The Ph.D. program is divided into three separate concentrations. Some requirements are the same across concentrations, and other requirements are concentration specific. Click below for specific details. Also, see our Deadlines & Forms page for a brief overview of what is due when.
Molecular, Cellular, Developmental and Genetic (Cell/Mol)
Integrative/Organismal (I/O)
Ecology, Evolution and Population Biology (Eco/Evo)
Requirements for all students
1st Year Requirements
Autumn Quarter: Faculty members are assigned to serve on a student's first year advising committee. This committee evaluates the student's background, recommends an academic program, and helps in choosing the eventual dissertation research advisor and dissertation advising committee. The advising committee is comprised of faculty members from the student's proposed area of specialization.
Meetings take place during orientation week, the first week of classes or at another mutually agreed upon time. Together they will establish a course of study, taking into consideration (1) area of specialization; (2) training in accessory areas such as language, math, physical sciences, and computer science; and (3) breadth in Biology. Students who have not chosen a specific area will need to work closely with their committee to plan for exploration of alternatives. The first year advising committee will also help students select and arrange lab rotations (if applicable), teaching opportunities, and remind students of their academic and administrative responsibilities. Students should bring the First Year Advising Committee Meeting form to their meeting and return the signed form to Student Services following the meeting, no later than the Monday following the study list deadline.
Winter Quarter: The First Year Advising Committee will meet with the student early in Winter Quarter to evaluate his or her progress. Discussions should cover the student’s progress in coursework, teaching and lab rotations. A signed First Year Winter Progress Report form must be submitted to the Student Services Office following the meeting and no later than January 31.
Spring Quarter: In spring quarter of the first year, the advising committee will meet again with the student to evaluate his or her progress. A signed First Year Evaluation Report form must be submitted to the Student Services Office by May 15 of the student’s first year in the Ph.D. program. The faculty will use the committee’s recommendations during their spring quarter review meeting. Once a student's continuation is approved, the committee is expected to help develop an academic plan for the second year and select a dissertation committee.
Ethics Course
All students are required to take an Ethics course. This course should be taken in the first year of the program.
BIO 312: Ethical Issues in Ecology and Evolutionary Biology – required for Eco/Evo students. Offered Autumn quarter.
MED 255: Responsible Conduct of Research – required for Molecular, Cell, Developmental and Genetics, and Integrative/Organismal students. Offered all four quarters.
Individual Development Plan and Annual Planning Meetings
All students are required to meet on an annual basis with their faculty advisor by August 1st to create and discuss their Individual Development Plan (IDP) on an annual basis.
The IDP and annual planning meeting with the advisor are intended to help the student:
- Take ownership of their training and professional development.
- Pause and reflect! Amidst daily research activities, it is easy to lose sight of longer-term goals.
- Think intentionally about their short-, mid-, and long-term training and development goals.
- Establish clear expectations/steps.
- negatively impact Stanford's abilit to receive NIH funding; and
- incur a hold on student registration that prevents stipends from being funded.
Teaching
Regardless of the source of support, each Ph.D. student is required to teach two quarters.
One quarter must be in the core lecture courses (BIO 41, 42, or 43), or undergraduate core labs (BIO 44X or 44Y). Summer teaching positions cannot be used to fulfill teaching requirements. Textbooks for courses are provided free of charge for teaching assistants. Please ask the instructor for a free desk copy; if one is not available, you can purchase any required texts – see student services staff.
The department requires teaching experience for two reasons. First, the department has practical needs for teaching assistance and must satisfy some of these needs with graduate teaching assistants (TAs). Second, the teaching experience is valuable for students who later choose to pursue academic careers where they will be expected to teach and develop courses.
Students should satisfy their teaching requirements ideally within the first two years of the program. In order to secure a TA position, faculty should be contacted well in advance of the quarter a course is to be offered.
Teaching responsibilities should be clearly understood before a student accepts a teaching position. Typical teaching responsibilities include the following:
- Assist in the preparation and grading of exams, problem sets, etc.
- Hold regular office hours
- Assist in preparation and distribution of course handouts
- Attend lectures
- Provide student course feedback to instructor
- Initiate and plan discussion sections
- For lab courses: set up experiments, check equipment, and supervise clean-up
Grading papers and exams is a part of teaching assistant (TA) duties and is not considered to be supplementary work.
