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"Journal of Proteome Research" } }, { "doi": "10.1038/s42004-024-01386-x", "pmid": "39702463", "pmcid": "PMC11659399", "type": [ "Primary" ], "version": "3.0", "note": "MS Annika 3.0 for non-cleavable crosslink identification", "metadata": { "title": "Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex", "abstract": "", "date": "2024-12-01T00:00:00Z", "citationCount": 2, "authors": [], "journal": "Communications Chemistry" } } ], "credit": [ { "name": "Viktoria Dorfer", "email": "viktoria.dorfer@fh-hagenberg.at", "url": "http://bioinformatics.fh-hagenberg.at/", "orcidid": "https://orcid.org/0000-0002-5332-5701", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Micha Birklbauer", "email": "micha.birklbauer@fh-hagenberg.at", "url": "http://bioinformatics.fh-hagenberg.at/", "orcidid": "https://orcid.org/0009-0005-1051-179X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "michabirklbauer", "additionDate": "2023-07-26T14:40:01.768324Z", "lastUpdate": "2025-10-26T02:38:48.643054Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SHAMAN", "description": "SHiny application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. It is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, as suggested in [McMurdie and Holmes 2014, Jonsson2016]. It robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014].", "homepage": "http://shaman.c3bi.pasteur.fr/", "biotoolsID": "shaman", "biotoolsCURIE": "biotools:shaman", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression analysis" }, { "uri": "http://edamontology.org/operation_3221", "term": "Species frequency estimation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [] } ], "note": "Quantitative metagenomics Count table & taxonomy Diversity, barplot, boxplot, scatterplot, rarefaction curves, heatmap", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/aghozlane/shaman", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "http://shaman.c3bi.pasteur.fr/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1073/pnas.1523899113", "pmid": "27140611", "pmcid": "PMC4878514", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection", "abstract": "Listeria monocytogenes is responsible for gastroenteritis in healthy individuals and for a severe invasive disease in immunocompromised patients. Among the three identified L. monocytogenes evolutionary lineages, lineage I strains are overrepresented in epidemic listeriosis outbreaks, but the mechanisms underlying the higher virulence potential of strains of this lineage remain elusive. Here, we demonstrate that Listeriolysin S (LLS), a virulence factor only present in a subset of lineage I strains, is a bacteriocin highly expressed in the intestine of orally infected mice that alters the host intestinal microbiota and promotes intestinal colonization by L. monocytogenes, as well as deeper organ infection. To our knowledge, these results therefore identify LLS as the first bacteriocin described in L. monocytogenes and associate modulation of host microbiota by L. monocytogenes epidemic strains to increased virulence.", "date": "2016-05-17T00:00:00Z", "citationCount": 87, "authors": [ { "name": "Quereda J.J." }, { "name": "Dussurget O." }, { "name": "Nahori M.-A." }, { "name": "Ghozlane A." }, { "name": "Volant S." }, { "name": "Dillies M.-A." }, { "name": "Regnault B." }, { "name": "Kennedy S." }, { "name": "Mondot S." }, { "name": "Villoing B." }, { "name": "Cossart P." }, { "name": "Pizarro-Cerda J." } ], "journal": "Proceedings of the National Academy of Sciences of the United States of America" } } ], "credit": [ { "name": "Stevenn Volant", "email": null, "url": "https://research.pasteur.fr/en/member/stevenn-volant/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Hugo Varet", "email": null, "url": "https://research.pasteur.fr/en/member/hugo-varet/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pierre Lechat", "email": null, "url": "https://research.pasteur.fr/en/member/pierre-lechat/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Amine Ghozlane", "email": null, "url": "https://research.pasteur.fr/en/member/amine-ghozlane/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Institut Pasteur", "email": null, "url": "https://research.pasteur.fr", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "C3BI", "email": null, "url": "https://research.pasteur.fr/en/center/c3bi/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "Bioinformatics and Biostatistics Hub", "email": null, "url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider" ], "note": null }, { "name": "SHAMAN team", "email": "shaman@pasteur.fr", "url": "https://research.pasteur.fr/en/software/shaman-shiny-application-for-metagenomic-analysis/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aghozlane", "additionDate": "2016-11-28T10:07:16Z", "lastUpdate": "2025-10-23T10:46:59.953305Z", "editPermission": { "type": "group", "authors": [ "hmenager", "khillion", "vashokan" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { 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"elixirCommunity": [], "link": [ { "url": "https://gcanudo-barreras.github.io/ViVo-Platform/", "type": [ "Service" ], "note": null }, { "url": "https://www.biorxiv.org/content/10.1101/2025.10.14.682266v1", "type": [ "Other" ], "note": "bioRxiv preprint" }, { "url": "https://github.com/gcanudo-barreras/ViVo-Platform", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/gcanudo-barreras/ViVo-Platform/blob/main/README.md", "type": [ "General" ], "note": null }, { "url": "https://github.com/gcanudo-barreras/ViVo-Platform/blob/main/ViVo_USER_MANUAL.md", "type": [ "User manual" ], "note": null }, { "url": "https://www.biorxiv.org/content/10.1101/2025.10.14.682266v1", "type": [ "Other" ], "note": "Full methodology" }, { "url": "https://github.com/gcanudo-barreras/ViVo-Platform/releases/tag/v1.0-beta", "type": [ "Release notes" ], "note": null } ], "publication": [ { "doi": "10.1101/2025.10.14.682266", "pmid": null, "pmcid": null, "type": 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