Full Text Journal Articles by
Author Emmanuelle Becker

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Exposure of human fetal kidneys to mild analgesics interferes with early nephrogenesis.

Sabrina Leverrier-Penna, Alain Michel, Laetitia L Lecante, Nathalie Costet, Antonio Suglia, Christèle Desdoits-Lethimonier, Hugoline Boulay, Roselyne Viel, Jonathan M Chemouny, Emmanuelle Becker, Vincent Lavoué, Antoine D Rolland, Nathalie Dejucq-Rainsford, Cécile Vigneau, Séverine Mazaud-Guittot,

Acetaminophen, aspirin, and ibuprofen are mild analgesics commonly used by pregnant women, the sole current recommendation being to avoid ibuprofen from the fifth month of gestation. The nephrotoxicity of these three analgesics is well documented in adults, as is their interference with prostaglandins biosynthesis. Here we investigated the effect of ... Read more >>

FASEB J (FASEB journal : official publication of the Federation of American Societies for Experimental Biology)
[2021, 35(7):e21718]

Cited: 0 times

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PAX2GRAPHML: a Python library for large-scale regulation network analysis using BIOPAX.

François Moreews, Hugo Simon, Anne Siegel, Florence Gondret, Emmanuelle Becker,

<h4>Summary</h4>PAX2GRAPHML is an open source Python library that allows to easily manipulate BioPAX source files as regulated reaction graphs described in .graphml format. The concept of regulated reactions, which allows connecting regulatory, signaling and metabolic levels, has been used. Biochemical reactions and regulatory interactions are homogeneously described by regulated reactions ... Read more >>

Bioinformatics (Bioinformatics (Oxford, England))
[2021, :]

Cited: 0 times

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Plasma microRNA signature in presymptomatic and symptomatic subjects with C9orf72-associated frontotemporal dementia and amyotrophic lateral sclerosis.

Virgilio Kmetzsch, Vincent Anquetil, Dario Saracino, Daisy Rinaldi, Agnès Camuzat, Thomas Gareau, Ludmila Jornea, Sylvie Forlani, Philippe Couratier, David Wallon, Florence Pasquier, Noémie Robil, Pierre de la Grange, Ivan Moszer, Isabelle Le Ber, Olivier Colliot, Emmanuelle Becker, ,

<h4>Objective</h4>To identify potential biomarkers of preclinical and clinical progression in chromosome 9 open reading frame 72 gene (<i>C9orf72)</i>-associated disease by assessing the expression levels of plasma microRNAs (miRNAs) in <i>C9orf72</i> patients and presymptomatic carriers.<h4>Methods</h4>The PREV-DEMALS study is a prospective study including 22 <i>C9orf72</i> patients, 45 presymptomatic <i>C9orf72</i> mutation carriers and ... Read more >>

J Neurol Neurosurg Psychiatry (Journal of neurology, neurosurgery, and psychiatry)
[2021, 92(5):485-493]

Cited: 0 times

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The anti-cancer drug 5-fluorouracil affects cell cycle regulators and potential regulatory long non-coding RNAs in yeast.

Bingning Xie, Emmanuelle Becker, Igor Stuparevic, Maxime Wery, Ugo Szachnowski, Antonin Morillon, Michael Primig,

5-fluorouracil (5-FU) was isolated as an inhibitor of thymidylate synthase, which is important for DNA synthesis. The drug was later found to also affect the conserved 3'-5' exoribonuclease EXOSC10/Rrp6, a catalytic subunit of the RNA exosome that degrades and processes protein-coding and non-coding transcripts. Work on 5-FU's cytotoxicity has been ... Read more >>

RNA Biol (RNA biology)
[2019, 16(6):727-741]

Cited: 1 time

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TOXsIgN: a cross-species repository for toxicogenomic signatures.

Thomas A Darde, Pierre Gaudriault, Rémi Beranger, Clément Lancien, Annaëlle Caillarec-Joly, Olivier Sallou, Nathalie Bonvallot, Cécile Chevrier, Séverine Mazaud-Guittot, Bernard Jégou, Olivier Collin, Emmanuelle Becker, Antoine D Rolland, Frédéric Chalmel,

Motivation:At the same time that toxicologists express increasing concern about reproducibility in this field, the development of dedicated databases has already smoothed the path toward improving the storage and exchange of raw toxicogenomic data. Nevertheless, none provides access to analyzed and interpreted data as originally reported in scientific publications. Given ... Read more >>

Bioinformatics (Bioinformatics (Oxford, England))
[2018, 34(12):2116-2122]

Cited: 5 times

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Clinicopathological characteristics of ROS1- and RET-rearranged NSCLC in caucasian patients: Data from a cohort of 713 non-squamous NSCLC lacking KRAS/EGFR/HER2/BRAF/PIK3CA/ALK alterations.

