Graduate Program Handbook | Integrative Neuroscience Ph.D. and M.S.

Program handbook

Please note: this represents the program handbook for the current academic year only. For an archived version of a previous year's handbook, please contact the program directors.

Program description

Neuroscience is an interdisciplinary program, drawing on faculty and courses from many campus units, including the Colleges of Liberal Arts, Science, and Engineering, and the School of Medicine. Study programs lead to the Master of Science and the Doctor of Philosophy degree. The program provides training in the core foundations of neuroscience, ranging from cellular mechanisms to cognition and behavior, with a wide range of options for advanced training and specialization within specific subdisciplines.

The program is designed to provide training in fundamental concepts and methods in modern neuroscience, and emphasize interdisciplinary and integrative approaches which are seen as central to major advances in the field. The program also emphasizes the development of research skills that will position students to be competitive in academic and research-oriented careers. Student learning outcomes include 1) comprehensive understanding and ability to critically evaluate current knowledge and theories in neuroscience; 2) research skills to effectively identify, design and carry out independent research; and 3) professional development including communication and teaching, grant-writing, and ethics.

Doctor of Philosophy degree

A. Program entrance requirements

An applicant to the program at the doctoral level must meet all requirements established by the Graduate School. Students admitted to the program will be expected to have obtained at least a 3.0 undergraduate grade point average (4 point system). Combined GRE scores of 300 (2012 scoring system) are recommended but not required for admission. Course preparation for the program will be determined on an individual basis. However, all students will be expected to have a basic background in science including a minimum of 3 semester credits each in Calculus, Physics, Chemistry, and Biology. Students lacking this background may be admitted with the provision that appropriate remedial coursework is completed.

B. Program requirements

Academic requirements as determined by the Graduate School and the Program must be met by all program students. Required and elective courses must be chosen from the program curriculum outlined below, and the plan of study requires approval of the student’s advisor/examination committee and the program director.

Neuroscience core courses (46 units)
Please note, this is an example. Please refer to your advisor and the for the current requirements.

BIOL 601 – Journal club/ research presentations (4 units)
BIOL 675 – Neurobiology (3 units)
PSY 721 – Advanced Psychophysiology (3 units)
BIOL/PSY/CMPP – First year project (6 units)
BIOL/PSY/CMPP – Second year research (6 units)
BIOL/PSY/CMPP 799 – Dissertation research (24 units)

Courses meeting the first and second year research requirement:

BIOL 691 – Independent study (1 to 3 units) AND
BIOL 792 – Independent research (1 to 3 units)

CMPP 770 – Research rotation (3 units) AND
CMPP 793 – Independent study (1 to 6 units)

PSY 752 – Graduate research (1 to 5 units) AND
PSY 755 – Individual reading (1 to 5 units)

Additional Course Requirements (8 units)

PSY 706 (or equivalent) – Intermediate Statistics (4 units)
PSY/CS/BCH – Computing or bioinformatics options (3 units)
PHAR 725 – Ethics and scientific research (2 units)

Electives (18 units)

Note electives must include at least one course from each of the following clusters:

Cognitive Neuroscience (PSY)

PSY 627 – Computer applications (3 units)
PSY 674 – Integrative Neuroscience (3 units)
PSY 709 – Comparative sensory neuroscience (3 units)
PSY 720 – Seminar in Sensation and Perception (3 units)
PSY 729 – Human Memory (3 units)
PSY 755 – Individual reading (multiple units)
PSY 761 – Contemporary Issues in Psychology (3 units), OR
PSY 762 – Contemporary Issues in Psychology (3 units), OR
PSY 763 – Special topics in Experimental Psychology (multiple units)

Cellular and Molecular Neuroscience

CMB 710 – Molecular Cell Biology (4 units)
BCH 705 – Molecular Genetics (3 units)
BCH 706 – Functional Genomics (3 units)
BCH 709 – Introduction to Bioinformatics (3 units)
BIOL 650 – Special topics (Systems neuroscience) (3 units)
BIOL 654 – Genomic Conflict, Epigenetics & Human Disease (3 units)
BIOL 666 – Developmental Biology (3 units)
BIOL 671 – Neurobiology of Mental Illness (3 units)
BIOL 674 – Integrative Neuroscience (3 units)
BIOL 676 – Clocks, Rhythms and Disease (3 units)
BIOL 677 – Genes, Brain and Behavior (3 units)
BIOL 681 – Principles of animal behavior (3 units)
BIOL 691 – Independent Study (3 units)
BIOL 705 – Current topics in cellular and molecular biology (multiple units)
PHAR 710 – Molecular Pharmacology (3 units)