In order to fulfill their teaching requirements, students have their teaching supervisors complete the Teaching Requirement Evaluation form. Students must deliver this completed form to the Student Services Office where it will be kept in their file.
Students who plan to TA for one of the core labs (BIO 44X or 44Y) are required to attend a training course, BIO 291, the preceding quarter. Registering for BIO 291 to obtain units is optional. If interested please contact Dr. Shyamala Malladi at smalladi@stanford.edu.
Optional Teaching: Students who wish to do more teaching after they have fulfilled the requirement may ask to be considered, though faculty must give first priority to students who have not yet completed their requirements.
Pre-Doctoral Fellowship Applications
All first and second year Ph.D. students who are eligible to apply for a National Science Foundation Graduate Research Fellowship are required to do so. If a student already has an outside fellowship, s/he is not required to apply for the NSF. Typically the application deadline is early November. Please see the NSF website for deadlines
All students are encouraged to apply for any/all fellowships for which they are eligible. Students are encouraged to consult their faculty advisors when preparing fellowship applications.
Laboratory Safety Training
All Biology Lab personnel are required, under regulations from various governmental agencies, to be trained in laboratory safety pertaining to their lab. During orientation, each new graduate student is required to attend the Health and Safety Training Session. Prior to working in the lab, new students are required to complete a number of SU EH&S safety training, online courses and any specialized classroom training that is required for the lab he or she will be entering. The Dept. Safety Officer will give a general safety overview and provide a Safety Training Certificate form, outlining the required and suggested courses for each student.
Required courses may include but are not limited to some of the following:
- General Safety & Emergency Preparedness
- Chemical Safety for Labs
- Biosafety
- Ergonomics
- Radiation Safety
- Laser Safety
- Compressed Gas Safety
- DOT: Shipping Biological Goods or Dry Ice
Students must complete their training, have the Safety Training Certificate form signed by their P.I., and return the form to the Safety Officer, in the main office in Gilbert Bldg., Room 109. After hours access to the Biology buildings, WILL BE REVOKED if the completed form is not returned.
Every laboratory has a Stanford Safety Manual, which describes the Health and Safety program at Stanford, and the Emergency Response Plan for the department. Reference materials can be found on the EH&S website, with a list of training videos and journals. There are CD-ROMs containing Material Safety Data Sheets (MSDS) and the Hazardous Waste Training Program available in the Falconer Biology Library.
Additional training is required when students begin to use protocols involving radioactivity and or animals. Students who may be using radioisotopes must also attend the University radiation safety course and pass the radiation safety examination. Arrangements to take this class are made through the Health Physics Division of the Department of Environmental Health and Safety. Students involved with animals may be required to take additional veterinary training.
2nd Year Requirements
Dissertation Proposal
During the second year, each student must pass a two-part qualifying exam. The student must prepare and defend a dissertation proposal that outlines the student’s projected dissertation research.
- Written dissertation proposal that outlines the student’s projected dissertation research
- Oral defense of the dissertation proposal
The dissertation proposal is submitted to the Dissertation Proposal Committee, and an oral examination is held.
Cell/Mol and I/O: The student’s advisor is present (but not as a voting member) at the oral examination, which is administered by the other three members of the Dissertation Proposal Committee (ideally two from the department and one from an outside department to serve as examiners).
Cell/Mol: The Dissertation Proposal (paper) must be submitted to the Student Services Office no later than November 1 and the Dissertation Proposal form and oral exam must be completed by November 15.
I/O: The Dissertation Proposal (paper) must be submitted to the Student Services Office no later than May 15 and the Dissertation Proposal form and oral exam must be completed by June 15.
Eco/Evo: The dissertation proposal is evaluated by a committee of three faculty members in an oral presentation. The Dissertation Proposal paper must be submitted to the Student Services Office no later than May 15 and the Dissertation Proposal form and oral exam must be completed by June 15.
Candidacy
All students must advance to candidacy by the end of their second year. This is contingent upon satisfactory completion of course work, teaching, and the dissertation proposal. If a student does not meet the requirements for advancing to candidacy by the end of 2nd year, the student is subject to dismissal from the Ph.D. program. PLEASE NOTE: Prior to candidacy, at least 3 units of work must be taken with each of four Stanford faculty members. Three units of work can include lectures, labs, seminars, teaching, research, directed readings, and independent study. Candidacy application form.
