1. Genetics 701, Advanced Genetics, 3 credits- Year 1 Fall
2. Genetics 708, Methods and Logics in Genetic Analysis, 3 credits- Year 1 Spring
3. Med Genetics 702, Advanced Genetics, 3 credits- Year 1 Spring
4. Med Genetics 707, Genetic Analysis of Human Biology, 3 credits- Year 2 Spring
5. Oncology 675, Appropriate Conduct in Science, 1 credit- Year 2 Spring
6. Elective: Any graduate level Genetics course (including special topics) or Biochemistry 620
7. Four seminars
8. Specialized elective coursework at the discretion of your thesis committee
Descriptions of courses, as well as information about when they are offered can be found here.
Evaluation of performance
Your continuation is dependent on satisfactory performance. The Graduate School requires an average of a B (3.0) or better in all coursework taken as a graduate student. However, Genetics considers anything less than a B in any major courses as unsatisfactory.
The normal full-time enrollment is 8-12 graduate credits during Fall and Spring semesters. You may not register for more than a total of 12 credits. The majority of your courses should be in the 600-999 range, but courses numbered 300-599 may be taken for graduate credit if in outlined in the course attributes of the catalog.
An orientation will be held the week before classes start for your first year. During orientation you will fill out the required paperwork for payroll and for insurance and register for your classes. Most of the week will be spent with scheduled rotation talks given by faculty and trainers who are recruiting graduate students to join their lab.
In your first semester, you will spend time in the labs of three or four professors whose work interests you. One of these will probably become your major professor. Arranging these round robin lab rotations is, therefore, one of the most important things that you will do in your first year in Madison. The brief descriptions of research given in the rotation talks should assist you in selecting the laboratories to visit. Expect to spend about four to five weeks in each of the three to four labs during the first semester.
Students are responsible for scheduling their own rotations. You may start scheduling these as soon as you hear a rotation talk of interest. Feel free to consult the Student Services Coordinator if you need help in choosing labs to visit. To avoid disappointment, you should plan to do your rotations through the laboratories of trainers in the Genetics Program who have openings. It is suggested that three or four rotations be completed by the end of the fall semester. Your schedule should be registered with Martha Reck (firstname.lastname@example.org) as soon as it is established.
Selection of a Major Professor
Normally students will decide on a major professor in mid-December. Until a major professor is determined students will be assigned to a member of the First Year Committee.
Your first paycheck will arrive October 1.
Building Access and Mail
You will be issued keys, as needed. As you set-up rotations, be sure to speak with the professor about what spaces and buildings you need to access. Your student ID will allow you entrance into the Genetics building after hours by electronic swipe. Please see Marj Haanstad (1432 Genetics) to obtain keys and building access. In 1422 Genetics there is a mailroom, all new students mail will be in the box labeled New Grads. 1421 Genetics is available as work space/office space for new students.
When you have identified a major professor and joined their lab, that professor will assume the duties of your primary advisor. At that time you will form a PhD Advisory Committee consisting of three to five faculty members (ultimately it must be five) three of whom must be Genetics trainers, including two members of the Laboratory of Genetics faculty, and one minor advisor, if needed. The PhD Advisory Committee should be established no later than the end of the second semester. Under normal circumstances, the committee membership will remain in effect for the entire tenure of the student's graduate career.
The PhD Advisory Committee will advise you with regard to major and minor requirements, certification, teaching requirements, and research topic and execution. It will also act as your Prelim B Examination Committee and as the Final Oral PhD Examination Committee. After your major professor, this committee is the primary monitoring instrument to assure satisfactory progress toward your degree. The PhD Advisory Committee will meet with you at least once per year. During these annual meetings anticipated timelines for progress of the thesis project should be discussed and concrete guidance should be given about completing the thesis. The annual committee meeting form will be completed each year prior to Fall Term. The meeting and form must be completed for you to register for (and be paid for) Fall term. The annual meeting should address the assessment or your progress and outline any suggestions or recommendations, in addition to verifying the discussion of your Individualized Development Plan.
