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{ "count": 1095, "next": "?page=2", "previous": null, "list": [ { "name": "iSnoDi-MDRF", "description": "Identifying snoRNA-disease associations based on multiple biological data by ranking framework.", "homepage": "http://bliulab.net/iSnoDi-MDRF/", "biotoolsID": "isnodi_mdrf", "biotoolsCURIE": "biotools:isnodi_mdrf", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1772", "term": "Score" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_3361", "term": "Laboratory techniques" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1109/TCBB.2023.3258448", "pmid": "37030816", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "iSnoDi-MDRF: identifying snoRNA-disease associations based on multiple biological data by ranking framework", "abstract": "Accumulating evidence indicates that the dysregulation of small nucleolar RNAs (snoRNAs) is relevant with diseases. Identifying snoRNA-disease associations by computational methods is desired for biologists, which can save considerable costs and time compared biological experiments. However, it still faces some challenges as followings: (i) Many snoRNAs are detected in recent years, but only a few snoRNAs have been proved to be associated with diseases; (ii) Computational predictors trained with only a few known snoRNA-disease associations fail to accurately identify the snoRNA-disease associations. In this study, we propose a ranking framework, called iSnoDi-MDRF, to identify potential snoRNA-disease associations based on multiple biological data, which has the following highlights: (i) iSnoDi-MDRF integrates ranking framework, which is not only able to identify potential associations between known snoRNAs and diseases, but also can identify diseases associated with new snoRNAs. (ii) Known gene-disease associations are employed to help train a mature model for predicting snoRNA-disease association. Experimental results illustrate that iSnoDi-MDRF is very suitable for identifying potential snoRNA-disease associations. The web server of iSnoDi-MDRF predictor is freely available at <uri>http://bliulab.net/iSnoDi-MDRF/</uri>.", "date": "2023-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Zhang W." }, { "name": "Liu B." } ], "journal": "IEEE/ACM Transactions on Computational Biology and Bioinformatics" } } ], "credit": [ { "name": "Bin Liu", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-3685-9469", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-09-25T17:45:48.313559Z", "lastUpdate": "2023-09-25T17:45:48.316096Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ANISEED", "description": "ANISEED is the main model organism database for the worldwide community of scientists working on tunicates (sister-group of vertebrates). 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": "includes" }, { "biotoolsID": "go", "type": "uses" }, { "biotoolsID": "morphonet", "type": "uses" }, { "biotoolsID": "morphonet", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0567", "term": "Phylogenetic tree visualisation" }, { "uri": "http://edamontology.org/operation_3208", "term": "Genome visualisation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" }, { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" }, { "uri": "http://edamontology.org/operation_2478", "term": "Nucleic acid sequence analysis" }, { "uri": "http://edamontology.org/operation_2495", "term": "Expression analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2042", "term": "Evidence" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2042", "term": "Evidence" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Ontology", "Web API", "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_3064", "term": "Developmental biology" }, { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" }, { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data submission, annotation and curation" }, { "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": "SSA", "description": "SSA (Signal Search Analysis) is a software package for the analysis of nucleic acid sequence motifs that are postionally correlated with a functional site (e.g a transcription or translation initiation site).", "homepage": "https://epd.expasy.org/ssa/", "biotoolsID": "ssa", "biotoolsCURIE": "biotools:ssa", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_0238", "term": "Sequence motif discovery" }, { "uri": "http://edamontology.org/operation_0240", "term": "Sequence motif comparison" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl", "Fortran", "C" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://epd.expasy.org/ssa/doc/ssa_tutorial.php", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": null, "pmid": "12824379", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Signal