Wesleyan Department of Molecular Biology & Biochemistry Graduate Student Handbook


  • Welcome and Some Initial Advice

    Welcome to our Molecular Biology and Biochemistry Department and to the Ph.D. program at Wesleyan University. You have chosen to embark on the exciting prospect of earning a doctoral degree in the molecular and cellular life sciences, and more broadly on becoming a thoughtful and skilled scientist in those fields. Given the exciting and explosive developments in our area, there is no better time than the present to be embarking on your journey.

    We thought that it would be helpful to initially underline some major themes that will help you in making your transition into our graduate program. First, to succeed and excel in a Ph.D. program of any type, it is important to quickly recognize that your priorities and actions must be quite different than those during your undergraduate years, when a sole prioritization of your coursework was sufficient for success. Graduate study, by contrast, requires much more self-directed work as well as multi-tasking to be successful. You should always be reading scientific articles in your areas of interest on your own, and thinking deeply and critically about them. Remember also that science is its own language, and thus both formal and informal scientific discussions among your peers, as well as your professors, are a must if you are going to become an accomplished practitioner. You will also be splitting up your time between formal coursework (where you learn core theory), journal clubs and seminars (where you learn critical thinking and scientific literacy), rotations in faculty laboratories (where you learn methodology, how to design good experiments to test hypotheses, and also find a thesis lab), and teaching assistantships (where you learn how to teach effectively), and each of these areas will fully engage you, and thus defy the 40-hour workweek. You will soon get used to working long hours if that wasn’t a habit in your recent past.

    Beyond these obvious changes to your work life, there are more subtle adjustments that you will need to make to your learning style. You will be learning from a wider array of people at various levels: fellow graduate students that may be your senior or just have good ideas, professors that may spot something in your work that you may have overlooked, or undergraduates that give you feedback on your teaching effectiveness. In short, collaborative learning, intellectual maturity and tact, and careful discernment about the true merits of ideas and how to successfully implement them will be required to negotiate this new learning space and make the most of it.

    Of course any major transition in one’s life is met with both excitement and anxiety. However, we are confident that you will rise to the occasion and succeed, and we are here to help you in any way that we can. The first of this aid is to offer you a brief guide to the structure of our graduate program here at Wesleyan University. This brochure focuses specifically on our department. Please note that another, more service-oriented brochure for all Wesleyan graduate students is available online from our Office of Graduate Student Services. The Table of Contents from this latter brochure is included at the end of this document for your information.
  • Overview of the Ph.D. Process

    Most of this brochure is dedicated to spelling out the details of the various stages in our Ph.D.-minting process. Our procedures and requirements are similar to many other Ph.D. programs in the Molecular and Cellular Life Sciences within the US. In particular, they include (1) a mixture of course work, journal clubs and seminars, laboratory rotations, and teaching assistant duties during the first couple of years of study, (2) choosing a thesis mentor(s)/laboratory after the first or during the second year of residency, (3) written and oral qualifying examinations during the second year of residency followed by admission to Ph.D. candidacy upon successful completion of both stages (Stage I: a comprehensive written examination, and Stage II: drafting a grant-style proposal on a topic of your choice, and orally defending it), and (4) supervision and approval of your Ph.D. thesis by your advisor along with a small committee of professors. These stages are spelled out in the relevant sections below along with other peripheral information that you should find helpful in settling into and thriving in graduate school.

Beginning Your First Year

  • Course Work

    Because you are busy with an array of different activities, first and second year graduate students typically take only 1 or 2, ‘lecture-style’, full (1.0) credit courses. There are a number of objectives in choosing your courses each semester: (1) to acquire good core knowledge in the areas of molecular genetics, molecular biology, biochemistry, and molecular biophysics and structural biology, (2) to experience and grow an area/areas of expertise suitable for thesis research and production, (3) to enroll in courses that will help prepare you for the qualifying examinations, and (4) to expand your horizons into other fields or specialties that will broaden you as a scientist and influence your post-graduate choices, and lastly and more logistically (5) to seize the opportunity to take a given course since it may be offered only once every year or every other year, and specialty courses may be offered even less frequently. Because of such curricular constraints, Third Year Graduate Students and beyond often continue to take additional courses that are not required as they expand their fields of expertise or finally get to take a course of interest that was not offered during their first two years in our program.

    The Advising Process

    You will be assigned to a First Year Graduate Student Advisor, who will meet with you at the beginning of your first semester to assist you in your course selection. Before you meet with her/him, be sure to go online into your electronic portfolio under WesMaps to look for available courses not only within the Molecular Biology and Biochemistry Department, but also for relevant courses within Chemistry, Biology, Physics, and Mathematics and Computer Sciences. Bear in mind that the first two weeks of each semester is the ‘add-drop’ period when you can add and drop courses freely (subject to course availability) in order to achieve the right course schedule. This allows you to assess your level of interest in a given course as well as to determine whether you are taking too few or two many courses given your other obligations.

    Minimal Graduate Course Credits

    Graduate students must take at least 3.0 credits of ‘lecture-style’ courses in order to be eligible to take the Stage I Qualifying examination, which is generally taken in January of the Second year.

    Graduate Course Grading Scale

    Incoming graduate students should be aware that they are graded on a different scale from undergraduates. Whereas undergraduates are graded on a traditional ‘A-F’ grading scale, graduate students are graded on an ‘A-C’ scale, where the various ‘A’ grades signify excellent knowledge and mastery of course material (factored up or down with + or – modifiers, respectively), B+ or B grades signify acceptable knowledge of course material, while a ‘B-‘ is a low passing grade, often signifying the need to do additional course work in that area in order to have sufficient knowledge and mastery of it. A grade of ‘C+’ or below is a failing grade, signifying the need for further course work in that area, and it will require repetition of the course or a facsimile (with the exception of journal clubs, seminars, or rotations).

  • Journal Clubs and Graduate Research Seminars

    In addition to taking 1 or 2 ‘lecture-style’ courses each semester during your first two years here, graduate students take at least one journal club as well as the Graduate Research Seminar Series each semester of residence. We host two journal clubs: one in molecular genetics & molecular biology (MB&B 585 Fall/586 Spring) and another in molecular biophysics, biochemistry and structural biology (MB&B 507 Fall/508 Spring). Initially it is advisable to take the journal club that corresponds to the field affiliation of your rotation advisor, and some more advanced students even elect to take both journal clubs in a given semester in order to broaden their scientific training.

