BIOC-PHD - Biochemistry (PhD)
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Program Overview
Biochemistry is a department within the School of Medicine, with offices and labs in the Beckman Center for Molecular and Genetic Medicine at the Stanford Medical Center, the Shriram Center for Bioengineering and Chemical Engineering, and the Stanford Genome Technology Center. Undergraduates and graduate and medical school students may take courses the department offers.
The Department of Biochemistry focuses on the molecular basis of life by studying the structures and functions of proteins and nucleic acids, the control of development, molecular motors and the cytoskeleton, trafficking of proteins between organelles, regulation of gene expression, protein homeostasis, structure and design, genetic and epigenetic control of chromosome function, and the application of genomics, all toward the understanding of health and disease. Advanced courses in more specialized areas emphasize the most recent developments in biochemistry, biophysics, cell biology, and molecular biology. These courses include the physical chemistry of proteins and nucleic acids, membrane biology and biochemistry, the cytoskeleton, mechanisms and regulation of nucleic acid replication and recombination, the biochemistry of bacterial and animal viruses, the molecular basis of morphogenesis, and the structure and function of both eukaryotic and prokaryotic chromosomes.
The Department of Biochemistry offers a PhD program that begins in autumn quarter of each year. The program of study is designed to prepare students for productive careers in biochemistry; its emphasis is training in research, and each student works closely with faculty members. Opportunities exist for directed reading and research in biochemistry and molecular biology using the most advanced research facilities, including those for light and electron microscopy, chromatography and electrophoresis, protein and nucleic acid purification, rapid kinetic analysis, synthesis and analysis, single-molecule analyses using laser light traps, microarray generation and analysis, and computer graphic workstation facilities for protein and nucleic acid structural analysis. Ongoing research uses a variety of organisms, from bacteria to animal cells.
Admissions Information
The Department of Biochemistry welcomes graduate applications from individuals with a broad range of life experiences, perspectives, and backgrounds who would contribute to our community of scholars. The review process is holistic and individualized, considering each applicant’s academic record and accomplishments, letters of recommendation, prior research experience, and admissions essays to understand how an applicant’s life experiences have shaped their past and potential contributions to their field and how they might enrich the learning community at Stanford.
The Department of Biochemistry recognizes that the Supreme Court issued a ruling in June 2023 about the consideration of certain types of demographic information as part of an admission review. All applications submitted during upcoming application cycles will be reviewed in conformance with that decision.
The Stanford Biosciences Admissions Office, not the Department of Biochemistry, processes applications for the Ph.D. program. Information on how to apply for graduate study at Stanford is available on the university’s Graduate Admissions website. All materials should be uploaded electronically to the online application.
2025-2026 Admissions Timeline
Application Opens: Mid-September 2025
Application Deadline: December 2, 2025 at 11:59:59 PM (PST)
Interview Session (in-person): March 4 through March 8, 2026
Those applying for graduate study should have at least a baccalaureate degree and complete work in cell and developmental biology, basic biochemistry and molecular biology, and genetics. Also required are: at least one year of university physics; differential and integral calculus; and organic, inorganic, and physical chemistry. The department is especially interested in applicants with research experience in biology or chemistry. All applicants are urged to compete for non-Stanford fellowships or scholarships, and U.S. citizens should complete an application for a National Science Foundation Predoctoral Traineeship.
Postdoctoral research training is available to graduates with a PhD or an MD degree. Qualified individuals may write to individual faculty members for further information.
Minimum Units in the Program
Minimum University Units
Students graduating with a PhD in Biochemistry from Stanford are expected to be generally proficient in four core scientific areas relevant to biochemical research and the specific scientific areas most relevant to their particular thesis projects. The four core proficiency areas are:
Biochemistry and Biophysics
Quantitative and Computational Techniques
Genetics
Cell Biology
Proficiency can be demonstrated by successfully completing three full quarter graduate-level courses of these four areas or by other means with the permission of the graduate advisor. Each quarter course can be replaced by two mini-courses.
In addition to the requirement for a PhD dissertation based on original research, students must complete advanced courses in biochemistry and related areas in their first year as part of the 135 total units required for the Ph.D. We enthusiastically recommend elective courses based on scientific interests.
The Biochemistry Department will allow up to the University limit of 45 units of graduate level course work to apply towards department degree requirements.
An additional requirement involves the submission of two research proposals. The student presents these proposals to a small committee of departmental faculty members responsible for monitoring the progress of student curricular and research programs and a journal club presentation. All PhD students must participate actively in the department’s seminar program. Students are encouraged to attend and present papers at regional and national meetings in cellular biochemistry and molecular biology.
Teaching experience is an integral part of the PhD curriculum and is required for the degree. Students must notify the Student Services Administrator.
The Department of Biochemistry offers only an MS to students already enrolled in the PhD program. Students should contact the Graduate Studies advisor for more details.
First rotation must be in the Biochemistry Department. Length of rotation is flexible. Choose a lab at the end of first year, preferably by the end of spring quarter. First year students should be enrolling in BIOC 399 under Biochemistry's Graduate Advisor for all their rotations. Once a student has committed to a lab, the student should sign up for the "Graduate Research" course under their advisor; i.e., if a student committed to a lab under an advisor in Chemical and Systems Biology, the student must sign up for CSB 399 "Graduate Research" under the advisor.
