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Jacques Rougemont

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Related publications (46)

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A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing

Didier Trono, Philipp Bucher, Jacques Rougemont, Giovanna Ambrosini, Nadine Fournier, Adamantia Kapopoulou, Anna Claire Groner, Annamaria Kauzlaric

BACKGROUND: KRAB-ZFPs (Kruppel-associated box domain-zinc finger proteins) are vertebrate-restricted transcriptional repressors encoded in the hundreds by the mouse and human genomes. They act via an essential cofactor, KAP1, which recruits effectors respo ...

BioMed Central2011

Stochastic phase oscillator models for circadian clocks

Felix Naef, Jacques Rougemont

Periodic environments like we experience on the surface of planet earth lead living organisms to evolve molecular anticipation devices known a circadian clocks. The word circadian refers to the period of these oscillations which last about (circa) one day ...

Springer2008

Probabilistic base calling of Solexa sequencing data

Felix Naef, Jacques Rougemont, Christian Iseli, Arnaud Amzallag

BACKGROUND: Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput dat ...

BioMed Central2008

The Microbe browser for comparative genomics

Jacques Rougemont

The Microbe browser is a web server providing comparative microbial genomics data. It offers comprehensive, integrated data from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) database, displayed along with gene pr ...

Oxford University Press2009

Comparative genomic and phylogeographic analysis of Mycobacterium leprae

Stewart Cole, Jacques Rougemont, Philippe Busso, Pushpendra Singh

Reductive evolution and massive pseudogene formation have shaped the 3.31-Mb genome of Mycobacterium leprae, an unculturable obligate pathogen that causes leprosy in humans. The complete genome sequence of M. leprae strain Br4923 from Brazil was obtained b ...

2009

The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae

Felix Naef, Jacques Rougemont

Small nucleolar RNAs (snoRNAs) play a key role in ribosomal RNA biogenesis, yet factors controlling their expression are unknown. We found that the majority of Saccharomyces snoRNA promoters display an aRCCCTaa sequence motif at the upstream border of a TA ...

Elsevier2010

Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

Olivier Martin, Bart Deplancke, Felix Naef, Jacques Rougemont, Mauro Delorenzi, Nicolas Jean Philippe Guex, Laura Symul

Interactions of cell-autonomous circadian oscillators with diurnal cycles govern the temporal compartmentalization of cell physiology in mammals. To understand the transcriptional and epigenetic basis of diurnal rhythms in mouse liver genome-wide, we gener ...

Public Library Science2012

GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR

Bart Deplancke, Jacques Rougemont, Fabrice David, Andreas Massouras, Carine Delattre-Gubelmann

The vast majority of genes in humans and other organisms undergo alternative splicing, yet the biological function of splice variants is still very poorly understood in large part because of the lack of simple tools that can map the expression profiles and ...

2011

Structural Variation-Associated Expression Changes Are Paralleled by Chromatin Architecture Modifications

Jacques Rougemont, Marion Leleu, Nele Gheldof

Copy number variants (CNVs) influence the expression of genes that map not only within the rearrangement, but also to its flanks. To assess the possible mechanism(s) underlying this "neighboring effect", we compared intrachromosomal interactions and histon ...

Public Library of Science2013

Privacy-enhancing technologies for medical tests using genomic data

Jean-Pierre Hubaux, Jacques Fellay, Jacques Rougemont, Erman Ayday, Jean Louis Raisaro, Mathias Jacques Jean-Marc Humbert

In this invention, we propose privacy-enhancing technologies for medical tests and personalized medicine methods, which utilize patients' genomic data. Assuming the whole genome sequencing is done by a certified institution, we propose to store patients' g ...

2016

Genome-Wide Definition of the SigF Regulon in Mycobacterium tuberculosis

Stewart Cole, Jacques Rougemont, Claudia Sala, Ruben Hartkoorn, Philippe Busso, Swapna Uplekar

In Mycobacterium tuberculosis the alternative sigma factor SigF controls the expression of a particular subset of genes by altering RNA polymerase specificity. Here, we utilize two genome-wide approaches to identify SigF-binding sites: chromatin immunoprec ...

American Society for Microbiology2012

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription

Sebastian Maerkl, Felix Naef, Jacques Rougemont, Nicolas Dénervaud, Philippe Jacquet

In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and the molecular basis for their coregulation remains largely unknown. Here we ...

Cold Spring Harbor Laboratory Press2014

Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling

Jacques Rougemont

Plant growth is strongly influenced by the presence of neighbors that compete for light resources. In response to vegetational shading shade-intolerant plants such as Arabidopsis display a suite of developmental responses known as the shade-avoidance syndr ...

Wiley-Blackwell2012

High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis

Stewart Cole, Jacques Rougemont, Claudia Sala, Swapna Uplekar

To construct a regulatory map of the genome of the human pathogen, Mycobacterium tuberculosis, we applied two complementary high-resolution approaches: strand-specific RNA-seq, to survey the global transcriptome, and ChIP-seq, to monitor the genome-wide dy ...

Oxford University Press2013

Computational analysis of protein-DNA interactions from ChIP-seq data

Felix Naef, Jacques Rougemont

Chromatin immunoprecipitation experiments followed by ultra-high-throughput sequencing (ChIP-seq) is becoming the method of choice to identify transcription factor binding sites in prokaryotes and eukaryotes in vivo. Here, we review the computational steps ...

2011

GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms

Bart Deplancke, Jacques Rougemont

GETPrime (http://bbcftools.epfl.ch/getprime) is a database with a web frontend providing geneand transcript-specific, pre-computed qPCR primer pairs. The primers have been optimized for genome-wide specificity and for allowing the selective amplification o ...

Oxford University Press2017

Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L

Jacques Rougemont

TORC1 is a conserved multisubunit kinase complex that regulates many aspects of eukaryotic growth including the biosynthesis of ribosomes. The TOR protein kinase resident in TORC1 is responsive to environmental cues and is potently inhibited by the natural ...

2011

Processing and analyzing ChIP-seq data: from short reads to regulatory interactions

Jacques Rougemont, Marion Leleu

Chromatin-immunoprecipitation and sequencing (ChIP-seq) is a rapidly maturing technology that draws on the power of high-throughput short-read sequencing to decipher chromatin states with unprecedented precision and breadth. Although some aspects of the ex ...

2010

Functional characterization of the TERRA transcriptome at damaged telomeres

Joachim Lingner, Jacques Rougemont, Antonio Porro, Sascha Feuerhahn

Telomere deprotection occurs during tumorigenesis and aging upon telomere shortening or loss of the telomeric shelterin component TRF2. Deprotected telomeres undergo changes in chromatin structure and elicit a DNA damage response (DDR) that leads to cellul ...

Nature Publishing Group2014

Probable zoonotic leprosy in the southern United States

Stewart Cole, Jacques Rougemont, Philippe Busso, Pushpendra Singh, Adamantia Kapopoulou, Rahul Sharma

In the southern region of the United States, such as in Louisiana and Texas, there are autochthonous cases of leprosy among native-born Americans with no history of foreign exposure. In the same region, as well as in Mexico, wild armadillos are infected wi ...

2011