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Ph.D in Neuroscience
Degree Requirements
2022-2023 Neurosciences Graduate Program Handbook (PDF)
The following requirements must be met to obtain a PhD in Neurosciences:
- Participate in Boot Camp
- Complete 3 Research Rotations
- Complete Coursework
- 6 Core Courses covering molecular, cellular, systems, and clinical neuroscience, behavior, anatomy, statistics, and ethics
- Minor Proposition Course & Exam
- 12 units of Electives to expand knowledge in specific areas of neuroscience
- Research Rounds for 2 years (6 quarters) to learn about NGP students' research and improve presenting skills
- Complete TA requirement (1 quarter)
- Advance to Candidacy
- Defend your Dissertation
Timeline
Normal progress toward the degree means that each student is expected to move through a series of milestones necessary to obtain the PhD at a reasonable pace and at the proper level of performance.
Under normal circumstances, students in the Neurosciences Program should be able to earn the PhD in less than 6 years.
Requirements
Advancement to Candidacy
To Advance to Candidacy students must assemble their full Doctoral Thesis Committee and meet with them for the Qualifying Exam. The Qualifying Exam is required by the Graduate Council of the Academic Senate to evaluate the quality of the dissertation work completed to date as well as the proposed additional experiments. The emphasis of the exam is on the conceptual rationale of the dissertation proposal. In addition, it is the charge of the Doctoral Committee to estimate the time required to complete the project. Passing the qualifying exam advances the student to candidacy, effectively changing their status from Doctoral student to Doctoral candidate.
The Neurosciences Graduate Program encourages all students to Advance to Candidacy by the end of their third year. MSTP students are required to advance by the end of spring quarter their third year. Non-MSTP Neuroscience students are required to advance by the end of spring quarter of their fourth year.
More information on advancing can be found in the NGP Handbook.
Boot Camp (NEU 210)
All incoming first-year neuroscience graduate students participate in Boot Camp, which is designed to:
- Familiarize them with the basic ideas and techniques of neuroscience
- Acquaint them with senior graduate students (who serve as TAs)
- Introduce them to faculty members and their research
- Help them get to know their classmates
This course, based on summer courses at the Marine Biological Laboratory in Woodshole, MA, is a series of intensive lab exercises that runs for two weeks from morning until midnight. At lunchtime students give short talks about research they have done. The course is held in September just before fall quarter begins. Topics covered include single-cell electrophysiology, computational modeling, molecular techniques, slice electrophysiology, both fly and rodent behavior and electrophysiology and imaging. In addition, faculty members highlight the major research interests being pursued in their laboratories and entering students give informal talks about the research they have done before entering the graduate program.
All incoming students participate in Boot Camp. Students are required to enroll in NEU 210 (Neurobiology Boot Camp Course) during the fall quarter enrollment period to receive credit for this two week course.
Core Courses
By the end of the second year, students are expected to demonstrate competence in the basics of neuroscience by taking the following mandatory course work:
Students must take the NEU 200 series during their first year.
- NEU 200A Basic Neuroscience: Cellular, Molecular & Developmental (4 units)
Instructors: Brenda Bloodgood and Byungkook Lim
This course is offered every fall and covers cellular & molecular neuroscience. Each week, there is one lecture and one discussion section in which research papers are discussed. Topics include cellular physiology, synaptic transmission, neurotransmitters and receptors, plasticity, and neural development. - NEU 200B Basic Neuroscience: Systems Neurobiology (4 units)
Instructors: John Reynolds, Sreekanth Chalasani and Eiman Azim
This course is offered every winter and covers systems neuroscience. Lectures are given by researchers in various fields, coupled with discussion sections on research papers. Topics include visual, auditory, olfactory, somatosensory, and motor systems. - NEU 200C Basic Neuroscience: Cognitive & Behavioral (4 units)
This course is offered every spring and deals with the methods of cognitive neuroscience, and then various topics including object recognition, attention, long-term and working memory, reinforcement learning and executive function.
- NEU 257 Neuroanatomy
Instructor: Eric Halgren
This course is offered every winter and provides a hands-on look at the anatomy of the central nervous system including the key structures and their connectivity and the types of information they carry. MSTP students are waived from NEU 257 if they took SOMC 227 and 237 in Medical School. In addition, the MSTP student will receive an additional 4 units of elective credit for this course.
