graduate student handbook · 2015. 12. 8. · graduate student handbook program directors:...

GRADUATE STUDENT

HANDBOOK

PROGRAM DIRECTORS: Christine Beeton, Ph.D.

713-798-5030

George Rodney, Jr., Ph.D.

713-798-5797

PROGRAM ADMINISTATOR: Elizabeth Haynes 713-798-5109

GRADUATE EDUCATION COMMITTEE:

Christine Beeton, Ph.D. 713-798-5030

William Lagor, Ph.D. 713-798-8666

Sean Marrelli, Ph.D. 713-798-7892

Joel Neilson, Ph.D. 713-798-8851

Ross Poche, Ph.D. 713-798-6911

George Rodney Jr., Ph.D. 713-798-5797

Joshua Wythe, Ph.D. 713-798-6911

*Policy and procedures set forth in the Program's guidelines are addenda to the Policy Handbook, Graduate School, and

Baylor College of Medicine. Program procedures supplement Graduate School policies; they do not supersede them. While

every effort has been made to verify the accuracy of information in this publication, the department of Molecular Physiology

and Biophysics reserves the freedom to change without notice any information published herein. This Publication is not to be

regarded as a contract.*

Last Revision: December 8, 2015

1

TABLE OF CONTENTS

INTRODUCTION ................................................................................................................................ 2

PROGRAM CO-DIRECTORS ............................................................................................................ 2

GRADUATE EDUCATION COMMITTEE ...................................................................................... 2

I. ADMISSION ............................................................................................................................ 3

A. REQUIREMENTS FOR ADMISSION ...................................................................... 3

B. ACADEMIC YEAR .................................................................................................... 3

C. FINANCIAL AID AND HEALTH INSURANCE .................................................... 3

II. PROGRAM REQUIREMENTS .............................................................................................. 4

A. CREDIT REQUIREMENTS FOR THE Ph.D. DEGREE .......................................... 4

B. COURSE WORK ........................................................................................................ 4

C. SEMINAR SERIES ..................................................................................................... 6

D. LAB ROTATIONS ...................................................................................................... 7

E. MAJOR DISSERTATION ADVISOR ....................................................................... 8

F. DISSERTATION ADVISORY COMMITTEE ......................................................... 9

G. STUDENT SYMPOSIUM AND DEPARTMENTAL RETREAT .......................... 9

H. STATUS REPORTS ...................................................................................................10

I. QUALIFYING EXAM ............................................................................................. 11

J. DISSERTATION DEFENSE .................................................................................... 14

K. ETHICAL CONDUCT IN SCIENCE............. ...........................................................14

L. INDIVIDUAL DEVELOPMENT PLAN...................................................................15

CURRICULUM AND ELECTIVE COURSES………………………………………………….. 16

TYPICAL COURSE OF STUDY FOR FIRST YEAR ..................................................................... 17

FACULTY MEMBERS (PRIMARY AND SECONDARY FACULTY) ....................................... 23 *** (Required Graduate School forms can be downloaded from the Graduate School website http://www.bcm.edu/gradschool/grad-forms.html) ***

http://www.bcm.edu/gradschool/grad-forms.html

2

INTRODUCTION

The Department of Molecular Physiology and Biophysics at Baylor College of Medicine offers a

research-oriented program of graduate study leading to a Ph.D. This program applies cutting-edge methods of

molecular and cell biology, electrophysiology, imaging, biophysics, immunology, protein biochemistry, and

pharmacology to the study of problems of physiological importance. The Department participates in Baylor

College of Medicine’s M.D./Ph.D. Program whose candidates earn the degrees of M.D. and Ph.D.

The departmental faculty members are very interactive with ongoing research in the areas of structure

and function of ion channels and transport proteins, signal transduction, synaptic plasticity, developmental

biology, cardiovascular diseases, cell cycle control, reactive oxygen species, neuronal morphology, drug and

gene delivery, the development of biosensors for genetic diagnosis, and small animal magnetic resonance

imaging (MRI). In addition, knockout and transgenic mice are used for a number of different types of whole

animal studies, including the study of muscle and cardiovascular function, learning and memory, Alzheimer’s

Disease, diabetes and cancer.

PROGRAM CO-DIRECTORS

The Co-Directors of Graduate Studies coordinate the graduate program within the Department. The Co-

Directors are appointed by the Chairman of the Department and serve as Co-Chairman of the Graduate Education

Committee (GEC). The Co-Directors are responsible for transmitting information between the Graduate School

office and the departmental faculty and represent the Department as a member of the Executive Council of the

Graduate School.

GRADUATE EDUCATION COMMITTEE (GEC)

The Graduate Education Committee (GEC) formulates and executes the policies and practices that pertain

to graduate education in Molecular Physiology and Biophysics. The major areas of responsibility for the

Committee include recruitment, admission, orientation, establishment and review of curriculum, examinations

(qualifying and defense of dissertation), and monitoring the progress of students through the graduate program.

The members of the Committee are appointed by the Chairman of the Department.

3

I. ADMISSION

A. REQUIREMENTS FOR ADMISSION

1. The requirements and procedures for admission are those of the Graduate School, as set

forth in the Graduate School catalogue.

2. Successful applicants are selected on the basis of their undergraduate academic records,

scores on the Graduate Record Examination (GRE), past research experience, letters of

recommendation, and an interview. Scores on the Test of English as a Foreign Language

(TOEFL) are also considered for foreign applicants.

