Pathobiology, PhD

Program Overview

Pathology is an integrative discipline that examines, in an integrative and quantitative manner, the whole organism and its component tissues, cells, and molecules to identify the causes and mechanisms of disease and how diseases can be treated and managed for patient care. Thus, pathology is a clinical, experimental, and translational endeavor. Contemporary pathology uses a vast array of state-of-the-art techniques and methods including, but not limited to, histology, high-resolution microscopy, genomics, transcriptomics, proteomics, genome editing (CRISPR-Cas9/TALENS), induced pluripotent stem cells (iPSCs), and cell and transgenic animals of human disease. The Pathobiology Graduate Program is committed to rigorously training students in basic science concepts underlying human disease, translational therapeutics, and related technologies and methods for therapeutic target discovery to prepare students for academic, research, teaching, and biotechnology careers.

Program of Study

The Graduate Program in Pathobiology of the Department of Pathology offers a program of study leading to the PhD degree in Pathobiology.

The Program provides students with opportunities to elucidate the mechanisms and origins of human diseases through an integrative approach emphasizing systemic processes based on molecular and cellular pathologic underpinnings. Students have formalized classroom instruction in all general areas of human disease mechanisms and undertake specialized doctoral training (including thesis research) in a programmatic area of their choosing, including Immunopathology, Microbiology & Infectious Disease, Neoplasia, Neuropathology, Developmental Pathology, Transplantation Biology, Nanobiology, Vascular Biology & Hemostasis.

Applicants are not required to be committed to a specific programmatic field of interest at the time of application or matriculation. Laboratory rotations across multiple disciplines are typical for students in the Program and are designed to assist in the discovery of the topic of interest for their doctoral work. Translational rotations in more clinical laboratories are designed to allow students to fully experience applications of basic science to human disease and patient healthcare. Thus, students in the Pathobiology program are prepared for careers in the translation of basic biological principles to solve specific disease problems.

Facilities

Classroom instruction is conducted in the lecture, seminar, and conference rooms of the School of Medicine. Student research is conducted in the state-of-the-art research facilities of program faculty. These fully equipped laboratories support studies ranging from molecular, cellular, and physicochemical analyses through whole animal and informatics-based techniques. The Program takes special advantage of its clinical service laboratories and clinical activities to familiarize students with and provide resources for translational research.

Financial Aid

Candidates accepted into the Program are offered full support providing payment of tuition, health, dental and vision benefits as well as a stipend for the duration of their studies. For more details regarding financial aid opportunities, please visit the Financial Aid page: Financial Aid | Johns Hopkins Medicine.

Admission Requirements

Students typically matriculate in late August. Starting the first laboratory rotation earlier is an option. Requirements for application and admission consideration into the Program:

1. a bachelor’s degree from an accredited college or university;
2. a curriculum vitae (CV) with current position and most recent institutional training;
3. relevant coursework, including laboratory in inorganic & organic chemistry, biochemistry, general biology, with anatomy and physiology, and basic cellular and molecular biology recommended;
4. unofficial transcripts of undergraduate grades (official transcripts required for admission);
5. a minimum of three letters of recommendation (preferably on institutional letterhead); and
6. a personal statement, including your research experience and career goals as well as describing a personal formative experience -- combined into a maximally two-page document.

GRE Scores Not Required. As of September, 2019, when applying to the Graduate Program in Pathobiology, we no longer require the GRE General or Subject Tests scores, however if taken, applicants are permitted to share their scores.

More details about applying and admissions can be found here: Admissions.

Vivien Thomas PhD Trainee Scholars

The Vivien Thomas Scholars Initiative (VTSI) is an endowed fellowship program at Johns Hopkins for PhD students in STEM fields. It provides full tuition, stipend, and benefits while also providing targeted mentoring, networking, community, and professional development opportunities. Students who have attended eligible institutions, including historically Black colleges and universities (HBCUs), community colleges, and regional institutions in Maryland, Virginia, and the District of Columbia for undergraduate study, are eligible to apply. More information about the VTSI program, including application deadlines is available at this link: https://provost.jhu.edu/about/vivien-thomas-scholars-initiative/.

Pathobiology Program Inquiries should be directed to the program contact listed on the program webpage.

