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 – 12:10Roger AlexanderExtracellular RNA Communication ConsortiumWorkshop Introduction
12:10 – 12:35Rob KitchenMassachusetts General Hospital and Harvard Medical SchoolOpen Problems in exRNA Data Analysis
12:35 – 12:50Juan Pablo TosarInstitut Pasteur de Montevideo, UruguayNon-coding RNA Annotations
Session 2) exRNA Data Sources
1:00 – 1:20Matt RothBaylor College of MedicineThe exRNA Atlas
1:20 – 1:35Pieter MestdaghOncoRNAlab, Cancer Research Institute GhentThe Human Biofluid RNA Atlas
1:35 – 1:50Joel RozowskyYale UniversityexceRpt: the extracellular RNA processing toolkit
Session 3) Data Visualization
2:00 – 2:25Justin ChangYale UniversityThe exRNA Explorer tool
2:25 – 2:50Discussion of open problems in exRNA data visualization
Session 4) Case Studies in exRNA Data Analysis I
3:00 – 3:20Ryan SpenglerUniversity of Wisconsin MadisonCharacterization and analysis of cell free mRNA fragments in human circulation
3:20 – 3:35Klaas MaxRockefeller UniversityReference profiles of extracellular RNA in serum and plasma
3:35 – 3:50Karolina Kaczor UrbanowiczUniversity of California Los AngelesBioinformatic analysis of salivary RNA sequencing data for biomarker development
Session 5) Questions and Answers
4:00 – 4:50This session gives the audience a chance to ask questions of the day’s speakers.

Tuesday, April 20th

Session 6) Deconvolution
12:00 – 12:15Rongshan YuDepartment of Computer Science, Xiamen University and Aginome ScientificA deep neural network based approach for tumor deconvolution – The Tumor Deconvolution DREAM Challenge winning algorithm
12:15 – 12:35Aleks MilosavljevicBaylor College of MedicineexRNA Atlas analysis reveals distinct extracellular RNA cargo types and carriers
12:35 – 12:50Brian WhiteJackson Laboratory, Manager of the Tumor Deconvolution DREAM challengeThe CIBERSORTx deconvolution algorithm
Session 7) exRNA and RNA binding proteins
1:00 – 1:20Eric Van NostrandBaylor College of MedicineENCORE: The ENCODE RNA regulatory element project
1:20 – 1:35Bogdan MateescuUniversity of Zurich / ETH ZurichRNA binding proteins and exRNAs
1:35 – 1:50Emily LaPlanteBaylor College of MedicineA look at the exRNA Atlas from the RBP perspective
Session 8) Case Studies in exRNA Data Analysis II
2:00 – 2:20Elizabeth HutchinsTranslational Genomics Research InstituteProfiling the extracellular long RNA transcriptome in human biofluids
2:20 – 2:35

Leonora BalajMassachusetts General Hospital and Harvard Medical SchoolDiscovery and validation of novel mRNA signatures in gliomas
2:35 – 2:50Bojan LosicIcahn School of Medicine at Mount SinaiSmall 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 – 3:50Open Discussion with Speaker Panel
Session 10) Formulating an exRNA data analysis challenge
4:00 – 4:15Gustavo StolovitzkyChair, IBM Exploratory Life Sciences Council andCan we use a crowdsourcing challenge to benchmark exRNA transcriptomics analyses?
4:15 – 4:25Roger AlexanderExtracellular RNA Communication ConsortiumPossible exRNA data analysis challenges: Problem definition and datasets
4:25 – 4:50Discussion

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.