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  1. Article ; Online: La chimiothérapie intra-péritonéale dans le traitement de la carcinose péritonéale d’origine colorectale. CHIP, PIPAC, état des lieux et perspectives.

    Quénet, François / Carrère, Sébastien / Sgarbura, Olivia

    Bulletin du cancer

    2024  Volume 111, Issue 3, Page(s) 285–290

    Abstract: After more than a decade of good results using the combination of cytoreductive surgery (CRS) plus hyperthermic intraperitoneal chemotherapy (HIPEC) in the treatment of peritoneal carcinosis of colorectal origin, the PRODIGE7 study, which specifically ... ...

    Title translation Contribution of intraperitoneal chemotherapy in the treatment of colorectal peritoneal carcinoma. HIPEC, PIPAC, state of the art and future directions.
    Abstract After more than a decade of good results using the combination of cytoreductive surgery (CRS) plus hyperthermic intraperitoneal chemotherapy (HIPEC) in the treatment of peritoneal carcinosis of colorectal origin, the PRODIGE7 study, which specifically evaluated the role of HIPEC, failed to show any superiority in terms of overall and disease-free survival for the CRS+HIPEC combination compared with CRS alone. This study constituted a radical change in the knowledge and therapeutic attitudes observed to date. After reviewing the literature and the consensus of national and international experts, a synthesis is provided, together with an outlook on the questions raised and the therapeutic trials and innovations of the near future. An analysis of recent advances due to the advent of a new technique, PIPAC, is also proposed, as well as a review of current therapeutic trials in this field.
    MeSH term(s) Humans ; Hyperthermic Intraperitoneal Chemotherapy ; Hyperthermia, Induced/methods ; Chemotherapy, Cancer, Regional Perfusion/methods ; Colorectal Neoplasms/drug therapy ; Carcinoma/therapy ; Peritoneal Neoplasms/drug therapy ; Combined Modality Therapy ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Survival Rate
    Language French
    Publishing date 2024-02-07
    Publishing country France
    Document type English Abstract ; Journal Article ; Review
    ZDB-ID 213270-9
    ISSN 1769-6917 ; 0007-4551
    ISSN (online) 1769-6917
    ISSN 0007-4551
    DOI 10.1016/j.bulcan.2023.10.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Peritoneal metastases of unknown primary with hepatoid features.

    Khellaf, Lakhdar / Nougaret, Stéphanie / Carrère, Sébastien / Bibeau, Frédéric

    Pleura and peritoneum

    2022  Volume 7, Issue 3, Page(s) 157–158

    Language English
    Publishing date 2022-08-19
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2861909-2
    ISSN 2364-768X ; 2364-7671
    ISSN (online) 2364-768X
    ISSN 2364-7671
    DOI 10.1515/pp-2022-0113
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: MtExpress, a Comprehensive and Curated RNAseq-based Gene Expression Atlas for the Model Legume Medicago truncatula.

    Carrere, Sebastien / Verdier, Jerome / Gamas, Pascal

    Plant & cell physiology

    2021  Volume 62, Issue 9, Page(s) 1494–1500

    Abstract: Although RNA sequencing (RNAseq) has been becoming the main transcriptomic approach in the model legume Medicago truncatula, there is currently no genome-wide gene expression atlas covering the whole set of RNAseq data published for this species. ... ...

