Anne-Laure Abraham

Ingénieur de recherche - MaIAGE - INRAE
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Publications

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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 Chapron et al.

Scientific Reports, 2019, 9 (1), pp.8897. ⟨10.1038/s41598-019-45173-4⟩

Article dans une revue hal-02466120v1
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Serine protease inhibitors and human wellbeing interplay: new insights for old friends

Hela Mkaouar , Nizar Akermi , Aicha Kriaa , Anne-Laure Abraham , Amin Jablaoui et al.

PeerJ, 2019, 7, pp.e7224. ⟨10.7717/peerj.7224⟩

Article dans une revue (article de synthèse) hal-02318313v1
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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 Rué et al.

Cahier des Techniques de l'INRA, 2019, 97, pp.46-69

Article dans une revue (article de synthèse) hal-02311421v1
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Identification of New Factors Modulating Adhesion Abilities of the Pioneer Commensal Bacterium Streptococcus salivarius

Benoit Couvigny , Saulius Kulakauskas , Nicolas Pons , Benoit Quinquis , Anne-Laure Abraham et al.

Frontiers in Microbiology, 2018, 9 (article 273), ⟨10.3389/fmicb.2018.00273⟩

Article dans une revue hal-01713777v1
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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 Chiapello et al.

Scientific Reports, 2017, 7, pp.1-11. ⟨10.1038/srep44331⟩

Article dans une revue hal-01509688v1
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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 Abraham et 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 Peucelle et al.

Environmental Microbiology, 2016, 18 (5), pp.1484-1497. ⟨10.1111/1462-2920.13181⟩

Article dans une revue istex hal-03372071v1
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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
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Multiple recent horizontal transfers of a large genomic region in cheese making fungi

Kevin Cheeseman , Jeanne Ropars , Pierre Renault , Joelle Dupont , Jerome Gouzy et al.

Nature Communications, 2014, 5 (5), pp.2876. ⟨10.1038/ncomms3876⟩

Article dans une revue hal-01302473v1
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Genome Sequence of the Lactic Acid Bacterium <i>Lactococcus lactis</i> subsp. <i>lactis</i> TOMSC161, Isolated from a Nonscalded Curd Pressed Cheese

Hélène Velly , Pierre Renault , Anne-Laure Abraham , Valentin Loux , Agnes Delacroix-Buchet et al.

Genome Announcements, 2014, 2 (6), ⟨10.1128/genomeA.01121-14⟩

Article dans une revue hal-01193999v1
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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 Monnet et 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 Bapaume et 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
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Genetic modifiers of chromatin acetylation antagonize the reprogramming of epi-polymorphisms.

Anne-Laure Abraham , Muniyandi Nagarajan , Jean-Baptiste Veyrieras , Hélène Bottin , Lars M Steinmetz et al.

PLoS Genetics, 2012, 8 (9), pp.e1002958. ⟨10.1371/journal.pgen.1002958⟩

Article dans une revue ensl-00811503v1

Genetic Modifiers of Chromatin Acetylation Antagonize the Reprogramming of Epi-Polymorphisms

Anne-Laure Abraham , Muniyandi Nagarajan , Jean-Baptiste Veyrieras , Hélène Bottin , Lars M. Steinmetz et al.

PLoS Genetics, 2012, 8 (e1002958), pp.e1002958

Article dans une revue ensl-00807474v1
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Natural single-nucleosome epi-polymorphisms in yeast.

Muniyandi Nagarajan , Jean-Baptiste Veyrieras , Maud de Dieuleveult , Hélène Bottin , Steffen Fehrmann et 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
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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
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Characterization and quantification of antibiotic resistance gene variants in gut microbiota

Ouléye Sidibe , Anne-Carmen Sanchez , Guillaume Kon Kam King , Fanny Calenge , Benoît Doublet et 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 Bouchon et 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
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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 Bidaut et al.

Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jul 2021, Paris, France

Communication dans un congrès hal-03451266v1
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A metagenomic tool for cheese ecosystems

Anne-Laure Abraham , Quentin Cavaillé , Thibaut Guirimand , Pierre Renault , Sandra Derozier et 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
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Food-Microbiomes Transfert, a shotgun metagenomic tool and a database to analyze cheese ecosystems

Thibaut Guirimand , Anne-Laure Abraham , Sandra Derozier , Charlie Pauvert , Mahendra Mariadassou et al.

JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France

Communication dans un congrès hal-02788899v1
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Microbial transfers in dairy systems under changing climate and farming practices

Sébastien Theil , Mahendra Mariadassou , Philippe Ruiz , Guillaume Kon Kam King , Matthieu Bouchon et al.

JOBIM 20025, Jul 2025, Bordeaux, France

Poster de conférence hal-05168268v1
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Microbial transfers in dairy systems under changing climate and farming practices

Sébastien Theil , Mahendra Mariadassou , Philippe Ruiz , Guillaume Kon Kam King , Matthieu Bouchon et al.

FROGS Days, Dec 2025, Toulouse, France

Poster de conférence hal-05462857v1
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Intra-species diversity in metagenomic datasets

Anne-Laure Abraham , Guillaume Kon Kam King , Solène Pety , Anne-Carmen Sanchez , Hélène Chiapello et al.

JOBIM 2024, Jun 2024, Toulouse, France. , 2024

Poster de conférence hal-04631038v1
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Characterization and quantification of antibiotic resistance gene variants in gut microbiota

Ouléye Sidibe , Anne-Carmen Sanchez , Guillaume Kon Kam King , Fanny Calenge , Benoît Doublet et 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 Bouchon et 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 Doublet et 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 Plauzolles et al.

3rd International Conference on Holobionts, Jul 2022, Lyon, France. 2022

Poster de conférence hal-04176902v1
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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 Chiapello et al.

JOBIM, Jul 2022, Rennes, France

Poster de conférence hal-04313747v1
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Precise detection of antibiotic resistance genes in chicken microbiota

Anne-Carmen Sanchez , Guillaume Kon Kam King , Sylvie Baucheron , Fanny Calenge , Hélène Chiapello et al.

Journées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM - colloque virtuel, Jul 2021, Paris, France.

Poster de conférence hal-03337234v1
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Shallow sequencing: a cost-effective and accurate alternative to WGS for taxonomic profiling ?

Benoit Goutorbe , Anne-Laure Abraham , Mahendra Mariadassou , Valentin Loux , Olivier Rué et al.

JOBIM, Jun 2020, Montpellier, France.

Poster de conférence hal-03451271v1
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Metagenomic analysis of an african beer ecosystem using Food Microbiome Transfert application

Anne-Laure Abraham , Sandra Derozier , Quentin Cavaillé , Thibaut Guirimand , Solange Aka et al.

jobim 2019, Jul 2019, Nantes, France. 2019

Poster de conférence hal-02789073v1
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FoodMicrobiome transfert: Web based metagenomic analysis

Quentin Cavaillé , Thibaut Guirimand , Sandra Derozier , Anne-Laure Abraham , Bedis Dridi et al.

JOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. , 2018

Poster de conférence hal-02008726v1
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Cheese ecosystems insights with shotgun metagenomics and a metadata extended genomics database.

Thibaut Guirimand , Charlie Pauvert , Sandra Derozier , Anne-Laure Abraham , Mahendra Mariadassou et al.

JOBIM 2016 : Journées ouvertes de biologie informatique et mathématiques, Jun 2016, Lyon, France. , 2016

Poster de conférence hal-01512085v1
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Food Microbiome-Transfert a database to characterize cheese ecosystems.

Thibaut Guirimand , Sandra S. Derozier , Charlie Pauvert , Anne-Laure Abraham , Valentin Loux et 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 Mariadassou et 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-Bony et al.

JOBIM 16. Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , 2015

Poster de conférence hal-01195512v1
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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 Schbath et al.

ECCB'08: 7. European Conference on Computational Biology, Sep 2014, Strasbourg, France. , 2014

Poster de conférence hal-01204320v1