- BGGN 216 Biostatistics
This statistics course is offered in the spring quarter and covers fundamentals of biostatistics and their practical application, including central tendency and variability, hypothesis testing, parametric and nonparametric inferential techniques, correlation and regression. Practice sets are drawn from the lab and primary literature. Students develop a conceptual understanding of basic principles of probability and statistics, to build a working understanding of how these principles are applied in biology and an appreciation for why good statistics are essential to sound conclusions. Students acquire practical skills using biostatistics software in realistic research scenarios. Recommended for students with little prior experience who desire the minimum required set of competencies. - BIOM 285 Statistical Inference and Experimental Design
This statistics course is offered every winter and spring and is recommended if you’re looking to augment a basic level of competence with more advanced techniques. Please contact one of the NGP Graduate Coordinators for a copy of the syllabus. - COGS 243 Statistical Inference and Data Analysis
This statistics course is offered winter quarter and provides a rigorous treatment of hypothesis testing, statistical inference, model fitting, and data analysis techniques used in neural sciences. Students acquire an understanding of mathematical foundations and hands-on coding experience in Matlab. Facility with calculus, linear algebra and elementary probability theory is assumed. - PSYC 201A/B Quantitative Methods
This statistics course is offered as part of a series every fall and winter, and is recommended if you’re starting from scratch and want to obtain an advanced level of competence.
- NEU 241 Research Ethics
Ethics courses are offered fall, winter and spring quarter each year. This course will cover “ethical” issues in academia, including dishonesty, plagiarism, attribution, sexual misconduct, etc. Also discussed are “survival” issues, including job hunting, grant preparation, journal reviews, writing letters of recommendation, mentoring, etc. Students are required to take an Ethics Course by the end of their second year. Course information and enrollment details are available online through UCSD's Research Ethics Program.
For more information see the NGP Course Catalog and the UC San Diego Course Catalog.
Defense of Dissertation
The Dissertation Defense consists of a public presentation of the dissertation work, followed by public discussion. As well as an oral defense, in closed session, with the student’s Doctoral Committee. Neurosciences Doctoral students are required to defend by the end of their sixth year.
More information on the Dissertation Defense can be found in the Student Handbook.
Electives
Students are required to take 12 units of electives at the graduate level (200+) to expand their knowledge in specific areas. The courses may be taken in almost any department including neurosciences, biology, cognitive science, psychology, medicine, mathematics, or engineering. At least 4 credits need to be advanced topics courses based on reading of primary literature. This can be satisfied either by completing NEU 221 courses or by completing graduate level readings based courses offered by any related discipline. For a list of current and recent offerings, take a look at the NGP Course Catalog. Course offerings are always changing. See the UC San Diego Course Catalog for descriptions of these and other courses.
Electives for Students in the Computational Neuroscience Specialization
Core course requirements for students in the Computational Neuroscience Specialization can be used to fulfill the elective requirement (must be 200 level courses). However, CN students must also fulfill the 4 credits of advanced topics courses based on reading primary literature.
Electives for MSTP Students
MSTP students may petition to receive credit for neuroscience related coursework taken as a medical student, including clerkship, for a maximum of 8 units. A petition to waive an elective requirement should be submitted in writing to the Program Director with a copy of the syllabus of the previous course, and a copy of the transcript showing the grade earned. All MSTP students must take at least 2 units of a reading based elective, and are encouraged to take other neuroscience related electives to broaden their education and subject knowledge.
Example Elective Courses
- NEU 268 Molecular and Cellular Neurobiology (Dr. Pamela Mellon)
- NEU 221 Advanced Topics in Neuroscience (recent offerings):
- Landmark Papers in Neurosciences (Kristan, Issacson)
- Neurobiology of Circadian Clocks (Welsh)
- Principles of Communicating Science (Voytek)
- Glia (Allen, Lemke, Nimmerjahn)
- RNA/Epigenetics in Neural Development and Disease (Wilkinson)
- Genetic Tools in Neuroscience (Hnasko)
- Neural Circuits (Leutgeb), Quantitative Behavior Genetics (Palmer)
- Neurotransmitter-based synaptic plasticity (Dulcis)
- Philosophy in Neuroscience (Bechtel)
- Neurobiology of Learning and Memory (Mayford).