A good guideline for the annual meeting is to prepare ~20-30 slides (which will expand to a longer discussion with questions from your committee). Your presentation should include an update on your progress, restating your aims (or changes made to the original aims), and should also provide a plan for future directions and a timeline for completion through to graduation. Remember to complete your Annual Committee Form and send it out to your committee before the meeting. Completed forms should be turned into Martha Reck in 1426 Genetics.
Certification is a planning process in which you and your committee decide the courses needed to prepare you for your chosen field. The process of certification should be completed as soon as possible. Most students schedule their certification meeting in the spring semester of their first year. You and your major professor should agree upon the minor field or the minor option before presenting your proposal to your committee. It is your responsibility to contact the minor professor, if you choose to do an external minor.
It is useful to prepare a short (15-20 slides) presentation of what your project is/will be so that your committee has an idea of your research area. Together, you will decide upon the specific course work necessary to ensure that your curriculum satisfies both the major and minor departmental and Graduate School requirements. Courses suggested by the committee may be influenced by your research topic and past courses you have taken, which are to be summarized on the Certification form.
All students are required to be a teaching assistant for one semester for an undergraduate general Genetics class (Genetics 466, 467 or 468). Responsibilities include leading discussions sessions and holding office hours weekly. In addition, most TA’s provide exam review sessions. You will TA during your second year, a week long required training will be held the summer before.
Prelim A is a week-long written take-home examination. The purpose of the Preliminary A Examination is to evaluate your general knowledge in genetics, your competency in critically analyzing original genetic literature and your ability to formulate experimental solutions to genetic problems. Administration of the Prelim A exam is the responsibility of the Preliminary A Examination Committee, a standing committee of 5-6 faculty and up to two graduate students of advanced standing (i.e., who have passed Prelim A).
You will take the Prelim A Examination at the end of your fourth semester, usually during the first week of June. The exam is handed out on a Monday morning and turned in the following Friday afternoon.
designed to take students from two hours to a half-day. The emphasis is on problem solving that draws on knowledge of fundamental aspects of a genetic sub-discipline, including the ability to integrate the use of multiple concepts and analytical approaches.
During the exam students are free to use any published references and any databases to answer the questions, and may contact the Exam Committee chair if in need of clarification. While taking the exam students may not consult any other person for help in answering the exam questions.
Students identify their exams with a code rather than their name, so that grading is double-blind until after the prelim committee has met and finalized the exam results, at which time the exams will be decoded. This process ensures that graders and the Prelim Committee do not know the identities of students until after the results are finalized.
There are two graders for each prelim question. One person is the author of the question. Both have copies of the student’s exam answers. Each grader reviews the question and assigns a score. The two scores are averaged to give the final score for the question. The two graders may confer on scoring but are not required to do so.. After grading is complete the Prelim Committee reviews the scoring of all the questions across all exams and finalizes the outcome.
5 excellent- perfect or nearly perfect answer, with only minor errors or omissions.
4 good- may contain a few errors or lack organization or clarity, but generally indicates a grasp of the subject.
3 borderline- acceptable, but has substantial errors or omissions. It may also lack organizational clarity. A score less than 3 is considered unacceptable.
2 poor- major errors or omissions.
1 completely unacceptable- little or no work towards an acceptable answer.
To pass the exam a student must have an overall average score of 3.0 or better and a grade of 3.0 or better on at least 2/3 of the exam questions (interpreted as at least 6 out of 10).
Students are allowed to request re-grading of one or more questions. Such requests are addressed in writing to the Prelim A Committee Chair, who then makes arrangements with the original graders. Re-grade results are reviewed by the Prelim A committee before a final decision is returned to the student.
If a student fails to pass the Preliminary A Examination on the first try, a second chance (i.e., to retake the following year) is automatically granted. A second failure nominally results in dismissal from the Program, although dismissal may be appealed by the student to the Genetics Graduate Curriculum Committee.
