Contact Info

Email:	dbbsphdadmissions@wustl.edu
Website:	http://dbbs.wustl.edu

Computational & Systems Biology

Doctoral Candidacy

To earn a PhD at Washington University, a student must complete all courses required by their department; maintain satisfactory academic progress; pass certain examinations; fulfill residence and Mentored Experience Requirements; write, defend, and submit a dissertation; and apply to graduate via Workday Student. For the details of doctoral degree general requirements in Arts & Sciences, including an explanation of Satisfactory Academic Progress, students should review the Doctoral Degree Academic Information page of the Arts & Sciences Bulletin.

Program Requirements

• Total Units Required: 36 credits
• Degree Length: 7 years
  • Students are expected to maintain satisfactory academic progress in accordance with academic milestones. Students entering their seventh year in the program will receive a warning letter in regards to reaching their stated degree length. Students entering their eighth year in the program will be required to obtain permission from the Associate Dean of Graduate Education.
  • Note: Students must be enrolled in 9 graduate credits each semester to retain full-time status. As students complete their course work, if enrolled in fewer than 9 graduate credits, they must enroll in a specific Arts & Sciences graduate course that will show 0 units but does count as full-time status. Students should connect with their department to ensure proper enrollment prior to Add/Drop.
  • Continued support is guaranteed for the duration of your graduate studies, provided that you maintain satisfactory progress towards completion of the degree. 
• Grade Requirement: Required courses generally consist of four to nine courses in areas fundamental to the student's program. Students are expected to maintain a B average in graduate courses.

Required Courses

DBBS Required Courses

• BIOL 5098 Graduate Research Fundamentals
• BIOL 5011 Ethics and Research Science

Program Required Courses

• BIOL 5495 Algorithms for Computational Biology
• BIOL 5488 Genomics

Three Advanced Electives

In consultation with their advisor, students choose a minimum of 3 advanced electives or special topics of at least 3 unit credits each. Students may substitute one of these three elective requirements by combining multiple 1–2 credit courses totaling at least three credits. To pursue this substitution option, students must submit a petition in advance to the Program Directors for each 1-2 credit course that they wish to substitute with a brief rationale. Because students will be expected to demonstrate substantive command of molecular biology, applied mathematics, and computer science in their qualifying exam, the advanced electives will typically be chosen in areas in which the student does not feel adequately prepared or will emphasize areas of primary interest for the student. The interdisciplinary nature of the program allows considerable flexibility in choosing these courses, depending upon the student's needs. Common choices for these electives include the following:

• BIOL 5357 Chemistry and Physics of Biomolecules
• BIOL 5483 Human Genetic Analysis
• BIOL 5491 Advanced Genetics 
• SDS 5210 Statistical Computation 
• SDS 5010 Probability 
• SDS 5020 Mathematical Statistics 
• CSE 5104 Data Mining 
• SDS 5480 Topics in Statistics: Machine Learning Methods in Biological Sciences  
• INFO 5558 Applications of Deep Neural Networks 
• MSB 5555 Computational Statistical Genetics  

Three Semesters of Journal Clubs 

Students are required to register for three semesters of journal clubs. Participation in BIOL 5496 Seminar in Computational Molecular Biology is strongly encouraged.

Laboratory Rotations

Selecting a thesis advisor is the most important decision a student makes in graduate school. To help each student make an informed, thoughtful choice, the Division builds in flexibility to explore options. Students usually participate in three lab rotations during their first year. Additional rotations can be arranged, and rotation lengths are flexible. Students usually begin their thesis research by the end of their first year.

Scientific Scholarship

Keeping abreast of scientific developments is critical for faculty and students alike. The Division offers many ways to stay current. More than 15 weekly biology seminars provide excellent opportunities to meet outstanding scientists from outside Washington University. Several annual symposia bring internationally recognized speakers to campus. Journal clubs meet weekly for students, postdoctoral fellows and faculty to present and discuss current scientific literature. A number of Interdisciplinary Research Pathways allow students to enhance their PhD program. Program retreats allow for informal interaction among students and faculty. The Division also provides funds for each student for professional development.

