The goal of the PhD program is to prepare students to take creative and sophisticated approaches to new scientific problems in various career settings. Graduating students are awarded the PhD degree in biomedical sciences or in neurosciences by ISMMS in New York City.

Students are at the heart of these investigative activities as partners in the work. They receive the most significant part of their doctoral training in a mentor-student relationship leading to the PhD dissertation. This research centerpiece of their training is preceded by a period of exploration of the Graduate Faculty and Multidisciplinary Training Areas in a year of core courses, special seminars/journal clubs, and laboratory rotations. It is further enhanced by an individualized program of advanced coursework within one of seven Multidisciplinary Training Areas, a format at the cutting-edge of modern science research training.

Website: https://icahn.mssm.edu/education/phd/biomedical-sciences

Email: phd@mssm.edu

This chapter covers the PhD in Biomedical Sciences and Neuroscience Program. Students can find the following information in this section.

• Program Information

• Program Requirements

  • Curricular Requirements

  • Requirements to Graduate

  • Standards for Maintaining Satisfactory Progress

• Curriculum

  • Seminars, Works-in-Progress, and Journal Clubs

  • Lab Rotations

• Selecting a Multidisciplinary Training Area

• Advising

  • Academic Advisor

  • Selecting a Research Mentor

  • Thesis Advisory Committee

• Thesis Proposal

  • General Considerations

  • The Written Document

  • The Oral Presentation

  • The Thesis Proposal Committee

  • Deadline

• Dissertation Defense

  • Written Document Format Options

  • The Dissertation Committee

  • The Defense and Seminar

  • Dissertation Deposit

• Transfer to Master Degree

• Program-Specific Policies

  • Program Alumni

All PhD students will be expected to fulfill the following course requirements for the PhD degree:

1. Core Curriculum – According to MTA requirements.

2. Laboratory Rotation – At least one rotation or equivalent (except for transfer/ advanced students) must be completed. See detailed description below.

3. RCR: Responsible Conduct in Research – Fall semester, first-year (except MD/PhD students who take the course during the first year in their PhD phase)

4. Rigor and Responsibility – Spring semester, first-year (except MD/PhD students who take the course during the first year in their PhD phase).

5. Biostatistics – Fall or Spring semester, first-year (except MD/PhD students who take the course during the first year in their PhD phase)

6. Advanced Coursework – Advanced coursework is required as defined by each MTA. See the MTA chapter, for a description of the individual course requirements, typical MTA requirements, and criteria for advancement to candidacy.

7. Transfer Credits – Students who have completed relevant graduate courses elsewhere will be granted exemption and/or graded credits at the discretion of the Dean, in consultation with the course and MTA Directors. See corresponding policy in Chapter 3 of the Handbook for details of this policy.

After the rotation period, students are expected to:

1. Formally choose a research mentor.

2. Decide on the Multidisciplinary Training Area if he/she/they has not already done so. The MTA will be the student’s area of focus for his/her/their advanced coursework, journal clubs, and seminars.

3. Choose three members for an Advisory Committee with whom they will be meeting at least once each semester to assess progress.

All students will need to meet the following degree requirements in order to successfully earn the PhD degree:

• Complete a minimum of 72 credits, with an average grade of B or better in all required core courses (i.e., Biostatistics and Core) and a cumulative GPA of 3.0 or higher.

• Complete at least 14 letter-graded credits of coursework

• Submit and successfully defend a Thesis Proposal

• Write an original dissertation that is accepted by the student’s Thesis Committee and is defended orally in front of a panel of experts.

• Deposit Thesis on Proquest

• Submit all required forms including student checkout form

See Standards for Maintaining Satisfactory Progress

It is crucial that students, Advisory Committees, and/or Program Directors monitor the students’ progress throughout the duration of their academic training. Continued financial support is contingent upon maintaining satisfactory progress at all times. Additionally, failure to achieve and maintain satisfactory progress, after counseling is sought from the Program, Advisory Committee and/or Dean of the Graduate School, can result in academic probation and ultimately, dismissal from the Program. Students who do not complete their degree within the maximum duration allowed will be dismissed from the program.

Under exceptional circumstances, the dissertation advisor, with the support of the student’s Advisory Committee, may petition the Dean of the Graduate School in writing to let a student continue his/her/their studies beyond the 7-year time limit for PhD students or 6 years in the PhD phase for MD/PhD students in Biomedical Sciences or Neuroscience and 5 years for students in the PhD in Clinical Research program. For those receiving a stipend, there is no guarantee that full stipend support will continue under these circumstances and each case will be reviewed and approved by the Dean of the Graduate School of Biomedical Sciences.

Satisfactory progress is maintained in the following ways for PhD students by:

• Matriculating on a full-time basis

• Demonstrating the potential for research and timely progress toward the choice of dissertation advisor and training area through their rotation activities in the first year

• Submitting a completed Laboratory Rotation Agreement Form and a completed Laboratory Rotation Evaluation Form for each rotation on time (see Lab Rotations)

• Maintaining of a minimum cumulative 3.0 GPA and achieving of a cumulative 3.0 GPA for all of the Core Curricula (see details under General Program Requirements). For this program, the Core Curriculum consists of a year-long core course (BMS or Neuro) AND an approved biostatistics course.

• Completing at least 14 letter-graded credits of coursework (see Requirements to Graduate)

• Completing the Thesis Proposal Exam by the end of the 4th semester in the program (see Thesis Proposal)

• Reaching and passing each of the Program Milestones by the required deadlines (see details in section on Program Milestones), and submitting of registration and documentation memos on time

• Forming within three months of lab declaration and then meeting with the full Advisory Committee at least once per semester and submitting an Advisory Committee Meeting Form following each meeting (see Thesis Advisory Committee)

• Enrolling in journal clubs, works-in-progress, and seminars as required by the student’s MTA (see Seminars, Works-in- Progress, and Journal Clubs)

• Demonstrating the ability to grow in research skills and moving towards project goals following the selection of a dissertation advisor (see Thesis Advisory Committee)

• Developing a research project, under the supervision of one or more faculty members, which results in a thesis that reports new findings, and is presented, defended and deposited by student (see Dissertation Defense)

• Producing data equivalent to that needed for a first author publication in a high-quality, peer-reviewed journal. A manuscript need not be submitted or accepted (see Dissertation Defense)

• Defending and revising within the prescribed time (5 weeks for no or minor revisions; 8 weeks for major revisions) (see Dissertation Deposit)

• Depositing the approved Dissertation within the time limits of the Program, i.e., (defend and deposit by June 30 of the seventh year in the Program) (see Dissertation Deposit)

• Successfully reaching and passing each of the Program Milestones by the required deadlines and timely submission of registration and documentation memos (see Program Milestones)

If the dissertation advisor is dissatisfied with the academic progress of a student and is considering removing the student from the laboratory the following steps must be taken:

1. The advisor will document sources of dissatisfaction.

2. The advisor will have direct discussions with the student to clarify the issues and to set a plan to correct the problems. A summary of the discussions should be documented by the advisor.

3. If dissatisfaction continues, mediation between the student and advisor should be sought by meeting with the MTA Director and the student’s Advisory Committee.

4. If required, a discussion between the student, the advisor, and the Dean or Senior Associate Dean should be also sought to determine whether the issues are potentially irrevocable.

5. The Dean may place the student on probation for a period not exceeding a semester.

If the student is placed on probation and fails to achieve sufficient academic progress during the following semester, the Committee for Academic Review will review the student’s status and may recommend dismissal from the PhD program.

The maximum registered time by which a PhD student must complete all doctoral requirements is 7 years. By the end of the 6th year in the PhD program, students must have successfully held an advisory committee meeting at which the committee has signed the Progress Form indicating that the student is planning to defend his/her/their dissertation in the next 3-6 months. If this step does not occur by the end of the 6th year, the student’s dissertation mentor must petition the Dean in writing for permission to extend the student’s status. The petition must include a written certification of progress from the student’s advisory committee that must be signed by the student. The petition must include a timetable for completing the dissertation and must also be signed by the student.

Upon entry into the 6th year of a PhD program, a student can no longer switch labs. If, at end of the 6th year, the PI, advisory committee, and CAR do not think sufficient progress has been achieved and the PI will not continue to support the student, the student will be dismissed from the program.