You will take the Prelim B Examination within one year of completing the Prelim A Examination. It is recommended that students should meet with their full committee (5 members) after their first summer colloquium (if not before) in order to set a timeline for Prelim B. Should a student fail the Prelim A on the first try, Prelim B may be taken before retaking the Prelim A Examination at the discretion of the student's Committee. Satisfactory completion of the Prelim B, along with relevant course, teaching, and minor requirements, is necessary for a student to acquire dissertator status.
The Prelim B generally consists of 30-40 minutes of presentation and allows for 1-2 hours of questions and answers. Questions typically focus on the proposal and presentation, however can be more far ranging or probe for a genetic concept or method. The questions are at the committees discretion.
The Prelim B Examination determines each student's future in the training program. Three outcomes are possible:
1.the student is given a pass and admitted into candidacy for the Ph.D. degree,
2.the student is given a deferred decision with a further meeting with the Prelim B Committee within six months to determine pass or fail, or
3.the student fails the exam outright and plans are formulated for early withdrawal from the program, usually with a Masters degree instead of a Ph.D.
Prior to taking prelim B, you must request from Martha Reck (email@example.com)a preliminary examination warrant from the Graduate School. You must request the warrant 2-3 weeks prior to the proposed exam date. If the residence requirement has been met and all unsatisfactory grades have been cleared or compensated, the warrant is issued. After you have passed prelim B, the warrant is signed by the members of your prelim committee and submitted to the Martha Reck. If your records are in order, you are formally admitted as a candidate for the Ph.D. degree.
You must maintain continuous registration from the time of admission to candidacy until all degree requirements have been completed, even if you should leave campus. A candidate for the Ph.D. degree who fails to take the final oral examination within five years of submitting the signed warrant may be required to take another preliminary examination to be admitted to candidacy a second time.
Proposals for Prelim B Examination
The purpose of the following outline is to provide some guidance for students as to the form and function of Prelim B proposals. The scaled down model for the particular version used below is the NIH plan for Public Health Service grants. As in the case of a "full-scale" grant proposal, your goal should be to persuade a reviewing group that your goals are interesting and important, that you have chosen a plan of experimentation that is highly likely to return interesting and interpretable results in a reasonable time frame, and that you have the background and understanding to bring this plan to fruition. In any such proposal, clarity is key. The people who review the proposal will not all be experts in your field and you must therefore provide significant information to document the above goals to this group. In line with this idea, you should avoid unnecessary arguments and information, since they will distract from the essential arguments. Begin the overall outline of the proposal well before the fact and discuss the goals and approaches with others before writing the proposal. You are therefore strongly encouraged to obtain input from other students and colleagues, and particularly from your advisor, prior to distribution of the proposal to your committee. The proposal description below contains information about the overall structure of the proposal as well as suggestions about each of the individual sections. If you have further questions concerning the proposal, contact either your research advisor or the Program Director.
This is the critical initial contact with the reader. Distill the necessary parts of your proposal down to one‑half page or less, stating the problem and what you intend to do about it. Make it understandable to the intelligent, but inexpert, reader.
Under the Major Goal of your proposed thesis, list the specific questions in your research and the specific approaches that will be used to address each of those questions. This is typically done in an outline form of no more than one‑half page. It should also provide the framework for the Experimental Design section, so its organization is key to the entire proposal. Try to be realistic and propose an amount of work that you are likely to accomplish in the next 2‑3 years; excessively optimistic proposals suggest a lack of critical thought. Like all research proposals, Prelim B should not be viewed as a contract; the successful dissertator may pursue other related topics/aims for completion of the Ph.D. The purpose of Pelim B is to demonstrate the ability to synthesize in writing a reasonable and coherent research plan and to discuss it intelligently with one’s faculty committee. It is often advisable to divide the following sections into subsections with titles to orient the reader.