Program Requirements

Required Core Courses:

Course List

Code	Title	Credits
ME.300.800	Pathology Research (ongoing throughout PhD study) 1	1-18
ME.300.803	Pathobiology Journal Club (ongoing throughout PhD study)	3
ME.800.811	Introduction to Responsible Conduct of Research	1
ME.300.713	Pathology for Graduate Students: Basic Mechanisms	3
ME.100.716	Analysis of Macromolecules	2
ME.260.709	Molecular Biology and Genomics	1.5
ME.110.733	Principles of Genetics	2
ME.110.728	Cell Structure and Dynamics	1.5
ME.360.728	Pathways and Regulation	2
ME.250.703	Graduate Immunology	4
ME.300.710	Pathobiology and Disease Mechanisms	3
ME.300.714	Pathology for Graduate Students: Cancer	1
ME.300.716	Pathology for Graduate Students: Immunology/Infectious Disease	1
ME.300.715	Pathology for Graduate Students: Neuropathology	1
ME.300.717	Grant Writing 101 (2nd Year)	3
ME.300.711	Introduction to Translational Research Rotation 1 (during or after 3rd Year)	1

1    Variable credit (modify to adjust total credits/semester).

Approach to Choosing Laboratory Rotations and a Thesis Environment

Each student will complete 3 research rotations prior to selecting a thesis laboratory. Declaring a thesis laboratory before the completion of 3 rotations is an option. A fourth rotation may be completed if necessary/desired. Generally, each research rotation will be about 3 months in length, with the exception of summer rotations. A full-time summer rotation (July-August) will be about 2 months in length. It is critical for rotating students to consult with rotation mentors (PIs) about available funding for students for a 4-year training period before a rotation is engaged.

Upon starting a rotation, students and their rotation mentors will complete the Rotation Plan form, provided within the student's Program Policy Manual. Upon completion of the rotation, the mentor will provide an evaluation grade for the student’s work. Students will present their rotation work at the Pathobiology Journal Club or at the annual Pathobiology retreat.

The 3 required rotations must be completed during the first year and are traditionally completed with Pathobiology faculty members. Outside Pathobiology faculty rotations may be completed, however these must be approved by the program director(s). If a student chooses to undertake their thesis research with an outside faculty member, the faculty member will need to be considered first by the Pathobiology Executive Committee before joining the program faculty.

Oral Examination

The Doctoral Board Oral (DBO) Examination tests the breadth and depth of the graduate student’s scientific knowledge and readiness to begin thesis research. The examination is based fundamentally on the collective content of the first-year courses. A thesis proposal is not required at the time of the examination. This preliminary oral examination is administered by the Pathobiology Program and will be scheduled by lottery during October at the beginning of the second year, after the student has successfully completed all required first-year courses. The examination committee consists of 5 faculty members. The committee is approved by the registrar. Passing the examination is required for graduation.

Thesis Advisor and Advisory Committee

After the first year is completed, the student will choose an advisor or co-advisors from the Pathobiology faculty. The student must select a thesis advisor no later than 1 year from the date of admission to the program. In general, if students have worked in a laboratory prior to becoming a Pathobiology student, they will not be permitted to conduct their thesis research in this laboratory. Any exceptions to this policy will be determined by the Pathobiology Executive Committee. After completing the DBO Examination for the Ph.D. Degree for the School of Medicine Programs, a Thesis Advisory Committee will be formed to monitor the student’s thesis research and academic progress. The student, with the guidance of their advisor(s), decides on the composition of the thesis committee. The thesis committee, in addition to the student's advisor(s), consists of at least three experts in the student’s field of study or related fields. Committee members help with research direction and technical challenges and oversee the student’s progress until research is completed and the doctorate is awarded. 

Academic Progress is observed during annual thesis committee meetings. Students are required to meet with their committee at least once per year to review progress. Additionally, per University guidelines, it is required that each student also complete an Individual Development Plan (IDP) form each year and meet with their mentor(s) to discuss. Thesis meeting and IDP forms are to be completed through an online tracking system. This online resource allows students to have better consolidation and control (take ownership) of their academic records and training while at JHU.

Faculty Advisory Groups: each student, along with a group of other students, will be assigned a faculty advisor(s) during the time period between starting the program and choosing a thesis advisor. The group will meet AT LEAST once every 4 months. These meetings will be initiated by the group's senior student leader (appointed by the Program).

Electives

All students in their third year and beyond are required to take a one-semester elective course for credit in each academic year. Elective courses in statistical analysis are encouraged. Courses may be taken for a grade or pass/fail. Students may choose a course offered in the Johns Hopkins Medical Institutions, or on the Homewood Campus subject to approval by the Program Director. 

