* Original version put together in the summer of 2004 (updated May 2005) by Dr. Carl Hashimoto (Director of Graduate Studies) and Rebecca Lackman (Cell Biology Ph.D. Student), with editorial input from Steve Becker, Mari Kawaguchi, Dr. Ira Mellman, and Jordan Yelinek. Please send any comments or suggestions for improving the handbook to carl.hashimoto@yale.edu.
Please confirm the currentness and accuracy of the contents of this handbook with your DGS and the Graduate School Registrar's Office.
This handbook is intended to be a source of information for graduate students studying for the Ph.D. degree in the Department of Cell Biology at Yale. Here, students as well as faculty should be able to find answers to questions that may occur to them from time to time about the Cell Biology Ph.D. program and its specific policies. The Programs and Policies bulletin of the Graduate School of Arts and Sciences (http://www.yale.edu/bulletin/html/grad/introduction.html), which is updated annually, is the definitive source of information about academic rules and regulations as well as general policies that apply to all graduate programs.
Students interested in pursuing a Ph.D. in Cell Biology apply to the Biological and Biomedical Sciences (BBS) graduate program, generally choosing the Molecular Cell Biology, Genetics and Development (MCGD) track as their primary interest on the application form. At the end of the 1st year, any student choosing to carry out thesis research in the lab of a faculty member with a primary or secondary appointment in the Cell Biology Department automatically enters the Cell Biology Ph.D. program. A student choosing to do thesis research that is cell biological in nature but in the laboratory of a faculty member not formally affiliated with the department can also request to be in the Cell Biology program.
Formally, to join the Cell Biology program, a student must fill out the “Advisor and Degree Program Selection Form” available from the BBS office (see Contacts below) and have it signed by the thesis advisor and DGS of Cell Biology. This form is submitted to the BBS office. The deadline is July 1.
Students should aim for finishing the Ph.D. in 5-6 years. Described below is an idealized timetable with major events of each year toward the Ph.D.
Year 1: Devoted mainly to laboratory rotations and coursework. Students do 3 rotations during the academic year in any of the labs in the MCGD track or in the wider BBS program. Some students occasionally elect to do a 4th rotation during the summer. By the end of the 1st year, students choose a lab in which to carry out thesis research.
Year 2: A major activity during this year is the qualifying exam, which is usually taken during the Spring semester. Course requirements are usually also completed this year. Students may teach during this year.
Year 3: This is the year that most students begin to devote full time to thesis research. Students teach; some complete the teaching requirement this year. Admission to candidacy usually occurs by the end of this year.
Year 4-5: Devoted mostly if not exclusively to thesis research. Even after fulfilling their teaching requirement, students may elect to teach as a teaching fellow for extra pay. Some students write manuscripts of their research to be submitted for publication. (By the end of the 4th year, a student should have a clear idea of the direction of the thesis project, as a period of only 1 year and 6 months is left to complete experiments and the dissertation for the March deadline to be awarded the Ph.D. degree toward end of the 6th year.)
Year 5-6: Finishing thesis research, writing the dissertation, and graduation! Manuscripts are also written during this time.
Students requiring additional time beyond the 6th year to complete the dissertation will only be allowed to register (and thus to receive financial aid and to use University facilities) with permission from the Graduate School. See Registration beyond the 6th year below.
The formal requirements for the Ph.D. in the Cell Biology program are successful completion of the course requirement, 2 semesters of teaching, the qualifying exam and a dissertation. Each of these requirements is described in detail below.
Students must meet the Graduate School requirement of a grade of Honors in 2 courses, if necessary taking additional courses beyond the 5 required in the department to fulfill this requirement.
Students must also maintain an average grade of High Pass in all courses.
2 semesters as a teaching assistant (TA) in any of numerous lecture, laboratory, and seminar courses offered at the undergraduate, graduate, and medical school levels. Students can also receive credit for teaching science to New Haven middle school students through the Science Education Outreach Program (http://www.yale.edu/onhsa/seop.htm). For further information, contact the director of the program, Paula Kavathas, Professor of Laboratory Medicine, Immunobiology, and Genetics (785-6223; paula.kavathas@yale.edu).
