W01 RADIANT Workshop

Analysis of Differential Isoform Usage by RNA-seq: Statistical Methodologies and Open Software

7th September 2014

There are many computational and statistical challenges in the analysis of differential isoform usage by RNA-Seq. The workshop addresses users and method developers who are interested in better understanding the features of current tools and exploring approaches to method benchmarking. The workshop will cover the most important current statistical and computational challenges, including:

  • Statistical characterisation of exon/isoform quantitative variation across samples/conditions
  • Methods for identification of differential exon/isoform usage
  • Methods for transcript discovery in non-model organisms
  • Inference algorithms for large-scale datasets
  • Establishing best practice in method benchmarking
  • Open software and end-to-end pipelines
  • Emerging long-read and small sample technologies, and future perspectives

The workshop is aimed at computational biologists, statisticians and genome biologists with an interest in data analysis and statistical methods and applications in transcriptomics.

Invited Speakers

David Kreil (University of Warwick and Boku University Vienna)

Jernej Ule (University College London)

Alyssa Frazee (John Hopkins Bloomberg School of Public Health)

Elsa Bernard (Mines Paris Tech/Institut Marie Curie)

David Rossell (University of Warwick)

Alejandro Reyes (EMBL)

Mar Gonzalez Porta (EBI)


Workshop schedule

Session 1 (9.00-9.05 Welcome)

9.05-9.40 Jernej Ule (Institute of Neurology, University College London, UK): Regulation of cryptic splicing elements within long neuronal genes

9.40-10.15 Mar Gonzales-Porta (EMBL-EBI, Cambridge, UK): Identification, annotation and visualisation of extreme changes in splicing from RNA-seq experiments with SwitchSeq

10.15-10.30 Axel Rasche (Max Planck Institute for Molecular Genetics, Berlin, Germany): ARH/ARH-Seq ‚Äď Discovery tool for differential splicing in High-throughput data

10.30-10.45 Coffee Break

Session 2

10.45-11.20 Alejandro Reyes (EMBL, Heidelberg, Germany): Studying differential usage of exons with the DEXSeq package

11.20-11.35 Thomas Risch (Max Planck Institute for Molecular Genetics, Berlin, Germany): Prediction of subtype-specific alternative exon usage in medulloblastoma

11.35-11.50 Jose M. Garcia-Manteiga (OSR, Milan, Italy): Alternative splicing in response to hypoxia in HUVEC cells by differential exon usage and differential expression of isoforms

11.50-12.00 Benchmarking team activity

12.00-13.30 Lunch

Session 3

13.30-14.05 Alyssa Frazee (John Hopkins Bloomberg School of Public Health, Baltimore, USA): Engineering annotation-agnostic tools for differential expression analysis

14.05-14.20 Daniel Gautheret (Insitut de Génétique et Microbiologie, Paris, France): Detecting Differential RNA-processing Events from RNA-seq data

14.20-14.55 David Rossell (Dept. of Statistics, University of Warwick): Casper for efficient summarization and design of RNA-seq studies

14.55-15.30 Elsa Bernard (Institut Curie, Paris): Fast isoform detection from RNA-Seq data with network flow techniques

15.30-15.45 Malgorzata Nowicka (Institute of Molecular Sciences, University of Zurich, Switzerland): Dirichlet-multinomial model for differential splicing detection in RNA-seq data

15.45-16.00 Panos Papastamoulis (Faculty of Life Sciences, University of Manchester, UK): Identifying differentially expressed transcripts via a Reversible Jump MCMC sampler

16.00-16.20 Coffee Break 

Session 4

16.20-16.55 David Kreil (Bioinformatics Research Group, Boku University Vienna, Austria) : Benchmarking gene transcript expression profiling - challenges and platform specific results

16.55-17.10 Azra Krek (Memorial Sloan-Kettering Cancer Center, New York, USA): Comparison of isoform quantification methods for short-reads sequencing data using SEQC data

17.10-18.00 Benchmarking team presentations and discussion



Short abstracts (max. 1500 chars) can be submitted through EasyChair via the RADIANT workshop submission page.

Abstract submission deadline: June 30th, 2014

Notification of acceptance: July 14th, 2014

Talk abstract submission is now closed. If you would like to submit a poster abstract then email a short abstract to This email address is being protected from spambots. You need JavaScript enabled to view it.  


Organising committee

Simon Anders (EMBL)

Wolfgang Huber (EMBL)

Magnus Rattray (University of Manchester)

Mark Robinson (University of Zurich)


Workshop Venue

Palais de la Musique et des Congrès
Place de Bordeaux
67082 Strasbourg


Sponsored by RADIANT  

RADIANT is funded by the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 305626.






Latest News

Awards ECCB'14 awards have been announced during the closing ceremony of ECCB'14 on Wednesday September... Read more
Next conferences: ISMB/ECCB & JOBIM 2015 Next ECCB will be held in conjunction with ISMB in Dublin, Ireland, July 10-14, 2015: ISMB/ECCB... Read more

Silver Sponsors

Other Exhibitors