    The Graduate Research Seminar series (MB&B 557 Fall/558 Spring) consists of research presentations by our graduate students as well as undergraduates doing Honors theses. First year graduate students give their seminars based on their rotation research at the end of each semester. Rotation talks are typically ~25 minutes in length with an additional ~5 minutes allotted for questions. It is advisable to give a practice talk ahead of your seminar in front of your rotation advisor (often done at a lab meeting with feedback from both students as well as your research advisor). Second year and higher graduate students, who have settled into a thesis lab, give longer talks that consume the entire class period (~50 min with ~5 min allotted for questions). It has been customary to excuse a graduate student from a final seminar in MB&B 557/558 if s/he will definitely be giving a public thesis defense seminar during their final semester of residency.

  • External Seminar Series

    The Biology and MB&B departments share an outside seminar series that brings in distinguished speakers from around the US and occasionally abroad. Attendance is a requirement. The seminar series is an ideal time for you to expand your knowledge of other fields, learn the intricacies of doing cutting-edge science, and giving polished professional talks. In addition, our graduate students meet informally with the seminar speaker over lunch, and such opportunities are valuable for professional networking (e.g. they have resulted in postdoctoral positions). We encourage our graduate students to meet as a group at least annually to invite a seminar speaker of interest to them.

    In addition to the Biology/MB&B seminar series, there are often important external seminars in other departments, particularly Chemistry and Physics. You should pay close attention to the seminar postings in the hallways and your email Inbox, and you should avail yourself of these valuable seminars as well. It is important to recognize that many of the most important scientific breakthroughs are occurring on the boundaries of two or more fields, so such seminars represent an ideal opportunity to broaden yourself as a scientist and potentially increase the impact of your science.

  • Rotations

    Incoming graduate students should arrange a laboratory rotation based on their field(s) of interest with one of the departmental faculty members or a faculty affiliate within one of our sister departments. A list of laboratories accepting rotation students is available from the Departmental Administrative Assistant (AA) in the MB&B office. Once you arrive at Wesleyan, you should approach (electronically or in person) any faculty member of interest to you and ask them for an appointment to sit down and discuss a potential rotation with them. Second rotations are conveniently arranged during the final few weeks of the previous semester. It is unwise to delay rotation selection, since rotation slots do fill up, or alternatively, faculty do accept other obligations (e.g. new undergraduate research students) and may be unable to start a rotation once the semester is underway.

    In sitting down with a potential rotation supervisor, it is important to clarify whether s/he is accepting new thesis students into her/his laboratory (rotation openings and thesis student opening are not always concordant). You may or may not wish to rotate with a professor if s/he is not accepting thesis students into her/his lab.

    Rotations are done on a semester-long basis, and graduate students generally do two rotations (Fall & Spring) before choosing a thesis advisor/laboratory. Occasionally a student may wish to do a third rotation (generally over the summer) before making their final decision. Two rotations are a requirement of our program with the exception that graduate students entering our program with a Masters degree may choose their thesis advisor/laboratory after a single rotation, but seek formal approval of this decision from the department, appealed through the department chair.

    It is important to recognize that choosing a thesis lab is a two-way street, and the PI needs to accept you into her/his laboratory as well as you wanting to matriculate into that lab. Therefore, a seriousness of purpose, hard work and scientific promise are important antecedents in the selection process. In addition to being assigned a letter grade in the rotation, PIs do also write up formal rotation evaluations that become part of your permanent record (i.e. they are contained in your electronic file).

  • Teaching Assistantships and Other Support

    Graduate students typically work as teaching assistants (TAs) during their first two years of study, and often longer, subject to the availability of grant funding in the thesis laboratory. Three semesters of teaching assistantship is our minimal requirement. 

    The Departmental AA will notify you of your TA course assignment at the beginning of each semester. In addition, you should initially register for the Graduate Pedagogy course during the fall of your first year (the course number is 500 and the department affiliation is based on the instructor which changes from year to year). This course is a teaching methods ‘nuts and bolts’ course that will help you improve your teaching skills. You only need to take this course once.

    Being a TA is an important part of developing your professional skills, regardless of whether you want to go into higher education, industry or government, since teaching, communication, and supervision skills are universally requisite for Ph.D.-level jobs. Therefore it is important that you allocate sufficient time and energy not only to successfully teach your students, but also to teach yourself as well. 

    Teaching assignments and their demands vary according to the course that you are assigned to. The department is aware of this fact, and we do try to rotate students in and out of more difficult TA assignments, subject to our ability to do so. It is important to point out that graduate students can learn a lot in the more difficult TA course assignments (e.g. upper level laboratories), and these courses can often become part of your teaching portfolio in your first academic job.

  • Development of Oral and Writing Skills and Resources

    The ability to speak and write science well is paramount to your success in it. Nearly all of the highly successful scientists that we have met over the years are excellent speakers and writers. Beyond our advice to practice speaking and writing science as much as possible, you should consider whether you need the resources of our ‘Writing Center’, that can assign you a tutor to help with your written compositions. This advice is particularly germane for ‘English as a Second Language’ speakers/writers. If you need this resource, the earlier that you visit the center, the more likely you are to successfully navigate your graduate career with us and thrive in the years beyond.

  • Policy on Vacation Time and Leaves of Absence

    In addition to the week between Christmas and New Year’s Day when many of us are away, our graduate students are allowed 3 weeks of vacation per year. It is important to communicate with your thesis or rotation advisor about your intended vacation time so that appropriate project coordination can be achieved.

    Given the expense of traveling abroad, foreign students sometimes accumulate their annual vacation time and use it once every two years. If any visa issues are anticipated, it is important that a foreign student has solicited the help and advice of the appropriate personnel in the Office of Graduate Student Services. Lengthy delays in re-entry into the US have occurred with certain of our students in the past, and such episodes have the potential to delay your progress through our program.