3rd Year Requirements
All students in their third year must meet with their Dissertation Committee in Spring Quarter. Students are required to submit a two page written progress report to their committee at each meeting. It should contain an overview of the information to be presented/discussed at the meeting (1 ½ pages) as well as goals for the next meeting (½ page). Both the report and signed Committee Meeting Form must be submitted to the Student Services Office following the committee meeting and no later than May 15.
4th Year Requirements
TGR Form: Due when student has completed 135 units and all degree requirements, except the defense and submission of the dissertation
Reading Committee form: Due with TGR form
Fourth Year Committee Meeting: Due by May 15
The 4th year committee meeting written progress report should describe the following:
- Progress towards goals
- A timeline to graduation within 5.5 years
- A timeline towards a publication(s)
- If applicable, a written petition for extending the time to graduation beyond 5.5 years with an explicit anticipated date for graduation; a petition could be for health, personal or scientific reasons.
The advising committee should discuss and approve the progress report at the meeting. The meeting must also include a formal slide presentation and timeline to degree completion with specific milestones outlined. Career planning should begin at the time of this meeting.
5th Year Requirements
Student will send each thesis committee member an updated progress report of work done and the timeline of experiments to graduation no later than November 15. Student Services should be formally notified that the Report was generated, sent, and evaluated by committee. No meeting is required unless committee requires an in-person meeting. Progress report should be 2 pages maximum, using bullet points for key topics, and student must request feedback from committee within 2 weeks of submitting report.
Formal committee meeting no later than the end of 5th year to finalize degree completion (no later than winter quarter of 6th year = 5.5 years total in the PhD program). Committee meeting form
Final Oral Exam (Defense) and Dissertation Submission
The conferral of the Ph.D. is dependent upon successful completion of an oral exam and dissertation submission, along with completion of all other departmental and university requirements. The oral exam is a public seminar followed by a closed session with the student’s Oral Examination Committee. At least one month before the oral exam, a complete final draft of the dissertation must be turned in to the student’s Oral Examination Committee. At least two weeks before the oral exam, the student should check in with the committee and incorporate any changes by the time of the exam. The exam cannot be formally scheduled or publicly announced until the student receives approval from the Committee. The student should, however, start scheduling a date and time with the committee earlier than that, to assure that everyone is available on the projected date. The dissertation presented at the defense is expected to be in the final form that will be submitted to the University barring any changes suggested by a student’s committee at the defense. University guidelines for dissertations and resources are available online at http://studentaffairs.stanford.edu/registrar/students/dissertation-thesis.
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Molecular, Cellular, Developmental and Genetic (Cell/Mol)
Courses
All courses must be completed prior to Spring Quarter of the 4th year, except for the required first year courses as noted. Students are required to pass all courses in which they are enrolled and earn a grade of B- or better in all courses applicable to the degree that are taken for a letter grade.
- BIO 301: Frontiers in Biology - two quarter course taken Autumn and Winter quarters of first year
- MED 255: Responsible Conduct of Research – Autumn, Winter or Spring quarters of first year
- BIOS 200: Foundations in Experimental Biology - Autumn Quarter of first year
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One additional course in each of the following four scientific areas to be decided upon by the student and the First Year Advising Committee. Up to two of these courses may be “mini courses” in the Biosciences (BIOS).
- Cell Biology
- Biology of Molecules
- Genetics/Genomics
- Quantitative Methods
Completion of rotations in at least two different laboratories for a total of 20 weeks during Autumn and Winter quarters is required of all first year students. At least one lab rotation must be with faculty in the Department of Biology. Due to potentially limited lab space, students are encouraged to set up rotations as early as possible. Signed Lab Rotation Evaluation forms are due at the conclusion of each rotation.
Seminar Presentation
The seminar requirement is fulfilled by presenting a 50-minute talk in BIO 301. At least two faculty members from the Department of Biology must attend the seminar and evaluate the presentation. Evaluation will consist of meeting with each faculty member within one week following the seminar to obtain comments. If the faculty members approve the presentation, they will sign the Seminar Evaluation form at this time. In some cases, they may require an additional talk before signing.
Advisor/Dissertation Lab
By May 1, each first year student is required to join a lab in which to perform their dissertation research. The faculty member in charge of the lab must agree to accept the student, becoming the student’s advisor. The student must email student services and cc the advisor of their lab decision.
Note: Written petitions for exemptions to requirements are considered by a student’s Advising Committee and the Graduate Studies Committee Chair. Approval is contingent on special circumstances and is not routinely granted.
