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@article{Krischuns2022, abstract = {During annual influenza epidemics, influenza B viruses (IBVs) co-circulate with influenza A viruses (IAVs), can become predominant and cause severe morbidity and mortality. Phylogenetic analyses suggest that IAVs (primarily avian viruses) and IBVs (primarily human viruses) have diverged over long time scales. Identifying their common and distinctive features is an effective approach to increase knowledge about the molecular details of influenza infection. The virus-encoded RNA-dependent RNA polymerases (FluPolB and FluPolA) are PB1-PB2-PA heterotrimers that perform transcription and replication of the viral genome in the nucleus of infected cells. Initiation of viral mRNA synthesis requires a direct association of FluPol with the host RNA polymerase II (RNAP II), in particular the repetitive C-terminal domain (CTD) of the major RNAP II subunit, to enable “cap-snatching” whereby 5'-capped oligomers derived from nascent RNAP II transcripts are pirated to prime viral transcription. Here, we present the first high-resolution co-crystal structure of FluPolB bound to a CTD mimicking peptide at a binding site crossing from PA to PB2. By performing structure-based mutagenesis of FluPolB and FluPolA followed by a systematic investigation of FluPol-CTD binding, FluPol activity and viral phenotype, we demonstrate that IBVs and IAVs have evolved distinct binding interfaces to recruit the RNAP II CTD, despite the CTD sequence being highly conserved across host species. We find that the PB2 627 subdomain, a major determinant of FluPol-host cell interactions and IAV host-range, is involved in CTD-binding for IBVs but not for IAVs, and we show that FluPolB and FluPolA bind to the host RNAP II independently of the CTD. Altogether, our results strongly suggest that the CTD-binding modes of IAV and IBV represent avian- and human-optimized binding modes, respectively, and that their divergent evolution was shaped by the broader interaction network between the FluPol and the host transcriptional machinery. Authors summary During seasonal influenza epidemics, influenza B viruses (IBVs) co-circulate with influenza A viruses (IAVs) and can cause severe outcomes. The influenza polymerase is a key drug target and it is therefore important to understand the common and distinctive molecular features of IBV and IAV polymerases. To achieve efficient transcription and replication in the nucleus of infected cells, influenza polymerases closely cooperate with the cellular RNA polymerase II (RNAP II) and interact with the repetitive C-terminal domain (CTD) of its major subunit. Here we gained new insights into the way IBV and IAV polymerases interact with the CTD of RNAP II. High-resolution structural data was used to perform structure-based mutagenesis of IBV and IAV polymerases followed by a systematic investigation of their interaction with RNAP II, transcription/replication activity and viral phenotype. Strikingly, we found that IBVs and IAVs have evolved distinct interfaces to interact with the host transcriptional machinery, in particular with the CTD of RNAP II. We provide evidence that these differences may have evolved as a consequence of the differences in IBV and IAV host range. Our findings are of significant importance with regard to the development of broad-spectrum antivirals that target the virus-host interface. {\#}{\#}{\#} Competing Interest Statement The authors have declared no competing interest.}, author = {Krischuns, Tim and Isel, Catherine and Drncova, Petra and Lukarska, Maria and Pflug, Alexander and Paisant, Sylvain and Navratil, Vincent and Cusack, Stephen and Naffakh, Nadia}, doi = {10.1101/2022.02.04.479088}, file = {:Users/navratil/Documents/Mendeley Desktop/2022/Krischuns et al/bioRxiv/bioRxiv{\_}Krischuns et al.{\_}Type B and Type A influenza polymerases have evolved 3 distinct binding interfaces to recruit the RNA polymeras.pdf:pdf}, journal = {bioRxiv}, month = {feb}, pages = {2022.02.04.479088}, publisher = {Cold Spring Harbor Laboratory}, title = {{Type B and Type A influenza polymerases have evolved 3 distinct binding interfaces to recruit the RNA polymerase II CTD 4 5 6}}, url = {https://doi.org/10.1101/2022.02.04.479088}, year = {2022} } @article{Touzot2022a, abstract = {Artificial light at night (ALAN) affects numerous physiological and behavioural mechanisms in various species by potentially disturbing circadian timekeeping systems and modifying melatonin levels. However, given the multiple direct and indirect effects of ALAN on organisms, large-scale transcriptomic approaches are essential to assess the global effect of ALAN on biological processes. Moreover, although studies have focused mainly on variations in gene expression during the night in the presence of ALAN, it is necessary to investigate the effect of ALAN on gene expression during the day. In this study, we combined de novo transcriptome sequencing and assembly, and a controlled laboratory experiment to evaluate the transcriptome-wide gene expression response using high-throughput (RNA-seq) in Bufo bufo tadpoles exposed to ecologically relevant light levels. Here, we demonstrated for the first time that ALAN affected gene expression at night (3.5{\%} and 11{\%} of differentially expressed genes when exposed to 0.1 and 5 lx compared to controls, respectively), but also during the day (11.2{\%} of differentially expressed genes when exposed to 5 lx compared to controls) with a dose-dependent effect. ALAN globally induced a downregulation of genes (during the night, 58{\%} and 62{\%} of the genes were downregulated when exposed to 0.1 and 5 lx compared to controls, respectively, and during the day, 61.2{\%} of the genes were downregulated when exposed to 5 lx compared to controls). ALAN effects were detected at very low levels of illuminance (0.1 lx) and affected mainly genes related to the innate immune system and, to a lesser extend to lipid metabolism. These results provide new insights into understanding the effects of ALAN on organism. ALAN impacted the expression of genes linked to a broad range of physiological pathways at very low levels of ALAN during night-time and during daytime, potentially resulting in reduced immune capacity under environmental immune challenges.}, author = {Touzot, Morgane and Lefebure, Tristan and Lengagne, Thierry and Secondi, Jean and Dumet, Adeline and Konecny-Dupre, Lara and Veber, Philippe and Navratil, Vincent and Duchamp, Claude and Mondy, Nathalie}, doi = {10.1016/j.scitotenv.2021.151734}, issn = {18791026}, journal = {Science of the Total Environment}, keywords = {Amphibian,Immune system,Light pollution,Lipid metabolism,RNA-seq,Transcriptome}, month = {apr}, pmid = {34808173}, publisher = {Elsevier B.V.}, title = {{Transcriptome-wide deregulation of gene expression by artificial light at night in tadpoles of common toads}}, volume = {818}, year = {2022} } @article{Lerat2021, abstract = {Transposable elements (TEs) are middle-repeated DNA sequences that can move along chromosomes using internal coding and regulatory regions. By their ability to move and because they are repeated, TEs can promote mutations. Especially they can alter the expression pattern of neighboring genes and have been shown to be involved in the mammalian regulatory network evolution. Human and mouse share more than 95{\%} of their genomes and are affected by comparable diseases, which makes the mouse a perfect model in cancer research. However not much investigation concerning the mouse TE content has been made on this topics. In human cancer condition, a global activation of TEs can been observed which may ask the question of their impact on neighboring gene functioning. In this work, we used RNA sequences of highly aggressive pancreatic tumors from mouse to analyze the gene and TE deregulation happening in this condition compared to pancreas from healthy animals. Our results show that several TE families are deregulated and that the presence of TEs is associated with the expression divergence of genes in the tumor condition. These results illustrate the potential role of TEs in the global deregulation at work in the cancer cells.}, author = {Lerat, Emmanuelle and Burlet, Nelly and Navratil, Vincent and No{\^{u}}s, Camilles}, doi = {10.1101/2021.07.16.452652}, journal = {bioRxiv}, month = {jul}, pages = {2021.07.16.452652}, publisher = {Cold Spring Harbor Laboratory}, title = {{Transposable element activity in the transcriptomic analysis of mouse pancreatic tumors}}, url = {https://doi.org/10.1101/2021.07.16.452652}, year = {2021} } @article{Oger-Desfeux2021, abstract = {We report the complete genome sequence of Bradyrhizobium sp. strain BDV5040, representative of Bradyrhizobium genospecies B, which symbiotically associates with legume hosts belonging to all three Fabaceae subfamilies across the Australian continent. The complete genome sequence provides a genetic reference for this Australian genospecies.}, author = {Oger-Desfeux, Christine and Briolay, J{\'{e}}r{\^{o}}me and Oger, Philippe M and Lafay, B{\'{e}}n{\'{e}}dicte}, doi = {10.1128/MRA.01326-20}, file = {:Users/navratil/Documents/Mendeley Desktop/2021/Oger-Desfeux et al/Microbiology resource announcements/Microbiology resource announcements{\_}Oger-Desfeux et al.{\_}Complete Genome Sequence of Bradyrhizobium sp. Strain BDV5040, Representative of.pdf:pdf}, issn = {2576-098X}, journal = {Microbiology resource announcements}, month = {jan}, number = {3}, pmid = {33479000}, publisher = {American Society for Microbiology}, title = {{Complete Genome Sequence of Bradyrhizobium sp. Strain BDV5040, Representative of Widespread Genospecies B in Australia.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/33479000 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC8407762}, volume = {10}, year = {2021} } @article{Oger-Desfeux2021a, abstract = {We report the complete genome sequence of Bradyrhizobium sp. strain BDV5419, representative of Bradyrhizobium genospecies L, which symbiotically associates with the Australian native legume Hardenbergia violaceae and is expected to represent a novel Bradyrhizobium species. The complete genome sequence provides a genetic reference for this Australian genospecies.}, author = {Oger-Desfeux, Christine and Briolay, J{\'{e}}r{\^{o}}me and Oger, Philippe M and Lafay, B{\'{e}}n{\'{e}}dicte}, doi = {10.1128/MRA.00042-21}, file = {:Users/navratil/Documents/Mendeley Desktop/2021/Oger-Desfeux et al/Microbiology resource announcements/Microbiology resource announcements{\_}Oger-Desfeux et al.{\_}Complete Genome Sequence of Bradyrhizobium sp. Strain BDV5419, Representative of.pdf:pdf}, issn = {2576-098X}, journal = {Microbiology resource announcements}, month = {feb}, number = {8}, pmid = {33632854}, publisher = {American Society for Microbiology}, title = {{Complete Genome Sequence of Bradyrhizobium sp. Strain BDV5419, Representative of Australian Genospecies L.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/33632854 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC7909079}, volume = {10}, year = {2021} } @article{Touzot2021, author = {Touzot, Morgane and Lefebure, Tristan and Lengagne, Thierry and Secondi, Jean and Dumet, Adeline and Konecny-Dupre, Lara and Veber, Philippe and Navratil, Vincent and Duchamp, Claude and Mondy, Nathalie}, doi = {10.1016/j.scitotenv.2021.151734}, issn = {00489697}, journal = {Science of The Total Environment}, keywords = {MEDLINE,Morgane Touzot,NCBI,NIH,NLM,Nathalie Mondy,National Center for Biotechnology Information,National Institutes of Health,National Library of Medicine,PubMed Abstract,Tristan Lefebure,doi:10.1016/j.scitotenv.2021.151734,pmid:34808173}, month = {nov}, pages = {151734}, publisher = {Sci Total Environ}, title = {{Transcriptome-wide deregulation of gene expression by artificial light at night in tadpoles of common toads}}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969721068108}, year = {2021} } @misc{Hufsky2021, abstract = {SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de}, author = {Hufsky, Franziska and Lamkiewicz, Kevin and Almeida, Alexandre and Aouacheria, Abdel and Arighi, Cecilia and Bateman, Alex and Baumbach, Jan and Beerenwinkel, Niko and Brandt, Christian and Cacciabue, Marco and Chuguransky, Sara and Drechsel, Oliver and Finn, Robert D. and Fritz, Adrian and Fuchs, Stephan and Hattab, Georges and Hauschild, Anne Christin and Heider, Dominik and Hoffmann, Marie and H{\"{o}}lzer, Martin and Hoops, Stefan and Kaderali, Lars and Kalvari, Ioanna and {Von Kleist}, Max and Kmiecinski, Ren{\'{o}} and K{\"{u}}hnert, Denise and Lasso, Gorka and Libin, Pieter and List, Markus and L{\"{o}}chel, Hannah F. and Martin, Maria J. and Martin, Roman and Matschinske, Julian and McHardy, Alice C. and Mendes, Pedro and Mistry, Jaina and Navratil, Vincent and Nawrocki, Eric P. and O'Toole, A{\'{i}}ne Niamh and Ontiveros-Palacios, Nancy and Petrov, Anton I. and Rangel-Pineros, Guillermo and Redaschi, Nicole and Reimering, Susanne and Reinert, Knut and Reyes, Alejandro and Richardson, Lorna and Robertson, David L. and Sadegh, Sepideh and Singer, Joshua B. and Theys, Kristof and Upton, Chris and Welzel, Marius and Williams, Lowri and Marz, Manja}, booktitle = {Briefings in Bioinformatics}, doi = {10.1093/bib/bbaa232}, issn = {14774054}, keywords = {SARS-CoV-2,drug design,epidemiology,sequencing,tools,virus bioinformatics}, month = {mar}, number = {2}, pages = {642--663}, pmid = {33147627}, publisher = {Oxford University Press}, title = {{Computational strategies to combat COVID-19: Useful tools to accelerate SARS-CoV-2 and coronavirus research}}, url = {https://pubmed.ncbi.nlm.nih.gov/33147627/}, volume = {22}, year = {2021} } @article{Ashraf2020, abstract = {{\textless}p{\textgreater}Influenza A viruses (IAVs) use diverse mechanisms to interfere with cellular gene expression. Although many RNA-seq studies have documented IAV-induced changes in host mRNA abundance, few were designed to allow an accurate quantification of changes in host mRNA splicing. Here, we show that IAV infection of human lung cells induces widespread alterations of cellular splicing, with an overall increase in exon inclusion and decrease in intron retention. Over half of the mRNAs that show differential splicing undergo no significant changes in abundance or in their 3′ end termination site, suggesting that IAVs can specifically manipulate cellular splicing. Among a randomly selected subset of 21 IAV-sensitive alternative splicing events, most are specific to IAV infection as they are not observed upon infection with VSV, induction of interferon expression or induction of an osmotic stress. Finally, the analysis of splicing changes in RED-depleted cells reveals a limited but significant overlap with the splicing changes in IAV-infected cells. This observation suggests that hijacking of RED by IAVs to promote splicing of the abundant viral NS1 mRNAs could partially divert RED from its target mRNAs. All our RNA-seq datasets and analyses are made accessible for browsing through a user-friendly Shiny interface (http://virhostnet.prabi.fr:3838/shinyapps/flu-splicing or https://github.com/cbenoitp/flu-splicing).{\textless}/p{\textgreater}}, author = {Ashraf, Usama and Benoit-Pilven, Clara and Navratil, Vincent and Ligneau, C{\'{e}}cile and Fournier, Guillaume and Munier, Sandie and Sismeiro, Odile and Copp{\'{e}}e, Jean-Yves and Lacroix, Vincent and Naffakh, Nadia}, doi = {10.1093/nargab/lqaa095}, issn = {2631-9268}, journal = {NAR Genomics and Bioinformatics}, month = {nov}, number = {4}, publisher = {Oxford Academic}, title = {{Influenza virus infection induces widespread alterations of host cell splicing}}, url = {https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqaa095/5998301}, volume = {2}, year = {2020} } @article{Sabatier2020, abstract = {{\textless}p{\textgreater}Viral metagenomics next-generation sequencing (mNGS) is increasingly being used to characterize the human virome. The impact of viral nucleic extraction on virome profiling has been poorly studied. Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods used for viral mNGS: two automated platforms (eMAG; MagNA Pure 24, MP24) and the manual QIAamp Viral RNA Mini Kit (QIAamp). Clinical respiratory samples (positive for Respiratory Syncytial Virus or Herpes Simplex Virus), one mock sample (including five viruses isolated from respiratory samples), and a no-template control (NTC) were extracted and processed through an mNGS workflow. QIAamp yielded a lower proportion of viral reads for both clinical and mock samples. The sample cross-contamination was higher when using MP24, with up to 36.09{\%} of the viral reads mapping to mock viruses in the NTC (vs. 1.53{\%} and 1.45{\%} for eMAG and QIAamp, respectively). The highest number of viral reads mapping to bacteriophages in the NTC was found with QIAamp, suggesting reagent contamination. Our results highlight the importance of the extraction method choice for accurate virome characterization.{\textless}/p{\textgreater}}, author = {Sabatier, Marina and Bal, Antonin and Destras, Gr{\'{e}}gory and Regue, Hadrien and Qu{\'{e}}rom{\`{e}}s, Gr{\'{e}}gory and Cheynet, Val{\'{e}}rie and Lina, Bruno and Bardel, Claire and Brengel-Pesce, Karen and Navratil, Vincent and Josset, Laurence}, doi = {10.3390/microorganisms8101539}, issn = {2076-2607}, journal = {Microorganisms}, keywords = {acid nucleic extraction,kitome,next-generation sequencing,sample cross-contamination,viral metagenomics}, month = {oct}, number = {10}, pages = {1539}, publisher = {Multidisciplinary Digital Publishing Institute}, title = {{Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses}}, url = {https://www.mdpi.com/2076-2607/8/10/1539}, volume = {8}, year = {2020} } @article{Galia2015, abstract = {Volume 3, no. 1, e01568-14, 2015. Page 1: The byline and affiliation line should read as given above.}, author = {Galia, Wessam and Mariani-Kurkdjian, Patricia and Bastien, Sylvere and Loukiadis, Estelle and Blanquet-Diot, St{\'{e}}phanie and Leriche, Françoise and Brugère, Hubert and Shima, Ayaka and Oswald, Eric and Cournoyer, Benoit and Thevenot-Sergentet, Delphine}, doi = {10.1128/genomeA.00880-15}, file = {:Users/navratil/Documents/Mendeley Desktop/2015/Galia et al/Genome announcements/Genome announcements{\_}Galia et al.{\_}Correction for Galia et al., Genome Sequence and Annotation of a Human Infection Isolate of Escherichi.pdf:pdf}, issn = {2169-8287}, journal = {Genome announcements}, number = {4}, pmid = {26227612}, publisher = {American Society for Microbiology}, title = {{Genome Sequence and Annotation of a Human Infection Isolate of Escherichia coli O26:H11 Involved in a Raw Milk Cheese Outbreak.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26227612 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4520910}, volume = {3}, year = {2015} } @article{Despres2014, abstract = {Background: Despite the intensive use of Bacillus thuringiensis israelensis (Bti) toxins for mosquito control, little is known about the long term effect of exposure to this cocktail of toxins on target mosquito populations. In contrast to the many cases of resistance to Bacillus thuringiensis Cry toxins observed in other insects, there is no evidence so far for Bti resistance evolution in field mosquito populations. High fitness costs measured in a Bti selected mosquito laboratory strain suggest that evolving resistance to Bti is costly. The aim of the present study was to identify transcription level and polymorphism variations associated with resistance to Bti toxins in the dengue vector Aedes aegypti. We used RNA sequencing (RNA-seq) for comparing a laboratory-selected strain showing elevated resistance to Bti toxins and its parental non-selected susceptible strain. As the resistant strain displayed two marked larval development phenotypes (slow and normal), each phenotype was analyzed separately in order to evidence potential links between resistance mechanisms and mosquito life-history traits. Results: A total of 12,458 genes were detected of which 844 were differentially transcribed between the resistant and susceptible strains. Polymorphism analysis revealed a total of 68,541 SNPs of which 12,571 SNPs exhibited more than 40{\%} frequency difference between the resistant and susceptible strains, affecting 2,953 genes. Bti resistance is associated with changes in the transcription level of enzymes involved in detoxification and chitin metabolism. Among previously described Bti-toxin receptors, four alkaline phosphatases (ALPs) were differentially transcribed between resistant and susceptible larvae, and non-synonymous changes affected the protein sequence of one cadherin, six aminopeptidases (APNs) and four a-amylases. Other putative Cry receptors located in lipid rafts, such as flotillin and glycoside hydrolases, were under-transcribed and/or contained non-synonymous substitutions. Finally, immunity-related genes showed contrasted transcription and polymorphisms patterns between the two developmental resistant phenotypes, suggesting the existence of trade-offs between Bti-resistance, life-history traits and immunity. Conclusions: The present study is the first to analyze the whole transcriptome of Bti-resistant mosquitoes by RNA-seq, shedding light on the importance of studying both transcription levels and sequence polymorphism variations to get a comprehensive view of insecticide resistance.}, author = {Despr{\'{e}}s, Laurence and Stalinski, Renaud and Tetreau, Guillaume and Paris, Margot and Bonin, Aur{\'{e}}lie and Navratil, Vincent and Reynaud, St{\'{e}}phane and David, Jean Philippe}, doi = {10.1186/1471-2164-15-926}, file = {:Users/navratil/Documents/Mendeley Desktop/2014/Despr{\'{e}}s et al/BMC Genomics/BMC Genomics{\_}Despr{\'{e}}s et al.{\_}Gene expression patterns and sequence polymorphisms associated with mosquito resistance to Bacillus thur(2).pdf:pdf}, issn = {14712164}, journal = {BMC Genomics}, keywords = {Bacillus thuringiensis israelensis toxins,Bio-insecticide resistance,Evolutionary trade-offs,Lipid rafts,Mosquito,RNA-seq,Resistance costs,Toxin receptors}, number = {1}, pmid = {25341495}, publisher = {BioMed Central Ltd.