Completing Your First Year

  • Choosing a Thesis Advisor/Laboratory

    Choosing a thesis advisor/laboratory is a multi-faceted decision. You need to think carefully about several things: (1) both your short and long term interest in the proposed field of study and what you want to do with your training post graduation, (2) your intellectual and personal compatibility with your potential thesis advisor and her/his style of training, (3) your aptitude for the proposed field of study, and your advisor’s productivity with similar students in terms of publications and eventual job placement (the latter is not applicable for new faculty members, who are in the process of establishing such a track record). 

    Of course, having had a great rotation experience and enthusiasm for what you have done is a given, but the more thoughtful you can be about this important decision, the better off you are likely to be. Sometimes evaluating the progress of more senior students in that laboratory (if they exist) can be helpful in anticipating where you might be in 2 or 3 more years, if you think that such parallelism applies to your circumstance.

  • Attendance at Scientific Meetings and Conferences

    As you wrap up your first year in graduate school and have a more concrete idea of your field(s) of interest, you should consider attending one of the many scientific meetings or conferences that occur during the summer or coming academic year. If you have chosen a thesis laboratory, then your thesis advisor can discuss some logical potential meetings to attend. Such attendance is strongly encouraged, since it is an opportunity to be immersed in a particular field of molecular life science and to hear cutting edge scientists ply their trade. It is never too early to start networking with other scientists and their research groups, or to think about your science in a broader context and get important ideas from others.

    The department allots $1000 for each incoming Ph.D. student for attendance of scientific meetings and conferences, and additional funds are often available from your Ph.D. advisor or by application to our department through its chair. Once you decide on a particular meeting, then you should plan out the finances. Sharing a hotel room with another fellow graduate student is often a mechanism to stay within budget. Be sure to touch base with the AA in planning out your meeting as well as to save all your receipts for reimbursement. If you need to make a payment in advance of attendance and this is difficult for you to afford, often the AA can help pay for it with departmental funds.

    You should also be aware that our Molecular Biophysics Program has an annual 1-day retreat at the Wadsworth Mansion in the latter part of September. The program includes a number of excellent internal and external speakers, including an illustrious guest speaker, as well as a student-led poster session.  Working around the constraints of your course and teaching schedule, you are required to attend this retreat even if you are not considering becoming a member of the Molecular Biophysics Program, since you are guaranteed to learn some important science in a beautiful and convenient setting.

  • Planning Next Year’s Course Work
    As you complete your first two semesters with us, you should plan out your course work for next year (you can obtain next year’s graduate course offerings from the AA or your First Year Advisor, if they are not yet available on WesMaps). You also need to think about what gaps you may need to fill with self study in order to adequately prepare for the Stage I Qualifying exam in January. Finally, as you finish your first year in graduate school, it is also a time for self-assessment. How am I doing? Is my method of study effective to master the material? Am I reading the literature enough—particularly in potential thesis areas? How are my scientific literacy skills progressing? Have I made good progress in my rotations and my bench skills? Am I ready to choose a thesis advisor/laboratory? If so, why or why not? Based on the particular area of self-assessment, speaking with your first year graduate advisor, a course Instructor, or your rotation or potential thesis advisor should be helpful in your deliberations and conclusions.
  • Preparing for Qualifying Examinations

    The summer between your first and second year in graduate school is an important time to excel in your thesis laboratory, if you have chosen one by this time. It is also an important time to begin preparing in earnest for the Stage I Qualifying examination that you will ordinarily take the following January. As you evaluate your past and intended course work and knowledge gaps, you should also obtain the faculty reading lists for the qualifying examination (described below) from the AA and begin to study and work up that material during the summer and fall months. You should also obtain a copy of the previous year’s examination in order to know the approximate depth of coverage of the relevant topics (based on the complexity of the questions and expected length of the answers). In addition, rising second year graduate students have often self-initiated a qualifying examination study group among themselves that met weekly in order to tackle the relevant subjects in a group manner.

Second Year Matters

  • Candidacy

    Advancement to candidacy for the Ph.D. degree includes three important steps:

    1. Taking a written qualifying examination normally during the second week of January of the second year (referred to as Stage I of the qualifying process).
    2.  Writing an NIH-style Research Proposal normally due the first Monday after Spring break.
    3. Giving an oral presentation of your research proposal, which is examined by a committee of Faculty who has read your research proposal.  The oral exam should be held sometime during the second week after spring break (items 2 & 3 are referred to as Stage II of the qualifying process).
  • Guidelines for the Qualifying Examination: Stage I


    Normally our students have prepared sufficiently during their first 3 semesters in our graduate program to take the Qualifying examination on time. However, students who feel the need to delay the examination should discuss their concern with their second year graduate Advisor and their thesis Advisor, and based on these conversations, they can seek departmental permission for a delay (typically one year) by submitting a brief petition to the faculty (through the Departmental Chair).


    You are eligible to take the Qualifying examination only if (i) you have taken at least 3.0 credits of lecture-style graduate courses and have received a grade of B- or better in all of them, or (ii) you petition the Faculty and receive permission to take the Qualifying examination despite deficient performance in a graduate course(s).  You are reminded that a grade lower than B- is considered failing in a graduate course, and all failed courses (with the exception of rotations, graduate seminars and journal clubs) must be retaken or replaced with a suitable course in a comparable subject area (approved of in writing by the class-year graduate or thesis Advisor).  

    Submission of Faculty Syllabi to Students

    During the spring of a given academic year all faculty will submit to the Administrative Assistant a brief list of topics that may be covered on their Qualifying examination question(s) along with appropriate reading lists.  This material will be collated by the AA and distributed by July 1 to students taking the qualifying examination in January. The AA will also ask Faculty for updates to their syllabi over the summer, and ensure that a complete set of updated syllabi are distributed to appropriate students by September 1.  Such syllabi are not an all-inclusive guide for preparation for the examination, but they should be very helpful. In order to gauge the scope, depth and rigor of the upcoming examination, students are encouraged to look at questions from the previous year’s qualifying examination (available through the AA). 

    Submission of Qualifying Examination Question(s)

    All Faculty will help design the Qualifying examination by submission of one or more questions to the two Faculty members in charge of the examination (the examiners: one in charge of questions in molecular genetics and molecular biology, and the other in charge of questions in biochemistry, molecular biophysics and structural biology).  The questions should test both general and specific knowledge in these fields with some reference to the course background that we have offered to the graduate students at the time of the examination. Each question should be marked as to whether it is an elementary or advanced question. Students should be able to answer any given question within a one-hour period.  Questions should be submitted to the Examiners no later than January 2nd.  The Administrative Assistant should send out a solicitation for questions to the Faculty by December 1.

