BIO-PHD - Biology (PhD)
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Program Overview
The training for a PhD in Biology is focused on learning skills required to be a successful research scientist and teacher, including how to ask important questions and devise and carry out experiments to answer these questions. The Biology PhD Program includes two subplans: Cell, Molecular, and Organismal Biology (CMOB) and Ecology/Evolution (Eco/Evo). Students work closely with an established advisor and meet regularly with a committee of faculty members to ensure they understand the importance of diverse perspectives on experimental questions and approaches. Students learn to evaluate critically pertinent original literature to stay abreast of scientific progress in their areas of interest. They also learn how to make professional presentations, write manuscripts for publication, and become effective teachers.
Minimum Units in the Program
Minimum University Units
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 making one formal seminar presentation 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
Each student must complete one publishable manuscript (paper) for which they ares/he is the major contributor. This work should be of recognized high quality by the primary research advisor and thesis committee and published or being prepared for publication in a reputable journal.This is to be completed by the time of graduation.
Residency requirement
Graduate students are expected to maintain a significant physical presence on campus unless the degree program has granted an exception, for example, to conduct fieldwork.
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.
Students must take a course on the ethical conduct of research in the first year of study.
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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 TAing.
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Teaching experience and training are part of the graduate curriculum. Each student assists in teaching one course at
The intro/foundational level (BIO 40s and 80s level courses). Note: Students with a primary working location of Hopkins Marine Station, will complete at least one TA requirement on campus during the first year. Any remaining TA requirements can be met at Hopkins.
And a second course that can be either an intro/foundational course or another biology or Hopkins Marine Station course.
Teaching is core to the academic and professional training of doctoral students in our program. All students are required to complete 2 quarters of teaching Biology courses by Autumn of their 3rd year in the program regardless of their financial support. The opportunities to gain teaching experience and training in specific courses are assigned using the departmental matching system during the Spring and Summer quarters before the next academic year.
CMOB students will complete rotations in year 1.
Rotation 1 (eight weeks): Monday September 22nd - Friday November 14th. Note that this first rotation is a bit longer than rotations #2 and #3 to help accommodate the transition to Stanford.
Rotation 2 (seven weeks): Monday November 17th - Friday January 16th. Note: Stanford Winter Closure is Dec 22nd to Jan 2nd and should be considered the winter holiday period.
Rotation 3 (seven weeks, optional): Monday January 19th - Friday March 6th.
Following the completion of the second or third rotation a lab should be selected in consultation with the desired PI/Lab.
EcoEvo 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 in the Department of Biology include required coursework, [research rotations, identification of an advisor by the end of the first year of the program, and completion of degree milestones, etc.]. Additional details on qualifying procedures 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
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
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One additional course in a scientific area decided upon by the student and the advising committee.
Cell Biology
Biology of Molecules
Genetics/Genomics
Quantitative Methods
Organismal Biology
BIO 265: Quantitative Biology: Rigor and Reproducibility*
*Or more advanced course in statistics or coding with approval from the DGS.
Students are required to take BIO 302, 303, and 304 in the first year.
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Students specializing in ecology and evolution may be required to take additional courses as the committee advises.
First-year paper: The paper should be read, commented upon, and agreed to as satisfactory by two EcoEvo faculty by June 1. This can be satisfied in several ways involving new writing undertaken since entering the Stanford program. These may include:
A new draft research manuscript (a previously published paper is unacceptable).
Some other pieces 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 ten double-spaced pages in standard-sized font and not more than ten single-spaced pages, plus references. It should be written in the style of a standard scientific paper.