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It integrates for each species: \ni) a main knowledge base with extended functional, gene expression, phenotyping, anatomical and phylogenetic information; \nii) A multispecies genomic browser; \niii) a Genomicus gene synteny browser.", "homepage": "https://www.aniseed.fr", "biotoolsID": "ANISEED", "biotoolsCURIE": "biotools:ANISEED", "version": [ "2019" ], "otherID": [ { "value": "DOI:10.1093/nar/gkx1108", "type": "doi", "version": "2017" }, { "value": "DOI:10.1093/nar/gkv966", "type": "doi", "version": "2015" }, { "value": "DOI:10.1101/gr.108175.110", "type": "doi", "version": "2010" }, { "value": "DOI:10.1016/j.cub.2005.12.044", "type": "doi", "version": "2006" } ], "relation": [ { "biotoolsID": "interpro", "type": "uses" }, { "biotoolsID": "blast", "type": "uses" }, { "biotoolsID": "genomicus-tunicates", "type": "uses" }, { "biotoolsID": "ciona_robusta_anatomy_and_development_ontology", "type": "uses" }, { "biotoolsID": "ciona_robusta_anatomy_and_development_ontology", "type": 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"uri": "http://edamontology.org/topic_3065", "term": "Embryology" }, { "uri": "http://edamontology.org/topic_3383", "term": "Biological imaging" }, { "uri": "http://edamontology.org/topic_3679", "term": "Animal study" }, { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0194", "term": "Phylogenomics" } ], "operatingSystem": [ "Linux" ], "language": [ "PHP", "JavaScript", "Python" ], "license": "GPL-3.0", "collectionID": [ "elixir-fr-sdp-2019" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Data", "Interoperability" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://www.aniseed.fr", "type": [ "Service" ], "note": null }, { "url": "https://twitter.com/Aniseed_DB", "type": [ "Social media" ], "note": "Twitter for ANISEED" }, { "url": "https://www.facebook.com/TunicateCommunity", "type": [ "Social media" ], "note": "Facebook for ANISEED" }, { "url": "https://morphonet.org/", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://www.aniseed.fr/aniseed/download/download_data", "type": "Biological data", "note": null, "version": "2019" } ], "documentation": [ { "url": "https://www.aniseed.fr/api", "type": [ "API documentation" ], "note": null }, { "url": "https://www.aniseed.fr/aniseed/default/privacyPolicy", "type": [ "Contributions policy" ], "note": null }, { "url": "https://www.aniseed.fr/aniseed/default/termOfUse", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkx1108", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "2017", "note": null, "metadata": { "title": "ANISEED 2017: Extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets", "abstract": "ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.", "date": "2018-01-01T00:00:00Z", "citationCount": 62, "authors": [ { "name": "Brozovic M." }, { "name": "Dantec C." }, { "name": "Dardaillon J." }, { "name": "Dauga D." }, { "name": "Faure E." }, { "name": "Gineste M." }, { "name": "Louis A." }, { "name": "Naville M." }, { "name": "Nitta K.R." }, { "name": "Piette J." }, { "name": "Reeves W." }, { "name": "Scornavacca C." }, { "name": "Simion P." }, { "name": "Vincentelli R." }, { "name": "Bellec M." }, { "name": "Aicha S.B." }, { "name": "Fagotto M." }, { "name": "Gueroult-Bellone M." }, { "name": "Haeussler M." }, { "name": "Jacox E." }, { "name": "Lowe E.K." }, { "name": "Mendez M." }, { "name": "Roberge A." }, { "name": "Stolfi A." }, { "name": "Yokomori R." }, { "name": "Brown C.T." }, { "name": "Cambillau C." }, { "name": "Christiaen L." }, { "name": "Delsuc F." }, { "name": "Douzery E." }, { "name": "Dumollard R." }, { "name": "Kusakabe T." }, { "name": "Nakai K." }, { "name": "Nishida H." }, { "name": "Satou Y." }, { "name": "Swalla B." }, { "name": "Veeman M." }, { "name": "Volff J.-N." }, { "name": "Lemaire P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkv966", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "2015", "note": null, "metadata": { "title": "ANISEED 2015: A digital framework for the comparative developmental biology of ascidians", "abstract": "Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalisembryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalisgenome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.", "date": "2016-01-01T00:00:00Z", "citationCount": 53, "authors": [ { "name": "Brozovic M." }, { "name": "Martin C." }, { "name": "Dantec C." }, { "name": "Dauga D." }, { "name": "Mendez M." }, { "name": "Simion P." }, { "name": "Percher M." }, { "name": "Laporte B." }, { "name": "Scornavacca C." }, { "name": "Di Gregorio A." }, { "name": "Fujiwara S." }, { "name": "Gineste M." }, { "name": "Lowe E.K." }, { "name": "Piette J." }, { "name": "Racioppi C." }, { "name": "Ristoratore F." }, { "name": "Sasakura Y." }, { "name": "Takatori N." }, { "name": "Brown T.C." }, { "name": "Delsuc F." }, { "name": "Douzery E." }, { "name": "Gissi C." }, { "name": "McDougall A." }, { "name": "Nishida H." }, { "name": "Sawada H." }, { "name": "Swalla B.J." }, { "name": "Yasuo H." }, { "name": "Lemaire P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1101/gr.108175.110", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "2010", "note": null, "metadata": { "title": "The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program", "abstract": "Developmental biology aims to understand how the dynamics of embryonic shapes and organ functions are encoded in linear DNA molecules. Thanks to recent progress in genomics and imaging technologies, systemic approaches are now used in parallel with small-scale studies to establish links between genomic information and phenotypes, often described at the subcellular level. Current model organism databases, however, do not integrate heterogeneous data sets at different scales into a global view of the developmental program. Here, we present a novel, generic digital system, NISEED, and its implementation, ANISEED, to ascidians, which are invertebrate chordates suitable for developmental systems biology approaches. ANISEED hosts an unprecedented combination of anatomical and molecular data on ascidian development. This includes the first detailed anatomical ontologies for these embryos, and quantitative geometrical descriptions of developing cells obtained from reconstructed three-dimensional (3D) embryos up to the gastrula stages. Fully annotated gene model sets are linked to 30,000 high-resolution spatial gene expression patterns in wild-type and experimentally manipulated conditions and to 528 experimentally validated cis-regulatory regions imported from specialized databases or extracted from 160 literature articles. This highly structured data set can be explored via a Developmental Browser, a Genome Browser, and a 3D Virtual Embryo module. We show how integration of heterogeneous data in ANISEED can provide a system-level understanding of the developmental program through the automatic inference of gene regulatory interactions, the identification of inducing signals, and the discovery and explanation of novel asymmetric divisions. © 2010 by Cold Spring Harbor Laboratory Press.", "date": "2010-01-01T00:00:00Z", "citationCount": 90, "authors": [ { "name": "Tassy O." }, { "name": "Dauga D." }, { "name": "Daian F." }, { "name": "Sobral D." }, { "name": "Robin F." }, { "name": "Khoueiry P." }, { "name": "Salgado D." }, { "name": "Fox V." }, { "name": "Caillol D." }, { "name": "Schiappa R." }, { "name": "Laporte B." }, { "name": "Rios A." }, { "name": "Luxardi G." }, { "name": "Kusakabe T." }, { "name": "Joly J.