}, title = {{Gene expression patterns and sequence polymorphisms associated with mosquito resistance to Bacillus thuringiensis israelensis toxins}}, volume = {15}, year = {2014} } @article{Lehembre2013, abstract = {Heavy metals are pollutants which affect all organisms. Since a small number of eukaryotes have been investigated with respect to metal resistance, we hypothesize that many genes that control this phenomenon remain to be identified. This was tested by screening soil eukaryotic metatranscriptomes which encompass RNA from organisms belonging to the main eukaryotic phyla. Soil-extracted polyadenylated mRNAs were converted into cDNAs and 35 of them were selected for their ability to rescue the metal (Cd or Zn) sensitive phenotype of yeast mutants. Few of the genes belonged to families known to confer metal resistance when overexpressed in yeast. Several of them were homologous to genes that had not been studied in the context of metal resistance. For instance, the BOLA ones, which conferred cross metal (Zn, Co, Cd, Mn) resistance may act by interfering with Fe homeostasis. Other genes, such as those encoding 110- to 130-amino-acid-long, cysteine-rich polypeptides, had no homologues in databases. This study confirms that functional metatranscriptomics represents a powerful approach to address basic biological processes in eukaryotes. The selected genes can be used to probe new pathways involved in metal homeostasis and to manipulate the resistance level of selected organisms. {\textcopyright} 2013 John Wiley {\&} Sons Ltd and Society for Applied Microbiology.}, author = {Lehembre, Fr{\'{e}}d{\'{e}}ric and Doillon, Didier and David, Elise and Perrotto, Sandrine and Baude, Jessica and Foulon, Julie and Harfouche, Lamia and Vallon, Laurent and Poulain, Julie and {Da Silva}, Corinne and Wincker, Patrick and Oger-Desfeux, Christine and Richaud, Pierre and Colpaert, Jan V. and Chalot, Michel and Fraissinet-Tachet, Laurence and Blaudez, Damien and Marmeisse, Roland}, doi = {10.1111/1462-2920.12143}, issn = {14622912}, journal = {Environmental Microbiology}, month = {oct}, number = {10}, pages = {2829--2840}, pmid = {23663419}, title = {{Soil metatranscriptomics for mining eukaryotic heavy metal resistance genes}}, volume = {15}, year = {2013} } @article{Navratil2009, abstract = {Infectious diseases caused by viral agents kill millions of people every year. The improvement of prevention and treatment of viral infections and their associated diseases remains one of the main public health challenges. Towards this goal, deciphering virus-host molecular interactions opens new perspectives to understand the biology of infection and for the design of new antiviral strategies. Indeed, modelling of an infection network between viral and cellular proteins will provide a conceptual and analytic framework to efficiently formulate new biological hypothesis at the proteome scale and to rationalize drug discovery. Therefore, we present the first release of VirHostNet (Virus-Host Network), a public knowledge base specialized in the management and analysis of integrated virus-virus, virus-host and host-host interaction networks coupled to their functional annotations. VirHostNet integrates an extensive and original literature-curated dataset of virus-virus and virus-host interactions (2671 non-redundant interactions) representing more than 180 distinct viral species and one of the largest human interactome (10 672 proteins and 68 252 non-redundant interactions) reconstructed from publicly available data. The VirHostNet Web interface provides appropriate tools that allow efficient query and visualization of this infected cellular network. Public access to the VirHostNet knowledge-based system is available at http://pbildb1.univ-lyon1.fr/virhostnet. {\textcopyright} 2008 The Author(s).}, author = {Navratil, Vincent and De chassey, Beno{\^{i}}t and Meyniel, Laur{\`{e}}ne and Delmotte, St{\'{e}}phane and Gautier, Christian and Andr{\'{e}}, Patrice and Lotteau, Vincent and Rabourdin-Combe, Chantal}, doi = {10.1093/nar/gkn794}, file = {:Users/navratil/Documents/Mendeley Desktop/2009/Navratil et al/Nucleic Acids Research/Nucleic Acids Research{\_}Navratil et al.{\_}VirHostNet A knowledge base for the management and the analysis of proteome-wide virus-host inter.pdf:pdf}, issn = {03051048}, journal = {Nucleic Acids Research}, number = {SUPPL. 1}, pmid = {18984613}, title = {{VirHostNet: A knowledge base for the management and the analysis of proteome-wide virus-host interaction networks}}, volume = {37}, year = {2009} } @article{Billoir2014, abstract = {The number of samples needed to identify significant effects is a key question in biomedical studies, with consequences on experimental designs, costs and potential discoveries. In metabolic phenotyping studies, sample size determination remains a complex step. This is due particularly to the multiple hypothesis-testing framework and the top-down hypothesis-free approach, with no a priori known metabolic target. Until now, there was no standard procedure available to address this purpose. In this review, we discuss sample size estimation procedures for metabolic phenotyping studies. We release an automated implementation of the Data-driven Sample size Determination (DSD) algorithm for MATLAB and GNU Octave. Original research concerning DSD was published elsewhere. DSD allows the determination of an optimized sample size in metabolic phenotyping studies. The procedure uses analytical data only from a small pilot cohort to generate an expanded data set. The statistical recoupling of variables procedure is used to identify metabolic variables, and their intensity distributions are estimated by Kernel smoothing or log-normal density fitting. Statistically significant metabolic variations are evaluated using the Benjamini-Yekutieli correction and processed for data sets of various sizes. Optimal sample size determination is achieved in a context of biomarker discovery (at least one statistically significant variation) or metabolic exploration (a maximum of statistically significant variations). DSD toolbox is encoded in MATLAB R2008A (Mathworks, Natick, MA) for Kernel and log-normal estimates, and in GNU Octave for log-normal estimates (Kernel density estimates are not robust enough in GNU octave). It is available at http://www.prabi.fr/redmine/projects/dsd/repository, with a tutorial at http://www.prabi.fr/redmine/projects/dsd/wiki.}, author = {Billoir, Elise and Navratil, Vincent and Blaise, Benjamin J.}, doi = {10.1093/bib/bbu052}, file = {:Users/navratil/Documents/Mendeley Desktop/2014/Billoir, Navratil, Blaise/Briefings in Bioinformatics/Briefings in Bioinformatics{\_}Billoir, Navratil, Blaise{\_}Sample size calculation in metabolic phenotyping studies{\_}2014.pdf:pdf}, issn = {14774054}, journal = {Briefings in Bioinformatics}, keywords = {Chemometrics,Metabolic phenotyping,Sample size determination}, month = {nov}, number = {5}, pages = {813--819}, pmid = {25600654}, publisher = {Oxford University Press}, title = {{Sample size calculation in metabolic phenotyping studies}}, volume = {16}, year = {2014} } @article{Lassalle2017, abstract = {Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species. We identified clade-specific blocks of cotransferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacterium clades. This pattern of gene coevolution rejects a neutral model of transfer, in which neighboring genes would be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of cofunctioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches, which consistently hint at a strong selective role of host plant rhizospheres.}, author = {Lassalle, Florent and Planel, R{\'{e}}mi and Penel, Simon and Chapulliot, David and Barbe, Val{\'{e}}rie and Dubost, Audrey and Calteau, Alexandra and Vallenet, David and Mornico, Damien and Bigot, Thomas and Gu{\'{e}}guen, Laurent and Vial, Ludovic and Muller, Daniel and Daubin, Vincent and Nesme, Xavier}, doi = {10.1093/gbe/evx255}, file = {:Users/navratil/Documents/Mendeley Desktop/2017/Lassalle et al/Genome Biology and Evolution/Genome Biology and Evolution{\_}Lassalle et al.{\_}Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacter.pdf:pdf}, issn = {17596653}, journal = {Genome Biology and Evolution}, keywords = {Agrobacterium tumefaciens,HGT,ancestral genome,cotransferred genes,reverse ecology,tree reconciliation}, month = {dec}, number = {12}, pages = {3413--3431}, pmid = {29220487}, publisher = {Oxford University Press}, title = {{Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium}}, volume = {9}, year = {2017} } @article{Hommais2008, abstract = {Pathogenicity of the enterobacterium Erwinia chrysanthemi (Dickeya dadantii), the causative agent of soft-rot disease in many plants, is a complex process involving several factors whose production is subject to temporal regulation during infection. PecS is a transcriptional regulator that controls production of various virulence factors. Here, we used microarray analysis to define the PecS regulon and demonstrated that PecS notably regulates a wide range of genes that could be linked to pathogenicity and to a group of genes concerned with evading host defenses. Among the targets are the genes encoding plant cell wall-degrading enzymes and secretion systems and the genes involved in flagellar biosynthesis, biosurfactant production, and the oxidative stress response, as well as genes encoding toxin-like factors such as NipE and hemolysin-coregulated proteins. In vitro experiments demonstrated that PecS interacts with the regulatory regions of five new targets: an oxidative stress response gene (ahpC), a biosurfactant synthesis gene (rhlA), and genes encoding exported proteins related to other plant-associated bacterial proteins (nipE, virK, and avrL). The pecS mutant provokes symptoms more rapidly and with more efficiency than the wild-type strain, indicating that PecS plays a critical role in the switch from the asymptomatic phase to the symptomatic phase. Based on this, we propose that the temporal regulation of the different groups of genes required for the asymptomatic phase and the symptomatic phase is, in part, the result of a gradual modulation of PecS activity triggered during infection in response to changes in environmental conditions emerging from the interaction between both partners. Copyright {\textcopyright} 2008, American Society for Microbiology. All Rights Reserved.}, author = {Hommais, Florence and Oger-Desfeux, Christine and {Van Gijsegem}, Fr{\'{e}}d{\'{e}}rique and Castang, Sandra and Ligori, Sandrine and Expert, Dominique and Nasser, William and Reverchon, Sylvie}, doi = {10.1128/JB.00553-08}, file = {:Users/navratil/Documents/Mendeley Desktop/2008/Hommais et al/Journal of Bacteriology/Journal of Bacteriology{\_}Hommais et al.{\_}PecS is a global regulator of the symptomatic phase in the phytopathogenic bacterium Erwinia chry.pdf:pdf}, issn = {00219193}, journal = {Journal of Bacteriology}, number = {22}, pages = {7508--7522}, pmid = {18790868}, publisher = {American Society for Microbiology}, title = {{PecS is a global regulator of the symptomatic phase in the phytopathogenic bacterium Erwinia chrysanthemi 3937}}, volume = {190}, year = {2008} } @article{Aouacheria2007, abstract = {Background: A promising application of the huge amounts of genetic data currently available lies in developing a better understanding of complex diseases, such as cancer. Analysis of publicly available databases can help identify potential candidates for genes or mutations specifically related to the cancer phenotype. In spite of their huge potential to affect gene function, no systematic attention has been paid so far to the changes that occur in untranslated regions of mRNA. Results: In this study, we used Expressed Sequence Tag (EST) databases as a source for cancer-related sequence polymorphism discovery at the whole-genome level. Using a novel computational procedure, we focused on the identification of untranslated region (UTR)-localized non-coding Single Nucleotide Polymorphisms (UTR-SNPs) significantly associated with the tumoral state. To explore possible relationships between genetic mutation and phenotypic variation, bioinformatic tools were used to predict the potential impact of cancer-associated UTR-SNPs on mRNA secondary structure and UTR regulatory elements. We provide a comprehensive and unbiased description of cancer-associated UTR-SNPs that may be useful to define genotypic markers or to propose polymorphisms that can act to alter gene expression levels. Our results suggest that a fraction of cancer-associated UTR-SNPs may have functional consequences on mRNA stability and/or expression. Conclusion: We have ndertaken a comprehensive effort to identify cancer-associated polymorphisms in untranslated regions of mRNA and to characterize putative functional UTR-SNPs. Alteration of translational control can change the expression of genes in tumor cells, causing an increase or decrease in the concentration of specific proteins. Through the description of testable candidates and the experimental validation of a number of UTR-SNPs discovered on the secreted protein acidic and rich in cysteine (SPARC) gene, this report illustrates the utility of a cross-talk between in silico transcriptomics and cancer genetics. {\textcopyright} 2007 Aouacheria et al; licensee BioMed Central Ltd.}, author = {Aouacheria, Abdel and Navratil, Vincent and L{\'{o}}pez-P{\'{e}}rez, Ricardo and Guti{\'{e}}rrez, Norma C. and Churkin, Alexander and Barash, Danny and Mouchiroud, Dominique and Gautier, Christian}, doi = {10.1186/1471-2164-8-2}, file = {:Users/navratil/Documents/Mendeley Desktop/2007/Aouacheria et al/BMC Genomics/BMC Genomics{\_}Aouacheria et al.{\_}In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA.pdf:pdf}, issn = {14712164}, journal = {BMC Genomics}, pmid = {17201911}, title = {{In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions}}, volume = {8}, year = {2007} } @article{Davidovic2011, abstract = {Fragile X syndrome (FXS) is the first cause of inherited intellectual disability, due to the silencing of the X-linked Fragile X Mental Retardation 1 gene encoding the RNA-binding protein FMRP. While extensive studies have focused on the cellular and molecular basis of FXS, neither human Fragile X patients nor the mouse model of FXS-the Fmr1-null mouse-have been profiled systematically at the metabolic and neurochemical level to provide a complementary perspective on the current, yet scattered, knowledge of FXS. Using proton high-resolution magic angle spinning nuclear magnetic resonance (1H HR-MAS NMR)-based metabolic profiling, we have identified a metabolic signature and biomarkers associated with FXS in various brain regions of Fmr1-deficient mice. Our study highlights for the first time that Fmr1 gene inactivation has profound, albeit coordinated consequences in brain metabolism leading to alterations in: (1) neurotransmitter levels, (2) osmoregulation, (3) energy metabolism, and (4) oxidative stress response. To functionally connect Fmr1-deficiency to its metabolic biomarkers, we derived a functional interaction network based on the existing knowledge (literature and databases) and show that the FXS metabolic response is initiated by distinct mRNAtargets and proteins interacting with FMRP, and then relayed by numerous regulatory proteins. This novel "integrated metabolome and interactome mapping" (iMIM) approach advantageously unifies novel metabolic findings with previously unrelated knowledge and highlights the contribution of novel cellular pathways to the pathophysiology of FXS. These metabolomic and integrative systems biology strategies will contribute to the development of potential drug targets and novel therapeutic interventions, which will eventually benefit FXS patients. {\textcopyright} 2011 by Cold Spring Harbor Laboratory Press.}, author = {Davidovic, Laetitia and Navratil, Vincent and Bonaccorso, Carmela M. and Catania, Maria Vincenza and Bardoni, Barbara and Dumas, Arc Emmanuel}, doi = {10.1101/gr.116764.110}, file = {:Users/navratil/Documents/Mendeley Desktop/2011/Davidovic et al/Genome Research/Genome Research{\_}Davidovic et al.{\_}A metabolomic and systems biology perspective on the brain of the Fragile X syndrome mouse model{\_}2011.pdf:pdf}, issn = {10889051}, journal = {Genome Research}, month = {dec}, number = {12}, pages = {2190--2202}, pmid = {21900387}, title = {{A metabolomic and systems biology perspective on the brain of the Fragile X syndrome mouse model}}, volume = {21}, year = {2011} } @article{Blaise2010, abstract = {The development of Statistical Total Correlation Spectroscopy (STOCSY), a representation of the autocorrelation matrix of a spectral data set as a 2D pseudospectrum, has allowed more reliable assignment of one- and two-dimensional NMR spectra acquired from the complex mixtures that are usually used in metabolomics/metabonomics studies, thus, improving precise identification of candidate biomarkers contained in metabolic signatures computed by multivariate statistical analysis. However, the correlations obtained cannot always be interpreted in terms of connectivities between metabolites. In this study, we combine statistical recoupling of variables (SRV) and STOCSY to identify perturbed metabolite systems. The resulting Recoupled-STOCSY (R-STOCSY) method provides a 2D correlation landscape based on the SRV clusters representing physical, chemical, and biological entities. This enables the identification of correlations between distant clusters and extends the recoupling scheme of SRV, which was previously limited to the association of neighboring clusters. This allows the recovery of only meaningful correlations between metabolic signals and significantly enhances the interpretation of STOCSY. The method is validated through the measurement of the distances between the metabolites involved in these correlations, within the whole metabolic network, which shows that the average shortest path length is significantly shorter for the correlations detected in this new way compared to metabolite couples randomly selected from within the entire KEGG metabolic network. This enables the identification without any a priori knowledge of the perturbed metabolic network. The R-STOCSY completes the recoupling procedure between distant clusters, further reducing the high dimensionality of metabolomics/metabonomics data set and finally allows the identification of composite biomarkers, highlighting disruption of particular metabolic pathways within a global metabolic network. This allows the perturbed metabolic network to be extracted through NMR based metabolomics/metabonomics in an automated, and statistical manner. {\textcopyright} 2010 American Chemical Society.}, author = {Blaise, Benjamin J. and Navratil, Vincent and Domange, C{\'{e}}line and Shintu, Laetitia and Dumas, Marc Emmanuel and Elena-Herrmann, B{\'{e}}n{\'{e}}dicte and Emsley, Lyndon and Toulhoat, Pierre}, doi = {10.1021/pr1002615}, issn = {15353893}, journal = {Journal of Proteome Research}, keywords = {NMR,STOCSY,metabolic profiling,network}, month = {sep}, number = {9}, pages = {4513--4520}, pmid = {20590164}, title = {{Two-dimensional statistical recoupling for the identification of perturbed metabolic networks from NMR spectroscopy}}, volume = {9}, year = {2010} } @article{Muyle2018, abstract = {Sex chromosomes have repeatedly evolved from a pair of autosomes. Consequently, X and Y chromosomes initially have similar gene content, but ongoing Y degeneration leads to reduced expression and eventual loss of Y genes1. The resulting imbalance in gene expression between Y genes and the rest of the genome is expected to reduce male fitness, especially when protein networks have components from both autosomes and sex chromosomes. A diverse set of dosage compensating mechanisms that alleviates these negative effects has been described in animals2–4. However, the early steps in the evolution of dosage compensation remain unknown, and dosage compensation is poorly understood in plants5. Here, we describe a dosage compensation mechanism in the evolutionarily young XY sex determination system of the plant Silene latifolia. Genomic imprinting results in higher expression from the maternal X chromosome in both males and females. This compensates for reduced Y expression in males, but results in X overexpression in females and may be detrimental. It could represent a transient early stage in the evolution of dosage compensation. Our finding has striking resemblance to the first stage proposed by Ohno6 for the evolution of X inactivation in mammals.}, author = {Muyle, Aline and Zemp, Niklaus and Fruchard, C{\'{e}}cile and Cegan, Radim and Vrana, Jan and Deschamps, Clothilde and Tavares, Raquel and Hobza, Roman and Picard, Franck and Widmer, Alex and Marais, Gabriel A.B.}, doi = {10.1038/s41477-018-0221-y}, issn = {20550278}, journal = {Nature Plants}, month = {sep}, number = {9}, pages = {677--680}, pmid = {30104649}, publisher = {Palgrave Macmillan Ltd.