Program Description
Graduate Program Overview
The graduate program in Genome Sciences trains students at the interface of several disciplines to prepare them for the challenges of modern biology and medicine. Our goal is to develop and apply technologies from the fields of genetics, genomics, proteomics, and bioinformatics to gain leading edge insights into the biology of humans, model organisms and a host of other species. The program emphasizes extensive research experience within an interdisciplinary and state-of-the-art research environment.
First Year of Graduate School:
Welcome to the Department
New students are welcomed to the department during an annual retreat. This is a time for everyone in the department to interact in a peaceful setting, and allows new students the opportunity to hear about the research in the different faculty laboratories. This opportunity is an important venue for new students to “shop around” for their first quarter rotation advisors. Students from other UW programs such as Molecular and Cellular Biology may also attend this first year retreat and rotate in Genome Sciences labs, but the number of available rotation slots generally exceeds the number of students looking to fill them, leaving students with plenty of freedom to choose a lab to suit their preferences.
Research Rotations
Although students are asked on their applications to name specific faculty they might be interested in working with, admitted students are not committed to working with any of these particular faculty (and the faculty they name might not be accepting students in the current year). Instead, each student spends the first year of the program rotating through the labs of three different faculty, one during each of the three ten-week quarters that make up the UW academic year.
Between the department retreat and the start of the fall quarter two weeks later, first year students are expected to approach one or more faculty to inquire about a first rotation, taking into account their research interests and desired lab environment. The student can approach potential second-rotation and third-rotation advisors anytime during the first and second quarters of the academic year, and is normally expected to choose a dissertation lab during the final month of the third rotation.
Course Work
Genome Sciences graduate students take a common set of core courses:
Genome 550: Methods and Logic
This is a literature review/discussion class designed to develop your ability for evaluation of the research literature, from pioneering works to the latest research reports.
Genome 551: Mechanisms of Gene Regulation in Prokaryotes and Eukaryotes
A detailed examination of the mechanisms of transcription and translation as determined by experimental genetics, molecular biology, and biochemistry.
Genome 552: Genomics
Discussion of current and newly-emerging technologies in genome analysis with regard to applications in biology and medicine and to potential advantages and limitations.
Genome 553: Advanced Genetic Analysis
Classical genetic analysis is a powerful approach to dissect complex biological processes. Selective removal, addition, or alteration of specific proteins to identify and order genes in a pathway, define protein function, determine tissue and temporal requirements for gene function, and distinguish among competing hypotheses to explain biological phenomena.
Genome 555: Proteomics
Focuses on current and emerging technologies and approaches in protein analysis, and considers applications of these technologies in biology, biotechnology, and medicine.
Genome 560: Statistics for Genome Sciences
The data-intensive nature of 21st-century biology makes it very important for scientists to have a basic proficiency in statistics. Whether it is thousands of gene expression levels as measured by a RNA-Seq, millions of polymorphisms that have been genotyped in a case-control study or more general questions of how to properly design an experiment, you will constantly be confronted with how to collect, analyze and interpret data. This course provides the key statistical concepts and methods necessary for extracting biological insights from data. (Students with prior undergraduate coursework in statistics are exempt.)
Genome 561: Population Genetics
Surveys recent literature to gain an understanding of the basic principles of molecular population genetics and evolution as applied to analysis of genome data. Requires some computer analysis of genome data.
Genome 599: Grant Writing
This course will serve as a writer’s workshop where each student will write a fellowship application, usually for the NSF GRFP. Students will learn strategies for effective grantsmanship and workshop drafts of their application components with their peers and the instructor.
In addition to these courses, students with little or no programming experience will take Genome 559 (Intro to Statistical and Computational Genomics). Students with more programming experience and an interest in Computational Biology often take Genome 540 & Genome 541 to learn about the development of bioinformatic algorithms. Most graduate level Genome Sciences classes are small and discussion-oriented, consisting of first year Genome Sciences students and a small number of graduate students from other departments.
In addition to these classes, students may elect to take other courses depending on their interests and research aims. These courses may include classes from within Genome Sciences and any other UW departments.
Students may continue to take courses during their second year of study. These usually concern disciplines relevant to the student's dissertation research. In addition, beginning in the second year, graduate students are expected to regularly practice their oral presentation skills through annual research reports and journal club presentations.
Journal Club, Research Reports, and Department Seminars
All members of the Department of Genome Sciences gather together weekly for Journal Club, Research Reports, and the Departmental Seminar. Journal Clubs are presentations of work published by researchers from outside our department which are led by both students and faculty and designed to increase the breadth of community knowledge. Research reports are a unique Genome Sciences tradition in which each graduate student gives an annual presentation of their work in progress to the entire department. Departmental seminars are presentations by faculty from other universities who are flown out to UW to exchange ideas with members of our community.