-S." }, { "name": "Darras S." }, { "name": "Christiaen L." }, { "name": "Contensin M." }, { "name": "Auger H." }, { "name": "Lamy C." }, { "name": "Hudson C." }, { "name": "Rothbacher U." }, { "name": "Gilchrist M.J." }, { "name": "Makabe K.W." }, { "name": "Hotta K." }, { "name": "Fujiwara S." }, { "name": "Satoh N." }, { "name": "Satou Y." }, { "name": "Lemaire P." } ], "journal": "Genome Research" } }, { "doi": "10.1016/j.cub.2005.12.044", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "2006", "note": null, "metadata": { "title": "A quantitative approach to the study of cell shapes and interactions during early chordate embryogenesis", "abstract": "Background: The prospects of deciphering the genetic program underlying embryonic development were recently boosted by the generation of large sets of precisely organized quantitative molecular data. In contrast, although the precise arrangement, interactions, and shapes of cells are crucial for the fulfilment of this program, their description remains coarse and qualitative. To bridge this gap, we developed a generic software, 3D Virtual Embryo, to quantify the geometry and interactions of cells in interactive three-dimensional embryo models. We applied this approach to early ascidian embryos, chosen because of their simplicity and their phylogenetic proximity to vertebrates. Results: We generated a collection of 19 interactive ascidian embryos between the 2- and 44-cell stages. We characterized the evolution with time, and in different cell lineages, of the volume of cells and of eight mathematical descriptors of their geometry, and we measured the surface of contact between neighboring blastomeres. These analyses first revealed that early embryonic blastomeres adopt a surprising variety of shapes, which appeared to be under strict and dynamic developmental control. Second, we found novel asymmetric cell divisions in the posterior vegetal lineages, which gave birth to sister cells with different fates. Third, during neural induction, differences in the area of contact between individual competent animal cells and inducing vegetal blastomeres appeared important to select the induced cells. Conclusions: In addition to novel insight into both cell-autonomous and inductive processes controlling early ascidian development, we establish a generic conceptual framework for the quantitative analysis of embryo geometry that can be applied to other model organisms. ©2006 Elsevier Ltd All rights reserved.", "date": "2006-02-21T00:00:00Z", "citationCount": 116, "authors": [ { "name": "Tassy O." }, { "name": "Daian F." }, { "name": "Hudson C." }, { "name": "Bertrand V." }, { "name": "Lemaire P." } ], "journal": "Current Biology" } }, { "doi": "10.1093/nar/gkz955", "pmid": null, "pmcid": null, "type": [], "version": "2019", "note": null, "metadata": { "title": "ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates", "abstract": "ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.", "date": "2020-01-01T00:00:00Z", "citationCount": 31, "authors": [ { "name": "Dardaillon J." }, { "name": "Dauga D." }, { "name": "Simion P." }, { "name": "Faure E." }, { "name": "Onuma T.A." }, { "name": "Debiasse M.B." }, { "name": "Louis A." }, { "name": "Nitta K.R." }, { "name": "Naville M." }, { "name": "Besnardeau L." }, { "name": "Reeves W." }, { "name": "Wang K." }, { "name": "Fagotto M." }, { "name": "Gueroult-Bellone M." }, { "name": "Fujiwara S." }, { "name": "Dumollard R." }, { "name": "Veeman M." }, { "name": "Volff J.-N." }, { "name": "Roest Crollius H." }, { "name": "Douzery E." }, { "name": "Ryan J.F." }, { "name": "Davidson B." }, { "name": "Nishida H." }, { "name": "Dantec C." }, { "name": "Lemaire P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkz955", "pmid": null, "pmcid": null, "type": [], "version": "2019", "note": null, "metadata": null } ], "credit": [ { "name": "Patrick Lemaire", "email": "patrick.lemaire@crbm.cnrs.fr", "url": "http://www.crbm.cnrs.fr/en/team/lemaire/", "orcidid": "https://orcid.org/0000-0003-4925-2009", "gridid": null, "rorid": "01xpc6869", "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Christelle Dantec", "email": "christelle.dantec@crbm.cnrs.fr", "url": "http://www.crbm.cnrs.fr/en/team/lemaire/", "orcidid": "https://orcid.org/0000-0001-7247-6460", "gridid": null, "rorid": "01xpc6869", "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": null, "email": "contact@aniseed.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null } ], "community": null, "owner": "cdantec", "additionDate": "2019-10-19T13:23:03Z", "lastUpdate": "2023-09-25T14:25:18.910230Z", "editPermission": { "type": "group", "authors": [ "delphinedauga" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MorphoNet", "description": "MorphoNet is an interactive morphodynamic web browser designed to help scientists, teachers and students share, analyze and visualize the large 3D morphological datasets that can be generated by modern imaging technology, ranging from live light sheet microscopy of cells and embryos to X Ray tomography of fossils.", "homepage": "https://morphonet.org", "biotoolsID": "morphonet", "biotoolsCURIE": "biotools:morphonet", "version": [ "2.1.3-35b3182" ], "otherID": [], "relation": [ { "biotoolsID": "aniseed", "type": "usedBy" }, { "biotoolsID": "aniseed", "type": "uses" }, { "biotoolsID": "ciona_robusta_anatomy_and_development_ontology", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal", "Desktop application", "Web application", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_3064", "term": "Developmental biology" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" }, { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://morphonet.org/help", "type": [ "Helpdesk", "Helpdesk" ], "note": null }, { "url": "https://www.aniseed.fr", "type": [ "Service" ], "note": null }, { "url": "https://twitter.com/MorphoTweet", "type": [ "Social media" ], "note": null } ], "download": [ { "url": "https://morphonet.org/downloads", "type": "Downloads page", "note": null, "version": null }, { "url": "https://morphonet.org/helpfiles/API/index.html", "type": "API specification", "note": null, "version": null } ], "documentation": [ { "url": "https://morphonet.org/help", "type": [ "General" ], "note": null }, { "url": "https://forum.image.sc/", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1038/s41467-019-10668-1", "pmid": null, "pmcid": "PMC6597584", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MorphoNet: an interactive online morphological browser to explore complex multi-scale data", "abstract": "Powerful novel imaging and image-processing methods are revolutionizing many fields of biology, at scales ranging from the molecule to the functional organ. To support this big-data revolution, we develop a concept of generic web-based morphodynamic browser to interactively visualize complex image datasets, with applications in research and education. MorphoNet handles a broad range of natural or simulated morphological data, onto which quantitative geometric or genetic data can be projected.", "date": "2019-12-01T00:00:00Z", "citationCount": 26, "authors": [ { "name": "Leggio B." }, { "name": "Laussu J." }, { "name": "Carlier A." }, { "name": "Godin C." }, { "name": "Lemaire P." }, { "name": "Faure E." } ], "journal": "Nature Communications" } }, { "doi": "10.1093/nar/gkz955", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates", "abstract": "ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.", "date": "2020-01-01T00:00:00Z", "citationCount": 31, "authors": [ { "name": "Dardaillon J." }, { "name": "Dauga D." }, { "name": "Simion P." }, { "name": "Faure E." }, { "name": "Onuma T.A." }, { "name": "Debiasse M.B." }, { "name": "Louis A." }, { "name": "Nitta K.R." }, { "name": "Naville M." }, { "name": "Besnardeau L." }, { "name": "Reeves W." }, { "name": "Wang K." }, { "name": "Fagotto M." }, { "name": "Gueroult-Bellone M." }, { "name": "Fujiwara S." }, { "name": "Dumollard R." }, { "name": "Veeman M." }, { "name": "Volff J.