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Fields of Study

  • Cancer Biology: leukemogenesis, metastasis, growth control, genome integrity, immune checkpoint therapy
  • Cell Biology: cytoskeleton, nuclear structure and dynamics
  • Cell Signaling: kinases, phosphatases, growth signaling
  • Epithelial cell biology: epithelial patterning, skin development and disease
  • Immunology: autoimmune disease, immunotherapy, systems biology
  • Genetics: disease etiology, birth defects
  • Lung function: cystic fibrosis, lung disease, idiopathic lung fibrosis
  • Maternal-Fetal Medicine
  • Metabolism: signaling and systems biology, diabetes
  • Neuroscience: pathogenesis of brain disease, neurogenomics
  • Organ homeostasis and injury: pancreatitis, kidney injury, macular degeneration, scleroderma
  • Physiology


PHAR 504a / PTB 504a, Molecular Mechanisms of Drug Actions

Elias Lolis
This course covers the molecular mechanisms of therapeutics, which are presented in a conceptual framework to increase understanding but decrease memorization. Topics include (but are not limited to) receptor affinity, efficacy, multiple equilibria, pharmacokinetics, and toxicity; enzyme kinetics and inhibition, drug discovery and design; molecular basis of antimicrobial therapy, cardiology drugs, anticancer and antiviral therapies; and therapeutics for inflammatory disorders, asthma, and allergy.

PHAR 550a / C&MP 550a / ENAS 550a / MCDB 550a / PTB 550a, Physiological Systems

Stuart Campbell
The course develops a foundation in human physiology by examining the homeostasis of vital parameters within the body, and the biophysical properties of cells, tissues, and organs. Basic concepts in cell and membrane physiology are synthesized through exploring the function of skeletal, smooth, and cardiac muscle. The physical basis of blood flow, mechanisms of vascular exchange, cardiac performance, and regulation of overall circulatory function are discussed. Respiratory physiology explores the mechanics of ventilation, gas diffusion, and acid-base balance. Renal physiology examines the formation and composition of urine and the regulation of electrolyte, fluid, and acid-base balance. Organs of the digestive system are discussed from the perspective of substrate metabolism and energy balance. Hormonal regulation is applied to metabolic control and to calcium, water, and electrolyte balance. The biology of nerve cells is addressed with emphasis on synaptic transmission and simple neuronal circuits within the central nervous system. The special senses are considered in the framework of sensory transduction. Weekly discussion sections provide a forum for in-depth exploration of topics. Graduate students evaluate research findings through literature review and weekly meetings with the instructor.

CBIO 604b / PTB 604b, Physiologic Function and Cellular Structure of Organ Systems

Agnes Vignery and Richard Kibbey
This course is an introduction to the organization and function of cells within complex multicellular systems as encountered in the human body. You will cover major tissues and organs as well as the cardiovascular, immune, and nervous systems, with special emphasis on the molecular and cellular bases of developmental processes and human diseases. Each week the lectures are supplemented with an active learning session including clinical correlations and student presentations.

PATH 690a / PTB690a, Molecular Mechanisms of Disease

Demetrios Braddock and Carlos Fernandez-Hernando
This course covers aspects of the fundamental molecular and cellular mechanisms underlying various human diseases. Many of the disorders discussed represent major forms of infectious, degenerative, vascular, neoplastic, and inflammatory disease. Additionally, certain rarer diseases that illustrate good models for investigation and/or application of basic biologic principles are covered in the course. The objective is to highlight advances in experimental and molecular medicine as they relate to understanding the pathogenesis of disease and the formulation of therapies.

Joining a Lab for the Dissertation Research

The single most important decision made by a graduate student is the selection of a dissertation advisor and laboratory. Students are encouraged to use the rotations to learn about potential advisors holistically, taking into account variables such as scientific focus, mentorship style, laboratory resources, and the past training record of the potential advisor. Other useful sources of information are prior trainees of the advisor, the Director of Graduate Studies and other faculty. The DGS must approve the selection of a laboratory, which requires commitment on the part of the advisor and their primary department. The selection of a lab marks the assignment of a student from a track to the PTB.

