Emeriti Faculty

Frederick Greenaway, Ph.D.

Thomas Leonard, Ph.D

Timothy Lyerla, Ph.D


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