-N." }, { "name": "Roest Crollius H." }, { "name": "Douzery E." }, { "name": "Ryan J.F." }, { "name": "Davidson B." }, { "name": "Nishida H." }, { "name": "Dantec C." }, { "name": "Lemaire P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Emmanuel FAURE", "email": "emmanuel.faure@lirmm.fr", "url": null, "orcidid": "https://orcid.org/0000-0003-2787-0885", "gridid": null, "rorid": "013yean28", "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "cdantec", "additionDate": "2023-09-25T13:33:15.447513Z", "lastUpdate": "2023-09-25T14:12:08.944886Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CellTrackVis", "description": "interactive browser-based visualization for analyzing cell trajectories and lineages.", "homepage": "http://github.com/scbeom/celltrackvis", "biotoolsID": "celltrackvis", "biotoolsCURIE": "biotools:celltrackvis", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3890", "term": "Trajectory visualization" }, { "uri": "http://edamontology.org/operation_3446", "term": "Cell migration analysis" }, { "uri": "http://edamontology.org/operation_0244", "term": "Simulation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_3068", "term": "Literature and language" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://scbeom.github.io/ctv_tutorial", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1186/S12859-023-05218-Y", "pmid": "36991341", "pmcid": "PMC10053428", "type": [], "version": null, "note": null, "metadata": { "title": "CellTrackVis: interactive browser-based visualization for analyzing cell trajectories and lineages", "abstract": "Background: Automatic cell tracking methods enable practitioners to analyze cell behaviors efficiently. Notwithstanding the continuous development of relevant software, user-friendly visualization tools have room for further improvements. Typical visualization mostly comes with main cell tracking tools as a simple plug-in, or relies on specific software/platforms. Although some tools are standalone, limited visual interactivity is provided, or otherwise cell tracking outputs are partially visualized. Results: This paper proposes a self-reliant visualization system, CellTrackVis, to support quick and easy analysis of cell behaviors. Interconnected views help users discover meaningful patterns of cell motions and divisions in common web browsers. Specifically, cell trajectory, lineage, and quantified information are respectively visualized in a coordinated interface. In particular, immediate interactions among modules enable the study of cell tracking outputs to be more effective, and also each component is highly customizable for various biological tasks. Conclusions: CellTrackVis is a standalone browser-based visualization tool. Source codes and data sets are freely available at http://github.com/scbeom/celltrackvis with the tutorial at http://scbeom.github.io/ctv_tutorial.", "date": "2023-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Shim C." }, { "name": "Kim W." }, { "name": "Nguyen T.T.D." }, { "name": "Kim D.Y." }, { "name": "Choi Y.S." }, { "name": "Chung Y.D." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Yon Dohn Chung", "email": "ydchung@korea.ac.kr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-09-25T12:40:15.653732Z", "lastUpdate": "2023-09-25T12:40:15.656573Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "A2TEA", "description": "A2TEA is a software workflow facilitating identification of candidate genes for stress adaptation based on comparative genomics and transcriptomics. It combines differential gene expression with gene family expansion as an indicator for the evolution of adaptive traits.", "homepage": "https://github.com/tgstoecker/A2TEA.Workflow", "biotoolsID": "a2tea", "biotoolsCURIE": "biotools:a2tea", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression profiling" }, { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_3192", "term": "Sequence trimming" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [ { "uri": "http://edamontology.org/format_2306", "term": "GTF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3754", "term": "GO-term enrichment data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0928", "term": "Gene expression profile" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Workflow", "Web application", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python", "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/tgstoecker/A2TEA.WebApp", "type": [ "Repository" ], "note": null }, { "url": "https://tgstoecker.shinyapps.io/A2TEA-WebApp", "type": [ "Other" ], "note": null }, { "url": "https://tgstoecker.github.io/A2TEA.WebApp", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.12688/F1000RESEARCH.126463.2", "pmid": "37224329", "pmcid": "PMC10186066", "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Tyll Stöcker", "email": "tyll.stoecker@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0001-7184-9472", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Heiko Schoof", "email": "schoof@uni-bonn.de", "url": null, "orcidid": "https://orcid.org/0000-0002-1527-3752", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-09-22T11:57:14.178569Z", "lastUpdate": "2023-09-22T11:57:14.182267Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "DEPIB", "description": "Analysis pipeline using Snakemake for RNAseq analysis in order to find differentially expressed genes.", "homepage": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/RNAseq_quantif_pipeline", "biotoolsID": "DEPIB", "biotoolsCURIE": "biotools:DEPIB", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3800", "term": "RNA-Seq quantification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3768", "term": "Clustered expression profiles" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [], "language": [ "R", "Python" ], "license": null, "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/RNAseq_quantif_pipeline", "type": "Source code", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1002/stem.3014", "pmid": "30977188", "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Low-Dose Pesticide Mixture Induces Accelerated Mesenchymal Stem Cell Aging In Vitro", "abstract": "The general population is chronically exposed to multiple environmental contaminants such as pesticides. We have previously demonstrated that human mesenchymal stem cells (MSCs) exposed in vitro to low doses of a mixture of seven common pesticides showed a permanent phenotype modification with a specific induction of an oxidative stress-related senescence. Pesticide mixture also induced a shift in MSC differentiation toward adipogenesis. Thus, we hypothesized that common combination of pesticides may induce a premature cellular aging of adult MSCs. Our goal was to evaluate if the prolonged exposure to pesticide mixture could accelerate aging-related markers and in particular deteriorate the immunosuppressive properties of MSCs. MSCs exposed to pesticide mixture, under long-term culture and obtained from aging donor, were compared by bulk RNA sequencing analysis. Aging, senescence, and immunomodulatory markers were compared. The protein expression of cellular aging-associated metabolic markers and immune function of MSCs were analyzed. Functional analysis of the secretome impacts on immunomodulatory properties of MSCs was realized after 21 days' exposure to pesticide mixture. The RNA sequencing analysis of MSCs exposed to pesticide showed some similarities with cells from prolonged culture, but also with the MSCs of an aged donor. Changes in the metabolic markers MDH1, GOT and SIRT3, as well as an alteration in the modulation of active T cells and modifications in cytokine production are all associated with cellular aging. A modified functional profile was found with similarities to aging process. Stem Cells 2019;37:1083–1094.", "date": "2019-08-01T00:00:00Z", "citationCount": 12, "authors": [ { "name": "Leveque X." }, { "name": "Hochane M." }, { "name": "Geraldo F." }, { "name": "Dumont S." }, { "name": "Gratas C." }, { "name": "Oliver L." }, { "name": "Gaignier C." }, { "name": "Trichet V." }, { "name": "Layrolle P." }, { "name": "Heymann D." }, { "name": "Herault O." }, { "name": "Vallette F.M." }, { "name": "Olivier C." } ], "journal": "Stem