BIO-PHD - Biology (PhD)

All students must be enrolled in exactly ten units during autumn, winter, spring, and summer quarters until reaching Terminal Graduate Registration (TGR) status. Satisfactory completion of each year’s general and track-specific requirements listed below is required for satisfactory progress toward the degree. Students not making satisfactory degree progress are subject to departmental academic review and/or dismissal.

Note: A student’s Advising Committee and the Graduate Studies Committee Chair consider written petitions for exemptions to requirements. Approval is contingent on special circumstances and is not routinely granted.

• First-year advising
  Entering CMOB students will meet with the DGS in the first quarter to discuss rotations and year 1 recommendations. In the first quarter, students in the Eco/Evo subplan must also meet with their first-year advising committee. The committee reviews the student's previous academic work and current goals and advises the student on a program of Stanford courses, some of which may be required and others recommended. All students must complete the core curriculum listed below under Subplan Specific Requirements.

• Seminars
  Graduate seminars devoted to current literature and research in particular fields of biology are an essential means of attaining professional perspective and competence. Seminars are presented under individual course listings or are announced by various research groups.
  During the first year of study, graduate students must attend seminars. For CMOB, this includes enrolling in BIO 301 and attending the corresponding department seminar series. For Eco/Evo, this includes enrolling in and attending BIO 302/303/304 in Autumn, Winter, and Spring of the first year, making one formal seminar presentation, and writing a research paper, both of which must be evaluated by a minimum of two Biology faculty members.

• Committee meetings
  Students must meet regularly with their advising committees. These meetings will be annual or semi-annual for advanced students in year 5+.

• Individual Development Plan meetings
  Students must meet once a year with their advisor by August 1 of that academic year.

• Publishable manuscript
  Over the course of the PhD, each student must complete one publishable manuscript (paper) for which they are the major contributor and first author. This work should be of recognized high quality by the primary research advisor and thesis committee and be published or being prepared for publication in a reputable journal. This is to be completed by the time of graduation. In some fields, students should have multiple first-authored research papers, which serve as thesis chapters. Decisions about how much primary research constitutes a PhD dissertation are made in consultation between the advisor, faculty committee, and PhD student

Subplan Specific Requirements

In addition to the general requirements listed above, students must complete requirements within their Subplan (see Subplan Options Categories below). The advising committee and the graduate studies committee chair consider written petitions for exemptions to core curriculum and lab rotation requirements. Approval is contingent upon special circumstances and is not routinely granted.

BIO 290 is to be taken concurrently with each quarter of required teaching. BIO 296 is to be taken concurrently with the first quarter of required teaching. Enrollment should be commensurate with the course for which they are teaching. Please see the handbook on the program requirement page for enrollment guidelines.

CMOB Rotations

CMOB students will complete rotations in year 1.

Rotation 1: Autumn quarter

Rotation 2 : Winter quarter 

Rotation 3 ( optional): Spring quarter 

Following the completion of the second or third rotation a lab should be selected in consultation with the desired PI/Lab.

Eco/Evo Rotations

Eco/Evo PhD students may rotate with and select any faculty member as the primary PhD advisor with a primary appointment in one of the Biosciences Home Programs. While rotations are not required to choose the primary advisor, they are possible. Many students collaborate with faculty in addition to their primary advisor in order to increase breadth and depth. This is usually accomplished with the advice and encouragement of the primary PhD advisor.

Admission to candidacy is a prospective judgement by the faculty of a student’s potential to successfully complete the requirements of the degree program. Students are expected to complete qualifying procedures and apply for candidacy by the end of their second year in the program. Qualifying procedures include required coursework, research rotations, identification of an advisor before the start of summer quarter of their first year, and successful completion of an oral qualifying exam with their advisor and faculty committee, in which they present an overview of their proposed dissertation research, respond to faculty questions, and discuss plans for their PhD.  Failure to pass the qualifying exam as part of the admission to candidacy process could result in dismissal from the program.  Additional details on qualifying procedures, including procedures for subsequent attempts to advance to candidacy in the event that the student does not successfully complete the qualifying exam,  can be found in the Graduate Handbook .  

Candidacy is valid for five years, subject to satisfactory academic progress. In the Department of Biology the procedure is outlined for each subplan in the Graduate Handbook

PhD students are required to give a ~50 minute research seminar summarizing their dissertation research, followed by 10 minutes of audience questions, which is attended by the committee and other department members and is open to the broader university and members of the public. Candidates and their committee then participate in a closed-door examination session in which candidates respond to further questions from the committee about the dissertation research.  The timing of the oral exam is determined through joint consultations between the student, the primary research advisor, and all members of the thesis committee. Candidates are expected to provide each member of their PhD Oral Examination Committee (see below) a copy of their written dissertation at least 14 days before the scheduled oral defense date. This dissertation is expected to be in final or near-final form, pending any changes suggested by the student’s committee at the defense itself. The student should check in with the committee and incorporate any changes before or right after the exam.

Along with completion of all Departmental and University requirements noted above, conferral of the PhD requires a written dissertation and successful completion of an oral exam. The written thesis is a document that expresses the contributions that the candidate has made (alone and/or in collaboration with others) to advancing knowledge. Typically, the written document contains several chapters, at minimum one chapter of introduction, one chapter of results, and one chapter of discussion or future directions. Additional chapters of results are common, and often correspond to distinct published or submitted manuscripts. Typically, the student is the first or co-first author on all their chapters. Regardless, the component of the work that was done by the candidate themself must be clearly identified and distinguishable from other aspects of the work. The evaluation of the Reading and Oral Committee should focus mainly on the component performed by the candidate. The specific roles of other major coauthors must be made clear in the thesis, and other presentations of the work.

Students are required to take the following courses by the end of their of the 4th year, except for the required first year courses as noted.

Complete the following courses in Year 1: 

-BIOS 200-Foundations in Experimental Biology

-BIO 312-Responsible Conduct in Cellular and Molecular Biology 

-BIO 301-Frontiers in Biology

-BIO 265-Quantitative Approaches in Modern Biology

Two additional courses in a scientific area decided upon by the student and the advising committee.

1. Cell Biology

2. Biology of Molecules

3. Genetics/Genomics

4. Quantitative Methods

5. Organismal Biology

Students are required to take BIO 302, 303, and 304 and MED 255 in the first year.

Students specializing in ecology and evolution may be required to take additional courses as the committee advises.