2015 CRI Bioinformatics Workshop

The CRI’s 2015 Bioinformatics Workshop took place from December 2-5, 2015 at Harper Court at the University of Chicago. This four-day, hands-on workshop focused on the bioinformatics analysis of integrative -omics data, with a focus on linking TF binding, DNA binding, and regulation with expression.

academic photography, conference photography, event photography of Center for Research Informatics Conference taken in Chicago, at University of Chicago Hyde Park Campus, IL for University of Chicago All photos ©2015 Brent Knepper http://www.brentknepper.com

See more photos from the workshop here!

Curriculum

The focus of our 2015 workshop was on the integration of multiple -omic/clinical datasets to answer complex questions in biomedical research, with strong focus on the use of NGS-based ChIP-seq analysis and its integration with gene expression and clinical information.

Topics included:

  • Conducting reproducible research
  • Use of Galaxy
  • Statistical considerations for ChIP-seq analysis
  • Identification of high- and low-quality samples
  • Understanding the types of questions ChIP-seq can answer
  • Use of publicly available annotation databases and web applications
  • Applied R programming
  • Use of Bioconductor
  • Interpretation of ChIP-seq results
  • Visualization
  • Integration of expression and transcription factor binding sites

For more details, download the PDF of the full workshop schedule.

Speakers

In addition to the CRI’s team of bioinformaticians, speakers included:

  • Suzanne Conzen, MD, Professor in the Department of Medicine, Comprehensive Cancer Center, Ben May Department for Cancer Research, and Committee on Cancer Biology
  • Devendra Mistry, PhD, from the Qiagen Applied Advanced Genomics team
  • Nan Xiao, an R developer who has authored two web applications and seven R/Bioconductor packages, such as liftr, sbgr, and hdnom
  • Samuel Volchenboum, MD, PhD, Associate Chief Research Informatics Officer and director of the Center for Research Informatics

Participation and Feedback

The workshop was attended by faculty, graduate students, post-doctoral fellows, and staff from the University of Chicago and five other institutions, as well as industry and research professionals. Thanks to our partnership with the Institute for Translational Medicine and Center for Health and the Social Sciences, three students received University of Chicago course credit for their participation in the workshop.

The workshop was well-received, with 92% of those who responded to our feedback survey indicating that the workshop was very or extremely useful and calling the quality of instruction excellent or very good.

Sponsors

The success of our 2015 workshop was made possible in part by the generosity of our institutional partner the Institute for Translational Medicine and of our sponsors IBM and QIAGEN Bioinformatics.