Cells" } }, { "doi": "10.1038/s41419-019-2200-2", "pmid": null, "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Identification of a transient state during the acquisition of temozolomide resistance in glioblastoma", "abstract": "Drug resistance limits the therapeutic efficacy in cancers and leads to tumor recurrence through ill-defined mechanisms. Glioblastoma (GBM) are the deadliest brain tumors in adults. GBM, at diagnosis or after treatment, are resistant to temozolomide (TMZ), the standard chemotherapy. To better understand the acquisition of this resistance, we performed a longitudinal study, using a combination of mathematical models, RNA sequencing, single cell analyses, functional and drug assays in a human glioma cell line (U251). After an initial response characterized by cell death induction, cells entered a transient state defined by slow growth, a distinct morphology and a shift of metabolism. Specific genes expression associated to this population revealed chromatin remodeling. Indeed, the histone deacetylase inhibitor trichostatin (TSA), specifically eliminated this population and thus prevented the appearance of fast growing TMZ-resistant cells. In conclusion, we have identified in glioblastoma a population with tolerant-like features, which could constitute a therapeutic target.", "date": "2020-01-01T00:00:00Z", "citationCount": 40, "authors": [ { "name": "Rabe M." }, { "name": "Dumont S." }, { "name": "Alvarez-Arenas A." }, { "name": "Janati H." }, { "name": "Belmonte-Beitia J." }, { "name": "Calvo G.F." }, { "name": "Thibault-Carpentier C." }, { "name": "Sery Q." }, { "name": "Chauvin C." }, { "name": "Joalland N." }, { "name": "Briand F." }, { "name": "Blandin S." }, { "name": "Scotet E." }, { "name": "Pecqueur C." }, { "name": "Clairambault J." }, { "name": "Oliver L." }, { "name": "Perez-Garcia V." }, { "name": "Nadaradjane A." }, { "name": "Cartron P.-F." }, { "name": "Gratas C." }, { "name": "Vallette F.M." } ], "journal": "Cell Death and Disease" } } ], "credit": [ { "name": "Eric Charpentier", "email": "eric.charpentier@univ-nantes.fr", "url": "https://pf-bird.univ-nantes.fr/qui-sommes-nous-/membres/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Support" ], "note": null }, { "name": "Audrey Bihouée", "email": "audrey.bihouee@univ-nantes.fr", "url": "https://pf-bird.univ-nantes.fr/qui-sommes-nous-/membres/", "orcidid": "https://orcid.org/0000-0002-8689-2083", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "BiRD bioinformatics facility", "email": "pf-bird@univ-nantes.fr", "url": "https://pf-bird.univ-nantes.fr", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider" ], "note": null }, { "name": "Erwan Delage", "email": "erwan.delage@univ-nantes.fr", "url": "https://pf-bird.univ-nantes.fr/qui-sommes-nous-/membres/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Solenne Dumont", "email": "solenne.dumont@univ-nantes.fr", "url": "https://pf-bird.univ-nantes.fr/qui-sommes-nous-/membres/", "orcidid": "https://orcid.org/0000-0003-3237-7382", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Damien Vintache", "email": "Damien.Vintache@univ-nantes.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "community": null, "owner": "audrey.bihouee", "additionDate": "2019-09-24T13:59:07Z", "lastUpdate": "2023-09-19T15:06:32.072285Z", "editPermission": { "type": "group", "authors": [ "echarpentier" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "3SRP", "description": "A Snakemake-based pipeline for 3' sequencing RNA profiling data analysis. This 3’ Digital gene expression sequencing technique allows a precise and low-cost transcriptome profiling.\n\nThe main steps of the pipeline are:\n- Samples demultiplexing transform the raw paired-end fastq files into a single-end fastq file for each sample.\n- Alignment on refseq reference transcriptome is performed using bwa.\n- Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix.\nIf secondary analysis has been asked (providing a comparisons file), the expression matrix is normalized and differentially expressed genes (DEG) are searched using deseq2.\n- If DEG are found, annotation is performed using the database GO and KEGG.\n- A report is provided listing the main quality controls performed and the results found.\n\nCite : https://dx.doi.org/10.21203/rs.3.pex-1336/v1", "homepage": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline", "biotoolsID": "3SRP", "biotoolsCURIE": "biotools:3SRP", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2935", "term": "Clustering profile plotting" }, { "uri": "http://edamontology.org/operation_3563", "term": "RNA-seq read count analysis" }, { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression analysis" }, { "uri": "http://edamontology.org/operation_0531", "term": "Heat map generation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1931", "term": "FASTQ-illumina" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3768", "term": "Clustered expression profiles" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] }, { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": "First generate a configuration file and then run the pipeline with the Snakemake engine.", "cmd": "python SCRIPTS/make_dge_config.py -s TESTDATA/samplesheet.tsv -r TESTDATA/REFERENCES/ -w RESULTS -f TESTDATA/fastqFiles.txt -c TESTDATA/conditions.tsv --minGenes 0 --minReads 0 > config.json ; \nsnakemake -rp --config conf=\"config.json\"" } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [ "Linux" ], "language": [ "R", "Python" ], "license": null, "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/wikis/home", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/s41467-017-02107-w", "pmid": "29367672", "pmcid": "PMC5783949", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Parallel derivation of isogenic human primed and naive induced pluripotent stem cells", "abstract": "Induced pluripotent stem cells (iPSCs) have considerably impacted human developmental biology and regenerative medicine, notably because they circumvent the use of cells of embryonic origin and offer the potential to generate patient-specific pluripotent stem cells. However, conventional reprogramming protocols produce developmentally advanced, or primed, human iPSCs (hiPSCs), restricting their use to post-implantation human development modeling. Hence, there is a need for hiPSCs resembling preimplantation naive epiblast. Here, we develop a method to generate naive hiPSCs directly from somatic cells, using OKMS overexpression and specific culture conditions, further enabling parallel generation of their isogenic primed counterparts. We benchmark naive hiPSCs against human preimplantation epiblast and reveal remarkable concordance in their transcriptome, dependency on mitochondrial respiration and X-chromosome status. Collectively, our results are essential for the understanding of pluripotency regulation throughout preimplantation development and generate new opportunities for disease modeling and regenerative medicine.", "date": "2018-12-01T00:00:00Z", "citationCount": 78, "authors": [ { "name": "Kilens S." }, { "name": "Meistermann D." }, { "name": "Moreno D." }, { "name": "Chariau C." }, { "name": "Gaignerie A." }, { "name": "Reignier A." }, { "name": "Lelievre Y." }, { "name": "Casanova M." }, { "name": "Vallot C." }, { "name": "Nedellec S." }, { "name": "Flippe L." }, { "name": "Firmin J." }, { "name": "Song J." }, { "name": "Charpentier E." }, { "name": "Lammers J." }, { "name": "Donnart A." }, { "name": "Marec N." }, { "name": "Deb W." }, { "name": "Bihouee A." }, { "name": "Le Caignec C." }, { "name": "Pecqueur C." }, { "name": "Redon R." }, { "name": "Barriere P." }, { "name": "Bourdon J." }, { "name": "Pasque V." }, { "name": "Soumillon M." }, { "name": "Mikkelsen T.S." }, { "name": "Rougeulle C." }, { "name": "Freour T." }, { "name": "David L." }, { "name": "Abel L." }, { "name": "Alcover A." }, { "name": "Astrom K." }, { "name": "Bousso P." }, { "name": "Bruhns P." }, { "name": "Cumano A." }, { "name": "Duffy D." }, { "name": "Demangel C." }, { "name": "Deriano L." }, { "name": "DI Santo J." }, { "name": "Dromer F." }, { "name": "Eberl G." }, { "name": "Enninga J." }, { "name": "Fellay J." }, { "name": "Freitas A." }, { "name": "Gelpi O." }, { "name": "Gomperts-Boneca I." }, { "name": "Hercberg S." }, { "name": "Lantz O." }, { "name": "Leclerc C." }, { "name": "Mouquet H." }, { "name": "Patin E." }, { "name": "Pellegrini S." }, { "name": "Pol S." }, { "name": "Rogge L." }, { "name": "Sakuntabhai A." }, { "name": "Schwartz O." }, { "name": "Schwikowski B." }, { "name": "Shorte S." }, { "name": "Soumelis V." }, { "name": "Tangy F." }, { "name": "Tartour E." }, { "name": "Toubert A." }, { "name": "Ungeheuer M.