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    Pathobiology student Andrew Soerens. Photo credit: Katherine Turner/School of Public Health.
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    Advanced Research Training

    Pathobiology students are working to address global health issues that affect millions of people including malaria, HIV, and HPV.

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    A white board in the lab at Fred Hutch. Photo credit: Katherine Turner/ School of Public Health.
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    Rigorous Coursework

    Coursework includes basic courses in pathobiology, epidemiology, and molecular biology. Students may also choose electives from other basic medical sciences, such as microbiology, biochemistry, pathology, and genetics.

Select from the following:

Current Courses

Autumn Quarter

PABIO 551: Biochemistry and Genetics of Pathogens and Their Hosts (4 credits) - Lee Ann Campbell, Lakshmi Rajagopal
G H 580: Global Health Doctoral Seminar: Diseases in Global Health (2 credits) - Sheila Lukehart, S.O. Soge
PABIO 581: Current Literature in Pathobiology (1 credit) - Justin Taylor

Winter Quarter

PABIO 552: Cell Biology of Human Pathogens and Disease (4 credits) - Christoph Grundner, Kevin Hybiske
PABIO 553: Survival Skills for Scientific Research (2 credits) - Don Sodora
PABIO 580: Pathobiology Seminar (1 credit) - Steve Polyak

Spring Quarter

PABIO 536: Bioinformatics and Gene Sequence Analysis (3 credits) - David Sherman
PABIO 582: Critical Thinking and Research Design (1.5 credits) - Lorenzo Giacani
PABIO 591 A: Minicourse: Scientific Writing (1 credit) - Jairam Lingappa
PABIO 591 B: Minicourse: TBD (1 credit) - Instructor TBD

 

Required Courses

PABIO 551: Biochemistry and Genetics of Pathogens and Their Hosts (4)
Provides a strong foundation in biochemistry, molecular biology, and genetics for students interested in disease. Principles will be illustrated through examples focusing on pathogens, and infectious and non-infectious disease. Prerequisite: Undergraduate level course work in molecular biology or biochemistry or permission of instructor.

PABIO 552: Cell Biology of Human Pathogens, Disease, and Public Health (4)
Cell biology and immunology explored through diseases of public health importance with examples of pathogen interaction with host cell biology and immune systems, unique aspects of the cell biology of pathogens, perturbations of these systems in non-infectious diseases and design of therapeutics and vaccines to combat diseases of public health importance.  Prerequisite: Undergraduate level coursework in biology or molecular biology or permission of instructor.

PABIO 553: Survival Skills for Scientific Research (2)
Focuses on skills needed for scientific career: writing abstracts, curriculum vitae, research proposals; preparing for oral presentations; lab management skills; discussion of mentorship/trainee relationships; case-based discussions of various topics in ethics and scientific misconduct.

PABIO 580: Pathobiology Seminar (1, max. 21)
Research from students, faculty members, and invited speakers is presented and discussed. Topics include immunochemistry, viruses, membranes, infectious diseases, immune response and other related topics. Note:  students are also required to attend the presentations of dissertation research in the Final Exam of students completing the Pathobiology doctoral program. 

PABIO 581: Current Literature in Pathobiology (1, max. 15)
Develop skills in analyzing data and assessing conclusions through an analysis of current literature in Pathobiology. Focuses on breadth and analytical skills. Prerequisite: enrollment in the Pathobiology graduate program. 

PABIO 582: Critical Thinking and Research Design in Pathobiology (1.5)
Analysis of issues, hypothesis and experimental design and testing. Credit/no credit only. Prerequisite: graduate standing in Pathobiology.

PABIO 591: Rotating Pathobiology Minicourses (1)
Intensive 3-week offerings focusing on topics such as pathogenesis, immunology, virology, disease agents, bioinformatics and grant writing. Topics differ from year to year. Prerequisite: permission of instructor.

PABIO 598: Didactic Pathobiology (2)
Supervised teaching experience in Pathobiology courses for Enrolled graduate students in the Interdisciplinary Pathobiology program on the PhD track. Prerequisite: permission of instructor.

Department of Epidemiology

EPI 511: Introduction to Epidemiology (4)
For the graduate student wanting an overview of epidemiologic methods. Description of ways in which variation in disease occurrence is documented, and how that variation is studied to understand causes of disease. Prerequisite: graduate standing.