    Design of the Examination

    The examination has two sections, which are given on consecutive days: (Section I) questions relating to molecular genetics and molecular biology, and (Section II) questions relating to molecular biophysics, biochemistry and structural biology.  There will be 5 questions for each section. Students specializing in molecular genetics and molecular biology will answer any 4 questions from Section I, and any 2 questions from Section II. Students who are specializing in molecular biophysics, biochemistry and structural biology will answer any 2 questions from Section I, and any 4 questions from Section II.  In addition to answering these 6 total questions (2 from one section, 4 from the other section), the examination will contain a question in the area of Biochemistry, which all students answer during the Section II examination day. Alternatively, students may instead demonstrate competency in the area of Biochemistry by receiving a grade of “B” or better in the MB&B 383 Biochemistry course (typically offered during fall semesters) prior to taking the examination, in which case they would not need to answer the Biochemistry question on the examination.

    Implementation of the Examination 

    The examination will ordinarily be given on Monday and Tuesday of the second week of January. The Examiners will inform the students of proper conduct during the examination.  The following rules must be adhered to:

    1. You will have all day (9 AM to 4 PM) to complete each part of the examination.
    2. You should answer each question on a separate Blue Book. 
    3. You must adhere to the Wesleyan University honor code.  In particular, you are on your honor not to consult with any written material (notes, journals, books, etc.) or any other student or individual during the examination.
    4. The site of the examination is at the examiner’s discrimination.  Often a departmental classroom or conference room is reserved. 
    5. You are accorded brief breaks as needed, but you are on your honor to comply with all rules.  The AA will coordinate lunch for the students.   


    The Examiners will return student's answers to individual Faculty for grading.  Once Faculty have assigned a letter grade to their question(s) and have made appropriate comments, they should communicate their grade to the Examiners and the AA and return the Blue Book to you.  The AA will prepare a summary sheet of student performance for each question for the next Faculty meeting, which ordinarily should be held within 1-2 weeks after the exam. The Faculty will discuss each student's performance on the examination, their course work, laboratory work, and all other matters germane to their academic performance and promise in our Graduate Program.  Individual circumstances and special backgrounds of students will be duly noted at this time. Based on these deliberations the Faculty will generally recommend one of the following course of actions:

    1. If you received a passing grade on all of the exam questions, and there are no serious concerns regarding your academic performance, then you will be allowed to proceed immediately to Stage II of the qualifying process.  If serious concerns exist, the Faculty will take whatever actions it considers are in your best interests and that of the Graduate Program. 
    2. If you received a B- on any of the questions on the exam, then this will be considered a “low pass” and you may be given additional reading or be required to participate in a course on the subject. You will often be allowed to proceed immediately to Stage II of the qualifying process, if the Faculty concludes that you are likely prepared for the challenge.
    3. If you received a failing grade (C+ or lower) on one of the exam questions, and there are no other serious concerns regarding your academic performance, then you have two options: (i) you can be re-examined on the failed question(s) by answering (orally or in written form at the discretion of the relevant Faculty member) a new question(s) composed by that Faculty member within 30 days after receiving written notification of unsatisfactory performance, or (ii) you can take a graduate course in the failed subject area(s) within one year and receive a passing grade (B- or better).  If serious concerns exist at the time of evaluation, or if you fail the make-up exam question or course, the faculty will take whatever actions it considers are in your best interests and that of the Graduate Program.
    4.  If you received a failing grade (C+ or lower) on two or more of the exam questions, then the faculty will have discussed your case at length and arrived at one of the following courses of action: (i) you will be asked to re-take the entire examination or significant portions of the examination within one year, or (ii) you will be dismissed from the Ph.D. Program.  Which option is pursued is at the discretion of the Faculty and will be based on your record and demonstrated promise to date. 

    The recommendations of the Faculty will be communicated to you both orally and in writing by one or both examiners.  Letters should be sent to you within one week of the relevant faculty meeting or no later than 3 weeks following the examination.  Copies of the letter should also be sent to your intended thesis advisor and AA and placed within your electronic file (e-file) in the Departmental WesFiles server.  Letters requiring a student to leave the Graduate Program require the Department Chair’s or Graduate Program Director’s signature in addition to the Examiners, and copies of this letter should be sent to the student's intended thesis Advisor, the AA, the Graduate Office, and placed within the student's e-file.

  • Guidelines for Qualifying Examination: Stage II Proposal and Examination

    Upon successful completion of the Qualifying Examination (Stage I) you will proceed to the second stage of the qualifying process, which includes drafting of a research Proposal and its oral defense.  Students who passed the Qualifying Examination must have made up any deficiencies by this time or be enrolled in or intending to enroll in the appropriate fall semester course in order to be allowed to proceed with a proposal.  You may write a proposal on any topic within the department’s array of fields (molecular genetics, molecular biology, biochemistry, molecular biophysics and structural biology), providing that it meets with the approval of your thesis advisor and they agree to supervise its preparation.  Topics generally include, but need not be limited to, your intended area of thesis specialization. The proposal should be original in nature, and it should follow the format of an NIH research proposal (see below). The thesis advisor may lend whatever aid they see fit. Such aid normally includes (i) discussion of the research topic with you and help in broadening or narrowing its focus, (ii) suggestions with the literature, (iii) feedback on your outline of the proposal (that was sent to your thesis Advisor by February 1), and (iv) feedback on your rough draft of the proposal (that was sent to your thesis advisor no later than the first day of Spring Break unless s/he needs it sooner).  Although such guidance is encouraged, it is your responsibility to uncover all the literature pertinent to the proposal, read and distill it, and write an original, focused research proposal of the highest quality both in regard to style and content. You should have been reading the literature regularly during your first and second years in preparation for your proposal. During this period you and your thesis advisor should also select an examining committee consisting of 3 departmental (or affiliated) faculty, of which one member needs to be designated and willing to serve as Chair. Normally Faculty members who constitute the Examining Committee are chosen from within the department, but if circumstances warrant, a faculty member outside of the department can be included as long as they meet with departmental approval. The Chair of your committee should be a member of the MB&B Department.  In order to insure your complete autonomy during the oral examination, the thesis advisor is excluded from the Examining Committee. Care should be exercised in the selection of your Examining Committee, since at least two of its members will ordinarily matriculate to your Thesis Advisory Committee (see below). You need to distribute final copies of your proposal to members of your Examining Committee by the first Monday after spring break.  Preferably before that time, you should have also consulted with them and set a specific time for the oral examination, which should be held sometime during the second week after spring break.  You should also book a room with computer projection capability for the oral examination with the aid of the AA.  