Background and Significance: This section should be several pages long and contain enough information to make the subsequent sections understandable to the reader. It should also give the reader an understanding of the state of the field before your participation. It should therefore cite any critical information that is either published, or known to you through personal communication. Your accomplishments will be described in the following sections, but it may be necessary to allude to some of your results in this section for clarity or argument. Results from others in your laboratory should be described in this section. This section should also serve to convince the reader that the general questions chosen is in important one.
Your Results To Date (Previous Results):
Describe the progress you personally have made while in the lab. The goal of this section is to convince the reader that you have made some progress and/or that you have developed laboratory and analytical skills that will be necessary to complete the proposed work.
Typically the sections in this part will follow in the order laid out in the Specific Aims. The goal here is to show that the approach you have chosen will yield interpretable results and that you really understand those approaches. If there are intermediate goals that are absolutely critical to the whole project, either defend why your single approach must work, or propose alternative "backup" approaches. Provide enough information to make it clear that you understand each technique; this does not mean an abundance of detail, but a terse description of potential problems and shortfalls in the experiment or its analysis. If there are obvious experiments that will not be done, briefly say why. Throughout this section, make your priorities clear; not every experiment is equally important, and some approaches will be pursued only under certain circumstances. Continually orient the reader by explaining how each intermediate goal fits into the overall plan.
This short section should be a realistic estimate of when the critical intermediate goals in the proposal will be accomplished. It should also make clear when the primary approaches will be dropped and the alternatives adopted. You wish to show that, no matter what happens, you will return with an investigation suitable for a thesis in a reasonable time period, no matter how the “cards fall”.
Using a standard format (authors' names and journal citation including titles), list the references cited throughout the proposal. This should not only document your understanding of the current state of information, but also that you know the critical sources of information on the methods you have proposed to use.
It is suggested that you keep the proposal, including figures and tables, but not the literature cited, to no more than 15 double‑spaced pages. This is the scale permitted in a laboratory-scale research proposal. Thus, your single-investigator proposal can be developed deeply. Use 1" margins, 12‑pt type, and page numbers throughout the proposal. Be sure to confer with your thesis committee regarding expectations.
Your thesis must be submitted to your committee members no later than two weeks before the date of the examination. You have five years from the date of passing your prelim exams to take your final oral exam and submit your dissertation. At least three weeks prior to your final oral exam you must request a warrant from Martha Reck (firstname.lastname@example.org).
To pass the examination, you must receive no more than one dissenting vote from your committee. A missing signature is considered a dissent. After you pass the exam, the committee must sign the warrant and the warrant must be submitted during the final review appointment.
The Committee must consist of at least five current graduate faculty members (UW-Madison) of professorial rank with at least one of the five from outside the major department, this is usually the minor professor if you are pursuing the external minor. At least two members must be Laboratory of Genetics faculty, and three members must be trainers. With permission of the candidate, other faculty members might be invited to participate in the examination.
After the exam, you must submit to the Graduate School a completed and approved library copy of your thesis and appropriate additional documents, and pay the required fee for microfilming and binding the thesis. With the appropriate receipts, you then submit your thesis to Memorial Library. You must also submit a final bound copy of your thesis to the Genetics department, as well as a copy to your major professor.
In addition, you must have a final review appointment with the Graduate School and notify the Payroll and Benefits Specialist of your resignation.
Changing Major Professor
If you fail the Ph.D. preliminary examination and do not choose to retake it, or fail the examination twice, or for other reasons choose not to be a Ph.D. candidate, you may still earn a Master's degree provided that you complete the requirements.
Parking and Bus Passes
You will need your WISC card to ride the Metro buses and campus bus lines.
Colloquium- Every Wednesday at 3:30 during Fall, Spring, and Summer terms Genetics hosts a colloquium presentation. Fall and Spring are invited speakers. During Summer the Colloquium is presented by 3rd and 4th year (and older) students.
Retreat- Each Fall Genetics hosts an annual retreat to promote interaction between members of the genetics community on campus.
Smithies Symposium- Each May Genetics hosts the Smithies Symposium.