Offered every third year:

PHAR 730 - Introduction to Imaging and Optics (3 units)
CMPP 740 - Neuroeffector Pharmacology (3 units)
PHAR 750 - Molecular and Cellular Mechanisms of Excitability (3 units)

Total units: 72

General time-line for degree completion

General timeline for degree completion - Example
Year	Fall semester	Spring semester	Summer
Year 1	First-year research project Core coursework Neuro Journal Club	First-year research project Core coursework Neuro Journal Club	First-year project exam Research
Year 2	Neuro Journal Club Advanced Graduate Coursework Research Strongly encouraged to submit NSF application	Neuro Journal Club Advanced Graduate Coursework Research	Research
Year 3	Research	Research Dissertation Proposal/Fellowship Application (Qualifying Exam)	Research
Year 4	Research	Research	Research
Year 5	Research/Thesis Defense	Research/Thesis Defense	Research/Thesis Defense

Additional program requirements

First year research project

Doctoral students in the Neuroscience program will complete 2 semesters of research in their first year. This is designed to expose students to research methods and questions in the discipline and to aid them in selecting an advisor.

Second year fellowship application

All doctoral students will be strongly encouraged to prepare and submit an application for an NSF graduate student fellowship (or equivalent) in fall semester of their second year. The application should be developed in collaboration with their faculty research advisor and is designed both to build grant writing skills and develop their research program.

Pre-doctoral fellowship submission requirement

Students must submit at least one fellowship or grant application during their graduate studies. Students are strongly encouraged to submit a NSF graduate student fellowship, or a NIH F31 pre-doctoral fellowship, or equivalent proposal, as part of this requirement.

Faculty advisor

Upon completion of the first-year project and before the third semester in the program, each student must select a faculty advisor in consultation with the program directors and the desired faculty member, who must be an affiliate member of the program. The advisor must agree to take the student on and will be responsible for supporting the student’s research and providing a stipend according to Neuroscience program guidelines. The advisor will serve as chair of the student’s advisory/examination committee. Once an advisor is chosen the student is required to complete the declaration of advisor/committee chair form (see below) and submit to the Graduate School by the end of the third semester.

Students who are unable to identify an advisor by the end of the third semester will seek advice from the program directors. If an advisor cannot be found, the program directors may recommend that the student be dismissed from the program.

Committee Selection

Each Neuroscience student with advice from their faculty advisor selects a first-year project exam committee and advisory/examination (or dissertation) committee. It is the responsibility of the student to select their committee(s) in a timely manner.

First-year project committee

The committee is required to include the faculty advisor of the project and two additional faculty members in the Neuroscience program, at least one of which is outside the advisor’s home department. Completion of the first-year project exam under a given advisor does not commit the student to working with that advisor or vice versa subsequent to the exam (see below).

Dissertation committee

The advisory/examination committee for the dissertation is required to be chosen by the end of the third semester. The committee must exist of at least five members of the graduate faculty: 1) the committee chair/permanent advisor; 2) at least two faculty members affiliated with the Neuroscience graduate program; 3) at least one faculty member from a department in a field related to the student's major; and 4) at least one member of the graduate faculty from outside the student’s and advisor’s home department who is the Graduate School Representative. The committee may include the same faculty members as the first-year project exam committee. The committee will approve the dissertation proposal/fellowship application (Qualifying Exam), the program study, and the dissertation. It will also conduct the students’ oral dissertation defense and serve in an advisory capacity of the student in the program.

The student and committee should meet annually with the committee to discuss and prepare a written progress report consisting of a dissertation outline, a list of the courses the student has taken, the courses proposed for the next year, and the tentative date for the dissertation proposal/fellowship application (see below). The committee should review the students program of study form (see below), which should be submitted by the student to the Graduate School at least one semester before their defense date.