Qualifying Examination


The qualifying exam will consist of 1) a written research proposal based on the prospective thesis project and 2) an oral exam in which the student defends the research proposal before a qualifying exam committee.


PTB students are expected to prepare for and complete the qualifying exam in the fall semester of the second year. Students needing extra time to prepare for the exam (for example, a student who carried out additional lab rotations or transferred between labs) may be allowed to have an extension of the deadline or to take the exam in the following spring term, but only with approval from the thesis advisor and the DGS. All students are required to complete the qualifying exam within one year of joining the program.

Qualifying exam committee

The student will assemble a qualifying exam committee of three faculty members (excluding the thesis advisor) in consultation with their advisor and the DGS, who must approve the committee. The chair of the committee must have an appointment as a PTB trainer.

Preparation for the qualifying exam

The student should develop a one-page outline draft of their proposal in the form of an NIH “Specific Aims” page that will be shared with their committee members in the early fall of their second year, typically two months prior to the exam. In consultation with the exam committee and thesis advisor, the student will define several (at least three) research areas broadly relevant to the thesis project that the student will be expected to be knowledgeable about from reading the literature. The student is encouraged to meet with qualifying exam committee members for advice and guidance in reading the literature.

Preparation and submission of the written research proposal

The written proposal should include a single Specific Aims page (Arial 11 pt font, 0.5 inch margins, single spaced) and be in the format of an NIH F31 grant: 6 pages, Arial 11 pt font, 0.5 inch margins, single spaced including figures. The proposal should include a Significance (Introduction) section, Research Strategy section, and References; References do not count towards the page limit. The written proposal should be provided to the committee at least a week prior to the oral exam date. Should the proposal be submitted in less than a week’s time, there may be a need to reschedule the defense at the discretion of the qualifying exam committee.

Oral exam

The student will prepare an oral presentation that covers the background and topic of their proposal (~maximum of 20 slides). The committee will ask questions both conceptual and technical in nature on topics related to the content of the proposal. At the conclusion of the exam the committee will consider the written proposal and oral defense and unanimously agree on a Pass, Fail, Conditional Pass outcome. In the case of a conditional pass, specific guidance and a timeline will be provided to the student including possible rewriting of the proposal and/or second oral defense. In all cases, students must successfully complete the qualifying exam by the end of their sixth term.

Prospectus & Thesis Committee

Upon completing the qualifying exam and moving towards engaging in full-time research, a thesis/prospectus committee will be formed which will consist of the student’s thesis advisor and a minimum of three additional faculty members; in most cases this is expected to include the members of the qualifying exam committee. This committee will be selected by the student, but each committee must have a Chair who is a PTB-affiliated trainer and must be approved by the PTB DGS.


The committee must be convened and hold its first meeting (the prospectus meeting) within a year after the qualifying exam, typically prior to the end of the fifth term. Once the student’s Prospectus is approved and they are admitted to candidacy, which must occur by the end of the sixth term, the thesis committee will meet every six months until the time of degree.

Format and Prospectus Approval

One week prior to the prospectus (first thesis committee) meeting, the student will provide the committee with 1) a Specific Aims page that the student has updated from the materials included as part of the qualifying exam; and 2) an “Introduction to revision” page that describes the changes made to the Specific Aims over the first year as the student has engaged in the research project. These documents and the oral presentation by the student will be the basis on which the committee will recommend approval of the prospectus to the PTB DGS, who will oversee the submission of the Prospectus materials and their approval to the GSAS registrar.

Individual Professional Development Plan (IDP)

Prior to the prospectus meeting (and all subsequent thesis committee meetings) the student is expected to complete an IDP and discuss it with their mentor. For example, use the resource: or another similar mechanism. This is a valuable time to step back and assess your accomplishments and future goals and to ensure that your PhD training is preparing you for future success.