New Student Recruitment
Every January and February potential new Genetics PhD students are invited to campus for three days to meet with faculty, meet with current students, learn about research happening with genetics, and explore Madison. Current student participation is vital in this recruitment and selection process. Current students will participate in lunches, dinners, meetings and tours.
You will be required to take a series of online courses (Biosafety 101, 104, and 201) designed to inform and prepare you for work in campus biological research laboratories in compliance with standards set forth by the NIH and CDC. Courses are taught through Learn @UW. Information is available at: http://www.ehs.wisc.edu/biosafetytraining.htm
You will also be required to take an in person chemical safety class. This courses teaches you how to work safely in the laboratory with hazardous materials in accordance with the OSHA Lab Standard. It is available for registration through UW-Madison’s OHRD site: https://www.ohrd.wisc.edu/OHRDCatalogPortal/Default.aspx?tabid=29&CourseGroupKey=18911
|Gilbert, Zhang, Hansen, Mayer, Robinson, Winden
Dean, Murphy, Young, Chevrette, Onder
||Yoon, Pfannenstiel, Tuholski, Lange, Cyrus, Santistevan, Sprengelmeyer,
Seitz, Serre, Frayer, Marischu, VandenHuevel, Bortolazzo
Robinson, Peterson, Crocker,
| 2012 Class
Langdon, Lewis, Keel
| 2011 Class
Welch, Jessen, Gnazzo, Shao, Wu,
| 2010 Class
Dimitrova, Traeger, Lucas, York,
| 2009 Class
Woods, Forshey, Muir, Gratz, Eno,
Rytz, Cao, Henning, Pleiman, Lamb,
| 2008 Class
Kang, Cunningham Williams,
Stone Travel Award
Genetics students are eligible to apply for the Stone Travel Award for funding to attend conferences or meetings in which they are giving an oral or written presentation. To apply send the following to Bill Engels (email@example.com) and Martha Reck (firstname.lastname@example.org):
Name of Genetics Graduate Student
Title of meeting
Location of the meeting
Dates of meeting
Estimated total cost of travel
Brief statement from faculty mentor supporting the nomination and indicating whether the student would attend the meeting without an award.
Training Grant Travel Funds
Genetics students may be eligible for a small amount of travel money while on the training grant. Please contact Pat Litza (email@example.com) for details.
Professional Development Opportunities
WARF Ambassador program:
WARF Ambassadors receive training in WARF's technology transfer process and learn how to access resources offered by WARF and other campus organizations designed to support technology development and entrepreneurial activity. They spend five to 10 hours per month promoting awareness of WARF's role across campus and WARF's engagement with campus research through departmental seminars, informal contacts and more.
Wisconsin Entrepreneurial Bootcamp:
The Wisconsin Entrepreneurial Bootcamp (WEB) is a one-week intensive training program in technology entrepreneurship for graduate students in the sciences, engineering, and math.
R short courses:
Special Topics course is the prototype for a new statistics course suite, Stat 327, "Learning a Statistical Language." Each 1-credit module will be half-semester in length: Beginning Data Analysis with R, Intermediate Data Analysis with R, Advanced Data Analysis with R:
Courses on teaching through the Delta program:
Examples include Teaching in Science and Engineering, Effective Teaching with Technology, and others.
Mentored Research Training:
The Delta Program (through an NIH grant with ICTR) offers a 1-credit course on Research Mentor Training
Outreach and training opportunities through WiSCIENCE:
Programs and resources to provide training and activities to educators.
Campus Information- Individualized Development Plan:
Science Career IDP Template:
OHRD – Principals of Supervision and Management:
11 half-day or 5 1/2 full day workshops. These are foundation workshops intended primarily for new managers and supervisors.
A full library of self-study software (Adobe, Office, lots more)
DoIT Student Technology Training – (Students Only):
In person trainings (LaTeX, Excel, Python, Adobe)
Doctoral minor in entrepreneurship:
Certificate in strategic innovation:
Graduate certificate in bioinformatics: