Saad, Chadi Noé, Laurent Richard, Hugues Leclerc, Julie Buisine, Marie-Pierre Touzet, Hélène Figeac, Martin
Published in
BMC Bioinformatics
BackgroundDiscovering over-represented approximate motifs in DNA sequences is an essential part of bioinformatics. This topic has been studied extensively because of the increasing number of potential applications. However, it remains a difficult challenge, especially with the huge quantity of data generated by high throughput sequencing technologi...
Saad, Chadi
L'arrivée des technologies de séquençage d’ADN à haut-débit a représenté une révolution dans le domaine de la génomique personnalisée, en raison de leur résolution et leur faible coût. Toutefois, ces nouvelles technologies présentent un taux d’erreur élevé, qui varie entre 0,1% et 1% pour les séquenceurs de seconde génération. Cette valeur est prob...
Merhej, Jawad Thiebaut, Antonin Blugeon, Corinne Pouch, Juliette Chaouche, Mohammed El Amine Ali Jean-Michel Camadro Crom, Stephane Le Lelandais, Gaëlle Devaux, Frédéric
Published in
Frontiers in Microbiology
The yeast Candida glabrata has become the second cause of systemic candidemia in humans. However, relatively few genome-wide studies have been conducted in this organism and our knowledge of its transcriptional regulatory network is quite limited. In the present work, we combined genome-wide chromatin immunoprecipitation (ChIP-seq), transcriptome a...
Boeva, Valentina
Published in
Frontiers in Genetics
Eukaryotic genomes contain a variety of structured patterns: repetitive elements, binding sites of DNA and RNA associated proteins, splice sites, and so on. Often, these structured patterns can be formalized as motifs and described using a proper mathematical model such as position weight matrix and IUPAC consensus. Two key tasks are typically carr...
Angelini, Claudia Heller, Ruth Volkinshtein, Rita Yekutieli, Daniel
Published in
BMC Bioinformatics
BackgroundChip-seq experiments are becoming a standard approach for genome-wide profiling protein-DNA interactions, such as detecting transcription factor binding sites, histone modification marks and RNA Polymerase II occupancy. However, when comparing a ChIP sample versus a control sample, such as Input DNA, normalization procedures have to be ap...
Schweikert, Gabriele Cseke, Botond Clouaire, Thomas Bird, Adrian Sanguinetti, Guido
Published in
BMC Genomics
BackgroundCell-specific gene expression is controlled by epigenetic modifications and transcription factor binding. While genome-wide maps for these protein-DNA interactions have become widely available, quantitative comparison of the resulting ChIP-Seq data sets remains challenging. Current approaches to detect differentially bound or modified reg...
Neri, Francesco Incarnato, Danny Krepelova, Anna Rapelli, Stefania Pagnani, Andrea Zecchina, Riccardo Parlato, Caterina Oliviero, Salvatore
Published in
Genome Biology
BackgroundTen-Eleven Translocation (TETs)proteins mediate the oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Tet1 is expressed at high levels in mouse embryonic stem cells (ESCs), where it mediates the induction of 5hmC decoration on gene-regulatory elements. While the function of Tet1 is known, the mechanisms of its specifi...