Courses having TA positions are listed on the “TA Position Form” available from the BBS office. During the summer, students formally request TA assignments by indicating their top 3 choices on this form, which they submit to the Cell Biology Registrar. The form in turn will be forwarded to the department giving the course that is the student’s first choice. The instructor in charge of the course ultimately chooses the TA’s. Students are encouraged beforehand to seek out the instructor of any course to express their interest in being a TA for that course (e.g., it is okay while taking a course to approach the instructor about being a TA the next time the course is offered; however, the instructor should not commit to any student prior to receiving the TA Position Form from all interested students). Students may start to TA in the second year.
The qualifying exam in Cell Biology consists of 1) a research proposal based on the thesis project, 2) two reading periods on topics broadly relevant to the thesis project, and 3) an oral exam in which the student is examined on the research proposal as well as the reading periods by the qualifying exam committee.
The qualifying exam committee consists of 3 faculty members, with at least one having a primary or secondary appointment in Cell Biology. It is common that 2-3 members of this committee will become the student’s thesis committee. The members of the committee are chosen by the student in consultation with the thesis advisor and with approval from the DGS. The student will read with two committee members and write the proposal with guidance from the third committee member.
The student will ask one Cell Biology faculty to be the chair of the committee. The chair is responsible for preparing, after the oral exam, a short assessment of the student’s performance in the qualifying exam to be emailed to the DGS and other members of the committee. The chair also acts as moderator of the oral exam.
The DGS should be contacted if any serious problem is encountered during the qualifying exam period.
The student should assemble the qualifying exam committee by mid-December of the 2nd year. The qualifying exam is taken in the following Spring term, and should be completed by July 1. Typically, 8-10 weeks are required from start to finish. During this period, students are allowed to take time away from laboratory work but are not exempt from classes.
The student reads with 2 committee members on 2 different topics broadly relevant to the research proposal, with each topic chosen in consultation with the committee member and thesis advisor. Each reading period consists of 5 or more sessions of about 1 hour per week. We recommend that the student do one reading period at a time. There is no prescribed number of papers that must be read during each reading period; however, it is expected that the student will delve deeply into the literature in order to become an expert in a field. The faculty and student together can decide how the reading sessions will be conducted (e.g., the choice and number of papers to be discussed).
The student will write the proposal (see guidelines below) with guidance from one of the qualifying exam committee members (the “writing faculty”). As one of the goals of the qualifying exam is for the student to learn how to write a research proposal, enough time should be allowed for several rounds of revision. The student should make the first version a best effort to be read by the writing faculty, who will provide critical comments or suggestions to improve the proposal. Only when this committee member decides the proposal is ready for distribution to the rest of the committee can possible dates for the oral exam be considered. It is acceptable for the student to discuss and to receive feedback about the proposal from the thesis advisor.
Please follow the format below for the qualifying exam proposal.
1) Specific Aims. State the specific purposes of the research proposal and the hypotheses to be tested. Should not be longer than 1 page.
2) Background and Significance. Sketch briefly the background to the proposal. State concisely the importance of the research described in the proposal by relating the specific aims to broad, long-term objectives.
3) Research Design and Methods. Describe the following:
The proposal should be single spaced in 12-point font with 1-inch margins and not exceed 10 pages including tables, figures and references.
Prior to the beginning of the actual oral exam, the student may be asked to step out of the room temporarily so that the committee can discuss the student’s performance in the reading periods and the quality of the proposal. The thesis advisor, who is present at the exam but does not participate, can also comment on the student’s performance in the lab. At the beginning of the exam, the student will give a short (15-20 min) presentation on the research proposal, including background, rationale, and aims. The actual presentation may take longer because the committee is likely to interrupt with questions about the research proposal. The committee may also ask questions about the reading periods. Typically, the exam lasts about 2 hours. At the end, with the student temporarily out of the room, the committee discusses the student’s performance in the oral exam before informing the student of their assessment. A student can receive a pass or a conditional pass contingent on fulfillment of an additional requirement, e.g., writing a paper to remedy an inadequate knowledge of the literature. (In other programs, students have found it helpful to prepare for the oral exam by taking a mock oral exam involving other students and postdocs.)
