Doctor of Philosophy
PhDOverview
The Stanford Stem Cell Biology and Regenerative Medicine (SCBRM) program is dedicated to doctoral education that translates basic science to clinical applications, typically called Translational Science, and is of intense interest internationally in medical schools and universities. Our doctoral program provides exceptional didactic education and research experience in the basic sciences underlying stem cell biology. In addition, program participants will receive specialized training in developing and clinically applying discoveries in the basic sciences to achieve regenerative therapies. Thus, our graduates will be uniquely positioned to develop successful translational careers in Stem Cell Biology and Regenerative Medicine. They will emerge prepared to deliver on their passion for improving the human condition. The core curriculum combines unique research and clinical/professional immersion rotations to provide opportunities for doctoral students to specialize in the broad subject of translational medicine and yet focus specifically on the fundamentals of SCBRM. The curriculum combines genetics and developmental biology education with an introductory laboratory-based stem cell course, an advanced course in stem cell biology and regenerative medicine, and a clinical rotation with alternative law, business, and/or engineering opportunities.
Requirements
Program Requirements
Requirements Overview
Each student should complete three one-quarter laboratory rotations during their first year, with two one-quarter laboratory rotations being the minimum in special circumstances.
Students must perform two full quarter rotations in two different ISCBRM labs. Your first rotation (autumn quarter) must be with a member of the Institute of Stem Cell and Regenerative Medicine. If you are an ADVANCE student, your rotation in autumn quarter must be with a member of the Institute (even if you rotated with a member of the Institute in the summer).
All rotations outside of the Institute must be approved by the first-year faculty mentor or the Director of Graduate Studies via email prior to the start of the rotation.
At the end of their rotations, students will select a lab for thesis work with the signed approval of their first-year advisor. We encourage students to select a lab within the Institute, but it is possible to join labs that are outside the Institute.
Joining a lab outside the Institute requires approval from the Faculty Executive Committee who will give permission based on mentorship record, area of study, and funding capacity of the chosen lab. To initiate this process, the student must submit a one page description stating why they want to join the particular out-of-Institute lab for the executive committee to review.
The final deadline to choose a dissertation advisor is before the end of spring quarter of the first year.
SCBRM graduate students must be registered in all quarters. All required courses, including those counting toward the 10 units of elective credit, must be taken for a letter grade if offered and must be passed with a B grade or better. The course must be repeated if a student does not earn a B grade or better.
Core Courses
BIOS 200
Foundations in Experimental Biology
DBIO 210
Developmental Biology
MED 255
The Responsible Conduct of Research
STEMREM 201B
Ethical Issues in Stem Cell Biology
STEMREM 200
Stem Cell Intensive
STEMREM 201A
Stem Cell Biology & Regenerative Medicine
STEMREM 205
Bioinformatics for Stem Cell and Cancer Biology
STEMREM 250
Regenerative Medicine Seminar Series
STEMREM 280
Stem Cell Biology and Regenerative Medicine Journal Club
STEMREM 399
Graduate Research
Other Mandatory Courses
STEMREM 802 TGR (Register for 0 units each quarter once Terminal Graduate Registration (TGR) is achieved. TGR is achieved after completing 135 total units (spring quarter of year 4) and all required core coursework.)
STEMREM 802
TGR Dissertation
Electives
Complete a total of 10 units from Elective 1, Elective 2, and Elective 3 sections below.
Elective 1: Biochemistry Elective
Students must complete
BIOC 241
Biological Macromolecules
BIOE 331
Protein Engineering
BIOE 361
Biomaterials in Regenerative Medicine
BIOE 385
Biomaterials for Drug Delivery
BIOS 204
Modeling Cell Signaling
BIOS 294
Chemistry for Biologists and Others
CSB 250
The Biology of Chromatin Templated Processes
CSB 260
Concepts and Applications in Chemical Biology
Elective 3: Science Elective(s)
BIO 152
Imaging: Biological Light Microscopy
BIOE 374A
Biodesign Innovation: Needs Finding and Concept Creation
BIOE 390
Introduction to Bioengineering Research
BIOS 217
Foundations of statistics and reproducible research
BIOS 224
Stem Cell Biology and Applications
BIOS 227
Mass Spectrometry and Proteomics: Opening the Black Box
BIOS 229
Open Source Prototyping: Translating Ideas to Reality using Rapid Prototyping Methods
BIOS 268
Biology and Applications of CRISPR/Cas9: Genome Editing and Epigenome Modifications
BIOS 272
Science and Art
BIOS 296
Preparation & Practice: Biotechnology Business
BIOS 319
Analysis of Public Companies in the Life Sciences
BIOS 412
Antibody Anywhere All at Once: An Introduction to Techniques in Immunology
BIOS 420
Building Connections, Defining the Future of Biosciences
BMDS 210
Modeling Biomedical Systems
CBIO 240
Molecular and Genetic Basis of Cancer
COMPMED 210
Form and Funkiness of Lab Animals : Anatomy, Histology, and Pathology
CS 106A
Programming Methodology
CSB 243
Biotechnology and Development of Therapeutics
CSB 245
Economics of Biotechnology
ENGR 208
Patent Law and Strategy for Innovators and Entrepreneurs
IMMUNOL 201
Advanced Immunology I
MCP 256
How Cells Work: Energetics, Compartments, and Coupling in Cell Biology
OTOHNS 204
Biology and Physics of Hearing
STATS 195
Introduction to R
STEMREM 223
Biology and Disease of Hematopoiesis
STRAMGT 353
Entrepreneurship: Formation of New Ventures
135 units of coursework: including research, required courses, and approved electives.