Qualifying Examinations

Progress toward the PhD is contingent upon the student passing examinations that are variously called preliminary, qualifying, general, comprehensive, or major field exams. The qualifying process varies according to the program. In some programs, it consists of a series of incremental, sequential, and cumulative exams over a considerable time. In others, the exams are held during a relatively short period of time. Exams may be replaced by one or more papers. The program, which determines the structure and schedule of the required examinations, is responsible for notifying the Office of Graduate Studies, Arts & Sciences, of the student’s outcome, whether successful or unsuccessful.

Program-specific information: Students must pass/complete their qualifying exam within 9 months of lab affiliation. Following a successful QE defense, students will identify and finalize their committee and complete their thesis proposal by December 31 of Year 3.

Mentored Experience Requirements

Doctoral students at Washington University must complete a department-defined Mentored Experience. The Mentored Experience Requirement is a doctoral degree requirement that is notated on the student’s transcript when complete. Each department has an established Mentored Experience Implementation Plan in which the number of units that a student must earn through Mentored Teaching Experience(s) and/or Mentored Professional Experience(s) is defined. The Mentored Experience Implementation Plans outline how doctoral students within the discipline will be mentored to achieve competencies in teaching at basic and advanced levels. Some departments may elect to include Mentored Professional Experiences as an avenue for completing some units of the Mentored Experience Requirement. Doctoral students will enroll in ASGS 8005, 8010, or 8015 Mentored Teaching Experience - Assistant in Instruction; ASGS 8020 Mentored Teaching Experience - Mentored Independent Teaching; or ASGS 8120 Mentored Professional Experience to signify their progression toward completing the overall Mentored Experience Requirement for the degree.

The Doctoral Dissertation

A Research Advisory Committee (RAC) must be created no later than the end of the student's third year; departments may set shorter timelines (e.g., by the end of the student's second year) for this requirement. As evidence of the mastery of a specific field of knowledge and of the capacity for original scholarly work, each candidate must complete a dissertation that is approved by their RAC.

A Title, Scope & Procedure Form for the dissertation must be signed by the committee members and by the program chair. It must be submitted to the Office of Graduate Studies, Arts & Sciences, at least six months before the degree is expected to be conferred or before the beginning of the fifth year of full-time enrollment, whichever is earlier.

A Doctoral Dissertation Guide and a Dissertation Template that give instructions regarding the format of the dissertation are available on the website of the Office of Graduate Studies, Arts & Sciences. Both should be read carefully at every stage of dissertation preparation.

The Office of Graduate Studies, Arts & Sciences, requires each student to make the full text of the dissertation available to the committee members for their review at least one week before the defense. Most degree programs require two or more weeks for the review period; students should check with their faculty.

The Dissertation Defense

Approval of the written dissertation by the Research Advisory Committee (RAC) is strongly recommended before the student can orally defend the dissertation. The Doctoral Dissertation Committee that examines the student during the defense consists of at least five members. Normally, the members of the RAC also serve on the Doctoral Dissertation Committee. The dissertation committee is then additionally augmented to ensure that the following criteria are met:

1. Three of the five members (or a similar proportion of a larger committee) must be full-time Washington University in St. Louis faculty members or, for programs involving Washington University in St. Louis-affiliated partners, full-time members of a Washington University in St. Louis-affiliated partner institution. All members must be authorized to supervise PhD students and have appropriate expertise in the proposed field of study. One of these three members must be the PhD student's primary thesis advisor, and one may be a member of the emeritus faculty.
2. All other committee members must be active in research/scholarship and have appropriate expertise in the proposed field of study whether at Washington University in St. Louis, at another university, in government, or in industry.
3. At least one of the five members must bring expertise outside of the student's field of study to the committee, as judged by the relevant department/program and approved by the Office of Graduate Studies, Arts & Sciences.

The approval processes outlined in the RAC section of the Doctoral Council bylaws also apply to the doctoral dissertation committee, including approval of each dissertation committee by the Office of Graduate Studies, Arts & Sciences.

