Program collaborations and projects

Table of Contents


Overview

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:

Figure 1 summarizes the sources and types of projects analyzed by the Informatic Fellows.

Project types and status. The majority of projects involve single-cell mRNA sequencing, alongside a variety of other RNA sequencing experiments.

Figure 1: Project types and status. The majority of projects involve single-cell mRNA sequencing, alongside a variety of other RNA sequencing experiments.

The RBI purchased a Chromium Controller from 10x Genomics to facilitate the construction of single-cell mRNA sequencing libraries. Due to the success of this method, 65 experiments to-date have focused on single-cell mRNA sequencing, but the fellows have engaged in a wide variety of RNA-related projects.

RBI-funded projects

The RBI has funded several seed and pilot grants with campus investigators to catalyze interest in and adoption of cutting-edge RNA sequencing technologies. Funded projects are designed, executed, and analyzed by the Informatics Fellows. The RBI has funded projects via several mechanisms:

Figure 2 summarizes the sources of RBI-funded projects that the Fellow have analyzed, comprising a total of 102 collaborative projects.

Project source organized by RFA. The RBI provides funds via several mechanisms to facilitate collaborative RNA sequencing experiments that are analyzed by the Informatic Fellows.

Figure 2: Project source organized by RFA. The RBI provides funds via several mechanisms to facilitate collaborative RNA sequencing experiments that are analyzed by the Informatic Fellows.

Fellow-Initiated Projects

The fellows have initiated several of their own projects in collaboration with the Hesselberth lab. These include software development (i.e., 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
Description Type Status
single cell PAS-Seq analysis Method Development ongoing
Targeted single cell RNA-Seq resampling Method Development completed
R Package development (valr) Method Development completed
single cell classification from bulk RNA-Seq Method Development ongoing
Practical Biological Data Analysis in R Teaching completed
Mentoring RBI summer student Teaching completed
scRNA-Seq short course Teaching initiated
Mentoring single cell RNA-Seq fellow Teaching ongoing
RBI Office Hours Teaching ongoing
Genome Analysis Workshop Teaching completed
RNA secondary structure short course Teaching initiated

RBI Faculty Collaborations

The RBI faculty hires are supported by the Fellows in long-term projects that involve substantial analysis. Data generated by the Fellows will be instrumental in helping these new faculty publish original research studies and obtain external funding.

Collaborative Projects with RBI Faculty Hires
PI Description
Jagannathan Escape from NMD in the 1000 genomes dataset
Mukherjee Regulatory mechanisms control steroidogenic responses
Ramachandran Mapping DNA-chromatin contacts using MINCE-Seq
Rissland Comparative evolutionary analysis of Maternal to Zygotic transitions
Taliaferro Patterns and mechanisms of 3' end variations in human cancers