3. Undergraduate academic records must be complete and presented in the form of an official

transcript.

4. Applicants must submit official GRE scores obtained within three years prior to the

application deadline. The General Test is required and a Subject Test in either Biology,

Chemistry, Physics or Biochemistry is recommended.

5. At least three letters of recommendation from undergraduate faculty members or research

sponsors must be submitted. If the applicant has had professional or graduate training, a

letter from a faculty member of the professional or graduate institution that the applicant

attended is also required.

6. An interview is required for all applicants.

B. ACADEMIC YEAR

1. The academic year is from approximately August 1 to July 31 and terms are designated 1,

2, 3, 4 and 5. Normally, students begin their studies in August, Term 1.

2. The week after the finals of terms 1, 3, and 4 are not vacation weeks and are to be spent

finishing the current term’s lab work. If a student wishes to take time off during these weeks, he/she

must obtain prior approval from the co-directors of the graduate program and the principal

investigator of their rotation lab. Upper level students must secure approval from their advisor prior

to making travel arrangements.

C. FINANCIAL AID AND HEALTH INSURANCE

1. Students accepted into the program usually receive a tuition scholarship, an annual stipend

of $29,000 (2015-2016 academic year), and health coverage (student only).

4

II PROGRAM REQUIREMENTS

A. CREDIT REQUIREMENTS FOR THE Ph.D. DEGREE

1. The Ph.D. degree requires satisfactory completion of 135 term hours.

a. A minimum of 60 term hours of course work is required of which 12 graded hours

must be taken outside the student's department (special projects are counted as

course work hours excluding the 12 required outside the department). 30 term hours

of graded coursework must be completed prior to standing for the Qualifying Exam.

b. The remaining 75 term hours may be course work, special projects or dissertation

research.

c. Students must be enrolled for at least 12 term hours per term, five terms per year.

Students wishing to take more than 17 hours per term must obtain written

permission from their advisor and have the approval of the Dean. Students will

receive notification from the Graduate School when on-line registration is open and

when registration is due. Late registration is subject to a $25.00 late fee.

B. COURSE WORK

1. Required Courses (and Term offered)

Didactic

GS-GS-501 - Organization of the Cell (T1)

GS-GS-521 - Introduction to Biostatistics (T4)

GS-PY-430 - Human Physiology I (T2)

GS-PY-431 - Human Physiology II (T3)

GS-PY-465 - Transmembrane Signaling (T4)

GS-PY-415 - Cell Physiology (T2)

Non-didactic

GS-GS-513 - Science as a Profession (T1)

GS-GS-514 - Science as a Profession-Ethics-Year 1 (T1)



GS-PY-413 - Grant Writing Skill-Year 2 (T2)

(Each Year, All Terms)

Physiology 549 - Research Rotation (All Terms, 1st year)

Physiology 435 - Special Project (All Terms, 2nd year)

Physiology 466 - Seminar in Molecular Physiology (All Terms)

Dissertation – (After Admitted into Candidacy)

5

After the completion of first year in the program, students must have completed the required 60

course term hours including all required courses. Graduate students must earn a grade of "B" or

better in all required course work. If a grade of "C" is received in a required course, the course must

be retaken. If a grade "C" is made a second time, the student will be subject to dismissal from the

program. If a grade of "F" is made in any required course, the student will be subject to dismissal

from the program.

Graduate students are expected to obtain passing grades of “B” or higher in all required course

work. Grades of marginal pass or “C” will place the student on academic warning. A single grade of

“F,” or two cumulative grades of “C,” will move the student to academic probation. Academic

probation is a serious situation, in which the student is in danger of dismissal from the program if

performance does not improve.

Placement on either academic probation or academic warning and eventual removal from

probation or warning requires formulation and approval of a remediation plan. This plan will be

formulated and signed by the Graduate Co-Directors, the major advisor, and the student, in mutual

consultation. It must be approved by the Promotions Committee.

Required courses may be waived upon request by the student. The student must submit evidence of

having achieved a passing grade (A or B) on a graduate level course or courses with similar content.

Such evidence should include a transcript and a course syllabus. The request will be reviewed by

the Graduate Education Committee, and forwarded to the Graduate School for approval to ensure

compliance with course requirements and to avoid redundancy. Any of these courses may be

waived at the discretion of the Graduate Education Committee.

MSTP students may request to transfer courses taken during their first two year of medical school.

The required courses available for such transfer are:

GS-GS-501 - Organization of the Cell (T1)

GS-PY-430 - Human Physiology I (T2)

GS-PY-431 - Human Physiology II (T3)

MSTP students will be required to take the remainder of the courses required by the program.

All students must attempt to complete the required 30 didactic hours by the end of term 5.

2. Recommended Elective Courses

Recommended elective courses are listed in the appendix for each of the 5 areas of emphasis.

Students may focus on a single area of emphasis or may combine electives from various areas.

Students will need prior approval from the Directors to take courses that will conflict with the

Seminar Series schedule.

6

C. SEMINAR SERIES

The Seminar Series consist of three types of seminars: Departmental Faculty, Postdoctoral/

Students and Dissertation.

1. Departmental Seminars Lunch with the Speaker

The seminar coordinator will send an email soliciting students to attend lunch with the

speakers.