- Using animal models to study neuropsychiatric disorders (Dulawa)
- Chromatin and transcription in the brain: from omics to single cell (Telese)
- Any of the computational neuroscience courses
Course offerings are always changing. See the UC San Diego Course Catalog for descriptions of these and other courses.
Journal Club
The Student Journal Club is organized entirely by students. Each week the student host of the Neuroscience Seminar Series presents a paper from the laboratory of the seminar speaker. The goal of the journal club is to create an open venue for friendly but lively scientific discussion. First year students are required to attend. Refreshments are provided.
First year students who maintain attendance of 70% or better for Journal Club will receive 2 units of NEU 221 credit to count towards elective requirements. Upon approval, and during the fall quarter of their second year, students will enroll in a NEUG 221 section, 2 units, S/U grade option.
Minor Proposition Course & Exam
The Minor Proposition course preparation begins winter quarter of the second year. The minor proposition proposal must be completed and the oral exam passed by the end of spring quarter. Students will enroll in Minor Proposition (NEUG 280), 4 units.
Minor Proposition is an intensive writing course required for second-year neuroscience graduate students. This course provides an overview on the preparation, submission, and response to feedback of a NRSA F30/31 grant application. Students prepare an entire application on the topic of their choice – likely on their research interest and in support from their primary mentor. Target deadlines for application components are provided with overview lectures on navigating the NIH system, descriptions on the importance of the Training Plan, and opportunities to write, discuss, and obtain feedback throughout the process. At the end of the course, students ‘submit’ their application for review, which is subsequently discussed at a mock study section and feedback provided. Upon receipt of feedback, the students prepare a response in addition to an oral defense to the reviewers of their application.
Students completing their application and defending their application and response to reviewers will receive a passing grade, those incomplete will not pass. Student with the best ranked score will receive a $500 award to go toward conference travel or educational needs. Students must receive a passing grade in the course, based on a successful written proposal and oral exam, to continue in the graduate program. Students are eligible to receive a continuing Master’s degree upon passing the Minor Proposition Course.
Pre-Thesis & Thesis Committees
Pre-Thesis Committee
Before the end of their second-year, students are required to assemble a Pre-Thesis Committee. This committee provides scientific input on the dissertation project and evaluates students at the end of each year after the first (i.e. once they have joined a laboratory) and until they advance to candidacy. This evaluation is primarily related to the students’ research rather than to their course work. The committee consists of the Thesis Advisor and two other members of the Graduate Program faculty group (one of the members may be from outside the program by approval of the Program Director). Typically, the Pre-Thesis Committee would become the nucleus of the Doctoral Committee. The full four member Doctoral Committee must be formed by winter quarter of the third year.
All students are required to meet with their Pre-Thesis or full Doctoral Committee, once formed, every spring. This meeting serves as the annual Spring Evaluation. This evaluation is primarily related to the students’ research rather than their course work. The meeting should contain an oral presentation by the student, outlining progress made and plans for the future. Students must submit a 1-2 page written thesis proposal to their committee prior to the first pre-thesis spring evaluation meeting.
Thesis Committee
Prior to advancing to candidacy, students must assemble their full Doctoral Committee, during their third or fourth year. Students meet yearly with this committee to evaluate their progress to date, recommend the modifications to the dissertation’s scope or methodology, timetable for completion, and recommendation for support in the following year. The Doctoral Committee conducts the qualifying examination, conducts the students annual Spring Evaluation, supervises the preparation and passes upon the dissertation, and administers the final examination.
The Doctoral Committee should comprise a minimum of four members. Names of the proposed committee members must be submitted to the Graduate Program Administrator at least one month prior to the anticipated advancement exam date. After review, the Administrator will send the nomination form to the GEPA for review and approval. Students should not schedule their advancement until they have received final approval for the appointment of their doctoral committee by GEPA.
Effective Fall 2021, the Doctoral Committee should comprise of a minimum of four members. Names of the proposed committee members must be submitted to the Graduate Program Administrator at least one month prior to the anticipated advancement exam date. After review, the Administrator will
send the nomination form to GEPA for review and approval. Students should not schedule their advancement until they have received final approval for the appointment of their doctoral committee by GEPA.
More information on Pre-Thesis and Thesis Committees can be found in the NGP Handbook.
Research Rotations
Research rotations provide the opportunity for first-year students to obtain hands-on research experience in several different laboratories. Through the rotations, students identify a faculty member under whose sponsorship and in whose laboratory their dissertation research will be completed.
