Joint ENS-CSI Workshop 2014

9.00am Registration/Breakfast


9.30 Welcome Address

By Prof Daniel Tenen, Director of CSI Singapore.


9.45am Chipseq data generation, from cells to the sequencer

Talk by Dr Annouck Luyten (CSI, NUS, Singapore)


ChIP-Seq is a powerful tool to provide genome-wide data regarding protein-DNA interactions. The combination of transcription factor (TF) binding, histone modifications and gene expression will give us valuable information on how protein-chromatin interactions lead to expression of a specific gene set in each tissue/cell line. Before we can analyze the chromatin on the sequencer, several well controlled steps are done in the lab, starting from harvesting cells or tissue to preparing a “DNA library”.


10.30 Mapping sequenced reads to a reference genome and quality control

Instructor: Dr Touati Benoukraf (CSI, NUS, Singapore)


After sequencing, the bioinformatics analysis starts with the assessment of data quality and the mapping of reads onto a reference genome. We will show how to use the read alignerbowtie, how to handle the main conventional file format (fastq, SAM, BAM), and how to identify the major bias (ie. genomic divergence, amplification effect) in order to assess library and sequencing quality.


12.30pm Lunch Break


1.30pm Signal extraction, peaks calling

Instructors: Dr Henry Yang (CSI, NUS, Singapore) &Samuel Collombet (ENS Paris)


Main step in the analysis of ChIP-seq data is the extraction of signal from background noise, i.e. to identify regions of reads enrichment (peaks). This step is necessary for both assessing ChIP efficiency, and for further functional analysis. First, we will see the statistical basis of signal identification, and how they are implemented for peak calling in different software. Then, we will see how to visualize data, using the online UCSC genome browser. Finally, we will see how to annotate these data to get insight into the underlying biological processes (peaks-to-genes association, gene set and gene ontology terms enrichment).


4.30pm Tea Break



4.45pm Data visualization

Instructors: Dr Nicolas Bertin (CSI, NUS, Singapore) &Dr Morgane Thomas-Chollier (ENS, Paris)


Although many genome data analysis tasks can be accomplished with automated processes, some steps continue to require human judgment and are frequently rate limiting. Beyond facilitating the interpretation of genome-anchored data and their contextualization, genome browsers also provide a common platform for investigators to share, store and publish scientific discoveries. We will present several browsers and illustrate their usage and respective advantages via specific case studies drawn from publicly available datasets.


7.00pm End of the session.



March 25th, 2014


9.00am Motif analysis and prediction of cofactors

Instructor: Dr Morgane Thomas-Chollier (ENS, Paris)



Starting from the ChIP-seq peaks, a motif analysis allows us to discover binding motifs that capture the binding specificity of the pulled-down factor, and predict their possible co-regulators. Specialized software tools have recently been developed for such analyses, but most can barely treat the thousands of peaks produced by ChIP-seq experiments. In this tutorial, we will first, provide a general overview of motif analyses, and second, focus on the RSAT peak-motif software ( for de novo motif-discovery in complete datasets, and CENTDIST for global enrichment of collections of known motifs.

(Tea break at 11am)


12.00pm presentation of ENS Master and PhD program
Talk by: Prof Denis Thieffry (ENS, Paris)


12.30pm Lunch Break



1.30pm Transcriptome-wide mapping of the Exon Juncion Complex with the CLIP-seq method

Talk by: Dr Herve le Hir (ENS, Paris)


Eucaryotic gene expression requires multiple steps including mRNA processing, transport, translation and finally degradation. All these steps are functionally coupled to finely tune and control the integrity of the message vehiculated. The communication between the different cellular machineries is ensured by the proteins that cover mRNA to form mRNP particles. We are interested in mRNP assembly and its influence on gene expression. More precisely, we study the multiprotein complex called EJC standing for « Exon Junction Complex ». This molecular signature accompanies mRNAs during their cellular travel and it couples splicing to mRNA transport, translation, degradation and quality control. If we made important progress to understand EJC structure, nothing is known about EJC assembly in vivo. We used the CLIP-seq (CrossLinking and ImmunoPrecipitation coupled to high-throughput sequencing) method to establish the first map of EJC in human cells. I will present the CLIP-seq data as well as the advantages and the limitations of this approach.


2.30pm Dynamical modeling of gene networks: introduction to the logical framework

Instructor: Prof Denis Thieffry (ENS, Paris)


The logical framework is being increasingly used to model the dynamical behaviour of large cellular signalling/regulatory networks. In this context, a range of computational tools have been developed to support model definition and analysis. In this tutorial, we will first provide a general overview of this framework, before focusing on the general (asynchronous) logical modelling approach implemented in the software GINsim ( Examples of applications to large signalling/regulatory networks will be provided, including prospects regarding the inclusion of information from large-scale ChIP-seq essays. A hands-on tutorial will be proposed to the most motivated students.

(Tea break at 3.30pm)


5.00pm Closing remarks and open discussions.


5.45pm End of the workshop.