Anne-Laure Abraham Ingénieur de recherche - MaIAGE - INRAE

Publications

Article dans une revue (18)

A Guide for Ex Vivo Handling and storage of stool samples Intended for Fecal Microbiota transplantation Sebastian D Burz,Anne-Laure Abraham,Fernanda Fonseca,Olivier David,Audrey Chapronet al. Scientific Reports, 2019, 9 (1), pp.8897. ⟨10.1038/s41598-019-45173-4⟩ Article dans une revue hal-02466120v1
Serine protease inhibitors and human wellbeing interplay: new insights for old friends Hela Mkaouar,Nizar Akermi,Aicha Kriaa,Anne-Laure Abraham,Amin Jablaouiet al. PeerJ, 2019, 7, pp.e7224. ⟨10.7717/peerj.7224⟩ Article dans une revue (article de synthèse) hal-02318313v1
Guide pratique à destination des biologistes, bioinformaticiens et statisticiens qui souhaitent s’initier aux analyses métabarcoding Hélène Falentin,Lucas Auer,Mahendra Mariadassou,Géraldine Pascal,Olivier Ruéet al. Cahier des Techniques de l'INRA, 2019, 97, pp.46-69 Article dans une revue (article de synthèse) hal-02311421v1
Identification of New Factors Modulating Adhesion Abilities of the Pioneer Commensal Bacterium Streptococcus salivarius Benoit Couvigny,Saulius Kulakauskas,Nicolas Pons,Benoit Quinquis,Anne-Laure Abrahamet al. Frontiers in Microbiology, 2018, 9 (article 273), ⟨10.3389/fmicb.2018.00273⟩ Article dans une revue hal-01713777v1
Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue Hela El Kafsi,Valentin Loux,Mahendra Mariadassou,Camille Blin,Hélène Chiapelloet al. Scientific Reports, 2017, 7, pp.1-11. ⟨10.1038/srep44331⟩ Article dans une revue hal-01509688v1
A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic Orlane Patrascu,Fabienne Beguet-Crespel,Ludovica Marinelli,Emmanuelle Le Chatelier,Anne-Laure Abrahamet al. Scientific Reports, 2017, 7, ⟨10.1038/srep40248⟩ Article dans une revue hal-01606551v1
Beneficial metabolic effects of selected probiotics on diet-induced obesity and insulin resistance in mice are associated with improvement of dysbiotic gut microbiota Jeanne Alard,Véronique Lehrter,Moez Rhimi,Irène Mangin,Véronique Peucelleet al. Environmental Microbiology, 2016, 18 (5), pp.1484-1497. ⟨10.1111/1462-2920.13181⟩ Article dans une revue istex hal-03372071v1
Functional comparison of bacteria from the human gut and closely related non-gut bacteria reveals the importance of conjugation and a paucity of motility and chemotaxis functions in the gut environment Dragana Dobrijevic,Anne-Laure Abraham,Alexandre Jamet,Emmanuelle Maguin,Maarten van de Guchte PLoS ONE, 2016, 11 (7), pp.e0159030. ⟨10.1371/journal.pone.0159030⟩ Article dans une revue hal-01353535v1
Genomics of Streptococcus salivarius, a major human commensal Christine Delorme,Anne-Laure Abraham,Pierre Renault,Eric Guédon Infection, Genetics and Evolution, 2014, 33, ⟨10.1016/j.meegid.2014.10.001⟩ Article dans une revue hal-01154007v1
Multiple recent horizontal transfers of a large genomic region in cheese making fungi Kevin Cheeseman,Jeanne Ropars,Pierre Renault,Joelle Dupont,Jerome Gouzyet al. Nature Communications, 2014, 5 (5), pp.2876. ⟨10.1038/ncomms3876⟩ Article dans une revue hal-01302473v1
Genome Sequence of the Lactic Acid Bacterium &lt;i&gt;Lactococcus lactis&lt;/i&gt; subsp. &lt;i&gt;lactis&lt;/i&gt; TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese Hélène Velly,Pierre Renault,Anne-Laure Abraham,Valentin Loux,Agnes Delacroix-Buchetet al. Genome Announcements, 2014, 2 (6), ⟨10.1128/genomeA.01121-14⟩ Article dans une revue hal-01193999v1
Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products Mathieu Almeida,Agnes Hebert,Anne-Laure Abraham,Simon Rasmussen,Christophe Monnetet al. BMC Genomics, 2014, 15, article 1101 (16 p.). ⟨10.1186/1471-2164-15-1101⟩ Article dans une revue hal-01195502v1
Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense Agnès Yu,Gersende Lepère,Florence Jay,Jingyu Wang,Laure Bapaumeet al. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (6), pp.2389-2394. ⟨10.1073/pnas.1211757110⟩ Article dans une revue hal-02318315v1
Genetic modifiers of chromatin acetylation antagonize the reprogramming of epi-polymorphisms. Anne-Laure Abraham,Muniyandi Nagarajan,Jean-Baptiste Veyrieras,Hélène Bottin,Lars M Steinmetzet al. PLoS Genetics, 2012, 8 (9), pp.e1002958. ⟨10.1371/journal.pgen.1002958⟩ Article dans une revue ensl-00811503v1
Natural single-nucleosome epi-polymorphisms in yeast. Muniyandi Nagarajan,Jean-Baptiste Veyrieras,Maud de Dieuleveult,Hélène Bottin,Steffen Fehrmannet al. PLoS Genetics, 2010, 6 (4), pp.e1000913. ⟨10.1371/journal.pgen.1000913⟩ Article dans une revue ensl-00811500v1
Alternative to homo-oligomerisation: the creation of local symmetry in proteins by internal amplification Anne-Laure Abraham,Joël Pothier,Eduardo P.C Rocha Journal of Molecular Biology, 2009, 394 (3), pp.522-534. ⟨10.1016/j.jmb.2009.09.031⟩ Article dans une revue hal-02319387v1
Genesis, effects and fates of repeats in prokaryotic genomes Todd J. Treangen,Anne-Laure Abraham,Marie Touchon,Eduardo P.C Rocha FEMS Microbiology Reviews, 2009, 33 (3), pp.539-571. ⟨10.1111/j.1574-6976.2009.00169.x⟩ Article dans une revue (article de synthèse) hal-02319386v1
Swelfe: a detector of internal repeats in sequences and structures. Anne-Laure Abraham,Eduardo P C Rocha,Joël Pothier Bioinformatics, 2008, 24 (13), pp.1536-7. ⟨10.1093/bioinformatics/btn234⟩ Article dans une revue pasteur-00336123v1