Frédéric Dugay, Francisco Llamas-Gutierrez, Marjory Gournay, Sarah Medane, François Mazet, Dan Christian Chiforeanu, Emmanuelle Becker, Régine Lamy, Hervé Léna, Nathalie Rioux-Leclercq, Marc-Antoine Belaud-Rotureau, Florian Cabillic,

Targeted therapies have substantially changed the management of non-small cell lung cancer (NSCLC) patients with driver oncogenes. Given the high frequency, <i>EGFR</i> and <i>ALK</i> aberrations were the first to be detected and paved the way for tyrosine kinase inhibitor (TKI) treatments. Other kinases such as <i>ROS1</i> and more recently <i>RET</i> ... Read more >>

Oncotarget (Oncotarget)
[2017, 8(32):53336-53351]

Cited: 10 times

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The protein expression landscape of mitosis and meiosis in diploid budding yeast.

Emmanuelle Becker, Emmanuelle Com, Régis Lavigne, Marie-Hélène Guilleux, Bertrand Evrard, Charles Pineau, Michael Primig,

Saccharomyces cerevisiae is an established model organism for the molecular analysis of fundamental biological processes. The genomes of numerous strains have been sequenced, and the transcriptome and proteome ofmajor phases during the haploid and diploid yeast life cycle have been determined. However, much less is known about dynamic changes of ... Read more >>

J Proteomics (Journal of proteomics)
[2017, 156:5-19]

Cited: 2 times

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Ndt80 activates the meiotic ORC1 transcript isoform and SMA2 via a bi-directional middle sporulation element in Saccharomyces cerevisiae.

Bingning Xie, Joe Horecka, Angela Chu, Ronald W Davis, Emmanuelle Becker, Michael Primig,

The origin of replication complex subunit ORC1 is important for DNA replication. The gene is known to encode a meiotic transcript isoform (mORC1) with an extended 5'-untranslated region (5'-UTR), which was predicted to inhibit protein translation. However, the regulatory mechanism that controls the mORC1 transcript isoform is unknown and no ... Read more >>

RNA Biol (RNA biology)
[2016, 13(9):772-782]

Cited: 6 times

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The epigenetic processes of meiosis in male mice are broadly affected by the widely used herbicide atrazine.

Aurore Gely-Pernot, Chunxiang Hao, Emmanuelle Becker, Igor Stuparevic, Christine Kervarrec, Frédéric Chalmel, Michael Primig, Bernard Jégou, Fatima Smagulova,

<h4>Background</h4>Environmental factors such as pesticides can cause phenotypic changes in various organisms, including mammals. We studied the effects of the widely used herbicide atrazine (ATZ) on meiosis, a key step of gametogenesis, in male mice.<h4>Methods</h4>Gene expression pattern was analysed by Gene-Chip array. Genome-wide mapping of H3K4me3 marks distribution was done ... Read more >>

BMC Genomics (BMC genomics)
[2015, 16:885]

Cited: 15 times

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Global alterations of the transcriptional landscape during yeast growth and development in the absence of Ume6-dependent chromatin modification.

Aurélie Lardenois, Emmanuelle Becker, Thomas Walther, Michael J Law, Bingning Xie, Philippe Demougin, Randy Strich, Michael Primig,

Chromatin modification enzymes are important regulators of gene expression and some are evolutionarily conserved from yeast to human. Saccharomyces cerevisiae is a major model organism for genome-wide studies that aim at the identification of target genes under the control of conserved epigenetic regulators. Ume6 interacts with the upstream repressor site ... Read more >>

Mol Genet Genomics (Molecular genetics and genomics : MGG)
[2015, 290(5):2031-2046]

Cited: 5 times

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Integrated RNA- and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development.