PhD students are required to meet key program milestones, register for all required courses, and complete all general program requirements to ensure timely completion of the degree. The maximum time limit for completing all PhD degree requirements is seven years after matriculation in the PhD Program. Students can review for the PhD program. Students who do not meet program deadlines will be subject to disciplinary action, up to and including academic probation and expulsion.

Key PhD Milestones/Deadlines

Seminars, works-in-progress, and journal clubs are central to the educational program. The opportunities to regularly encounter scientists and build critical analysis and presentation skills are of major importance. All students are required to participate in seminars and journal club activities during the entire duration of their Program.

First-year students will fulfill the journal club requirement within their Core Curriculum. They are encouraged to attend additional seminars and journal clubs in areas of their particular interest or in areas that they wish to explore.

Advanced students are expected to participate in the journal club and seminar activities of their MTAs and to participate in laboratory journal clubs and departmental seminars that are recommended by their dissertation advisor.

See

Core Curriculum

All PhD students must complete a Core Curriculum. The Core Curriculum will vary depending on the training area and the specific PhD degree (Biomedical Sciences or Neuroscience). The Core Curriculum provides the students with a strong set of general concepts and vocabulary that underpins much of the cutting-edge biomedical research in their area of interest.

All MD/PhD students take "Biomedical Sciences for the MD/PhD Student" as their Core Curriculum. This Core has been developed with the unique training needs of the dual MD and PhD degree students.

Students in the PhD in Biomedical Sciences program will complete the Biomedical Sciences Core, a yearlong course that consists of six units. They are BMS Fall: Enzymes and Metabolism; Genetics and Genomics and Gene Expression and Biological Chemistry); BMS Spring: Cell Biology; Development and Regeneration and Mechanisms of Disease.

Students in the Neuroscience PhD program must complete the Neuroscience Core curriculum, found in the.

In exceptional cases, students who have had prior graduate level coursework relevant to a Core Curriculum may seek exemption from a core course. Refer to for information about course waivers and transfer credits.

Satisfactory completion of the initial General Program Requirements (i.e., excluding advanced coursework and seminars) will be evaluated at the end of the first year in the Program:

Biomedical Sciences Core

Fall

BSR1006 Laboratory Rotation - Fall (4 credits)

BSR1012 Biomedical Science - Fall (6 credits)

BSR1021 Responsible Conduct in Research (0.5 credits)

MPH0300 Introduction to Biostatistics (3 credits) or BIO6400 Biostatistics for Biomedical Research (3 credits) - or BSR1715 Modern Statistics for Modern Biology in the Spring (3 credits)

Spring

BSR1007 Laboratory Rotation - Spring (4 credits)

BSR1013 Biomedical Science - Spring (6 credits)

BSR1022 Rigor and Reproducibility (0.5 credits)

BSR1715 Modern Statistics for Modern Biology (3 credits) - if MPH0300 or BIO6400 not taken in Fall

Neuroscience Core

Fall

BSR1006 Laboratory Rotation - Fall (4 credits)

BSR1021 Responsible Conduct of Research (0.5 credits)

BSR1705 – Cellular and Molecular Neuroscience (3 credits)

BSR1706 – Systems Neuroscience (3 credits)

BSR2707 Techniques and Approaches in Neuroscience (1 credit)

BSR4702 Selected Topics in Neuroscience (1 credit)

BSR5701 Seminar in Neuroscience (1 credit)

MPH0300 Introduction to Biostatistics (3 credits) or BIO6400 Biostatistics for Biomedical Research (3 credits) - or BSR1715 Modern Statistics for Modern Biology in the Spring (3 credits)

Spring

BSR1007 Laboratory Rotation - Spring (4 credits)

BSR1022 Rigor and Reproducibility (0.5 credits)

BSR1707 – Behavioral and Cognitive Neuroscience (3 credits)

BSR1708 – Pathophysiology of Neurological and Psychiatric Disorders (2.5 credits)

BSR4702 Selected Topics in Neuroscience (1 credit)

BSR5701 Seminar in Neuroscience (1 credit)

BSR6705 Clinical Topics in Neuroscience (0.5 credits)

BSR1715 Modern Statistics for Modern Biology (3 credits) - if MPH0300 or BIO6400 not taken in Fall

Advanced Coursework

Laboratory rotations are an important part of the first year of the Graduate Program. They give students the opportunity to experience different research projects, different laboratory and mentoring styles, and allow the faculty to assess the interests and aptitude of the students. All PhD and MD/PhD students must complete rotation(s) in laboratories before declaring a dissertation advisor and a Multidisciplinary Training Area. While it is acceptable to join a lab after 1 successful rotation, students are encouraged to find two matches before terminating their rotations and joining a lab. If an incoming students worked as a research technician in an ISMMS laboratory prior to becoming a graduate student, he/she/they may choose their former employer as their dissertation advisor, but only after rotating in at least one other laboratory. The rotation facilitates the choice of dissertation advisor and also offers students exposure to problems and techniques of interest to them.

THE GOAL OF THE ROTATION IS TO FIND A LAB. This should be an environment that provides a training experience in which students can thrive and reach their full potential.

See Standards for Maintaining Satisfactory Progress

MD/PhD students complete summer rotations:

• In year 1, MD/PhD students rotate in one lab for ~4-5 weeks.

• Going into year 2, MD/PhD students generally complete 2 more rotations, each of 4-5 weeks.

• Rotations need not be identical in length.

Rotation guidelines are as follows:

• Students are encouraged to use web resources and the current student body to explore possible labs before and during discussions with their advisors. Students are urged to consult multiple sources including current and previous laboratory members to gain a better idea of the laboratory’s approach to science and training and the success of previous trainees.

• In order to take a rotation student, labs must have sufficient financial and personnel resources to support a PhD student for at least 2 years following lab declaration. Labs that cannot support a student and his/her/their training CANNOT have a rotation student. Rotation students will work with their first-year advisors and/or MTA Directors to select labs that can take rotation students. If a lab cannot support a student’s financial package, the student SHOULD NOT rotate in that lab. If there is no chance that they will be able to take the student in the lab, no matter how good and interesting the work is, the rotation will be a waste of the student’s time.

• To facilitate and optimize the rotation experience for both the student and the faculty mentor, it is important that this student-faculty pair meet prior to the start of the rotation to discuss and align expectations, goals, requirements and laboratory guidelines. The discussion must be recorded on the Laboratory Rotation Agreement Form so that both the student and the rotation advisor are in agreement about what each expects from the other. The Form must be submitted at the beginning of the rotation.

• During the laboratory rotation, the student has to be aware of the balance that needs to be maintained between research and study time for ongoing courses. Students are expected to spend an average of about 50% of their time (about 20 hours/week) on the laboratory rotation. Good time management can optimize the experience in that particular laboratory.

• A “match” between student and lab is defined as an offer from the research mentor for the student to join the lab. This may be a hard yes, or could be pursuant to other conditions, such as the outcome of other rotation students in the research mentor’s lab.

• Students with prior experience at Mount Sinai -

  1. PREP or MSBS students who matriculate into the PhD program can use their research time in place of a rotation.

  2. Former SURP scholars who have spent two summers at ISMMS and are now in the PhD program, can use that research time in place of a rotation.

  3. Staff who become PhD students and who feel it necessary to do a rotation in their lab of employment before deciding to join that lab, may not do so until after completing a rotation in another lab. If, on the other hand, the student and the research mentor are confident about joining the lab of employment, other rotations are not strictly required.

• Starting in week 3 of the rotation, the research mentor and student should review progress and the possibility of joining the lab. This does not have to be a detailed conversation, but can be a simple update, and has three possible outcomes regarding joining the lab: yes, no, or maybe. If either the research mentor or the student has a firm idea that the lab is not a good match, the rotation should be terminated immediately. If the research mentor and the student believe it is a good match, it is recommended that the rotation continue for the full 6-8-week duration to ensure the lab continues to be a good fit. At some time during the final weeks of the rotation, terms for joining the lab should be reached, a Laboratory Rotation Evaluation form should be completed and turned in to the Graduate School, a lab Dissertation Advisor - MTA Declaration Form should be completed and turned in to the Graduate School, and the student should cancel other planned rotations. Finally, if either person is unsure if the lab is a good fit (and the other is not a “no”), the rotation should be continued with check-ins, as outlined above, occurring every week. The outcome of these discussions should be conveyed by the students to their first-year advisors and/or MTA co-directors.

• When rotations end, regardless of whether the lab is a match or not, a Laboratory Rotation Evaluation form must be completed by the student and rotation advisor and filed with the Graduate School.

• When the student is the person deciding the lab is not a match, it is customary for the student to provide the rotation advisor with a brief explanation of the reason why the match does not work. While this is not a strict requirement, it is recommended because it is important to remain in good communication with one's rotation advisor.

• The maximum time for a rotation is typically 6-8 weeks. An extension would be considered if there were circumstances that warrant one. A request for an extension should be made in writing, via email, to the PhD Program Manager.

• In some cases, rotations will span winter or spring breaks. When this occurs, the time off does not count towards the rotation.

• The schedule outlined above would permit up to four rotations (if needed) prior to spring break, although three rotations is more typical.

• Rotation times could be shortened further if the student is not taking classes while rotating because the student can work full time in the lab instead of balancing lab with class time.

• While it is acceptable to join a lab after one successful rotation, students are encouraged to find two matches before terminating rotations and joining a lab.

• Individual MTAs may require rotation presentations. Presentations may not be synchronized with the end of each rotation, so students should be prepared to describe work that they may have concluded weeks earlier.

• Grading of rotations will be on a Pass/Fail basis. If a student in the PhD in Biomedical Sciences or Neuroscience programs is not accepted into a laboratory by the conclusion of the second semester (fourth semester for MD/PhD students), he/she/they will be reviewed by the Committee for Academic Review for a failure to make satisfactory academic progress. Dismissal from the program is a possible outcome of this review.

This section covers advising for the PhD in Biomedical Sciences and Neuroscience Program. Students can find the following information in this section.

• Academic Advisor

• Selecting a Research Mentor

• Thesis Advisory Committee

Students matriculate in the PhD program without a formal commitment to a particular training area, unless interested in the neuroscience program. While students affiliate closely with a group of researchers in an initial area of interest, they are encouraged to consider new combinations or interests during the first year. Students pursue a series of rotations through diverse research laboratories before formally choosing a PhD research mentor and one of seven multidisciplinary training areas by the end of the second semester. See detailed chapter on MTAs here.

Entering students are assigned a graduate faculty advisor who will handle student questions about courses, rotations, or problems that surface throughout the first year. This faculty advisor is generally from the first choice MTA on the student’s application to the Graduate Program. In cases where the student is unsure about their choice of MTA, a second advisor from another MTA may be assigned. Once a student selects a dissertation advisor and a Multidisciplinary Training Area, with the help of the research mentor, he/she/they selects an Advisory Committee.

Also available to MD/PhD students are the Physician-Scientist Career Advisors, and peer networks, the Office of Diversity and Inclusion, and the Office of Well-Being and Resilience.

• Mentoring Changes due to the Relocation of the Research Mentor

• Mentoring Changes due to an Unproductive Partnership

• Procedures for Dispute Resolution

Selecting a Research Mentor The choice of a research mentor and an associated multidisciplinary training area (MTA) by the student (mentee), as well as the mentor’s acceptance of the mentee, should be regarded as a mutual commitment. This partnership is based on the understanding that the student will remain with their chosen research mentor until the thesis is completed. Students should select a mentor only after completing a period of research rotation. Both mentor and mentee should use the Compact for PhD Students and Preceptors as a basis to make sure that both parties are aware of their respective responsibilities and expectations, and apply the knowledge and skills from the “Responsible Conduct of Research” training (Course Code BSR1021). Such a partnership relies on open and transparent lines of communication to ensure understanding of the mentoring partnership and enhance the mentee’s training experience.

Students must understand that their research mentor is a primary mentor, providing research direction and career guidance. Research mentors are expected to foster the student’s independence, encourage collaborative work, presentations, and departmental seminar participation, introduce the student to colleagues, assist with manuscript writing and submission for publication, help identify and address strengths and weaknesses, and support career development. However, other faculty who take particular interest in the student’s growth and development as scientists may also serve as important mentors. Students are encouraged, with the guidance of their mentors and advisors, to develop relationships with those faculty whom they feel can provide significant research, career, and personal guidance, and may choose to include these faculty members on their thesis advisory committee (see section on Thesis Advisory Committee to follow).

Disagreements or disputes may arise between a mentee and their research mentor, thesis advisory committee, or MTA. These disputes may arise from the student’s laboratory training experiences or from concerns that the student’s academic progress is not meeting the expectations of the thesis advisory committee, MTA, and/or mentor. In such circumstances, every effort should be made to rectify these issues before they escalate into a situation that could make the mentor(s)-mentee partnership non-productive. Procedures for mediating disputes are outlined in Changes to a Mentor-Mentee Partnership which follow.

Irreconcilable differences that are not resolved by mediation may necessitate a change in the mentor(s)-mentee partnership, thesis advisory committee, or MTA. Such changes may be instigated by the mentor(s) or mentee, and policies and procedures to make such changes are outlined in Changes to a Mentor-Mentee Partnership which follow.

For MD/PhD students, the choice of a research mentor and MTA is done through lab rotations during the first two summers in the MD/PhD program. MD/PhD students end their second year in the program with being accepted into the laboratory of a Graduate Faculty member.

Each PhD student should complete the Dissertation Advisor/MTA Declaration Form before the end of the second semester in the Program. MD/PhD program strongly encourages its students to submit this form by March 1 of the second year/ fourth semester in the Program; however, for the form deadline is June 30 of that year. At this time, the student must also select at least three members for an Advisory Committee. Committee members should be selected because of their ability to provide scientific and/or technical support for the dissertation project. Advisory Committee members must be members of the Graduate Faculty. Two Advisory Committee members are experts in the area of the student’s research; a third member must be from a related field but need not be expert in the student’s area of research.

MD/PhD students are encouraged to add a clinical/translational (C/T) investigator, who need not be a member of the Graduate Faculty, to their Advisory Committee to provide feedback about the C/T impact of their research. This Form should be submitted to the Graduate School Office with all the required signatures as soon as possible, but no later than June 30.

One indication of satisfactory progress in the Program is the demonstration of the potential for research and the timely selection of a mentor and MTA. PhD students are expected to declare a dissertation advisor and MTA no later than 12 months after matriculation. MD/PhD students are expected to declare by the end of the second year in the Program.

The choice of a research mentor by the student and the acceptance of that student by the future research mentor should be considered a commitment on the part of both parties that the student will remain with the chosen research mentor until the thesis is completed. If a student is contemplating a change in research mentor or MTA, or, if the research mentor is unsatisfied with the academic progress of the student, mediation should be sought to remedy this situation by first meeting with the MTA Director and the student’s Advisory Committee. (MD/PhD students should also confer with the MSTP directors.) If necessary, the Dean of the Graduate School may also meet with the student and their research mentor. Movement between MTAs is permitted if the student is certified, in writing by the MTA Director(s), to be in good academic standing by the original MTA and is accepted, in writing, by the proposed MTA. Students who are contemplating a change must discuss this fully with the current research mentor. These changes invariably involve some loss of time and dislocation to both student and research mentor and possibly extra coursework. Careful guidance by the student’s Advisory Committee will reduce the number of such changes and will increase the likelihood that those changes that do occur are productive.

A. Responsibilities of a departing research mentor and newly assigned research mentor at Mount Sinai When a research mentor relocates to another institution, the mentee will need to realign their mentoring team, whether the mentee stays at ISMMS or relocates with the mentor while remaining enrolled at ISMMS. In all cases, the student must have a primary mentor who is a mentoring faculty of the GSBS. All formal mentors will be non-voting members of advisory committees. If a student’s new mentor was formerly a member of the student’s thesis advisory committee, that advisory role will need to be assumed by appointment of a new member who is a mentoring faculty of the GSBS.

The relocation of a research mentor presents three options for a new mentoring arrangement:

i) If the student has not yet passed their qualifying exam, they may opt to change their laboratory and begin their PhD with a new research mentor, project, and possibly multidisciplinary training area (MTA). This will require the same rotation, laboratory declaration, and mentor selection procedures that would be applicable to a new student. If the research mentor departs during the student’s first year, and the new mentor is willing to take the student as a mentee immediately, then this can occur with the new mentor assuming financial and training responsibilities for the student. If new rotations are required, the student will receive a 3-month window of support from the GSBS to pursue these rotations prior to selecting a new laboratory. The student and new Mentor must submit a new laboratory declaration form electronically to the Manager of PhD programs in Biomedical Sciences and Neuroscience to document any changes in the mentoring team.

ii) If the student is at least halfway through their training (3 years or longer in the program), and wishes to continue their research project in another laboratory with a new research mentor at ISMMS, the previous research mentor and student must identify the new mentor and agree to a collaboration to continue the work that was initiated in the original laboratory without further laboratory rotation. This may also require realignment of the thesis advisory committee, and possibly a change in the MTA. The new mentor assumes the role of primary mentor, and the departing mentor may (or may not) agree to remain as a secondary mentor so long as they hold an adjunct faculty position at ISMMS. This plan must be documented in writing as a transition plan submitted electronically via the GSBS Airtables, and agreed to by relevant MTA Director(s) and the Senior Associate Dean for PhD Programs. Academic requirements and student support services following this mentoring change will not be altered. The student must submit a new laboratory declaration form electronically to the Manager of PhD programs to document any changes in the mentoring team.

iii) Regardless of the stage of their studies, the student may opt to remain enrolled at ISMMS, and complete their experiments in the new laboratory of their existing research mentor at their new institution. In this case, the departing mentor must complete a transition plan form via the GSBS Airtables to indicate: 1) the names of all affected mentees; 2) a transition plan for relocating mentees, including a new primary mentor based at ISMMS, and a plan for financial support of the mentees. This plan must be completed in writing and agreed to by relevant MTA Director(s) and the Senior Associate Dean for PhD Programs. Academic requirements and student support services following this mentoring change will not be altered. The student must submit a new laboratory declaration form electronically to the Manager of PhD programs to document any changes in the mentoring team.

In cases where the student wishes to transfer to another program, they must withdraw from the relevant PhD program offered by the GSBS, and enroll at the new institution. International students should be aware that any changes to the locations of their activities may have implications for their visa/immigration status, and should check this with personnel at the new institution well in advance of any relocation.

B. Responsibilities of the mentee Any changes to the mentoring team due to relocation of the original research mentor do not change the responsibilities of the mentee, even if they are performing their experiments at another institution. Academic requirements and thesis advisory committee meeting requirements do not change. Policies regarding publication and use of data, protocols, or code generated during the PhD remain those of ISMMS, and the mentee’s affiliation as a student of the GSBS on publications and communications do not change. Finally, changes to the mentoring team do not change the maximum time for completion of a degree.

C. Responsibilities of the MTA director and thesis advisory committee regarding the research mentor(s) and mentee (including thesis proposal and thesis defense exams) If mentoring changes do not affect the MTA or thesis advisory committee, these entities continue to guide and assess the academic progress of the student. The absence of such changes will be documented on the transition plan.

If mentoring changes result in a change of MTA, this should be documented as part of the transition plan, and approved by the original and new MTA Director, as well as the Senior Associate Dean for PhD programs. Such changes may alter academic requirements of the new MTA, which must be clearly communicated to the student and included in the transition plan.

If changes are made to the thesis advisory committee, these must also be documented and approved by the (new) MTA.

The post-transition MTA and thesis advisory committee will oversee the thesis proposal and thesis defense exams of the mentee. These exams will be conducted under the same criteria, and to the same standards, as if no changes had occurred. In situations where the changes to the mentoring arrangements had a significant impact on the academic progress of the student, the student may apply for an extension to complete the qualifying exam, but the maximum time for completion of a degree does not change.

See Standards for Maintaining Satisfactory Progress

The thesis advisory committee is an essential, independent advisory panel that adds to the mentoring provided by the student’s research mentor. The membership of the committee should be determined after discussion between the mentor(s) and the mentee, and consist of at least three mentoring faculty members of the GSBS who can provide advice and support to the student. The student should declare the thesis advisory committee simultaneously with declaring the mentor(s) and laboratory, or as close as is possible to the time (not to exceed 3 months) the laboratory is declared.

The thesis advisory committee must meet with the student at least once per semester starting from the point of laboratory declaration. It is the responsibility of the student to ensure these meetings occur each semester, and that the appropriate progress reports are submitted electronically to the PhD program manager. Early meetings will focus on developing aims for a research proposal to act as the basis of the qualifying exam, as well as review initial progress and the relevant literature. At any time, the thesis advisory committee also acts to advise and support the student with their training experience, academic progress, and career development. Throughout the student’s candidacy phase, the thesis advisory committee plays an important role in working with both the mentor and mentee to refine and resolve any substantive or professional divergences.

The qualifying exam, comprising a thesis proposal (written document and oral defense) and discussion of relevant general knowledge from core classes, confirms candidacy for the Doctor of Philosophy degree. This exam is evaluated by the thesis advisory committee, plus an MTA director or their delegate (a senior faculty from their MTA). PhD students should successfully complete the qualifying exam by the end of their fourth semester (June 30th), and MD/PhD students by the end of their first year in the PhD-phase (MP1). Further details regarding registration and expectations for this exam can be found in “Thesis Proposal” to follow.

Following confirmation of candidature, the thesis advisory committee continues to advise on research directions and scope, preparations for thesis defense and publications, as well as responsible generation and handling of data arising from their research in the mentor’s laboratory. The thesis advisory committee will also advise on career development and on any other challenges or difficulties students may encounter during their PhDs. On occasions where additional help or focusing of effort is required, the thesis advisory committee may require more frequent meetings.

See Standards for Maintaining Satisfactory Progress

A. Disputes between research mentor(s) and mentee Disputes between the research mentor(s) and mentee range in origin and severity, and can be reported by either or both parties. Open communication between the mentor(s) and mentee is the key to avoiding disputes and, when they occur, resolving them. In cases where resolution cannot be reached in communications between the parties, there are procedures and resources that aim to resolve disputes. In the event that the mentor(s) and mentee cannot resolve their disputes through such procedures and resources, either the mentor(s) or mentee may opt to change the nature of the mentoring team.

i) Scientific disputes. When the research mentor(s) and mentee cannot themselves resolve a scientific dispute, they should promptly present the relevant issues to the student’ thesis advisory committee. After hearing from the research mentor(s) and mentee, the thesis advisory committee must ultimately decide on the scientific issue. If the scientific dispute concerns data ownership, the thesis advisory committee should refer to The Ownership of Research Data policy. Please note that in case of suspected research misconduct by either the student or mentor (with the priviso that disagreements of opinions are not reseach misconduct) the issue should be immediately reported to the Office of Research Integrity Note: Anonymous Reporting is also available at the Hotline: 1-800-853-9212.

ii) Non-scientific disputes. It is critical that all research is carried out in a safe and professional environment. Any form of mistreatment, bullying, harassment, is not tolerated, may violate NIH Anti-Harassment Policy and Guidance, and should be reported to one or more of the contacts listed below. The mentor is responsible to provide a professional laboratory environment, and should be the student’s first contact if they believe they are experiencing inappropriate or unprofessional behavior in the laboratory. If a mentee believes that they are experiencing such behavior by their mentors, they may initially contact an MTA Director, a faculty advisor, or the Senior Associate Dean for PhD Programs. Depending on the nature of the dispute, the MTA Director, faculty advisor and/or Senior Associate Dean for PhD Programs may directly recommend a course of action, refer the matter to a responsible office, and/or refer the mentee for further advice. Mentees may also seek confidential advice from the Ombuds Office (Dr. George.Huntley@mssm.edu). There are additional resources available for mentees to report inappropriate behavior that are discussed in Responsible Conduct of Research (BSR1021). These resources include:

• The mistreatment feedback form

• Title IX Coordinator Rebecca Anderson (212-540-8669 or TitleIX@mssm.edu)

• Human Resources (212-241-4097)

• Office of Gender Equity in Sci/Med (Carolyn Horowitz, Dean, 212-659-9552)

• Compliance Online Form (can be anonymous)—legal, ethical, behavioral, practical concerns)

• Compliance Hotline 1-800-853-9212

B. Disputes between the thesis advisory committee and a research mentor(s) or mentee All disputes between the thesis advisory committee and the research mentor(s) and/or mentee should be presented to the MTA directors and, if necessary, the Senior Associate Dean for PhD Programs. The Senior Associate Dean for PhD Programs has the ultimate responsibility for resolving any such disputes (whether scientific or non-scientific) and can institute changes to the thesis advisory committee membership to do so.

Students and faculty are urged to understand that the advisory system is their strongest ally in identifying and helping to resolve problems, in maintaining a realistic set of expectations for progress, and as a source of extra ideas and new approaches. Students should take the initiative in scheduling meetings. Timely meetings are imperative.

Students should recognize that their thesis advisor is usually their most important mentor, someone who can advise the student on research directions and may also provide career guidance. It is expected that thesis advisors provide opportunities for the student to develop independence, encourage the student to participate in collaborations, presentations, departmental seminars, introduce the student to colleagues, help the student to learn about writing and submitting manuscripts for publication, help the student to identify and work with their strengths and weaknesses and be committed to help the student make the next move in their career development. However, other faculty who take particular interest in the student’s growth and development as scientists may often also serve as important mentors. Students are encouraged to develop relationships with those faculty whom they feel can provide significant research, career, and personal guidance.

Formal progress reports must be filed twice annually with the Graduate School Office. To meet this requirement, students are expected to meet each semester with the full Advisory Committee. The student should review the Progress Form and correct/update as necessary. The Advisory Committee must use the last page of the Progress Form to evaluate the student’s progress, clearly identify strengths and weaknesses and indicate plans for development. All members of the Advisory Committee should then sign and date the Progress Form.

When a student fails to demonstrate satisfactory academic progress, the Advisory Committee or Program Director may mandate more frequent advisory committee meetings.

When a research mentor thinks his/her/their student is nearing a point of completion, the Advisory Committee should meet with the student and advisor to assess the student’s readiness to write a dissertation. This meeting should take place approximately 6 months before the anticipated dissertation defense. Students should update their list of publications and manuscripts in press on the Progress Report form before this meeting. At this meeting, the Advisory Committee will certify that the student is ready to write his/her/their dissertation and to schedule a defense date.

This approval should be granted and a date set only if the student has, at a minimum, achieved the following:

• met all of the required program milestones,

• completed all coursework and met the academic standards of the Graduate School,

• demonstrated mastery of the literature, conceptual skills, analytical skills, writing and presentation skills, experimental skills, record keeping skills and work ethic meets doctoral-level standards

• contributed intellectually as a lead author, or equivalent, to at least one manuscript, published, in review, or ready for submission in a peer-reviewed journal. An exception to this requirement will require the unanimous approval by the Advisory Committee.

When these criteria have been met, the student will be given a green light to enter the dissertation writing phase.

A. Responsibilities of former and new research mentors A mentorship change may be necessary based on irreconcilable differences or incompatibility between the research mentor(s) and mentee – whether based on scientific, academic, or personal issues – such that the mentoring partnership is no longer productive. In such cases, there are two possible outcomes that affect the role(s) of former and new mentors:

i) The mentee ceases to work on the former project. If no data, protocols, or code from the former research mentor’s laboratory is to be published, included in a thesis, or publically reported in any way, the former mentor no longer has responsibility for the mentee’s publication or reporting activities. If data, protocols, or code generated by the mentee in former mentor’s laboratory is to be published, the former mentor must document in writing (as part of the transition plan) that the former mentee will gain (co)authorship in accordance with ISMMS’s policy on authorship. If data, protocols, or code generated by the mentee in the former mentor’s laboratory is to be included in their PhD thesis, the former mentor and mentee must document inwriting such inclusion as part of the transition plan, and such an agreement must be approved by the Senior Associate Dean for PhD Programs, and recorded electronically in the student’s file. If the former mentor does not agree that the former mentee’s work is worthy of publication, including in the former mentee’s thesis, the dispute must be referred to, and handled by, the departmental Chair, similar to other authorship disputes.

ii) The mentee continues their research project in the laboratory of a new mentor. The former research mentor must approve in writing (and record electronically in the student’s file) the mentee’s continuation of a project originated in their laboratory. The new mentor assumes all the training responsibilities of any PhD mentor in research, academic progress, career development, etc. Continuation of the mentee’s research project must be accompanied by details of financial costs for experiments and publications, as well as plans for authorship, data sharing, and data usage, as would be part of any formal research collaboration. Such details must be included in the transition plan, approved by the Senior Associate Dean for PhD Programs, and recorded electronically in the student’s file. In addition, if any data, protocols, or code derived by the mentee in the former mentor’s laboratory is to be included in the PhD thesis, written permission for such inclusion must be provided from the former mentor prior to submission of the thesis. Such permission should be sought by the chair of the thesis advisory committee, and forwarded to the Senior Associate Dean for PhD Programs. If the former mentor does not agree that the mentee’s work is worthy of publication or inclusion in the former mentee’s thesis, the dispute must be referred to, and handled by, the departmental Chair, similar to other authorship disputes.

iii) The student opts to change their laboratory and start a new PhD research project with a new research mentor, project, and/or MTA. This scenario will require the same rotation, laboratory declaration, and research mentor selection procedures that would be applicable to a new student. If the research mentor departs during the student’s first year, and the new mentor is willing to take the student as a mentee immediately, then this can occur with the new mentor assuming financial and training responsibilities for the student. If new rotations are required, the student will receive a 3-month window of support from the GSBS to pursue these rotations prior to selecting a new laboratory. Procedures for the latter scenario can be found in Chapter 2, Funding Package and Direct Compensation. The student must submit a new laboratory declaration form electronically to the Manager of PhD programs in Biomedical Sciences and Neuroscience to document any changes in the mentoring team.

B. Responsibilities of the mentee If changes to the mentoring team are a result of unresolved disputes, the mentee will be responsible to continue their studies as outlined in the agreed mentoring plan. The overall academic responsibilities will remain those imposed by the GSBS and the MTA. Depending on the post-dispute agreement, in cases where the student is continuing the same research project in a different laboratory, the mentee, through the new mentor, may be required to communicate research results to the former research mentor. In all situations, mentees must abide by publication and data use rules under which their research was performed; this may affect plans for publication, thesis writing, and data reporting into public databases and at scientific meetings. If the former mentor agrees to publication or presentation of data, protocols, or code derived by the mentee while they were in the former mentor’s laboratory, permission from the former mentor must be obtained in writing and forwarded to the Senior Associate Dean for PhD programs and the Manager of PhD Programs, who will record such permission electronically in the student’s file.

C. Responsibilities of the MTA director and thesis advisory committee interactions with research mentor(s) and mentee (including thesis proposal and thesis defense exams) If changes to the mentoring team are a result of unresolved disputes, the new MTA and/or thesis advisory committees continue to assume the same roles as otherwise set forth in this Handbook in ensuring the completion of the academic requirements of the PhD as outlined above for changes induced by mentor relocation.

Specific criteria for the members of the Thesis Advisory Committee are:

1. The committee chair: The chair is a voting member of the committee chosen by the MTA co-directors in consultation with the trainee and their Thesis Advisor. This committee member is typically an MTA co-director or a voting committee member delegated by an MTA co-director. The chair must be someone who does not directly collaborate on the student’s project, will not co-author papers or abstracts with the student, has no financial conflicts of interest with the student or project, and does not supervise the work.

2. The Thesis Advisor: the PhD Thesis Advisor of the trainee. The PhD Thesis Advisor is not a voting member of the committee and is a silent observer at the Thesis Proposal and the Thesis Dissertation. However, after committee meetings, the Thesis Advisor should discuss the feedback of the committee with the student and advise on how to act on their advice as the project evolves.

3. The voting members: There must be two voting members on the committee in addition to the chair. Both these individuals must be members of the Graduate Faculty and have no financial conflicts of interest with the student or project and cannot directly supervise the student’s work. Voting members may not be collaborators on the project; collaborators may attend committee meetings but may not vote. These committee members can be collaborators on the student’s project and co-authors on papers and abstracts with the student.