Journal Club

The journal club is designed to expose students to important current work in the field as well as familiarize them with diverse approaches and ongoing research within the program. The club is also an important venue for students to present their own projects and develop their scientific communication skills. Active participation is required.

Annual research retreat

The Neuroscience program schedules an annual research retreat for graduate students, faculty, and research fellows. All graduate students are required to attend. Furthermore, students are required to present their research findings at this conference, either as a poster or talk, as determined by the retreat organizing committee. Graduate students who have completed their first or second year of studies may present their findings by either the poster or oral presentation method.

Seminar series

The program also participates in an ongoing colloquium series hosting speakers from both within and outside the university. Graduate students play an active role in identifying the speakers and scheduling their visits as members of the Colloquium Committee, and are expected to attend the talks as well as additional opportunities to interact with the speakers.

Continuous enrollment

Graduate students without an assistantship must enroll for three (3) graduate credits each fall and spring semester until graduation (this includes enrolling in three graduate credits in your final semester). Graduate students with an assistantship must enroll for six (6) graduate credits each fall and spring semester. Graduate students may also enroll in at least 1 credit during the summer sessions. For non-resident aliens who are not taxed, it is important to enroll in at least 1 credit in two of the three summer sessions to maintain student status and hence non-taxable status.

C. Program completion requirements

It is the student’s responsibility to fulfill all requirements in a timely manner, and all courses must be completed with a letter grade of B or higher. Failure to meet these requirements may result in academic probation, loss of funding, or dismissal from the program.

Academic requirements

Academic requirements as determined by the Graduate School and the Program will be met by all Neuroscience students. Required courses will be chosen from core and elective courses as outlined above. The final decision on courses to be taken is made by each individual student’s advisory/examination committee, and approval by the program directors.

First-year project exam

Neuroscience graduate students are required to take a written and oral examination of their first-year research project. However, students entering the program with a prior Master’s degree are exempt from this requirement. The first-year exam will be based on a research project conducted by the student in the first year. For students in rotation they may choose which lab to base the report on. For students working on multiple projects the student and their advisor should agree which project to use for the exam.

Written exam component

Students will prepare a written report describing their first-year research project. The report should be 4-6 pages excluding references and follow NIH formatting. The report must include the following components:

Abstract
Background and significance. This section should demonstrate basic comprehension of the background literature on the project topic, the aims and hypotheses of the project, and why the experiment(s) in the project were important to pursue.
This section should demonstrate basic comprehension of the methods employed and why they are appropriate for addressing the aims.
This section should demonstrate basic understanding and evaluation of the results obtained including appropriate statistical assessments. For projects that did not yield results, the report should discuss potential findings.
This section should demonstrate an understanding of the theoretical implication of the results. For projects that did not yield results, this section should discuss potential implications.
Figures should be used where appropriate to illustrate models, methods, or results.
References should be included for all cited work.

While the first-year report can be developed in discussion with the advisor, the report must be written entirely by the student and not edited by the advisor.

Oral exam component

The student should submit the report to their committee at least one week prior to the oral exam. The committee will evaluate the report and conduct a private oral defense with the student. During the defense the student should present a ~20 minute ppt presentation giving an overview of the project followed by question and answer session with the committee.

First-year project examination committee

Evaluation

The committee will decide by majority vote whether to pass or fail the exam. The evaluation will be submitted to the program directors using a standard form and kept as part of the student’s record.

Outcome

Pass: students will continue as planned in the Neuroscience program.

Fail: students will be given three options:

Termination from the program.
Complete a terminal non-thesis Master’s degree, or
Retake the exam by the end of their third semester. The exam may be retaken with the same project or with a new project and/or advisor.

Students that pass the retake will continue as planned in the program. Students who fail the retake will be given the option of a non-thesis terminal Master’s degree (see below). Students who have failed the exam and wish to appeal the results must do so in writing to the Neuroscience program directors within two weeks after notification of the results of the exam. Appeals will be decided by the program directors and the Neuroscience steering committee, who will consult with the student and the committee before issuing a decision. If the student's appeal is rejected, the student may then appeal the results to the Dean of the Graduate School.

Timeline

The exam must be completed before the beginning of the student’s third semester in the program (i.e. by August for fall admission or January for spring admission).

Advisors

Completion of the first-year project exam under a given advisor does not commit the student to working with that advisor or vice versa subsequent to the exam.