Emmanuelle Becker, Yuchen Liu, Aurélie Lardenois, Thomas Walther, Joe Horecka, Igor Stuparevic, Michael J Law, Régis Lavigne, Bertrand Evrard, Philippe Demougin, Michael Riffle, Randy Strich, Ronald W Davis, Charles Pineau, Michael Primig,

<h4>Unlabelled</h4>Diploid budding yeast undergoes rapid mitosis when it ferments glucose, and in the presence of a non-fermentable carbon source and the absence of a nitrogen source it triggers sporulation. Rich medium with acetate is a commonly used pre-sporulation medium, but our understanding of the molecular events underlying the acetate-driven transition ... Read more >>

J Proteomics (Journal of proteomics)
[2015, 119:30-44]

Cited: 2 times

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Extreme multifunctional proteins identified from a human protein interaction network.

Charles E Chapple, Benoit Robisson, Lionel Spinelli, Céline Guien, Emmanuelle Becker, Christine Brun,

Moonlighting proteins are a subclass of multifunctional proteins whose functions are unrelated. Although they may play important roles in cells, there has been no large-scale method to identify them, nor any effort to characterize them as a group. Here, we propose the first method for the identification of 'extreme multifunctional' ... Read more >>

Nat Commun (Nature communications)
[2015, 6:7412]

Cited: 39 times

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The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community.

Thomas A Darde, Olivier Sallou, Emmanuelle Becker, Bertrand Evrard, Cyril Monjeaud, Yvan Le Bras, Bernard Jégou, Olivier Collin, Antoine D Rolland, Frédéric Chalmel,

We report the development of the ReproGenomics Viewer (RGV), a multi- and cross-species working environment for the visualization, mining and comparison of published omics data sets for the reproductive science community. The system currently embeds 15 published data sets related to gametogenesis from nine model organisms. Data sets have been ... Read more >>

Nucleic Acids Res (Nucleic acids research)
[2015, 43(W1):W109-16]

Cited: 17 times

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The conserved histone deacetylase Rpd3 and the DNA binding regulator Ume6 repress BOI1's meiotic transcript isoform during vegetative growth in Saccharomyces cerevisiae.

Yuchen Liu, Igor Stuparevic, Bingning Xie, Emmanuelle Becker, Michael J Law, Michael Primig,

BOI1 and BOI2 are paralogs important for the actin cytoskeleton and polar growth. BOI1 encodes a meiotic transcript isoform with an extended 5'-untranslated region predicted to impair protein translation. It is, however, unknown how the isoform is repressed during mitosis, and if Boi1 is present during sporulation. By interpreting microarray ... Read more >>

Mol Microbiol (Molecular microbiology)
[2015, 96(4):861-874]

Cited: 6 times

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The histone deacetylase Rpd3/Sin3/Ume6 complex represses an acetate-inducible isoform of VTH2 in fermenting budding yeast cells.

Igor Stuparevic, Emmanuelle Becker, Michael J Law, Michael Primig,

The tripartite Rpd3/Sin3/Ume6 complex represses meiotic isoforms during mitosis. We asked if it also controls starvation-induced isoforms. We report that VTH1/VTH2 encode acetate-inducible isoforms with extended 5'-regions overlapping antisense long non-coding RNAs. Rpd3 and Ume6 repress the long isoform of VTH2 during fermentation. Cells metabolising glucose contain Vth2, while the ... Read more >>

FEBS Lett (FEBS letters)
[2015, 589(8):924-932]

Cited: 1 time

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Combining RNA and protein profiling data with network interactions identifies genes associated with spermatogenesis in mouse and human.

Fabrice G Petit, Christine Kervarrec, Soazik P Jamin, Fatima Smagulova, Chunxiang Hao, Emmanuelle Becker, Bernard Jégou, Frédéric Chalmel, Michael Primig,

Genome-wide RNA profiling studies have identified hundreds of transcripts that are highly expressed in mammalian male germ cells, including many that are undetectable in somatic control tissues. Among them, genes important for spermatogenesis are significantly enriched. Information about mRNAs and their cognate proteins facilitates the identification of novel conserved target ... Read more >>

Biol Reprod (Biology of reproduction)
[2015, 92(3):71]

Cited: 12 times

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The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development.