    Format of the Proposal

    The proposal should follow the format of an NIH research grant proposal.  There is a 10-page limit (10 font, 1 inch margins all around, single spaced) excluding figures, tables, and references.  In particular the proposal should be divided into the following sections: 

    1. Specific Aims.  List the broad, long-term objectives and describe concisely and realistically what the specific research described in the proposal is intended to accomplish and any hypotheses to be tested.  0.5-1 page recommended.
    2. Background and Significance.  Briefly sketch the background literature to the present proposal, critically evaluate existing knowledge, and specifically identify the gaps that the project is intended to fill.  State concisely the importance of the research described in the proposal by relating the specific aims to the broad long-term objectives. 2 pages recommended.
    3. Research Design and Methods Including Any Preliminary Studies.  Describe the research design and the procedures to be used to accomplish the specific aims of the project, along with any progress made by the student to date.  Include the means by which the data will be collected, analyzed, and interpreted. Describe any new methodology and its advantage over existing methodologies. Discuss the potential difficulties and limitations of the proposed procedures and alternative approaches to achieve the aims.  Provide a tentative sequence or time-table for the investigation. 6.5-7.5 pages recommended.
    4. Significance and Future Directions (optional).  If you have not already done so in section 2, then it may be helpful to conclude the proposal with a section summarizing the overall significance of the proposed studies to the field and indicating any long-term future directions that may be anticipated by you, but which are beyond your participation in the project. 0-0.5 pages recommended.
    5. References.  Use a format that includes titles of each article.
    6. Figures and Tables.  Use figures, tables, and flow-diagrams to aid in the clear and succinct presentation of the proposal.  These items should be helpful as audio visual aids during your oral presentation. It is often best to embed the figures and tables at the relevant section of your proposal in order to aid the reader in following your logic.

    Common Deficiencies in Past Proposals

    While it is difficult to anticipate each and every student deficiency in preparing a proposal, there are a number of common problems that routinely occur: (1) Students don’t know how to properly write Specific Aims. A given specific aim must (i) identify the gap in the literature that it intends to address, (ii) state a hypothesis that will be tested, (iii) provide the approach or methodology that will utilized to test that hypothesis, and (iv) indicate the anticipated result(s) and its significance. These four objectives are achieved in 1 or 2 succinct and well-crafted sentences. (2) Students provide too many specific aims that go well beyond the ability of a single student to accomplish within a 3 or 4 year period. (3) Students have an inadequate review of the relevant literature with insufficient depth or breadth in their area, and/or they are not sufficiently knowledgeable or critical of what was done previously. (4) Students have an underdeveloped Research Design and Methods section with insufficient detail about necessary controls that need to be included in order to properly interpret the data, and/or lack back-up or alternative plans in cases where proposed experiments may fail or give unexpected results for unknown reasons. Even if a given experiment works, it is often best to try to prove something in two different ways in order to be thoroughly convincing (e.g. often required to publish it). (5) Students often fail to put their anticipated results into a broader context that makes the most out of their proposed dataset(s). Many of these problems ultimately relate to insufficient time and effort being invested by the student in reading the relevant literature during her/his first 3 semesters in graduate school or spending insufficient time in the laboratory with the thesis advisor in rigorous scientific discussions of the project.

    Oral Examination

    You should prepare a ~50 min presentation of your proposal with appropriate illustrations.  After allowing for questioning during this period, the actual presentation will generally take ~1.5-2 hrs.  The examination will emphasize the proposal, but it includes broader topics in molecular genetics, molecular biology, biochemistry, molecular biophysics and structural biology, particularly those areas that impact the proposed research.  Immediately before or after the presentation, the Examining Committee may question you on your performance in any courses, rotations, or the Qualifying examination (Stage I) in order to solicit information that it will need to evaluate your overall performance and promise in our Ph.D. Program.  Following this, the committee will excuse you from the examination to confer and reach its recommendations before calling you back to convey its findings. During the examination and deliberation by the Examining Committee, the Chair will keep notes regarding your evaluation that serve as a basis for both oral and written communication with you (see below).


    The Examining Committee will meet with you immediately following its deliberations to communicate the results of the examination.  The committee chair will tell you whether you passed the examination or not, and each member of the Examining Committee will point out the strengths and weaknesses of your proposal and defense, as well as discuss any other concerns that it has with your performance to date in our Ph.D. Program.  The recommendations of the Examining Committee will then be considered in a Faculty meeting along with your entire performance in the Graduate Program. Based on its deliberations the Faculty will decide on one of the following actions:

    1.  If you received a passing grade on your proposal and defense, then you will be admitted to Ph.D. Candidacy.
    2.  If you received a conditional passing grade on your proposal and/or defense, then you will need to thoroughly satisfy the conditions set out by your Examining Committee as well as any other requirements of the Graduate Program in order to be admitted to Candidacy.    
    3.  If you received a failing grade on your proposal and/or defense, but your overall academic record is good and the Faculty feel that you show promise, then you may be allowed to write another proposal or revise the present one and defend/re-defend it. This course must be completed within one year of the date of the first defense, but it may occur much sooner depending on the circumstances surrounding the case and under the direction of the Examining Committee. If you fail to receive a passing grade during re-examination, then you will be dismissed from the Ph.D. Program. You may be allowed to complete a terminal Master’s Degree (subject to approval of the faculty and thesis advisor).
    4. If you received a failing grade on your proposal and/or defense, and the Faculty feel that there are serious academic deficiencies that are evident in your record, then you will be dismissed from the Graduate Program.  You may be allowed to complete a terminal Master’s Degree (subject to the approval of the faculty and thesis Advisor).

