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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 launch the RNA Bioscience Initiative (RBI). As one of its first acts, the RBI established the Informatics Fellows Program to recruit bioinformatics post-docs who would develop and apply computational approaches to RNA biology. In addition, the RBI Informatics Fellows have been tasked with training RNA biologists to use these methods in their own research, thereby alleviating the current bottleneck in analysis created by these large sequencing data sets.
A unique feature of this program is that RBI Informatics Fellows are themselves card-carrying RNA biologists who have significant training at the lab bench. This background gives fellows a rare 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 collective capabilities to push the limits of RNA sequencing technologies.
It was the RBI Informatics Fellows Program that made me want to come to CU Anschutz. This program is an innovative way of facilitating collaborations between “wet labs” and bioinformaticians. The collaborations have been interesting and effective, pushing the RBI to be early adopters of novel RNA technologies– a great way to put CU Anschutz at the forefront of transformative science.
The objective of the RBI Informatics Fellows Program is to train the next generation of bioinformatic analysts. By the conclusion of their fellowship, these newly minted bioinformaticians will have mastered the skills, from both RNA biology and computer science, required to complete RNA sequencing experiments including design, execution, and analysis.
RBI Informatics 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:
The success of the Informatics Program can be measured in part by its impact on our collaborators’ publications and grants. Since the Program’s inception in 2016, the Informatics Fellows have:
In 2017 the RBI purchased a Chromium Controller from 10x Genomics to facilitate the construction of single-cell mRNA sequencing libraries (this instrument is maintained in the Genomics Core). Due to the success of this method, 103 experiments to-date have focused on single-cell mRNA sequencing. Figure 1 below details these scRNA-sequencing experiments, as well as a wide variety of other RNA-related projects.
Figure 1: Project types and status.
Through its Pilot Grant Program, the RBI has funded more than 119 RNA-focused projects, catalyzing interest in and adoption of cutting-edge technologies among campus investigators. Funded projects are designed, executed, and analyzed by the RBI Informatics Fellows. In addition to the projects funded through the RBI Pilot Grant Program, the RBI has provided both experimental and bioinformatic support via several mechanisms:
Figure 2 summarizes the 161 RBI-funded projects analyzed by the Informatics Fellows to date.
Figure 2: Project source organized by RFA.
In collaboration with the Hesselberth Lab , the RBI Informatics Fellows also work on their own projects. These include software development, e.g., R packages for genome interval analysis and for the analysis of single-cell functional heterogeneity, new molecular methods focused on single-cell RNA-seq, and bioinformatics curriculum development.
|Fellow-Initiated Internal Projects|
|single cell PAS-Seq analysis||Method Development||ongoing|
|Targeted single cell RNA-Seq resampling||Method Development||completed|
|R Package development (valr)||Method Development||completed|
|R Package development (scrunchy)||Method Development||completed|
|R Package development (djvdj)||Method Development||ongoing|
|single cell classification from bulk RNA-Seq||Method Development||completed|
|Practical Biological Data Analysis in R||Teaching||completed|
|Genome Analysis Workshop||Teaching||completed|
|RNA secondary structure short course||Teaching||initiated|
|scRNA-Seq short course||Teaching||ongoing|
|RBI Office Hours||Teaching||ongoing|
|Mentoring- RBI interns, students, fellows||Teaching||ongoing|
The RBI can also provide letters of support to investigators for their grant applications that detail the Informatics Fellows program and the broader RNA sequencing and other single cell analytic capabilities on campus. Please contact Jay Hesselberth (firstname.lastname@example.org) or details.
The RBI Informatics Fellows also host office hours to provide help with programming, software, pipelines, and experimental design questions. Please visit the RBI Office Hours page for scheduling.