2. Seminar Attendance

a. Attendance to departmental Faculty and Postdoctoral/Student

seminars is mandatory for all Physiology Students.

b. Seminars remain a Pass/Fail course for all Physiology Students.

c. First year students are however required to present a journal club at

the Postdoctoral/Student seminar.

d. Attendance of dissertation defenses is mandatory for all

Physiology Students.

e. Students must attend 80% of seminars in each term or the student

will be given an ‘F’. Sign-in sheets will be used to monitor

attendance at all seminars.

f. Students planning on attending a meeting, going on a job

interview, attending classes or trainings, or giving/attending a

seminar elsewhere should contact the Seminar Director in advance

to obtain permission to miss one or several departmental seminars

without using an excused absence.

g. Please arrive at seminar on time. Late arrival will count as an

absence.

3. Student Host Responsibilities

Students, 2nd year and above (1st year only if requested), are required to host faculty

speakers as a Student Host. Selection of student hosts will be made by the faculty host. The

selected student will be notified via email by the seminar coordinator when he or she is selected

to host and will also be provided with a copy of the Student Host Duties and Responsibilities

document.

4. Guidelines for first year students' journal club:

a. Choose a paper of general interests from a leading biomedical

journal. The paper has to be approved by the student seminar director

at least one week before the scheduled journal club.

7

b. Once a paper is chosen, send a .PDF file to the program administrator

who will distribute copies to Physiology graduate students.

c. It is mandatory that the presenter read background material.

d. The presentation should consist of 5 min background and

introduction, 15 min results, and 10 min discussion of the results.

When preparing the presentation, keep the following in mind:

i. Issues/questions/hypothesis the paper is trying to address;

ii. Methods used in acquiring the data

iii. Were there proper controls?

iv. Why the data support the conclusion

v. What are alternative explanations for the data?

vi. Do the conclusions drawn address the hypothesis?

e. All students are required to read and critique the paper.

5. Guidelines for 2nd year and higher student seminar presentations.

Upper-year students will deliver a 20-25 min seminar on their current research followed

by a critique session attended by the students and faculty.

D. LAB ROTATIONS

During the first term, all students will be introduced to faculty research projects by attending faculty

presentations. The time and location of the presentations will be arranged by the program

administrator. The students will receive 1 credit of Research Rotation (360-549) for attending these

presentations. In addition, first year students may rotate in laboratories the first term or arrange for

individual readings with faculty.

The student must contact the faculty supervisor of the lab they have chosen to rotate in at least two

weeks prior to the start of the rotation for permission to rotate in their lab and to obtain rotation

requirements. Rotations begin at the start of the term and end at the beginning of the next term.

After the completion of the first year in the program, students must have rotated through at least 3

different labs. The time spent in each lab and the number of credit hours awarded will be decided

by the student and the faculty supervisors. Credit for 1-12 hours is given through the course

"Research Rotation (360-549)". Rotations should be used by the student to identify the student's

mentor for the dissertation research, to learn a variety of techniques, and to become familiar with the

research work in the department.

The primary goal of a rotation is to determine whether the laboratory and faculty mentor will be

suitable for the student’s dissertation research. It is also expected that students will use this time to

learn new techniques and more broadly familiarize themselves with research in the department.

Consistent and active participation in lab activities is strongly encouraged to ensurea good fit for

their dissertation research.

8

E. MAJOR DISSERTATION ADVISOR

Near the completion of the first year in the program, students must choose a Major Dissertation

Advisor from the training faculty. Students must submit a form of their preference for a Major

Dissertation Advisor. The student and advisor should review and sign the Student/Mentor compact

(GS form). The student should notify the program administrator of their chosen mentor by

July 1st. Students who do not join a lab by the end of Term 5 (July 1, will have failed to

register for directed research and will be administratively withdrawn from the graduate

program, in accordance with policies of the Graduate School (Section 6.9.2)

Options to students upon the resignation of the Major Dissertation Advisor are as follows:

1. Students who have not been admitted to candidacy for the Ph.D. This applies to

students who have not completed the qualifying examination or other requirements for

admission to candidacy.

a. If the student wishes to remain in the Department, the student must select a new

Major Dissertation Advisor.

b. The student may withdraw from the Department and follow the advisor, if the

circumstances permit.

c. If the student wishes to complete the dissertation as a remote student, all

requirements for candidacy and residency must be completed. Until such

requirements are met, the payment of the stipend is not guaranteed, but will be

decided upon discussion of the circumstances among the advisor and the program

directors and the graduate education committee.

2. Students who have been admitted to candidacy for the Ph.D. This applies to students

who have passed the qualifying exam and all course requirements and have been admitted to

candidacy by the Graduate School (form GS6) and are engaged in dissertation research.

a. If the student wishes to remain in the Department, the student must select a new

Local Advisor.

b. The student may elect to withdraw from the Department and follow the dissertation

advisor to complete the dissertation research.

c. The student may elect to follow their advisor but to remain a member of the

Departmental Graduate Program and to receive the degree from Baylor.

In the latter case (c), the student must choose a new advisor from the Departmental faculty.

The resigned faculty advisor is appointed as an outside member of the committee and

continues to serve as the operational preceptor for the student.

Evidence must be provided to the Graduate Education Committee that the new institution

accepts the student in an appropriate category and provides facilities and physical resources

to continue the dissertation research. Proof also must be provided that the student will

receive a stipend and health and dental insurance coverage from the new institution that is

9

comparable to the support provided by Baylor. The student must apply to the Promotions

Committee, through the Director of Graduate Studies, to be placed on “Remote Status”.