    The Chair of the Examining Committee will send written notification of the faculty's recommendation to you, typically within one week following the faculty meeting during which results are discussed. Copies of this letter should be sent to your thesis Advisor and AA, as well as placed within your e-file.  In cases that involve a student’s dismissal from the Graduate Program, the Chair of the Examining Committee should obtain the signature of the Director of the Graduate Program or the Departmental Chair, and copies of this letter should be sent to the student's thesis Advisor, AA, the Graduate office, and placed within their e-file.

  • Choosing a Thesis Committee

    Upon receiving notification of advancement to Candidacy, you and your thesis advisor should form a Thesis Advisory Committee.  You should give this matter careful thought to ensure that your Committee has the appropriate expertise and depth to provide you with the best possible advice in the coming years. The committee must consist of at least two Faculty members in addition to your thesis advisor, but students not uncommonly add an additional Faculty member that brings needed expertise or perspective to the table.  Of these members, one (not the Advisor nor a Faculty member outside of the MB&B department) should be asked by you and agree to serve as Chair of your committee. Typically, faculty who were on your Stage-II Examining Committee are enlisted to serve on your Thesis Advisory Committee, although you and your thesis Advisor are free to make any necessary changes that enhance the advising and oversight process.  An additional, expert Faculty member outside of Wesleyan sometimes joins the committee, but s/he need the approval of the Faculty and often is added at a more advanced stage of thesis research as warranted. You should send the names of your committee members to the AA within one month of receiving your letter of Advancement to Candidacy, and the AA will distribute them to Faculty in a timely fashion.

Candidacy and Completion

  • Annual Thesis Committee Meetings
    Our Doctoral Program requires you to have at least annual meetings with your Thesis Advisory Committee, and more frequent meetings are often requested by the committee or you for cause. You should not be shy about soliciting help from your Committee, particularly when you are having difficulties with your experiments and an outside perspective might be helpful.  Annual meetings should be scheduled within one or two weeks following your presentation in our graduate research seminar series (MB&B 557/558).  It is your responsibility to schedule these meetings and to book a room for them (with the assistance of the AA). At least one week prior to your committee meeting, you should provide the Committee with a detailed written Progress Report of your thesis research that includes important figures and tables (up to 10 pages is typical). As you progress through your dissertation research and have more of a story to tell, these Progress Reports should naturally transition into the format of a publication, and you should also forward copies of any of your thesis publications (as PDF files) to your Committee members prior to the meeting. Within one week following such meetings, you are also responsible for sending your Committee Chair a brief Summary (typically 1-2 pages) of the Committee’s major comments and recommendations as well as complying with any other stipulations that were made during the meeting (e.g. revision of your Progress Report is not an uncommon request).  The Chair will add whatever comments they deem appropriate to your Summary and return it to you and the other Committee members for the record.
  • Notification of Intent to Complete a Ph.D. Thesis
    In addition to the normal meetings with your Thesis Advisory Committee, you should meet with them approximately 6 months prior to your anticipated thesis defense and discuss your plans for finishing your dissertation and graduation. This is an important meeting where your Committee and you need to reach a mutually agreeable template for completion of your outstanding work. As in annual Committee meetings, the same reporting requirements are expected (i.e. need for a Progress Report preceding, and a Summary following the meeting). The normative standard for receiving permission to defend your thesis is the completion of at least one peer-reviewed first-author publication and with a second peer-reviewed publication in progress. In addition, your Thesis Advisory Committee evaluates your readiness for a Ph.D. defense more broadly, including strengths/weaknesses in the lab, written and oral abilities, knowledge in the field, etc.
  • Completion of the Ph.D

    Completion of a Ph.D. thesis is a complex process, so you need to pay close attention to its various requirements in order to successfully negotiate it while preserving a professional sense of calm in yourself and those around you. 

    Scheduling Your Thesis Production

    You should check with your thesis advisor to work out a satisfactory schedule for the preparation, writing, and revising of your thesis.  You should also meet with the staff in the Office of Graduate Student Services in order to be aware of the various deadlines for submission of your thesis title and Committee-approved thesis to that office, as well as the required Exit interview, in order to obtain your Ph.D. degree in time for Commencement. A list of requirements is available both online and in written form from the Office of Graduate Student Services. The timing of these processes may be more flexible if you are not trying to complete your thesis during the spring in time for Commencement (in which case your official graduation date will be the following spring). 

    Distribution of Your Thesis and Setting a Defense Date

    Once a satisfactory copy of the thesis has been produced, you should distribute it to your full Thesis Advisory Committee, along with your publications (as PDF files), and schedule a Thesis Defense date with your Committee members that allows them at least 2 weeks to read and critique your thesis. Given busy and often conflicting faculty schedules (particularly toward the end of the spring semester), it is often advisable to work out a Thesis Defense date before distribution of your thesis.

    Your Thesis Defense

    Your thesis defense is not unlike a normal committee meeting with a presentation interrupted by faculty questions and comments. However it is best to prepare a flexible presentation in case the Committee asks you to skip over some part of your work or briefly summarize important, but older findings. Most Committees tend to emphasize your most recent work, which is explored in greater detail during a defense, since it is assumed that older work has already been reviewed. You will be examined orally at the defense, and any recommendations for additional work or thesis revisions will be communicated to you and your Advisor (often marked up versions of the thesis are conveyed to you by individual committee members).  After asking you to step out of the room for a few minutes, the Committee will carefully discuss the thesis and your defense, and it will take a vote with the following three options: pass, conditional pass, or fail. A pass is contingent on satisfactory completion of any recommended (often minor) changes to the thesis (the Advisor normally monitors this task on behalf of the Committee). A conditional pass will be granted when the Committee has determined that additional experimental work is needed to complete the thesis, and this option may or may not necessitate a second defense depending on the importance of the outstanding work (it is not uncommon for the thesis Advisor to monitor and affirm that this condition has been met without the need for another meeting). A failing determination is made if the thesis is poorly conceived or written, or alternatively, if the student is unable to adequately orally defend it. In either case, this option will necessitate a second defense. Once the Committee has reached its decision, you will be called back into the room, and the Chair and other members of the Committee will give you their determination along with sufficient detail to understand all corrective and performance-related matters. Last but not least, you should remember to bring the necessary paperwork for the Committee members to (hopefully) sign in order to grant the Ph.D. degree (available from the Office of Graduate Student Services and online). Of note, you officially obtain your Ph.D. degree status upon completion of the defense and your Thesis Committee signs the defense form that specifies that you have met all degree requirements, after which you are eligible to begin post-doctoral work even if your formal graduation occurs at the following year’s Commencement. 