-N." }, { "name": "Quintana-Murci L." }, { "name": "Albert M.L." } ], "journal": "Nature Communications" } }, { "doi": null, "pmid": "29445370", "pmcid": "PMC5797797", "type": [ "Usage" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1016/j.jaut.2017.10.005", "pmid": null, "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "An intermediate level of CD161 expression defines a novel activated, inflammatory, and pathogenic subset of CD8 + T cells involved in multiple sclerosis", "abstract": "Several lines of evidence support a key role for CD8 + T cells in central nervous system tissue damage of patients with multiple sclerosis. However, the precise phenotype of the circulating CD8 + T cells that may be recruited from the peripheral blood to invade the CNS remains largely undefined to date. It has been suggested that IL-17 secreting CD8 (Tc17) T cells may be involved, and in humans these cells are characterized by the expression of CD161. We focused our study on a unique and recently described subset of CD8 T cells characterized by an intermediate expression of CD161 as its role in neuroinflammation has not been investigated to date. The frequency, phenotype, and function of CD8 + T cells with an intermediate CD161 expression level were characterized ex-vivo, in vitro, and in situ using RNAseq, RT-PCR, flow cytometry, TCR sequencing, and immunohistofluorescence of cells derived from healthy volunteers (n = 61), MS subjects (n = 90), as well as inflammatory (n = 15) and non-inflammatory controls (n = 6). We report here that CD8 + CD161 int T cells present characteristics of effector cells, up-regulate cell-adhesion molecules and have an increased ability to cross the blood-brain barrier and to secrete IL-17, IFNγ GM-CSF, and IL-22. We further demonstrate that these cells are recruited and enriched in the CNS of MS subjects where they produce IL-17. In the peripheral blood, RNAseq, RT-PCR, high-throughput TCR repertoire analyses, and flow cytometry confirmed an increased effector and transmigration pattern of these cells in MS patients, with the presence of supernumerary clones compared to healthy controls. Our data demonstrate that intermediate levels of CD161 expression identifies activated and effector CD8 + T cells with pathogenic properties that are recruited to MS lesions. This suggests that CD161 may represent a biomarker and a valid target for the treatment of neuroinflammation.", "date": "2018-03-01T00:00:00Z", "citationCount": 17, "authors": [ { "name": "Nicol B." }, { "name": "Salou M." }, { "name": "Vogel I." }, { "name": "Garcia A." }, { "name": "Dugast E." }, { "name": "Morille J." }, { "name": "Kilens S." }, { "name": "Charpentier E." }, { "name": "Donnart A." }, { "name": "Nedellec S." }, { "name": "Jacq-Foucher M." }, { "name": "Le Frere F." }, { "name": "Wiertlewski S." }, { "name": "Bourreille A." }, { "name": "Brouard S." }, { "name": "Michel L." }, { "name": "David L." }, { "name": "Gourraud P.-A." }, { "name": "Degauque N." }, { "name": "Nicot A.B." }, { "name": "Berthelot L." }, { "name": "Laplaud D.-A." } ], "journal": "Journal of Autoimmunity" } }, { "doi": "10.1172/jci.insight.90088", "pmid": "28194440", "pmcid": "PMC5291739", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Transient antibody targeting of CD45RC induces transplant tolerance and potent antigen-specific regulatory T cells", "abstract": "Rat and human CD4+ and CD8+ Tregs expressing low levels of CD45RC have strong immunoregulatory properties. We describe here that human CD45 isoforms are nonredundant and identify distinct subsets of cells. We show that CD45RC is not expressed by CD4+ and CD8+ Foxp3+ Tregs, while CD45RA/RB/RO are. Transient administration of a monoclonal antibody (mAb) targeting CD45RC in a rat cardiac allotransplantation model induced transplant tolerance associated with inhibition of allogeneic humoral responses but maintained primary and memory responses against cognate antigens. Anti-CD45RC mAb induced rapid death of CD45RChigh T cells through intrinsic cell signaling but preserved and potentiated CD4+ and CD8+ CD45RClow/- Tregs, which are able to adoptively transfer donor-specific tolerance to grafted recipients. Anti-CD45RC treatment results in distinct transcriptional signature of CD4+ and CD8+ CD45RClow/- Tregs. Finally, we demonstrate that anti-human CD45RC treatment inhibited graft-versus-host disease (GVHD) in immune-humanized NSG mice. Thus, short-term anti-CD45RC is a potent therapeutic candidate to induce transplantation tolerance in human.", "date": "2017-02-09T00:00:00Z", "citationCount": 34, "authors": [ { "name": "Picarda E." }, { "name": "Bezie S." }, { "name": "Boucault L." }, { "name": "Autrusseau E." }, { "name": "Kilens S." }, { "name": "Meistermann D." }, { "name": "Martinet B." }, { "name": "Daguin V." }, { "name": "Donnart A." }, { "name": "Charpentier E." }, { "name": "David L." }, { "name": "Anegon I." }, { "name": "Guillonneau C." } ], "journal": "JCI Insight" } }, { "doi": "10.1038/s41598-017-14892-x", "pmid": "29116112", "pmcid": "PMC5676863", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "A Comparison of mRNA Sequencing with Random Primed and 3′-Directed Libraries", "abstract": "reating a cDNA library for deep mRNA sequencing (mRNAseq) is generally done by random priming, creating multiple sequencing fragments along each transcript. A 3′-end-focused library approach cannot detect differential splicing, but has potentially higher throughput at a lower cost, along with the ability to improve quantification by using transcript molecule counting with unique molecular identifiers (UMI) that correct PCR bias. Here, we compare an implementation of such a 3′-digital gene expression (3′-DGE) approach with \"conventional\" random primed mRNAseq. Given our particular datasets on cultured human cardiomyocyte cell lines, we find that, while conventional mRNAseq detects ∼15% more genes and needs ∼500,000 fewer reads per sample for equivalent statistical power, the resulting differentially expressed genes, biological conclusions, and gene signatures are highly concordant between two techniques. We also find good quantitative agreement at the level of individual genes between two techniques for both read counts and fold changes between given conditions. We conclude that, for high-throughput applications, the potential cost savings associated with 3′-DGE approach are likely a reasonable tradeoff for modest reduction in sensitivity and inability to observe alternative splicing, and should enable many larger scale studies focusing on not only differential expression analysis, but also quantitative transcriptome profiling.", "date": "2017-12-01T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Xiong Y." }, { "name": "Soumillon M." }, { "name": "Wu J." }, { "name": "Hansen J." }, { "name": "Hu B." }, { "name": "Van Hasselt J.G.C." }, { "name": "Jayaraman G." }, { "name": "Lim R." }, { "name": "Bouhaddou M." }, { "name": "Ornelas L." }, { "name": "Bochicchio J." }, { "name": "Lenaeus L." }, { "name": "Stocksdale J." }, { "name": "Shim J." }, { "name": "Gomez E." }, { "name": "Sareen D." }, { "name": "Svendsen C." }, { "name": "Thompson L.M." }, { "name": "Mahajan M." }, { "name": "Iyengar R." }, { "name": "Sobie E.A." }, { "name": "Azeloglu E.U." }, { "name": "Birtwistle M.R." } ], "journal": "Scientific Reports" } }, { "doi": "10.3390/ijms21041368", "pmid": null, "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Characterization of glyceollins as novel aryl hydrocarbon receptor ligands and their role in cell migration", "abstract": "Recent studies strongly support the use of the aryl hydrocarbon receptor (AhR) as a therapeutic target in breast cancer. Glyceollins, a group of soybean phytoalexins, are known to exert therapeutic effects in chronic human diseases and also in cancer. To investigate the interaction between glyceollin I (GI), glyceollin II (GII) and AhR, a computational docking analysis, luciferase assays, immunofluorescence and transcriptome analyses were performed with different cancer cell lines. The docking experiments predicted that GI and GII can enter into the AhR binding pocket, but their interactions with the amino acids of the binding site differ, in part, from those interacting with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Both GI and GII were able to weakly and partially activate AhR, with GII being more potent. The results from the transcriptome assays showed that approximately 10% of the genes regulated by TCDD were also modified by both GI and GII, which could have either antagonistic or synergistic effects upon TCDD activation. In addition, we report here, on the basis of phenotype, that GI and GII inhibit the migration of triple-negative (ER-, PgR-, HER2NEU-) MDA-MB-231 breast cancer cells, and that they inhibit the expression of genes which code for important regulators of cell migration and invasion in cancer tissues. In conclusion, GI and GII are AhR ligands that should be further investigated to determine their usefulness in cancer treatments.", "date": "2020-02-02T00:00:00Z", "citationCount": 8, "authors": [ { "name": "Pham T.H." }, { "name": "Lecomte S." }, { "name": "Le Guevel R." }, { "name": "Lardenois A." }, { "name": "Evrard B." }, { "name": "Chalmel F." }, { "name": "Ferriere F." }, { "name": "Balaguer P." }, { "name": "Efstathiou T." }, { "name": "Pakdel F." } ], "journal": "International Journal of Molecular Sciences" } }, { "doi": "10.3390/nu12051464", "pmid": "32438566", "pmcid": "PMC7284977", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Maternal protein restriction in rats alters the expression of genes involved in mitochondrial metabolism and epitranscriptomics in fetal hypothalamus", "abstract": "Fetal brain development is closely dependent on maternal nutrition and metabolic status. Maternal protein restriction (PR) is known to be associated with alterations in the structure and function of the hypothalamus, leading to impaired control of energy homeostasis and food intake. The objective of this study was to identify the cellular and molecular systems underlying these effects during fetal development. We combined a global transcriptomic analysis on the fetal hypothalamus from a rat model of maternal PR with in vitro neurosphere culture and cellular analyses. Several genes encoding proteins from the mitochondrial respiratory chain complexes were overexpressed in the PR group and mitochondrial metabolic activity in the fetal hypothalamus was altered. The level of the N6-methyladenosine epitranscriptomic mark was reduced in the PR fetuses, and the expression of several genes involved in the writing/erasing/reading of this mark was indeed altered, as well as genes encoding several RNA-binding proteins. Additionally, we observed a higher number of neuronal-committed progenitors at embryonic day 17 (E17) in the PR fetuses. Together, these data strongly suggest a metabolic adaptation to the amino acid shortage, combined with the post-transcriptional control of protein expression, which might reflect alterations in the control of the timing of neuronal progenitor differentiation.", "date": "2020-05-01T00:00:00Z", "citationCount": 5, "authors": [ { "name": "Frapin M." }, { "name": "Guignard S." }, { "name": "Meistermann D." }, { "name": "Grit I." }, { "name": "Moulle V.S." }, { "name": "Paille V." }, { "name": "Parnet P." }, { "name": "Amarger V." } ], "journal": "Nutrients" } }, { "doi": "10.1038/s41419-020-2505-1", "pmid": null, "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Dual targeting of BCL2 and MCL1 rescues myeloma cells resistant to BCL2 and MCL1 inhibitors associated with the formation of BAX/BAK hetero-complexes", "abstract": "Multiple myeloma is a plasma cell malignancy that escapes from apoptosis by heterogeneously over-expressing anti-apoptotic BCL2 proteins. Myeloma cells with a t(11;14) translocation present a particular vulnerability to BCL2 inhibition while a majority of myeloma cells relies on MCL1 for survival. The present study aimed to determine whether the combination of BCL2 and MCL1 inhibitors at low doses could be of benefit for myeloma cells beyond the single selective inhibition of BCL2 or MCL1. We identified that half of patients were not efficiently targeted neither by BCL2 inhibitor nor MCL1 inhibitor. Seventy percent of these myeloma samples, either from patients at diagnosis or relapse, presented a marked increase of apoptosis upon low dose combination of both inhibitors. Interestingly, primary cells from a patient in progression under venetoclax treatment were not sensitive ex vivo to neither venetoclax nor to MCL1 inhibitor, whereas the combination of both efficiently induced cell death. This finding suggests that the combination could overcome venetoclax resistance. The efficacy of the combination was also confirmed in U266 xenograft model resistant to BCL2 and MCL1 inhibitors. Mechanistically, we demonstrated that the combination of both inhibitors favors apoptosis in a BAX/BAK dependent manner. We showed that activated BAX was readily increased upon the inhibitor combination leading to the formation of BAK/BAX hetero-complexes. We found that BCLXL remains a major resistant factor of cell death induced by this combination. The present study supports a rational for the clinical use of venetoclax/S63845 combination in myeloma patients with the potential to elicit significant clinical activity when both single inhibitors would not be effective but also to overcome developed in vivo venetoclax resistance.", "date": "2020-05-01T00:00:00Z", "citationCount": 27, "authors": [ { "name": "Seiller C." }, { "name": "Maiga S." }, { "name": "Touzeau C." }, { "name": "Bellanger C." }, { "name": "Kervoelen C." }, { "name": "Descamps G." }, { "name": "Maillet L." }, { "name": "Moreau P." }, { "name": "Pellat-Deceunynck C." }, { "name": "Gomez-Bougie P." }, { "name": "Amiot M." } ], "journal": "Cell Death and Disease" } }, { "doi": "10.1016/j.celrep.2020.108419", "pmid": null, "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Induction of Human Trophoblast Stem Cells from Somatic Cells and Pluripotent Stem Cells", "abstract": "Human trophoblast stem cells (hTSCs) derived from blastocysts and first-trimester cytotrophoblasts offer an unprecedented opportunity to study the placenta. However, access to human embryos and first-trimester placentas is limited, thus preventing the establishment of hTSCs from diverse genetic backgrounds associated with placental disorders. Here, we show that hTSCs can be generated from numerous genetic backgrounds using post-natal cells via two alternative methods: (1) somatic cell reprogramming of adult fibroblasts with OCT4, SOX2, KLF4, MYC (OSKM) and (2) cell fate conversion of naive and extended pluripotent stem cells. The resulting induced/converted hTSCs recapitulated hallmarks of hTSCs including long-term self-renewal, expression of specific transcription factors, transcriptomic signature, and the potential to differentiate into syncytiotrophoblast and extravillous trophoblast cells. We also clarified the developmental stage of hTSCs and show that these cells resemble day 8 cytotrophoblasts. Altogether, hTSC lines of diverse genetic origins open the possibility to model both placental development and diseases in a dish. Castel et al. report the generation of patient-specific human induced trophoblast stem cells via two methods: (1) somatic cell reprogramming with OSKM and (2) conversion of naive and extended hiPSCs. Their findings open avenues to study placental diseases and relations between the trophoblast lineage, pluripotency, and the human embryo.", "date": "2020-11-24T00:00:00Z", "citationCount": 84, "authors": [ { "name": "Castel G." }, { "name": "Meistermann D." }, { "name": "Bretin B." }, { "name": "Firmin J." }, { "name": "Blin J." }, { "name": "Loubersac S." }, { "name": "Bruneau A." }, { "name": "Chevolleau S." }, { "name": "Kilens S." }, { "name": "Chariau C." }, { "name": "Gaignerie A." }, { "name": "Francheteau Q." }, { "name": "Kagawa H." }, { "name": "Charpentier E." }, { "name": "Flippe L." }, { "name": "Francois--Campion V." }, { "name": "Haider S." }, { "name": "Dietrich B." }, { "name": "Knofler M." }, { "name": "Arima T." }, { "name": "Bourdon J." }, { "name": "Rivron N." }, { "name": "Masson D." }, { "name": "Fournier T." }, { "name": "Okae H." }, { "name": "Freour T." }, { "name": "David L." } ], "journal": "Cell Reports" } }, { "doi": "10.21203/rs.3.pex-1336/v1", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Eric Charpentier", "email": "eric.charpentier@univ-nantes.fr", "url": "https://pf-bird.univ-nantes.fr/about-us/members/", "orcidid": "https://orcid.org/0000-0002-8571-7603", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Support" ], "note": null }, { "name": "BiRD bioinformatics facility", "email": "pf-bird@univ-nantes.fr", "url": "https://pf-bird.univ-nantes.fr", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider", "Support" ], "note": null }, { "name": "Solenne Dumont", "email": "solenne.dumont@univ-nantes.fr", "url": "https://pf-bird.univ-nantes.fr/qui-sommes-nous-/membres/", "orcidid": "https://orcid.org/0000-0003-3237-7382", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Dimitri MEISTERMANN", "email": "dimitri.meistermann@univ-nantes.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Broad Institute", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": "Some scripts of the pipeline regarding sample demultiplexing and UMI counting have been adapated and modified from this paper:\nXiong, Y., Soumillon, M., Wu, J. et al. A Comparison of mRNA Sequencing with Random Primed and 3′-Directed Libraries. Sci Rep 7, 14626 (2017)." }, { "name": "Philippe Bordron", "email": "philippe.bordron@univ-nantes.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Audrey Bihouée", "email": "audrey.bihouee@univ-nantes.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-8689-2083", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "community": null, "owner": "alban.gaignard@univ-nantes.fr", "additionDate": "2019-08-30T10:28:42Z", "lastUpdate": "2023-09-19T14:54:48.081069Z", "editPermission": { "type": "group", "authors": [ "audrey.bihouee", "echarpentier" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SynBioTools", "description": "A catalog of tools for synthetic biology.", "homepage": "https://synbiotools.lifesynther.com/", "biotoolsID": "synbiotools", "biotoolsCURIE": "biotools:synbiotools", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3907", "term": "Information extraction" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3895", "term": "Synthetic biology" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3068", "term": "Literature and language" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": "Freeware", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/S12859-023-05281-5", "pmid": "37069545", "pmcid": "PMC10111727", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "SynBioTools: a one-stop facility for searching and selecting synthetic biology tools", "abstract": "Background: The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry or catalog addresses all aspects of synthetic biology. Results: We constructed SynBioTools, a comprehensive collection of synthetic biology databases, computational tools, and experimental methods, as a one-stop facility for searching and selecting synthetic biology tools. SynBioTools includes databases, computational tools, and methods extracted from reviews via SCIentific Table Extraction, a scientific table-extraction tool that we built. Approximately 57% of the resources that we located and included in SynBioTools are not mentioned in bio.tools, the dominant tool registry. To improve users’ understanding of the tools and to enable them to make better choices, the tools are grouped into nine modules (each with subdivisions) based on their potential biosynthetic applications. Detailed comparisons of similar tools in every classification are included. The URLs, descriptions, source references, and the number of citations of the tools are also integrated into the system. Conclusions: SynBioTools is freely available at https://synbiotools.lifesynther.com/. It provides end-users and developers with a useful resource of categorized synthetic biology databases, tools, and methods to facilitate tool retrieval and selection.", "date": "2023-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Cai P." }, { "name": "Liu S." }, { "name": "Zhang D." }, { "name": "Xing H." }, { "name": "Han M." }, { "name": "Liu D." }, { "name": "Gong L." }, { "name": "Hu Q.-N." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Qian-Nan Hu", "email": "qnhu@sibs.ac.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-09-18T11:55:41.488018Z", "lastUpdate": "2023-09-18T11:55:41.490558Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Cellcano", "description": "Supervised cell type identification for single-cell ATAC-seq data.", "homepage": "https://marvinquiet.github.io/Cellcano/", "biotoolsID": "cellcano", "biotoolsCURIE": "biotools:cellcano", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_0417", "term": "PTM site prediction" }, { "uri": "http://edamontology.org/operation_0313", "term": "Expression profile clustering" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3173", "term": "Epigenomics" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_3940", "term": "Chromosome conformation capture" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python", "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/marvinquiet/Cellcano", "type": [ "Repository" ], "note": null }, { "url": "https://pypi.org/project/Cellcano/", "type": [ "Repository" ], "note": null }, { "url": "https://anaconda.org/marvinquiet/cellcano-all", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/S41467-023-37439-3", "pmid": "37012226", "pmcid": "PMC10070275", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Cellcano: supervised cell type identification for single cell ATAC-seq data", "abstract": "Computational cell type identification is a fundamental step in single-cell omics data analysis. Supervised celltyping methods have gained increasing popularity in single-cell RNA-seq data because of the superior performance and the availability of high-quality reference datasets. Recent technological advances in profiling chromatin accessibility at single-cell resolution (scATAC-seq) have brought new insights to the understanding of epigenetic heterogeneity. With continuous accumulation of scATAC-seq datasets, supervised celltyping method specifically designed for scATAC-seq is in urgent need. Here we develop Cellcano, a computational method based on a two-round supervised learning algorithm to identify cell types from scATAC-seq data. The method alleviates the distributional shift between reference and target data and improves the prediction performance. After systematically benchmarking Cellcano on 50 well-designed celltyping tasks from various datasets, we show that Cellcano is accurate, robust, and computationally efficient. Cellcano is well-documented and freely