}, title = {{Genomic imprinting mediates dosage compensation in a young plant XY system}}, volume = {4}, year = {2018} } @article{Navratil2020, abstract = {Following the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) in 2002 and Middle East Respiratory Syndrome coronavirus (MERS-CoV) in 2012, the novel coronavirus SARS-CoV-2 emerged at the end of 2019 as a highly pathogenic infectious agent that rapidly spread around the world. SARS-CoV-2 shares high sequence homology with SARS-CoV and causes acute, highly lethal pneumonia coronavirus disease 2019 (COVID-19) with clinical symptoms similar to those reported for SARS-CoV. Like other betacoronaviruses, SARS-CoV-2 encode four major structural proteins: Spike (S), Membrane (M), Nucleocapsid (N) and Envelope (E). SARS-CoV E protein is abundant in infected cells and plays a crucial role in viral particle assembly. Moreover, SARS coronaviruses lacking E are attenuated in vivo, suggesting that CoV E may act as a critical virulence factor not only in SARS-CoV but also in the case of the new coronavirus SARS-CoV-2. Ectopic expression of SARS-CoV E was previously shown to trigger apoptosis (cell suicide) of T lymphocytes, lymphopenia being a common feature observed in fatal cases following viral infections. Importantly, T-cell apoptosis was shown to involve interaction between the C-terminal region of SARS-CoV E and the Bcl-2 family member Bcl-xL, which acts as a potent anti-apoptotic protein. Here we provide the first observation that the SARS-CoV E and SARS-CoV-2 E proteins share a conserved Bcl-2 Homology 3 (BH3)-like motif in their C-terminal region, a well-studied motif shown to be necessary for SARS-CoV E binding to Bcl-xL. We used available sequence data for SARS-CoV-2 and related coronaviruses, in combination with structural information, to study the structure to biological activity relationships of SARS-CoV-2 E in relation with its BH3-like motif. Our analysis of the SARS-CoV E interactome further revealed that the predicted SARS-CoV-2 network is extensively wired to the Bcl-2 apoptotic switch. Research is therefore needed to establish if SARS-CoV-2 E targets prosurvival Bcl-2 homologs to modulate cell viability, as part of a coronavirus strategy to interfere with apoptosis. The identification of small molecules (or the repurposing of existing drugs) able to disrupt SARS-CoV-2 E BH3-mediated interactions might provide a targeted therapeutic approach for COVID-19 treatment. Recombinant SARS-CoV-2 expressing an E protein with a deleted or mutated BH3-like motif might also be of interest for the design of a live, attenuated vaccine. {\#}{\#}{\#} Competing Interest Statement The authors have declared no competing interest.}, author = {Navratil, Vincent and Lionnard, Loic and Longhi, Sonia and Combet, Christophe and Aouacheria, Abdel}, doi = {10.1101/2020.04.09.033522}, file = {:Users/navratil/Documents/Mendeley Desktop/2020/Navratil et al/bioRxiv/bioRxiv{\_}Navratil et al.{\_}The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein harbors a conserved BH3-li.pdf:pdf}, journal = {bioRxiv}, month = {jun}, pages = {2020.04.09.033522}, publisher = {Cold Spring Harbor Laboratory}, title = {{The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein harbors a conserved BH3-like motif}}, url = {https://doi.org/10.1101/2020.04.09.033522}, year = {2020} } @article{Navratil2008, abstract = {Single nucleotide polymorphisms (SNPs), which are the most abundant form of genetic variations in numerous organisms, have emerged as important tools for the study of complex genetic traits and deciphering of genome evolution. High-throughput genome sequencing projects worldwide provide an unprecedented opportunity for whole-genome SNP analysis in a variety of species. To facilitate SNP discovery in vertebrates, we have developed a web-based, user-friendly, and fully automated application, DigiPINS, for genome-wide identification of exonic SNPs from EST data. Currently, the database can be used to the mining of exonic SNPs in six complete genomes (Homo sapiens, Mus musculus, Rattus norvegicus, Canis familiaris, Gallus gallus and Danio rerio). In addition to providing information on sequence conservation, DigiPINS allows compilation of comprehensive sets of polymorphisms within cancer candidate genes or identification of novel cancer markers, making it potentially useful for cancer association studies. The DigiPINS server is available via the internet at http://pbil.univ-lyon1.fr/gem/DigiPINS/query{\_}DigiPINS.php. {\textcopyright} 2007 Elsevier Masson SAS. All rights reserved.}, author = {Navratil, Vincent and Penel, Simon and Delmotte, St{\'{e}}phane and Mouchiroud, Dominique and Gautier, Christian and Aouacheria, Abdel}, doi = {10.1016/j.biochi.2007.09.017}, issn = {03009084}, journal = {Biochimie}, keywords = {Cancer association,Comparative genomics,Expressed sequenced tag,Single nucleotide polymorphism,Web server}, month = {apr}, number = {4}, pages = {563--569}, pmid = {17988782}, title = {{DigiPINS: A database for vertebrate exonic single nucleotide polymorphisms and its application to cancer association studies}}, volume = {90}, year = {2008} } @article{Oger2017, abstract = {Members of the order Thermococcales are common inhabitants of hightemperature hydrothermal vent systems (black smokers) that are represented in clone libraries mostly by isolates from the Thermococcus genus. We report the complete sequence of a novel species from the Pyrococcus genus, P. kukulkanii strain NCB100, which has been isolated from a flange fragment of the Rebecca's Roost hydrothermal vent system in the Guaymas Basin.}, author = {Oger, Philippe M. and Callac, Nolwenn and Oger-Desfeux, Christine and Hughes, Sandrine and Gillet, Benjamin and Jebbar, Mohamed and Godfroy, Anne}, doi = {10.1128/genomeA.01667-16}, file = {:Users/navratil/Documents/Mendeley Desktop/2017/Oger et al/Genome Announcements/Genome Announcements{\_}Oger et al.{\_}Complete genome sequence of the hyperthermophilic piezophilic archaeon Pyrococcus kukulkanii NCB100 iso.pdf:pdf}, issn = {21698287}, journal = {Genome Announcements}, number = {7}, publisher = {American Society for Microbiology}, title = {{Complete genome sequence of the hyperthermophilic piezophilic archaeon Pyrococcus kukulkanii NCB100 isolated from the Rebecca's Roost hydrothermal vent in the Guaymas Basin}}, volume = {5}, year = {2017} } @article{Faucon2015, abstract = {The capacity of mosquitoes to resist insecticides threatens the control of diseases such as dengue and malaria. Until alternative control tools are implemented, characterizing resistance mechanisms is crucial for managing resistance in natural populations. Insecticide biodegradation by detoxification enzymes is a common resistance mechanism; however, the genomic changes underlying this mechanism have rarely been identified, precluding individual resistance genotyping. In particular, the role of copy number variations (CNVs) and polymorphisms of detoxification enzymes have never been investigated at the genome level, although they can represent robust markers of metabolic resistance. In this context, we combined target enrichment with high-throughput sequencing for conducting the first comprehensive screening of gene amplifications and polymorphisms associated with insecticide resistance in mosquitoes. More than 760 candidate genes were captured and deep sequenced in several populations of the dengue mosquito Ae. aegypti displaying distinct genetic backgrounds and contrasted resistance levels to the insecticide deltamethrin. CNV analysis identified 41 gene amplifications associated with resistance, most affecting cytochrome P450s overtranscribed in resistant populations. Polymorphism analysis detected more than 30,000 variants and strong selection footprints in specific genomic regions. Combining Bayesian and allele frequency filtering approaches identified 55 nonsynonymous variants strongly associated with resistance. Both CNVs and polymorphisms were conserved within regions but differed across continents, confirming that genomic changes underlying metabolic resistance to insecticides are not universal. By identifying novel DNA markers of insecticide resistance, this study opens the way for tracking down metabolic changes developed by mosquitoes to resist insecticides within and among populations.}, author = {Faucon, Frederic and Dusfour, Isabelle and Gaude, Thierry and Navratil, Vincent and Boyer, Frederic and Chandre, Fabrice and Sirisopa, Patcharawan and Thanispong, Kanutcharee and Juntarajumnong, Waraporn and Poupardin, Rodolphe and Chareonviriyaphap, Theeraphap and Girod, Romain and Corbel, Vincent and Reynaud, Stephane and David, Jean Philippe}, doi = {10.1101/gr.189225.115}, file = {:Users/navratil/Documents/Mendeley Desktop/2015/Faucon et al/Genome Research/Genome Research{\_}Faucon et al.{\_}Identifying genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by.pdf:pdf}, issn = {15495469}, journal = {Genome Research}, month = {sep}, number = {9}, pages = {1347--1359}, pmid = {26206155}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Identifying genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing}}, volume = {25}, year = {2015} } @article{Shintu2012, abstract = {The world faces complex challenges for chemical hazard assessment. Microfluidic bioartificial organs enable the spatial and temporal control of cell growth and biochemistry, critical for organ-specific metabolic functions and particularly relevant to testing the metabolic dose- response signatures associated with both pharmaceutical and environmental toxicity. Here we present an approach combining a microfluidic system with 1H NMR-based metabolomic footprinting, as a high-throughput small-molecule screening approach. We characterized the toxicity of several molecules: ammonia (NH 3), an environmental pollutant leading to metabolic acidosis and liver and kidney toxicity; dimethylsulfoxide (DMSO), a free radical-scavenging solvent; and N-acetyl-para-aminophenol (APAP, or paracetamol), a hepatotoxic analgesic drug. We report organ-specific NH 3 dose-dependent metabolic responses in several microfluidic bioartificial organs (liver, kidney, and cocultures), as well as predictive (99{\%} accuracy for NH 3 and 94{\%} for APAP) compound-specific signatures. Our integration of microtechnology, cell culture in microfluidic biochips, and metabolic profiling opens the development of so-called "metabolomics-on-a-chip" assays in pharmaceutical and environmental toxicology. {\textcopyright} 2012 American Chemical Society.}, author = {Shintu, Laetitia and Baudoin, R{\'{e}}gis and Navratil, Vincent and Prot, Jean Matthieu and Pontoizeau, Cl{\'{e}}ment and Defernez, Marianne and Blaise, Benjamin J. and Domange, C{\'{e}}line and P{\'{e}}ry, Alexandre R. and Toulhoat, Pierre and Legallais, C{\'{e}}cile and Brochot, C{\'{e}}line and Leclerc, Eric and Dumas, Marc Emmanuel}, doi = {10.1021/ac2011075}, issn = {00032700}, journal = {Analytical Chemistry}, month = {feb}, number = {4}, pages = {1840--1848}, pmid = {22242722}, title = {{Metabolomics-on-a-chip and predictive systems toxicology in microfluidic bioartificial organs}}, volume = {84}, year = {2012} } @article{Navratil2013, abstract = {Supervised multivariate statistical analyses are often required to analyze the high-density spectral information in metabolic datasets acquired from complex mixtures in metabolic phenotyping studies. Here we present an implementation of the SRV-Statistical Recoupling of Variables-algorithm as an open-source Matlab and GNU Octave toolbox. SRV allows the identification of similarity between consecutive variables resulting from the high-resolution bucketing. Similar variables are gathered to restore the spectral dependency within the datasets and identify metabolic NMR signals. The correlation and significance of these new NMR variables for a given effect under study can then be measured and represented on a loading plot to allow a visual and efficient identification of candidate biomarkers. Further on, correlations between these candidate biomarkers can be visualized on a two-dimensional pseudospectrum, representing a correlation map, helping to understand the modifications of the underlying metabolic network. {\textcopyright} 2013 The Author. Published by Oxford University Press. All rights reserved.}, author = {Navratil, Vincent and Pontoizeau, Cl{\'{e}}ment and Billoir, Elise and Blaise, Benjamin J.}, doi = {10.1093/bioinformatics/btt136}, file = {:Users/navratil/Documents/Mendeley Desktop/2013/Navratil et al/Bioinformatics/Bioinformatics{\_}Navratil et al.{\_}SRV An open-source toolbox to accelerate the recovery of metabolic biomarkers and correlations from metab.pdf:pdf}, issn = {13674803}, journal = {Bioinformatics}, month = {may}, number = {10}, pages = {1348--1349}, pmid = {23508967}, title = {{SRV: An open-source toolbox to accelerate the recovery of metabolic biomarkers and correlations from metabolic phenotyping datasets}}, volume = {29}, year = {2013} } @article{Aouacheria2006, abstract = {Collagens are thought to represent one of the most important molecular innovations in the metazoan line. Basement membrane type IV collagen is present in all Eumetazoa and was found in Homoscleromorpha, a sponge group with a well-organized epithelium, which may represent the first stage of tissue differentiation during animal evolution. In contrast, spongin seems to be a demosponge-specific collagenous protein, which can totally substitute an inorganic skeleton, such as in the well-known bath sponge. In the freshwater sponge Ephydatia m{\"{u}}lleri, we previously characterized a family of short-chain collagens that are likely to be main components of spongins. Using a combination of sequence- and structure-based methods, we present evidence of remote homology between the carboxyl-terminal noncollagenous NC1 domain of spongin short-chain collagens and type IV collagen. Unexpectedly, spongin short-chain collagen-related proteins were retrieved in nonsponge animals, suggesting that a family related to spongin constitutes an evolutionary sister to the type IV collagen family. Formation of the ancestral NC1 domain and divergence of the spongin short-chain collagen-related and type IV collagen families may have occurred before the parazoan-eumetazoan split, the earliest divergence among extant animal phyla. Molecular phylogenetics based on NC1 domain sequences suggest distinct evolutionary histories for spongin short-chain collagen-related and type IV collagen families that include spongin short-chain collagen-related gene loss in the ancestors of Ecdyzosoa and of vertebrates. The fact that a majority of invertebrates encodes spongin short-chain collagen-related proteins raises the important question to the possible function of its members. Considering the importance of collagens for animal structure and substratum attachment, both families may have played crucial roles in animal diversification. {\textcopyright} The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.}, author = {Aouacheria, Abdel and Geourjon, Christophe and Aghajari, Nushin and Navratil, Vincent and Del{\'{e}}age, Gilbert and Lethias, Claire and Exposito, Jean Yves}, doi = {10.1093/molbev/msl100}, file = {:Users/navratil/Documents/Mendeley Desktop/2006/Aouacheria et al/Molecular Biology and Evolution/Molecular Biology and Evolution{\_}Aouacheria et al.{\_}Insights into early extracellular matrix evolution Spongin short chain collagen-relate.pdf:pdf}, issn = {07374038}, journal = {Molecular Biology and Evolution}, keywords = {Basement membrane,Collagen,Extracellular matrix,Metazoan evolution,Remote homology,Spongin}, month = {dec}, number = {12}, pages = {2288--2302}, pmid = {16945979}, title = {{Insights into early extracellular matrix evolution: Spongin short chain collagen-related proteins are homologous to basement membrane type IV collagens and form a novel family widely distributed in invertebrates}}, volume = {23}, year = {2006} } @article{Badouin2020, abstract = {BACKGROUND: A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype (Yh) and that the sex locus is small, but it has not previously been precisely characterized. RESULTS: We generate a high-quality de novo reference genome for V. sylvestris, onto which we map whole-genome re-sequencing data of a cross to locate the sex locus. Assembly of the full X, Y, and Yh haplotypes of V. sylvestris and V. vinifera sex locus and examining their gene content and expression profiles during flower development in wild and cultivated accessions show that truncation and deletion of tapetum and pollen development genes on the X haplotype likely causes male sterility, while the upregulation of a Y allele of a cytokinin regulator (APRT3) may cause female sterility. The downregulation of this cytokinin regulator in the Yh haplotype may be sufficient to trigger reversal to hermaphroditism. Molecular dating of X and Y haplotypes is consistent with the sex locus being as old as the Vitis genus, but the mechanism by which recombination was suppressed remains undetermined. CONCLUSIONS: We describe the genomic and evolutionary characterization of the sex locus of cultivated and wild grapevine, providing a coherent model of sex determination in the latter and for transition from dioecy to hermaphroditism during domestication.}, author = {Badouin, H{\'{e}}l{\`{e}}ne and Velt, Amandine and Gindraud, Fran{\c{c}}ois and Flutre, Timoth{\'{e}}e and Dumas, Vincent and Vautrin, Sonia and Marande, William and Corbi, Jonathan and Sallet, Erika and Ganofsky, J{\'{e}}r{\'{e}}my and Santoni, Sylvain and Guyot, Dominique and Ricciardelli, Eugenia and Jepsen, Kristen and K{\"{a}}fer, Jos and Berges, H{\'{e}}l{\`{e}}ne and Duch{\^{e}}ne, Eric and Picard, Franck and Hugueney, Philippe and Tavares, Raquel and Bacilieri, Roberto and Rustenholz, Camille and Marais, Gabriel A.B.}, doi = {10.1186/s13059-020-02131-y}, file = {:Users/navratil/Documents/Mendeley Desktop/2020/Badouin et al/Genome biology/Genome biology{\_}Badouin et al.{\_}The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during.pdf:pdf}, issn = {1474760X}, journal = {Genome biology}, keywords = {Dioecy,Grapevine,Sex chromosomes,Sex-determining genes}, month = {sep}, number = {1}, pages = {223}, pmid = {32892750}, publisher = {NLM (Medline)}, title = {{The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication}}, volume = {21}, year = {2020} } @article{Stockinger2008, abstract = {Programmatic access to data and tools through the web using so-called web services has an important role to play in bioinformatics. In this article, we discuss the most popular approaches based on SOAP/WS-I and REST and describe our, a cross section of the community, experiences with providing and using web services in the context of biological sequence analysis. We briefly review main technological approaches as well as best practice hints that are useful for both users and developers. Finally, syntactic and semantic data integration issues with multiple web services are discussed. {\textcopyright} The Author 2008. Published by Oxford University Press.}, author = {Stockinger, Heinz and Attwood, Teresa and Chohan, Shahid Nadeem and C{\^{o}}t{\'{e}}, Richard and Cudr{\'{e}}-Mauroux, Philippe and Falquet, Laurent and Fernandes, Pedro and Finn, Robert D. and Hupponen, Taavi and Korpelainen, Eija and Labarga, Alberto and Laugraud, Aurelie and Lima, Tania and Pafilis, Evangelos and Pagni, Marco and Pettifer, Steve and Phan, Isabelle and Rahman, Nazim}, doi = {10.1093/bib/bbn029}, file = {:Users/navratil/Documents/Mendeley Desktop/2008/Stockinger et al/Briefings in Bioinformatics/Briefings in Bioinformatics{\_}Stockinger et al.{\_}Experience using web services for biological sequence analysis{\_}2008.pdf:pdf}, issn = {14675463}, journal = {Briefings in Bioinformatics}, keywords = {Internet technologies,REST,SOAP,Sequence analysis,Web services}, number = {6}, pages = {493--505}, pmid = {18621748}, title = {{Experience using web services for biological sequence analysis}}, volume = {9}, year = {2008} } @article{Palmeira2011, abstract = {Fast viral adaptation and the implication of this rapid evolution in the emergence of several new infectious diseases have turned this issue into a major challenge for various research domains. Indeed, viruses are involved in the development of a wide range of pathologies and understanding how viruses and host cells interact in the context of adaptation remains an open question. In order to provide insights into the complex interactions between viruses and their host organisms and namely in the acquisition of novel functions through exchanges of genetic material, we developed the PhEVER database. This database aims at providing accurate evolutionary and phylogenetic information to analyse the nature of virus-virus and virus-host lateral gene transfers. PhEVER (http:// pbil.univ-lyon1.fr/databases/phever) is a unique database of homologous families both (i) between sequences from different viruses and (ii) between viral sequences and sequences from cellular organisms. PhEVER integrates extensive data from up-to-date completely sequenced genomes (2426 non-redundant viral genomes, 1007 non-redundant prokaryotic genomes, 43 eukaryotic genomes ranging from plants to vertebrates) and offers a clustering of proteins into homologous families containing at least one viral sequences, as well as alignments and phylogenies for each of these families. Public access to PhEVER is available through its webpage and through all dedicated ACNUC retrieval systems. {\textcopyright} The Author(s) 2010.}, author = {Palmeira, Leonor and Penel, Simon and Lotteau, Vincent and Rabourdin-Combe, Chantal and Gautier, Christian}, doi = {10.1093/nar/gkq1013}, file = {:Users/navratil/Documents/Mendeley Desktop/2011/Palmeira et al/Nucleic Acids Research/Nucleic Acids Research{\_}Palmeira et al.{\_}PhEVER A database for the global exploration of virus-host evolutionary relationships{\_}2011.pdf:pdf}, issn = {13624962}, journal = {Nucleic Acids Research}, keywords = {Christian Gautier,Cluster Analysis,Databases,Evolution,Gene Transfer,Genes,Genetic*,Genome,Genomics,Horizontal,Host-Pathogen Interactions / genetics*,Leonor Palmeira,MEDLINE,Molecular*,NCBI,NIH,NLM,National Center for Biotechnology Information,National Institutes of Health,National Library of Medicine,Non-U.S. Gov't,PMC3013642,Phylogeny,PubMed Abstract,Research Support,Sequence Homology,Simon Penel,User-Computer Interface,Viral,Viral Proteins / chemistry,Viral Proteins / classification,Viral Proteins / genetics,Viruses / classification,Viruses / genetics*,doi:10.1093/nar/gkq1013,pmid:21081560}, number = {SUPPL. 