Translational Rotation (1 required)

The objective of the Translational Rotation is to give graduate students an interactive exposure with the clinical diagnostic dimension of Pathology. Students should learn the fundamental clinical questions, the current state of the technologies to address these questions, and how basic science can be translated to advances in diagnostic and therapeutic approaches. Students must complete a translational rotation within a year or earlier of the student's expected completion date, as a graduation requirement, (unless otherwise directed by the Program Director(s)). The rotation need not require an experimental project involving bench work. If the student wishes to complete such a project, it should be decided jointly between the student and rotation advisor. 

Departmental Thesis Seminar

Shortly before the program submits your graduation materials, you must formally present your thesis work to the Department and Program in the form of a public presentation. 

Seminars, Journal Clubs, and Lab Meetings

All Pathobiology students are required to attend the Pathobiology Journal Club course, occurring every other week, as well as all lab meetings in their mentor/thesis advisor’s departments throughout their training period. All first-year Pathobiology students are expected to attend weekly Pathobiology lunch meetings (Wednesdays). Students are also encouraged to attend the many seminars presented by invited speakers who are involved in cutting-edge research.

Pathobiology Annual Retreat

The annual Pathobiology Retreat (held in early Fall), from 8:00 a.m. to 4:00 p.m. includes a series of short research talks by senior students and poster presentations by third year and beyond students. Attending keynote speaker(s) will deliver a special lecture and faculty members and alumni will discuss their research and career options. All students in the Pathobiology Graduate Program are expected to participate in this event; Pathobiology faculty make every effort to participate in the event as well.    

Pathology Young Investigators' Day (students are encouraged to participate)

The Departmental Young Investigators’ Day (held in May) provides residents, fellows, and students with the opportunity to present their clinical, basic, or translational research efforts. This activity allows faculty, fellows, residents, and students to learn more about the diverse ongoing research in the Pathology department. All fellows, residents, graduate students and medical students working with a faculty member who holds an appointment in the Department of Pathology, or the Pathobiology Program are invited to submit abstracts and present posters at the annual event. 

Graduate Student Association Poster Session (students are encouraged to participate)

The Graduate Student Association Poster Session is held every year. This gives the students the opportunity to showcase their research to both faculty and peers.

Learning Outcomes

Over about a 5-year period, Pathobiology Program trainees will become competent and competitive for career placement and leadership positions in academia, industry, medicine, clinical laboratory medicine, entrepreneurship, consulting, business, government, and science writing. Trainees are sculpted to become transformational leaders and make an important, global impact on the pathological basis of human disease and health-related research.

This outcome will be achieved by:

1. Instruction on the fundamentals of human disease biology and mechanisms. Students will learn the historical and contemporary drivers of many human diseases ranging from neoplasia, infectious disease, and neurodegeneration.
2. Honing of critical and incisive thinking skills for distinguishing important and less important research, strong and weak science, mundane and visionary research. We accomplish our mission through a curriculum and environment that are different and uniquely designed for understanding and empathizing with human disease and the myriad of unmet therapeutic needs for human disease treatment.
3. Learning state-of-the-art and high-throughput elegant analytical skills for normative and pathological assessments using histological, cellular, and molecular, and the vast array of omics approaches to interrogate human disease at the gene level to the organism level.
4. Engaging in fully rigorous, transparent, and reproducible research.
5. Sharing in the deep satisfaction of the outstanding, interdisciplinary, and diverse programmatic and collaborative faculty and resource-rich environment, including human disease biorepositories.
6. Developing sophisticated skills in logic and communication involving creative-thinking, speaking, and writing at the peer-review level.
7. Reinforcement of the humanity, compassion, and importance of each student’s research project with a clear understanding that the ultimate goal is a Kantian categorical imperative to better alleviate the suffering caused by human diseases.

We accomplish our mission through a curriculum and environment that are different and unique. We encourage change, creativity, and out-of-the-box reasoning. The intensive coursework during the first year of training is designed to build a foundation in contemporary molecular, cell, and structural biology, signal transduction pathways, neurobiology, genetics and genomics, immunology, and bioinformatics, all filtered through the prism of human pathology, therapeutics, and translational medicine. These classes, along with 3 lab rotations and oral presentations based on this work, culminate with the student selection of a thesis lab headed by a faculty member who is accredited for mentor compliance by institutional and programmatic review.

