Students who are granted a Ph.D. degree from the Department of Biochemistry have demonstrated their ability to (i) design, conduct and evaluate high quality, independent research and (ii) possess broad-based knowledge of the field of Biochemistry. Students are expected to demonstrate their acquisition of these skills principally in their thesis research and through graduate course performance, student journal club participation, seminar attendance and performance on the qualifying examination.
Research Requirements
The Ph.D. degree in Biochemistry is a research degree. Research training begins with laboratory research rotations during the 1st year of study and continues with the selection of a thesis research advisor and development of an original research project.
Students’ typically rotate in three laboratories during their 1st year. Students who matriculate directly to the laboratory of a member of the department are required to rotate in at least one other laboratory in order to gain breadth in their research training. Students who matriculate with a M.S. or equivalent research experience and have selected a thesis laboratory may obtain an exemption from laboratory rotations if the request is endorsed by their mentor, their advisory committee and the Chair of Biochemistry.
Students should plan to complete the majority of their course work including required departmental courses during the first year. (The department recognizes that special circumstances may delay completion of the required courses.) Advanced courses appropriate to their thesis research may be taken in the second and subsequent years.
Once students join a thesis laboratory in the department, their advisory committee is responsible for monitoring their progress. Ph.D. thesis research involves meaningful, critical thinking and the execution of ideas in the laboratory through the use of the scientific method. Students are expected to embrace full-time research upon declaration of their thesis mentor following a twelve-month calendar. The qualifying exam is scheduled to take place during the latter half of the second year, allowing timely advancement to candidacy. Upon joining a thesis laboratory, it is expected that students’ research continue in concert with their course work and examinations.
The research conducted by a Biochemistry Ph.D. candidate should be an original contribution to scientific knowledge. The quality of the candidate's research is expected to be equivalent to that found in reputable, refereed scientific journals. Research progress is documented by the reports of the student’s advisory committee meetings and by the student's progress reports submitted before these meetings. Filing these reports with both the Chair of Biochemistry and with the Graduate Division office is a departmental requirement. Reports of student advisory committees should discuss research progress and research. To download the advisory committee forms – Click Here.
Course Requirements for the Ph.D. Degree in Biochemistry
First year students must fulfill the general course requirements of the graduate division. While thesis research is necessarily highly focused, a broad foundation in chemistry and modern biology is required to carry out scholarly studies in biochemistry. A student’s curriculum should provide breadth and fundamental information as well as specialized education in the chosen area of research. Click Here – for a list of the courses offered by the Graduate Division. The Biochemistry faculty has identified three courses that all of our students should endeavor to complete during their 1st year of study. These courses are:
Required Courses for Ph.D. and M.D.-Ph.D. Students (taught annually):
- (Block 1) Biochemistry - This course continues building the foundation in understanding of biological macromolecules, energetics, biochemical methods and enzymatic activity presented in undergraduate biochemistry courses.
- (Block 2) Gene Expression: Beyond the Double Helix - This course covers the molecular mechanisms of biological information content of cellular processes such as transcription, translation, splicing and replication.
- (Block 3) Human Metabolism: Regulation and Disease - This course explores the metabolic pathways relevant to human health and disease.
Students may request exemption from these courses if they have completed substantial graduate level courses on these topics during either their undergraduate or masters training. Students should contact the leader(s) of each course upon matriculation for a review of their placement request. The decision of a course leader on an exemption request is final.
First year students are encouraged to seek out faculty for advice on crafting an effective curriculum that will support their future studies in biochemistry and related disciplines studied by members of our department. Since a goal of the graduate curriculum is for students to complete the majority of their didactic training during the first year, serious thought should be given about charting the optimal pathway through the available options remembering that educational breath as well as depth is important to future success. Students who have joined a thesis laboratory should discuss additional course work with their mentor and advisory committee members.
Students must pass the required courses to be in good academic standing with the department. Students who fail a course may take it one additional time; passage will restore a student’s good academic standing. (Students should be aware that a grade of ‘fail’ is a permanent mark on their academic transcripts.) Lastly, students may not graduate with an incomplete on their academic record. Departmental students who are not in good standing or who fail to progress in Thesis Research are referred to the Academic Affairs Committee (AAC) of the Graduate Division for review. As part of this review, the student’s advisory committee will prepare a written plan for the student, the mentor and the AAC, outlining the requirements for a return to good academic standing.
Biochemistry Student Journal Club and Works in Progress Seminars
Upon declaring the Department of Biochemistry for their thesis research, graduate students participate in the Journal Club (JC) and Works in Progress (WIP) held at noon on Fridays in the departmental seminar room. Attendance at the weekly meetings begins immediately. Presentations by the student begin at the start of the semester following declaration. This is typically the fall semester of the second year for students entering the department from the rotational pathway. Each student presents one journal club and one works in progress each calendar year. Students completing their thesis studies may be excused from the journal club presentation by the faculty advisor to the program. However, all students will present yearly works in progress until they successfully defend their thesis.
For both journal club and works-in-progress presentations, students are randomly assigned a faculty advisor for their presentation at the beginning of the semester. Journal club and works in progress presentation scheduling is at the discretion of the faculty advisor to the program as discussed below. A written record for each Journal Club and Works in Progress is filed with the departmental office. Forms for evaluation of the Journal Club and Works in Progress performance is in the Appendix. The criteria for the evaluations are discussed below. A detailed description of Journal Club and Works in Progress guidelines can be found in the Appendix.
Journal Club Guidelines and Procedures
A journal club presentation is an analysis of a recent scientific article chosen for its general interest and importance. The Journal Club requirement is met by (i) presentation of literature seminars in consultation with the assigned faculty member; and (ii) participation in the discussion during and following seminar presentations. Students are required to attend the Biochemistry Journal Club and Works in Progress during each semester they are enrolled in the Biochemistry Graduate Program. Rotational students are also encouraged to attend.
The student and faculty advisor will jointly select an article that is outside the scope of the student’s thesis research. The assigned faculty advisor will mentor the student through a critical reading of the journal article and preparation of the student’s presentation. The faculty advisor will meet with the student prior to the JC to provide guidance for the presentation. The faculty advisor will be present during the presentation and provide the student with critical feedback on the effectiveness of the presentation. Each faculty member can serve only once per semester as a journal club advisor. A student’s thesis advisor cannot serve as an advisor for their journal club presentation. However, thesis advisors are expected to be present during their student’s journal club presentations and provide critical, if informal, feedback. In addition, journal clubs will be evaluated by fellow students. The purpose of these evaluations is to help students develop the skill of public presentation.
At least three weeks before the presentation date, in consultation with the faculty advisor, the student must choose the article to be presented. The articles must be primary research papers, not review articles or short research communications. The selected article must be from an area not directly related to the student’s thesis research; students can take best advantage of the expertise of their faculty advisor by selecting a paper that the advisor can comment on with some authority. A pdf file of the selected article should be provided to the faculty advisor to the program or the current student organizer at least one week before the presentation date. If the student does not provide a copy of the article in time, he/she will be responsible for the article’s distribution.
The faculty advisor will be available to guide the Journal club preparation process during the three weeks following article selection and prior to the presentation. In the event that the faculty advisor cannot fulfill his/her responsibility, another faculty member should be sought to substitute as the advisor. The student should make every effort to give a practice talk before the presentation date. After the presentation, the faculty advisor will meet with the student to discuss the presentation. The journal club presentation should contain Introduction and background, Experimental methods, Results, Conclusions and Critique sections as described below. Students should aim for a 20 minute presentation in order to allow time for discussion during and at the end of the presentation. Careful consideration should be given to the time allocated to each of these sections in order to craft an effective, enjoyable and informative presentation.
- Introduction and Background: Informs the audience on both basic concepts and latest developments impacting the article that is being presented. The background should point out the questions answered by the article to be presented. In crafting their presentation, students should remember that many in the audience will be unfamiliar with the subject of the presented paper. It is very important to put the paper in context. Why is the work important?
- Experimental methods: Describes the experimental techniques used in the article. Common techniques can be described in a few phrases or sketches. Specialized or novel techniques should be explained in greater detail. It is often helpful to an audience to know why a particular technique and not another was used.
- Results: All data acquired in the experiments should be presented and described in great detail. The student should assume that the audience does not know the significance of the results. Do not simply recapitulate the results. Explain them!
- Conclusions: Describes the inferences drawn by the authors from the data obtained. The student should refer back to result slides as needed.
- Critique: This is the most important part of the journal club. The student will present his/her opinion regarding strengths and weaknesses of the article. The critique should be treated as a peer-reviewed publication process. Do you believe that this paper will have an impact on its field? If so, why?
Students may use Microsoft PowerPoint or other graphics display aids. However, fancy formatting and animation should only be used if warranted by the nature of the article. In preparing the presentation, the emphasis should be in reviewing the science, not on demonstrating computer graphics skill. Students should keep their slides simple, only presenting the information that they wish to convey to their audience.
Works In Progress
The works in progress presentation is prepared with the thesis mentor as advisor. Additionally, the faculty advisor for the WIP presentation will provide outside critique and guidance on the presentation. The student should arrange a meeting with the faculty advisor prior to the WIP. This presentation should contain Introduction and background, Experimental methods, Results and Conclusion sections.
- Introduction and Background: Informs the audience on “the big picture” and where your thesis project fits into this big picture. The background should point out what questions you hope to answer with your research.
- Experimental methods: Describes the experimental techniques that will be used in your research. Common techniques can be described in a few phrases or sketches. Specialized or novel techniques should be explained in greater detail.
- Results: Results are not required for a works in progress. Second year students often do not have results to present. In this instance the student should focus his/her presentation on the background and experimental methods to be used.
Each section can be as long as necessary, taking into account that the presentation should allow plenty of time for questions. Each student should aim for a 20 minute presentation to allow time for questions and discussion during and at the end of the presentation.
Student Advisory Committees
Upon declaration of a thesis laboratory within the department, an advisory committee must be formed by the student and mentor consisting of three additional faculty. At least one and preferably two members of this committee should be members of the department. The role of the advisory committee is to advise the student during their Ph.D. research, nurture and evaluate their scholarly development and ultimately grant permission to defend the Ph.D. thesis. The faculty who comprise a student’s advisory committee can play a central role in graduate student training by providing additional areas of expertise and perspective to the conduct of a student’s thesis study.
The Department of Biochemistry requires that advisory committee meetings be held twice each year. Initially, a committee can provide guidance in crafting the thesis project, selection of courses and preparation for the qualifying examination. Subsequently, they can evaluate the laboratory work that constitutes the research component of the Ph.D. degree. The regular meetings of these committees and the filing of written reports of their content with the departmental are required for a student to remain in good departmental standing.
As the direction of a student’s thesis research may change as the project progresses, the student and their advisor may wish to make changes to the composition of a student’s advisory committee. Such changes must be approved by the Chair of the advisory committee. The Chair of the Department is an ex officio member of all advisory committees and may attend a meeting at his/her discretion. Other policies governing student academics and responsibilities can be found in the Academic Policies and Guidelines of the Sue Golding Graduate Division, which is available on the program’s website – Click Here.
Students are responsible for scheduling the two required advisory meetings each year. Additional meetings may be scheduled as needed, as requested by the student, mentor or committee. Prior to a meeting, the student must distribute to the committee a short (1 - 2) page summary of academic and research progress since the last meeting. A synopsis of the meeting and committee recommendations will be summarized by the committee chairperson and communicated to the student and his/her mentor.
Student progress reports and Advisory Committee reports on all meetings are included in the student's academic file. Copies of these reports are also distributed to the Chair of the Department of Biochemistry. The written reports of the required advisory committee meetings must be on file with the departmental office before the Ph.D. degree is granted. An advisory committee report form and other relevant forms can be found on the Graduate Division’s website – Click Here.
Research Seminars in Biochemistry
Students enrolled in the Graduate Program are required to attend the research seminars presented in the Seminar Programs of the Department of Biochemistry. Notices are posted on the Departmental bulletin board near the Departmental Office, on the Einstein homepage Calendar of Events and in e-blast announcements.
Qualifying Examination
The Graduate Division administers the qualifying examination for advancement to candidacy for the Ph.D. degree. Passage of the qualifying examination is required for continued study in the department.
Thesis Examination
The preparation and defense of the Ph.D. thesis in Biochemistry is a culmination of a student's independent laboratory research. During the course of thesis research, the advisory committee will assist the student and the thesis advisor in defining the nature and scope of the research project that will form the basis of the doctoral dissertation. The Graduate Division has established procedures for preparation of the thesis and its defense that can be found on the program’s website. As per the Department of Biochemistry requirements, one member of the thesis committee should be an outside examiner.
Students must remain in residence until the thesis research has been completed to the satisfaction of the Ph.D. mentor and the advisory committee. A student must request a waiver of this requirement from the Chair of the Advisory Committee who will then make a recommendation to the Chair of the Department for a final decision.
Time to Degree
The faculty of the department shares the national concern with the increasing time to achieve the Ph.D. degree. Our goal is to reverse this trend. Students typically complete their graduate training 4 to 6 years from their entry into the graduate school. Written permission of the mentor, the student advisory committee and the Chair of the Department of Biochemistry is required for study to continue beyond 6 calendar years. The Graduate School requires that students admitted to doctoral programs register each semester, unless a leave of absence has been applied for and granted. This requirement applies to students engaged in thesis research who are not enrolled in any courses.
Members of the Graduate Faculty in Biochemistry serve as thesis research advisors for Ph.D. research. The Graduate Faculty of Biochemistry are tenure-track faculty with a primary appointment in the Department of Biochemistry or with a secondary appointment in Biochemistry and a primary appointment in a clinical department that does not grant a Ph.D. degree (e.g., Medicine). Permission of the Chair of the Department of Biochemistry is required of faculty with a secondary appointment in the department to serve as a thesis research mentor. Emeritus Professors are not eligible as Ph.D. mentors of Biochemistry Graduate Students.
Acknowledgement of Research Support – All publications, theses, reports, etc. resulting from research conducted during the candidate’s degree program must include an appropriate acknowledgement of the sources of funding. Examples include research grants to the faculty sponsor, training grants, equipment grants for equipment essential to the research, core facilities, scholarship support provided by the school, and fellowships from external sources.