Publications de Jacques Rougemont

Multicenter analysis of sputum microbiota in tuberculosis patients

Stewart Cole, Claudia Sala, Jacques Rougemont, Philippe Busso, Marion Leleu, Andrej Benjak

The impact of tuberculosis and of anti-tuberculosis therapy on composition and modification of human lung microbiota has been the object of several investigations. However, no clear outcome has been presented so far and the relationship betweenM.tuberculos ...

2020

Two-Tier Mapper, an unbiased topology-based clustering method for enhanced global gene expression analysis

Kathryn Hess Bellwald, Cathrin Brisken, Jacques Rougemont, Rachel Marcone

Motivation: Unbiased clustering methods are needed to analyze growing numbers of complex data sets. Currently available clustering methods often depend on parameters that are set by the user, they lack stability, and are not applicable to small data sets. ...

2019

Differential regulation of RNA polymerase III genes during liver regeneration

Felix Naef, Philippe Jacquet, Nicolas Jean Philippe Guex, Jonathan Aryeh Sobel, Cristian Carmeli, Olivier Martin, Irina Krier, Mauro Delorenzi, Nouria Hernandez, Bart Deplancke, Jacques Rougemont, François Mange, Laura Symul, Fabrice David, Sunil Kumar Raghav, Julien Delafontaine, Marion Leleu, Julia Catharina Cajan, Winship Herr, Kyle Gustafson, Maykel Lopes, Dominic Villeneuve, Ioannis Xenarios

Mouse liver regeneration after partial hepatectomy involves cells in the remaining tissue synchronously entering the cell division cycle. We have used this system and H3K4me3, Pol II and Pol III profiling to characterize adaptations in Pol III transcriptio ...

Oxford University Press (OUP)2019

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

Privacy-enhancing technologies for medical tests using genomic data

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

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

Bicaudal C1 promotes pancreatic NEUROG3+ endocrine progenitor differentiation and ductal morphogenesis

Daniel Constam, Anne Grapin-Botton, Joan Goulley, Laurence Anne E Lemaire, Jacques Rougemont, Yung Hae Kim

In human, mutations in bicaudal C1 (BICC1), an RNA binding protein, have been identified in patients with kidney dysplasia. Deletion of Bicc1 in mouse leads to left-right asymmetry randomization and renal cysts. Here, we show that BICC1 is also expressed i ...

Company Of Biologists Ltd2015

Phage-dependent variability of Candidatus ‘Accumulibacter phosphatis’ populations in aerobic granular sludge

Aline Sondra Adler, Christof Holliger, Julien Maillard, Jacques Rougemont

During the past 20 years, aerobic granular sludge (AGS) has been extensively studied with the aim to develop an attractive alternative to conventional activated sludge for wastewater treatment. The phosphate-accumulating organism (PAO) Candidatus ‘Accumuli ...

2015

Analysis of S. pombe SIN protein association to the SPB reveals two genetically separable states of the SIN

Michaël Unser, Daniel Sage, Viesturs Simanis, Daniel Andreas Schmitter, Andrea Krapp, Jacques Rougemont, Anastasia Chasapi, Ioannis Xenarios

The Schizosaccharomyces pombe septation initiation network (SIN) regulates cytokinesis, and asymmetric association of SIN proteins with the mitotic spindle pole bodies (SPBs) is important for its regulation. Here, we have used semi-automated image analysis ...

Company Of Biologists Ltd2015

The Intestinal Microbiota Contributes to the Ability of Helminths to Modulate Allergic Inflammation

Alexis Rapin, Jacques Rougemont, Laure Menin, Luc Xavier Marie Lebon, Ilaria Mosconi, Nicola Harris, Benjamin John Marsland, Mario Michael Zaiss, Lalit Kumar Dubey, Alessandra Piersigilli, Andrew J. Macpherson

Intestinal helminths are potent regulators of their host's immune system and can ameliorate inflammatory diseases such as allergic asthma. In the present study we have assessed whether this anti-inflammatory activity was purely intrinsic to helminths, or w ...

Elsevier2015

Progesterone and Wnt4 control mammary stem cells via myoepithelial crosstalk

Cathrin Brisken, Renuga Devi Rajaram, Ayyakkannu Ayyanan, Jacques Rougemont, Marian Caikovski, Duje Buric

Ovarian hormones increase breast cancer risk by poorly understood mechanisms. We assess the role of progesterone on global stem cell function by serially transplanting mouse mammary epithelia. Progesterone receptor (PR) deletion severely reduces the regene ...

Wiley-Blackwell2015

The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in Mycobacterium tuberculosis

Stewart Cole, Claudia Sala, Swapna Uplekar, Jacques Rougemont, Andrej Benjak

The PhoPR two-component system is essential for virulence in Mycobacterium tuberculosis where it controls expression of approximately 2% of the genes, including those for the ESX-1 secretion apparatus, a major virulence determinant. Mutations in phoP lead ...

Public Library of Science2014

Functional characterization of the TERRA transcriptome at damaged telomeres

Joachim Lingner, Jacques Rougemont, Antonio Porro, Sascha Feuerhahn, Julien Delafontaine

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

Genome-wide re-sequencing of multidrug-resistant Mycobacterium leprae Airaku-3

Stewart Cole, Jacques Rougemont, Philippe Busso, Pushpendra Singh, Andrej Benjak, Charlotte Avanzi

Genotyping and molecular characterization of drug resistance mechanisms in Mycobacterium leprae enables disease transmission and drug resistance trends to be monitored. In the present study, we performed genome-wide analysis of Airaku-3, a multidrug-resist ...

Wiley-Blackwell2014

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

Philipp Bucher, Amos Bairoch, Olivier Michielin, Heinz Stockinger, Mauro Delorenzi, Jacques Rougemont, Ioannis Xenarios

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRI ...

Oxford University Press2014

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

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

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

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

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

Stewart Cole, Claudia Sala, Swapna Uplekar, Jacques Rougemont

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

Protecting and Evaluating Genomic Privacy in Medical Tests and Personalized Medicine

Jean-Pierre Hubaux, Jacques Rougemont, Erman Ayday, Jean Louis Raisaro

In this paper, we propose privacy-enhancing technologies for medical tests and personalized medicine methods that use patients' genomic data. Focusing on genetic disease-susceptibility tests, we develop a new architecture (between the patient and the medic ...

2013

PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data

Christof Holliger, Julien Maillard, David Gregory Weissbrodt, Lucas Sinclair, Pierre Rossi, Noam Shani, Jacques Rougemont

Background: In molecular microbial ecology, massive sequencing is gradually replacing classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for the characterization of microb ...

BioMed Central2012

Virulence Regulator EspR of Mycobacterium tuberculosis Is a Nucleoid-Associated Protein

Benjamin Blasco, Stewart Cole, Claudia Sala, Florence Pojer, Jeffrey Chen, Swapna Uplekar, Jacques Rougemont, Ruben Hartkoorn

The principal virulence determinant of Mycobacterium tuberculosis (Mtb), the ESX-1 protein secretion system, is positively controlled at the transcriptional level by EspR. Depletion of EspR reportedly affects a small number of genes, both positively or neg ...

Public Library of Science2012