4. The non-voting members: One or more non-voting members can attend the committee meetings. These might include a clinical/translational (C/T) investigator, who need not be a member of the Graduate Faculty, to provide feedback about C/T impact of the research (encouraged for MD/PhD students) or others with particular expertise of value to the trainee, including collaborators. Individuals other than the Thesis Advisor who are directly involved in supervising the work (e.g., a computational mentor or co-advisor) can also attend committee meetings. In addition, experts who are not members of the training faculty of the GSBS may be invited to attend in an ad hoc manner to extend their expertise in one or more meetings.

Successful passage of the Thesis Proposal should be completed by the end of the fourth semester (June 30th) for PhD students, and by the end of the first year in the PhD-phase (June 30th) for MD/PhD students. To schedule the Thesis Proposal (or re-examination), the student should check the proposed date and time with the Examination Committee members before submitting the Thesis Proposal Registration Form. The student needs to submit the Registration Form, with the appropriate signatures, to the Graduate School for approval, at least 4 weeks before the scheduled dates of these Examinations. Failure to register in a timely manner may result in the cancellation of the Examination. If a student does not register for an Examination that is conducted, the Graduate School reserves the right to require a re-examination or to require a notarized statement from the student and the Examination Committee certifying the number of times the student has been examined. The Chair of the Examination Committee complete the Thesis proposal voting form at the completion of the examination. If the Committee determines that a re-examination must occur, or that revisions must be made to the Thesis Proposal, the details, including a deadline within the allowable time, must be communicated to the student, in writing.

No extensions will be granted except under extenuating circumstances. Requests for extensions of established Examination deadlines should be made at least one month prior to that deadline. Request for an extension should be made by completing the Thesis Proposal - Request for Extension form and turning it in to the Senior Associate Dean for Student Affairs; final decision are made by the Dean of the Graduate School. Students who fail to meet the Examination deadlines will be placed on academic probation.

See Standards for Maintaining Satisfactory Progress

The written document must be in the format of an NIH F30/31. As such, the document should not exceed 7 pages, excluding references. The Thesis Proposal must be submitted to the Thesis Proposal Review Committee at least three weeks in advance of the Oral Presentation. When writing the Thesis Proposal, it should contain:

1. Specific Aims (1 page): Describe the hypothesis(es) you are testing. What are your research objectives? What conclusions could be made from your findings? Be concise, clear and logical. Provide an approximate timetable for accomplishing these aims. Your aims are the test(s) of your hypothesis

2. Research Proposal (6 pages): The research proposal portion typically includes the following sections:

   • A clear statement of the scientific premise. The purpose of this will be covered in the Rigor and Reproducibility course in Year 1.

   • Background/Significance: Provide a critical review – evaluate, don't just cite! – of the most pertinent work that raised the question you are answering, spawned the idea for your plans, made your approach feasible, etc. Critically evaluate what others have done. How does your dissertation relate to other problems or areas of biomedical sciences and/or contemporary biology? Identify any concerns. Explain how your hypothesis and planned accomplishments fit. This is an opportunity to relate your plans to the ongoing tradition in science and explain why your work is important.

   • Preliminary Studies: Describe what you have already accomplished. Where appropriate, provide data, even if preliminary. You do not need an enormous amount of preliminary data; it is far better to take this Examination near the beginning of the project. Explain how these results fit in with your plans.

   • Research Design and Methods: Describe the primary techniques you will use. Critique them - exactly what will they show? With how much assurance? How will you evaluate them? What kinds of artifacts have been observed or could be expected? Are the methods adequate to test your hypothesis(es)? Can other procedures be applied to achieve the same goals? Why are yours better?

   • Literature Cited: Not included in the page limit.

3. Formatting Instructions:

   • Font: Use single-spaced, 11-point Arial font (A Symbol font may be used to insert Greek letters or special characters; the font size requirement still applies.)

   • Page Margins: Use at least one-half inch margins (top, bottom, left, and right) for all pages.

4. Figures, Graphs, Diagrams, Charts, Tables, Figure Legends, and Footnotes: You may use a smaller type size, but it must be in a black font color, readily legible, and follow the font typeface requirement. Color can be used in figures; however, all text must be in a black font color, clear and legible.

The Thesis Proposal consists of the presentation, written and oral, of a research proposal that is based on the thesis work already begun by the candidate. For additional detailed instructions, refer to the Thesis Proposal webpage.

The thesis proposal should:

• Be based on the student's own work, not that of the research mentor

• Allow the student to organize his/her/their thoughts and plans and place them in perspective

• Allow the research mentor and the student's Advisory Committee to assess the level of scientific sophistication of the student

• Provide both the student and the Committee a measure against which to determine subsequent progress.

The Committee should evaluate the student’s ability to:

• evaluate and synthesize relevant literature

• articulate and elaborate on the aims

• show and evaluate preliminary data

• discuss experimental design as it applies to work planned.

The Thesis Proposal Committee is composed of the Thesis Advisory Committee with the possible addition of an MTA co-director or another senior MTA faculty member designated by the MTA-Director(s) who will serve as chair of the committee for the Thesis Proposal exam. If an MTA co-director or other senior MTA faculty member are already a member of the Thesis Advisory Committee, no additional members are needed for the Thesis Proposal Committee. If the chair of the Thesis Advisory Committee does not have extensive experience with Thesis Proposal Exams, an MTA co-Director or a senior MTA faculty member (delegated by the MTA co-Directors in consultation with the trainee and their Thesis Advisor) will be added to the committee to serve in this role. The chair of the Proposal Committee must meet the same criteria as the chair of the advisory committee. Participation of nonvoting members of the advisory committee in the Thesis Proposal exam is optional; if they are present, they must remain silent.

The Chair of the Committee must enforce all rules of the Examination, including those pertaining to the role of the dissertation advisor, as outlined below. In addition, each student is strongly encouraged to discuss the expectations of the Thesis Proposal Committee Chair as they develop their Thesis Proposal.

The meeting should be structured as detailed in the Thesis Proposal webpage

If the Committee determines further work necessary, the Chair will provide this information, in writing, to the student. A copy of this memo, detailing conditions and deadline, must accompany the Voting Form, which should be submitted electronically within two days of the proposal presentation. The Chair of the Committee will report the discussion to the dissertation advisor.

It is possible for a Committee to consider a student’s performance satisfactory for the oral presentation of the work achieved and work planned, but still consider the written proposal to be inadequate (in detail, style, citation quality, figure/table/legend presentation, etc.). The student may only be permitted one re-take the oral presentation, but the Committee may ask for as many revisions of the written proposal as are necessary to achieve a satisfactory proposal. This process can occur under the supervision of a subcommittee and must be completed before the student can be advanced to Candidacy.

Advancement to Candidacy

Students will automatically be advanced to candidacy after all the General Program Requirements, the Advanced Coursework for the MTA, and the Thesis Proposal Exam have been successfully completed.

All PhD students must complete the Thesis Proposal by the end of their fourth semester in the Program. MD/PhD students must present the Thesis Proposal by the end of the first year in the PhD-phase in Program. If a student fails to meet this deadline, he/she/they will automatically be placed on Academic Probation. If Academic Probation is not removed by the end of the next semester, the student will be dismissed from the program. Under extenuating circumstances, students may request an extension of this deadline by submitting the appropriate form to the Dean of the Graduate School prior to the deadline for successful completion of the Thesis Proposal.

The student whose Thesis Proposal is deemed unsatisfactory will usually be given one opportunity to address the particular area(s) of weakness. The conditions and timing for a re-presentation must be established at the time of the initial presentation. However, it must occur within 4 months of the initial presentation. The information concerning a re-presentation should be communicated to the student and the Graduate School Office, in writing, within two days of the initial presentation. If the student (with support of the mentor) wishes to change the membership of the Re-Examination Committee from that of the Examination Committee, she/he/they should discuss this with the MTA co-directors and/or the Dean of the Graduate School, prior to registration for the Re-Examination. In rare instances, the Committee may refuse the student the opportunity to redress the Proposal where students who have failed to show sufficient research progress and ability.