1}, publisher = {Oxford University Press}, title = {{PhEVER: A database for the global exploration of virus-host evolutionary relationships}}, url = {https://pubmed.ncbi.nlm.nih.gov/21081560/}, volume = {39}, year = {2011} } @article{Navratil2011, abstract = {Background: Comprehensive understanding of molecular mechanisms underlying viral infection is a major challenge towards the discovery of new antiviral drugs and susceptibility factors of human diseases. New advances in the field are expected from systems-level modelling and integration of the incessant torrent of high-throughput "-omics" data.Results: Here, we describe the Human Infectome protein interaction Network, a novel systems virology model of a virtual virus-infected human cell concerning 110 viruses. This in silico model was applied to comprehensively explore the molecular relationships between viruses and their associated diseases. This was done by merging virus-host and host-host physical protein-protein interactomes with the set of genes essential for viral replication and involved in human genetic diseases. This systems-level approach provides strong evidence that viral proteomes target a wide range of functional and inter-connected modules of proteins as well as highly central and bridging proteins within the human interactome. The high centrality of targeted proteins was correlated to their essentiality for viruses' lifecycle, using functional genomic RNAi data. A stealth-attack of viruses on proteins bridging cellular functions was demonstrated by simulation of cellular network perturbations, a property that could be essential in the molecular aetiology of some human diseases. Networking the Human Infectome and Diseasome unravels the connectivity of viruses to a wide range of diseases and profiled molecular basis of Hepatitis C Virus-induced diseases as well as 38 new candidate genetic predisposition factors involved in type 1 diabetes mellitus.Conclusions: The Human Infectome and Diseasome Networks described here provide a unique gateway towards the comprehensive modelling and analysis of the systems level properties associated to viral infection as well as candidate genes potentially involved in the molecular aetiology of human diseases. {\textcopyright} 2011 Navratil et al; licensee BioMed Central Ltd.}, author = {Navratil, Vincent and de Chassey, Benoit and Combe, Chantal R. and Lotteau, Vincent}, doi = {10.1186/1752-0509-5-13}, file = {:Users/navratil/Documents/Mendeley Desktop/2011/Navratil et al/BMC Systems Biology/BMC Systems Biology{\_}Navratil et al.{\_}When the human viral infectome and diseasome networks collide Towards a systems biology platform for.pdf:pdf}, issn = {17520509}, journal = {BMC Systems Biology}, month = {jan}, number = {SUPPL. 1}, pmid = {21255393}, publisher = {BioMed Central Ltd.}, title = {{When the human viral infectome and diseasome networks collide: Towards a systems biology platform for the aetiology of human diseases}}, volume = {5}, year = {2011} } @article{Horard2009, abstract = {Half of the human genome consists of repetitive DNA sequences. Recent studies in various organisms highlight the role of chromatin regulation of repetitive DNA in gene regulation as well as in maintainance of chromosomes and genome integrity. Hence, repetitive DNA sequences might be potential "sensors" for chromatin changes associated with pathogenesis. Therefore, we developed a new genomic tool called RepArray. RepArray is a repeat-specific microarray composed of a representative set of human repeated sequences including transposon-derived repeats, simple sequences repeats, tandemly repeated sequences such as centromeres and telomeres. We showed that combined to anti-methylcytosine immunoprecipitation assay, the RepArray can be used to generate repeat-specific methylation maps. Using cell lines impaired chemically or genetically for DNA methyltransferases activities, we were able to distinguish different epigenomes demonstrating that repeats can be used as markers of genome-wide methylation changes. Besides, using a well-documented system model, the thermal stress, we demonstrated that RepArray is also a fast and reliable tool to obtain an overview of overall transcriptional activity on whole repetitive compartment in a given cell type. Thus, the RepArray represents the first valuable tool for systematic and genome-wide analyses of the methylation and transcriptional status of the repetitive counterpart of the human genome. {\textcopyright} 2009 Landes Bioscience.}, author = {Horard, B{\'{e}}atrice and Eymery, Ang{\'{e}}line and Fourel, Genevi{\`{e}}ve and Vassetzky, Nikita and Puechberty, Jacques and Roizes, G{\'{e}}rard and Lebrigand, Kevin and Barbry, Pascal and Laugraud, Aur{\'{e}}lie and Gautier, Christian and Simon, Elisa Ben and Devaux, Fr{\'{e}}d{\'{e}}ric and Magdinier, Fr{\'{e}}d{\'{e}}rique and Vourc'h, Claire and Gilson, Eric}, doi = {10.4161/epi.4.5.9284}, file = {:Users/navratil/Documents/Mendeley Desktop/2009/Horard et al/Epigenetics/Epigenetics{\_}Horard et al.{\_}Global analysis of DNA methylation and transcription of human repetitive sequences{\_}2009.pdf:pdf}, issn = {15592308}, journal = {Epigenetics}, keywords = {DNA methylation,Epigenetic,Human repetitive DNA,Microarray,Non coding transcripts}, month = {jul}, number = {5}, pages = {66--77}, pmid = {19633427}, publisher = {Taylor and Francis Inc.}, title = {{Global analysis of DNA methylation and transcription of human repetitive sequences}}, volume = {4}, year = {2009} } @article{Teulier2012, abstract = {The passage from shore to marine life of juvenile penguins represents a major energetic challenge to fuel intense and prolonged demands for thermoregulation and locomotion. Some functional changes developed at this crucial step were investigated by comparing pre-fledging king penguins with sea-acclimatized (SA) juveniles (Aptenodytes patagonicus). Transcriptomic analysis of pectoralis muscle biopsies revealed that most genes encoding proteins involved in lipid transport or catabolism were up-regulated, while genes involved in carbohydrate metabolism were mostly downregulated in SA birds. Determination of muscle enzymatic activities showed no changes in enzymes involved in the glycolytic pathway, but increased 3-hydroxyacyl-CoA dehydrogenase, an enzyme of the b-oxidation pathway. The respiratory rates of isolated muscle mitochondria were much higher with a substrate arising from lipid metabolism (palmitoyl-L-carnitine) in SA juveniles than in terrestrial controls, while no difference emerged with a substrate arising from carbohydrate metabolism (pyruvate). In vivo, perfusion of a lipid emulsion induced a fourfold larger thermogenic effect in SA than in control juveniles. The present integrative study shows that fuel selection towards lipid oxidation characterizes penguin acclimatization to marine life. Such acclimatization may involve thyroid hormones through their nuclear beta receptor and nuclear coactivators.}, author = {Teulier, Loic and D{\'{e}}gletagne, Cyril and Rey, Benjamin and Tornos, J{\'{e}}r{\'{e}}my and Keime, C{\'{e}}line and de Dinechin, Marc and Raccurt, Mireille and Rouanet, Jean Louis and Roussel, Damien and Duchamp, Claude}, doi = {10.1098/rspb.2011.2664}, file = {:Users/navratil/Documents/Mendeley Desktop/2012/Teulier et al/Proceedings of the Royal Society B Biological Sciences/Proceedings of the Royal Society B Biological Sciences{\_}Teulier et al.{\_}Selective upregulation of lipid metabolism in skeletal muscle of f.pdf:pdf}, issn = {14712954}, journal = {Proceedings of the Royal Society B: Biological Sciences}, keywords = {Energy substrates,In vivo,Mitochondria,Transcriptomic analysis}, month = {jun}, number = {1737}, pages = {2464--2472}, pmid = {22357259}, publisher = {Royal Society Publishing}, title = {{Selective upregulation of lipid metabolism in skeletal muscle of foraging juvenile king penguins: An integrative study}}, url = {https://pubmed.ncbi.nlm.nih.gov/22357259/}, volume = {279}, year = {2012} } @article{Muyle2012, abstract = {Silene latifolia is a dioecious plant with heteromorphic sex chromosomes that have originated only {\~{}}10 million years ago and is a promising model organism to study sex chromosome evolution in plants. Previous work suggests that S. latifolia XY chromosomes have gradually stopped recombining and the Y chromosome is undergoing degeneration as in animal sex chromosomes. However, this work has been limited by the paucity of sex-linked genes available. Here, we used 35 Gb of RNA-seq data from multiple males (XY) and females (XX) of an S. latifolia inbred line to detect sex-linked SNPs and identified more than 1,700 sex-linked contigs (with X-linked and Y-linked alleles). Analyses using known sex-linked and autosomal genes, together with simulations indicate that these newly identified sex-linked contigs are reliable. Using read numbers, we then estimated expression levels of X-linked and Y-linked alleles in males and found an overall trend of reduced expression of Y-linked alleles, consistent with a widespread ongoing degeneration of the S. latifolia Y chromosome. By comparing expression intensities of X-linked alleles in males and females, we found that X-linked allele expression increases as Y-linked allele expression decreases in males, which makes expression of sex-linked contigs similar in both sexes. This phenomenon is known as dosage compensation and has so far only been observed in evolutionary old animal sex chromosome systems. Our results suggest that dosage compensation has evolved in plants and that it can quickly evolve de novo after the origin of sex chromosomes. {\textcopyright} 2012 Muyle et al.}, author = {Muyle, Aline and Zemp, Niklaus and Deschamps, Clothilde and Mousset, Sylvain and Widmer, Alex and Marais, Gabriel A.B.}, doi = {10.1371/journal.pbio.1001308}, file = {:Users/navratil/Documents/Mendeley Desktop/2012/Muyle et al/PLoS Biology/PLoS Biology{\_}Muyle et al.{\_}Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromo.pdf:pdf}, issn = {15449173}, journal = {PLoS Biology}, month = {apr}, number = {4}, pmid = {22529744}, title = {{Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes}}, volume = {10}, year = {2012} } @article{Royer2011, abstract = {Serial analysis of gene expression (SAGE) profiles, from posterior and median cells of the silk gland of Bombyx mori, were analyzed and compared, so as to identify their respective distinguishing functions. The annotation of the SAGE libraries was performed with a B. mori reference tag collection, which was extracted from a novel set of Bombyx ESTs, sequenced from the 3' side. Most of the tags appeared at similar relative concentration within the two libraries, and corresponded with region-specific and highly abundant silk proteins. Strikingly, in addition to tags from silk protein mRNAs, 19 abundant tags were found (≥ 0.1{\%}), in the median cell library, which were absent in the posterior cell tag collection. With the exception of tags from SP1 mRNA, no PSG specific tags were found in this subset class. The analysis of some of the MSG-specific transcripts, suggested that middle silk gland cells have diversified functions, in addition to their well characterized role in silk sericins synthesis and secretion.}, author = {Royer, Corinne and Briolay, J{\'{e}}r{\^{o}}me and Garel, Annie and Brouilly, Patrick and Sasanuma, Shun-ichi and Sasanuma, Motoe and Shimomura, Michihiko and Keime, C{\'{e}}line and Gandrillon, Olivier and Huang, Yongping and Chavancy, G{\'{e}}rard and Mita, Kazuei and Couble, Pierre}, doi = {10.1016/j.ibmb.2010.11.003}, issn = {1879-0240}, journal = {Insect biochemistry and molecular biology}, keywords = {Bombyx,SAGE,Silk gland,Transcriptome}, month = {feb}, number = {2}, pages = {118--24}, pmid = {21078388}, publisher = {Elsevier Ltd}, title = {{Novel genes differentially expressed between posterior and median silk gland identified by SAGE-aided transcriptome analysis.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21078388}, volume = {41}, year = {2011} } @article{Sanguin2006, abstract = {The microarray approach has been proposed for high throughput analysis of the microbial community by providing snapshots of the microbial diversity under different environmental conditions. For this purpose, a prototype of a 16S rRNA-based taxonomic microarray was developed and evaluated for assessing bacterial community diversity. The prototype microarray is composed of 122 probes that target bacteria at various taxonomic levels from phyla to species (mostly Alphaproteobacteria). The prototype microarray was first validated using bacteria in pure culture. Differences in the sequences of probes and potential target DNAs were quantified as weighted mismatches (WMM) in order to evaluate hybridization reliability. As a general feature, probes having a WMM {\textgreater} 2 with target DNA displayed only 2.8{\%} false positives. The prototype microarray was subsequently tested with an environmental sample, which consisted of an Agrobacterium-related polymerase chain reaction amplicon from a maize rhizosphere bacterial community. Microarray results were compared to results obtained by cloning-sequencing with the same DNA. Microarray analysis enabled the detection of all 16S rRNA gene sequences found by cloning-sequencing. Sequences representing only 1.7{\%} of the clone library were detected. In conclusion, this prototype 16S rRNA-based taxonomic microarray appears to be a promising tool for the analysis of Alphaproteobacteria in complex ecosystems. {\textcopyright} 2005 Society for Applied Microbiology and Blackwell Publishing Ltd.}, author = {Sanguin, Herv{\'{e}} and Herrera, Aude and Oger-Desfeux, Christine and Dechesne, Arnaud and Simonet, Pascal and Navarro, Elisabeth and Vogel, Timothy M. and Mo{\"{e}}nne-Loccoz, Yvan and Nesme, Xavier and Grundmann, Genevi{\`{e}}ve L.}, doi = {10.1111/j.1462-2920.2005.00895.x}, issn = {14622920}, journal = {Environmental Microbiology}, number = {2}, pages = {289--307}, pmid = {16423016}, publisher = {Blackwell Publishing Ltd}, title = {{Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria}}, volume = {8}, year = {2006} } @article{Ghayad2008, abstract = {Activation of the Akt/mammalian target of rapamycin (mTOR) pathway has been shown to be associated with resistance to endocrine therapy in estrogen receptor alpha (ER$\alpha$)-positive breast cancer patients. Utmost importance is attached to strategies aimed at overcoming treatment resistance. In this context, this work aimed to investigate whether, in breast cancer cells, the use of an mTOR inhibitor would be sufficient to reverse the resistance acquired after exposure to endocrine therapy. The ER$\alpha$-positive human breast adenocarcinoma derived-MCF-7 cells used in this study have acquired both cross-resistance to hydroxy-tamoxifen (OH-Tam) and to fulvestrant and strong activation of the Akt/mTOR pathway. Cell proliferation tests in control cells demonstrated that the mTOR inhibitor rapamycin enhanced cell sensitivity to endocrine therapy when combined to OH-Tam or to fulvestrant. In resistant cells, rapamycin used alone greatly inhibited cell proliferation and reversed resistance to endocrine therapy by blocking the agonist-like activity of OH-Tam on cell proliferation and bypassing fulvestrant resistance. Reversion of resistance by rapamycin was associated with increased ER$\alpha$ protein expression levels and modification of the balance of phospho-ser167 ER$\alpha$/total ER$\alpha$ ratio. Pangenomic DNA array experiments demonstrated that the cotreatment of resistant cells with fulvestrant and rapamycin allowed the restoration of 40{\%} of the fulvestrant gene-expression signature. Taken together, data presented herein strongly support the idea that mTOR inhibitor might be one of the promising therapeutic approaches for patients with ER$\alpha$-positive endocrine therapy-resistant breast cancers. {\textcopyright} 2008 Japanese Cancer Association.}, author = {Ghayad, Sandra E. and Bieche, Ivan and Vendrell, Julie A. and Keime, Celine and Lidereau, Rosette and Dumontet, Charles and Cohen, Pascale A.}, doi = {10.1111/j.1349-7006.2008.00955.x}, file = {:Users/navratil/Documents/Mendeley Desktop/2008/Ghayad et al/Cancer Science/Cancer Science{\_}Ghayad et al.{\_}mTOR inhibition reverses acquired endocrine therapy resistance of breast cancer cells at the cell prolifera.pdf:pdf}, issn = {13497006}, journal = {Cancer Science}, number = {10}, pages = {1992--2003}, pmid = {19016759}, publisher = {Blackwell Publishing Ltd}, title = {{mTOR inhibition reverses acquired endocrine therapy resistance of breast cancer cells at the cell proliferation and gene-expression levels}}, volume = {99}, year = {2008} } @article{Carrouel2016, abstract = {In oral health, the interdental spaces are a real ecological niche for which the body has few or no alternative defenses and where the traditional daily methods for control by disrupting biofilm are not adequate. The interdental spaces are the source of many hypotheses regarding their potential associations with and/or causes of cardiovascular disease, diabetes, chronic kidney disease, degenerative disease, and depression. This PCR study is the first to describe the interdental microbiota in healthy adults aged 18-35 years-old with reference to the Socransky complexes. The complexes tended to reflect microbial succession events in developing dental biofilms. Early colonizers included members of the yellow, green, and purple complexes. The orange complex bacteria generally appear after the early colonizers and include many putative periodontal pathogens, such as Fusobacterium nucleatum. The red complex (Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola) was considered the climax community and is on the list of putative periodontal pathogens. The 19 major periodontal pathogens tested were expressed at various levels. F. nucleatum was the most abundant species, and the least abundant were Actinomyces viscosus, P. gingivalis, and Aggregatibacter actinomycetemcomitans. The genome counts for Eikenella corrodens, Campylobacter concisus, Campylobacter rectus, T. denticola, and Tannerella forsythensis increased significantly with subject age. The study highlights the observation that bacteria from the yellow complex (Streptococcus spp., S. mitis), the green complex (E. corrodens, Campylobacter gracilis, Capnocytophaga ochracea, Capnocytophaga sputigena, A. actinomycetemcomitans), the purple complex (Veillonella parvula, Actinomyces odontolyticus) and the blue complex (A. viscosus) are correlated. Concerning the orange complex, F. nucleatum is the most abundant species in interdental biofilm. The red complex, which is recognized as the most important pathogen in adult periodontal disease, represents 8.08{\%} of the 19 bacteria analyzed. P. gingivalis was detected in 19{\%} of healthy subjects and represents 0.02{\%} of the interdental biofilm. T. forsythensis and T. denticola (0.02 and 0.04{\%} of the interdental biofilm) were detected in 93 and 49{\%} of healthy subjects, respectively. The effective presence of periodontal pathogens is a strong indicator of the need to develop new methods for disrupting interdental biofilm in daily oral hygiene.}, author = {Carrouel, Florence and Viennot, St{\'{e}}phane and Santamaria, Julie and Veber, Philippe and Bourgeois, Denis}, doi = {10.3389/fmicb.2016.00840}, file = {:Users/navratil/Documents/Mendeley Desktop/2016/Carrouel et al/Frontiers in Microbiology/Frontiers in Microbiology{\_}Carrouel et al.{\_}Quantitative molecular detection of 19 major pathogens in the interdental biofilm of periodont.pdf:pdf}, issn = {1664302X}, journal = {Frontiers in Microbiology}, keywords = {Interdental microbiota,Oral biofilm,P. gingivalis,Periodontology,Socransky complexes}, number = {JUN}, publisher = {Frontiers Research Foundation}, title = {{Quantitative molecular detection of 19 major pathogens in the interdental biofilm of periodontally healthy young adults}}, url = {https://pubmed.ncbi.nlm.nih.gov/27313576/}, volume = {7}, year = {2016} } @article{Blaise2011, abstract = {Supervised multivariate statistical analyses of NMR spectroscopic data sets are often required to identify metabolic differences between sample classes, and the use of orthogonal filters has proven to be highly efficient even when dealing with weak perturbations. In this note, we associate orthogonal filters to the recently reported recoupled-statistical total correlation spectroscopy (RSTOCSY). An initial supervised deflation of the spectral matrix is applied to remove all information orthogonal to the effect of interest and is followed by an RSTOCSY analysis to extract a list of pairs of metabolites that experience correlated perturbations. This list can then be used to find possibilities for the perturbed metabolic network. This supervised RSTOCSY approach, dubbed OR-STOCSY, yields metabolites related to perturbations of biological interest, even if they make a minor contribution to the global variance of a complex data set compared to other (possibly confounding) effects under study. The method is demonstrated with the application to genetic phenotypes in Caenorhabditis elegans. {\textcopyright} 2011 American Chemical Society.}, author = {Blaise, Benjamin J. and Navratil, Vincent and Emsley, Lyndon and Toulhoat, Pierre}, doi = {10.1021/pr200489n}, issn = {15353893}, journal = {Journal of Proteome Research}, keywords = {NMR,OSC filter,SRV,STOCSY,correlation matrix,metabolic network,metabonomics}, month = {sep}, number = {9}, pages = {4342--4348}, pmid = {21774548}, title = {{Orthogonal filtered recoupled-STOCSY to extract metabolic networks associated with minor perturbations from NMR spectroscopy}}, volume = {10}, year = {2011} } @article{Kojadinovic2008, abstract = {In the purple photosynthetic bacterium Rhodopseudomonas palustris, far-red illumination induces photosystem synthesis via the action of the bacteriophytochrome RpBphP1. This bacteriophytochrome antagonizes the repressive effect of the transcriptional regulator PpsR2 under aerobic condition. We show here that, in addition to photosystem synthesis, far-red light induces a significant growth rate limitation, compared to cells grown in the dark, linked to a decrease in the respiratory activity. The phenotypes of mutants inactivated in RpBphP1 and PpsR2 show their involvement in this regulation. Based on enzymatic and transcriptional studies, a 30{\%} decrease in the expression of the alpha-ketoglutarate dehydrogenase complex, a central enzyme of the Krebs cycle, is observed under far-red light. We propose that this decrease is responsible for the down-regulation of respiration in this condition. This regulation mechanism at the Krebs cycle level still allows the formation of the photosynthetic apparatus via the synthesis of key biosynthesis precursors but lowers the production of NADH, i.e. the respiratory activity. Overall, the dual action of RpBphP1 on the regulation of both the photosynthesis genes and the Krebs cycle allows a fine adaptation of bacteria to environmental conditions by enhancement of the most favorable bioenergetic process in the light, photosynthesis versus respiration. {\textcopyright} 2007 Elsevier B.V. All rights reserved.