Department of Global Health

G H 580: Global Health Doctoral Seminar: Diseases in Global Health (2)
The study of global health emphasizes a multidisciplinary perspective to understand the complex determinants of the health of the world’s population.  In meeting its goals for training students, the Department of Global Health (DGH) endeavors to provide each of our students with an appreciation of the complexity of global health determinants, exposing them to the most significant challenges that the field faces as well as currently available solutions. This four-quarter course series is designed to expose students to the most critical issues in global health, bringing in the complementary perspectives of Pathobiology, metrics and implementation science to build a multidisciplinary understanding of these issues, including effective and appropriate strategies for their control. 

University Conjoint Courses

UCONJ 510: Introductory Laboratory Based Biostatistics (2)
Introduces methods of data description and statistical inference for experiments. Covers principles of design and analysis of experiments; descriptive statistics; comparison of group means and proportions; linear regression; and correlation. Emphasizes examples from laboratory-based biomedical sciences, and provides demonstrations using standard statistical programs.

Department of Immunology

IMMUN 441: Introduction to Immunology (4)
General properties of immune responses; cells and tissues of immune system; lymphocyte activation and specificity; effector mechanisms; immunity to microbes; immunodeficiency and AIDS; autoimmune diseases; transplantation.

OR

IMMUN 532: Advanced Immunology (4)
Examines the molecular and cellular basis of immune function. Students must have completed a baccalaureate degree in a biological specialty and be conversant with molecular genetics. Topics include: hematopoiesis, antigen receptor structure, lymphocyte development, antigen presentation, and cytokines.

Electives

You must take two or more courses selected on the basis of your track and emphasis. PABIO 536: Bioinformatics is recommended for all students. Please consult with your advisor and your committee regarding your selection and schedule of electives. Your research advisory committee may advise you to take additional electives or electives in lieu of those designated for your track. If the latter occurs, this should be documented in your file in the program office. Some electives are more suitable for students with advanced backgrounds.

Elective Recommendations by Emphasis

Students should consult a current catalog to verify course offerings. Each student in the PhD program will select a track based on his or her research interests; this is done at the time of the formation of the student-mentor partnership (end of the third quarter in the first year). Students should choose electives based on their track.

Emphasis in Eukaryotic Pathogens

Strongly Recommended:

IMMUN 532: Advanced Immunology (4 credits, Winter)

Additional electives can be selected from the courses below to fulfill the total graded credit requirements, depending on the background and interests of the student:

EPI 520: Epidemiology of Infectious Diseases (3 credits, Winter)

EPI 532: Epidemiology of Infectious Diseases of Third World Importance (3 credits, Spring, odd years)

MICROM 444: Medical Mycology and Parasitology (4 credits, Spring)

CONJ 531-548: Select Modules from the Molecular Conjoint Series (varies)

Emphasis in Bacterial Pathogens

Strongly Recommended:

IMMUN 532: Advanced Immunology (4 credits, Winter)

Additional electives can be selected from the courses below to fulfill the total graded credit requirements, depending on the background and interests of the student:

MICROM 553: Molecular Mechanisms of Bacterial Pathogenesis (3 credits, Autumn, odd years)

MICROM 555: Advanced Clinical Microbiology (2.5 credits, Autumn, Winter, Spring)

EPI 520: Epidemiology of Infectious Diseases (3 credits, Winter)

EPI 529: Emerging Infections of International Public Health Importance (3 credits, Winter)

GENOME 576: Genetic and Genomic Analysis of Bacteria (1.5 credits, Autumn)

CONJ 548, 549, 557: Select Modules from the Molecular Conjoint Series (varies)

Emphasis in Viral Pathogens and Cellular Pathology

Two or more of the following are strongly recommended:

IMMUN 532: Advanced Immunology (4 credits, Winter)

MICROM 540: Virology (3 credits, Winter, even years)

CONJ 531-544: Select Modules from the Molecular Conjoint Series (varies)

MCB 532: Human Pathogenic Viruses (3 credits, Autumn, odd years)

Additional electives can be selected from the courses below to fulfill the total graded credit requirements, depending on the background and interests of the student:

EPI 520: Epidemiology of Infectious Diseases (3 credits, Winter)

EPI 530: AIDS: A Multidisciplinary Approach (2 credits, Autumn)

EPI 524: Epidemiology of Cancer (4 credits, Winter)

The PhD Program

Time to completion: ~ 5 years
Total Credit Requirement: 90 credits
Minimum: 18 graded credits

The Pathobiology Graduate Program has established learning objectives for its doctoral program. The goals of the program are the following:

  • Develop a fundamental understanding of basic cellular and molecular processes and techniques important in the application of basic biomedical research to diseases of global public health interest.  Specifically, this includes familiarity with the paradigms for control, prevention, and treatment of diseases of public health importance, an understanding of the epidemiology and processes of diseases of national and international importance, an understanding of how biomedical research can approach such diseases, and basic methodologies used in this type of research, including relevant areas of molecular biology, epidemiology, and biostatistics. Students are also expected to develop familiarity with the major classes of pathogens.

