PhD Thesis Guide

Years 1 - 2

• Students participating in lab rotations during year 1, may use the optional MEMP Rotation Registration Form, to formalize the arrangement and can earn academic credit by enrolling in HST.599. 
• Students should register for HST.ThG during any term in which they are conducting research towards their thesis. First- and second-year students registered for HST.ThG in a regular term (fall or spring) must meet with their supervisor and complete the Semi-Annual PhD Student Progress Review Form to receive credit.
• A first letter of intent (LOI-1) proposing a general area of thesis research and research supervisor is required by April 30th of the second year of registration.

Year 3

• Beginning in year 3, student and research supervisor must complete the Semi-Annual PhD Student Progress Review for each regular term (fall and spring).
• A second letter of intent (LOI-2) proposing a tentative thesis committee is required by April 30th of the third year of registration. The letter should indicate the research supervisor and general thesis area since these may have changed since the first LOI.

Year 4 

• Beginning in year 4, the student must meet with their tentative thesis committee at least once per semester until the formal thesis committee is formed.
• Students must finalize their thesis committee, formally defend their proposal before the committee, and submit their proposal to the HST Graduate Committee by April 30 of the forth year of registration.

Year 5

• Following submission of the thesis proposal, meetings with the thesis committee must be held at least once per semester. 

HST has developed these policies to help keep students on track as they progress through their PhD program. Experience shows that students make more rapid progress towards graduation when they interact regularly with a faculty committee and complete their thesis proposal by the deadline.

Check out these resources for finding a research lab.

Students perform doctoral thesis work under the guidance of a thesis committee consisting of at least three faculty members from Harvard and MIT (including a chair and a research supervisor) who will help guide the research. Students are encouraged to form their thesis committee early in the course of the research and in any case by the end of the third year of registration. The HST IMES Committee on Academic Programs (HICAP) approves the composition of the thesis committee via the letter of intent and the thesis proposal (described below). 

Research Supervisor

The research supervisor is responsible for overseeing the student's thesis project. The research supervisor is expected to:

• supervise the research and mentor the student;
• provide a supportive research environment, facilities, and financial support;
• discuss expectations, progress, and milestones with the student and complete the Semi-Annual PhD Student Progress Review Form each semester;
• assist the student to prepare for the oral qualifying exam;
• guide the student in selecting the other members of the thesis committee;
• help the student prepare for, and attend, meetings of the full thesis committee, to be held at least once per semester;
• help the student prepare for, and attend, the thesis defense;
• evaluate the final thesis document.

The research supervisor is chosen by the student and must be a faculty member of MIT* or Harvard University and needs no further approval.  HICAP may approve other individuals as research supervisors on a student-by-student basis. Students are advised to request approval of non-faculty research supervisors as soon as possible.  In order to avoid conflicts of interest, the research supervisor may not also be the student's academic advisor. In the event that an academic advisor becomes the research supervisor, a new academic advisor will be assigned.

The student and their research supervisor must complete the Semi-Annual PhD Student Progress Review during each regular term in order to receive academic credit for research. Download Semi Annual Review Form

*MIT Senior Research Staff are considered equivalent to faculty members for the purposes of supervising research. No additional approval is required.

Thesis Committee Chair

Each HST PhD thesis committee is headed administratively by a chair, chosen by the student in consultation with the research supervisor. The thesis committee chair is expected to:

• provide advice and guidance concerning the thesis research; 
• oversee meetings of the full thesis committee, to be held at least once per semester;
• preside at the thesis defense; 
• review and evaluate the final thesis document.

The thesis committee chair must be well acquainted with the academic policies and procedures of the institution granting the student's degree and be familiar with the student's area of research. The research supervisor may not simultaneously serve as thesis committee chair.

For HST PhD students earning degrees through MIT, the thesis committee chair must be an MIT faculty member. A select group of HST program faculty without primary appointments at MIT have been pre-approved by HICAP to chair PhD theses awarded by HST at MIT in cases where the MIT supervisor is an MIT faculty member.**

HST PhD students earning their degree through Harvard follow thesis committee requirements set by the unit granting their degree - either the Biophysics Program or the School of Engineering and Applied Sciences (SEAS).