The prospectus is a statement of what the student intends to do for the dissertation, and an approved prospectus must be submitted to the Graduate School in order for a student to be admitted to candidacy. Because in Cell Biology the proposal for the qualifying exam is based on the student’s thesis project, it is de facto the prospectus, and thus successful completion of the qualifying exam means the student’s prospectus has been approved. After a student has passed the qualifying exam, the DGS will submit to the Graduate School a “Qualifying Exam/Prospectus Certification” for that student along with a copy of the prospectus. For this purpose, rather than writing a new document, students may provide to the DGS a copy of their qualifying exam proposal but with a cover sheet entitled “Prospectus” and containing all other information requested by the Graduate School not in the original written proposal (see p. 395 of Graduate School of Arts and Sciences Programs and Policies).
“Admission to candidacy indicates that the department and the Graduate School consider the student prepared to do original and independent research” (p. 396 Graduate School of Arts and Sciences Programs and Policies). In order to be admitted to candidacy, students must have fulfilled the course requirement, passed the qualifying exam, and submitted an approved prospectus. When a student has met all of these requirements, the DGS will submit to the Graduate School the “Certification of Admission to Candidacy” for that student. Admission to candidacy normally occurs by the end of the third year. A student failing to be admitted to candidacy by the expected time will not be permitted by the Graduate School to register for the following term.
In the years following completion of the qualifying exam, students are required to conduct yearly meetings with their thesis committee to chart their progress towards the dissertation. Students are required to provide (email or hard copy) a brief one to two page summary of their past work and future experiments to their committee members at least several days prior to the meeting. A copy should also be given to the DGS. Every year the DGS will remind students to schedule a meeting, and students should notify the DGS of the meeting date.
The thesis committee, which may have been the qualifying exam committee, must have at least one member who holds a primary or secondary appointment in the Cell Biology Department. One of these Cell Biology faculty members should be chosen to be the chair of the committee. After each thesis committee meeting, it is the responsibility of the chair to email to the DGS, as well as to other members of the committee, a brief report of the meeting.
Students and thesis advisors may choose to alter the composition of the thesis committee in order to reflect changes in direction of the thesis project. Any changes must be approved by the DGS. Thesis committee meetings may also be held more frequently if necessary at the request of the student, thesis advisor, or other committee members.
The thesis committee has the major responsibility of deciding when a student has done sufficient work for the Ph.D. and is ready to begin writing the dissertation.
A question that probably comes up now and then in the minds of students and faculty as well is, what qualifies as sufficient work for the Ph.D. (and thus for the student to be given by the thesis committee the go-ahead to write the dissertation)? Or in other words, is there a minimal requirement for the Ph.D.? A Ph.D. should represent an original scholarly contribution to one’s field, which in Cell Biology and other experimental sciences means that the student has successfully carried out a series of experiments to test a hypothesis and in the process has gained new knowledge that advances a field. Such an accomplishment usually culminates in a first author paper (several in some cases) published in a peer-reviewed journal, and in fact some departments require the submission of a paper as a minimal requirement for the Ph.D. While not having such a requirement, the Cell Biology Department does expect that at least one paper published in a peer-reviewed journal will result from a student’s Ph.D. research. This expectation is usually not difficult to meet, and highlights the importance of regularly scheduled thesis committee meetings to ensure adequate and timely progress toward finishing the Ph.D.
Before beginning to write the dissertation, please read “Preparation and Submission of the Doctoral Dissertation” (see “Where to get forms” below), and obtain a dissertation packet from the Graduate School. The dissertation packet contains several forms, including the “Notification of Readers Form” that must be signed by the DGS and submitted with the dissertation to the Graduate School.
It may take a couple of months to write the dissertation, or less time for students who have already published papers that will form the core of the dissertation.
Published papers can be simply reformatted to form the core of the dissertation (including changing all the “we’s” to “I’s”). If another person obtained a result shown in the dissertation, then the contribution of this person must be explicitly acknowledged in the text and figure legend.
Copies of the dissertation are distributed to the committee members for their comments, which should be addressed in the final version before its submission to the Graduate School. Committee members should be given adequate time, at least 2 weeks, to read and evaluate the dissertation.
