Program description
Recent technological advances have transformed genetics research, and major shifts have occurred in best practices for graduate education, research training, and mentoring. The Genetic Mechanisms and Evolution (GME) Training Program, funded by an NIH T32 predoctoral training grant, is designed to meet these challenges. Students will develop multidisciplinary competence in molecular, statistical, and evolutionary genetics research, with strong foundations in quantitative analysis and scientific communication. The GME program emphasizes a positive training community with regular student advising, mentor training for PIs, peer-peer support, and opportunities to engage with societal dimensions of science.
Program structure
Trainees will be funded as NIH appointees in Years 2 and 3 of their studies, but they will participate in the GME program from matriculation to graduation.
- Year 1: Students are prepared for potential future appointment as GME trainees. They take GME-required courses and participate in the GME annual retreat, and they may participate in the hackathon and workshops (but this is not required). They receive advising from GME directors and peer mentoring from senior GME trainees.
- Years 2-3: Appointment as NIH-funded GME trainees. Students conduct research in labs of GME-approved trainers. They participate in a software hackathon and workshops on scientific writing and best practices in quantitative and computational analysis. They receive advising from GME directors and participate in peer mentoring and the GME annual retreat.
- Years 4+: Students continue their research in GME trainers’ labs. They receive advising from the GME program directors and training in oral presentation. They also serve as peer mentors and participate in the GME retreat.
Nomination and appointment process
At the end of each Spring quarter, graduate programs will nominate
- Rising Y2 and Y3 students for appointment as funded GME trainees, and
- Incoming Y1 students for participation in the GME program
Students are eligible if their research interests are in any area of genetics. Funded appointees must perform their research in the laboratory of a GME-approved trainer. Reappointment for Y3 is expected, subject to annual evaluation of the student and trainer. Participation during Y1 is strongly encouraged but not required for a student to be nominated for Y2 or Y3. Students in any BSD doctoral training program may be nominated.
Nominations are evaluated by the GME steering committee based on the following criteria: potential for scientific excellence (based on prior experience and Y1 coursework and rotations, if applicable), fit to the GME program area (i.e., strong interest in genetics, ideally with interdisciplinary interests), potential to benefit from the GME program, intent to perform research in the laboratory of a GME-approved research advisor (for Y2/3 students), potential for positive engagement in the GME community, and potential contribution to an engaged and diverse GME community.
Course requirements
GME trainees must fulfill the following course requirements. We have attempted to harmonize these requirements with those of the participating graduate programs to the greatest extent possible.
- Core course: All Y1 GME students should take the GME core course, Genetic Mechanisms from Variation to Evolution (HG 47500) during Autumn Quarter of their first year of graduate school. This course provides a rigorous interdisciplinary introduction to molecular, statistical, and evolutionary genetics.
- Statistics and programming fundamentals. GME trainees must take at least one graduate course in fundamentals of probability and statistics, unless they already have equivalent proficiency (to be determined by the GME directors). This requirement should generally be fulfilled in Y1. For most students, we recommend STAT 23400 Statistical Models and Methods. Students with a strong background in statistics, or whose research is focused on statistics and computation, should take Fundamentals of Probability and Statistics (STAT 24400). Statistical Methods and Applications (STAT 22000), Probability and Statistics for Geneticists (HGEN 47400 – Autumn Quarter), or Fundamentals of Biological Data Analysis (BCMB 33500, Winter) can also fulfill this requirement. Students who already have extensive training in probability and statistics may be excused from this requirement at the discretion of the GME directors.
- Breadth requirement: GME students are required to take at least one approved course in each of three major areas. These courses must be taken for credit. We recommend fulfilling as many of these requirements as possible during the first year of study, but continued coursework in the second year is acceptable.
- Genetic Mechanisms. Molecular Biology I: Mechanisms of Prokaryotic Transcription and Regulation and Prokaryotic and Eukaryotic Replication (MGCB 31200); Molecular Biology 2: Eukaryotic Gene Expression and Regulation (MGCB 31300); Genetic Analysis of Model Organisms (MGCB 31400); Genomics and Systems Biology (HGEN 47300); Developmental Mechanisms (BIOS 21237); Protein Fundamentals (BMB 30400); Biophysics of Biomolecules (BCMB 32200); Biophysics of Biomolecules); Neurogenetics (NURB 33480); Evolution of Biological Molecules (BCMB 31100)*; Decoding and engineering genes and genomes (HGEN 47900)*.