The student must submit semi-annual status reports documenting progress and must have at

two committee meetings a year, at least one at Baylor College of Medicine. The dissertation

is defended at Baylor College of Medicine.

F. DISSERTATION ADVISORY COMMITTEE

Within one month of selecting a Major Dissertation Advisor, the student should select a

Dissertation Advisory Committee. The committee should be selected in consultation with

the Major Dissertation Advisor according to the guidelines below.

1. The student's Dissertation Advisory Committee shall be appointed by the Dean upon written

request from the Departmental Program Director within 12 months following entry into the

program. Written request is submitted on a "Appointment of Advisory Committee (GS1)”

form.

2. The Dissertation Advisory Committee consists of a minimum of four faculty members: 1)

The chairperson of the committee, typically the Major Dissertation Advisor; 2) at least

one additional member whose primary appointment is within the student's department;

and, 3), at least one faculty member from outside the department. An outside member is a

faculty member who holds neither a primary nor a joint appointment in the Department.

A quorum of more than 50% of the committee members are required to hold a meeting.

3. The student will seek advice and counsel from all members of the Dissertation Advisory

Committee regarding dissertation research and the progress of the student’s graduate

education. The Dissertation Advisory Committee must meet every 6 months to review the

student's progress.

4. The initial meeting with the Dissertation Advisory Committee should be held prior to the

last business day preceding December 24thof the second year.

5. The student may change their Dissertation Advisory Committee upon approval of the

Advisor, Dean, and Graduate Program Director by submitting a new “Appointment of

Advisory Committee form”.

G. STUDENT SYMPOSIUM AND DEPARTMENTAL RETREAT

Students 3rd year and above are required to submit an abstract and a poster for the symposium

and departmental retreat, but may request an exemption with written approval from their advisor.

First and second year students may submit abstracts and present posters, but are not required to

do so.

10

H. STATUS REPORTS

1. After a student's Dissertation Advisory Committee has been appointed, progress reports

must be completed by 5:00 p.m. on the last business day preceding December 24 (Year 2

Fall Status Report) and the last business day in June (Year 2 Spring Status Report).

Meetings may be held any time prior to the deadline and students are encouraged to arrange

meetings early. Anyone who misses the deadlines will be required to meet with the program

directors promptly to discuss the reasons.

2. The student will schedule the meetings with their Dissertation Advisory Committee.

3. The student should prepare a written progress report of their dissertation work to date.

(Instruction on the second page of the Status Report Signature Page form) This report must

be given to the committee members at least 1 week in advance of the meeting.

4. After the meeting, the student appends the progress report with a summary of the meeting

including any special projects or additional work requested by the committee.

5. The student brings to the meeting the Status Report Signature Page form, which is signed by

all members of the committee (both attending and absent). There are distinct forms

depending on the student year. In addition, the advisor must write a summary of the

meeting, outlining any specific concerns about the student’s progress, prior to obtaining

signatures. The advisor must discuss the summary with the student. The original form

and progress report must be turned into the Graduate School office by the deadline. A copy

of this form must be returned to the Program Administrator along with the written progress

report, copy of presentation and summary of the meeting. An example is

included in the Appendix.

For students 3rd year and above, the status report deadlines are the last business day

of the student’s birth month and the last business day of the 6-month anniversary of

their birth month. The student may hold the committee meeting at any time but must

turn in the status report before these deadlines. The student will receive email

notifications from the Graduate School at 60 and 30 days prior to the deadline. The

program administrator can answer any questions concerning these deadlines.

If a report is not submitted by the appropriate Graduate School deadlines and the student

has had no prior late penalties assessed at previous deadlines, the student will be assessed

a $25 fine. If the completed status report is not submitted within 15 calendar days of the

original deadline, an additional $50 fine will be assessed and if still delinquent after 30

calendar days from the original deadline, the student will receive a grade of F for

Dissertation or Special Projects. The thesis committee will be notified of delinquent

status reports. On the second instance of status report delinquency, the initial fine will be

$50 and if still delinquent, 15 calendar days after the original deadline, the student will

receive a grade of F for Dissertation or Special Projects. On the third instance of status

report delinquency, the student will receive a grade of F for Dissertation or Special

Projects immediately after the original deadline. A grade of F in Dissertation or Special

Projects may be sufficient to cause dismissal from the Graduate School by the

Promotions Committee (Section 6.8). The student may appeal the grade of F, any fines,

and/or their dismissal through the appeals process of the Promotions Committee.

Extensions will not be granted unless there is an outstanding reason.

11

I. QUALIFYING EXAM

1. Eligibility, Examining Committee, and the Role of the Advisor:

Within 2 years following entry into the program, students must have taken their qualifying

exam. The exam comprises a preliminary abstract, a written research proposal, and an oral

defense of the proposal. To be eligible, the student must have completed 60 term hours of

course work, all the required courses, with 12 term hours outside the department and 30

hours of graded coursework. Exceptions to the course requirements can be petitioned to the

GEC.

The standing examination committee will be appointed each year by the GEC from the

departmental faculty. The committee or a subset of the committee will constitute the

examination committee. In addition, one outside examiner will be appointed by the standing

committee to provide expertise in the topic of the examination. The student may submit

suggestions for the outside examiner by February 1. The advisor is a nonvoting observer of

the exam – see section 4 below.