See Standards for Maintaining Satisfactory Progress

Dissertation

When a research mentor thinks his/her/their student is nearing a point of completion, the Advisory Committee should meet with the student and advisor to assess the student’s readiness to write a dissertation. This meeting should take place approximately 6 months before the anticipated dissertation defense. Students should update their list of publications and manuscripts in press on the Progress Report form before this meeting. At this meeting, the Advisory Committee will certify that the student is ready to write his/her/their dissertation and to schedule a defense date. This approval should be granted and a date set only if the student has, at a minimum, achieved the following:

• met all of the required program milestones

• completed all coursework and met the academic standards of the Graduate School

• demonstrated mastery of the literature, conceptual skills, analytical skills, writing and presentation skills, experimental skills, record keeping skills and work ethic meets doctoral-level standards

• contributing intellectually as a lead author, or equivalent, to at least one manuscript, published, in review, or ready for submission in a peer-reviewed journal. An exception to this requirement will require the unanimous approval by the Advisory Committee

When these criteria have been met, the student will be given a green light to enter the dissertation writing phase.

Copies of earlier successfully completed Program Dissertations are available for review in the Levy Library. Guidelines for the dissertation deposit can be found on Graduate School Forms website or at the Levy Library website.

Content

A student should not present tables or figures that are not entirely his/her/their own work unless this is unavoidable because the data are necessary to develop the story; in that case the precise contribution of the student must be made clear and indicated on the contributions page. Detailed methods should not be presented for work not actually conducted by the student, including work done by the Core Facilities or other colleagues; such presentations convey the impression that the student actually carried out the procedures.

See Standards for Maintaining Satisfactory Progress

The written proposal should be emailed to the committee no later than three weeks prior to the scheduled oral exam. Committee members may reschedule the Examination if not given the appropriate amount of time to prepare.

The committee members should read the proposal prior to the exam, and while they can provide informal feedback to the student if they wish, they cannot convey their consideration as to whether the document is acceptable or requires revision prior to the meeting of the committee at the oral exam.

Since the Committee members will have read the written document before this presentation, the student should use this opportunity to give a brief summary of the particulars of the research and the proposal. This presentation should not be a reiteration of the written proposal and should be limited to 20 minutes, a time limit that should be enforced by the Chair of the Committee. Prior to the presentation, the student should discuss, with the Chair of the Committee, whether he/she/they would prefer uninterrupted presentation vs. one in which questions will be asked as they arise during the presentation. If the latter is chosen, the 20-minute time limit does not apply. If the former format is chosen, there will be a questioning period following the presentation.

In either case, the student should be able to answer questions about the specifics of the proposal as well as general knowledge of the field as related to the proposal. The student should be able to defend the rationale for the particular approach(es) being used and explain how this will answer the questions being asked. Potential problems should also be anticipated with alternative approaches that could be used. Students will not be expected to defend these alternatives in great detail.

• The proposal should be written by the student, not the dissertation advisor. It is the role of the dissertation advisor to guide the student in preparing a coherent, intelligible document to be distributed to the members of the Thesis Proposal Committee. However, the dissertation advisor should also ensure, to the best of her/his/their ability, that the proposal is an original document and that the language of the proposal is that of the student. Ultimately, it is the responsibility of the student to provide an acceptable document.

• The whole proposal should be in the best traditions of scholarship, e.g., identify sources, and balance one's presentation by including conflicting data and counterarguments. The proposal should convince the Committee that the dissertation project is reasonably important and practicable.

• A student should not present tables that are not entirely his/her/their own work, unless this is unavoidable because the data are necessary to develop the story. In that case, the precise contribution of the student must be made clear and appropriate attribution should be made.

• Detailed methods should not be presented for work not actually conducted by the student, including work done by the Core Facilities or other colleagues; such presentations convey the impression that the student actually carried out the procedures.

Option 1: Students have the option of writing a traditional dissertation. The written dissertation should conform to the guidelines detailed in the Levy Library PhD instructions.

Option 2: Students who wish to use published manuscripts in their dissertation must comply with the following standards regarding inclusion of their published work:

1. When a student is first (or co-first) author on a publication he/she/they can include the entire manuscript as a dissertation chapter. There is no need to rewrite it.

   • The manuscript must be converted into the proper thesis format; typeset pdfs cannot be included in the dissertation.

   • Students must obtain copyright permission from the journal if necessary and follow all journal rules regarding inclusion in a dissertation.

   • When the work represents collaborative research, each chapter should include a page of attributions where the contributions of others are explicitly stated.

2. If a student is a middle author on a published manuscript, the dissertation cannot include the text of the full manuscript. Instead, the student should write a new description of the work that includes only his/her/their data.

3. A paper that has been submitted, but not yet accepted, can also be used as long as the above guidelines are followed. In addition, the following text should be added to the acknowledgements section of the manuscript: “The data in this paper were used in a dissertation as partial fulfillment of the requirements for a PhD degree at the Graduate School of Biomedical Sciences at Mount Sinai."

Either option must involve a substantive piece of original and independent research grounded in an appropriate body of literature and theory.The thesis must contain a Statement of Authorship page which is available on the Graduate School forms website.

The Dissertation Committee is composed of the Thesis Advisory Committee with the addition of an external committee member. Once constituted as such, the committee is considered the Dissertation Committee. The external committee member must: 1) hold a PhD, MD, or other appropriate advanced degree from an accredited institution; 2) have sufficient research experience and qualifications in the area of the student’s thesis to ensure an appropriate level of rigor for the examination; 3) be a member of a PhD granting institution and 4) not be a faculty member of ISMMS. Like the committee chair, this member must be someone that does/has not directly collaborated on the project of the student, has no coauthored papers or abstracts with the student, has no financial conflicts of interest with the student or project, and has not supervised any aspect of the work. The external committee member is a voting member of the committee. Prior to naming an external member to the committee, the student and mentor should write a brief summary of why the proposed external examiner is qualified for the role and state that they have no conflicts of interest. This document requires approval by the committee chair. Participation of non-voting members of the advisory committee in the Thesis Dissertation exam is optional; if they are present, they must remain silent.

When the student has completed the written dissertation document, it must be read and approved by the Dissertation Committee. The student should submit the Dissertation to each member of the Committee as early as possible, but no later than two weeks before the Defense. Committee members may reschedule the Examination if not given the appropriate amount of time to prepare for it. The Committee shall meet with the student for an oral Defense of the Dissertation. Before the final scheduling of the Defense, it is wise to obtain the Committee’s approval that the work is complete and appropriately presented. The student must register for the defense with the Registrar using the Dissertation Defense and Seminar Registration form. Once the defense has been registered, the Registrar will provide the Dissertation Defense Voting form. The student must include a Statement of Authorship page with the written document.

The possible outcomes are listed below. Dissertations approved as presented or pending minor revisions may be nominated for distinction.

Approved as Presented: No revisions required. Students must deposit within five weeks after the defense.

Approved Pending Minor Revisions: Minor additions and edits to the text, formatting and organizational changes, the addition of references to existing text, and additions/corrections to the preface. Minor revisions should be completed to the Chair's satisfaction and deposited within five weeks after the defense.

Approved Pending Major Revisions: Inclusion of additional data, the inclusion of additional data analysis, substantial additions to the text (e.g., the addition of subject matter to the introduction or discussion), or rewriting of whole sections. Major revisions must be resubmitted for approval by the Chair and two members of the examining committee and deposited within eight weeks after the defense.

Fail: The committee believes that the dissertation is not acceptable and will provide a detailed written description of the reservations about the examined dissertation and make further recommendations.

The mentor may apply to the Graduate School for reimbursement (up to $450) to defray travel expenses for the “outside” examiner. A letter of request, from the dissertation advisor, for the honorarium should be submitted to the Graduate School Office. The letter should include the name of the examiner, his/her/their social security number and mailing address. If the funds are being used to defray the cost of travel, original receipts should be sent with the letter of request. We will prepare and submit the check request. Unless otherwise instructed, the check will be sent directly to the examiner. If the dissertation advisor/department is covering a portion of the travel expenses, the letter of request should be sent with a check request (and original receipts), prepared by the dissertation advisor/department, indicating the amount and fund number (with appropriate signature) for the portion covered by the dissertation advisor/department. The Graduate School will complete the request and forward it to Accounts Payable. Unless otherwise instructed, the check will be sent directly to the examiner.

In addition to the closed session for the oral Defense, each student must present a 45-60 minute seminar on his/her/their work, open to the scientific community. The GSBS will announce the seminar to the "public” at least four weeks prior to the seminar. If the seminar is presented before the oral defense, the examiners should be invited to the seminar, but should be asked to refrain from asking questions, except those that will lead to making the seminar more interactive with the rest of the audience. More intensive questions will be asked in the actual private defense.