There are 2 deadlines for submission of the dissertation: October 1 for a December degree and March 15 for a May degree. The Graduate School does not make any exception to these deadlines, which have been picked to give readers adequate time to evaluate the dissertation.
Upon receipt, the Graduate School will send the dissertation out for evaluation by 3 readers, with at least 2 having tenure or a tenure track position at Yale. As Cell Biology does not require an outside reader (i.e., outside Yale), unlike some departments, 3 members of the thesis committee, except the thesis adviser, would be appropriate as readers. After all reader evaluation forms have been returned to the Graduate School and all requested changes to the dissertation have been made, the DGS acting on behalf of the entire Cell Biology faculty will sign the form recommending award of the Ph.D. degree. Then the Graduate School Degree Committee and finally the Yale Corporation will vote to approve conferral of the degree.
Students are required to present a seminar on their thesis work. This seminar is usually scheduled just prior to submission of the dissertation. Like all other Cell Biology seminars, the thesis seminar will be open to the university community. The thesis seminar is conducted like a defense, so the thesis committee will meet with the student after the seminar. At this time, the thesis committee may ask questions beyond those asked at the end of the seminar. Then the student may be asked to leave the room while the committee decides whether the thesis work presented in the seminar and in the dissertation is acceptable for award of the Ph.D. degree. After making any changes to the dissertation requested by the committee, the dissertation is submitted to the Graduate School. Occasionally, it may be necessary to submit the dissertation before the thesis seminar (e.g., if it is not possible to schedule the seminar before the submission deadline). However, in this case, the student still has to give the thesis committee plenty of time to read the dissertation and must make all requested changes to the dissertation before submitting it to the Graduate School.
The Master of Philosophy is awarded to Cell Biology graduate students en route to the Ph.D. A student is eligible for this degree after having been admitted to candidacy, and may petition for the degree at the earliest in the term that follows the term in which the requirement is met (e.g., in the Fall term if the requirement is met by the end of the Spring term).
The Master of Science is a terminal degree normally awarded only to graduate students who are withdrawing from the Ph.D. program. The minimum Graduate School requirement for students admitted for an M.S. degree is an overall grade average of High Pass, including a grade of Honors in at least two full-term graduate courses.
Please note that there are 2 deadlines, one in October and the other in March, for degree petitions to be submitted to the Graduate School. See below for where the petition can be obtained.
Many of the forms that graduate students will need to fill out during their studies, including petitions for degrees, are downloadable at: http://www.yale.edu/graduateschool/academics/forms.html
Students are required to submit an annual “Report on Dissertation Progress” to the Graduate School, mapping out their achievements in the past year, and goals and timeframe for the upcoming year.
For training grant purposes, students are requested to list on this form any publications, meeting abstracts, and meetings and retreats attended.
The deadline for submitting this form is May 1. At least a week before the deadline, please forward this form after it has been signed by the thesis advisor to the Cell Biology Registrar in order to obtain the signature of the DGS. Then the Registrar will send it to the Graduate School.
Students must register with the Graduate School each term until the dissertation is submitted or 6 years of study have been completed. Beginning the 5th year, students must submit the “Continuous Registration Form” to the Graduate School. The department will pay for the student’s continuous registration fee.
The Graduate School does not require students to register beyond the 6th year for submission of the dissertation or award of the Ph.D. degree. However, registration is required to receive financial support, including stipend and health insurance, and to use the University facilities. Thus, from this viewpoint it may be advantageous for students to register even if they only a few months beyond the end of the 6th year to finish the dissertation. This matter should be discussed with the thesis advisor.
Students intending to register beyond the 6th year must fill out a “Petition for Extended Registration,” which requires approval by the DGS. (Usually, students submit this form at the same time that they submit the annual Report on Dissertation Progress.) The Petition for Extended Registration should be filled out and given to the Cell Biology Registrar along with a copy of the most recent Report on Dissertation Progress and a letter to the DGS detailing the reasons for the petition. After obtaining the DGS signature, the Registrar will forward the petition to the Graduate School. Final approval by the Graduate School is contingent on certification from the thesis advisor and the DGS that the student will work full-time and is on track to complete the dissertation by the end of the extended registration period.
