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Doctor of Philosophy in Biology

For information on the University's basic requirements for the Ph.D. degree, see the "Graduate Degrees" section of this bulletin. The training for a Ph.D. in Biology is focused on learning skills required for being a successful research scientist and teacher, including how to ask important questions and then devise and carry out experiments to answer these questions. Students work closely with an established adviser and meet regularly with a committee of faculty members to ensure that they understand the importance of diverse perspectives on experimental questions and approaches. Students learn how to evaluate critically pertinent original literature in order 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.

ADMISSIONS

Preparation for Graduate Study—Students seeking entrance to graduate study in Biology ordinarily should have the equivalent of an undergraduate major in Biology at Stanford. However, students from other disciplines, particularly the physical sciences, are also encouraged to apply. Such students are advised at the time of initial registration on how they should complete background training during the first year of graduate study. In addition to the usual basic undergraduate courses in biology, it is recommended that preparation for graduate work include courses in chemistry through organic chemistry, general physics, and mathematics through calculus.

Application, Admission, and Financial Aid—Prospective graduate students must apply via Stanford's online graduate application.

The department's program is divided into three separate areas of concentration:

Included in these concentrations is the option to conduct research at Hopkins Marine Station. These concentrations are recorded in the department as part of the admissions process and for tracking degree progress for admitted students; they do not appear on official university records.

Applicants are required to take the Graduate Record Examination (GRE) general test. The GRE subject test is not required. Applicants should plan on taking the GRE at least one month prior to the application deadline to ensure that official scores are available when applications are evaluated.

Admission to the Ph.D. program is competitive, and in recent years it has been possible to offer admission to approximately 10 percent of the applicants.

Applicants who are eligible should apply for nationally competitive predoctoral fellowships, especially those offered by the National Science Foundation.

Admitted students are typically offered financial support in the form of Stanford Graduate Fellowships, research assistantships, NIH traineeships, or Biology fellowships.

GENERAL REQUIREMENTS

The following requirements must be completed by all students:

  1. First year advising. Each entering student meets with the first-year advising committee within the first two weeks of Autumn Quarter and again no later than May 15. 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. Completion of the core curriculum listed below under "Track Specific Requirements" is required of all students.
  2. Ethics. Students must take a course on the ethical conduct of research: BIO 312 for ecology/evolution/population studies; MED 255 for integrative/organismal and molecular/cellular/developmental/genetic/plant.
  3. Teaching. Teaching experience and training are part of the graduate curriculum. Each student assists in teaching one course in the department's core lecture (41, 42, or 43) or lab (44X, 44Y) series, and a second course that can be either a core course or other Biology or Hopkins Marine Station course. A third quarter of teaching is required for ecology, evolution, and population studies students.
  4. Seminars. Graduate seminars devoted to current literature and research in particular fields of biology are an important means of attaining professional perspective and competence. Seminars are presented under individual course listings or are announced by the various research groups. Topics of current biological interest are presented by speakers from Stanford and other institutions. During the first year of study, graduate students are required to attend seminars and make one formal seminar presentation which must be evaluated by a minimum of two Academic Council faculty members.
  5. Fellowship application. All eligible first and second year students must apply for a National Science Foundation fellowship.
  6. Adviser/lab selection. By April, each first-year student is required to have selected a lab in which to perform dissertation research and to have been accepted by the faculty member in charge.
  7. Qualifying exam and advancement to candidacy. During the second year, students are required to write a dissertation proposal which is evaluated by a committee of three faculty (the dissertation advising committee) in an oral presentation. Track-specific deadlines are listed below. Advancement to candidacy depends on satisfactory completion of the dissertation proposal.
  8. Advising meetings. Students must meet regularly with their advising committees. For more details, see the Biology PhD Handbook.
  9. Publishable manuscript. Each student must complete one publishable manuscript (paper) for which s/he is the major contributor.
  10. Residency requirement. A minimum of 135 units of graduate registration is required of each candidate at the time of graduation.
  11. Doctoral dissertation. A completed draft of the dissertation must be turned in to the student's oral examination at least one month before the oral exam is scheduled to take place. The dissertation must be presented to an oral examination committee comprised of at least five faculty members. In addition, the final written dissertation must be approved by the student's reading committee (a minimum of three approved faculty), and submitted to the Registrar's Office. Upon completion of this final requirement, a student is eligible for conferral of the degree.

