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Computational analysis of cis-regulatory sequences

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Computational analysis 2017-2018 Planning

Coordination : Morgane Thomas-Chollier, Biology Department, ENS (MC ENS)
Hours : 30h
Credits : 3 ECTS
Semester : 1st semester
Pre-requisite : This teaching unit follows the course “High-throughput data analysis for genomics”. In practice, it is highly recommended to enroll to this course as a pre-requisite, as it presents some introductory concepts (firsts steps of high-throughput sequencing data processing) that are considered as previous knowledge for this teaching unit.

Aims : Mastering of concepts and software tools for the analysis of cis-regulatory sequences from ChIP-seq experiments. Practical experience of the analysis of high-throughput datasets. Develop a critical view on the dataset quality.

Themes : This teaching unit introduces the experimental approaches used for the detection of cis-regulatory elements in genomic sequences. It then focuses on ChIP-seq experiments. It covers the main bioinformatic and statistical concepts enabling the processing of raw data to obtain peaks, and then downstream analyses to extract meaningful biological information to answer the biological question initially asked. Discovery of motifs in ChIP-seq peaks for different transcription factors is also introduced.

To complement the lectures and practical hands-on sessions, seminars will be given by researchers, to highlight the biological and medical applications of ChIP-seq and the joint work between experimentalists and bioinformaticians, to present analyses taking into account the tridimensional organisation of the chromatin, and the analysis of variations in cis-regulatory elements.

Organization : The teaching unit will be organised over one week, with hands-on sessions, in addition to a practical project for which time is dedicated for personal work.

Teaching team 2016 :
Samuel Collombet (ENS, Paris)
Sebastiaan H. Meijsing (MPIMG Berlin, Germany)
Alejandra Medina Rivera (UNAM Queretaro, Mexico)
Morgane Thomas-Chollier (ENS, Paris)