Journal Clubs and Research Reports give students regular opportunities to develop their presentation skills. The Department takes the training of its graduate students seriously, and a big part of that is learning to communicate in a professional manner. In addition to such departmental events, students often present their work at technical intra-group lab meetings as well as national or international scientific meetings. Research Reports also serves to keep each member of the department current with the diversity of research in the department, and facilitates the free exchange of ideas.
Second Year and Beyond:
Research
At the start of the summer, most students join one of their three rotation labs and begin working on their thesis research. They will focus on research for most of their second year, perhaps taking one or two elective courses. After working for several months to generate preliminary data, the student assembles a supervisory committee consisting of three or four faculty with relevant expertise. The committee guides the student's training program with regard to further course work, research, and the Ph.D. dissertation, and conducts the General Examination (see below), which is taken at the end of the second year.
Additional coursework
The only required second-year course is the special topics course Genome 599: Scientific Speaking. This course is designed to improve students’ research presentation skills. Rather than attending class weekly, students meet the requirements of this course by giving two practice Research Reports talks to the course instructors and two advanced graduate student mentors, who offer extensive feedback for the student to incorporate before presenting their first formal Research Report to the entire department.
In the third year, students take an NIH-mandated ethics course designed to teach them to identify and avoid research misconduct, as well as recognize and mitigate the impact of the cultural biases that can make science and academia inhospitable to historically underrepresented groups.
Evaluation of Progress and The General Examination
The Department monitors each student's scientific development to encourage timely progress toward the completion of thesis research. At the end of a student’s first year, the faculty will meet to evaluate written reports prepared by those who have interacted with the student during classwork or research rotations. A timely discussion with the student will then provide the opportunity for the student to work toward making improvements where needed and to develop specific strengths that the intended research may demand. The faculty will discuss the student’s progress at the end of every subsequent year to ensure that they are progressing toward completion of their Ph.D.
During the second year, students will begin preparation for the Oral General Examination by writing a research proposal in the format of an NIH grant proposal to be submitted for evaluation by their advisory committee. This proposal will outline their preliminary work as well as a plan for achieving three total research aims by the end of the 5-year Ph.D. The committee will promptly provide feedback to the student, who will then revise the proposal. The revised proposal will serve as the basis for the oral general examination to be conducted by the committee at the end of the second academic year. Critical evaluation of the research project in this manner is intended to ensure that preparation is thorough and well-conceived, thus providing the student with a solid basis for timely performance and publication of the research. During the oral exam, the student is also expected to answer questions designed to test the breadth and depth of their knowledge beyond the scope of their specific project.
Teaching
All graduate students in Genome Sciences participate in undergraduate instruction by serving as teaching assistants for Genome Sciences courses for a total of two quarters, generally once in the department’s flagship introductory genetics course during Year Three and a second time in an upper level elective or graduate course during Year Four. Student course preferences are respected whenever possible. This experience prepares students for teaching responsibilities after receipt of the Ph.D.
Graduation
The graduate program in Genome Sciences is designed to take approximately 5 years. On average, our students graduate in 5.1 years. Prior to obtaining the Ph.D. degree, the student must defend the dissertation in a presentation to the department in a seminar format, which is followed by closed-door questioning by the student’s thesis committee. Approval of both the written thesis and the oral defense by the supervisory committee qualifies the student to receive the Ph.D. degree.
Financial Support
Full funding is provided for the duration of studies, including a stipend for living expenses (currently $40,008 per year as of July 2021), tuition waiver, and health insurance.
Environment
The Department is relatively small, with about 70 graduate students in residence at any given time. This not only provides a nurturing environment, but also encourages close associations and scientific interactions. Many of our faculty are affiliated with other graduate programs such as Molecular and Cellular Biology, Biochemistry, Bioengineering, and Statistics, whose students may also choose to do thesis work in Genome Sciences and bring different disciplinary perspectives to the department. All students in our department will be assigned space in the laboratories of the faculty members with whom they do their rotations or dissertation research. State-of-the-art research facilities are available in the department for cellular, protein, and DNA analysis. Extensive computer resources are also available to students. In addition, the Seattle area houses many prestigious scientists in other departments at the University of Washington, at the Fred Hutchinson Cancer Research Center, and at several large biotechnology companies. Many labs are members of the yeast, fly, worm, or mouse clubs, which hold meetings regularly, and which include labs from each of these institutions.
Applying to the Graduate Program
The complete application process is outlined in the application section.
For additional information on applying to the Genome Sciences Ph.D. program, please contact Brian Giebel at bgiebel
[ a t ] uw.edu or (206) 616-7297.