2. Qualifying Exam Timeline*

a. The student may suggest an outside examining committee member no later than

February 1. If the student does not suggest an outside member, one will be

assigned by the program director.

b. Abstract due to program administrator no later than February 15.

c. Abstract meeting about 1 week later, as scheduled by the program

administrator. Turn in abstract approval form.

d. Full proposal due 6 weeks from abstract approval date.

e. Submit Qualifying Examination Date form to graduate school (date will be

scheduled by the program administrator).

f. Oral defense within two weeks of proposal submission.

g. Submit the Qualifying Examination Results form to the graduate

school.

h. Complete Admission to Candidacy form and submit to GS.

* The submission schedule will be determined by the GEC for students who have

not completed the requirements on time, are not in good standing, or did not

matriculate in term 1.

12

3. Purpose and Guidelines for the Format of the Exam

a. Purpose:

The exam constitutes the definition of a research problem and the

development of a written proposal to address the stated question on a topic of the

student’s choice. This may be the student’s dissertation research or an entirely

different topic. The written proposal will be defended orally. Although the exam is

designed to assess creativity and rationality in the design of research, the student's

basic knowledge of molecular physiology and biophysics will also be examined and

the student is responsible for all information gained during the student’s course of

study (i.e., course work and lab rotations).

b. Abstract:

(i) Students must submit an abstract of the proposal to the program

administrator for review and approval by the Qualifying Exam Committee. The

abstract style should conform to the Grants Writing Course and the NIH Specific

Aims Page. It may be no more than 1 page in length in 11 point Arial or larger

type (12 point for times roman) with 0.5" margins, single spaced.

(ii) Approximately 7 days after submission, students will meet with the

examination committee to discuss the abstract. The meeting will be scheduled by

the program administrator. At this meeting, the student may be asked to briefly

describe the abstract to the committee and answer questions. The committee, in

consultation with the student, will approve the abstract to be used for the qualifying

exam by majority vote and may make suggestions for improvements at this time.

Alternatively the committee may request a new abstract or refer the student to the

GEC. After the abstract has been approved, the student will submit a “Qualifying

Exam Abstract Approval” form, signed by each committee member and the advisor,

to the graduate program administrator. Note – the student is not expected to bring

refreshments to this or any other meetings.

c. Proposal:

The student has 6 weeks from abstract approval to electronically submit the

completed proposal to the graduate program administrator. The graduate program

administrator will distribute the proposal to the committee. The proposal must be

written independently and defended by the student. Students may ask other students

or postdocs to review and critique their proposal prior to submission. Faculty may

only comment on the format, syntax, and grammar prior to submission. In all cases,

the writing and the experimental design must be performed independently by the

student.

The significance and feasibility of the proposal and the relationship of the proposal

to current literature are important criteria for evaluation. Performance on the

qualifying exam determines the student's eligibility for admission to candidacy for

the Ph.D. degree.

d. The proposal should be written in the following format:

i. Specific Aims. List the broad, long-term objectives and describe

concisely and realistically what the specific research described in this

proposal is intended to accomplish and any hypotheses to be tested. One

page is suggested.

13

ii. Background and Significance. Briefly describe the background to

the present proposal, critically evaluate existing knowledge, and specifically

identify the gaps which the project is intended to fill. State concisely the

importance of the research described by relating the specific aims to the

broad long-term objectives. Two to three pages are suggested.

iii. Preliminary Studies. Use this section to provide an account of any

preliminary studies pertinent to the proposal. (Optional).

iv. Research Designs and Methods. Describe the research design and

the procedures to be used to accomplish the specific aims of the project.

Include the means by which the data will be collected, analyzed, and

interpreted. Describe any new methodology and its advantage over existing

methodologies. Discuss the potential difficulties and limitations of the

proposed procedures and alternative approaches to achieve the aims.

Provide a tentative sequence of timetable for the investigation. Although no

specific number of pages is suggested for this section, the total for items 1-4

should be approximately 10 pages and may not exceed 20 single spaced

pages (12 point), including all tables and figures.

v. Literature Citations. All literature cited in the proposal must be

listed with titles.

4. Conduct of the Exam and Outcomes:

a. The Qualifying Exam date, time and place will be scheduled by the graduate

program administrator upon approval of the abstract. The graduate program

administrator will notify the student and the committee of the schedule and distribute

the proposal. All members of the Qualifying Exam Committee must be present as

described in the Policy Handbook of the Graduate School.

b. During the oral examination, the student will be expected to give a brief (20 - 30

minute) presentation of the research proposal. The student will be asked questions

by each member of the committee.

c. Failure to meet any of the examination deadlines constitutes failure of the exam.

d. The student's advisor will be allowed to ask questions during the oral exam but

should not lead the student in answering questions posed by other members of the

committee. The chairperson will intervene if the advisor or any other member of the

committee acts inappropriately.

e. The student and the advisor leave the room while the remainder of the Committee

discusses the examination and vote on the results. If necessary, the advisor may be

asked to return to clarify any issues for the Committee. In the case of “Incomplete”,

the student will have to complete specific requirements stipulated by the examining

committee to achieve a pass. Such requirements may include, but are not excluded

14

to, revision of the written proposal, a new oral defense, or both. Failure to complete

the conditions will constitute failure of the exam.

f. If the student fails the qualifying exam, the student may be permitted to retake the

exam one time, upon recommendation of the Qualifying Examining Committee,

This may include complete rewriting of the proposal, a new oral defense, or both. In

the event of a second failure, the student will be recommended for dismissal by the

department.