}, author = {Kojadinovic, Mila and Laugraud, Aur{\'{e}}lie and Vuillet, Laurie and Fardoux, Jo{\"{e}}l and Hannibal, Laure and Adriano, Jean Marc and Bouyer, Pierre and Giraud, Eric and Verm{\'{e}}glio, Andr{\'{e}}}, doi = {10.1016/j.bbabio.2007.09.003}, file = {:Users/navratil/Documents/Mendeley Desktop/2008/Kojadinovic et al/Biochimica et Biophysica Acta - Bioenergetics/Biochimica et Biophysica Acta - Bioenergetics{\_}Kojadinovic et al.{\_}Dual role for a bacteriophytochrome in the bioenergetic control of Rhod.pdf:pdf}, issn = {00052728}, journal = {Biochimica et Biophysica Acta - Bioenergetics}, keywords = {Alpha-ketoglutarate,Bacteriophytochrome,Photosynthesis,Regulation,Respiration,Rhodopseudomonas palustris}, month = {feb}, number = {2}, pages = {163--172}, pmid = {17988648}, title = {{Dual role for a bacteriophytochrome in the bioenergetic control of Rhodopsdeudomonas palustris: Enhancement of photosystem synthesis and limitation of respiration}}, volume = {1777}, year = {2008} } @article{Gregoire2011, abstract = {Autophagy is a conserved degradative pathway used as a host defense mechanism against intracellular pathogens. However, several viruses can evade or subvert autophagy to insure their own replication. Nevertheless, the molecular details of viral interaction with autophagy remain largely unknown. We have determined the ability of 83 proteins of several families of RNA viruses (Paramyxoviridae, Flaviviridae, Orthomyxoviridae, Retroviridae and Togaviridae), to interact with 44 human autophagy-associated proteins using yeast two-hybrid and bioinformatic analysis. We found that the autophagy network is highly targeted by RNA viruses. Although central to autophagy, targeted proteins have also a high number of connections with proteins of other cellular functions. Interestingly, immunity-associated GTPase family M (IRGM), the most targeted protein, was found to interact with the autophagy-associated proteins ATG5, ATG10, MAP1CL3C and SH3GLB1. Strikingly, reduction of IRGM expression using small interfering RNA impairs both Measles virus (MeV), Hepatitis C virus (HCV) and human immunodeficiency virus-1 (HIV-1)-induced autophagy and viral particle production. Moreover we found that the expression of IRGM-interacting MeV-C, HCV-NS3 or HIV-NEF proteins per se is sufficient to induce autophagy, through an IRGM dependent pathway. Our work reveals an unexpected role of IRGM in virus-induced autophagy and suggests that several different families of RNA viruses may use common strategies to manipulate autophagy to improve viral infectivity. {\textcopyright} 2011 Gr{\'{e}}goire et al.}, author = {Gr{\'{e}}goire, Isabel Pombo and Richetta, Cl{\'{e}}mence and Meyniel-Schicklin, Laur{\`{e}}ne and Borel, Sophie and Pradezynski, Fabrine and Diaz, Olivier and Deloire, Alexandre and Azocar, Olga and Baguet, Jo{\"{e}}l and {Le Breton}, Marc and Mangeot, Philippe E. and Navratil, Vincent and Joubert, Pierre Emmanuel and Flacher, Monique and Vidalain, Pierre Olivier and Andr{\'{e}}, Patrice and Lotteau, Vincent and Biard-Piechaczyk, Martine and Rabourdin-Combe, Chantal and Faure, Mathias}, doi = {10.1371/journal.ppat.1002422}, file = {:Users/navratil/Documents/Mendeley Desktop/2011/Gr{\'{e}}goire et al/PLoS Pathogens/PLoS Pathogens{\_}Gr{\'{e}}goire et al.{\_}IRGM is a common target of RNA viruses that subvert the autophagy network{\_}2011(2).pdf:pdf}, issn = {15537366}, journal = {PLoS Pathogens}, month = {dec}, number = {12}, pmid = {22174682}, title = {{IRGM is a common target of RNA viruses that subvert the autophagy network}}, volume = {7}, year = {2011} } @article{Simonis2012, abstract = {Background: Human T-cell leukemia virus type 1 (HTLV-1) and type 2 both target T lymphocytes, yet induce radically different phenotypic outcomes. HTLV-1 is a causative agent of Adult T-cell leukemia (ATL), whereas HTLV-2, highly similar to HTLV-1, causes no known overt disease. HTLV gene products are engaged in a dynamic struggle of activating and antagonistic interactions with host cells. Investigations focused on one or a few genes have identified several human factors interacting with HTLV viral proteins. Most of the available interaction data concern the highly investigated HTLV-1 Tax protein. Identifying shared and distinct host-pathogen protein interaction profiles for these two viruses would enlighten how they exploit distinctive or common strategies to subvert cellular pathways toward disease progression.Results: We employ a scalable methodology for the systematic mapping and comparison of pathogen-host protein interactions that includes stringent yeast two-hybrid screening and systematic retest, as well as two independent validations through an additional protein interaction detection method and a functional transactivation assay. The final data set contained 166 interactions between 10 viral proteins and 122 human proteins. Among the 166 interactions identified, 87 and 79 involved HTLV-1 and HTLV-2 -encoded proteins, respectively. Targets for HTLV-1 and HTLV-2 proteins implicate a diverse set of cellular processes including the ubiquitin-proteasome system, the apoptosis, different cancer pathways and the Notch signaling pathway.Conclusions: This study constitutes a first pass, with homogeneous data, at comparative analysis of host targets for HTLV-1 and -2 retroviruses, complements currently existing data for formulation of systems biology models of retroviral induced diseases and presents new insights on biological pathways involved in retroviral infection. {\textcopyright} 2012 Simonis et al; licensee BioMed Central Ltd.}, author = {Simonis, Nicolas and Rual, Jean Fran{\c{c}}ois and Lemmens, Irma and Boxus, Mathieu and Hirozane-Kishikawa, Tomoko and Gatot, Jean St{\'{e}}phane and Dricot, Am{\'{e}}lie and Hao, Tong and Vertommen, Didier and Legros, S{\'{e}}bastien and Daakour, Sarah and Klitgord, Niels and Martin, Maud and Willaert, Jean Fran{\c{c}}ois and Dequiedt, Franck and Navratil, Vincent and Cusick, Michael E. and Burny, Ars{\`{e}}ne and {Van Lint}, Carine and Hill, David E. and Tavernier, Jan and Kettmann, Richard and Vidal, Marc and Twizere, Jean Claude}, doi = {10.1186/1742-4690-9-26}, file = {:Users/navratil/Documents/Mendeley Desktop/2012/Simonis et al/Retrovirology/Retrovirology{\_}Simonis et al.{\_}Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses{\_}2012.pdf:pdf}, issn = {17424690}, journal = {Retrovirology}, keywords = {HBZ,HTLV,Interactome,ORFeome,Retrovirus,Tax}, month = {mar}, pmid = {22458338}, title = {{Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses}}, volume = {9}, year = {2012} } @article{Galia2017, abstract = {Background: Enterohemorrhagic Escherichia coli (EHEC) are zoonotic agents associated with outbreaks worldwide. Growth of EHEC strains in ground beef could be inhibited by background microbiota that is present initially at levels greater than that of the pathogen E. coli. However, how the microbiota outcompetes the pathogenic bacteria is unknown. Our objective was to identify metabolic pathways of EHEC that were altered by natural microbiota in order to improve our understanding of the mechanisms controlling the growth and survival of EHECs in ground beef. Results: Based on 16S metagenomics analysis, we identified the microbial community structure in our beef samples which was an essential preliminary for subtractively analyzing the gene expression of the EHEC strains. Then, we applied strand-specific RNA-seq to investigate the effects of this microbiota on the global gene expression of EHEC O2621765 and O157EDL933 strains by comparison with their behavior in beef meat without microbiota. In strain O2621765, the expression of genes connected with nitrate metabolism and nitrite detoxification, DNA repair, iron and nickel acquisition and carbohydrate metabolism, and numerous genes involved in amino acid metabolism were down-regulated. Further, the observed repression of ftsL and murF, involved respectively in building the cytokinetic ring apparatus and in synthesizing the cytoplasmic precursor of cell wall peptidoglycan, might help to explain the microbiota's inhibitory effect on EHECs. For strain O157EDL933, the induced expression of the genes implicated in detoxification and the general stress response and the repressed expression of the peR gene, a gene negatively associated with the virulence phenotype, might be linked to the survival and virulence of O157:H7 in ground beef with microbiota. Conclusion: In the present study, we show how RNA-Seq coupled with a 16S metagenomics analysis can be used to identify the effects of a complex microbial community on relevant functions of an individual microbe within it. These findings add to our understanding of the behavior of EHECs in ground beef. By measuring transcriptional responses of EHEC, we could identify putative targets which may be useful to develop new strategies to limit their shedding in ground meat thus reducing the risk of human illnesses.}, author = {Galia, Wessam and Leriche, Francoise and Cruveiller, St{\'{e}}phane and Garnier, Cindy and Navratil, Vincent and Dubost, Audrey and Blanquet-Diot, St{\'{e}}phanie and Thevenot-Sergentet, Delphine}, doi = {10.1186/s12864-017-3957-2}, file = {:Users/navratil/Documents/Mendeley Desktop/2017/Galia et al/BMC Genomics/BMC Genomics{\_}Galia et al.{\_}Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground b.pdf:pdf}, issn = {14712164}, journal = {BMC Genomics}, keywords = {16S metagenomics analysis,EHEC,Ground beef,Natural microbiota,RNA-Seq}, month = {aug}, number = {1}, pmid = {28774270}, publisher = {BioMed Central Ltd.}, title = {{Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: Interactions between microorganisms in raw meat}}, volume = {18}, year = {2017} } @article{Moccia2009, abstract = {Background: Expressed sequence tag (EST) databases represent a valuable resource for the identification of genes in organisms with uncharacterized genomes and for development of molecular markers. One class of markers derived from EST sequences are simple sequence repeat (SSR) markers, also known as EST-SSRs. These are useful in plant genetic and evolutionary studies because they are located in transcribed genes and a putative function can often be inferred from homology searches. Another important feature of EST-SSR markers is their expected high level of transferability to related species that makes them very promising for comparative mapping. In the present study we constructed a normalized EST library from floral tissue of Silene latifolia with the aim to identify expressed genes and to develop polymorphic molecular markers. Results: We obtained a total of 3662 high quality sequences from a normalized Silene cDNA library. These represent 3105 unigenes, with 73{\%} of unigenes matching genes in other species. We found 255 sequences containing one or more SSR motifs. More than 60{\%} of these SSRs were trinucleotides. A total of 30 microsatellite loci were identified from 106 ESTs having sufficient flanking sequences for primer design. The inheritance of these loci was tested via segregation analyses and their usefulness for linkage mapping was assessed in an interspecific cross. Tests for crossamplification of the EST-SSR loci in other Silene species established their applicability to related species. Conclusion: The newly characterized genes and gene-derived markers from our Silene EST library represent a valuable genetic resource for future studies on Silene latifolia and related species. The polymorphism and transferability of EST-SSR markers facilitate comparative linkage mapping and analyses of genetic diversity in the genus Silene. {\textcopyright} 2009 Moccia et al; licensee BioMed Central Ltd.}, author = {Moccia, Maria Domenica and Oger-Desfeux, Christine and Marais, Gabriel A.B. and Widmer, Alex}, doi = {10.1186/1471-2164-10-243}, file = {:Users/navratil/Documents/Mendeley Desktop/2009/Moccia et al/BMC Genomics/BMC Genomics{\_}Moccia et al.{\_}A white campion (Silene latifolia) floral expressed sequence tag (EST) library Annotation, EST-SSR characteri.pdf:pdf}, issn = {14712164}, journal = {BMC Genomics}, month = {may}, pmid = {19467153}, title = {{A white campion (Silene latifolia) floral expressed sequence tag (EST) library: Annotation, EST-SSR characterization, transferability, and utility for comparative mapping}}, volume = {10}, year = {2009} } @article{Regnault2014, abstract = {Background: Despite numerous studies suggesting that amphibians are highly sensitive to cumulative anthropogenic stresses, the role pollutants play in the decline of amphibian populations remains unclear. Amongst the most common aquatic contaminants, polycyclic aromatic hydrocarbons (PAHs) have been shown to induce several adverse effects on amphibian species in the larval stages. Conversely, adults exposed to high concentrations of the ubiquitous PAH, benzo[a]pyrene (BaP), tolerate the compound thanks to their highly efficient hepatic detoxification mechanisms. Due to this apparent lack of toxic effect on adults, no studies have examined in depth the potential toxicological impact of PAH on the physiology of adult amphibian livers. This study sheds light on the hepatic responses of Xenopus tropicalis when exposed to high environmentally relevant concentrations of BaP, by combining a high throughput transcriptomic approach (mRNA deep sequencing) and a characterization of cellular and physiological modifications to the amphibian liver.Results: Transcriptomic changes observed in BaP-exposed Xenopus were further characterized using a time-dependent enrichment analysis, which revealed the pollutant-dependent gene regulation of important biochemical pathways, such as cholesterol biosynthesis, insulin signaling, adipocytokines signaling, glycolysis/gluconeogenesis and MAPK signaling. These results were substantiated at the physiological level with the detection of a pronounced metabolic disorder resulting in a possible insulin resistance-like syndrome phenotype. Hepatotoxicity induced by lipid and cholesterol metabolism impairments was clearly identified in BaP-exposed individuals.Conclusions: Our data suggested that BaP may disrupt overall liver physiology, and carbohydrate and cholesterol metabolism in particular, even after short-term exposure. These results are further discussed in terms of how this deregulation of liver physiology can lead to general metabolic impairment in amphibians chronically exposed to contaminants, thereby illustrating the role xenobiotics might play in the global decline in amphibian populations.}, author = {Regnault, Christophe and Worms, Isabelle A.M. and Oger-Desfeux, Christine and MelodeLima, Christelle and Veyrenc, Sylvie and Bayle, Marie Laure and Combourieu, Bruno and Bonin, Aur{\'{e}}lie and Renaud, Julien and Raveton, Muriel and Reynaud, St{\'{e}}phane}, doi = {10.1186/1471-2164-15-666}, file = {:Users/navratil/Documents/Mendeley Desktop/2014/Regnault et al/BMC Genomics/BMC Genomics{\_}Regnault et al.{\_}Impaired liver function in Xenopus tropicalis exposed to benzoapyrene Transcriptomic and metabolic evidence.pdf:pdf}, issn = {14712164}, journal = {BMC Genomics}, keywords = {Benzo[a]pyrene,Insulin resistance-like syndrome,Liver,Metabolic disorders,RNA sequencing,Xenopus}, month = {aug}, number = {1}, pmid = {25103525}, publisher = {BioMed Central Ltd.}, title = {{Impaired liver function in Xenopus tropicalis exposed to benzo[a]pyrene: Transcriptomic and metabolic evidence}}, volume = {15}, year = {2014} } @article{Duchemin2018, abstract = {Motivation: A reconciliation is an annotation of the nodes of a gene tree with evolutionary events—for example, speciation, gene duplication, transfer, loss, etc.—along with a mapping onto a species tree. Many algorithms and software produce or use reconciliations but often using different reconciliation formats, regarding the type of events considered or whether the species tree is dated or not. This complicates the comparison and communication between different programs. Results: Here, we gather a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative—albeit flexible—specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities.}, author = {Duchemin, Wandrille and Gence, Guillaume and Chifolleau, Anne Muriel Arigon and Arvestad, Lars and Bansal, Mukul S. and Berry, Vincent and Boussau, Bastien and Chevenet, Fran{\c{c}}ois and Comte, Nicolas and Dav{\'{i}}n, Adri{\'{a}}n A. and Dessimoz, Christophe and Dylus, David and Hasic, Damir and Mallo, Diego and Planel, R{\'{e}}mi and Posada, David and Scornavacca, Celine and Sz{\"{o}}llősi, Gergely and Zhang, Louxin and Tannier, {\'{E}}ric and Daubin, Vincent}, doi = {10.1093/bioinformatics/bty389}, file = {:Users/navratil/Documents/Mendeley Desktop/2018/Duchemin et al/Bioinformatics/Bioinformatics{\_}Duchemin et al.{\_}RecPhyloXML A format for reconciled gene trees{\_}2018.pdf:pdf}, issn = {14602059}, journal = {Bioinformatics}, number = {21}, pages = {3646--3652}, pmid = {29762653}, publisher = {Oxford University Press}, title = {{RecPhyloXML: A format for reconciled gene trees}}, volume = {34}, year = {2018} } @article{Pontoizeau2011, abstract = {Maintaining homeostasis in higher organisms involves a complex interplay of multiple ubiquitous and organ-specific molecular mechanisms that can be characterized using functional genomics technologies such as transcriptomics, proteomics, and metabonomics and dissected out through genetic investigations in healthy and diseased individuals. We characterized the genomic, metabolic, and physiological divergence of several inbred rat strains-Brown Norway, Lewis, Wistar Kyoto, Fisher (F344)-frequently used as healthy controls in genetic studies of the cardiometabolic syndrome. Hierarchical clustering of 1H NMR-based metabolic profiles (n = 20 for urine, n = 16 for plasma) identified metabolic phenotype (metabotype) divergence patterns similar to the phylogenetic variability based on single nucleotide polymorphisms. However, the observed urinary metabotype variation exceeded that explainable by genetic polymorphisms. To understand further this natural variation, we used an integrative, knowledge-based network biology metabolic pathway analysis approach, coined Metabolite-Set Enrichment Analysis (MSEA). MSEA reveals that homeostasis and physiological plasticity can be achieved despite widespread divergences in glucose, lipid, amino acid, and energy metabolism in the host, together with different gut microbiota contributions suggestive of strain-specific transgenomic interactions. This work illustrates the concept of natural metabolomic variation, leading to physiologically stable albeit diverse strategies within the range of normality, all of which are highly relevant to animal model physiology, genetical genomics, and patient stratification in personalized healthcare. {\textcopyright} 2011 American Chemical Society.}, author = {Pontoizeau, Cl{\'{e}}ment and Fearnside, Jane F. and Navratil, Vincent and Domange, C{\'{e}}line and Cazier, Jean Baptiste and Fern{\'{a}}ndez-Santamar{\'{i}}a, Cristina and Kaisaki, Pamela J. and Emsley, Lyndon and Toulhoat, Pierre and Bihoreau, Marie Th{\'{e}}r{\`{e}}se and Nicholson, Jeremy K. and Gauguier, Dominique and Dumas, Marc E.}, doi = {10.1021/pr101000z}, issn = {15353893}, journal = {Journal of Proteome Research}, keywords = {NMR spectroscopy,cardiometabolic syndrome,metabolite-set enrichment analysis,metabonomics/metabolomics,natural variation,pathway analysis,single nucleotide polymorphism}, month = {apr}, number = {4}, pages = {1675--1689}, pmid = {21322573}, title = {{Broad-ranging natural metabotype variation drives physiological plasticity in healthy control inbred rat strains}}, volume = {10}, year = {2011} } @article{Navratil2010, abstract = {Infection caused by pathogens kills millions of people every year. Comprehensive understanding of molecular pathogen-host interactions, i.e. the infectome, is one of the key steps towards the development of novel diagnostic, therapeutic and preventive strategies. In this quest, progress in high-throughput « omics » technologies applied to pathogens, i.e. infectomics, opens new perspectives toward systemic understanding of perturbations induced during infection. Deciphering the pathogen-host system also relies on the analytical and predictive power of molecular systems biology and by developing in silico models taking into account the whole picture of the molecules and their interactions. In this context, we have reconstructed a prototype of the human virtual infected cell based on 30 years of intensive research in the field of molecular virology. This model contains more than one hundred viral infectomes, including major human pathogens (HCV, HBV, HIV, HHV, HPV) and has led to the generation of novel systems-level hypotheses that could be suitable for the development of innovative antiviral strategies based on the control of cellular functions.}, author = {Navratil, Vincent and Lotteau, Vincent and Rabourdin-Combe, Chantal}, doi = {10.1051/medsci/2010266-7603}, file = {:Users/navratil/Documents/Mendeley Desktop/2010/Navratil, Lotteau, Rabourdin-Combe/MedecineSciences/MedecineSciences{\_}Navratil, Lotteau, Rabourdin-Combe{\_}The virtual infected cell A systems biology rational for antiviral drug discovery{\_}20.pdf:pdf}, issn = {07670974}, journal = {Medecine/Sciences}, number = {6-7}, pages = {603--609}, pmid = {20619162}, publisher = {Editions EDK}, title = {{The virtual infected cell: A systems biology rational for antiviral drug discovery}}, volume = {26}, year = {2010} } @article{Francois2016, abstract = {The field of stoichiogenomics aims at understanding the influence of nutrient limitations on the elemental composition of the genome, transcriptome, and proteome. The 20 amino acids and the 4 nt differ in the number of nutrients they contain, such as nitrogen (N). Thus, N limitation shall theoretically select for changes in the composition of proteins or RNAs through preferential use of N-poor amino acids or nucleotides, which will decrease the N-budget of an organism. While these N-saving mechanisms have been evidenced in microorganisms, they remain controversial in multicellular eukaryotes. In this study, we used 13 surface and subterranean isopod species pairs that face strongly contrasted N limitations, either in terms of quantity or quality. We combined in situ nutrient quantification and transcriptome sequencing to test if N limitation selected for N-savings through changes in the expression and composition of the transcriptome and proteome. No evidence of N-savings was found in the total N-budget of transcriptomes or proteomes or in the average protein N-cost. Nevertheless, subterranean species evolving in N-depleted habitats displayed lower N-usage at their third codon positions. To test if this convergent compositional change was driven by natural selection, we developed a method to detect the strand-asymmetric signature that stoichiogenomic selection should leave in the substitution pattern. No such signature was evidenced, indicating that the observed stoichiogenomic-like patterns were attributable to nonadaptive processes. The absence of stoichiogenomic signal despite strong N limitation within a powerful phylogenetic framework casts doubt on the existence of stoichiogenomic mechanisms in metazoans.}, author = {Francois, Cl{\'{e}}mentine M. and Duret, Laurent and Simon, Laurent and Mermillod-Blondin, Florian and Malard, Florian and Konecny-Dupr{\'{e}}, Lara and Planel, R{\'{e}}mi and Penel, Simon and Douady, Christophe J. and Lef{\'{e}}bure, Tristan}, doi = {10.1093/molbev/msw131}, file = {:Users/navratil/Documents/Mendeley Desktop/2016/Francois et al/Molecular Biology and Evolution/Molecular Biology and Evolution{\_}Francois et al.{\_}No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Tran.pdf:pdf}, issn = {15371719}, journal = {Molecular Biology and Evolution}, keywords = {C:N mismatch,N availability,RNA and protein composition,comparative approach,nitrogen cost,orthologous gene families,stoichiogenomics}, month = {oct}, number = {10}, pages = {2605--2620}, pmid = {27401232}, publisher = {Oxford University Press}, title = {{No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes}}, volume = {33}, year = {2016} } @article{Lassalle2011, abstract = {The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome-one on the circular chromosome and six on the linear chromosome-suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species. {\textcopyright} The Author(s) 2010.}, author = {Lassalle, Florent and Campillo, Tony and Vial, Ludovic and Baude, Jessica and Costechareyre, Denis and Chapulliot, David and Shams, Malek and Abrouk, Danis and Lavire, C{\'{e}}line and Oger-Desfeux, Christine and Hommais, Florence and Gu{\'{e}}guen, Laurent and Daubin, Vincent and Muller, Daniel and Nesme, Xavier}, doi = {10.1093/gbe/evr070}, file = {:Users/navratil/Documents/Mendeley Desktop/2011/Lassalle et al/Genome Biology and Evolution/Genome Biology and Evolution{\_}Lassalle et al.{\_}Genomic species are ecological species as revealed by comparative genomics in Agrobacterium.pdf:pdf}, issn = {17596653}, journal = {Genome Biology and Evolution}, keywords = {Agrobacterium,Bacterial evolution,Bacterial species,Ecological niche,Linear chromosome}, number = {1}, pages = {762--781}, pmid = {21795751}, title = {{Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens}}, volume = {3}, year = {2011} } @article{Gautier2007, abstract = {To evaluate and compare the extent of LD in cattle, 1536 SNPs, mostly localized on BTA03, were detected in silico from available sequence data using two different methods and genotyped on samples from 14 distinct breeds originating from Europe and Africa. Only 696 SNPs could be validated, confirming the importance of trace-quality information for the in silico detection. Most of the validated SNPs were informative in several breeds and were used for a detailed description of their genetic structure and relationships. Results obtained were in agreement with previous studies performed on microsatellite markers and using larger samples. In addition, the majority of the validated SNPs could be mapped precisely, reaching an average density of one marker every 311 kb. This allowed us to analyze the extent of LD in the different breeds. Decrease of LD with physical distance across breeds revealed footprints of ancestral LD at short distances ({\textless}10 kb). As suggested by the haplotype block structure, these ancestral blocks are organized, within a breed, into larger blocks of a few hundred kilobases. In practice, such a structure similar to that already reported in dogs makes it possible to develop a chip of ,300,000 SNPs, which should be efficient for mapping purposes in most cattle breeds. Copyright {\textcopyright} 2007 by the Genetics Society of America.}, author = {Gautier, Mathieu and Faraut, Thomas and Moazami-Goudarzi, Katayoun and Navratil, Vincent and Foglio, Mario and Grohs, C{\'{e}}cile and Boland, Anne and Garnier, Jean Guillaume and Boichard, Didier and Lathrop, G. Mark and Gut, Ivo G. and Eggen, Andr{\'{e}}}, doi = {10.1534/genetics.107.075804}, file = {:Users/navratil/Documents/Mendeley Desktop/2007/Gautier et al/Genetics/Genetics{\_}Gautier et al.{\_}Genetic and haplotypic structure in 14 European and African cattle breeds{\_}2007.pdf:pdf}, issn = {00166731}, journal = {Genetics}, month = {oct}, number = {2}, pages = {1059--1070}, pmid = {17720924}, title = {{Genetic and haplotypic structure in 14 European and African cattle breeds}}, volume = {177}, year = {2007} } @article{Hunter2009, abstract = {The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or 'signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total ∼ 58 000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein-protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8{\%} of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/). {\textcopyright} 2008 The Author(s).}, author = {Hunter, Sarah and Apweiler, Rolf and Attwood, Teresa K. and Bairoch, Amos and Bateman, Alex and Binns, David and Bork, Peer and Das, Ujjwal and Daugherty, Louise and Duquenne, Lauranne and Finn, Robert D. and Gough, Julian and Haft, Daniel and Hulo, Nicolas and Kahn, Daniel and Kelly, Elizabeth and Laugraud, Aur{\'{e}}lie and Letunic, Ivica and Lonsdale, David and Lopez, Rodrigo and Madera, Martin and Maslen, John and Mcanulla, Craig and McDowall, Jennifer and Mistry, Jaina and Mitchell, Alex and Mulder, Nicola and Natale, Darren and Orengo, Christine and Quinn, Antony F. and Selengut, Jeremy D. and Sigrist, Christian J.A. and Thimma, Manjula and Thomas, Paul D. and Valentin, Franck and Wilson, Derek and Wu, Cathy H. and Yeats, Corin}, doi = {10.1093/nar/gkn785}, file = {:Users/navratil/Documents/Mendeley Desktop/2009/Hunter et al/Nucleic Acids Research/Nucleic Acids Research{\_}Hunter et al.{\_}InterPro The integrative protein signature database{\_}2009(2).pdf:pdf}, issn = {03051048}, journal = {Nucleic Acids Research}, number = {SUPPL. 1}, pmid = {18940856}, title = {{InterPro: The integrative protein signature database}}, volume = {37}, year = {2009} } @article{Meunier2005, abstract = {In mammals, several studies have suggested that levels of methylation are higher in repetitive DNA than in nonrepetitive DNA, possibly reflecting a genome-wide defense mechanism against deleterious effects associated with transposable elements (TEs). To analyze the determinants of methylation patterns in primate repetitive DNA, we took advantage of the fact that the methylation rate in the germ line is reflected by the transition rate at CpG sites. We assessed the variability of CpG substitution rates in nonrepetitive DNA and in various TE and retropseudogene families. We show that, unlike other substitution rates, the rate of transition at CpG sites is significantly (37{\%}) higher in repetitive DNA than in nonrepetitive DNA. Moreover, this rate of CpG transition varies according to the number of repeats, their length, and their level of divergence from the ancestral sequence (up to 2.7 times higher in long, lowly divergent TEs compared with unique sequences). This observation strongly suggests the existence of a homology-dependent methylation (HDM) mechanism in mammalian genomes. We propose that HDM is a direct consequence of interfering RNA-induced transcriptional gene silencing. {\textcopyright} 2005 by The National Academy of Sciences of the USA.}, author = {Meunier, Julien and Khelifi, Adel and Navratil, Vincent and Duret, Laurent}, doi = {10.1073/pnas.0408986102}, file = {:Users/navratil/Documents/Mendeley Desktop/2005/Meunier et al/Proceedings of the National Academy of Sciences of the United States of America/Proceedings of the National Academy of Sciences of the United States of America{\_}Meunier et al.{\_}Homology-dependent methylation in primate.pdf:pdf}, issn = {00278424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, keywords = {CpG,RNA interference,Substitution rate,Transposable element}, month = {apr}, number = {15}, pages = {5471--5476}, pmid = {15797989}, title = {{Homology-dependent methylation in primate repetitive DNA}}, volume = {102}, year = {2005} } @article{DeChassey2013, abstract = {Virus-host interactomes are instrumental to understand global perturbations of cellular functions induced by infection and discover new therapies. The construction of such interactomes is, however, technically challenging and time consuming. Here we describe an original method for the prediction of high-confidence interactions between viral and human proteins through a combination of structure and high-quality interactome data. Validation was performed for the NS1 protein of the influenza virus, which led to the identification of new host factors that control viral replication. {\textcopyright} 2013 European Molecular Biology Organization.}, author = {{De Chassey}, Beno{\^{i}}t and Meyniel-Schicklin, Laur{\`{e}}ne and Aublin-Gex, Anne and Navratil, Vincent and Chantier, Thibaut and Andr{\'{e}}, Patrice and Lotteau, Vincent}, doi = {10.1038/embor.2013.130}, file = {:Users/navratil/Documents/Mendeley Desktop/2013/De Chassey et al/EMBO Reports/EMBO Reports{\_}De Chassey et al.{\_}Structure homology and interaction redundancy for discovering virus-host protein interactions{\_}2013.pdf:pdf}, issn = {1469221X}, journal = {EMBO Reports}, keywords = {interactome,prediction,protein interaction,structure,virus}, month = {oct}, number = {10}, pages = {938--944}, pmid = {24008843}, title = {{Structure homology and interaction redundancy for discovering virus-host protein interactions}}, volume = {14}, year = {2013} } @article{Mitchell2015, abstract = {The InterPro database (http://www.ebi.ac.uk/interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and sites. Central to the InterPro database are predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches to classify protein families and domains. InterPro integrates these signatures, capitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource. Here, we report on the status of InterPro as it enters its 15th year of operation, and give an overview of new developments with the database and its associated Web interfaces and software. In particular, the new domain architecture search tool is described and the process of mapping of Gene Ontology terms to InterPro is outlined. We also discuss the challenges faced by the resource given the explosive growth in sequence data in recent years. InterPro (version 48.0) contains 36 766 member database signatures integrated into 26 238 InterPro entries, an increase of over 3993 entries (5081 signatures), since 2012.}, author = {Mitchell, Alex and Chang, Hsin Yu and Daugherty, Louise and Fraser, Matthew and Hunter, Sarah and Lopez, Rodrigo and McAnulla, Craig and McMenamin, Conor and Nuka, Gift and Pesseat, Sebastien and Sangrador-Vegas, Amaia and Scheremetjew, Maxim and Rato, Claudia and Yong, Siew Yit and Bateman, Alex and Punta, Marco and Attwood, Teresa K. and Sigrist, Christian J.A. and Redaschi, Nicole and Rivoire, Catherine and Xenarios, Ioannis and Kahn, Daniel and Guyot, Dominique and Bork, Peer and Letunic, Ivica and Gough, Julian and Oates, Matt and Haft, Daniel and Huang, Hongzhan and Natale, Darren A. and Wu, Cathy H. and Orengo, Christine and Sillitoe, Ian and Mi, Huaiyu and Thomas, Paul D. and Finn, Robert D.}, doi = {10.1093/nar/gku1243}, file = {:Users/navratil/Documents/Mendeley Desktop/2015/Mitchell et al/Nucleic Acids Research/Nucleic Acids Research{\_}Mitchell et al.{\_}The InterPro protein families database The classification resource after 15 years{\_}2015.pdf:pdf}, issn = {13624962}, journal = {Nucleic Acids Research}, month = {jan}, number = {D1}, pages = {D213--D221}, pmid = {25428371}, publisher = {Oxford University Press}, title = {{The InterPro protein families database: The classification resource after 15 years}}, volume = {43}, year = {2015} } @article{Aouacheria2006a, abstract = {Background: Owing to the explosion of information generated by human genomics, analysis of publicly available databases can help identify potential candidate genes relevant to the cancerous phenotype. The aim of this study was to scan for such genes by whole-genome in silico subtraction using Expressed Sequence Tag (EST) data. Methods: Genes differentially expressed in normal versus tumor tissues were identified using a computer-based differential display strategy. Bcl-xL, an anti-apoptotic member of the Bcl-2 family, was selected for confirmation by western blot analysis. Results: Our genome-wide express ion analysis identified a set of genes whose differential expression may be attributed to the genetic alterations associated with tumor formation and malignant growth. We propose complete lists of genes that may serve as targets for projects seeking novel candidates for cancer diagnosis and therapy. Our validation result showed increased protein levels of Bcl-xL in two different liver cancer specimens compared to normal liver. Notably, our EST-based data mining procedure indicated that most of the changes in gene expression observed in cancer cells corresponded to gene inactivation patterns. Chromosomes and chromosomal regions most frequently associated with aberrant expression changes in cancer libraries were also determined. Conclusion: Through the description of several candidates (including genes encoding extracellular matrix and ribosomal components, cytoskeletal proteins, apoptotic regulators, and novel tissue-specific biomarkers), our study illustrates the utility of in silico transcriptomics to identify tumor cell signatures, tumor-related genes and chromosomal regions frequently associated with aberrant expression in cancer. {\textcopyright} 2006 Aouacheria et al; licensee BioMed Central Ltd.}, author = {Aouacheria, Abdel and Navratil, Vincent and Barthelaix, Audrey and Mouchiroud, Dominique and Gautier, Christian}, doi = {10.1186/1471-2164-7-94}, file = {:Users/navratil/Documents/Mendeley Desktop/2006/Aouacheria et al/BMC Genomics/BMC Genomics{\_}Aouacheria et al.{\_}Bioinformatic screening of human ESTs for differentially expressed genes in normal and tumor tissues{\_}2006.pdf:pdf}, issn = {14712164}, journal = {BMC Genomics}, month = {apr}, pmid = {16640784}, title = {{Bioinformatic screening of human ESTs for differentially expressed genes in normal and tumor tissues}}, volume = {7}, year = {2006} } @article{Ashraf2019, abstract = {Alteration of host cell splicing is a common feature of many viral infections which is underappreciated because of the complexity and technical difficulty of studying alternative splicing (AS) regulation. Recent advances in RNA sequencing technologies revealed that up to several hundreds of host genes can show altered mRNA splicing upon viral infection. The observed changes in AS events can be either a direct consequence of viral manipulation of the host splicing machinery or result indirectly from the virus-induced innate immune response or cellular damage. Analysis at a higher resolution with single-cell RNAseq, and at a higher scale with the integration of multiple omics data sets in a systems biology perspective, will be needed to further comprehend this complex facet of virus–host interactions.}, author = {Ashraf, Usama and Benoit-Pilven, Clara and Lacroix, Vincent and Navratil, Vincent and Naffakh, Nadia}, doi = {10.1016/j.tim.2018.11.004}, issn = {18784380}, journal = {Trends in Microbiology}, keywords = {alternative splicing,genome-wide transcriptomics,systems biology,virus–host interaction}, month = {mar}, number = {3}, pages = {268--281}, pmid = {30577974}, publisher = {Elsevier Ltd}, title = {{Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing}}, volume = {27}, year = {2019} } @misc{Sonnhammer2014, abstract = {Given the rapid increase of species with a sequenced genome, the need to identify orthologous genes between them has emerged as a central bioinformatics task. Many different methods exist for orthology detection, which makes it difficult to decide which one to choose for a particular application. Here, we review the latest developments and issues in the orthology field, and summarize the most recent results reported at the third 'Quest for Orthologs' meeting. We focus on community efforts such as the adoption of reference proteomes, standard file formats and benchmarking. Progress in these areas is good, and they are already beneficial to both orthology consumers and providers. However, a major current issue is that the massive increase in complete proteomes poses computational challenges to many of the ortholog database providers, as most orthology inference algorithms scale at least quadratically with the number of proteomes. The Quest for Orthologs consortium is an open community with a number of working groups that join efforts to enhance various aspects of orthology analysis, such as defining standard formats and datasets, documenting community resources and benchmarking.}, author = {Sonnhammer, Erik L.L. and Gabaldon, Toni and {Sousa Da Silva}, Alan W. and Martin, Maria and Robinson-Rechavi, Marc and Boeckmann, Brigitte and Thomas, Paul D. and Dessimoz, Christophe}, booktitle = {Bioinformatics}, doi = {10.1093/bioinformatics/btu492}, file = {:Users/navratil/Documents/Mendeley Desktop/2014/Sonnhammer et al/Bioinformatics/Bioinformatics{\_}Sonnhammer et al.{\_}Big data and other challenges in the quest for orthologs{\_}2014.pdf:pdf}, issn = {14602059}, month = {may}, number = {21}, pages = {2993--2998}, pmid = {25064571}, publisher = {Oxford University Press}, title = {{Big data and other challenges in the quest for orthologs}}, volume = {30}, year = {2014} } @article{David2014, abstract = {Background:Mosquito control programmes using chemical insecticides are increasingly threatened by the development of resistance. Such resistance can be the consequence of changes in proteins targeted by insecticides (target site mediated resistance), increased insecticide biodegradation (metabolic resistance), altered transport, sequestration or other mechanisms. As opposed to target site resistance, other mechanisms are far from being fully understood. Indeed, insecticide selection often affects a large number of genes and various biological processes can hypothetically confer resistance. In this context, the aim of the present study was to use RNA sequencing (RNA-seq) for comparing transcription level and polymorphism variations associated with adaptation to chemical insecticides in the mosquito Aedes aegypti. Biological materials consisted of a parental susceptible strain together with three child strains selected across multiple generations with three insecticides from different classes:the pyrethroid permethrin, the neonicotinoid imidacloprid and the carbamate propoxur.Results:After ten generations, insecticide-selected strains showed elevated resistance levels to the insecticides used for selection. RNA-seq data allowed detecting over 13,000 transcripts, of which 413 were differentially transcribed in insecticide-selected strains as compared to the susceptible strain. Among them, a significant enrichment of transcripts encoding cuticle proteins, transporters and enzymes was observed. Polymorphism analysis revealed over 2500 SNPs showing {\textgreater} 50{\%} allele frequency variations in insecticide-selected strains as compared to the susceptible strain, affecting over 1000 transcripts. Comparing gene transcription and polymorphism patterns revealed marked differences among strains. While imidacloprid selection was linked to the over transcription of many genes, permethrin selection was rather linked to polymorphism variations. Focusing on detoxification enzymes revealed that permethrin selection strongly affected the polymorphism of several transcripts encoding cytochrome P450 monooxygenases likely involved in insecticide biodegradation.Conclusions:The present study confirmed the power of RNA-seq for identifying concomitantly quantitative and qualitative transcriptome changes associated with insecticide resistance in mosquitoes. Our results suggest that transcriptome modifications can be selected rapidly by insecticides and affect multiple biological functions. Previously neglected by molecular screenings, polymorphism variations of detoxification enzymes may play an important role in the adaptive response of mosquitoes to insecticides. {\textcopyright} 2014 David et al.; licensee BioMed Central Ltd.}, author = {David, Jean Philippe and Faucon, Fr{\'{e}}d{\'{e}}ric and Chandor-Proust, Alexia and Poupardin, Rodolphe and Riaz, Muhammad A. and Bonin, Aur{\'{e}}lie and Navratil, Vincent and Reynaud, St{\'{e}}phane}, doi = {10.1186/1471-2164-15-174}, file = {:Users/navratil/Documents/Mendeley Desktop/2014/David et al/BMC Genomics/BMC Genomics{\_}David et al.{\_}Comparative analysis of response to selection with three insecticides in the dengue mosquito Aedes aegypti (2).pdf:pdf}, issn = {14712164}, journal = {BMC Genomics}, keywords = {CYP,Cuticle,Cytochrome P450 monooxygenase,Dengue,Detoxification enzymes,Insecticide resistance,Mosquito,RNA sequencing,RNA-seq,Transporters}, month = {mar}, number = {1}, pmid = {24593293}, publisher = {BioMed Central Ltd.