Publications de René Dreos | EPFL Graph Search

Computational identification and experimental characterization of preferred downstream positions in human core promoters

Author summary Transcription of genes by the RNA polymerase II enzyme initiates at a genomic region termed the core promoter. The core promoter is a regulatory region that may contain diverse short DNA sequence motifs/elements that confer specific properti ...

2021

EPD in 2020: enhanced data visualization and extension to ncRNA promoters

Philipp Bucher, Giovanna Ambrosini, Romain Fernand Pietro Groux, René Dreos, Patrick Meylan

The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome bro ...

2020

Opposing chromatin remodelers control transcription initiation frequency and start site selection

Philipp Bucher, René Dreos

Precise nucleosome organization at eukaryotic promoters is thought to be generated by multiple chromatin remodeler (CR) enzymes and to affect transcription initiation. Using an integrated analysis of chromatin remodeler binding and nucleosome occupancy fol ...

NATURE PUBLISHING GROUP2019

MGA repository: a curated data resource for ChIP-seq and other genome annotated data

Rouayda Cavin Perier, Philipp Bucher, Giovanna Ambrosini, Romain Fernand Pietro Groux, René Dreos

Oxford University Press2018

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

Rouayda Cavin Perier, Philipp Bucher, Giovanna Ambrosini, Romain Fernand Pietro Groux, René Dreos

We present an update of the Eukaryotic Promoter Database EPD (http://epd.vital-it.ch), more specifically on the EPDnew division, which contains comprehensive organisms-specific transcription start site (TSS) collections automatically derived from next gene ...

2017

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data

Philipp Bucher, Giovanna Ambrosini, René Dreos, Sunil Kumar

ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrati ...

2016

Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters

Philipp Bucher, Giovanna Ambrosini, René Dreos

The recruitment of RNA-Pol-II to the transcription start site (TSS) is an important step in gene regulation in all organisms. Core promoter elements (CPE) are conserved sequence motifs that guide Pol-II to the TSS by interacting with specific transcription ...

Public Library Science2016

The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools

Rouayda Cavin Perier, Philipp Bucher, Giovanna Ambrosini, René Dreos

We present an update of EPDNew (http://epd. vital-it. ch), a recently introduced new part of the Eukaryotic Promoter Database (EPD) which has been described in more detail in a previous NAR Database Issue. EPD is an old database of experimentally character ...

Oxford University Press2015

Principles of ChIP-seq Data Analysis Illustrated with Examples

Philipp Bucher, Giovanna Ambrosini, René Dreos

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) is a powerful method to determine how transcription factors and other chromatin-associated proteins interact with DNA in order to regulate gene transcription. A single C ...

Copicentro Granada S L2014

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era

Rouayda Cavin Perier, Philipp Bucher, Giovanna Ambrosini, René Dreos

The Eukaryotic Promoter Database (EPD), available online at http://epd.vital-it.ch, is a collection of experimentally defined eukaryotic POL II promoters which has been maintained for more than 25 years. A promoter is represented by a single position in th ...

Oxford University Press2013

Critical assessment of automated flow cytometry data analysis techniques

Philipp Bucher, Pascal Meyer, Giovanna Ambrosini, Nima Aghaeepour, Slavica Dimitrieva Janeva, René Dreos

Traditional methods for flow cytometry (FCM) data processing rely on subjective manual gating. Recently, several groups have developed computational methods for identifying cell populations in multidimensional FCM data. The Flow Cytometry: Critical Assessm ...

Nature Publishing Group2013

Genetic and physiological analysis of Rht8 in bread wheat: an alternative source of semi-dwarfism with a reduced sensitivity to brassinosteroids

René Dreos

Oxford, Oxford University Press2012