    Your Public Seminar

    After successful completion of the Thesis Defense, you should schedule your Public Seminar at a time that is mutually agreeable to all parties (typically within one week of the Thesis Defense). The AA can help you with room scheduling, as well as advertising the event.

Postdoctoral and Job Advice

  • Professional Development

    It is never too early to have a vision about what kind of career you might wish to pursue. Indeed, such reflections are probably one of the reasons that you are in our Program today. Attendance at scientific meetings and conferences can help to bring career options into sharper focus, since among other things, they often have job boards and interview tables as well as career panel discussions incorporated into their structure. In addition, a number of the major scientific societies in our array of fields (e.g. The Genetics Society of America, The American Society of Biochemistry and Molecular Biology, The American Biophysical Society, The American Society for Microbiology, The American Chemical Society, etc.) have online Career Advice and Job sites that are important resources for career education and job placement. The Office of Graduate Students Services has also started hosting an annual career panel for our graduate students.

    It is important to recognize that Ph.D.-level job placement is not a rapid process, so it is a good idea to start looking for job opportunities once you are within 6 months or even 1 year from finishing your degree. Each type of job has its own time delay, so it is important to do some research in your chosen area to discern when job applications need to be made in order to land the right job shortly before or soon after your graduation.  Most employers of Ph.D.-level scientists know that it is normative to wait a couple of months for you to finish your thesis (particularly in cases of future postdoctoral advisors), so a precise finishing date is typically not an impediment in your job search.

  • Postdoctoral Study

    For those of you who are interested in pursuing postdoctoral training, you should consider a postdoctoral position that will broaden you in some manner (e.g. changing field, methodology, or system), since expanding your theoretical and experimental skill set will make you a better, and thus, more valuable scientist on the job market. Scientists with postdoctoral experience on their resumes often have the upper edge in job hiring, and the starting pay scale is typically higher as well. 

    Choosing a Postdoctoral Advisor

    All other things being equal, it is best to try to get a postdoctoral position with a top investigator and often at a well-recognized (i.e. prestigious) institution. Top investigators typically have the best track record of production of outstanding science and strong job placement of their students. Beyond this simple albeit general and thus incomplete rule, it is important to research a potential postdoc advisor/laboratory to find out their current publication track record, recent grant history, and hopefully visit or be interviewed to assess the environment first hand. Given the limited number of great labs with openings in them, it is prudent to cast a wide (i.e. national or international) net and apply for a number of postdoctoral vacancies, since such positions are highly competitive.


    When interviewing for a job, make sure that you have done your homework ahead of time. Read a number of recent papers from that PI (and even their competition), read about their most current work (typically summarized on their website), and be prepared to discuss it in an engaged fashion, hopefully having formulated some good questions or ideas of your own to display. Most potential PI’s ask for a presentation of your thesis work (often before their research group), and visits with group members are also interview situations for both parties (PI’s will ask their group members for their impressions of you, so don’t let your guard down).

    Job Timing

    It is important to try to get your various job applications and interviews on the same time line, since when a job offer does come, you may only have a couple of weeks to reach a decision. You will need to quickly assess the quality of the environment and the specific training offered as well as your interest in it, your ability to succeed in that environment, the terms of the contract (length of time, pay/benefits, etc.).

  • Other Types of Positions
    It is common for Ph.D.-level scientists to find employment opportunities in a variety of types of jobs within government and the private sector. The wide swath of possibilities defies generalizations here. It is probably accurate to say that a given position within industry or government looks for a more specific skill set than a postdoctoral advisor, who is likely to also consider your potential for breaking new ground and expanding your potential in unanticipated directions. Therefore, when considering an industry/government opportunity, it is prudent to pay careful attention to the set of qualifications and tasks when answering a given job advertisement. If fitting yourself into that job is a stretch in your mind, then you will probably not be competitive within the applicant pool.