The student is responsible for making the full text of the dissertation accessible to their committee members for their review in advance of the defense according to program rules. Washington University in St. Louis community members and guests of the student who are interested in the subject of the dissertation are normally welcome to attend all or part of the defense but may ask questions only at the discretion of the committee chair. Although there is some variation among degree programs, the defense ordinarily focuses on the dissertation itself and its relation to the student's field of expertise.

Attendance by a minimum of four members of the Doctoral Dissertation Committee, including the committee chair and an outside member, is required for the defense to take place. This provision is designed to permit the student's defense to proceed in case of a situation that unexpectedly prevents one of the five members from attending. Students should not plan in advance to only have four members in attendance. If four members cannot attend, the defense must be rescheduled. The absence of all outside members or of the committee chair also requires rescheduling the defense.

Students, with the support of their Doctoral Dissertation Committee chair, may opt to hold their dissertation defense in person or by utilizing a virtual or hybrid format.

Submission of the Dissertation

After the defense, the student must submit an electronic copy of the dissertation online to the Office of Graduate Studies, Arts & Sciences. The submission website requires students to choose among publishing and copyrighting services offered by ProQuest’s ETD Administrator. Students are asked to submit the Survey of Earned Doctorates separately. The degree program is responsible for delivering the final approval form, signed by the committee members at the defense and then by the program chair or director, to the Office of Graduate Studies, Arts & Sciences. Students who defend their dissertations successfully have not yet completed their PhD requirements; they finish earning their degree only when their electronic dissertation submission has been accepted by the Office of Graduate Studies, Arts & Sciences.

As part of their degree requirements, PhD students must complete a program-defined Mentored Experience Requirement (MER) as per these guidelines. The Mentored Experience Implementation Plan (MEIP) is the written articulation of a program-defined degree requirement for PhD students to engage in mentored teaching activities and/or mentored professional activities, collectively referred to as MERs.

Mentored Experience Requirements (MERs)

Philosophy of Teaching

Effective communication of information and concepts is a critical skill for biomedical research scientists. Although much of the teaching that scientists engage in is through one-on-one interactions with individuals in the laboratory, all scientists must have fundamental instruction in and experience with pedagogy principles, be able to deliver effective lectures to a wide audience, and be prepared to teach courses to undergraduate and graduate students. These represent the goals of the required Mentored Teaching Experience (MTE).

Preparatory Engagement

Preparatory Engagement activities are those that represent an introduction to the foundational skills associated with teaching or communication. Pedagogical preparation engagement activities are normally completed before students are permitted to engage in assisting or teaching in a classroom.

Prior to beginning their MTE and typically during their second graduate year, Division of Biology & Biomedical Sciences (DBBS) students will be required to complete the Graduate Student Teaching Orientation and two additional teaching workshops offered by the Center for Teaching and Learning. Students will meet with assigned course director(s) prior to the start of the semester and complete a teaching expectations form. 

Mentored Teaching Experiences (MTEs)

Assistant in Instruction (AI)

An Assistant in Instruction (AI) is a PhD student who is directly engaged in the organization, instruction, and/or support of a semester-long course primarily taught by a faculty member. An AI receives mentorship from a faculty member related to best practices in classroom engagement, instruction in the field, interpersonal engagement, and other relevant skills. Students and mentors complete a mentorship plan prior to the start of each AI experience. To complete each AI assignment and to ensure that it applies toward their degree requirements, students must register for the appropriate course number for each semester of engagement. Refer to the "Required Pathways for Completion" section below for course numbers and details.

DBBS students will serve as mentored AIs in courses approved by the Associate Dean. Units for a given course will be determined ahead of the assignment. A unit is equivalent to approximately one hour per week, so 5 units would involve five hours of support (on average per week) for a course. The PhD student is formally listed as instructional support in the course listings and receives mentorship from the faculty member in best practices for classroom engagement, instruction in the field, interpersonal engagement, and other relevant skills. The mentored teaching training must incorporate at least one of the following activities: delivering lectures, leading lab activities or discussion groups, or conducting review sessions for groups of students. Grading exams or papers, holding office hours, administrative tasks, one-on-one tutoring, and so on may also be components of the assistantship and should be counted in the 5 units; however, these activities are not sufficient to meet the DBBS teaching training requirement. In general, AI assignments connect to undergraduate or lower-level graduate courses that the AI has taken previously. Students must enroll in ASGS 8005 during the semester(s) of their assigned MTEs. 