Students who leave the PhD program may be eligible for transfer to the Masters of Philosophy (MPhil) or the Master of Science in Biomedical Sciences (MSBS) degree programs.

Transfer to MPhil

Students leaving the PhD program may be eligible to earn an MPhil. To be eligible for this exit pathway, students should have fulfilled the following criteria.

• be in good academic standing with a cumulative GPA of 3.0 or higher

• have successfully submitted and defended the PhD Thesis Proposal, and:

• completed the “Request for Transfer from PhD to Master of Philosophy” and have received all the required approvals.

If a student has met all of these requirement, he/she/they will be awarded an MPhil degree.

Transfer to MSBS

Students leaving the PhD program may be eligible to earn an MSBS. To be eligible for this exit pathway, students should have fulfilled the following criteria:

• be in good academic standing with a cumulative GPA of 3.0 or higher

• complete the coursework and credits necessary to fulfill all requirements of the MSBS degree

• demonstrate mastery of the literature in their field commensurate with a Master's-level student

• produce a substantial research portfolio consisting of independently conducted experiments, yielding results, analysis, and conclusions equivalent to a Master's-level thesis

If these criteria are fulfilled prior to the PhD thesis proposal, the student is not required to take and pass the thesis proposal exam

In order to initiate the PhD to MSBS transfer pathway, the student’s PhD Advisory Committee must consent to this plan. Consent from the dissertation advisor is not a requirement but should be obtained when strained relations between the research mentor and student is not a reason for the transfer.

The student must complete Page 1 of the form “Request for Transfer from PhD to Master of Science in Biomedical Sciences” (Page 2 will be completed after the MSBS Thesis is deposited as part of the program checkout process). It is important to note that the student’s transcript will reflect a withdrawal from the PhD Program and matriculation to the MSBS Program.

The research mentor and student, in conjunction with PhD Advisory Committee, will agree on a length of time, not to exceed 60 days, that the student will remain in the lab to finish up experiments and write the MSBS Thesis. During this time the student will continue to receive a stipend. The research mentor must commit to covering the student’s stipend, presumably via the same mechanism that had been supporting him/her prior to the transfer, for the duration of this period.

The student will write and defend an MSBS thesis within the time frame defined in the previous paragraph. The exam committee will consist of the existing PhD advisory committee plus one of the student’s MTA Co-directors (if he/she/they is not already a member of the committee), with the specific Co-Director to be chosen by the student. The student must deposit the thesis within one week of completing the thesis defense

The effective date of withdrawal from the PhD Program and Matriculation to the MSBS program will be the date of the defense, as defined in the above paragraphs. This will allow the student to: 1) receive a stipend; 2) remain in student housing; and 3) receive health insurance.

Once the MSBS Thesis is deposited, the student should complete Page 2 of the form “Request for Transfer from PhD to Master of Science in Biomedical Sciences”. Deposition of the thesis also initiates the process of terminating the student’s stipend, health insurance coverage and housing. These terminations will proceed as per Graduate School and Real Estate Office policies, which are detailed in other sections of this handbook.

See Standards for Maintaining Satisfactory Progress

Once a student has successfully defended the dissertation, makes all relevant revisions, and is ready to deposit the Dissertation, s/he should deposit the dissertation electronically according to the instructions in the Doctoral Thesis Deposit Instructions document, available on the Graduate School Forms webpage. Students should submit the Student Checkout form before depositing the dissertation. This form can also be found on the Graduate School forms webpage. Failure to do this can result in a delay of the student’s graduation.

MD/PhD students should note the additional requirements/instructions for depositing a dissertation, which are detailed in Chapter 2.

The dissertation may be deposited at any time during the year, but the following deposit deadlines and enrollment requirements determine the date of the degree.

The degree is awarded on September 30, January 31, or the date of ISMMS’s annual Commencement in May. Students depositing by the January or April deadline will receive their diploma at Commencement. Those students who have a dissertation or thesis defense scheduled between April 16th and June 30th MAY be eligible to participate in the spring Commencement ceremony even though they have not met the April 15th thesis/dissertation deposit deadline. In cases where a student is allowed to participate, he/she/they will not receive a diploma at graduation. Instead, a diploma will be awarded on the conferral date (September 30th, of January 31) following the successful defense. Only students in good academic standing will be offered this courtesy. In this case, good academic standing means that all coursework has been completed with passing grades and the student’s mentor/committee fully expect the student will successfully defend his/her/their thesis/dissertation prior to June 30th. If either of these criteria is not met, the student will not be allowed to participate in the spring graduation ceremony.

Additionally, any student whose written document or oral defense was not acceptable to their committee will not be allowed to participate in Commencement until after successfully defending and depositing.

By March 1, students must notify the Registrar of their intent to deposit their thesis on or before the April or September deposit deadlines in order to be included in the Commencement exercises of that year. Commencement information will be sent during the spring semester to the student’s ISMMS email address recorded with the Graduate School Office.

If a student fails to deposit their thesis by the end of their seventh year in the PhD program (6th PhD year for MD/PhD students), their dissertation advisor must petition the Dean of the Graduate School in writing for permission to extend their student status. The petition must include a timetable for completing the dissertation and must also be signed by the student.

It is the dissertation advisor’s responsibility to inform the Graduate School Office, in a timely manner, the expected date that financial support will be terminated.

PhD students can maintain student status, with the stipend and health benefits covered by the dissertation advisor, after the defense, according to the following timetable:

Exceptions to this schedule will only be considered under extenuating circumstances. The dissertation advisor must request this in writing to the Dean of the Graduate School. The request must include a timetable for revisions and must confirm advisor’s financial responsibility for stipend and health coverage.

Student Housing: the Real Estate Office provides 4-5 weeks after the dissertation defense to vacate. Extensions may be granted by the Real Estate Office pending availability.

See Standards for Maintaining Satisfactory Progress

ISMMS is proud of its alumni. Most of the students who complete the PhD program pursue a postdoctoral research-training period before entering a more permanent position and most of the MD/PhD graduates complete a residency and/or fellowship. The faculty of the program actively assists and guides the students in identifying an optimal position. After the immediate postdoctoral work, our graduates have gone on to a gratifying array of research positions in academic, medical, and industrial settings. The Graduate School alumni are invited to join the Associated Alumni of the Mount Sinai Medical Center, and they receive a quarterly bulletin that includes alumni and institutional news.

The ISMMS Alumni encompasses graduates of the Medical School and the Graduate School of Biomedical Sciences, former interns, residents and fellows, as well as past and active members of the basic science and clinical faculty. The association is dedicated to promoting enduring relationships among members, furthering ISMMS’s educational and charitable endeavors, and promoting scholarship for students and physicians-in-training, and honoring alumni with awards on an annual basis. Senior students will be asked to enroll in the association upon graduation, and will receive all benefits of membership, but will not be expected to become dues-paying members of the Alumni Association until postgraduate training is completed. The Student Council selects a member to serve as student liaison to the Alumni Executive Board; however, student input and participation in alumni-sponsored programs and activities is always encouraged. The Alumni Office is located in the plaza of the Annenberg Building. Students are welcome to visit the office at any time to speak with staff.

Teaching Policy

There is no program-wide teaching requirement, but many students seek to take advantage of the opportunities to teach in a variety of modes and settings either because it enforces the mastery of core material, is intrinsically rewarding or because it is a major part of their career plans. Teaching opportunities include: teaching assistantships for the Core courses; teaching assistantships for additional Medical and Graduate School courses; one-on-one tutoring opportunities for graduate or medical courses; tutoring and special teaching programs at the Life Sciences Secondary School with which ISMMS has a special relationship; student mentorships in the RCR course; and student mentorships in the Introduction to Journal Club course.

Vacation Policy

The vacation policy for PhD students in Biomedical Sciences or Neuroscience is clearly stated in the Leave Policies section of Chapter 3. Please refer to that section for the complete policy. In brief, PhD students in Biomedical Sciences or Neuroscience receive two weeks of paid vacation each year. Time spent studying for courses, preparing for examinations, etc. is not considered vacation time.