Take three full quarter courses. Each course may be selected from any of the following areas:
Biochemistry and Biophysics
Quantitative and Computational Techniques
Genetics
Cell Biology
Each quarter course can be replaced by two mini-courses (which run 1-3 weeks). We enthusiastically recommend additional elective courses based on scientific interests.
Other courses may be discussed with the Graduate Advisor.
Coding:
CS 106A - Programming Methodology
CS 106B - Programming Abstractions
STATS 101 - Data Science 101
Mini-courses in R from the Department of Biomedical Data Sciences
Genomics:
DBIO 173A - Foundations of Computational Human Genomics
GENE 214 - Representations and Algorithms for Computational Molecular Biology
BIOE 279 - Computational Biology: Structure and Organization of Biomolecules and Cells
BIOS 253 - Primary concepts in Bioinformatics - To Make Sense of Large Scale Biological and Biomedical Data (mini-course)
Statistics:
STATS 101 - Data Science 101
STATS 116 - Theory of Probability
Mathematical Modeling:
BIOE 209 - Mathematical Modeling of Biological Systems
BIOS 204 - Modeling Cell Signaling (mini-course)
Students may choose to take any graduate-level courses across science, engineering, or mathematics disciplines at Stanford to gain both breadth and depth; there is no required minimum number of electives. However, students must reach the university minimum requirement of 135 units. Students are encouraged to consult with their advisors to select courses that complement their research focus and long-term goals.
Preparation for the 1st Proposal starts as soon as one joins a lab. Second year graduate students will enroll in BIOC 350 "Development of Thesis Research" during the Autumn quarter. The class will meet once a week to prepare the student for writing and presenting their proposal. Second year graduate students will defend their proposals before their Thesis Committee by the end of Winter quarter.
Students will adapt their 1st Proposal into fellowship applications for submission in Autumn quarter of their 3rd year.
Third year graduate students will enroll in BIOC 360 "Developing an Original Research Proposal" during the Spring quarter. The aim of the 2nd Proposal is for students to explore their interests and develop their ability to find scientific questions.
Students will provide:
A 1-page Specific Aims (okay if it goes slightly over); this will be reviewed in meetings and will be handed out to the presentation audience.
A roughly 10 minute presentation to the department, with ample time for questions and discussion.
Any student not wanting to participate in the group activity (BIOC 360) should petition in writing to the Graduate Advisor, with an outline of their plan and timeline for completing the Proposal in time to present in one of the group presentations. The student must notify the Student Services Administrator.
Journal Club is designed to bring together students, post docs, and faculty to discuss interesting, exciting, and important topics from the literature. The aim of Journal Club is to provide a unique opportunity for students to hone their presentation skills and to bring the department up-to-date regarding recent scientific developments. It is designed to help advance students as they begin to present at scientific conferences and apply for post-doctoral and professional positions.
Every 4-6 weeks, one 4th year student and one faculty member will present a research discussion based on recent paper or developing scientific topics of general interest. Each student will present on a topic outside their thesis research to the Biochemistry Department.
Admission to candidacy is a judgment by the faculty in the department of the student's potential to successfully complete the requirements of the degree program. Students are expected to complete department qualifying procedures and apply for candidacy by the summer quarter of their second year in the PhD program. This form is forwarded to the Registrar's Office and indicates that the student is formally qualified for the PhD degree and is in good academic standing. The form requires listing completed Stanford course work with at least 3 units of course work taken with each of four Stanford faculty members.
Once a student is admitted to candidacy, the status is valid for five years; subject to termination by the department if progress is unsatisfactory. In special circumstances, it may be renewed by the submission and approval of a new application or extended upon the chairman's recommendation.
At the oral examination, a student will first present to an open audience a seminar on the thesis, after which there is an open question period. Then, the examining committee meets in private with the candidate for further discussion of the general area of the research works and to test the candidate's command of biochemistry and fitness for scholarly pursuits.
Student should see the Student Services Administrator for the appropriate instructions and forms before establishing a Dissertation Reading Committee and Oral Examination. The student's committee must consist of at least five members: four examiners (the student's thesis committee plus one) and one University chair (chair cannot have an appointment in the same department as the student or the student's advisor). Approval to deviate from this assemblage requires approval by the graduate advisor and the student's thesis advisor.
Students must complete a draft of the PhD thesis that is acceptable to the reading committee, which is typically, but not necessarily, the same as the proposal committee. Students must submit their finalized thesis following their oral examination.
Deadlines for submitting the thesis to the Registrar's Office and applying to graduate can be found on the Registrar's website at: https://studentservices.stanford.edu/my-academics/earn-my-degree/graduate-degree-progress/dissertations-and-theses/submit-your. The student must be registered in the quarter in which they will turn in their thesis. Tuition can be reduced in the student's final quarter by completing a "Petition for Graduation Quarter." Students must notify the Student Services Administrator if they plan to take a Graduation Quarter.