Anne-Laure Abraham

Ingénieur de recherche - MaIAGE - INRAE
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Publications

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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-02318313 v1
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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-02466120 v1
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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-02311421 v1
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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-01713777 v1
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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-01606551 v1
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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-01509688 v1

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-03372071 v1
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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-01353535 v1

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-01154007 v1
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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-01302473 v1
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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-01193999 v1
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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-01195502 v1

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-02318315 v1
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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-00811503 v1

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-00807474 v1
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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-00811500 v1

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-02319387 v1

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-02319386 v1
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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-00336123 v1
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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-04169802 v1

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-04826247 v1
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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-03451266 v1
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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-02789036 v1
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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-02788899 v1
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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-04631038 v1

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-04221437 v1

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-04170846 v1

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-04176902 v1
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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-04313747 v1
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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-03337234 v1
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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-03451271 v1
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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-02789073 v1
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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-02008726 v1
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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-01512085 v1
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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-02799027 v1

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-01195512 v1

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-01204484 v1
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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-01204320 v1