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Integrative/Organismal (I/O)
Courses
All courses must be completed prior to Spring Quarter of the 4th year, except for the required first year courses as noted. Students are required to pass all courses in which they are enrolled and earn a grade of B- or better in all courses applicable to the degree that are taken for a letter grade.
- BIO 301: Frontiers in Biology – two quarter course taken Autumn and Winter quarters of 1st year. *I/O Hopkins students may have the option of taking BIO 302, 303 and 304 and should consult with their advising committee
- MED 255: Responsible Conduct of Research – Autumn, Winter or Spring quarters of first year
- In addition to BIO 301 and MED 255, students may be required to take a set of courses to be determined by the advising committee.
Lab Rotations
In their first year, students are encouraged, but not required, to carry out research rotations to help them select an appropriate lab for their thesis studies. Since lab space is potentially limited, students are encouraged to set up rotations as early as possible. If students rotate in labs, they are required to submit signed Lab Rotation Evaluation forms at the conclusion of each rotation.
Seminar Presentation
The seminar requirement is fulfilled by presenting a 50-minute talk. The student must arrange for at least two faculty members from the Department of Biology to attend the seminar and evaluate the presentation. Evaluation will consist of meeting with each faculty member within one week following the seminar to obtain comments. If the faculty members approve the presentation, they will sign the form at this time. In some cases, they may require an additional talk before signing. The Seminar Evaluation form must be submitted to the Student Services Office no later than May 15th of a student's first year in the program.
First Year Paper
Each student must prepare and submit a paper before the end of the first year that will be evaluated by the advising committee. This paper should be a step toward the development of a dissertation proposal and may consist of an analysis of new data or a literature review and synthesis. The paper should be read, commented upon, and agreed to as satisfactory by a minimum of two faculty members. The First Year Paper Evaluation form and a copy of the first year paper itself must be submitted to the Student Services Office no later than May 15th of a student’s first year in the program.
Note: Written petitions for exemptions to requirements are considered by a student’s Advising Committee and the Graduate Studies Committee Chair. Approval is contingent on special circumstances and is not routinely granted.
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Ecology, Evolution and Population Biology (Eco/Evo)
Courses
All courses must be completed prior to Spring Quarter of the 4th year, except for the required first year courses as noted. Students are required to pass all courses in which they are enrolled and earn a grade of B- or better in all courses applicable to the degree that are taken for a letter grade.
- BIO 302, 303, 304: Current Topics and Concepts in Population Biology, Ecology and Evolution – Autumn, Winter and Spring quarters of first year
- BIO 312: Ethical Issues in Ecology and Evolutionary Biology – Autumn Quarter of first year
- In addition to BIO 302, 303, 304 and 312, students may be required to take a set of courses to be determined by the advising committee.
Seminar Presentation
The seminar requirement is fulfilled by presenting a 50-minute talk. The student must arrange for at least two faculty members from the Department of Biology to attend the seminar and evaluate the presentation. Evaluation will consist of meeting with each faculty member within one week following the seminar to obtain comments. If the faculty members approve the presentation, they will sign the form at this time. In some cases, they may require an additional talk before signing. The Seminar Evaluation form must be submitted to the Student Services Office no later than May 15th of a student's first year in the program.
First Year Paper
Each student must prepare and submit a paper before the end of the first year that will be evaluated by the advising committee. This paper should be a step toward the development of a dissertation proposal and may consist of an analysis of new data or a literature review and synthesis. The paper should be read, commented upon, and agreed to as satisfactory by a minimum of two EcoEvo faculty. The First Year Paper Evaluation form and a copy of the first year paper itself must be submitted to the Student Services Office no later than May 15th of a student’s first year in the program.
This can be satisfied in a number of ways which all involve new writing, undertaken since entering the Stanford program. These may include:
- a new draft research manuscript (a previously published paper will not do, because it may have received much editorial modification in the review process).
- some other piece of new writing, such as a review paper from a course, or an initial literature review of a potential thesis topic. In this case the paper should ordinarily be not less than 10 double-spaced pages in usual sized font, and not more than 10 single spaced pages, plus references. It should be written in the style of a standard scientific paper.
Note: Written petitions for exemptions to requirements are considered by a student’s Advising Committee and the Graduate Studies Committee Chair. Approval is contingent on special circumstances and is not routinely granted.
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