5. Required Forms to be Submitted:

Most forms can be obtained on the Graduate School of Biomedical Sciences website,

http://www.bcm.edu/gradschool/grad-forms.html

Abstract Approval Form

This is a departmental form that can be found on the Molecular Physiology and

Biophysics web site. It must be signed by the examining committee, the advisor and

the program director and submitted to the program administrator.

Qualifying Examination Date This form will be completed by the student, signed by the student's major advisor

and the departmental Program Director, and forwarded to the Graduate School

Office prior to the oral exam.

Qualifying Examination Results The student will take the form to the oral exam. The Program Director will indicate

on the form if the student passes or fails and the form is signed by all attending

members of the Examination Committee. The form is forwarded to the Graduate

School Office along with form SGS-12, if applicable.

Admission to Candidacy If the student passes the qualifying exam and all other requirements have been

satisfied, the student should submit the admission to candidacy form to the

administrator and after approval, obtain the other required signatures.

J. DISSERTATION DEFENSE

Upon written consent from the student's Dissertation Advisory Committee on the “Status Report

Signature Page”, the student should begin to write the dissertation following the standard format

outlined in the Policy Handbook of the Graduate School.

The student must submit the original “Defense of Dissertation Date (GS7)” form to the Graduate

School and a copy to the Program Director. The examining committee is the student’s Dissertation

Advisory Committee

Before the defense announcement can be sent, the student must submit a Defense Approval form to

the program administrator. This form affirms that the presented dissertation is submittable for

consideration by the Graduate School and must be submitted at least two weeks prior to the defense

date. If the defense approval form is submitted less than two weeks from the defense date, the

15

defense date will be cancelled and the student must coordinate with the program administrator to

reschedule.

The student must submit the dissertation to members of the Dissertation Advisory Committee not

less than two weeks prior to the defense.

A dissertation seminar is to be presented as a public event and should be scheduled as part of the

normal departmental seminar series (i.e., at Noon on Tuesdays). At the conclusion of the seminar

the student must answer any questions from the general audience. The Examining Committee will

meet in closed session with the student for the final defense of dissertation. Alternatively, if

scheduling is a problem, the dissertation defense can take place at some other date but should be

within one week of the formal seminar.

Successful defense of the dissertation is indicated by all committee signatures and the approval of

the Dean on the Defense of Dissertation Result Form.

In the case of a single dissenting vote, the Promotions Committee of the Graduate School will

review the decision of the Examining Committee upon appeal by the student or the student's

advisor. The Promotions Committee may recommend awarding the Ph.D., may recommend a new

committee, or may recommend another examination of the student.

K. ETHICAL CONDUCT IN SCIENCE

All students are expected to maintain high ethical standards and conduct throughout their scientific

career, including all academic and research work. Ethical standards are described in the ethics

courses (required for all students) and in the graduate school handbook. Violation of ethical

standards will be reviewed by the GEC to determine punishment, up to and including

recommendation of dismissal from the graduate school.

To help maintain standards, the department may screen all documents and materials written by the

students using plagiarism-detection software, including the qualifying exam, the dissertation and

other written coursework.

L. INDIVIDUAL DEVELOPMENT PLAN

Each student is required to complete an Individual Development Plan (IDP) at

myidp.sciencecareers.org during the first term of their first year. A summary of the IDP will be

given to the Program Administrator. This IDP will be used as a starting point for the student to

discuss career interests with the program co-directors in year-1 and with their advisor and

committee members in subsequent years. The IDP will be updated by the student as he/she

progresses through the years.

16

MOLECULAR PHYSIOLOGY & BIOPHYSICS CURRICULUM

(30 hours didactic credit required)

REQUIRED COURSES (* = Didactic credit courses)

Term 1 Organization of the Cell (2)* Science as a Profession 1 (0.5) Ethics Year 1 (0.5) Seminar in MPB (1) Research Rotation Term 2 Human Physiology I (3)* Cell Physiology (1)* Grant Writing Year 2 (1)

Ethics Year 2 (0.5) Seminar in MPB (1)

Research Rotation Term 3 Human Physiology II (3)* Ethics Year 3 (0.5) Seminar in MPB (1) Research Rotation Term 4 Introduction to Biostatistics (2)* Transmembrane Signaling (2)*

Seminar in MPB (1) Research Rotation Term 5 Research Rotation

Electives (choose at least 17 hours, to reach total of 30 didactic hours)

BIOPHYSICS and BIOENGINEERING

Term 1 Molecular Methods (3) Term 1 Fundamentals of Human Neuroimaging (3) Term 1 Electrical Signaling in the Brain (2) Term 1&2 Fundamentals of Human Neuroimaging (3) Term 2&3 Functional Magentic Resonance Imaging Lab (3) Term 3 Macromolecules: Structure and Interactions (3) Term 4 Structural Basis of Human Disease (1) Term 4 Cellular Neurophysiology (3)

(Rice courses 3 semester hours ~ 6 BCM credits each)

BIOE 505 Optical Imaging BIOE 507 Systems Biology of Blood Vessels BIOE 512 Biophotonics Instrumentation BIOE 516 Mechanics, Transport, and Cellular Signaling BIOE 517 Instrumentation and Molecular Analysis BIOE 519 Biomaterials Synthesis BIOE 540 Introduction to Synthesis