For the duration of their studies in the Cell Biology program, students will be given full financial support, including stipend, full tuition, health coverage, and a yearly allotment from the BBS for travel to meetings and courses. The annual stipend in 2004-5 will be $25,000.
Students are supported during the 1st 3 years by NIH training grants or other university funds. Some students receive fellowships from the National Science Foundation, the Howard Hughes Medical Institute, or other agencies. BBS students in the first year are requested to apply for these fellowships, and BBS faculty members have an obligation to help students with the research proposals for the fellowship applications.
After support from training grants and fellowships ends, the thesis advisor is responsible for providing full financial support, including stipend, tuition, and fees (health and registration).
The Cell Biology Department has a longstanding weekly progress report series in which graduate students and postdocs give talks about their research in front of the whole department. This is a great forum for everyone to hear and learn about the research going on in other labs, and for both graduate students and postdocs to hone their presentation skills.
Progress report is held in C429 SHM on Friday from 11 AM to noon during most of the year except in summer. Each speaker has 30 min for the talk and questions. During the summer, Jim Jamieson (james.jamieson@yale.edu) and Mari Kawaguchi (mari.kawaguchi@yale.edu) will request from each PI the names of postdocs to be put on the progress report speakers list for the coming year. Students 3rd year and up are required to give a progress report every year and are automatically scheduled unless a special waiver is requested by the student’s PI. It is the responsibility of the speaker, and ultimately of the speaker’s PI, to find a replacement in case the speaker cannot speak on the assigned date. Each speaker is required to submit the talk title to Mari 2 weeks prior to the scheduled date of the talk.
Refreshments of bagels, muffins, and coffee/tea are served. Click here for the schedule of the Cell Biology Progress Report Speakers.
The Cell Biology Department hosts a weekly seminar series in which scientists from other institutions or from other Yale departments are invited to talk about their research. The seminar is generally held on Wednesday at noon in varying rooms at the medical school, including C429 SHM and TAC Auditorium. Coffee/tea and cookies are available 15 minutes before the seminar. It is expected that all students will attend all of the seminars offered by the Cell Biology seminar series, regardless of topic.
Students and postdocs, in addition to faculty, are strongly encouraged to invite and host seminar speakers. Please discuss names of potential speakers with Peter Novick (peter.novick@yale.edu), the faculty currently in charge of the seminar series. Mari Kawaguchi (mari.kawaguchi@yale.edu) is in charge of travel arrangements, seminar announcements, and meeting appointments for seminar speakers. Hosts are responsible for ensuring a pleasant and productive visit for their speakers.
Students and postdocs are also strongly encouraged to attend the lunch with the seminar speaker held immediately after the seminar, usually in room C225 SHM. In addition to a free lunch, this is a great opportunity to meet the seminar speaker. Please contact Mari if interested in having lunch with a particular seminar speaker. Click here for the upcoming Cell Biology Seminar Series lectures.
Once a year in the Fall the whole department goes on a 2-day retreat. In the past couple of years, the retreat has been held jointly with the Microbial Pathogenesis Section at the Dolce Heritage resort in Southbury, CT. The retreat provides a relaxed setting for all members of the department to engage in scientific discussions and in social activities. In addition to talks and a poster session, a highlight of the retreat is a skit put on by 2nd year graduate students lampooning the faculty. The PI’s grants cover the cost of attending the retreat for students and postdocs. Contact Mari Kawaguchi (mari.kawaguchi@yale.edu) for further information about the retreat.
The department has a happy hour on Friday 5-7 PM, held once a month in BCMM 208. Derek Toomre (derek.toomre@yale.edu) is the organizer responsible for the excellent varieties of wine, beer, cheese and other food featured at the happy hour. Each happy hour is hosted by one or two labs, which are responsible for setting up the refreshments and cleanup. A flyer announcing the happy hour should also be created by the hosting labs and emailed to Mari Kawaguchi (mari.kawaguchi@yale.edu) about a week before the date of the happy hour so that it can be disseminated and posted. A list of the hosting labs is circulated. Admission is free, and all are encouraged to attend!
