Doctor of Philosophy
PhDJoint DegreeOverview
Learn how to approach and solve research problems by developing skills in modern methods of neuroscience research, the ability to appraise the scientific literature and make scientific judgments, and ultimately, to function as an independent creative neuroscientist.
Requirements
Program Requirements
Core Courses
Required courses must be taken for a letter grade and passed with a 3.0 (B) or better. MSTP students will take NEPR 209, NEPR 211, NEPR 212, and NEPR 288. MSTP students will take one of NEPR 201, NEPR 203, NEPR 207, or NEPR 208. MSTP students will also take either NEPR 202 or NEPR 204.
Students must also complete the Stanford Immersive Neurosciences (SIN) Boot Camp.
Students must complete special sessions in neuroanatomy. (Not required for MSTP students.)
9 quarters of NEPR 280 (Journal Club) are required. MSTP students in the Neurosciences PhD program are required to take 3 quarters of Journal Club and at least 2 quarters must be taken for 2 units.
NEPR 201
Neuro-Cellular Core
NEPR 202
Neurosciences Development Core
NEPR 203
Neuroscience Systems Core
NEPR 204
Neuroscience Molecular Core
NEPR 206
Neuroscience Data Basics
NEPR 207
Neurosciences Cognitive Core
NEPR 208
Neuroscience Computational Core
NEPR 209
Introduction to Mathematical Tools in Neuroscience
NEPR 211
Animal Behavior for Neuroscientists
NEPR 212
Responsible Conduct of Neuroscience Research
NEPR 213
Neurogenetics Core
NEPR 280
Neuroscience Journal Club and Professional Development Series
NEPR 288
Cellular/Molecular Neuroscience Laboratory
Statistics and Reproducible Research
Students must complete BIOS 217 as well as one graduate statistics course from the list below; pre-approval is required.
Foundations of Statistics and Reproducible Research
BIOS 217
Foundations of statistics and reproducible research
Additional Statistics Course
BIO 141
Introduction to Statistics for Biology
COMPMED 211
Robust, reproducible, real-world experimental design and analysis for life and biomedical scientists
CS 109
Introduction to Probability for Computer Scientists
CS 228
Probabilistic Graphical Models: Principles and Techniques
EE 178
Probabilistic Systems Analysis
EPI 258
Introduction to Probability and Statistics for Clinical Research
MS&E 226
Fundamentals of Data Science: Prediction, Inference, Causality
PSYCH 204B
Computational Neuroimaging: Data Analyses
PSYCH 252
Statistical Methods for Behavioral and Social Sciences
STATS 117
Introduction to Probability Theory
STATS 141
Introduction to Statistics for Biology
STATS 191
Introduction to Applied Statistics
STATS 200
Introduction to Theoretical Statistics
STATS 202
Statistical Learning and Data Science
STATS 207
Time Series Analysis
STATS 215
Statistical Models in Biology
STATS 217
Introduction to Stochastic Processes I
STATS 219
Stochastic Processes
STATS 220
Machine Learning Methods for Neural Data Analysis
STATS 305A
Applied Statistics I
STATS 315A
Modern Applied Statistics: Learning
STATS 320
Machine Learning Methods for Neural Data Analysis
STATS 325
Multivariate Analysis and Random Matrices in Statistics
STATS 369
Methods from Statistical Physics
Required courses must be taken for a letter grade and passed with a 3.0 (B) or better.
Advanced Courses
Our program embraces the highly interdisciplinary nature of neuroscience research by allowing students to create an individualized curriculum of advanced topic courses best suited to their research agenda and scientific development needs. This approach has empowered students to take advantage of the breadth of expertise across the university. A minimum of six credits of Advanced Topics coursework is required of each student. Students select the courses while meeting the following criteria: (1) at least one course must be taken with a minimum of three units, (2) the course must have a clear means of evaluation (i.e., problem sets, paper writing, class presentations), and (3) the student must detail how the course relates to the student’s project or domain of neuroscience. This information is submitted in writing along with the course syllabus and examples of problem sets to the co-directors/curriculum committee co-chairs for approval.Six units of advanced neuroscience coursework are required. To complete the six units, at least one course must be three units or more; the remaining units can be completed with a combination of smaller-unit courses (e.g., 3+2+1, 3+2+2, 4+2).
One course of 3 units of advanced neuroscience coursework are required for MSTP students.
Pre-approval for advanced courses is required.
Required courses must be taken for a letter grade and passed with a 3.0 (B) or better.
Rotations
NEPR 299
Directed Reading in Neurosciences
Students rotate through at least three labs during the first year, enrolling in NEPR 299 each quarter, while taking core courses. MSTP students are exempt from this requirement because they will have completed their rotations in the first year of their MD program.
First Author Publication
Students must publish at least one first-author paper in a peer-reviewed major scientific journal on the defended work before completing the PhD degree.
Advancement to Candidacy
Oral Exam
Passing a comprehensive qualifying examination given by the student’s advisory committee is required for admission to PhD candidacy.
The qualifying exam assesses whether the student is ready to advance to candidacy by proposing a thesis project of acceptable scope and feasibility, that the student is prepared to take on the research, has justified the research in terms of background, significance and innovation and has a well-justified approach.
The qualifying exam includes a qualifying exam proposal in the style of an NIH NRSA proposal and a written rigor document which outlines how the proposed research has addressed NIH's four key areas of rigor as well as a plan for dissemination for research outcomes and products.
The qualifying exam must be taken by May 31 of the second year for students starting AY26-27, and by June 30 for those starting AY25-26 and earlier.
Oral Exam
Oral Examination
Students must defend the dissertation in a University Oral Examination that includes a public seminar.
Dissertation
Dissertation
Students are required to prepare a PhD dissertation that is the result of an independent investigation accomplished while enrolled in the program that contributes to knowledge in an area of neuroscience.

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