METABOLISM

Term 1 Molecular Methods (3) Term 2 Cell Signaling (3) Term 3 Gene Regulation (3) Term 3 Macromolecules: Structure and Interactions (3) Term 4 Structural Basis of Human Disease (1) Term 4 Bioinformatics and Genomic Analysis (3) Term 4 Regulation of Energy Homeostasis (3) Term TBD Advanced Topics in Muscle Physiology (TBD) BIOE 540 Introduction to Systems Biology and Systems Biotechnology

CARDIOVASCULAR SCIENCES

All terms: Seminar in Cardiovascular Sciences Term 1 Genetics A (2) Term 2 Genetics B (2) Term 3 Cell Division (2) Term 3 Development (2) Term 3 Gene Regulation (3) Term 3 Neuroscience (1) Term 4 Cardiovascular Physiology (4) Term 5 Cardiovascular Disease and Pathology (4)

NEURAL AND MUSCLE PHYSIOLOGY Term 1 Brain Cell Biology (1) Term 1 Electrical Signaling in the Brain (3) Term 1&2 Fundamentals of Human Neuroimaging (3) Term 1&2 Theoretical Neuroscience: Cells, Circuits and Systems (3) Term 2 Anatomy & Development of the Nervous System (3) Term 2 Analyses of Neuronal Function (3) Term 2 Introduction to MatLab for Neuroscience (1) Term 3 Advanced MatLab for Neuroscience (2) Term 3&4 Functional Magnetic Resonance Imaging Lab (2) Term 4 Cellular Neurophysiology (3) Term 4 Neurobiology of Disease (3)

PHYSIOLOGY OF CANCER

Term 2 Cancer (3) Term 2 Translational Cancer Biology (2) Term 2 Cell Signaling (3) Term 2 Cell Division (2) Term 3 Immunology (3) Term 3 Gene Regulation (3) Term 4 Regulation of Energy Homeostasis (2)

17

Physiology Recommended Course of Study

Biophysics and Bioengineering

1st Year

* Didactic Credits

Total Term Credits = 12 Term 1

Aug. – Oct.

Course # Credit

Hours

Course Title Instructor’s Name

Required

GS-GS-501 2* Organization of the Cell Pedersen/Sifers

GS-GS-513/514 1 Science as a Profession/Ethic Gilbert

GS-PY-466 1 Seminar in Molecular Physiology Larina

GS-PY-549 Laboratory Rotation

Recommended

Rice BIOE 516 3* + Mechanics, Transport, and Cellular Signaling Raphael

3* Electrical Signaling in the Brain

GS-GS-502 3* Molecular Methods Gilbert/Highlander

Term 2

Oct. – Dec.

Course # Credit

Hours


Required

GS-PY-430 3* Human Physiology I Horrigan

GS-PY-415 1* Cell Physiology Pautler



Recommended

Rice BIOE 516 3* (cont’d) Mechanics, Transport, Cellular Signaling Raphael

3* Functional MRI Lab

Term 3

Jan. – Mar.

Course # Credit

Hours


Required

GS-PY-431 3* Human Physiology II Horrigan

GS-GS-518 3* Macromolecules:Structure and Interaction Prasad/Pedersen



Recommended

GS-GS-509 3* Functional MRI Lab

Rice BIOE512 3* BioPhotonics Instrumentation Tkaczyk

Term 4

Mar. - May

Course # Credit

Hours


Required

GS-PY-465 2 Transmembrane Signaling Beeton

GS-GE-407 3* Basic Biostatistics Paylor



Recommended

1 Structural Basis of Human Disease

GS-NE-464 3* Cellular Neurophysiology Wu

Rice BIOE512 3* BioPhotonics Instrumentation Tkaczyk

Term 5

May – Jul.

Course # Credit

Hours


Required



18


Metabolism

1st Year

* Didactic Credits


Aug. – Oct.

Course # Credit

Hours


Required





Recommended

BIOE 540 3* Introduction to Systems Biology and Systems Biotechnology Bio. Dept. Faculty


Term 2

Oct. – Dec.

Course # Credit

Hours


Required


GS-PY-415 1* Cell Physiology Bayle



Recommended

GS-CB-425 3* Cell Signaling Weigel

BIOE 540 3* Introduction to Systems Biology and Systems Biotechnology Bio. Dept. Faculty

Term 3

Jan. – Mar.

Course # Credit

Hours


Required




Recommended

GS-GS-509 3* Gene Regulation Rosen

GS-GS-518 3* Macromolecules:Structure & Interactions Prasad/Pedersen

Term 4

Mar. - May

Course # Credit

Hours


Required





Recommended

2* Regulation of Energy Homeostasis Moses

3* Adv. Top. Muscle Physiology Rodney

1 Structural Basis of Human Disease Prasad

Term 5

May – Jul.

Course # Credit

Hours


Required



19


Physiology of Cancer

1st Year

* Didactic Credits


Aug. – Oct.

Course # Credit

Hours


Required





Recommended

GS-GS-503 2* Genetics A Rosenberg/Kelley


Term 2

Oct. – Dec.

Course # Credit

Hours


Required


GS-PY-415 1* Cell Physiology



Recommended

2 Cell Division

1 Cancer

GS-MB-431 2* Translational Cancer Biology Yustein/Marriot

GS-GS-512 3* Immunology Levitt

Term 3

Jan. – Mar.

Course # Credit

Hours


Required




Recommended


Term 4

Mar. - May

Course # Credit

Hours


Required





Recommended

GS-MV-457J 3* Introduction to Molecular Carcinogenesis Li

GS-CB-468 2* Regulation of Energy Homeostasis Moses

Term 5

May – Jul.