** List of non-MIT HST faculty approved to chair MIT thesis proposals when the research supervisor is an MIT faculty member.

Readers

In addition to the research supervisor and the thesis committee chair, the thesis committee must include one or more readers. Readers are expected to:

• provide advice and guidance concerning the thesis research; 
• attend meetings of the full thesis committee, to be held at least once per semester;
• attend the thesis defense; 
• review and evaluate the final thesis document.

Faculty members with relevant expertise from outside of Harvard/MIT may serve as readers, but they may only be counted toward the required three if approved by HICAP.

The members of the thesis committee should have complementary expertise that collectively covers the areas needed to advise a student's thesis research. The committee should also be diverse, so that members are able to offer different perspectives on the student's research. When forming a thesis committee, it is helpful to consider the following questions: 

1. Do the individuals on the committee collectively have the appropriate expertise for the project?
2. Does the committee include at least one individual who can offer different perspectives on the student's research?  The committee should include at least one person who is not closely affiliated with the student's primary lab. Frequent collaborators are acceptable in this capacity if their work exhibits intellectual independence from the research supervisor.
3. If the research has a near-term clinical application, does the committee include someone who can add a translational or clinical perspective?  
4. Does the committee conform to HST policies in terms of number, academic appointments, and affiliations of the committee members, research supervisor, and thesis committee chair as described elsewhere on this page?

[Friendly advice: Although there is no maximum committee size, three or four is considered optimal. Committees of five members are possible, but more than five is unwieldy.]

Thesis Committee Meetings

Students must meet with their thesis committee at least once each semester beginning in the fourth year of registration. It is the student's responsibility to schedule these meetings; students who encounter difficulties in arranging regular committee meetings can contact Julie Greenberg at jgreenbe [at] mit.edu.

The format of the thesis committee meeting is at the discretion of the thesis committee chair. In some cases, the following sequence may be helpful:

• The thesis committee chair, research supervisor, and readers meet briefly without the student in the room;
• The thesis committee chair and readers meet briefly with the student, without the advisor in the room;
• The student presents their research progress, answers questions, and seeks guidance from the members of the thesis committee;

Please note that thesis committee meetings provide an important opportunity for students to present their research and respond to questions. Therefore, it is in the student's best interest for the research supervisor to refrain from defending the research in this setting.

Students must submit two letters of intent (LOI-1 and LOI-2) with applicable signatures. Download LOI Form.

LOI-1 identifies a research supervisor and a general area of thesis research, described in 100 words or less. It should include the area of expertise of the supervisor and indicate whether IRB approval (Institutional Review Board; for research involving human subjects) and/or IACUC approval (Institutional Animal Care and Use Committee; for research involving vertebrate animals) will be required and, if so, from which institutions. LOI-1 is due by April 30 of the second year of registration.

LOI-2 addresses the same topics as LOI-1 and also specifies at least two people who, in addition to the research supervisor, will tentatively serve on the thesis committee. At least one member of the tentative thesis committee must be eligible to serve as thesis committee chair, as described above. LOI-2 should also specify the research supervisor and general area of thesis research since these may have changed since LOI-1. LOI-2 is due by April 30th of the third year of registration.

The LOIs are understood to provide only a tentative thesis plan, and it is recognized that the research direction may change in the process of developing a formal thesis proposal. Students are strongly encouraged to identify tentative thesis committee members and begin meeting with them as early as possible. Following submission of LOI-2, students are required to hold at least one meeting per semester with their tentative thesis committee. The role of the tentative committee is to offer advice in formulating the research. In many cases, the tentative committee members may ultimately serve on the final thesis committee, although that is not required. The research topic and thesis committee are only considered final after the thesis proposal (see below) has been approved.

LOIs should be submitted to HICAP, c/o Traci Anderson in E25-518.

For MEMP students receiving their degrees through MIT, successful completion of the Oral Qualifying Exam is a prerequisite for the thesis proposal presentation. For MEMP students receiving their degrees through Harvard, the oral qualifying exam satisfies the proposal presentation requirement.

Proposal Document

Each student must present a thesis proposal to their thesis committee and submit an approved proposal to HICAP by April 30th of the fourth year of registration. The only exception is for students who substantially change their research focus after submitting their original letter of intent; in those cases the thesis proposal must be submitted within three semesters of joining a new lab. Students registering for thesis research (HST.THG) who have not met this deadline may be administratively assigned a grade of "U" (unsatisfactory) and receive a Dean's Warning.

