Planning for Online Workshop on exRNA Data Analysis

On Monday and Tuesday April 19–20, 2021, the ERCC will host a free online workshop on exRNA data analysis. There are three target audiences: experimentalists generating exRNA-seq data, computational and data scientists who have worked with those groups to analyze their data, and other interested data scientists. Our goal is to foster an open dialog about best practices and open problems in exRNA data analysis, focusing mainly on small exRNA sequencing data. Data scientists will gain domain knowledge about exRNA and the unique features to consider when analyzing exRNA data. Experimentalists will learn more about the bioinformatic tools available to them. We hope the interaction between the two communities will increase understanding and foster collaboration.

Participation in the workshop is free. Sessions will run from noon to 5pm US Eastern time both days. Registered participants will receive Zoom call-in information shortly before the meeting. Stay tuned to this page for details!

Workshop Schedule

Monday, April 19th

Session 1) Introduction: Open Problems in exRNA Data Analysis
12:00 – 12:10	Roger Alexander	Extracellular RNA Communication Consortium	Workshop Introduction
12:10 – 12:35	Rob Kitchen	Massachusetts General Hospital and Harvard Medical School	Open Problems in exRNA Data Analysis
12:35 – 12:50	Juan Pablo Tosar	Institut Pasteur de Montevideo, Uruguay	Non-coding RNA Annotations
Session 2) exRNA Data Sources
1:00 – 1:20	Matt Roth	Baylor College of Medicine	The exRNA Atlas
1:20 – 1:35	Pieter Mestdagh	OncoRNAlab, Cancer Research Institute Ghent	The Human Biofluid RNA Atlas
1:35 – 1:50	Joel Rozowsky	Yale University	exceRpt: the extracellular RNA processing toolkit
Session 3) Data Visualization
2:00 – 2:25	Justin Chang	Yale University	The exRNA Explorer tool
2:25 – 2:50	Discussion of open problems in exRNA data visualization
Session 4) Case Studies in exRNA Data Analysis I
3:00 – 3:20	Ryan Spengler	University of Wisconsin Madison	Characterization and analysis of cell free mRNA fragments in human circulation
3:20 – 3:35	Klaas Max	Rockefeller University	Reference profiles of extracellular RNA in serum and plasma
3:35 – 3:50	Karolina Kaczor Urbanowicz	University of California Los Angeles	Bioinformatic analysis of salivary RNA sequencing data for biomarker development
Session 5) Questions and Answers
4:00 – 4:50	This session gives the audience a chance to ask questions of the day’s speakers.

Tuesday, April 20th

Session 6) Deconvolution
12:00 – 12:15	Rongshan Yu	Department of Computer Science, Xiamen University and Aginome Scientific	A deep neural network based approach for tumor deconvolution – The Tumor Deconvolution DREAM Challenge winning algorithm
12:15 – 12:35	Aleks Milosavljevic	Baylor College of Medicine	exRNA Atlas analysis reveals distinct extracellular RNA cargo types and carriers
12:35 – 12:50	Brian White	Jackson Laboratory, Manager of the Tumor Deconvolution DREAM challenge	The CIBERSORTx deconvolution algorithm
Session 7) exRNA and RNA binding proteins
1:00 – 1:20	Eric Van Nostrand	Baylor College of Medicine	The ENCODE RNA binding protein project
1:20 – 1:35	Bogdan Mateescu	University of Zurich / ETH Zurich	RNA binding proteins and exRNAs
1:35 – 1:50	Emily LaPlante	Baylor College of Medicine	A look at the exRNA Atlas from the RBP perspective
Session 8) Case Studies in exRNA Data Analysis II
2:00 – 2:20	Elizabeth Hutchins	Translational Genomics Research Institute	Profiling the extracellular long RNA transcriptome in human biofluids
2:20 – 2:35	Leonora Balaj	Massachusetts General Hospital and Harvard Medical School	Discovery and validation of novel mRNA signatures in gliomas
2:35 – 2:50	Bojan Losic	Icahn School of Medicine at Mount Sinai	Small RNA clusters in circulating extracellular vesicles in liver and prostate cancer
Session 9) Workshop Round-up: Discussion of Progress on Open Problems in exRNA Data Analysis
3:00 – 3:50	Open Discussion with Speaker Panel
Session 10) Formulating an exRNA data analysis challenge
4:00 – 4:15	Gustavo Stolovitsky	Chair, IBM Exploratory Life Sciences Council and	Can we use a crowdsourcing challenge to benchmark exRNA transcriptomics analyses?
4:15 – 4:25	Roger Alexander	Extracellular RNA Communication Consortium	Possible exRNA data analysis challenges: Problem definition and datasets
4:25 – 4:50	Discussion

Open Problems

The workshop will focus on computational methods to understand and catalog the heterogeneity of exRNA carriers, with a particular emphasis on deconvolution.

Some specific open problems to be discussed at the workshop include the following:

biomarker discovery: given a set of case-control experiments for a specific disease, what are the most informative sets of exRNA biomarkers for diagnosing and tracking treatment progress for that disease?
housekeeping exRNAs: What is the core set of exRNAs expressed in each class of EVs, regardless of cell type of origin?
cell-type-specific housekeeping exRNAs: What are the additional core set of exRNAs expressed in specific classes of EVs secreted by specific cell types?
cell type of origin: For exRNA datasets from biofluid samples, is it possible to determine the cell type of origin of different clusters of EVs in the biofluid?
best practices for analysis of RNA modifications: like other non-coding RNAs, exRNAs can be highly modified. Most modifications are invisible to standard RNA sequencing methods. If each specific modification requires its own sequencing experiment, how can we integrate disparate datasets to create a clear picture of the entire modified exRNA-ome?
data visualization: the exRNA Atlas contains datasets from a wide variety of diseases, biofluids, and cell types. What are innovative ways that researchers have used to visualize and find interesting new biology in this complex collection of datasets?

exRNA Data Analysis Challenge

Our goal is for the Spring 2021 workshop to lay the foundation for creating an exRNA-themed DREAM challenge. The DREAM challenge is an ideal framework for presenting problems in exRNA data analysis to the wider scientific community. For more information, watch the February ERCC webinar presented by DREAM founder Gustavo Stolovitsky.