Course # Credit

Hours


Required



Recommended

GS-PG-413 Drug Discovery: From Bench to Bedside

20


Neural and Muscle Physiology

1st Year

* Didactic Credits


Aug. – Oct.

Course # Credit

Hours


Required





Recommended

GSNE400 3* Fundamentals of Human NeuroImaging Ress

Term 2

Oct. – Dec.

Course # Credit

Hours


Required


GS-PY-415 1* Cell Physiology



Recommended

3* Immunology

GSNE400 3* Fundamentals of Human NeuroImaging Ress

GS-NE430 3* Anatomy and Development of the Nervous

system

Rasband

Term 3

Jan. – Mar.

Course # Credit

Hours


Required




Recommended

GS-GS-511 1* Neuroscience Jankowski

GS-GS-512 1* Immunology Levitt

GS-NE441 3* Genetics for Neuroscience Deneen

Term 4

Mar. - May

Course # Credit

Hours


Required





Recommended

3 Adv. Top. Muscle Physiology Rodney

GS-CS-411 4* Cardiovascular Physiology Marrelli

GS-NE-462J 3* Concepts of Learning and Memory Costa-Mattioli/Ji

Term 5

May – Jul.

Course # Credit

Hours


Required



GS-CS-412 4* Cardiovascular Disease and Pathology Marrelli

21


Cardiovascular Sciences

1st Year

* Didactic Credits


Aug. – Oct.

Course # Credit Hours Course Title Instructor’s Name

Required





GS-CS-549 Laboratory Rotation

Recommended

GS-GS-503 2* Genetics A Rosenberg/Kelley

GS-CS-465-466 Seminar in Cardiovascular Sciences Marrelli

Term 2

Oct. – Dec.


Required


GS-PY-415 1* Cell Physiology Bayle



Recommended

GS-GS-504 2* Genetics B Zhou

GS-GS-505 2* Cell Division Sazer

GS-GS-506 2* Development S. Lee


Term 3

Jan. – Mar.


Required




Recommended

GS-GS-518 3* Macromolecules:Structure and Function Prasad/Pedersen


GS-GS-511 1* Neuroscience Jankowski


Term 4

Mar. - May


Required

GS-CS-411 4* Cardiovascular Physiology Marrelli





Recommended


Term 5

May – Jul.


Required

GS-CS-412 4* Cardiovascular Disease and Pathology Marrelli



22

Recommended Course of Study

2nd Year All Areas of Emphasis

Term 1

Aug. – Oct.


Required


GS-PY-435 Special Projects

Term 2

Oct. – Dec.


Required

GS-PY-413 1 Grand Writing Skills Pedersen/Dickinson


GS- PY -435 Special Projects

Term 3

Jan. – Mar.


Required



Term 4

Mar. - May


Required



Term 5

May – Jul.


Required


GS- PY-435 Special Projects

23

Primary Faculty Members in the Department of Molecular Physiology and Biophysics Susan L. Hamilton, Ph.D.

Christine Beeton, Ph.D.

Mary Dickinson, Ph.D.

Frank Horrigan, Ph.D.

William Lagor, Ph.D.

Irina Larina, Ph.D.

James Martin, M.D., Ph.D.

Joel Neilson, Ph.D.

Robia G. Pautler, Ph.D.

Steen E. Pedersen, Ph.D.

Ross Poché, Ph.D.

Ergun Sahin, Ph.D.

George Rodney, Ph.D.

Xander Wehrens, M.D., Ph.D.

Joshua Wythe, Ph.D.

Pumin Zhang, Ph.D.

Joint Faculty Members in the Department of Molecular Physiology and Biophysics Kjersti Aagaard-Tillery, Ph.D.

Christie Ballantyne, M.D.

Penelope Bonnen, Ph.D.

Aladin Boriek, Ph.D.

Biykem Bozkurt, M.D.

Malcolm Brenner, Ph.D.

Robert Bryan, Ph.D.

Wah Chiu, Ph.D

Thomas Cooper, M.D.

William Craigen, M.D., Ph.D.

Miguel Cruz, Ph.D.

Jing-Fei Dong, M.D., Ph.D.

Tony Eissa, M.D.

Mark Entman, M.D.

Xin Hua Feng, Ph.D.

Marta Fiorotto, Ph.D.

K. Jane Grande-Allen, Ph.D.

Yadollah Harati, M.D.

Craig Hartley, Ph.D.

Sandra Haudek, Ph.D.

Joseph Hyser, Ph.D.

Jeffery Jacot, Ph.D.

Amit Joshi, Ph.D.

Kirill Larin, Ph.D

Scott LeMaire, M.D.

Ali Jalilian Marian, M.D.

Sean Marrelli, Ph.D.

Lloyd Michael, Ph.D.

Jeffrey Neul, Ph.D.

Paul J. Pfaffinger, Ph.D.

Cecile Phan, M.D.

Florante A. Quiocho, Ph.D.

Amina Qutub, PhD

Peter Saggau, Ph.D.

Daryl Scott, M.D., Ph.D.

Richard Sifers, Ph.D.

George Taffet, M.D.

Addison Taylor, M.D., Ph.D.

Qiang Tong, Ph.D.

Vinod Vijayan, Ph.D.

Wainerdi, Richard, Ph.D.

Samuel M. Wu, Ph.D.

graduate student handbook · 2015. 12. 8. · graduate student handbook program directors:...

Documents