Communication dans un congrès (5)

Characterization and quantification of antibiotic resistance gene variants in gut microbiota Ouléye Sidibe,Anne-Carmen Sanchez,Guillaume Kon Kam King,Fanny Calenge,Benoît Doubletet al. 9; Symposium on Antimicrobial Resistance in Animals and the Environment - ARAE, INRAE, Jul 2023, Tours (France), France Communication dans un congrès hal-04169802v1
Microbial transfers at the crossroads of agro-ecological transitions in dairy systems Nicolas Chemidlin Prévost-Bouré,Anne-Laure Abraham,Annick Bernalier Donadille,Juliette Bloor,Matthieu Bouchonet al. Carrefours de l’innovation agronomique (CIAG) Les indicateurs de qualité des sols et leur usage dans un contexte de transitions agricoles, Nov 2022, Orléans, France Communication dans un congrès hal-04826247v1
Shallow Shotgun Metagenomics as a cost-effective and accurate alternative to WGS for taxonomic profiling and clinical diagnosis Benoit Goutorbe,Anne-Laure Abraham,Mahendra Mariadassou,Anne Plauzolles,Ghislain Bidautet al. Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2021, Paris, France Communication dans un congrès hal-03451266v1
A metagenomic tool for cheese ecosystems Anne-Laure Abraham,Quentin Cavaillé,Thibaut Guirimand,Pierre Renault,Sandra Derozieret al. 17. European Conference on Computational Biology (ECCB 2018, Workshop "Recent Computational Advances in Metagenomics (RCAM)", Sep 2018, Athenes, Greece Communication dans un congrès hal-02789036v1
Food-Microbiomes Transfert, a shotgun metagenomic tool and a database to analyze cheese ecosystems Thibaut Guirimand,Anne-Laure Abraham,Sandra Derozier,Charlie Pauvert,Mahendra Mariadassouet al. JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France Communication dans un congrès hal-02788899v1

Poster de conférence (17)