A unique aspect of the program is the inclusion of translational rotations in a clinical pathology setting. During their training, most students garner first author and collaborative co-author peer-reviewed publications, many in high-impact journals, including Nature, Cell, Science Translational Medicine, and Journal of Clinical Investigation, and some successfully compete for NIH F31 individual training grants. Collectively, the coursework, supplemental library-based teaching tools, the annual program retreat, journal club meetings and discussions, scientific ethics in rigor, reproducibility, transparency and logic, and moral values are inculcated as Kantian categorical imperatives. The outstanding, interdisciplinary, and diverse programmatic and collaborative faculty and resource-rich environment act as catalysts for students to explore, thrive, and consolidate their novel research to launch their exciting careers to become transformational leaders in their scientific fields of endeavor. 

Historically, Pathobiology PhD graduates are well-trained biomedical scientists, medical doctors (MD/PhDs), and veterinary doctors (DVM/PhDs) that have successfully embraced varied career paths.

The Pathobiology Graduate Program may confer an Intermediate Master's Degree (IMD) to recognize a student's achievements en route to their PhD. This is done upon the student's request and will be subject to the same standards as a Terminal Master's degree, as mentioned below. See policy statement referenced in the above link for more details. NOTE: Request for the IMD must be received at least one term before student plans to graduate with their PhD.

1. Successful completion of graduate program IMD course requirements. IMD course requirements must be the same as those for a Terminal Master's Degree.
2. Successful completion of additional SOM or University requirements (e.g., training in the Responsible Conduct of Research).
3. Completion of at least two consecutive semesters of full-time study prior to degree conferral.
4. All IMD students must have successfully passed a required Graduate Board Oral examination.
5. All graduate students receiving an IMD must be a current full-time student at the time of submitting their IMD application.

Process for Application and Awarding of IMD for Pathobiology

• PhD program requirements and procedures for the IMD must be clearly stated in the PhD Program's Handbook.
• Eligible students may submit a request for an IMD to their PhD Program at least one term before they plan to graduate with their PhD degree. Requests will be reviewed by the Committee on Master's and PhD Programs according to the regular degree conferral schedule (see below). Only one degree (IMD or PhD) may be conferred per term.
• Students who have graduated or left the SOM are not eligible to request an IMD.
• Students receiving an IMD are not eligible to participate in SOM Convocation, because these students have not completed their studies at the SOM.
• Students who receive an IMD but do not complete the requirements for the PhD degree should follow procedure for a Terminal Master's degree. The IMD and Terminal Master's degrees are equivalent. These students will not receive a second degree but will be eligible to participate in SOM Convocation.
• The SOM will provide the conferred IMD diploma by mail or by other means to the student.

Policy for Awarding the PhD Degree at the Johns Hopkins University

 Administered by the Doctor of Philosophy Board.
Degree Requirements:There are four fundamental requirements for the Ph.D. at Johns Hopkins University: dissertation, residence, oral examination, and RCR fulfillment. None of these requirements can be modified or changed without unanimous consent of the schools and the Provost.

1. Dissertation: All Ph.D. students must successfully complete a dissertation in accordance with relevant school and program guidelines prior to degree conferral.
2. Residence: All Ph.D. students must have completed two consecutive semesters of full-time study prior to degree conferral.
3. Oral Examination: All Ph.D. students must successfully pass a required oral examination conducted by five faculty members. The oral examination must include the chair and at least one other member from outside the candidate’s home department.

4. Responsible Conduct of Research: All graduate students must receive training in the Responsible Conduct of Research.

The SOM policy is based on NIH guidelines. Students must receive training that includes a significant small-group component, allowing issues to be openly discussed with fellow students and faculty discussion leaders. A training program should provide at least eight hours of class time -- with at least three hours of face-to-face discussion -- and address at least the following topics:

1. ​The scientist as a responsible member of society
2. Research misconduct
3. Data acquisition and management
4. Authorship and publication practices
5. Mentor and trainee responsibilities
6. Use of animals in research
7. Conflicts of interest
8. Collaborative research
9. Human subjects if applicable

It is the responsibility of each program to design a curriculum that satisfies these requirements. Contact the Associate Dean for Graduate Biomedical Education with any questions.

It is university policy that all program and university requirements for the Ph.D. must be completed in 9 years or less from start of the doctoral program. The Doctor of Philosophy Board reviews all candidates for the Ph.D. prior to conferral to ensure that the fundamental requirements for the Ph.D. have been met within the time frame delineated.

Documents provided by the Program to the student's Payroll Administrator, included in packet:

• PhD Student Payroll Termination Form

Deadlines for documentation:

• Deadline for submission of materials for December conferral: November 1st
• Deadline for submission of materials for May conferral: April 1st
• Deadline for submission of materials for August conferral: July 1st

Conferral Dates:

• Thursday before Memorial Day in May
• Last weekday before the fall term begins in August
• Last weekday in December