The written proposal should be no longer than 4500 words, excluding references. This is intended to help students develop their proposal-writing skills by gaining experience composing a practical proposal; the length is comparable to that required for proposals to the NIH R03 Small Research Grant Program. The proposal should clearly define the research problem, describe the proposed research plan, and defend the significance of the work. Preliminary results are not required. If the proposal consists of multiple aims, with the accomplishment of later aims based on the success of earlier ones, then the proposal should describe a contingency plan in case the early results are not as expected.

Proposal Presentation

The student must formally defend the thesis proposal before the full thesis committee.

Students should schedule the meeting and reserve a conference room and any audio visual equipment they may require for their presentation. To book a conference room and/or an LCD projector, please contact Joseph Stein (jrstein [at] mit.edu).

Following the proposal presentation, students should make any requested modifications to the proposal for the committee members to review. Once the committee approves the proposal, the student should obtain the signatures of the committee members on the forms described below as part of the proposal submission package.

[Friendly advice: As a professional courtesy, be sure your committee members have a complete version of your thesis proposal at least one week in advance of the proposal presentation.]

Submission of Proposal Package

When the thesis committee has approved the proposal, the student submits the proposal package to HICAP, c/o Traci Anderson in E25-518, for final approval. HICAP has responsibility for final approval of both the composition of the thesis committee and the proposal.

The proposal package includes the following: 

• the proposal document
• a properly formatted title page, including an abstract, the student's signature, IRB and/or IACUC approval numbers, institutions and dates if applicable. The abstract has a maximum length of 500 words and serves as a concise description of the proposed work that can be read independently of the full proposal. HICAP will use the abstract when reviewing the proposal for final approval. The abstract should be comprehensible to a general scientific audience, yet contain sufficient information for evaluation of the project. It should not include references. The components of the abstract are:
  • a brief description of the project background and significance that explains why the work is important;
  • the specific aims of the proposal, including a contingency plan if needed**; and
  • an indication of the methods to be used to accomplish the specific aims.
• signed supervisor agreement form;
• signed chair agreement form;
• signed reader agreement form(s);
• a cover letter signed by the thesis committee chair documenting the time and place of the thesis proposal presentation, the names and areas of expertise of the thesis committee members, and the committee's assessment of the proposal.

**If the proposal consists of multiple aims, with the accomplishment of later aims based on the success of earlier ones, then the abstract should briefly describe an alternate plan in case the early results are not as expected. For example, if Aim 1 involves developing a particular technology, and Aims 2 and 3 depend on utilizing that technology, the abstract should indicate what would happen in the event that the goals of Aim 1 are not met.

[Friendly advice: Be sure to take responsibility for obtaining the necessary signatures and submitting the proposal to Traci. The proposal serves as a contract between you and your committee, but only after it is approved by HICAP.]

Thesis Proposal Forms

• SAMPLE Cover Letter (doc)
• SAMPLE Title Page (doc)
• Supervisor Agreement Form (pdf)
• Chair Agreement Form (pdf)
• Reader Agreement Form (pdf)

Samples of Successful Proposal Abstracts

• SAMPLE 1 (pdf)
• SAMPLE 2 (pdf)
• SAMPLE 3 (pdf)

When the thesis is substantially complete and fully acceptable to the thesis committee, a public thesis defense is scheduled for the student to present his/her work to the thesis committee and other members of the community. The thesis defense is the last formal examination required for receipt of a doctoral degree. To be considered "public", a defense must be announced to the community at least five working days in advance. At the defense, the thesis committee determines if the research presented is sufficient for granting a doctoral degree. Following a satisfactory thesis defense, the student submits the final thesis document, approved by the research supervisor, to Traci Anderson via email (see instructions below).

[Friendly advice: Contact jrstein [at] mit.edu (Joseph Stein) at least two weeks before your scheduled date to arrange for advertising via email and posters. A defense can be canceled for insufficient public notice.]

[12.16.2021 UPDATE -  Thesis defenses through September 2022 may be conducted virtually, in-person or hybrid.  The policy will be reviewed again in fall 2022.]