Aurélie Lardenois, Igor Stuparevic, Yuchen Liu, Michael J Law, Emmanuelle Becker, Fatima Smagulova, Karl Waern, Marie-Hélène Guilleux, Joe Horecka, Angela Chu, Christine Kervarrec, Randy Strich, Mike Snyder, Ronald W Davis, Lars M Steinmetz, Michael Primig,

It was recently reported that the sizes of many mRNAs change when budding yeast cells exit mitosis and enter the meiotic differentiation pathway. These differences were attributed to length variations of their untranslated regions. The function of UTRs in protein translation is well established. However, the mechanism controlling the expression ... Read more >>

Nucleic Acids Res (Nucleic acids research)
[2015, 43(1):115-128]

Cited: 12 times

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Multifunctional proteins revealed by overlapping clustering in protein interaction network.

Emmanuelle Becker, Benoît Robisson, Charles E Chapple, Alain Guénoche, Christine Brun,

<h4>Motivation</h4>Multifunctional proteins perform several functions. They are expected to interact specifically with distinct sets of partners, simultaneously or not, depending on the function performed. Current graph clustering methods usually allow a protein to belong to only one cluster, therefore impeding a realistic assignment of multifunctional proteins to clusters.<h4>Results</h4>Here, we present ... Read more >>

Bioinformatics (Bioinformatics (Oxford, England))
[2012, 28(1):84-90]

Cited: 59 times

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Functional integrative levels in the human interactome recapitulate organ organization.

Ouissem Souiai, Emmanuelle Becker, Carlos Prieto, Alia Benkahla, Javier De las Rivas, Christine Brun,

Interactome networks represent sets of possible physical interactions between proteins. They lack spatio-temporal information by construction. However, the specialized functions of the differentiated cell types which are assembled into tissues or organs depend on the combinatorial arrangements of proteins and their physical interactions. Is tissue-specificity, therefore, encoded within the interactome? ... Read more >>

PLoS One (PloS one)
[2011, 6(7):e22051]

Cited: 10 times

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A strategy for interaction site prediction between phospho-binding modules and their partners identified from proteomic data.

Willy Aucher, Emmanuelle Becker, Emilie Ma, Simona Miron, Arnaud Martel, Françoise Ochsenbein, Marie-Claude Marsolier-Kergoat, Raphaël Guerois,

Small and large scale proteomic technologies are providing a wealth of potential interactions between proteins bearing phospho-recognition modules and their substrates. Resulting interaction maps reveal such a dense network of interactions that the functional dissection and understanding of these networks often require to break specific interactions while keeping the rest ... Read more >>

Mol Cell Proteomics (Molecular & cellular proteomics : MCP)
[2010, 9(12):2745-2759]

Cited: 9 times

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HMM-Kalign: a tool for generating sub-optimal HMM alignments.

Emmanuelle Becker, Aurélie Cotillard, Vincent Meyer, Hocine Madaoui, Raphaël Guérois,

Recent development of strategies using multiple sequence alignments (MSA) or profiles to detect remote homologies between proteins has led to a significant increase in the number of proteins whose structures can be generated by comparative modeling methods. However, prediction of the optimal alignment between these highly divergent homologous proteins remains ... Read more >>

Bioinformatics (Bioinformatics (Oxford, England))
[2007, 23(22):3095-3097]

Cited: 5 times

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Detection of a tandem BRCT in Nbs1 and Xrs2 with functional implications in the DNA damage response.

Emmanuelle Becker, Vincent Meyer, Hocine Madaoui, Raphaël Guerois,

<h4>Motivation</h4>Human Nbs1 and its homolog Xrs2 in Saccharomyces cerevisiae are part of the conserved MRN complex (MRX in yeast) which plays a crucial role in maintaining genomic stability. NBS1 corresponds to the gene mutated in the Nijmegen breakage syndrome (NBS) known as a radiation hyper-sensitive disease. Despite the conservation and ... Read more >>

Bioinformatics (Bioinformatics (Oxford, England))
[2006, 22(11):1289-1292]

Cited: 45 times

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Sequence search methods and scoring functions for the design of protein structures.

Hocine Madaoui, Emmanuelle Becker, Raphael Guerois,

This chapter focuses on the methods developed for the automatic or semiautomatic design of protein structures. We present several algorithms for the exploration of the sequence space and scoring of the designed models. There are now several successful designs that have been achieved using these approaches such as the stabilization ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2006, 340:183-206]

Cited: 1 time

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