Maintain satisfactory degree progress with a significant physical presence on campus during the duration of the degree (GAP 3.1.1).
Advance to Ph.D. candidacy through a University Oral Examination on proposed research (aka, “Qualifying Exam”)
Biochemistry proficiency is required by the end of the second year, as well as a total of 80 units and completed qualifying examinations. Students who do not pass the qualifying examination may retake a full qualifying exam, be retested in a few areas, or be asked to redo their presentation.
Students must take advanced science elective units relevant to the dissertation and career goals, totaling at least ten units.
All courses, including those counting toward the 10 science elective units, are taken for a letter grade when offered. Courses must be passed with a B or better; repeat the course if below a B is received.
Present research at Stem Cell Club.
Submit at least one first- or co-first-author peer-reviewed primary research manuscript to a journal (BioRxiv does not satisfy this requirement). Submission proof must be provided to the Student Services Officer and Director of Graduate Studies no later than the day the thesis is due.
Perform a University Oral Examination on thesis research (aka, “Thesis Defense”).
Submit a written dissertation approved by the Dissertation Reading Committee.
MSTP Requirements
If you are in the Medical Scientist Training Program (MSTP) MD-PhD program pursuing a PhD in Stem Cell Biology and Regenerative Medicine, unlike your SCBRM PhD peers, you are NOT required to take:
BIOS 200 - Foundations in Experimental Biology
DBIO 210 - Developmental Biology
STEMREM 200 - Stem Cell Intensive
10 units of science electives toward the PhD
You are also not required to do 3 rotations since you will come to us already in a lab.
MSTP Required Courses for the SCBRM PhD
Core
Complete ALL of the following Courses:
MED 255 (Take in year two. Your PhD cohort will take it in year 1) or STEMREM 201b
STEMREM 201A - Stem Cell Biology & Regenerative Medicine
STEMREM 205 - Bioinformatics for Stem Cell and Cancer Biology
STEMREM 250 - Regenerative Medicine Seminar Series (ReMS) (To be repeated 5 times. 5 units required.)
STEMREM 280 - SCBRM Journal Club (To be repeated 5 times. 5 units required.)
STEMREM 399 - Graduate Research
Grant Writing
Required Course
Complete one of the following courses:
BIOS 242 - Writing Compelling Fellowships and Career Development Awards
BIOS 299 - Online Proposal Bootcamp
BIOS 425 - Independent Study: Write a Grant Proposal in 9 Weeks
Advancement to Candidacy
Advancement to Candidacy
Prior to being formally admitted to candidacy for the PhD degree, the student must demonstrate knowledge of Stem Cell Biology and Regenerative Medicine fundamentals and a potential for research by passing a qualifying oral examination in their second year.
The exam consists of an NIH-style written grant proposal and an oral examination. The Qualifying Exam Committee includes three faculty members but does not include the student’s thesis advisor. The examining committee includes the committee chair, who is an Academic Council member outside of ISCBRM and outside of the research mentor's department, and 2 ISCBRM faculty members (not including the research mentor) who are Academic Council members.
The written and oral proposal should represent the student’s efforts to identify a question of interest and to develop appropriate experimental approaches. The proposal must be submitted to committee members no later than ten days before the examination. The first page is a Specific Aims page, and other sections include Background-Significance and Research Plan (including a discussion of alternative approaches). The qualifying exam must be completed by the end of Autumn quarter of the second year and successful outcome is required to continue in the PhD program. If necessary, one retake will be permitted in the quarter following the first exam attempt.
Oral Exam
Oral Exam
A University Oral Examination is also required for the PhD degree. In the Stem Cell Biology and Regenerative Medicine Program, the PhD candidate presents a public seminar (one hour), followed by a closed-door oral examination. The University Oral Examination Committee consists of at least four examiners, including the student’s PI and a chair from an academic department outside of SCBRM, for a total of five people. All members of the Committee are usually members of the Academic Council, and the oral examination chair must be AC. With the prior approval of the ISCBRM Director, one of the examiners may be a person who is not a member of the Academic Council if that individual contributes expertise not readily available from the Stanford faculty. Official responsibility for selecting the oral examination committee rests with the student and their dissertation advisor.
Dissertation
Dissertation Overview
The major accomplishment of each successful PhD student is the presentation of a written dissertation resulting from an independent investigation that contributes to knowledge in Stem Cell Biology and Regenerative Medicine.
Annual Dissertation Committee Meetings
In year one, a dissertation committee meeting is not required.
In year two, the qualifying exam is in place of the dissertation committee meeting.
In years three and four, each student must hold an annual dissertation committee meeting to assess progress toward the degree and for the committee to provide advice.
In the fifth year and beyond, students are required to meet with their thesis committee twice a year.
Failure to meet with your dissertation committee within the required time frame will result in academic probation.
The Annual Dissertation Committee Meeting Form should be completed and signed by all committee members attending each meeting. The form should be returned to the SCBRM SSO.
Dissertation TGR Course
STEMREM 802
TGR Dissertation

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