search analysis server", "abstract": "Signal search analysis is a general method to discover and characterize sequence motifs that are positionally correlated with a functional site (e.g. a transcription or translation start site). The method has played an instrumental role in the analysis of eukaryotic promoter elements. The signal search analysis server provides access to four different computer programs as well as to a large number of precompiled functional site collections. The programs offered allow: (i) the identification of non-random sequence regions under evolutionary constraint; (ii) the detection of consensus sequence-based motifs that are over- or under-represented at a particular distance from a functional site; (iii) the analysis of the positional distribution of a consensus sequence- or weight matrix-based sequence motif around a functional site; and (iv) the optimization of a weight matrix description of a locally over-represented sequence motif. These programs can be accessed at: http://www.isrec.isb-sib.ch/ssa/.", "date": "2003-07-01T00:00:00Z", "citationCount": 20, "authors": [ { "name": "Ambrosini G." }, { "name": "Praz V." }, { "name": "Jagannathan V." }, { "name": "Bucher P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "SIB Swiss Institute of Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "Prof. Philipp Bucher", "email": "epd@sib.swiss", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "sduvaud", "additionDate": "2017-01-13T13:16:40Z", "lastUpdate": "2023-09-05T10:29:08.667997Z", "editPermission": { "type": "group", "authors": [ "metanetx" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HaploDX", "description": "The HaploDX library provides a collection of functions to generate simulated population-specific genomic data in VCF format. The library includes parameters and functions to control mutation rates, linkage disequilibrium strength and block lengths, and number of individuals. 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However, analyzing miRNA-Seq data can be challenging because it requires multiple steps, from quality control and preprocessing to differential expression and pathway-enrichment analyses, with many tools and databases available for each step. Furthermore, reproducibility of the analysis pipeline is crucial to ensure that the results are accurate and reliable. Here, we present myBrain-Seq, a comprehensive and reproducible pipeline for analyzing miRNA-Seq data that incorporates miRNA-specific solutions at each step of the analysis. The pipeline was designed to be flexible and user-friendly, allowing researchers with different levels of expertise to perform the analysis in a standardized and reproducible manner, using the most common and widely used tools for each step. In this work, we describe the implementation of myBrain-Seq and demonstrate its capacity to consistently and reproducibly identify differentially expressed miRNAs and enriched pathways by applying it to a real case study in which we compared schizophrenia patients who responded to medication with treatment-resistant schizophrenia patients to obtain a 16-miRNA treatment-resistant schizophrenia profile.", "date": "2023-04-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Perez-Rodriguez D." }, { "name": "Agis-Balboa R.C." }, { "name": "Lopez-Fernandez H." } ], "journal": "Biomedicines" } }, { "doi": "10.1007/978-3-031-17024-9_4", "pmid": null, "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Towards a Flexible and Portable Workflow for Analyzing miRNA-Seq Neuropsychiatric Data: An Initial Replicability Assessment", "abstract": "In the last decade, miRNAs have attracted noticeable interest as potential biomarkers of neuropsychiatric conditions. However, a standard methodology for miRNA-Seq analysis does not yet exist, raising concerns about the reproducibility of the in-silico results and limiting their usefulness. This situation motivated us to design a miRNA-Seq pipeline specialized in the analysis of neuropsychiatric data, aiming to integrate the results of several bioinformatics tools in a highly reproducible workflow. In this study, we performed an initial test of the usefulness of our new pipeline, named myBrain-Seq, by reanalyzing four recent miRNA-Seq studies of neuropsychiatric conditions. We then compared the myBrain-Seq results with the original results and with an additional reanalysis done with another pipeline in order to make an estimation of the overall replicability. We found one of the three myBrain-Seq methodologies to be the one with best replicability, although the heterogeneity of the results and the absence of an experimental validation limits our conclusions. Further work is required to assess myBrain-Seq’ performance using a bigger