External examiner visit

Prior to or immediately after admission to candidacy, students are asked to work with their advisor to identify a faculty member from outside Yale who will ultimately serve on their dissertation committee. This individual will be invited as part of the Translational Science Seminar Series in the student’s third or fourth year of study to visit Yale, during which the student will have a dedicated hour to present and discuss their thesis research. After the student has prepared the thesis, the external examiner will read the thesis and make suggestions for edits. The external examiner is then invited back to campus (or may participate virtually) in the thesis defense of the student.

Responsible Conduct of Research

At the start of their first year of study, all master’s and Ph.D. students are required to attend sessions on professional ethics, including academic integrity, prevention of sexual misconduct, and discrimination and harassment reporting. Students must also complete an approved online training module in professional ethics before they can register for the spring term of their first year.


When the student is prepared to ask for permission to write their dissertation, they will convene a meeting of the thesis committee. The student should provide the committee with a written outline of the thesis prior to the meeting. If the progress of the student is deemed sufficient and the thesis outline is approved, the student will be given permission to proceed with writing the thesis and scheduling their defense. Approval of the committee at this stage will be contingent on the student either having a first-author publication (including in press) or having generated a prepared first-author manuscript for submission for publication that is provided to the committee; in most cases this is expected to be available online as a preprint. A complete draft of the dissertation must be distributed to the committee members (including the external examiner) no later than two weeks before the defense is to take place. The thesis defense consists of two parts: 1) An open seminar to which all members of the academic community will be invited; and 2) An oral defense of the thesis, which will include only the student and the thesis committee. When the defense has been completed, the committee will discuss acceptance of the thesis (with or without revisions). Once all changes have been made to the satisfaction of the committee, the student can submit the dissertation and all required paperwork to the GSAS. The dissertation should normally be submitted no later than March of year six.

Teaching Requirements

All PTB students are required to teach the equivalent of two courses at the TF-10 level (10 hours per week) or one course at the TF-20 level (20 hours per week). These can be chosen from numerous lecture, laboratory and seminar courses offered at the undergraduate, graduate or medical school levels. Students generally teach in the 3rd year but may also begin teaching during the spring of their 2nd year with permission of the thesis advisor and PTB DGS. MD/PhD students are only required to TA one course at the TF-10 level.

Prior to the first semester of teaching, each PTB student must attend the Teaching @ Yale Day Orientation. Students are also encouraged to take one or more of the short teaching courses and workshops offered by the Poorvu Center for Teaching and Learning.

Leave of Absence

Students who wish or need to interrupt their study temporarily may request a leave of absence. There are three types of leave—personal, medical, and parental.

General policies, as well as specific requirements for any type of leave may be found on the GSAS website.

Required Coursework Timeline

Term 1 – Year 1, Fall Semester

At least one but typically two of the following:

  • Physiological Systems
  • Molecular Mechanisms of Disease
  • Principles of Pharmacology

Seminar: Topics in Translational Molecular Medicine, Pharmacology and Physiology – fall

Laboratory Rotations, Responsible Conduct in Research (“Ethics in Science”)

Term 2 – Year 1, Spring Semester

Physiologic function and cellular structure of organ systems (new PTB course, will replace the former Systems Cell Biology)

Seminar: Topics in Translational Molecular Medicine, Pharmacology and Physiology – spring

Introduction to Biostatistics in Clinical Investigation (or other statistics-based course such as ENAS549).

Laboratory rotation(s)

Term 3 – Year 2, Fall Semester

Mentored Clinical Experience

Grant Writing Course

Additional electives (if needed or desired)

Term 4 – Year 2, Spring Semester

Mentored Clinical Experience

Additional electives (if needed or desired)

Note: Students who participate in the Medical Research Scholars Program, which currently serves students in all tracks and PhD programs of the BBS, would participate in an additional year of the Mentored Clinical Experience in Year 3.