GEN 800 Seminar Courses

Spring 2017

GEN 800 Section 001 (CMB800, BMB960)

Course Title: CRISPR Revolution

When: Weds. 3:30-4:50 PM
Where: TBD
Course Coordinators: David Arnosti, Robin Buell, Rebecca Grumet 
Course Description: 

Stemming from basic research on bacterial innate immunity and yogurt production, CRISPR technologies have taken the scientific world by storm. These tools offer both significant opportunities to advance goals in basic research and applied fields of medicine and agriculture. Technical methods are continuing to evolve as a wide community of users has adapted this approach to many different systems. In addition to opening new fields of study, as well as unleashing speculative waves in the stock market and in the halls of the Nobel Commission, the application of CRISPR technologies may result in significant impacts on human health, food production, and the environment. This GEN800 course will consider the natural history of CRISPR, its application to diverse basic research settings, potential application in industry and societal impacts of a designer genome feature. Weekly meetings will feature instructor-led overview sessions and student-led presentations of current literature.

Fall 2016

GEN 800 Section 301 (PHM 980 Sec 303)

Course Title: The Communication of Science and Risk/Uncertainty in the Current Media Landscape

When: Mondays September 19th - November 7th (except for Oct 5th) from 4:00 - 6:00 pm
Where: Life Sciences Building, Room B448
Course Coordinator(s): Jamie Bernard
Course Description:
One credit seminar course open to students in biomedical Ph.D. programs. This course will fulfill the Topics in Toxicology requirement for the Environmental and Integrative Toxicological Sciences doctoral program. The course explores science and risk communication at practical and theoretical levels.

Students will:

  • understand key concepts and gain skills for communicating scientific issues through various media, with an emphasis on risk from chemicals and other exposures and uncertainties surrounding such risk.
  • gain an appreciation for how risk communication can influence public perception of safety.
  • think critically about the role of scientists in society and how this is impacted by public engagement and professional engagement with policy makers.
  • think critically about the social and ethical implications of risk communication and engagement through different media outlets.

Course will be part lecture and part discussion/workshop based. Lecturers include: Jamie Bernard (Toxicology), Sarah Hendrickson (Improvisation for Scientists), Keri Szejda (Risk Communication; Arizona State University), Bruno Takahashi (Environmental Science Journalism), Mark Largent (Environment and Public Safety), Kevin Elliot (Ethical and Social Issues in Risk Communication). Discussion topics include: sunscreen, lead, Zika, GMOs, vaccines, endocrine disruptors. Grading: 65% attendance, 25% discussions/presentations, 10% writing assignment.

GEN 800 Section 002 (MMG 991 Sec 3)


Course Title: Statistical Analysis of Microbiomes

When: TBD, meeting 1-2 hours per week
Where: TBD
Course Coordinators: Ashley Shade
Course Description:
This one-credit literature-based course will explore the ways in which microbiome (microbial community) data can be analyzed using typical statistical methods. We will discuss fundamental approaches for microbiome analysis, including hypothesis testing (e.g., to answer the question are treatment and control communities different?) and gradient analyses (e.g., to answer the question do communities change with changes in the environment?). This course will consider downstream analysis of a sample by species community table (e.g., the "OTU table"), which is the output of sequence processing typically performed in mothur or QIIME. We will not discuss sequencing methodology and processing. Primary goals of the course include 1) to familiarize students with common approaches for analyzing a microbiome dataset 2) to discuss the benefits and limitations of those approaches, and, 3) to equip students to make informed choices about which analyses are most appropriate for their scientific question, experimental design, and type of dataset.

Outline of major concepts:

  • Reivew of fundamentals of statistics p-values, parametric and non-parametric tests, hypothesis testing
  • Data workflows
  • Types of microbiome data, OTU tables, contextual data
  • Assessing sampling and sequencing effort
  • Within-sample (alpha) diversity
  • Comparative (beta) diversity, ecological resemblence
  • Ordination
  • Hypothesis testing: are there differences across categrocial groups?
  • Gradient analysis: are there trends across environmental gradients, space, or time?
  • Determining a core microbiome
  • Specialty topics (TBD): Co-occurrence networks, experimental design, models of community assembly, diversity profiles, indicator species analysis, source tracking, temporal turnover, rare biosphere analysis, species abundance distributions


One, one-hour session per week for class meeting time, with student time outside of class required for discussion preparation. Some sessions will involve lecture and discussion sessions lead by the instructor. Other class sessions will be individual student-led paper or topic of interest, and, as time permits, specialty topics can be proposed by the students. A final paper (3-pages) will be due by the end of the semester. The paper can either be: 1) a workflow for analysis created by the student for her/his microbiome analysis; 2) a report describing a specialty analysis not covered in class (benefits and limitations, standard approaches) and a critique of the use of that technique from an example in the literature.


The course grade will be based on 60% Classroom participation, 20% Student-led paper discussion, 20% Final paper due the last day of class