Dissertation proposal and advancement to candidacy (qualifying exam)

During their 3th year, students should prepare a dissertation proposal outlining their planned research for the dissertation. The proposal should be written following the format of the NIH F31 Predoctoral Fellowship and include the following sections: 1) project summary; 2) specific aims; 3) research strategy; and 4) references cited. In cases where a different funding agency is deemed by the student’s advisory/examination committee to be more appropriate for the proposed work, the proposal may instead be prepared in the format appropriate for that agency. Students are expected to give a seminar (either public or private as determined by the committee) on the proposed research and will then hold a private oral defense with their committee. Approval by the committee (see evaluation) will qualify the student to advance to candidacy. The student is required to submit to Graduate School a doctoral degree admission-to-candidacy form (see below) signed by the committee and program director(s).

The plan of study may change during the course of conducting the dissertation research, but significant changes should be approved by the committee. The final proposal should be sent to the committee at least two weeks prior to the oral defense date to allow time for the committee to evaluate the proposal. Students are strongly encouraged to submit their proposal as a full F31 (or equivalent) application to NIH, taking advantage of the feedback from their committee. Students must submit at least one fellowship or grant application during their graduate studies.

Evaluation of the Qualifying Exam

The advisory/examination committee must reach a consensus that the student has written an acceptable proposal and performed satisfactory in the oral examination. To pass the examination, the student will need to be well-versed in the current literature in their field, and be able to defend their hypotheses, aims, research plan, and methodology. The proposal must be the student’s own work and not the same as any grant submitted by the advisor or collaborator If the oral defense and proposal is not considered acceptable and the committee cannot reach a consensus, a revised dissertation proposal and defense will be due within a period as determined by the committee. If the student fails the second examination, the program directors and advisory/examination committee will decide if the student’s work merits awarding a Master’s degree, or if the student should be dismissed from the program. Students who fail the Qualifying Exam cannot continue their graduate studies as determined by Graduate School policy.

Dissertation and final examination requirements

If a student has first author publications accepted in refereed journals at the time they have completed work, they may submit the publications to their advisory/examination committee and petition to write an introduction to the work and have the dissertation consist of this introduction and the papers. The committee may decide that additional chapters be required along with the published papers. Prior to formally choosing a date for the final oral examination, graduate students must submit a copy of their final dissertation for review by their examining committee. The dissertation does not have to be in its final form, e.g. thoroughly referenced, perfect grammar, etc., but must contain sufficient information to allow their committee to make an informed decision about the state of completion of their studies. The purpose of the review is to discern whether a student has sufficiently completed their studies to announce a date for their final examination.

Following acceptance of the dissertation by the advisory/examination committee, all doctoral candidates in the Neuroscience program will schedule and present a research seminar on their dissertation research, which will be open to the general public. This seminar will constitute part of the final examination and must be presented while the candidate is still in residence. This seminar requirement is in addition to the final examination requirement of the Graduate School. Following the public portion of this seminar, the advisory/examination committee, including all appointed Graduate School representatives, will conduct a final oral examination in closed session. This oral examination will be so conducted as to meet all relevant examination requirements of the Graduate School. Doctoral candidates may register for one credit of Graduate Seminar during the semester in which this seminar is presented.

Students are required to submit to Graduate School a doctoral degree notice of completion form, and final dissertation review approval form (see below).

D. Graduate student performance standards

All graduate students in the Neuroscience program are considered full-time scientists, and as such are expected to adhere to high standards of professional and personal behavior. Following are standards that are required of students, and disciplinary actions that may be taken if a student fails to measure up to these standards.

Ethics

All Neuroscience students are required to adhere to the scientific misconduct policy of the �Ƽ��Ӱ�ԭ�� (Ethical Standards in the Conduct of Research). Failure to adhere to these standards may be grounds for removal from the program, at the discretion of the Program Directors.

Disciplinary actions

In the event of a potential breach of ethics, evaluation of a student’s performance will be determined by the Student Advisory Committee (SAC). The SAC may receive input from individual faculty and students. After preliminary considerations, the committee will inform the student of areas of concern and may suggest disciplinary action. These can include i) probationary status, which may include loss of financial support and/or non-registration; ii) permanent expulsion from the program, which may be implemented without a probation period.

