Gene/DevBio/Bio203, "Advanced Genetics"

Fall Quarter 2010, 4 Units


Stuart Kim, Arend Sidow, and Tim Stearns

Teaching Assistants

Biff Mann, Edward Grow, Elizabeth Finn, Kathleen Xie. Click link for office hours/locations.


All students will meet Tuesday and Thursday, 9:00 AM - 10:50 AM, in LK101 (except on 11/11 when class meets in LK130).


Discussion sections will meet in various rooms at various times TBD.

This link to section assignments will be active as soon as assignments have been made.

Online Class Resource

Please refer to the course's site as your main web resource for this course.

Nature of the course

This course is designed for graduate students enrolled in the Ph.D. programs of any of the Biosciences Departments and Programs at Stanford University. Our emphasis is on developing the ability to solve problems using genetic ideas and methods, to understand the nature and reliability of genetic inference, and to apply genetic reasoning to biological research. The format is lectures twice a week, and a discussion session once a week. The discussions are (mostly) based on original research papers that define or illustrate the ideas and techniques covered in the lectures. It is essential that students read and understand the assigned readings in detail.


All students should have a working knowledge of basic concepts of genetics and molecular biology. If you are uncertain of your preparation, we urge you to review by reading and, more importantly, solving the problems in a good undergraduate genetics textbook. We recommend for this purpose any of several upper-level textbooks, such as
An Introduction to Genetic Analysis (Griffiths et al.) or
Genetics: from Genes to Genomes (Hartwell et al.) or
Genetics: Analysis of Genes and Genomes (Hartl and Jones)
You may also be interested in
Principles of Population Genetics (Hartl and Clark) and
Human Genetics: Problems and Approaches (Vogel and Motulsky)
Much of genetics, both "classical" and "genomic", depends on statistical analysis of experimental or observational data. In general, the more statistics you know, the better. At a minimum, if you do not have a strong working knowledge of undergraduate-level biostatistics, we recommend Biometry (Sokal and Rohlf) or Biostatistical Analysis (Zar).


The discussion sections work only if the number of students per section is small. Our priorities are to serve incoming Ph.D. and M.D.Ph.D. graduate students first, other students enrolled in graduate programs second, and to allow enrollment of undergraduate students only in special cases and by permission of the instructors. In particular, this course is not a suitable substitute for undergraduate genetics courses offered by the Biology department.

Course Requirements and Grades

The course grade will be based on four criteria:

  • eight weekly problem sets (5% each set)
  • a take-home final examination (30%)
  • participation in discussion section (30%)
  • Problem sets

    The purpose of the problem sets is to reinforce and further explore concepts and principles presented in class time and section. Students are encouraged to work together to discuss the problems but the answers need to be provided as an individual effort. Problem sets will be posted under "Assignments" on the coursework site.

    Discussion sections

    The weekly discussion sections are an essential part of learning about genetics. Most weeks, one or two research papers will be critically analyzed. The focus will be on the genetic logic used to dissect diverse biological processes. Students must thoroughly read the papers beforehand, and come prepared to discuss the experiments in depth.

    To help develop an ability to read and think critically, students will hand in short analytic proposals for four of the section papers. These proposals should focus on how the work described in a discussion paper might be carried one step further using a genetic method of your choice, and should demonstrate an understanding of the paper's main findings and limitations. Each proposal must be specific and well-defined, and must be less than 250 words. Here are some examples from a paper we did in previous years.

    The choice of which four of the discussion papers are used for the analytic proposal is completely up to the student. Proposals should be turned in at the beginning of the section, and the content of the proposals will be discussed by the group at the end. Attendance at, preparation for, and participation in discussion sections (together with completion of the four analytic proposals) will count towards 30% of the overall grade.

    Two out of the eight discussion sections will be spent solving a mock research project; one will be a mutant hunt, the other a structure/function analysis extravaganza.

    The section papers and schedule are posted on the 203 coursework web site off the "Materials" link.

    Final exam

    A take-home final exam will be handed out Thursday 12/02/2010, due back Tuesday, 12/07/2010, and will be designed similarly to the problem sets in both concept and level. The final exam is "open-book" (and open-note and open-internet), but unlike the problem sets, cooperation or discussion among students is not permitted. Students are expected to behave according to the Stanford honor code.