available at https://marvinquiet.github.io/Cellcano/.", "date": "2023-12-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Ma W." }, { "name": "Lu J." }, { "name": "Wu H." } ], "journal": "Nature Communications" } } ], "credit": [ { "name": "Hao Wu", "email": "wuhao@siat.ac.cn", "url": null, "orcidid": "https://orcid.org/0000-0003-1269-7354", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-09-18T10:03:04.971037Z", "lastUpdate": "2023-09-18T10:03:04.974549Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "dbMisLoc", "description": "A manually curated database of conditional protein mis-localization events.", "homepage": "https://dbml.pufengdu.org", "biotoolsID": "dbmisloc", "biotoolsCURIE": "biotools:dbmisloc", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_2489", "term": "Subcellular localisation prediction" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data submission, annotation and curation" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "JavaScript" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/quinlanW/dbMisLoc", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1007/S12539-023-00564-0", "pmid": "37000408", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "dbMisLoc: A Manually Curated Database of Conditional Protein Mis-localization Events", "abstract": "Over the last few years, an increasing number of protein mis-localization events have been reported under various conditions. It is important to understand these events and their relationship with complex disorders. Although many efforts had been made in establishing models with statistical or machine learning algorithms, a comprehensive database resource is still missing. Since the records of experimental-validated protein mis-localization events spread across many literatures, a collection of all these reports in a unique website is demanded. In this paper, we created the dbMisLoc database by manually curating conditional protein mis-localization events from various literatures. The dbMisLoc database records the protein localizations, mis-localizations, conditions for mis-localization, and the original reports. The dbMisLoc database allows the users to intuitively view, search, visualize and download protein mis-localization records. The dbMisLoc database integrates a BLAST search engine, which can search mis-localized proteins that are similar to user queries. The dbMisLoc database can be accessed directly through (https://dbml.pufengdu.org). The source code of dbMisLoc database is available from the GitHub repository (https://github.com/quinlanW/dbMisLoc) for free. Users can host their own mirrors of dbMisLoc database on their own servers. Graphical Abstract: [Figure not available: see fulltext.].", "date": "2023-09-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Wang R.-H." }, { "name": "Luo T." }, { "name": "Guo Y.-P." }, { "name": "Yang Z.-X." }, { "name": "Zhang H.-Y." }, { "name": "Hao H.-Y." }, { "name": "Du P.-F." } ], "journal": "Interdisciplinary Sciences – Computational Life Sciences" } } ], "credit": [ { "name": "Pu-Feng Du", "email": "pdu@tju.edu.cn", "url": null, "orcidid": "http://orcid.org/0000-0001-9897-3932", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-09-15T19:15:23.358224Z", "lastUpdate": "2023-09-15T19:15:23.360850Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "OTTERS", "description": "TWAS framework leveraging summary-level reference data.", "homepage": "https://github.com/daiqile96/OTTERS", "biotoolsID": "otters", "biotoolsCURIE": "biotools:otters", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3557", "term": "Imputation" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_0244", "term": "Simulation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_3517", "term": "GWAS study" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python", "R", "Shell" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/daiqile96/OTTERS_paper", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/S41467-023-36862-W", "pmid": "36882394", "pmcid": "PMC9992663", "type": [], "version": null, "note": null, "metadata": { "title": "OTTERS: a powerful TWAS framework leveraging summary-level reference data", "abstract": "Most existing TWAS tools require individual-level eQTL reference data and thus are not applicable to summary-level reference eQTL datasets. The development of TWAS methods that can harness summary-level reference data is valuable to enable TWAS in broader settings and enhance power due to increased reference sample size. Thus, we develop a TWAS framework called OTTERS (Omnibus Transcriptome Test using Expression Reference Summary data) that adapts multiple polygenic risk score (PRS) methods to estimate eQTL weights from summary-level eQTL reference data and conducts an omnibus TWAS. We show that OTTERS is a practical and powerful TWAS tool by both simulations and application studies.", "date": "2023-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Dai Q." }, { "name": "Zhou G." }, { "name": "Zhao H." }, { "name": "Vosa U." }, { "name": "Franke L." }, { "name": "Battle A." }, { "name": "Teumer A." }, { "name": "Lehtimaki T." }, { "name": "Raitakari O.T." }, { "name": "Esko T." }, { "name": "Agbessi M." }, { "name": "Ahsan H." }, { "name": "Alves I." }, { "name": "Andiappan A.K." }, { "name": "Arindrarto W." }, { "name": "Awadalla P." }, { "name": "Battle A." }, { "name": "Beutner F." }, { "name": "Jan Bonder M." }, { "name": "Boomsma D.I." }, { "name": "Christiansen M.W." }, { "name": "Claringbould A." }, { "name": "Deelen P." }, { "name": "Fave M.-J." }, { "name": "Frayling T." }, { "name": "Gharib S.A." }, { "name": "Gibson G." }, { "name": "Heijmans B.T." }, { "name": "Hemani G." }, { "name": "Jansen R." }, { "name": "Kahonen M." }, { "name": "Kalnapenkis A." }, { "name": "Kasela S." }, { "name": "Kettunen J." }, { "name": "Kim Y." }, { "name": "Kirsten H." }, { "name": "Kovacs P." }, { "name": "Krohn K." }, { "name": "Kronberg J." }, { "name": "Kukushkina V." }, { "name": "Kutalik Z." }, { "name": "Lee B." }, { "name": "Loeffler M." }, { "name": "Marigorta U.M." }, { "name": "Mei H." }, { "name": "Milani L." }, { "name": "Montgomery G.W." }, { "name": "Muller-Nurasyid M." }, { "name": "Nauck M." }, { "name": "Nivard M.G." }, { "name": "Penninx B." }, { "name": "Perola M." }, { "name": "Pervjakova N." }, { "name": "Pierce B.L." }, { "name": "Powell J." }, { "name": "Prokisch H." }, { "name": "Psaty B.M." }, { "name": "Ripatti S." }, { "name": "Rotzschke O." }, { "name": "Rueger S." }, { "name": "Saha A." }, { "name": "Scholz M." }, { "name": "Schramm K." }, { "name": "Seppala I." }, { "name": "Slagboom E.P." }, { "name": "Stehouwer C.D.A." }, { "name": "Stumvoll M." }, { "name": "Sullivan P." }, { "name": "'t Hoen P.A.C." }, { "name": "Thiery J." }, { "name": "Tong L." }, { "name": "Tonjes A." }, { "name": "van Dongen J." }, { "name": "van Iterson M." }, { "name": "van Meurs J." }, { "name": "Veldink J.H." }, { "name": "Verlouw J." }, { "name": "Visscher P.M." }, { "name": "Volker U." }, { "name": "Westra H.-J." }, { "name": "Wijmenga C." }, { "name": "Yaghootka H." }, { "name": "Yang J." }, { "name": "Zeng B." }, { "name": "Zhang F." }, { "name": "Epstein M.P." }, { "name": "Yang J." } ], "journal": "Nature Communications" } } ], "credit": [ { "name": "Michael P. Epstein", "email": "mpepste@emory.edu", "url": null, "orcidid": "https://orcid.org/0000-0001-9647-9738", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Jingjing Yang", "email": "jingjing.yang@emory.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-4191-4138", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Qile Dai", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Geyu Zhou", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Hongyu Zhao", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-09-15T17:25:38.681022Z", "lastUpdate": "2023-09-15T17:25:38.683660Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" } ] }