    Abstract Although RNA sequencing (RNAseq) has been becoming the main transcriptomic approach in the model legume Medicago truncatula, there is currently no genome-wide gene expression atlas covering the whole set of RNAseq data published for this species. Nowadays, such a tool is highly valuable to provide a global view of gene expression in a wide range of conditions and tissues/organs. Here, we present MtExpress, a gene expression atlas that compiles an exhaustive set of published M. truncatula RNAseq data (https://medicago.toulouse.inrae.fr/MtExpress). MtExpress makes use of recent releases of M. truncatula genome sequence and annotation, as well as up-to-date tools to perform mapping, quality control, statistical analysis and normalization of RNAseq data. MtExpress combines semi-automated pipelines with manual re-labeling and organization of samples to produce an attractive and user-friendly interface, fully integrated with other available Medicago genomic resources. Importantly, MtExpress is highly flexible, in terms of both queries, e.g. allowing searches with gene names and orthologous gene IDs from Arabidopsis and other legume species, and outputs, to customize visualization and redirect gene study to relevant Medicago webservers. Thanks to its semi-automated pipeline, MtExpress will be frequently updated to follow the rapid pace of M. truncatula RNAseq data publications, as well as the constant improvement of genome annotation. MtExpress also hosts legacy GeneChip expression data originally stored in the Medicago Gene Expression Atlas, as a very valuable and complementary resource.
    MeSH term(s) Databases, Genetic ; Genes, Plant ; Medicago truncatula/genetics ; RNA, Plant/genetics ; Sequence Analysis, RNA ; Transcriptome
    Chemical Substances RNA, Plant
    Language English
    Publishing date 2021-07-07
    Publishing country Japan
    Document type Journal Article
    ZDB-ID 208907-5
    ISSN 1471-9053 ; 0032-0781
    ISSN (online) 1471-9053
    ISSN 0032-0781
    DOI 10.1093/pcp/pcab110
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Symbiotic Nodule Development and Efficiency in the Medicago truncatula Mtefd-1 Mutant Is Highly Dependent on Sinorhizobium Strains.

    Jardinaud, Marie-Françoise / Carrere, Sebastien / Gourion, Benjamin / Gamas, Pascal

    Plant & cell physiology

    2022  Volume 64, Issue 1, Page(s) 27–42

    Abstract: Symbiotic nitrogen fixation (SNF) can play a key role in agroecosystems to reduce the negative impact of nitrogen fertilizers. Its efficiency is strongly affected by the combination of bacterial and plant genotypes, but the mechanisms responsible for the ...

    Abstract Symbiotic nitrogen fixation (SNF) can play a key role in agroecosystems to reduce the negative impact of nitrogen fertilizers. Its efficiency is strongly affected by the combination of bacterial and plant genotypes, but the mechanisms responsible for the differences in the efficiency of rhizobium strains are not well documented. In Medicago truncatula, SNF has been mostly studied using model systems, such as M. truncatula A17 in interaction with Sinorhizobium meliloti Sm2011. Here we analyzed both the wild-type (wt) A17 and the Mtefd-1 mutant in interaction with five S. meliloti and two Sinorhizobium medicae strains. ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes a transcription factor, which contributes to the control of nodule number and differentiation in M. truncatula. We found that, in contrast to Sm2011, four strains induce functional (Fix+) nodules in Mtefd-1, although less efficient for SNF than in wt A17. In contrast, the Mtefd-1 hypernodulation phenotype is not strain-dependent. We compared the plant nodule transcriptomes in response to SmBL225C, a highly efficient strain with A17, versus Sm2011, in wt and Mtefd-1 backgrounds. This revealed faster nodule development with SmBL225C and early nodule senescence with Sm2011. These RNA sequencing analyses allowed us to identify candidate plant factors that could drive the differential nodule phenotype. In conclusion, this work shows the value of having a set of rhizobium strains to fully evaluate the biological importance of a plant symbiotic gene.
    MeSH term(s) Medicago truncatula ; Sinorhizobium/genetics ; Sinorhizobium meliloti/genetics ; Nitrogen Fixation/genetics ; Transcription Factors/genetics ; Symbiosis/genetics ; Root Nodules, Plant/genetics ; Root Nodules, Plant/microbiology
    Chemical Substances Transcription Factors
    Language English
    Publishing date 2022-09-24
    Publishing country Japan
    Document type Journal Article
    ZDB-ID 208907-5
    ISSN 1471-9053 ; 0032-0781
    ISSN (online) 1471-9053
    ISSN 0032-0781
    DOI 10.1093/pcp/pcac134
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: First whole genome assembly and annotation of a European common bean cultivar using PacBio HiFi and Iso-Seq data.