TRACK SPECIFIC REQUIREMENTS

In addition to the general requirements listed above, students must also complete requirements within their concentration.

Molecular, Cellular, Developmental, Genetic, and Plant—

  1. First year:
    1. core curriculum:* Students are required to take the following courses for a letter grade:

          BIO 203. Advanced Genetics

          BIO 214/BIOC 224/MCP 221. Advanced Cell Biology

          BIO 301. Frontiers in Biology

              (satisfies first-year talk requirement; must be taken Autumn and Winter quarters)

      And one of the following for a letter grade :

          BIOC/BIOPHYS/SBIO 241. Biological Macromolecules

          BIOC 201. Advanced Molecular Biology

          CSB 210. Signal Transduction Pathways and Networks

          MCP 256. How Cells Work: Energetics, Compartments, and Coupling in Cell Biology

      And three additional courses in the student's area of interest, or as advised by committee. These courses must be offered for at least three units and must be taken for a letter grade.

    2. lab rotations:* First-year students are required to complete rotations in at least two but not more than three different laboratories. The first rotation must be in a lab in the Department of Biology.

* Written petitions for exemptions to core curriculum and lab rotation requirements are considered by the advising committee and the chair of the graduate studies committee. Approval is contingent upon special circumstances and is not routinely granted.

2. Second year: Each student must pass a two-part qualifying exam.

  1. dissertation proposal: During Autumn quarter of the second year, the student must prepare a written dissertation proposal that outlines the student's projected dissertation research, including an expert assessment of the current literature; deadline is November 1. An oral examination is held after submission of the written proposal to the dissertation advising committee; deadline is November 15. The student's adviser is a silent member of the examination committee; the other members of the dissertation advising committee can provide feedback. Advancement to candidacy is contingent upon completion of the dissertation proposal and oral exam.

Integrative/Organismal—

  1. First year:
    1. core curriculum: Students are required to take BIO 306. Current Topics in Integrative and Organismal Biology. Students specializing in integrative biology may also be asked to take appropriate graduate-level courses as advised by committee.
    2. first-year paper: Students must submit a paper that is evaluated by a minimum of two Academic Council faculty members by May 1. 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.
  2. Second year: Each student must pass a two-part qualifying exam.
    1. dissertation proposal: During Spring Quarter of the second year, the student must prepare a written dissertation proposal that outlines the student's projected dissertation research, including an expert assessment of the current literature. An oral examination is held after submission of the written proposal to the dissertation advising committee comprised of three faculty members. Advancement to candidacy depends on completion of the dissertation proposal and oral exam. The written proposal is due by May 15, and the oral defense must take place no later than June 15. Advancement to candidacy depends on completion of the dissertation proposal and oral exam.

Ecology, Evolution, and Population Studies—

  1. First year:
    1. core curriculum: Students are required to take BIO 302, 303, 304: Current Topics and Concepts in Population Biology, Ecology, and Evolution.
    2. first-year paper: The paper should be read, commented upon, and agreed to as satisfactory by two EcoEvo faculty by May 15. This can be satisfied in a number of ways which all involve new writing, undertaken since entering the Stanford program. These may include:
      1. a new draft research manuscript (a previously published paper is not acceptable).
      2. 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.
  2. Second year: Each student must pass a two-part qualifying exam.
    1. dissertation proposal: The student should form her/his thesis committee well before the anticipated date of dissertation proposal defense, and should consult committee members in a timely manner to make sure their expectations are clearly understood, and to allow time to produce a professionally effective written proposal. In general, the student should prepare a written document and spoken presentation sufficient to support a 30 minute presentation of the goals of the thesis, typically including preliminary data, models, etc. as appropriate which are relevant to at least the first goal, and should be prepared thereafter to discuss questions raised by the committee in professional scientific depth. An oral examination is held after submission of the written proposal to the dissertation advising committee comprised of three faculty members. The written proposal is due by May 15, and the oral defense must take place no later than June 15. Advancement to candidacy depends on completion of the dissertation proposal and oral exam.

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