RNA Bioscience Initiative Informatics Fellows Program

Jay Hesselberth
July 15, 2019

Table of Contents


Many facets of modern biological research involve the analysis of RNA to understand how cells control gene expression. These experiments involve powerful new sequencing methods that produce large data sets and require sophisticated bioinformatic analysis. In the Spring of 2016, faculty at the University of Colorado Anschutz Medical Campus were awarded $20 million to start the RNA Bioscience Initiative. To alleviate the bottleneck in analysis of these data sets, the RBI started the Informatics Fellows program and recruited postdoctoral fellows to develop and apply bioinformatic approaches and to educate other trainees on the use of these methods in their own research.

A unique feature of the program is that Fellows are card-carrying RNA biologists who have significant training at the lab bench. So while they no longer do “wet” experiments themselves, this background gives them a unique perspective on RNA-related research and has been instrumental in helping collaborators ask and answer fundamental questions in RNA biology.

It’s an exciting time to be an RNA biologist capable of analyzing large sequencing data sets. We discover something new every day in our collaborators’ data sets and are capitalizing on our unique capabilities to push the limits of RNA sequencing technologies.

Goals and activities

The goal of the Informatics Fellows program is train the next generation of bioinformatic analysts who span the disciplines required for completing RNA sequencing experiments including design, execution, and analysis.

The Fellows divide their time between bioinformatic collaborations with other groups on campus, internal projects involving software and method development, and teaching.

Their training involves several important areas of bioinformatic collaboration:

Current fellows

The program was formed and is led by Jay Hesselberth, Ph.D., Associate Professor of Biochemistry and Molecular Genetics.

Currently the program has four fellows:

  1. Kent Riemondy, Ph.D. did thesis work at the University of Colorado Boulder with Rui Yi studying the role of miRNA biogenesis and targeting in skin. Kent has been in the program for 3.01 years.

  2. Austin Gillen, Ph.D. did thesis work at Northwestern University with Ann Harris studying miRNA regulation of CFTR. Austin has been in the program for 2.37 years.

  3. Rui Fu, Ph.D. did thesis work at the University of California San Diego with Jens Lykke-Andersen studying the mechanism of nonsense-mediated mRNA decay. Rui has been in the program for 1.62 years.

  4. Ryan Sheridan, Ph.D. did thesis work at the University of Colorado Anschtuz Medical Campus with David Bentley studying the role of backtracking in RNA Polymerase II proofreading. Ryan has been in the program for 4.47 months.

Support

Collaborative projects with the Informatic Fellows are done through RBI pilot awards. We are not a service core, and so to facilitate fee-for-service projects we have established a relationship with CIDA to facilitate analysis of single-cell mRNA sequencing experiments. The cost of these analyses can be included in a grant budget. Please initiate a collaboration for more details.

We also provide letters of support to investigators for their grant applications that detail the Informatics Fellows program and broader RNA sequencing capabilities on campus. Please contact for details.

The Informatics Fellows also provide office hours to provide help with programming, software, pipelines, and experimental design questions. Please see our office hour page for additional details.

Education

Outreach and mentoring

The fellows hold weekly RBI Office Hours on Thursday afternoons from 1:00-4:00 PM. Office hours allow investigators across campus to ask questions about the design, execution, and analysis of RNA-related sequencing experiments. The Office Hours have been instrumental in educating investigators across campus on the appropriate design, execution, and analysis of RNA sequencing experiments.

The fellows mentor summer students as part of the RBI Summer Internship Program.

Classes and short courses

The Fellows help create and teach several courses focused on intersection of RNA biology and bioinformatics.

Courses

Workshops

The fellows are developing a short course on analysis of single-cell RNA sequencing experiments. This course will be offered on the Anschutz Medical Campus and will hopefully shift some of the workload of single-cell RNA-seq analysis into individual labs.

Other courses

The fellows taught the Genome Analysis Workshop in Spring 2017. This semester-long course teaches the basics of shell programming, analysis in R, and scripting in Python.