The Cell Biology Department has a graduate education committee of faculty that reviews policies, resolves issues, and makes recommendations and decisions pertaining to the Cell Biology graduate program. In addition to the DGS, the current members are Susan Ferro-Novick (susan.ferronovick@yale.edu), Peter Takizawa (peter.takizawa@yale.edu), and Graham Warren (graham.warren@yale.edu).
For required signatures on forms and for help in resolving questions and problems with regard to working in the Cell Biology Department and to graduate studies at Yale, students should contact the following individuals.
Carl Hashimoto
Office/Lab: SHM C215
Phone: 737-2746
Email: carl.hashimoto@yale.edu
The DGS is responsible for administration of the graduate program and for overseeing the academic and research progress of all students in the program. The DGS also acts as liaison between the students and the Graduate School Dean’s office. Students should feel free to contact the DGS to discuss any issue regarding their studies and research.
Mari Kawaguchi
Office: SHM C207
Phone: 785-4320
Fax: 785-7446
Email: mari.kawaguchi@yale.edu
The Registrar is the communication hub between students, the DGS, and the Graduate School, and assists the DGS in administering the graduate program.
Location: SHM C207
Fax: 785-7446
Marsha Maresca, Operations Manager
Phone: 785-7444
Email: marsha.maresca@yale.edu
The main contact for all Cell Biology departmental business matters, including payroll and personnel issues.
Mari Kawaguchi, Administrative Associate (also Registrar)
Phone: 785-4320
Email: mari.kawaguchi@yale.edu
Assistant to the Chair of the department; department website editor; and coordinator/organizer for seminar series, progress reports, immigration matters, retreat, business travels.
Pansy Walters, Senior Administrative Assistant
Phone: 785-4311
Email: pansy.walters@yale.edu
Responsible for orders, stockroom cards, ID’s, paycheck distribution, telecommunication, keys, reimbursements.
Veronica (Ronnie) Luedee, Grants Coordinator
Phone: 785-7462
Email: veronica.luedee@yale.edu
Responsible for grant applications.
John Alvaro, Administrative Director
Office: SHM L200c
Phone: 785-3735
Email: john.alvaro@yale.edu
Danielle Waterbury, Assistant Administrative Director
Office: SHM L203
Phone: 785-5663
Fax: 785-3734
Email: danielle.waterbury@yale.edu
Richard Sleight, Associate Dean
Office: HGS 132
Phone: 432-2744
Email: richard.sleight@yale.edu
Dean Sleight oversees all graduate programs in the natural sciences.
The Graduate Student Assembly (GSA) is the elected body of Yale students in the Graduate School of Arts and Sciences. The Assembly's goals are to (1) identify the needs and concerns of graduate students, consider possible solutions, and present these to the Dean and other administrators, (2) discuss and advise on changes to Graduate School policy proposed by the administration, and (3) provide a means for communication and deliberation both among graduate students and between grad students and other members of the university community. Student representatives are elected from each department in the Graduate School. The current Cell Biology representative is Stephen Francis (stephen.francis@yale.edu).
The Yale Graduate and Professional Student Senate (GPSS) is a student government organization representing over 5,000 graduate and professional students at Yale. Its goal is to foster interaction between graduate and professional students through the congregation of student groups at the Graduate and Professional Student Center at Yale (GPSCY), the sponsorship of academic, intellectual events, and social events, and through community service and charitable events. The GPSS influences the course of the University through, representation on University Committees, by expressing views of the student body to the administration, and by issuing statements of our position to the media and administration. The Senate stands at the intersection of subsets of the Yale Graduate and Professional Student community, Yale Undergraduates, Faculty and Staff of Yale University, Yale Alumni, and the New Haven Community. Two Cell Biology students, Jordan Yelinek (jordan.yelinek@yale.edu) and Steven Becker (steven.becker@yale.edu) are the current President and Student Advocate, respectively, of GPSS.
Please consult the Programs and Policies bulletin of the Graduate School of Arts and Sciences for additional resources available to graduate students.
http://www.yale.edu/bulletin/html/grad/introduction.html