dataset of studies with experimental validation data available.", "date": "2023-01-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Perez-Rodriguez D." }, { "name": "Perez-Rodriguez M." }, { "name": "Agis-Balboa R.C." }, { "name": "Lopez-Fernandez H." } ], "journal": "Lecture Notes in Networks and Systems" } }, { "doi": "10.1007/978-3-030-86258-9_5", "pmid": null, "pmcid": null, "type": [ "Review" ], "version": null, "note": null, "metadata": { "title": "On the Reproducibility of MiRNA-Seq Differential Expression Analyses in Neuropsychiatric Diseases", "abstract": "MiRNAs are attracting considerable interest as potential biomarkers on neuropsychiatric diseases due to their expression plasticity. In the last decade, a large number of studies have been published in this regard with promising results; however, there is widespread concern about the reproducibility of these results. This study aims to compare the differentially expressed miRNAs reported by 5 recent studies of neuropsychiatric diseases, with those obtained through the miARma-Seq pipeline [1]. In general, we found a low reproducibility (0–74%), and some variations related to the software used for the differential expression analysis. Our results support the idea that miRNAs reported as potential biomarkers in neuropsychiatric diseases are strongly correlated with the analytical methodology and the biological references used; nonetheless, further research is needed to establish the magnitude of this problem and spot its main causes.", "date": "2022-01-01T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Perez-Rodriguez D." }, { "name": "Lopez-Fernandez H." }, { "name": "Agis-Balboa R.C." } ], "journal": "Lecture Notes in Networks and Systems" } }, { "doi": "10.3390/ijms24031891", "pmid": null, "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "MiRNA Differences Related to Treatment-Resistant Schizophrenia", "abstract": "Schizophrenia (SZ) is a serious mental disorder that is typically treated with antipsychotic medication. Treatment-resistant schizophrenia (TRS) is the condition where symptoms remain after pharmacological intervention, resulting in long-lasting functional and social impairments. As the identification and treatment of a TRS patient requires previous failed treatments, early mechanisms of detection are needed in order to quicken the access to effective therapy, as well as improve treatment adherence. In this study, we aim to find a microRNA (miRNA) signature for TRS, as well as to shed some light on the molecular pathways potentially involved in this severe condition. To do this, we compared the blood miRNAs of schizophrenia patients that respond to medication and TRS patients, thus obtaining a 16-miRNA TRS profile. Then, we assessed the ability of this signature to separate responders and TRS patients using hierarchical clustering, observing that most of them are grouped correctly (~70% accuracy). We also conducted a network, pathway analysis, and bibliography search to spot molecular pathways potentially altered in TRS. We found that the response to stress seems to be a key factor in TRS and that proteins p53, SIRT1, MDM2, and TRIM28 could be the potential mediators of such responses. Finally, we suggest a molecular pathway potentially regulated by the miRNAs of the TRS profile.", "date": "2023-02-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Perez-Rodriguez D." }, { "name": "Penedo M.A." }, { "name": "Rivera-Baltanas T." }, { "name": "Pena-Centeno T." }, { "name": "Burkhardt S." }, { "name": "Fischer A." }, { "name": "Prieto-Gonzalez J.M." }, { "name": "Olivares J.M." }, { "name": "Lopez-Fernandez H." }, { "name": "Agis-Balboa R.C." } ], "journal": "International Journal of Molecular Sciences" } }, { "doi": "10.1016/j.compbiomed.2021.104603", "pmid": null, "pmcid": null, "type": [ "Review" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daniel Pérez-Rodríguez", "email": "daniel.prz.rodriguez@gmail.com", "url": "https://www.linkedin.com/in/daniel-p%C3%A9rez-rodr%C3%ADguez-26a921264/", "orcidid": "https://orcid.org/0000-0002-8110-3567", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Hugo López-Fernández", "email": "hlfernandez@uvigo.gal", "url": "https://es.linkedin.com/in/hugo-l%C3%B3pez-fern%C3%A1ndez-80307589", "orcidid": "https://orcid.org/0000-0002-6476-7206", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Roberto Carlos Agís-Balboa", "email": "roberto.carlos.agis.balboa@sergas.es", "url": "https://es.linkedin.com/in/robertocarlosagisbalboa", "orcidid": "https://orcid.org/0000-0001-9899-9569", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "dannyzimm", "additionDate": "2023-05-31T07:46:01.760391Z", "lastUpdate": "2023-05-31T07:46:52.130710Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }