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Author

Christophe Klopp

Bio: Christophe Klopp is an academic researcher from Institut national de la recherche agronomique. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 44, co-authored 207 publications receiving 11088 citations. Previous affiliations of Christophe Klopp include University of Toulouse & Centre national de la recherche scientifique.
Topics: Genome, Gene, Population, Transcriptome, Genomics


Papers
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Journal ArticleDOI
Shusei Sato, Satoshi Tabata, Hideki Hirakawa, Erika Asamizu  +320 moreInstitutions (51)
31 May 2012-Nature
TL;DR: A high-quality genome sequence of domesticated tomato is presented, a draft sequence of its closest wild relative, Solanum pimpinellifolium, is compared, and the two tomato genomes are compared to each other and to the potato genome.
Abstract: Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

2,687 citations

Journal ArticleDOI
TL;DR: jvenn is a new JavaScript library that processes lists and produces Venn diagrams and handles up to six input lists and presents results using classical or Edwards-Venn layouts.
Abstract: Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus allow the comparison between different experimental conditions or between different methods. However, when the number of input lists exceeds four, the diagram becomes difficult to read. Alternative layouts and dynamic display features can improve its use and its readability. jvenn is a new JavaScript library. It processes lists and produces Venn diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized. Finally, jvenn can easily be embeded in a web page, allowing to have dynamic Venn diagrams. jvenn is an open source component for web environments helping scientists to analyze their data. The library package, which comes with full documentation and an example, is freely available at http://bioinfo.genotoul.fr/jvenn .

1,265 citations

Journal ArticleDOI
TL;DR: It is shown that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization.
Abstract: Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate genome. Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here challenges the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions.

742 citations

Journal ArticleDOI
TL;DR: The 1000 bull genomes project supports the goal of accelerating the rates of genetic gain in domestic cattle while at the same time considering animal health and welfare by providing the annotated sequence variants and genotypes of key ancestor bulls.
Abstract: The 1000 bull genomes project supports the goal of accelerating the rates of genetic gain in domestic cattle while at the same time considering animal health and welfare by providing the annotated sequence variants and genotypes of key ancestor bulls. In the first phase of the 1000 bull genomes project, we sequenced the whole genomes of 234 cattle to an average of 8.3-fold coverage. This sequencing includes data for 129 individuals from the global Holstein-Friesian population, 43 individuals from the Fleckvieh breed and 15 individuals from the Jersey breed. We identified a total of 28.3 million variants, with an average of 1.44 heterozygous sites per kilobase for each individual. We demonstrate the use of this database in identifying a recessive mutation underlying embryonic death and a dominant mutation underlying lethal chrondrodysplasia. We also performed genome-wide association studies for milk production and curly coat, using imputed sequence variants, and identified variants associated with these traits in cattle.

690 citations

Journal ArticleDOI
Damian Smedley1, Syed Haider2, Steffen Durinck3, Luca Pandini4, Paolo Provero4, Paolo Provero5, James E. Allen6, Olivier Arnaiz7, Mohammad Awedh8, Richard Baldock9, Giulia Barbiera4, Philippe Bardou10, Tim Beck11, Andrew Blake, Merideth Bonierbale12, Anthony J. Brookes11, Gabriele Bucci4, Iwan Buetti4, Sarah W. Burge6, Cédric Cabau10, Joseph W. Carlson13, Claude Chelala14, Charalambos Chrysostomou11, Davide Cittaro4, Olivier Collin15, Raul Cordova12, Rosalind J. Cutts14, Erik Dassi16, Alex Di Genova17, Anis Djari10, Anthony Esposito18, Heather Estrella18, Eduardo Eyras19, Eduardo Eyras20, Julio Fernandez-Banet18, Simon A. Forbes1, Robert C. Free11, Takatomo Fujisawa, Emanuela Gadaleta14, Jose Manuel Garcia-Manteiga4, David Goodstein13, Kristian Gray6, José Afonso Guerra-Assunção14, Bernard Haggarty9, Dong Jin Han21, Byung Woo Han21, Todd W. Harris22, Jayson Harshbarger, Robert K. Hastings11, Richard D. Hayes13, Claire Hoede10, Shen Hu23, Zhi-Liang Hu24, Lucie N. Hutchins, Zhengyan Kan18, Hideya Kawaji, Aminah Keliet10, Arnaud Kerhornou6, Sunghoon Kim21, Rhoda Kinsella6, Christophe Klopp10, Lei Kong25, Daniel Lawson6, Dejan Lazarevic4, Ji Hyun Lee21, Thomas Letellier10, Chuan-Yun Li25, Pietro Liò26, Chu Jun Liu25, Jie Luo6, Alejandro Maass17, Jérôme Mariette10, Thomas Maurel6, Stefania Merella4, Azza M. Mohamed8, François Moreews10, Ibounyamine Nabihoudine10, Nelson Ndegwa27, Céline Noirot10, Cristian Perez-Llamas19, Michael Primig28, Alessandro Quattrone16, Hadi Quesneville10, Davide Rambaldi4, James M. Reecy24, Michela Riba4, Steven Rosanoff6, Amna A. Saddiq8, Elisa Salas12, Olivier Sallou15, Rebecca Shepherd1, Reinhard Simon12, Linda Sperling7, William Spooner29, Daniel M. Staines6, Delphine Steinbach10, Kevin R. Stone, Elia Stupka4, Jon W. Teague1, Abu Z. Dayem Ullah14, Jun Wang25, Doreen Ware29, Marie Wong-Erasmus, Ken Youens-Clark29, Amonida Zadissa6, Shi Jian Zhang25, Arek Kasprzyk8, Arek Kasprzyk4 
TL;DR: The latest version of the BioMart Community Portal comes with many new databases that have been created by the ever-growing community and comes with better support and extensibility for data analysis and visualization tools.
Abstract: The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.

664 citations


Cited by
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28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

Journal ArticleDOI
TL;DR: The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.
Abstract: The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.

4,658 citations

01 Feb 2015
TL;DR: In this article, the authors describe the integrative analysis of 111 reference human epigenomes generated as part of the NIH Roadmap Epigenomics Consortium, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression.
Abstract: The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

4,409 citations

Journal ArticleDOI
08 Jun 2012-Science
TL;DR: A deeper understanding of the axes that physiologically connect the gut, liver, muscle, and brain are a prerequisite for optimizing therapeutic strategies to manipulate the gut microbiota to combat disease and improve health.
Abstract: The composition and activity of the gut microbiota codevelop with the host from birth and is subject to a complex interplay that depends on the host genome, nutrition, and life-style. The gut microbiota is involved in the regulation of multiple host metabolic pathways, giving rise to interactive host-microbiota metabolic, signaling, and immune-inflammatory axes that physiologically connect the gut, liver, muscle, and brain. A deeper understanding of these axes is a prerequisite for optimizing therapeutic strategies to manipulate the gut microbiota to combat disease and improve health.

3,509 citations