  • Become an independent scholar capable of conducting independent research leading to the expansion of knowledge of Pathobiology.  This includes developing the skills to approach an unfamiliar experimental system, and identify and explore important questions concerning pathogenesis and infection.

  • Learn to collect, analyze, interpret, and use data for solving problems in Pathobiology. 

  • Develop advanced research skills and expertise in the area of his/her research concentration.

  • Develop skills in communicating research findings to scientific audiences through publications and oral presentations. 

The course of study outlined below will fulfill University of Washington regulations. On this website, those requirements will not be covered exhaustively. See the Graduate School's Doctoral Degree Policies for a summary of the University requirements. Ultimately, it is the student's responsibility to ensure that s/he meets the UW and program requirements and proceeds through the program in a timely fashion. 

Required Courses

PABIO 551: Biochemistry and Genetics of Pathogens and Their Hosts (4 credits, Graded)

PABIO 552: Cell Biology of Human Pathogens and Disease (4 credits, Graded)

PABIO 553: Survival Skills for Scientific Research (2 credits, C/NC)

PABIO 580: Pathobiology Seminar* (1 credit, C/NC)

G H 580: Global Health Doctoral Seminar: Diseases in Global Health (2 credits, Graded)

PABIO 581: Current Literature in Pathobiology** (1 credit, C/NC)

PABIO 582: Critical Thinking and Research Design in Pathobiology** (1.5 credits, C/NC)

PABIO 591: Rotating Pathobiology Minicourses** (1 credit, C/NC)

PABIO 598: Didactic Pathobiology (Teaching) (2 credits, C/NC)

PABIO 500: Rotation (3 credits, C/NC)

PABIO 600: Research (Variable, C/NC)

PABIO 800: Doctoral Dissertation (Variable, C/NC)

EPI 511: Introduction to Epidemiology (4 credits, Graded)

UCONJ 510: Introductory Laboratory Based Biostatistics (2 credits, Graded)

Plus one of these courses:

IMMUN 441: Introduction to Immunology (4 credits, Graded)

IMMUN 532: Advanced Immunology (4 credits, Graded)

Notes on Courses for Degree Progress

* Students are required to attend Seminar (PABIO 580) every Winter Quarter, and to attend the presentations of dissertation research in the Final Exam of students completing the Pathobiology PhD Program. Students in the writing stage of their dissertation are exempted from PABIO 580 for that quarter. 

** Students are required to enroll in Lit Review (PABIO 581) every Autumn Quarter for the first three years, Critical Thinking (PABIO 582) every Spring Quarter until they complete their General Exam, and a minicourse (PABIO 591) every Spring Quarter for the first four years in the PhD program.

Biostatistics Competency

Given the importance of understanding biostatistics, the Pathobiology Program requires students entering the PhD program in Autumn 2016 or later to have formal coursework in biostatistics. To allow for maximum flexibility, this requirement can be fulfilled in a number of ways. Doctoral students must complete one of the
items below by the end of the third year to demonstrate competency.

  1. Complete UCONJ 510: Introductory Laboratory Based Biostatistics (2 credits, offered in Summer Quarter)*
  2. Complete either BIOST 508: Biostatistical Reasoning in the Health Sciences (4 credits) or BIOST 511: Medical Biometry (4 credits) or BIOST 517: Applied Biostatistics (4 credits)
  3. Previous coursework in Biostatistics or Statistics – must be approved by Program Director
  4. Alternate approach to be discussed with the Program Director

*If taking UCONJ 510 in summer, students should register for no more than 2 credits total.

PhD Electives

You must take two or more courses selected on the basis of your track and emphasis. PABIO 536: Bioinformatics is strongly recommended for all students. Please consult with your advisor and your committee regarding your selection and schedule of electives. Your Doctoral Supervisory Committee may advise you to take additional electives or electives in lieu of those designated for your track. If the latter occurs, this should be documented in your file in the program office. Some electives are more suitable for students with advanced backgrounds. See the Pathobiology electives list for more information.

MSTP Coursework

Curriculum for first-year Pathobiology PhD Students in the MSTP Program:

The Graduate School requires 18 graded credits to complete the PhD. To meet this requirement, MSTP students following this recommended curriculum will need to take at least five graded elective credits in addition to the required courses outlined below. (Note that 6 - 8 graded credits are required if one or more of the mini-courses are not taken for a grade). The five graded elective credits may be fulfilled by a combination of courses including those listed below as optional or other PABIO, SPHCM, Conjoint, or MCB courses.

The rotation requirements are waived for MSTP students since these are fulfilled during the first years in Medical School.

MSTP students are required to take the same written and oral general examinations as other PhD students in the program.

MSTP students are required to have the same training in didactic teaching (PABIO 598) as other PhD students, unless they have served as a TA during Medical School prior to joining the Pathobiology Program. In that case, they are exempted from taking PABIO 598. 

Required Courses

PABIO 551: Biochemistry and Genetics of Pathogens and Their Hosts (4 credits, Graded)

PABIO 552: Cell Biology of Human Pathogens and Disease (4 credits, Graded)

PABIO 553: Survival Skills for Scientific Research (2 credits, C/NC)

PABIO 580: Pathobiology Seminar* (1 credit, C/NC)

G H 580: Global Health Doctoral Seminar: Diseases in Global Health (2 credits, Graded)

PABIO 581: Current Literature in Pathobiology** (1 credit, C/NC)

PABIO 582: Critical Thinking and Research Design in Pathobiology** (1.5 credits, C/NC)

PABIO 591: Rotating Pathobiology Minicourses** (1 credit, C/NC)

PABIO 598: Didactic Pathobiology (Teaching) (2 credits, C/NC)

PABIO 500: Rotation (3 credits, C/NC)

PABIO 600: Research (Variable, C/NC)

PABIO 800: Doctoral Dissertation (Variable, C/NC)

EPI 511: Introduction to Epidemiology (4 credits, Graded)

UCONJ 510: Introductory Laboratory Based Biostatistics (2 credits, Graded)

Optional Course

IMMUN 441: Introduction to Immunology (4 credits, Graded)

Notes on courses for degree progress

* Seminar (PABIO 580) is taken every Winter Quarter during the first three years.

** MSTP students are required to enroll in Lit Review (PABIO 581) every Autumn Quarter for the first three years, Critical Thinking (PABIO 582) every Spring Quarter until they complete their General Exam, and a minicourse (PABIO 591) every Spring Quarter for the first three years in the PhD program.

Biostatistics Competency

Given the importance of understanding biostatistics, the Pathobiology Program requires students entering the PhD program in Autumn 2016 or later to have formal coursework in biostatistics. To allow for maximum flexibility, this requirement can be fulfilled in a number of ways. Doctoral students must complete one of the items below by the end of the third year to demonstrate competency.

  1. Complete UCONJ 510: Introductory Laboratory Based Biostatistics (2 credits, offered in Summer Quarter)*
  2. Complete either BIOST 508: Biostatistical Reasoning in the Health Sciences (4 credits) or BIOST 511: Medical Biometry (4 credits) or BIOST 517: Applied Biostatistics (4 credits)
  3. Previous coursework in Biostatistics or Statistics – must be approved by Program Director
  4. Alternate approach to be discussed with the Program Director

*If taking UCONJ 510 in summer, students should register for no more than 2 credits total.

 

The MS Program

Time to completion: 2 years
Total Credit Requirement: 60 credits
Minimum: 18 graded credits

The Pathobiology Graduate Program is not currently accepting students directly into the MS program. However, the MS program remains an option under specific circumstances, such as failure to pass the General Examination or changes to academic goals. 

The Master's degree is designed to be a two-year program.

The Pathobiology Graduate Program has established learning objectives for its MS program. The goals of the program are the following: 

  • Learn the fundamental aspects of the application of basic biomedical research to diseases of public health interest.  Specifically, this includes developing an understanding of the applications of molecular biology to public health, epidemiology, and cellular or antigenic analysis, and microbiology or immunology.

  • Learn to collect, analyze, interpret, and use data for solving problems in Pathobiology.

  • Develop basic research skills and understanding of the scientific method.

  • Develop skills in communicating research findings through oral and written presentations.

The course of study outlined below will fulfill University of Washington regulations. On this website, those requirements will not be covered exhaustively. See the Graduate School's Master's Degree Policies for a summary of the University requirements. Ultimately, it is the student's responsibility to ensure that s/he meets the UW and program requirements and proceeds through the program in a timely fashion. 

Required Courses

PABIO 551: Biochemistry and Genetics of Pathogens and Their Hosts (4 credits, Graded)

PABIO 552: Cell Biology of Human Pathogens and Disease (4 credits, Graded)

PABIO 553: Survival Skills for Scientific Research (2 credits, C/NC)

PABIO 580: Pathobiology Seminar* (1 credit, C/NC)

G H 580: Global Health Doctoral Seminar: Diseases in Global Health (2 credits, Graded)

PABIO 581: Current Literature in Pathobiology** (1 credit, C/NC)

PABIO 582: Critical Thinking and Research Design in Pathobiology** (1.5 credits, C/NC)

PABIO 591: Rotating Pathobiology Minicourses** (1 credit, C/NC)

PABIO 500: Rotation (3 credits, C/NC)

PABIO 600: Research (Variable, C/NC)

PABIO 700: Master's Thesis

EPI 511: Introduction to Epidemiology (4 credits, Graded)

MS Electives

Additional courses in Pathobiology or the biomedical sciences may be taken to fulfill the graded course requirement, to encompass the interests of the student, or to fulfill any additional requirements set forth by the student’s committee.

All formal course work should be completed by the first quarter of the second year, except courses offered in alternate years.

Notes for Degree Progress

* Students are required to attend Seminar (PABIO 580) every Winter Quarter, and to attend the presentations of dissertation research in the Final Exam of students completing the Pathobiology doctoral program.

** MS students are required to enroll in Lit Review (PABIO 581) every Autumn Quarter, Critical Thinking (PABIO 582) every Spring Quarter, and a minicourse (PABIO 591) every Spring Quarter in each of the first two years in the MS program. Three credits each of Seminar and Current Literature may each be counted toward the degree. If an MS student decides to continue studies in the Pathobiology PhD program, additional years of PABIO 581/582/591 will be required commiserate with the PhD requirements.

Schedule for Coursework

To progress in a timely manner, students should anticipate taking 1-2 graded courses per quarter, plus Seminar, Current Literature, and Research (PABIO 600) or Thesis (PABIO 700) credits for a total of 10 credits per quarter. Students desiring to enroll in more than 10 credits per quarter need approval from the Graduate Program Director. All formal coursework should be completed by the end of the second year. Please consult with your advisor or a member of the Graduate Student Advisory Committee (GSAC) regarding your specific program. Individual students are likely to need different sets of electives and may want to take required courses at different times.

For offerings of other Pathobiology courses see the listing under the PhD program. Please check with your GSAC advisor or a member of the curriculum committee, as well as a current catalog, to verify course offerings.

MS Advisory Committee 

Your progress in the MS program will be followed by several individuals. Among these are your advisor, members of the Graduate Student Advisory Committee (GSAC), and your MS advisory committee. In the event that you perceive you are having problems with your academic or research program, please discuss this with a faculty member on one of these committees.

The GSAC will monitor your progress until the MS advisory committee is formed in the third quarter of your first year. One of the faculty members serving on the GSAC will be assigned as your GSAC advisor. Please bring questions concerning course offerings and curriculum to them. Once you choose an advisor and form the MS Advisory Committee, you must submit the Advisor Confirmation Form to the Program Manager to be placed in your permanent file. 

The MS advisory committee consists of three members including your research advisor. At least one of the two other members of the committee should be from the Pathobiology Graduate Program. The MS advisory committee meets every six months. For each Committee meeting, the student should prepare a brief oral presentation documenting their progress. The committee will complete a brief report regarding your progress after each meeting. You, your advisor, and the GSAC will receive a copy of that report. If you do not receive a copy, please contact the Program Manager.

MS Thesis Research Proposal 

The MS thesis research proposal should be done by the end of the fourth quarter of the first year. The proposal should contain the following, in this order:

I.          A brief synopsis of background relevant to the project.

II.         A summary of preliminary experiments.

III.       A description of experiments planned for the next year.

Students are encouraged to consult with their advisor and research advisory committee during the preparation of the proposal. The experiments should be designed such that they will form the basis of the student’s thesis. Appropriate references should be cited, although the list does not need to be exhaustive. This proposal should be 3‑4 single spaced pages, excluding references. It is turned in to the student's research advisory committee. The committee in turn will discuss the proposal and experimental options with the student. A copy of the proposal should be provided to the Program Manager for the student's file.

The MS Thesis

The thesis must be provided to the MS advisory committee two weeks prior to the oral presentation. Corrections should be made following their review before submission of the document to the Graduate School. 

The thesis is to be an original study of such quality as to be accepted by a reputable journal. The requirement for a thesis of publishable quality implies a substantial research commitment by the student. It is expected that the thesis work will be promptly submitted for publication, if that has not been done already. 

The thesis should be written in the format suggested by the Graduate School.

MS Oral Presentation and Defense

All students are required to give a formal seminar prior to the completion of the MS program. The research presentation given during the Graduate Research Symposium is not a substitute. The actual thesis presentation will consist of a concise verbal summary of the background, results, conclusions, and significance of the thesis project. Following this presentation, each committee member will question the student on any aspect of his or her research endeavors. The Oral Presentation and Defense is advertised campus wide and other Pathobiology students are encouraged to attend.