The PhD student should receive regular feedback or evaluation from the mentor throughout the semester, a formal evaluation of teaching skills by the faculty at the end of the semester, and evaluation by the students at the end of the term as part of the course evaluation. If the course director determines that the PhD student's facility with essential teaching skills is unsatisfactory, the student will be counseled by the course director and the Associate Dean of Graduate Education and then will complete another MTE to attain mastery of these skills. Mentored teaching opportunities will be reviewed annually to ensure that the experiences meets the requirements established in this policy.

Required Pathways for Completion

Students work with their faculty mentor and their Director of Graduate Studies to plan how and when they will complete their MERs. Students register during the normal registration period for courses in accordance with one of these approved pathways.

• Preparatory Engagement completed during the first year

Pathway #1

UG Spanish Seminar

ASGS 8005	Take one time

Optional Activity: Professional Intensive Pathway (PIP)

The PIP is an optional pathway for those students whose career interests lie outside of academia or who want to benefit from mentored professional experiences (MPEs). An MPE is an unpaid professional experience for PhD students that allows students to develop skills and experiences relevant to their intended career outcomes. Students and mentors complete a mentorship plan prior to the start of each MPE. Students who are interested in participating in this elective experience must formally request to participate, which is subject to program approval. Due to this experience being an elective, unpaid experience, students who participate in the PIP will not receive compensation. 

Students and mentors complete a mentorship plan prior to the start of each MPE. To complete each MPE assignment and ensure that it applies toward their degree requirements, students must submit the Mentorship Registration Request form for approval and register for the appropriate course number (ASGS 8120) for each semester of engagement.

The DBBS MPE via the PIP is an optional activity. Students should engage in activities that enhance their professional development and record these activities at their thesis update meetings. For some students, an optional MPE is encouraged. The DBBS MPE can be fulfilled by a wide range of activities that advance the careers and professional development of DBBS PhD students. These could include, for example, opportunities in biotech or pharmaceuticals (including at a startup or established company); science communication; science outreach; diversity, equity, and inclusion work; government or policy opportunities; consulting; or higher education administration. Academic-track students may use the MPE to learn a new technique at a core facility or other lab. The duties and responsibilities of the MPE should be intellectually substantive and offer opportunities for the student to develop new skills and experiences. MPEs are distinct from internships in that they are considered part of the PhD training and are recorded on students' transcripts as courses. The scope of the MPE will be determined in conversation among the student, the site mentor, and DBBS staff, and the final plan must be approved by the principal investigator and the program director. An average of 10 hours per week of MPE for a total of 150 to 180 hours is expected for each student. The nature of some MPEs may take students away from their academic pursuits for full-time participation. In these cases, coverage of a percentage of the student's stipend may be pursued by consulting DBBS leadership.

Prior to the start of an MPE, the student and the site mentor will submit a plan to DBBS detailing the scope of the project(s) to be undertaken and including a schedule and list of anticipated outcomes, and the mentor will provide an explicit commitment to the mentorship. This plan should be directly related to the goals developed via the student's recent completion of an Individual Development Plan, and students should enroll in ASGS 8120. During the semester, the mentor and the mentee should meet frequently (i.e., weekly or biweekly) to track the progress of the student's work. At the end of the MPE, the mentor should provide a written assessment (approximately 500 words) of the overall learning experience for the student and the quality of the work completed, and the student will submit a self-reflection statement detailing the skills and experiences gained and how their career goals may (or may not) have changed. The mentor will register the completion of ASGS 8120 as Pass/No Pass.

Optional Pathway

UG Spanish Seminar

ASGS 8120	Take one time