Master of Science degree

A. Program Entrance Requirements

An applicant to the program at the Masters level must meet all requirements established by the Graduate School. Students admitted to the program will be expected to have obtained at least a 3.0 undergraduate grade point average (4 point system). Combined GRE scores of 300 (2012 scoring system) are recommended but not required for admission. Course preparation for the program will be determined on an individual basis. However, all students will be expected to have a basic background in science including a minimum of 3 semester credits each in Calculus, Physics, Chemistry, and Biology. Students lacking this background may be admitted with the provision that appropriate remedial coursework is completed.

B. Program Requirements

Neuroscience Core Courses (16 units)

BIOL 675 - Neurobiology (3 units)
PSY 721 - Advanced Psychophysiology (3 units)
BIO/PSY/SOM - Journal club/ research presentations (4 units)
BIO/PSY 797 - Thesis research (6 units)

Additional Course Requirements (8 units)

PSY 706 (or equivalent) - Statistics (3 units)
PSY/CS/BCH - Computing or bioinformatics options (3 units)
PHAR 725 - Ethics and scientific research (2 units)

Electives (6 units)

Note all electives cannot be taken from the cluster below:

Cognitive Neuroscience (PSY)

PSY 627 - Computer applications (3 units)
PSY 709 - Comparative sensory neuroscience (3 units)
PSY 720 – Perception (3 units)
PSY 729 - Memory (3 units)
PSY 755 - Individual reading (multiple units)
PSY 761-3 - Special topics (multiple units)

Cellular and Molecular Neuroscience

CMB 710 - Molecular cell biology (4 units)
BCH 704 - Molecular genetics (3 units)
BCH 706 - Functional genomics (3 units)
BCH 709 - Introduction to bioinformatics (3 units)
BIOL 677 - Genes, Brain and Behavior (3 units)
BIOL 681 - Principles of animal behavior (3 units)
BIOL 654 - Genomic conflict, epigenetics (3 units)
BIOL 666 - Developmental biology (3 units)
BIOL 691 - Independent Study (3 units)
BIOL 705 - Current topics in cellular and molecular biology (multiple units)
BIOL 711 - Advanced cellular biology (3 units)
PHAR 710 - Molecular Pharmacology (3 units)

Total Units = 30

Additional program requirements thesis research

Students in the Neuroscience MS program will complete 2 semesters of thesis research during their second year. In the first year, they have the option of earning elective credits for additional research in their first year or substituting these credits with elective courses. MS students must complete a thesis based on an independent research project. The thesis must be defended orally before their examining committee.

Faculty advisor

Before the third semester in the program, each student must select a research/thesis advisor in consultation with the program director and the desired faculty member, who must be an affiliate member of the program. The advisor will serve as chair of the student’s advisory/examination committee. Once an advisor is chosen the student should complete the declaration of advisor/committee chair form (see below) and submit to the Graduate School by the end of the second semester.

Journal Club

Annual research retreat

Seminar series

Continuous enrollment

C. Program completion requirements

Academic requirements

Qualifying exam

There is no qualifying exam requirement for students enrolled in a terminal Masters degree.

General procedures and examination requirements

During the second semester of residence in the Neuroscience program, each MS student must select, in consultation with the program directors and the desired faculty member, a research/thesis advisor from among the program faculty. Selection depends on a mutual agreement between the student and the desired advisor, and the program cannot guarantee the availability of any particular advisor. This advisor will serve as chair of the student’s advisory/examination committee.

After having selected a research advisor, the student will arrange for one additional Neuroscience group faculty member to serve as an advisory/examination committee. At least one additional faculty will be appointed, representing the University at large, to meet Graduate School requirements. These additional appointments will be subject to approval of the committee chairperson (research/thesis advisor). Permanent constitution of the committee will be subject to the approval of the program directors. This committee will approve the final thesis, conduct the formal oral part of the thesis defense, and serve in an advisory capacity to the student during his or her tenure in the program.

