Video recordings of the workshop talks are now available on our Youtube channel. See https://exRNA.org/exRNAdata2021-videos/.

On Monday and Tuesday April 19–20, 2021, the ERCC hosted a free online workshop on exRNA data analysis. There were 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 was to foster an open dialog about best practices and open problems in exRNA data analysis, focusing mainly on small exRNA sequencing data. We hope that data scientists gained domain knowledge about exRNA and the unique features to consider when analyzing exRNA data, and that experimentalists learned more about the bioinformatic tools available to them. We will continue to work to foster interaction and collaboration between the two communities.


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Workshop Schedule

All times US Eastern daylight time (EDT, UTC-4)

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 ENCORE: The ENCODE RNA regulatory element 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 Stolovitzky 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 focused on computational methods to understand and catalog the heterogeneity of exRNA carriers, with a particular emphasis on deconvolution.

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

exRNA Data Analysis Challenge

A major goal for the Spring 2021 workshop was 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. We are now taking next steps to organize such a challenge.