}, title = {{Comparative analysis of response to selection with three insecticides in the dengue mosquito Aedes aegypti using mRNA sequencing}}, volume = {15}, year = {2014} } @article{Blavet2011, abstract = {Background: The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing functional variation and developing molecular markers, thereby laying the foundations for future studies on gene sequence and gene expression divergence. Here, we report the results of a comparative transcriptome sequencing study of eight individuals representing four Silene and one Dianthus species as outgroup. All sequences and annotations have been deposited in a newly developed and publicly available database called SiESTa, the Silene EST annotation database.Results: A total of 1,041,122 EST reads were generated in two runs on a Roche GS-FLX 454 pyrosequencing platform. EST reads were analyzed separately for all eight individuals sequenced and were assembled into contigs using TGICL. These were annotated with results from BLASTX searches and Gene Ontology (GO) terms, and thousands of single-nucleotide polymorphisms (SNPs) were characterized. Unassembled reads were kept as singletons and together with the contigs contributed to the unigenes characterized in each individual. The high quality of unigenes is evidenced by the proportion (49{\%}) that have significant hits in similarity searches with the A. thaliana proteome. The SiESTa database is accessible at http://www.siesta.ethz.ch.Conclusion: The sequence collections established in the present study provide an important genomic resource for four Silene and one Dianthus species and will help to further develop Silene as a plant model system. The genes characterized will be useful for future research not only in the species included in the present study, but also in related species for which no genomic resources are yet available. Our results demonstrate the efficiency of massively parallel transcriptome sequencing in a comparative framework as an approach for developing genomic resources in diverse groups of non-model organisms. {\textcopyright} 2011 Blavet et al; licensee BioMed Central Ltd.}, author = {Blavet, Nicolas and Charif, Delphine and Oger-Desfeux, Christine and Marais, Gabriel A.B. and Widmer, Alex}, doi = {10.1186/1471-2164-12-376}, file = {:Users/navratil/Documents/Mendeley Desktop/2011/Blavet et al/BMC Genomics/BMC Genomics{\_}Blavet et al.{\_}Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation dat.pdf:pdf}, issn = {14712164}, journal = {BMC Genomics}, keywords = {Database,ESTSNP,Silene,cDNA library}, month = {jul}, pmid = {21791039}, title = {{Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database}}, volume = {12}, year = {2011} } @article{Dumas2016, abstract = {Background: The genetic regulation of metabolic phenotypes (i.e., metabotypes) in type 2 diabetes mellitus occurs through complex organ-specific cellular mechanisms and networks contributing to impaired insulin secretion and insulin resistance. Genome-wide gene expression profiling systems can dissect the genetic contributions to metabolome and transcriptome regulations. The integrative analysis of multiple gene expression traits and metabolic phenotypes (i.e., metabotypes) together with their underlying genetic regulation remains a challenge. Here, we introduce a systems genetics approach based on the topological analysis of a combined molecular network made of genes and metabolites identified through expression and metabotype quantitative trait locus mapping (i.e., eQTL and mQTL) to prioritise biological characterisation of candidate genes and traits. Methods: We used systematic metabotyping by 1H NMR spectroscopy and genome-wide gene expression in white adipose tissue to map molecular phenotypes to genomic blocks associated with obesity and insulin secretion in a series of rat congenic strains derived from spontaneously diabetic Goto-Kakizaki (GK) and normoglycemic Brown-Norway (BN) rats. We implemented a network biology strategy approach to visualize the shortest paths between metabolites and genes significantly associated with each genomic block. Results: Despite strong genomic similarities (95-99 {\%}) among congenics, each strain exhibited specific patterns of gene expression and metabotypes, reflecting the metabolic consequences of series of linked genetic polymorphisms in the congenic intervals. We subsequently used the congenic panel to map quantitative trait loci underlying specific mQTLs and genome-wide eQTLs. Variation in key metabolites like glucose, succinate, lactate, or 3-hydroxybutyrate and second messenger precursors like inositol was associated with several independent genomic intervals, indicating functional redundancy in these regions. To navigate through the complexity of these association networks we mapped candidate genes and metabolites onto metabolic pathways and implemented a shortest path strategy to highlight potential mechanistic links between metabolites and transcripts at colocalized mQTLs and eQTLs. Minimizing the shortest path length drove prioritization of biological validations by gene silencing. Conclusions: These results underline the importance of network-based integration of multilevel systems genetics datasets to improve understanding of the genetic architecture of metabotype and transcriptomic regulation and to characterize novel functional roles for genes determining tissue-specific metabolism.}, author = {Dumas, Marc Emmanuel and Domange, C{\'{e}}line and Calderari, Sophie and Mart{\'{i}}nez, Andrea Rodr{\'{i}}guez and Ayala, Rafael and Wilder, Steven P. and Su{\'{a}}rez-Zamorano, Nicolas and Collins, Stephan C. and Wallis, Robert H. and Gu, Quan and Wang, Yulan and Hue, Christophe and Otto, Georg W. and Argoud, Kar{\`{e}}ne and Navratil, Vincent and Mitchell, Steve C. and Lindon, John C. and Holmes, Elaine and Cazier, Jean Baptiste and Nicholson, Jeremy K. and Gauguier, Dominique}, doi = {10.1186/s13073-016-0352-6}, file = {:Users/navratil/Documents/Mendeley Desktop/2016/Dumas et al/Genome Medicine/Genome Medicine{\_}Dumas et al.{\_}Topological analysis of metabolic networks integrating co-segregating transcriptomes and metabolomes in typ.pdf:pdf}, issn = {1756994X}, journal = {Genome Medicine}, keywords = {1H NMR,EQTL,Genome Mapping,MQTL,Metabolic networks,Metabolomics,Transcriptomics}, month = {sep}, number = {1}, pmid = {27716393}, publisher = {BioMed Central Ltd.}, title = {{Topological analysis of metabolic networks integrating co-segregating transcriptomes and metabolomes in type 2 diabetic rat congenic series}}, volume = {8}, year = {2016} } @article{Freyermuth2016, abstract = {Myotonic dystrophy (DM) is caused by the expression of mutant RNAs containing expanded CUG repeats that sequester muscleblind-like (MBNL) proteins, leading to alternative splicing changes. Cardiac alterations, characterized by conduction delays and arrhythmia, are the second most common cause of death in DM. Using RNA sequencing, here we identify novel splicing alterations in DM heart samples, including a switch from adult exon 6B towards fetal exon 6A in the cardiac sodium channel, SCN5A. We find that MBNL1 regulates alternative splicing of SCN5A mRNA and that the splicing variant of SCN5A produced in DM presents a reduced excitability compared with the control adult isoform. Importantly, reproducing splicing alteration of Scn5a in mice is sufficient to promote heart arrhythmia and cardiac-conduction delay, two predominant features of myotonic dystrophy. In conclusion, misregulation of the alternative splicing of SCN5A may contribute to a subset of the cardiac dysfunctions observed in myotonic dystrophy.}, author = {Freyermuth, Fernande and Rau, Fr{\'{e}}d{\'{e}}rique and Kokunai, Yosuke and Linke, Thomas and Sellier, Chantal and Nakamori, Masayuki and Kino, Yoshihiro and Arandel, Ludovic and Jollet, Arnaud and Thibault, Christelle and Philipps, Muriel and Vicaire, Serge and Jost, Bernard and Udd, Bjarne and Day, John W. and Duboc, Denis and Wahbi, Karim and Matsumura, Tsuyoshi and Fujimura, Harutoshi and Mochizuki, Hideki and Deryckere, Fran{\c{c}}ois and Kimura, Takashi and Nukina, Nobuyuki and Ishiura, Shoichi and Lacroix, Vincent and Campan-Fournier, Amandine and Navratil, Vincent and Chautard, Emilie and Auboeuf, Didier and Horie, Minoru and Imoto, Keiji and Lee, Kuang Yung and Swanson, Maurice S. and {De Munain}, Adolfo Lopez and Inada, Shin and Itoh, Hideki and Nakazawa, Kazuo and Ashihara, Takashi and Wang, Eric and Zimmer, Thomas and Furling, Denis and Takahashi, Masanori P. and Charlet-Berguerand, Nicolas}, doi = {10.1038/ncomms11067}, file = {:Users/navratil/Documents/Mendeley Desktop/2016/Freyermuth et al/Nature Communications/Nature Communications{\_}Freyermuth et al.{\_}Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in.pdf:pdf}, issn = {20411723}, journal = {Nature Communications}, month = {apr}, pmid = {27063795}, publisher = {Nature Publishing Group}, title = {{Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy}}, volume = {7}, year = {2016} } @article{Damon2012, abstract = {Eukaryotic organisms play essential roles in the biology and fertility of soils. For example the micro and mesofauna contribute to the fragmentation and homogenization of plant organic matter, while its hydrolysis is primarily performed by the fungi. To get a global picture of the activities carried out by soil eukaryotes we sequenced 2×10,000 cDNAs synthesized from polyadenylated mRNA directly extracted from soils sampled in beech (Fagus sylvatica) and spruce (Picea abies) forests. Taxonomic affiliation of both cDNAs and 18S rRNA sequences showed a dominance of sequences from fungi (up to 60{\%}) and metazoans while protists represented less than 12{\%} of the 18S rRNA sequences. Sixty percent of cDNA sequences from beech forest soil and 52{\%} from spruce forest soil had no homologs in the GenBank/EMBL/DDJB protein database. A Gene Ontology term was attributed to 39{\%} and 31.5{\%} of the spruce and beech soil sequences respectively. Altogether 2076 sequences were putative homologs to different enzyme classes participating to 129 KEGG pathways among which several were implicated in the utilisation of soil nutrients such as nitrogen (ammonium, amino acids, oligopeptides), sugars, phosphates and sulfate. Specific annotation of plant cell wall degrading enzymes identified enzymes active on major polymers (cellulose, hemicelluloses, pectin, lignin) and glycoside hydrolases represented 0.5{\%} (beech soil)-0.8{\%} (spruce soil) of the cDNAs. Other sequences coding enzymes active on organic matter (extracellular proteases, lipases, a phytase, P450 monooxygenases) were identified, thus underlining the biotechnological potential of eukaryotic metatranscriptomes. The phylogenetic affiliation of 12 full-length carbohydrate active enzymes showed that most of them were distantly related to sequences from known fungi. For example, a putative GH45 endocellulase was closely associated to molluscan sequences, while a GH7 cellobiohydrolase was closest to crustacean sequences, thus suggesting a potentially significant contribution of non-fungal eukaryotes in the actual hydrolysis of soil organic matter. {\textcopyright} 2012 Damon et al.}, author = {Damon, Coralie and Lehembre, Fr{\'{e}}d{\'{e}}ric and Oger-Desfeux, Christine and Luis, Patricia and Ranger, Jacques and Fraissinet-Tachet, Laurence and Marmeisse, Roland}, doi = {10.1371/journal.pone.0028967}, file = {:Users/navratil/Documents/Mendeley Desktop/2012/Damon et al/PLoS ONE/PLoS ONE{\_}Damon et al.{\_}Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils{\_}2012.pdf:pdf}, issn = {19326203}, journal = {PLoS ONE}, month = {jan}, number = {1}, pmid = {22238585}, title = {{Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils}}, volume = {7}, year = {2012} } @article{Aouacheria2005, abstract = {Last decade has led to the accumulation of large amounts of data on cancer genetics, opening an unprecedented access to the mapping of cancer genes in the human genome. Single-nucleotide polymorphisms (SNPs), the most common form of DNA variation in humans, emerge as an invaluable tool for cancer association studies. These genotypic markers can be used to assay how alleles of candidate genes correlate with the malignant phenotype, and may provide new clues into the genetic modifications that characterize cancer onset. In this cancer-oriented study, we detail an SNP mining strategy based on the analysis of expressed sequence tags among publicly available databases. Our whole-genome approach provides a comprehensive and unbiased description of nonsynonymous SNPs (nsSNPs) in tumoral versus normal tissues. To gain further insights into the possible relationships between genetic variation and altered phenotype, locations of a subset of nsSNPs were mapped onto protein domains known to be critical for protein function. Computational methods were also used to predict the potential impact of these cancer-associated nsSNPs on protein structure and function. We illustrate our approach through the detailed biochemical and structural characterization of a previously unknown cancer-associated mutation (G79C) affecting the 8 kDa dynein light chain (DNCL1). {\textcopyright} 2005 Nature Publishing Group All rights reserved.}, author = {Aouacheria, Abdel and Navratil, Vincent and Wen, Wenyu and Jiang, Ming and Mouchiroud, Dominique and Gautier, Christian and Gouy, Manolo and Zhang, Mingjie}, doi = {10.1038/sj.onc.1208745}, file = {:Users/navratil/Documents/Mendeley Desktop/2005/Aouacheria et al/Oncogene/Oncogene{\_}Aouacheria et al.{\_}In silico whole-genome scanning of cancer-associated nonsynonymous SNPs and molecular characterization of a d.pdf:pdf}, issn = {09509232}, journal = {Oncogene}, keywords = {Cancer association study,Cancer genomics,DNCL1,Dynein light chain,Expressed sequence tags,Single-nucleotide polymorphism}, month = {sep}, number = {40}, pages = {6133--6142}, pmid = {15897869}, title = {{In silico whole-genome scanning of cancer-associated nonsynonymous SNPs and molecular characterization of a dynein light chain tumour variant}}, volume = {24}, year = {2005} } @article{Pellet2009, abstract = {Abstract. Background. High-throughput screening of protein-protein interactions opens new systems biology perspectives for the comprehensive understanding of cell physiology in normal and pathological conditions. In this context, yeast two-hybrid system appears as a promising approach to efficiently reconstruct protein interaction networks at the proteome-wide scale. This protein interaction screening method generates a large amount of raw sequence data, i.e. the ISTs (Interaction Sequence Tags), which urgently need appropriate tools for their systematic and standardised analysis. Findings. We develop pISTil, a bioinformatics pipeline combined with a user-friendly web-interface: (i) to establish a standardised system to analyse and to annotate ISTs generated by two-hybrid technologies with high performance and flexibility and (ii) to provide high-quality protein-protein interaction datasets for systems-level approach. This pipeline has been validated on a large dataset comprising more than 11.000 ISTs. As a case study, a detailed analysis of ISTs obtained from yeast two-hybrid screens of Hepatitis C Virus proteins against human cDNA libraries is also provided. Conclusion. We have developed pISTil, an open source pipeline made of a collection of several applications governed by a Perl script. The pISTil pipeline is intended to laboratories, with IT-expertise in system administration, scripting and database management, willing to automatically process large amount of ISTs data for accurate reconstruction of protein interaction networks in a systems biology perspective. pISTil is publicly available for download at http://sourceforge.net/projects/pistil. {\textcopyright} 2009 Navratil et al; licensee BioMed Central Ltd.}, author = {Pellet, Johann and Meyniel, Laur{\`{e}}ne and Vidalain, Pierre Olivier and {De Chassey}, Benot and Tafforeau, Lionel and Lotteau, Vincent and Rabourdin-Combe, Chantal and Navratil, Vincent}, doi = {10.1186/1756-0500-2-220}, file = {:Users/navratil/Documents/Mendeley Desktop/2009/Pellet et al/BMC Research Notes/BMC Research Notes{\_}Pellet et al.{\_}PISTil A pipeline for yeast two-hybrid Interaction Sequence Tags identification and analysis{\_}2009.pdf:pdf}, issn = {17560500}, journal = {BMC Research Notes}, title = {{PISTil: A pipeline for yeast two-hybrid Interaction Sequence Tags identification and analysis}}, volume = {2}, year = {2009} } @article{Guirimand2015, abstract = {VirHostNet release 2.0 (http://virhostnet.prabi.fr) is a knowledgebase dedicated to the network-based exploration of virus-host protein-protein interactions. Since the previous VirhostNet release (2009), a second run of manual curation was performed to annotate the new torrent of high-throughput protein-protein interactions data from the literature. This resource is shared publicly, in PSI-MI TAB 2.5 format, using a PSICQUIC web service. The new interface of VirHostNet 2.0 is based on Cytoscape web library and provides a user-friendly access to the most complete and accurate resource of virus-virus and virus-host protein-protein interactions as well as their projection onto their corresponding host cell protein interaction networks. We hope that the VirHostNet 2.0 system will facilitate systems biology and gene-centered analysis of infectious diseases and will help to identify new molecular targets for antiviral drugs design. This resource will also continue to help worldwide scientists to improve our knowledge on molecular mechanisms involved in the antiviral response mediated by the cell and in the viral strategies selected by viruses to hijack the host immune system.}, author = {Guirimand, Thibaut and Delmotte, St{\'{e}}phane and Navratil, Vincent}, doi = {10.1093/nar/gku1121}, file = {:Users/navratil/Documents/Mendeley Desktop/2015/Guirimand, Delmotte, Navratil/Nucleic Acids Research/Nucleic Acids Research{\_}Guirimand, Delmotte, Navratil{\_}VirHostNet 2.0 Surfing on the web of virushost molecular interactions data{\_}2015.pdf:pdf}, issn = {13624962}, journal = {Nucleic Acids Research}, month = {jan}, number = {D1}, pages = {D583--D587}, pmid = {25392406}, publisher = {Oxford University Press}, title = {{VirHostNet 2.0: Surfing on the web of virus/host molecular interactions data}}, volume = {43}, year = {2015} } @article{Hanriot2008, abstract = {Background: "Open" transcriptome analysis methods allow to study gene expression without a priori knowledge of the transcript sequences. As of now, SAGE (Serial Analysis of Gene Expression), LongSAGE and MPSS (Massively Parallel Signature Sequencing) are the mostly used methods for "open" transcriptome analysis. Both LongSAGE and MPSS rely on the isolation of 21 pb tag sequences from each transcript. In contrast to LongSAGE, the high throughput sequencing method used in MPSS enables the rapid sequencing of very large libraries containing several millions of tags, allowing deep transcriptome analysis. However, a bias in the complexity of the transcriptome representation obtained by MPSS was recently uncovered. Results: In order to make a deep analysis of mouse hypothalamus transcriptome avoiding the limitation introduced by MPSS, we combined LongSAGE with the Solexa sequencing technology and obtained a library of more than 11 millions of tags. We then compared it to a LongSAGE library of mouse hypothalamus sequenced with the Sanger method. Conclusion: We found that Solexa sequencing technology combined with LongSAGE is perfectly suited for deep transcriptome analysis. In contrast to MPSS, it gives a complex representation of transcriptome as reliable as a LongSAGE library sequenced by the Sanger method. {\textcopyright} 2008 Hanriot et al; licensee BioMed Central Ltd.}, author = {Hanriot, Lucie and Keime, C{\'{e}}line and Gay, Nadine and Faure, Claudine and Dossat, Carole and Wincker, Patrick and Scot{\'{e}}-Blachon, C{\'{e}}line and Peyron, Christelle and Gandrillon, Olivier}, doi = {10.1186/1471-2164-9-418}, file = {:Users/navratil/Documents/Mendeley Desktop/2008/Hanriot et al/BMC Genomics/BMC Genomics{\_}Hanriot et al.{\_}A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of t.pdf:pdf}, issn = {14712164}, journal = {BMC Genomics}, keywords = {Animals,C{\'{e}}line Keime,DNA / methods*,Evaluation Study,Gene Expression Profiling / methods*,Gene Library,Hypothalamus / metabolism,Inbred Strains,Lucie Hanriot,MEDLINE,Male,Mice,NCBI,NIH,NLM,National Center for Biotechnology Information,National Institutes of Health,National Library of Medicine,Olivier Gandrillon,PMC2562395,PubMed Abstract,Sequence Analysis,doi:10.1186/1471-2164-9-418,pmid:18796152}, month = {sep}, pmid = {18796152}, publisher = {BioMed Central Ltd.}, title = {{A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome}}, url = {https://pubmed.ncbi.nlm.nih.gov/18796152/}, volume = {9}, year = {2008} } @article{Deniaud2009, abstract = {Background: The ubiquitous transcription factor Sp1 regulates the expression of a vast number of genes involved in many cellular functions ranging from differentiation to proliferation and apoptosis. Sp1 expression levels show a dramatic increase during transformation and this could play a critical role for tumour development or maintenance. Although Sp1 deregulation might be beneficial for tumour cells, its overexpression induces apoptosis of untransformed cells. Here we further characterised the functional and transcriptional responses of untransformed cells following Sp1 overexpression. Methodology and Principal Findings: We made use of wild-type and DNA-binding-deficient Sp1 to demonstrate that the induction of apoptosis by Sp1 is dependent on its capacity to bind DNA. Genome-wide expression profiling identified genes involved in cancer, cell death and cell cycle as being enriched among differentially expressed genes following Sp1 overexpression. In silico search to determine the presence of Sp1 binding sites in the promoter region of modulated genes was conducted. Genes that contained Sp1 binding sites in their promoters were enriched among down-regulated genes. The endogenous sp1 gene is one of the most down-regulated suggesting a negative feedback loop induced by overexpressed Sp1. In contrast, genes containing Sp1 binding sites in their promoters were not enriched among up-regulated genes. These results suggest that the transcriptional response involves both direct Sp1-driven transcription and indirect mechanisms. Finally, we show that Sp1 overexpression led to a modified expression of G1/S transition regulatory genes such as the down-regulation of cyclin D2 and the up-regulation of cyclin G2 and cdkn2c/p18 expression. The biological significance of these modifications was confirmed by showing that the cells accumulated in the G1 phase of the cell cycle before the onset of apoptosis. Conclusion: This study shows that the binding to DNA of overexpressed Sp1 induces an inhibition of cell cycle progression that precedes apoptosis and a transcriptional response targeting genes containing Sp1 binding sites in their promoter or not suggesting both direct Sp1-driven transcription and indirect mechanisms. {\textcopyright} 2009 Deniaud et al.