Thesis examination requirements

Prior to formally choosing a date for the final oral examination, graduate students must submit a copy of their final thesis for review by their examining committee. The thesis does not need to be in its final form, e.g. thoroughly referenced, perfect grammar, etc., but must contain sufficient information to allow their committee to make an informed decision about the state of completion of their studies. The purpose of the review is to discern whether a student has sufficiently completed their studies to announce a date for their final examination. After acceptance of the thesis (see Doctoral section for nature of thesis) by the advisory/examination committee, all MS candidates will schedule and present a research seminar on their thesis research which will be open to the public. This seminar will constitute part of the final examination and must be presented while the candidate is still in residence. Following the public portion of this seminar, the advisory/examination committee, expanded to include all appointed Graduate School representatives, will conduct, in closed session, a final oral examination, which will be so conducted as to meet all relevant examination requirements of the Graduate School.

Non-thesis MS option

In rare cases where the student’s advisor and committee deem it is not possible for the student to complete a research project for their thesis, at the discretion of the program the student may be allowed to complete a non-thesis MS degree. This option must be approved by the faculty advisor for the degree and by the program directors. Under this option the student will take additional course work in lieu of the thesis credits, and will prepare and defend a substantive critical review of the literature on a relevant topic in neuroscience. The specific topic and format of the review should be developed with and approved by the faculty advisor and committee. Award of the degree will be contingent on approval of the review by the committee.

D. Graduate Student Performance Standards

Ethics

Disciplinary actions

Graduate School Forms

You will need to become familiar with a set of forms from the Graduate School.

Graduate School forms

Important dates and information on dissertation and thesis guidelines

As you progress through the program:

Graduate Credit Transfer Evaluation Request Form
Program of Study Requirements (instructions & form)
Declaration of Advisor/Major Advisor/Committee Chair Form
- For Master’s students, the completed form must be submitted to Graduate School by the end of the student’s second semester.
- For Doctoral students, the completed form must be submitted to Graduate School by the end of the student’s third semester.
Change in program of Study
Change of Advisory Committee
Doctoral Degree Admission to Candidacy/Comprehensive Examination Report
- For doctoral students who completed all requirements except for the dissertation.
Application for Leave of Absence

For Ph.D. graduation:

Doctoral Committee Approval page (5 committee members)
Doctoral Committee Approval page (6 committee members)
Doctoral Microfilming Agreement (Only if you are submitting paper, print this)
Doctoral Complete Microfilming Agreement (see online form)
Doctoral Degree Notice of Completion
- Completed form should be submitted after all requirements have been met.
Doctoral Final Review Approval transmittal
Survey of Earned Doctorates (see online form)
Exit Survey

For MS graduation:

Master's Committee Approval page (3 committee members)
Master's Committee Approval page (4 committee members)
Master's Microfilming Agreement (Only if you are submitting paper, print this)
Master's Complete Microfilming Agreement (see online form)
Master's Degree - Notice of Completion
Master's Final Review Approval transmittal
Exit Survey

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Program handbook

Program description

Doctor of Philosophy degree

A. Program entrance requirements

B. Program requirements

Neuroscience core courses (46 units) Please note, this is an example. Please refer to your advisor and the for the current requirements.

Courses meeting the first and second year research requirement:

Electives (18 units)

General time-line for degree completion

Additional program requirements

First year research project

Second year fellowship application

Pre-doctoral fellowship submission requirement

Faculty advisor

Committee Selection

First-year project committee

Dissertation committee

Journal Club

Annual research retreat

Seminar series

Continuous enrollment

C. Program completion requirements

Academic requirements

First-year project exam

Written exam component

Oral exam component

First-year project examination committee

Evaluation

Outcome

Timeline

Advisors

Dissertation proposal and advancement to candidacy (qualifying exam)

Evaluation of the Qualifying Exam

Dissertation and final examination requirements

D. Graduate student performance standards

Ethics

Disciplinary actions

Master of Science degree

A. Program Entrance Requirements

B. Program Requirements

Neuroscience Core Courses (16 units)

Additional Course Requirements (8 units)

Electives (6 units)

Additional program requirements thesis research

Faculty advisor

Journal Club

Annual research retreat

Seminar series

Continuous enrollment

C. Program completion requirements

Academic requirements

Qualifying exam

General procedures and examination requirements

Thesis examination requirements

Non-thesis MS option

D. Graduate Student Performance Standards

Ethics

Disciplinary actions

Graduate School Forms

Neuroscience core courses (46 units)
Please note, this is an example. Please refer to your advisor and the for the current requirements.