    Carrère, Sébastien / Mayjonade, Baptiste / Lalanne, David / Gaillard, Sylvain / Verdier, Jérôme / Chen, Nicolas W G

    Data in brief

    2023  Volume 48, Page(s) 109182

    Abstract: Common bean ( ...

    Abstract Common bean (
    Language English
    Publishing date 2023-04-26
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2786545-9
    ISSN 2352-3409 ; 2352-3409
    ISSN (online) 2352-3409
    ISSN 2352-3409
    DOI 10.1016/j.dib.2023.109182
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Genome Sequences of 17 Strains from Eight Races of Xanthomonas campestris pv. campestris.

    Bellenot, Caroline / Carrère, Sébastien / Gris, Carine / Noël, Laurent D / Arlat, Matthieu

    Microbiology resource announcements

    2022  Volume 11, Issue 7, Page(s) e0027922

    Abstract: Xanthomonas campestris pv. campestris is a group of phytopathogenic bacteria causing black rot disease on Brassicaceae crops. Here, we report on draft genome sequences of 17 strains representing eight of nine known races of this pathogen, including the ... ...

    Abstract Xanthomonas campestris pv. campestris is a group of phytopathogenic bacteria causing black rot disease on Brassicaceae crops. Here, we report on draft genome sequences of 17 strains representing eight of nine known races of this pathogen, including the pathotype strain CFBP 6865.
    Language English
    Publishing date 2022-06-13
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00279-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: A high diversity of non-target site resistance mechanisms to acetolactate-synthase (ALS) inhibiting herbicides has evolved within and among field populations of common ragweed (Ambrosia artemisiifolia L.).

    Loubet, Ingvild / Meyer, Lucie / Michel, Séverine / Pernin, Fanny / Carrère, Sébastien / Barrès, Benoit / Le Corre, Valérie / Délye, Christophe

    BMC plant biology

    2023  Volume 23, Issue 1, Page(s) 510

    Abstract: Background: Non-target site resistance (NTSR) to herbicides is a polygenic trait that threatens the chemical control of agricultural weeds. NTSR involves differential regulation of plant secondary metabolism pathways, but its precise genetic ... ...

    Abstract Background: Non-target site resistance (NTSR) to herbicides is a polygenic trait that threatens the chemical control of agricultural weeds. NTSR involves differential regulation of plant secondary metabolism pathways, but its precise genetic determinisms remain fairly unclear. Full-transcriptome sequencing had previously been implemented to identify NTSR genes. However, this approach had generally been applied to a single weed population, limiting our insight into the diversity of NTSR mechanisms. Here, we sought to explore the diversity of NTSR mechanisms in common ragweed (Ambrosia artemisiifolia L.) by investigating six field populations from different French regions where NTSR to acetolactate-synthase-inhibiting herbicides had evolved.
    Results: A de novo transcriptome assembly (51,242 contigs, 80.2% completeness) was generated as a reference to seek genes differentially expressed between sensitive and resistant plants from the six populations. Overall, 4,609 constitutively differentially expressed genes were identified, of which none were common to all populations, and only 197 were shared by several populations. Similarly, population-specific transcriptomic response was observed when investigating early herbicide response. Gene ontology enrichment analysis highlighted the involvement of stress response and regulatory pathways, before and after treatment. The expression of 121 candidate constitutive NTSR genes including CYP71, CYP72, CYP94, oxidoreductase, ABC transporters, gluco and glycosyltransferases was measured in 220 phenotyped plants. Differential expression was validated in at least one ragweed population for 28 candidate genes. We investigated whether expression patterns at some combinations of candidate genes could predict phenotype. Within populations, prediction accuracy decreased when applied to an additional, independent plant sampling. Overall, a wide variety of genes linked to NTSR was identified within and among ragweed populations, of which only a subset was captured in our experiments.
    Conclusion: Our results highlight the complexity and the diversity of NTSR mechanisms that can evolve in a weed species in response to herbicide selective pressure. They strongly point to a non-redundant, population-specific evolution of NTSR to ALS inhibitors in ragweed. It also alerts on the potential of common ragweed for rapid adaptation to drastic environmental or human-driven selective pressures.
    MeSH term(s) Humans ; Ambrosia/genetics ; Herbicides/pharmacology ; Acetolactate Synthase ; Transcriptome ; Herbicide Resistance/genetics
    Chemical Substances Herbicides ; Acetolactate Synthase (EC 2.2.1.6) ; alpha-acetolactate (535-17-1)
    Language English
    Publishing date 2023-10-24
    Publishing country England
    Document type Journal Article
    ZDB-ID 2059868-3
    ISSN 1471-2229 ; 1471-2229
    ISSN (online) 1471-2229
    ISSN 1471-2229
    DOI 10.1186/s12870-023-04524-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Bacterial host adaptation through sequence and structural variations of a single type III effector gene.

    Lauber, Emmanuelle / González-Fuente, Manuel / Escouboué, Maxime / Vicédo, Céline / Luneau, Julien S / Pouzet, Cécile / Jauneau, Alain / Gris, Carine / Zhang, Zhi-Min / Pichereaux, Carole / Carrère, Sébastien / Deslandes, Laurent / Noël, Laurent D

    iScience

    2024  Volume 27, Issue 3, Page(s) 109224

    Abstract: Molecular mechanisms underlying quantitative variations of pathogenicity remain elusive. Here, we identified ... ...

    Abstract Molecular mechanisms underlying quantitative variations of pathogenicity remain elusive. Here, we identified the
    Language English
    Publishing date 2024-02-15
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2024.109224
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Development and characterization of a new sunflower source of resistance to race G of Orobanche cumana Wallr. derived from Helianthus anomalus.

    Fernández-Melero, Belén / Del Moral, Lidia / Todesco, Marco / Rieseberg, Loren H / Owens, Gregory L / Carrère, Sébastien / Chabaud, Mireille / Muños, Stéphane / Velasco, Leonardo / Pérez-Vich, Begoña

    TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

    2024  Volume 137, Issue 3, Page(s) 56

    Abstract: Key message: A new ... ...

    Abstract Key message: A new Or
    MeSH term(s) Helianthus/genetics ; Orobanche ; Plant Breeding ; Necrosis ; Phenols
    Chemical Substances Phenols
    Language English
    Publishing date 2024-02-22
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2170-2
    ISSN 1432-2242 ; 0040-5752
    ISSN (online) 1432-2242
    ISSN 0040-5752
    DOI 10.1007/s00122-024-04558-4
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    Zs.A 1692: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  10. Article: myGenomeBrowser: building and sharing your own genome browser

    Carrere, Sébastien / Gouzy, Jérôme

    Bioinformatics. 2017 Apr. 15, v. 33, no. 8

    2017  

    Abstract: myGenomeBrowser is a web-based environment that provides biologists with a way to build, query and share their genome browsers. This tool, that builds on JBrowse, is designed to give users more autonomy while simplifying and minimizing intervention from ... ...

    Abstract myGenomeBrowser is a web-based environment that provides biologists with a way to build, query and share their genome browsers. This tool, that builds on JBrowse, is designed to give users more autonomy while simplifying and minimizing intervention from system administrators. We have extended genome browser basic features to allow users to query, analyze and share their data. Availability and implementation: myGenomeBrowser is freely available at https://bbric-pipelines.toulouse.inra.fr/myGenomeBrowser and includes tutorial screencasts. Source code and installation instructions can be found at https://framagit.org/BBRIC/myGenomeBrowser. myGenomeBrowser is open-source and mainly implemented in Perl, JavaScript, Apache and Docker. Contact: sebastien.carrere@inra.fr
    Keywords Internet ; bioinformatics ; computer software ; genome
    Language English
    Dates of publication 2017-0415
    Size p. 1255-1257.
    Publishing place Oxford University Press
    Document type Article
    ZDB-ID 1468345-3
    ISSN 1460-2059 ; 1367-4811 ; 1367-4803
    ISSN (online) 1460-2059 ; 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btw800
    Database NAL-Catalogue (AGRICOLA)

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