Students must complete three rotations for a minimum period of nine weeks each. Rotation advisors should be selected from the Neurosciences Graduate Program Faculty; although, non-affiliated faculty may be selected upon pre-approval from the Program Director. Students must arrange their own rotations, but during Boot Camp students are exposed to many faculty looking for students. Students should enroll in NEUG 296 to receive credit. Contact the Program Coordinator for creation of NEUG 296 with rotating Faculty.
Prior to the beginning of the rotation, the student and faculty member should discuss their expectations and goals. Regular meetings between the student and the faculty advisor are required. At the conclusion of each rotation, the faculty member will submit a written evaluation of the student’s performance to the Graduate Program office.
All three rotations must be completed by the end of the spring quarter of the student’s first year. By this time, each student should have identified the Program Faculty member under whose sponsorship and in whose laboratory their dissertation research will be completed. A fourth rotation requires approval from the Program Director and should be undertaken only in special circumstances.
Research Rotations for MSTP Students
MSTP students are expected to have completed at least two research rotations before joining the graduate program, and must complete a total of three rotations before joining a thesis lab. At least two of the rotations must be in labs associated with the Neurosciences Graduate Program. MSTP students must complete all rotations by fall Quarter after entering the graduate program, and must select a thesis lab by the end of the fall Quarter.
Time Limits
Each Ph.D. program at UCSD has three time limits: 1) Pre-Candidacy, 2) Support, and 3) Total Registered. These are assigned at the end of a Ph.D. student's first year.
Pre-Candidacy Time Limit
Neurosciences Graduate Students are encouraged to advance to candidacy by the end of their third year. MSTP students are required to advance by the end of spring quarter of their third year. Non-MSTP Neuroscience students are required to advance by the end of spring quarter of their fourth year. The University will not allow students to register for the fall quarter following the advancement deadline or receive any financial support unless they have successfully advanced to candidacy.
Support Limit
This is the maximum time during which a doctoral student is eligible for support. Students must complete all requirements by the end of their sixth year. MSTP students must complete all requirements and defend within 6 years. Their total registered time limit is also 6 years. At the end of the sixth year, the student is no longer allowed to register at the University. Non-MSTP students may continue as a student for an additional seventh year, but will not be eligible for financial support during that year. This includes all stipend, fees/tuition payments, fellowships, scholarships, and employment administered by the University and its affiliated institutions (i.e. the Salk Institute, the Sanford-Burnham Institute, and the Scripps Research Institute), but does not affect financial aid loans. Since students cannot receive any support, they will be required to pay their own tuition/fees to be eligible for student health insurance and student housing.
Total Registered Time Limit
This is the maximum registered time in which a student must complete all Ph.D. requirements. As noted above, MSTP students must complete all Ph.D. requirements by the end of the sixth academic year, thereafter the student is no longer allowed to register at the University. Non-MSTP Neuro students must complete all Ph.D. requirements by the end of the seventh academic year. At the end of the seventh year, the student is no longer allowed to register at the University.Research Rounds
Research Rounds is a weekly seminar course that meets in Fall, Winter and Spring quarters, in which graduate students beyond their second year in the program present their current research. All students in their first and second years are required to take Neurosciences Research Rounds (NEU 276) for six quarters. Students engage in scientific discussion as well as constructive criticism on the presentations meant to enhance the skills of both the audience and presenters.
Teaching Apprenticeship
All students are required to be a teaching assistant (TA) for at least one quarter during their graduate career to develop their talents and gain experience as teachers. Opportunities to lecture and to assist in laboratory exercises and demonstrations are available through many departments, including Neurosciences, Biology, Cognitive Science and Psychology. The teaching requirement must be fulfilled before advancement to candidacy.
Furthermore, as TAships are a curriculum requirement for the program, they are not a source of supplementary income. In cases where the students’ TAships provide financial support, the total annual support will remain at the standard level, currently $36,000/year. Students are encouraged to complete their TA requirement during their second or third year, and should contact the instructor of the course they wish to TA. In addition, students must inform the Graduate Program Administrator at least three weeks prior to the beginning of the quarter when the TAship starts. Students TAing for NEUG courses or others that do not have a specific TA section listed should enroll in NEUG 500 Apprenticeship Teaching for 2 Units with the Program Director.