Microbial transfers in dairy systems under changing climate and farming practices Sébastien Theil,Mahendra Mariadassou,Philippe Ruiz,Guillaume Kon Kam King,Matthieu Bouchonet al. JOBIM 20025, Jul 2025, Bordeaux, France Poster de conférence hal-05168268v1
Microbial transfers in dairy systems under changing climate and farming practices Sébastien Theil,Mahendra Mariadassou,Philippe Ruiz,Guillaume Kon Kam King,Matthieu Bouchonet al. FROGS Days, Dec 2025, Toulouse, France Poster de conférence hal-05462857v1
Intra-species diversity in metagenomic datasets Anne-Laure Abraham,Guillaume Kon Kam King,Solène Pety,Anne-Carmen Sanchez,Hélène Chiapelloet al. JOBIM 2024, Jun 2024, Toulouse, France. , 2024 Poster de conférence hal-04631038v1
Characterization and quantification of antibiotic resistance gene variants in gut microbiota Ouléye Sidibe,Anne-Carmen Sanchez,Guillaume Kon Kam King,Fanny Calenge,Benoît Doubletet al. 35e colloque BIOTECHNOCENTRE, Oct 2023, Nouan le Fuzelier, France Poster de conférence hal-05190952v1
Microbial transfers across a food chain: from grassland to cheese using metagenetic high-throughput sequencing approaches Anne-Laure Abraham,Juliette Bloor,Céline Delbès,Annick Bernalier Donadille,Matthieu Bouchonet al. FORUM ON FERMENTED FOODS, May 2023, Lyon, France Poster de conférence hal-04221437v1
Characterization and quantification of antibiotic resistance gene variants in gut microbiota. Ouléye Sidibe,Anne-Carmen Sanchez,Guillaume Kon Kam King,Fanny Calenge,Benoît Doubletet al. JOBIM 2023, Jun 2023, Tours, France. 2023, JOBIM 2023 Proceedings Poster de conférence hal-04170846v1
Combining marker genes in amplicon sequencing: a novel approach enhancing taxonomic profiling of microbial ecosystems Benoît Goutorbe,Anne-Laure Abraham,Mahendra Mariadassou,Marion Bonnet,Anne Plauzolleset al. 3rd International Conference on Holobionts, Jul 2022, Lyon, France. 2022 Poster de conférence hal-04176902v1
Construction of a reference genome catalog to decipher shared strains along an agrifood chain with shotgun metagenomic data Fiona Bottin,Sébastien Theil,Céline Delbès,Panagiotis Sapountzsis,Hélène Chiapelloet al. JOBIM, Jul 2022, Rennes, France Poster de conférence hal-04313747v1
Precise detection of antibiotic resistance genes in chicken microbiota Anne-Carmen Sanchez,Guillaume Kon Kam King,Sylvie Baucheron,Fanny Calenge,Hélène Chiapelloet al. Journées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM - colloque virtuel, Jul 2021, Paris, France. Poster de conférence hal-03337234v1
Shallow sequencing: a cost-effective and accurate alternative to WGS for taxonomic profiling ? Benoit Goutorbe,Anne-Laure Abraham,Mahendra Mariadassou,Valentin Loux,Olivier Ruéet al. JOBIM, Jun 2020, Montpellier, France. Poster de conférence hal-03451271v1
Metagenomic analysis of an african beer ecosystem using Food Microbiome Transfert application Anne-Laure Abraham,Sandra Derozier,Quentin Cavaillé,Thibaut Guirimand,Solange Akaet al. jobim 2019, Jul 2019, Nantes, France. 2019 Poster de conférence hal-02789073v1
FoodMicrobiome transfert: Web based metagenomic analysis Quentin Cavaillé,Thibaut Guirimand,Sandra Derozier,Anne-Laure Abraham,Bedis Dridiet al. JOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. , 2018 Poster de conférence hal-02008726v1
Cheese ecosystems insights with shotgun metagenomics and a metadata extended genomics database. Thibaut Guirimand,Charlie Pauvert,Sandra Derozier,Anne-Laure Abraham,Mahendra Mariadassouet al. JOBIM 2016 : Journées ouvertes de biologie informatique et mathématiques, Jun 2016, Lyon, France. , 2016 Poster de conférence hal-01512085v1
Food Microbiome-Transfert a database to characterize cheese ecosystems. Thibaut Guirimand,Sandra S. Derozier,Charlie Pauvert,Anne-Laure Abraham,Valentin Louxet al. Journées Bioinformatique Inra, Mar 2016, Toulouse, France. , 2016 Poster de conférence hal-02799027v1
Accurate taxonomy assignments in cheeses ecosystems via a metagenomic approach Charlie Pauvert,Anne-Laure Abraham,Mathieu Almeida,Nicolas Pons,Mahendra Mariadassouet al. JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , pp.1, 2015 Poster de conférence hal-01204484v1
How to design an efficient and robust pipeline for 16S rRNA-gene sequence analysis to improve our understanding on microbial communities? Lucas Auer,Laurent Cauquil,Stephane Chaillou,Céline Delbès,Eric Dugat-Bonyet al. JOBIM 16. Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , 2015 Poster de conférence hal-01195512v1
A shotgun metagenomic method to characterise low abundant species and assign precisely taxonomy in complex microbial ecosystems Anne-Laure Abraham,Mathieu Almeida,Nicolas Pons,Charlie Pauvert,Sophie Schbathet al. ECCB'08: 7. European Conference on Computational Biology, Sep 2014, Strasbourg, France. , 2014 Poster de conférence hal-01204320v1

Pré-publication, Document de travail (1)

Characterizing the limits of shallow shotgun metagenomics for taxonomic profiling of human gut microbiota in clinical studies Benoit Goutorbe,Anne-Laure Abraham,Mahendra Mariadassou,Anne Plauzolles,Ghislain Bidautet al. 2022 Pré-publication, Document de travail hal-04316615v1

Thèse (1)

Caractérisation et analyse évolutive des répétitions intragéniques : une étude au niveau des gènes, des séquences protéiques et des structures tridimensionnelles Anne-Laure Abraham Sciences du Vivant [q-bio]. Université Pierre et Marie Curie - Paris VI, 2008. Français. ⟨NNT : ⟩ Thèse tel-00482373v1