}, author = {Deniaud, Emmanuelle and Baguet, Jo{\"{e}}l and Chalard, Roxane and Blanquier, Bariza and Brinza, Lilia and Meunier, Julien and Michallet, Marie C{\'{e}}cile and Laugraud, Aur{\'{e}}lie and Ah-Soon, Claudette and Wierinckx, Anne and Castellazzi, Marc and Lachuer, Jo{\"{e}}l and Gautier, Christian and Marvel, Jacqueline and Leverrier, Yann}, doi = {10.1371/journal.pone.0007035}, file = {:Users/navratil/Documents/Mendeley Desktop/2009/Deniaud et al/PLoS ONE/PLoS ONE{\_}Deniaud et al.{\_}Overexpression of transcription factor Sp1 leads to gene expression perturbations and cell cycle inhibition{\_}2009.pdf:pdf}, issn = {19326203}, journal = {PLoS ONE}, month = {sep}, number = {9}, pmid = {19753117}, title = {{Overexpression of transcription factor Sp1 leads to gene expression perturbations and cell cycle inhibition}}, volume = {4}, year = {2009} } @article{Despres2014a, abstract = {Worldwide evolution of mosquito resistance to chemical insecticides represents a major challenge for public health, and the future of vector control largely relies on the development of biological insecticides that can be used in combination with chemicals (integrated management), with the expectation that populations already resistant to chemicals will not become readily resistant to biological insecticides. However, little is known about the metabolic pathways affected by selection with chemical or biological insecticides. Here we show that Aedes aegypti, a laboratory mosquito strain selected with a biological insecticide (Bacillus thuringiensis israelensis, Bti) evolved increased transcription of many genes coding for endopeptidases while most genes coding for detoxification enzymes were under-expressed. By contrast, in strains selected with chemicals, genes encoding detoxification enzymes were mostly over-expressed. In all the resistant strains, genes involved in immune response were under-transcribed, suggesting that basal immunity might be a general adjustment variable to compensate metabolic costs caused by insecticide selection. Bioassays generally showed no evidence for an increased susceptibility of selected strains towards the other insecticide type, and all chemical-resistant strains were as susceptible to Bti as the unselected parent strain, which is a good premise for sustainable integrated management of mosquito populations resistant to chemicals.}, author = {Despr{\'{e}}s, Laurence and Stalinski, Renaud and Faucon, Fr{\'{e}}d{\'{e}}ric and Navratil, Vincent and Viari, Alain and Paris, Margot and Tetreau, Guillaume and Poupardin, Rodolphe and Riaz, Muhammad Asam and Bonin, Aur{\'{e}}lie and Reynaud, St{\'{e}}phane and David, Jean Philippe}, doi = {10.1098/rsbl.2014.0716}, file = {:Users/navratil/Documents/Mendeley Desktop/2014/Despr{\'{e}}s et al/Biology Letters/Biology Letters{\_}Despr{\'{e}}s et al.{\_}Chemical and biological insecticides select distinct gene expression patterns in Aedes aegypti mosquito{\_}.pdf:pdf}, issn = {1744957X}, journal = {Biology Letters}, keywords = {Cross resistance,Detoxification,Immunity,Transcriptomics}, month = {dec}, number = {12}, pmid = {25540155}, publisher = {Royal Society of London}, title = {{Chemical and biological insecticides select distinct gene expression patterns in Aedes aegypti mosquito}}, volume = {10}, year = {2014} } @article{Salvetti2016, abstract = {Nucleolin (NCL) is a major component of the cell nucleolus, which has the ability to rapidly shuttle to several other cells' compartments. NCL plays important roles in a variety of essential functions, among which are ribosome biogenesis, gene expression, and cell growth. However, the precise mechanisms underlying NCL functions are still unclear. Our study aimed to provide new information on NCL functions via the identification of its nuclear interacting partners. Using an interactomics approach, we identified 140 proteins co-purified with NCL, among which 100 of them were specifically found to be associated with NCL after RNase digestion. The functional classification of these proteins confirmed the prominent role of NCL in ribosome biogenesis and additionally revealed the possible involvement of nuclear NCL in several pre-mRNA processing pathways through its interaction with RNA helicases and proteins participating in pre-mRNA splicing, transport, or stability. NCL knockdown experiments revealed that NCL regulates the localization of EXOSC10 and the amount of ZC3HAV1, two components of the RNA exosome, further suggesting its involvement in the control of mRNA stability. Altogether, this study describes the first nuclear interactome of human NCL and provides the basis for further understanding the mechanisms underlying the essential functions of this nucleolar protein.}, author = {Salvetti, Anna and Cout{\'{e}}, Yohann and Epstein, Alberto and Arata, Loredana and Kraut, Alexandra and Navratil, Vincent and Bouvet, Philippe and Greco, Anna}, doi = {10.1021/acs.jproteome.6b00126}, issn = {15353907}, journal = {Journal of Proteome Research}, keywords = {mRNA processing,nucleolin,proteomics,tandem affinity purification}, month = {may}, number = {5}, pages = {1659--1669}, pmid = {27049334}, publisher = {American Chemical Society}, title = {{Nuclear functions of nucleolin through global proteomics and interactomic approaches}}, volume = {15}, year = {2016} } @article{Degletagne2010, abstract = {Background: Recent developments in high-throughput methods of analyzing transcriptomic profiles are promising for many areas of biology, including ecophysiology. However, although commercial microarrays are available for most common laboratory models, transcriptome analysis in non-traditional model species still remains a challenge. Indeed, the signal resulting from heterologous hybridization is low and difficult to interpret because of the weak complementarity between probe and target sequences, especially when no microarray dedicated to a genetically close species is available.Results: We show here that transcriptome analysis in a species genetically distant from laboratory models is made possible by using MAXRS, a new method of analyzing heterologous hybridization on microarrays. This method takes advantage of the design of several commercial microarrays, with different probes targeting the same transcript. To illustrate and test this method, we analyzed the transcriptome of king penguin pectoralis muscle hybridized to Affymetrix chicken microarrays, two organisms separated by an evolutionary distance of approximately 100 million years. The differential gene expression observed between different physiological situations computed by MAXRS was confirmed by real-time PCR on 10 genes out of 11 tested.Conclusions: MAXRS appears to be an appropriate method for gene expression analysis under heterologous hybridization conditions. {\textcopyright} 2010 Degletagne et al; licensee BioMed Central Ltd.}, author = {Degletagne, Cyril and Keime, C{\'{e}}line and Rey, Benjamin and de Dinechin, Marc and Forcheron, Fabien and Chuchana, Paul and Jouventin, Pierre and Gautier, Christian and Duchamp, Claude}, doi = {10.1186/1471-2164-11-344}, file = {:Users/navratil/Documents/Mendeley Desktop/2010/Degletagne et al/BMC Genomics/BMC Genomics{\_}Degletagne et al.{\_}Transcriptome analysis in non-model species A new method for the analysis of heterologous hybridization o.pdf:pdf}, issn = {14712164}, journal = {BMC Genomics}, keywords = {Animals,Claude Duchamp,Cyril Degletagne,C{\'{e}}line Keime,Developmental,Fluorescence,Gene Expression Profiling / methods*,Gene Expression Regulation,MEDLINE,NCBI,NIH,NLM,National Center for Biotechnology Information,National Institutes of Health,National Library of Medicine,Non-U.S. Gov't,Nucleic Acid Hybridization / methods*,Oceans and Seas,Oligonucleotide Array Sequence Analysis / methods*,PMC2901317,Pectoralis Muscles / growth {\&} development,Pectoralis Muscles / metabolism,Polymerase Chain Reaction,PubMed Abstract,Reproducibility of Results,Research Support,Spectrometry,Spheniscidae / genetics,Spheniscidae / growth {\&} development,doi:10.1186/1471-2164-11-344,pmid:20509979}, month = {may}, number = {1}, pmid = {20509979}, publisher = {BMC Genomics}, title = {{Transcriptome analysis in non-model species: A new method for the analysis of heterologous hybridization on microarrays}}, url = {https://pubmed.ncbi.nlm.nih.gov/20509979/}, volume = {11}, year = {2010} } @article{Jiang2016, abstract = {Dickeya species are soft rot disease-causing bacterial plant pathogens and an emerging agricultural threat in Europe. Environmental modulation of gene expression is critical for Dickeya dadantii pathogenesis. While the bacterium uses various environmental cues to distinguish between its habitats, an intricate transcriptional control system coordinating the expression of virulence genes ensures efficient infection. Understanding of this behaviour requires a detailed knowledge of expression patterns under a wide range of environmental conditions, which is currently lacking. To obtain a comprehensive picture of this adaptive response, we devised a strategy to examine the D. dadantii transcriptome in a series of 32 infection-relevant conditions encountered in the hosts. We propose a temporal map of the bacterial response to various stress conditions and show that D. dadantii elicits complex genetic behaviour combining common stress-response genes with distinct sets of genes specifically induced under each particular stress. Comparison of our dataset with an in planta expression profile reveals the combined impact of stress factors and enables us to predict the major stress confronting D. dadantii at a particular stage of infection. We provide a comprehensive catalog of D. dadantii genomic responses to environmentally relevant stimuli, thus facilitating future studies of this important plant pathogen.}, author = {Jiang, Xuejiao and Zghidi-Abouzid, Ouafa and Oger-Desfeux, Christine and Hommais, Florence and Greliche, Nicolas and Muskhelishvili, Georgi and Nasser, William and Reverchon, Sylvie}, doi = {10.1111/1462-2920.13267}, issn = {14622920}, journal = {Environmental Microbiology}, month = {nov}, number = {11}, pages = {3651--3672}, pmid = {26940633}, publisher = {Blackwell Publishing Ltd}, title = {{Global transcriptional response of Dickeya dadantii to environmental stimuli relevant to the plant infection}}, volume = {18}, year = {2016} } @article{Faucon2017, abstract = {Background: The capacity of Aedes mosquitoes to resist chemical insecticides threatens the control of major arbovirus diseases worldwide. Until alternative control tools are widely deployed, monitoring insecticide resistance levels and identifying resistance mechanisms in field mosquito populations is crucial for implementing appropriate management strategies. Metabolic resistance to pyrethroids is common in Aedes aegypti but the monitoring of the dynamics of resistant alleles is impeded by the lack of robust genomic markers. Methodology/Principal findings: In an attempt to identify the genomic bases of metabolic resistance to deltamethrin, multiple resistant and susceptible populations originating from various continents were compared using both RNA-seq and a targeted DNA-seq approach focused on the upstream regions of detoxification genes. Multiple detoxification enzymes were over transcribed in resistant populations, frequently associated with an increase in their gene copy number. Targeted sequencing identified potential promoter variations associated with their over transcription. Non-synonymous variations affecting detoxification enzymes were also identified in resistant populations. Conclusion /Significance: This study not only confirmed the role of gene copy number variations as a frequent cause of the over expression of detoxification enzymes associated with insecticide resistance in Aedes aegypti but also identified novel genomic resistance markers potentially associated with their cis-regulation and modifications of their protein structure conformation. As for gene transcription data, polymorphism patterns were frequently conserved within regions but differed among continents confirming the selection of different resistance factors worldwide. Overall, this study paves the way of the identification of a comprehensive set of genomic markers for monitoring the spatio-temporal dynamics of the variety of insecticide resistance mechanisms in Aedes aegypti.}, author = {Faucon, Frederic and Gaude, Thierry and Dusfour, Isabelle and Navratil, Vincent and Corbel, Vincent and Juntarajumnong, Waraporn and Girod, Romain and Poupardin, Rodolphe and Boyer, Frederic and Reynaud, Stephane and David, Jean Philippe}, doi = {10.1371/journal.pntd.0005526}, file = {:Users/navratil/Documents/Mendeley Desktop/2017/Faucon et al/PLoS Neglected Tropical Diseases/PLoS Neglected Tropical Diseases{\_}Faucon et al.{\_}In the hunt for genomic markers of metabolic resistance to pyrethroids in the mosquito Ae.pdf:pdf}, issn = {19352735}, journal = {PLoS Neglected Tropical Diseases}, month = {apr}, number = {4}, pmid = {28379969}, publisher = {Public Library of Science}, title = {{In the hunt for genomic markers of metabolic resistance to pyrethroids in the mosquito Aedes aegypti: An integrated next-generation sequencing approach}}, volume = {11}, year = {2017} } @article{Jordheim2011, abstract = {Purpose: The need for new treatment options for acute myeloid leukemia (AML) is increasing. AS602868 is a novel investigational drug with reported activity on AML cells. Methods: We studied gene expression profiles in AML blasts exposed to AS602868 in order to better understand its mechanism of action. We analyzed the in vitro cytotoxicity of AS602868 alone or in combination with daunorubicin, etoposide or cytarabine. To document AS602868-induced IKK2 inhibition in fresh AML cells, a flow cytometry analysis of I$\kappa$B was performed. Finally, the effect of AS602868 on gene expression in fresh AML cells was analyzed. Results: The results show that AML cells are globally as sensitive to AS602868 as they are to cytarabine, with large interindividual variations. Combinations with conventional antileukemic agents showed enhanced cytotoxic activity in subsets of patients. IKK2 appeared to be effectively inhibited by 100 $\mu$M AS602868 in fresh leukemic cells. Gene expression profiling and gene ontology analyses identified several groups of genes induced/inhibited by exposure to AS602868 and/or exhibiting a correlation with sensitivity to this agent in vitro. Of note, the expression of several genes related to immune function was found to be significantly altered after exposure to AS602868. Conclusion: These data suggest that AS602868 is cytotoxic against fresh human AML blasts and provide insights regarding the mechanisms of cytotoxicity. {\textcopyright} 2010 Springer-Verlag.}, author = {Jordheim, Lars Petter and Plesa, Adriana and Dreano, Michel and Cros-Perrial, Emeline and Keime, C{\'{e}}line and Herveau, St{\'{e}}phanie and Demangel, Delphine and Vendrell, Julie A. and Dumontet, Charles}, doi = {10.1007/s00280-010-1458-y}, issn = {03445704}, journal = {Cancer Chemotherapy and Pharmacology}, keywords = {AS602868,Acute myeloid leukemia,Gene expression,Microarray,Sensitivity}, month = {jul}, number = {1}, pages = {97--105}, pmid = {20844879}, title = {{Sensitivity and gene expression profile of fresh human acute myeloid leukemia cells exposed ex vivo to AS602868}}, volume = {68}, year = {2011} } @incollection{Aouacheria2019, abstract = {BCL-2 proteins correspond to a structurally, functionally, and phylogenetically heterogeneous group of regulators that play crucial roles in the life and death of animal cells. Some of these regulators also represent therapeutic targets in human diseases including cancer. In the omics era, there is great need for easy data retrieval and fast analysis of the molecular players involved in cell death. In this chapter, we present generic and specific computational resources (such as the reference database BCL2DB) as well as bioinformatics tools that can be used to investigate BCL-2 homologs and BH3-only proteins.}, author = {Aouacheria, Abdel and Navratil, Vincent and Combet, Christophe}, booktitle = {Methods in Molecular Biology}, doi = {10.1007/978-1-4939-8861-7_2}, issn = {10643745}, keywords = {Apoptosis,BCL-2,BH3,Bioinformatics,Cell death,Databases,Omics,Protein domains,Protein motifs,Structure–function relationships}, pages = {23--43}, pmid = {30535996}, publisher = {Humana Press Inc.}, title = {{Database and Bioinformatic Analysis of BCL-2 Family Proteins and BH3-Only Proteins}}, volume = {1877}, year = {2019} } @article{Hommais2011, abstract = {Background: Quantitative RT-PCR is the method of choice for studying, with both sensitivity and accuracy, the expression of genes. A reliable normalization of the data, using several reference genes, is critical for an accurate quantification of gene expression. Here, we propose a set of reference genes, of the phytopathogenic bacteria Dickeya dadantii and Pectobacterium atrosepticum, which are stable in a wide range of growth conditions. Results: We extracted, from a D. dadantii micro-array transcript profile dataset comprising thirty-two different growth conditions, an initial set of 49 expressed genes with very low variation in gene expression. Out of these, we retained 10 genes representing different functional categories, different levels of expression (low, medium, and high) and with no systematic variation in expression correlating with growth conditions. We measured the expression of these reference gene candidates using quantitative RT-PCR in 50 different experimental conditions, mimicking the environment encountered by the bacteria in their host and directly during the infection process in planta. The two most stable genes (ABF-0017965 (lpxC) and ABF-0020529 (yafS) were successfully used for normalization of RT-qPCR data. Finally, we demonstrated that the ortholog of lpxC and yafS in Pectobacterium atrosepticum also showed stable expression in diverse growth conditions. Conclusions: We have identified at least two genes, lpxC (ABF-0017965) and yafS (ABF-0020509), whose expressions are stable in a wide range of growth conditions and during infection. Thus, these genes are considered suitable for use as reference genes for the normalization of real-time RT-qPCR data of the two main pectinolytic phytopathogenic bacteria D. dadantii and P. atrosepticum and, probably, of other Enterobacteriaceae. Moreover, we defined general criteria to select good reference genes in bacteria. {\textcopyright} 2011 Hommais et al.}, author = {Hommais, Florence and Zghidi-Abouzid, Ouafa and Oger-Desfeux, Christine and Pineau-Chapelle, Emilie and van Gijsegem, Frederique and Nasser, William and Reverchon, Sylvie}, doi = {10.1371/journal.pone.0020269}, file = {:Users/navratil/Documents/Mendeley Desktop/2011/Hommais et al/PLoS ONE/PLoS ONE{\_}Hommais et al.{\_}LpxC and yafS are the most suitable internal controls to normalize real time RT-qPCR expression in the phytopath.pdf:pdf}, issn = {19326203}, journal = {PLoS ONE}, number = {5}, pmid = {21637857}, publisher = {Public Library of Science}, title = {{LpxC and yafS are the most suitable internal controls to normalize real time RT-qPCR expression in the phytopathogenic bacteria dickeya dadantii}}, volume = {6}, year = {2011} } @article{Durand2020, abstract = {Osteoarthritis (OA) is a degenerative disease of the joints which is associated with an impaired production of the cartilage matrix by the chondrocytes. Here, we investigated the role of Lysine-Specific Demethylase-1 (LSD1), a chromatin remodeling enzyme whose role in articular chondrocytes was previously associated with a catabolic activity and which is potentially involved during OA. Following a loss of function strategy and RNA sequencing analysis, we detail the genes which are targeted by LSD1 in human articular chondrocytes and identify COL9A1, a gene encoding the $\alpha$1 chain of the cartilage-specific type IX collagen, as negatively regulated by LSD1. We show that LSD1 interacts with the transcription factor SOX9 and is recruited to the promoter of COL9A1. Interestingly, we observe that OA cartilage displays stronger LSD1 immunostaining compared with normal, and we demonstrate that the depletion of LSD1 in OA chondrocytes prevents the decrease in COL9A1 following Il-1$\beta$ treatment. These results suggest LSD1 is a new regulator of the anabolic activity of articular chondrocytes potentially destabilizing the cartilage matrix, since it negatively regulates COL9A1, a gene encoding a crucial anchoring collagen molecule. This newly identified role played by LSD1 may thus participate in the alteration of the cartilage matrix during OA.}, author = {Durand, Anne Laure and Dufour, Alexandre and Aubert-Foucher, Elisabeth and Oger-Desfeux, Christine and Pasdeloup, Marielle and Lustig, Sebastien and Servien, Elvire and Vaz, Gualter and Perrier-Groult, Emeline and Mallein-Gerin, Frederic and Lafont, Jerome E.}, doi = {10.3390/ijms21176322}, file = {:Users/navratil/Documents/Mendeley Desktop/2020/Durand et al/International Journal of Molecular Sciences/International Journal of Molecular Sciences{\_}Durand et al.{\_}The lysine specific demethylase-1 negatively regulates the COL9A1 gene in huma.pdf:pdf}, issn = {14220067}, journal = {International Journal of Molecular Sciences}, keywords = {Articular chondrocytes,Lysine demethylase,Osteoarthritis,Type IX collagen}, month = {sep}, number = {17}, pages = {1--16}, pmid = {32878268}, publisher = {MDPI AG}, title = {{The lysine specific demethylase-1 negatively regulates the COL9A1 gene in human articular chondrocytes}}, volume = {21}, year = {2020} }
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