Frequently Asked Questions

  • General FAQs
    1. My spoken and/or written English is weak; what can I do to improve it? Wesleyan has a Writing Center that can help you hone your spoken and written English skills. Please go to that office for help. The sooner and more often you do it, the better the outcome will be. See section on Development of Oral and Writing Skills and Resources above.
    2. I need to petition the department about an item. How do I do that? Petitions generally originate with the departmental Chair, and are brought up at the next available Faculty meeting. You should speak to the Chair to discuss your problem and the format of the petition, which may or may not be required depending on the outcome of your meeting with her/him.
    3. I have a general question; who do I seek to answer it? The answer depends on the nature of the question. You can start by asking the AA within the departmental office, who can refer you to the appropriate person if they cannot address it.
    4. I am going to a Scientific Meeting; who can help pay for it? The department budgets $1000 for Ph.D. students to go to scientific meetings, and often your thesis Advisor or the Department can come up with more funds, if necessary. See section on Scientific Meetings and Conferences above.
    5. Does the department have a policy about my vacation time (timing and length)? Yes, the week between Christmas and the New Year is a de facto vacation week, and you are allowed an additional 3 weeks of vacation time per annum that does not interrupt your course, rotation or thesis work. See section on Policy on Vacation Time and Leaves of Absence above.
    6. I have a personal problem; whom should I speak to? Wesleyan has a number of resources depending on the nature of the problem. It is probably best to initially speak on a confidential basis with either the Department Chair or the Director of the Office of Graduate Student Services, who can refer you to the appropriate person. Advanced graduate students who have a close relationship with their thesis Advisor may wish to consider consulting them as well, since beyond any aid that they may be able to offer you, it is likely that the problem has or will affect your productivity in the lab, and they should be made aware of this fact.
    7. I have a Visa problem; whom should I speak to? The Office of Graduate Student Services can refer you to their legal council on campus.
    8. How many semesters do I need to TA? Three semesters is the minimal requirement, although four semesters is more normative. You may need to TA additional semesters depending on your source of support for your thesis Advisor/laboratory.
    9. I am not happy with my TA assignment; what do I do? The departmental Chair in consultation with the faculty and AA make all TA assignments. We try to balance those assignments as fairly as possible over the course of your years with us. You can discuss the matter with the Chair.
    10. I am having trouble with one of the undergraduates in my TA section; what should I do? The first course of action is to have a confidential discussion with the course instructor. Depending on the nature of the problem, they may refer you elsewhere.
  • FAQs on Courses
    1. How many lecture-style courses are required for the degree? Three full (1.0) credit courses or a number of lecture-style courses that add up to the requisite 3.0 credits.
    2. How do I know which Journal Club to register for? Students should generally register for the Journal Club that coincides with the field affiliation of their rotation supervisor or their thesis Advisor. Later in the program, it is not uncommon for advanced students to register for the other journal club in order to broaden their training, or even to register for both journal clubs in a given semester.
    3. Do I need to register for a Journal Club every semester? Yes.
    4. Do I need to register for the Graduate Research Seminar (MBB 557/558) every semester? Yes, with the exception of the final semester that you defend your thesis in, where such registration is optional.
    5. Is attendance at the joint Biology/MB&B Outside Seminar series optional, or should I attend only when we have MB&B speakers? No, attendance at ALL seminars is a requirement each and every week—no exceptions!
    6. What is a minimal passing grade for a graduate course? B-. See section on Graduate Course Grading Scale above.
    7. I received a C+ in one of my courses; do I need to repeat it? Yes, you need to repeat the course and obtain a B- or above, or you need to substitute it with a course of similar content and obtain at least a B-. See section on Graduate Course Grading Scale above.
  • FAQs on Qualifying
    1. What are the different stages of the Ph.D. Qualifying Process? There are two stages: a comprehensive written Qualifying examination (Stage I) generally taken in January of the second year, followed by a written Proposal and an Oral Defense of it (Stage II) taken later that spring. See section on Second Year Matters above. 
    2. Can I delay the Qualifying exam, and if so how long? Yes, if you provide a compelling Petition for cause to the Faculty, and they approve it, then you could obtain a 1 year delay or less depending on circumstances.
    3. If I delayed the Qualifying exam, would I still prepare a Proposal and Orally defend it that spring?  No, the Faculty would have deemed you underprepared for both requirements, and you would be need to complete Stage-II the following spring (one year later). 
    4. I received a C+ in one of my courses; can I still take the Stage I qualifying exam? No you cannot, unless you Petition the Faculty to do so, and they approve your request. See section on Guidelines for Qualifying Examination: Stage I above. 
    5. I failed one of the questions on the Qualifying exam; do I need to take the whole exam over again? No, you only need to retake that failed question within 30 days, or take a graduate level course that covers that material and obtain a grade of B- or better. These options will be discussed with you in order to arrive at the most suitable solution.
    6. I failed the Qualifying exam; can I redo it, and if so when? It depends on your level of failure as well as your overall record in our Graduate Program. If the Faculty allows you to retake the exam (they will notify you either way in writing), then it will occur within one year. See section on Guidelines for Qualifying Examination: Stage I above.
    7. Can I still write a proposal and orally defend it (Stage II) if I failed the Qualifying exam? If you failed a single question and have successfully passed the make-up question or will be registering for a graduate course in that area the subsequent fall semester, then the Faculty are likely to allow you to move on to Stage II, but it requires their explicit permission. If you failed two or more questions, then ‘no’ you cannot proceed to Stage II. You must either repeat the Qualifying exam or leave our program depending on your performance on the exam and program to date. The Faculty will make your options clear to you in writing. See section on Guidelines for Qualifying Examination: Stage I above.
    8. What are some of the most common mistakes in writing the Stage II Proposal? There are a number of them, which are listed in section Guidelines for Qualifying Examination: Stage II above.
    9. I have decided that a Ph.D. degree is not for me; can I get a Master’s degree? The answer to this question depends on how much progress you have made in your thesis laboratory and whether your thesis Advisor and the other Faculty believe that you can successfully finish the terminal Master’s degree expeditiously; this path requires permission from the department. You do not need to have gone through or passed the Stage I or Stage II Qualifying Process to receive a terminal M.A. degree.
    10. I completed the terminal Masters degree and would like to reapply to the Departmental Ph.D. program; is this allowed? Regrettably, no. If you want to obtain a Ph.D. degree, then you will need to apply to another school. 
  • FAQs on Thesis Production
    1. How many rotations should I do? Two rotations are standard, but some students do a third rotation (typically over the summer) before reaching a firm decision about a thesis Advisor and laboratory. Incoming students, who already have a Master’s degree, may be permitted to do just a single rotation after consultation with the faculty.
    2. Can I choose a Thesis Advisor outside of the MB&B department? Since students come to our department to specifically study our array of fields, they generally choose a Thesis Advisor among the MB&B Core or Affiliate Faculty. However, if you have had a highly successful rotation with a Faculty member in a related department (e.g. Biology, Chemistry, or Physics), then it is possible to make this choice, but it will require reaching an appropriate agreement between the two departments (via the relevant Chairs with Faculty approval).
    3. Who are the MB&B Departmental Affiliates that you refer to? These are faculty who are formally associated with our department and presently include Professors Weir (Biology), Smith (Chemistry), and Starr (Physics). 
    4. How do I choose a Thesis Advisory Committee? Your Thesis Advisor and you should carefully discuss this matter taking into account your need for various types of expertise and perspective in your intended thesis project(s).
    5. How often and when should my Thesis Advisory Committee meet? You are required to call an annual meeting of your Thesis Advisory Committee (typically immediately after your presentation in the Graduate Seminar series) as well as ~6 months prior to your anticipated Thesis Defense. However meeting more often with your committee and getting their perspective and input is a good thing and is often initiated by either party. See section on Completion of the Ph.D. above.
    6. What do I need to do before a meeting of my Thesis Advisory Committee? You should prepare a written Progress Report (typically ~10 pages including figures, tables, and references) and send it to your committee members at least one week prior to the scheduled meeting. You should work with your thesis advisor in drafting and revising that document before it is distributed. You also need to reserve a room for the meeting (often done via the Departmental AA). See section on Completion of the Ph.D. above.
    7. I am ready to defend my thesis; what do I need to do? You need to do many things that must be carefully orchestrated, often involving multiple parties. See section on Completion of the Ph.D. above for a complete list of instructions.