- Computational/Statistical Approaches to Genetics. Introductory Statistical Genetics (STAT35490); Fundamentals of Computational Biology: Models and Inference (HGEN 48600); Fundamentals of Computational Biology: Algorithms and Applications (HGEN 48800); Quantitative Genetics for the 21st Century (HGEN 47800*); Decoding and engineering genes and genomes (HGEN 47900)*.
- Evolution. Evolution of Biological Molecules (ECEV 31100)* ; Principles of Population Genetics (ECEV 35600); Molecular Phylogenetics (HGEN 36400 – not offered 2023); Molecular Evolution (ECEV 44001/2); Human Variation and Disease (HGEN 46900); Reconstructing the Tree of Life (EVOL35401); Evolution and Development (ORGB 33850); Quantitative Genetics for the 21st Century (HGEN 47800*), Macroevolution (EVOL 31700).
* Decoding and Engineering Genes and Genomes can fulfill the requirement for Area A or Area B but not both. Quantitative Genetics for the 21st Century can fulfill the requirement for a course in Area B or Area C, but not both. Evolution of Biological Molecules can fulfill the requirement for Area A or C but not both.
Other Training Activities
During your time as a GME trainee, you will participate in programmatic activities that we will offer, as described below.
GME research hackathon. To engage in team-based science and strengthen rigorous/reproducible research practices, we will host a GME hackathon annually. Participation in at least one hackathon during Y2 or Y3 is required. Participants will be organized into 2-person teams for a 2.5-day supervised hackathon to produce software that addresses a particular data analysis challenge.
Best Practices in Quantitative Biology workshop series. Existing courses effectively develop students’ capacity for critical analysis of the literature and conceptual design of well-controlled experiments. But practical training in many areas required for data intensive research biology is underemphasized. To address this need, we will offer a series of team-based, experiential workshop on rigorous data analysis, presentation, and data handling in genetics/genomics. DuringY2 and Y3, GME trainees are required to participate in two sessions of their choice per year. Topics will include handling, analyzing, reporting, and archiving sequencing and other large-scale datasets, as well as reproducible, well-controlled and quantitatively informative experimental design in genetics and genomics, automated image/video analysis, figure making/data visualization, archiving, and reporting. Workshops offered through the University of Chicago Research Computing Center (RCC) also are suitable.
Writing workshop. During Y2 or Y3, GME trainees participate in a special 6-session writing workshop, Advanced Principles and Practices of Scientific Writing. The program develops your capacity to write clear and effective scientific manuscripts, fellowship proposals, and grant proposals. The workshop is taught especially for GME by instructors from UChicago’s writing program and follows the renowned Little Red Schoolhouse curriculum. It is appropriate for students who enter at any level of writing proficiency.
Annual GME Retreat. Each fall, we will convene the GME training community (the faculty, Y1 participants, actively funded trainees, and senior trainees who were previously funded) for a one-day retreat on or near campus. The retreat will consist of discussion-based sessions that emphasize the GME program’s values, build a mutually supportive community, provide opportunities for professional development, and permit us to evaluate the program’s efficacy, progress, and environment.
Advising and mentor-mentee alignment. All GME trainees will receive advising by a GME advisor (a program director or steering committee member). Y1 participants will meet each quarter with their GME advisor to discuss progress and challenges in graduate school, receive advice about course selection and rotations, and answer any questions or provide advice about the GME or any other matters. All Y2 and Y3 trainees will meet semiannually with their GME advisors. Working with their research mentor, each student should prepare an Individual Development Plan consistent with the graduate school’s requirements, and the IDP should be shared with the student’s GME advisor. The goal of these advising meetings will be to review progress and challenges, discuss goals and plans, and address any problems or other issues that the student would like to discuss.
Peer mentoring. Peer mentoring has been shown to be an effective means of improving student training outcomes and morale and building community in a program. We have been using our monthly gathering as a mechanism for periodic peer mentoring, and will continue to alternate bimonthly between more formal peer-moderated discussions and open socials. To get the most out of these experiences, we offer a guidance document to help peer mentors to understand the goals, responsibilities, and limits of peer mentoring, the advising and support resources available to GME students, and strategies that are often useful for mentees who needs support. This activity will not only support the mentee but also provide a professional development activity for the mentor.
Program directors
The GME program directors are Joe Thornton (EE/HG), John Novembre (HG), Alex Ruthenburg (CMB). Please contact us with questions!