Before the Thesis Defense 

Committee Approves Student to Defend: The thesis committee, working with the student and reviewing thesis drafts, concludes that the doctoral work is complete. The student should discuss the structure of the defense (general guidelines below) with the thesis committee chair and the research supervisor. 

Schedule the Defense: The student schedules a defense at a time when all members of the thesis committee will be physical present. Any exceptions must be approved in advance by the IMES/HST Academic Office.

Reserve Room: It is the student's responsibility to reserve a room and any necessary equipment. Please contact imes-reservation [at] mit.edu (subject: E25%20Room%20Reservation) (IMES Reservation) to reserve rooms E25-140, E25-141, E25-119/121, E25-521. 

Guidelines for a Zoom Defense: Download PDF

Final Draft: A complete draft of the thesis document is due to the thesis committee two weeks prior to the thesis defense to allow time for review.  The thesis should be written as a single cohesive document; it may include content from published papers (see libraries website on "Use of Previously Published Material in a Thesis") but it may not be a simple compilation of previously published materials.

Publicize the Defense: The IMES/HST Academic Office invites the community to attend the defense via email, flyers, and a notice on the HST website. This requires that the student email a thesis abstract and supplemental information to jrstein [at] mit.edu (Joseph Stein) two weeks prior to the thesis defense. The following information should be included: Date and time, Location (Zoom invitation), Thesis Title, Names of committee members, with academic and professional titles and institutional affiliations. The abstract is limited to 250 words for the poster, but students may optionally submit a second, longer abstract for the email announcement.

Thesis Defense Guidelines

Public Defense: The student should prepare a presentation of 45-60 minutes in length, to be followed by a public question and answer period of 15–30 minutes at discretion of the chair.

Committee Discussion: Immediately following the public thesis presentation, the student meets privately with the thesis committee and any other faculty members present to explore additional questions at the discretion of the faculty. Then the thesis committee meets in executive session and determines whether the thesis defense was satisfactory. The committee may suggest additions or editorial changes to the thesis document at this point.

Chair Confirms Pass: After the defense, the thesis committee chair should inform Traci Anderson of the outcome via email to tanderso [at] mit.edu.

Submitting the Final Thesis Document

The student submits the signed thesis document to Traci Anderson in E25-518. Please refer to the thesis formatting guidelines.

Title page notes.
The Program line should read, "Submitted to the Harvard-MIT Program in Health Sciences and Technology, in partial fulfillment of the the requirements for the degree of ... "

Both the student and research supervisor should sign the title page. Thesis committee members are not required to sign. On the "Accepted by" line, please list: Emery N. Brown, MD, PhD/Director, Harvard-MIT Program in Health Sciences and Technology/Professor of Computational Neuroscience and Health Sciences and Technology. The Academic Office will obtain Professor Brown's signature.

Download sample thesis title page

Thesis Submission Components. 
As of 4/2021, the MIT libraries have changed their thesis submissions guidelines and are no longer accepting hard copy theses submissions. For most recent guidance from the libraries: https://libguides.mit.edu/mit-thesis-faq/instructions 

Submit to the Academic Office, via email (tanderso [at] mit.edu)

• pdf of the final thesis should include an UNSIGNED title page

• A separate file with a SIGNED title page by the student and supervisor, the Academic Office will get Dr. Emery Brown's signature.

• Submit a UMI ProQuest form 

For the MIT Library thesis processing, fill out the "Thesis Information" here: https://thesis-submit.mit.edu/

File Naming Information: https://libguides.mit.edu/

Survey of Earned Doctorates. The University Provost’s Office will contact all doctoral candidates via email with instructions for completing this survey.

General

• MEMP Rotation Form (optional)
• Semi-Annual Progress Review Form
• Letter of Intent (1 & 2)

Thesis Proposal Forms

• SAMPLE Cover Letter (doc)
• SAMPLE Title Page (doc)
• Supervisor Agreement Form (pdf)
• Chair Agreement Form (pdf)
• Reader Agreement Form (pdf)

Samples of Successful Proposal Abstracts

• SAMPLE 1 (pdf)
• SAMPLE 2 (pdf)
• SAMPLE 3 (pdf)

Final Thesis

• Sample thesis title page
• UMI Form