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{ "count": 724, "next": "?page=2", "previous": null, "list": [ { "name": "SwissTree", "description": "Aims to provide a collection of 100 Gold Standard gene phylogenies to the scientific community. This set of reference gene trees is suitable for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure. SwissTree is used for benchmarking at the Orthology Benchmarking web service.", "homepage": "https://swisstree.sib.swiss/", "biotoolsID": "swisstree", "biotoolsCURIE": "biotools:swisstree", "version": [], "otherID": [ { "value": "RRID:SCR_015881", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0552", "term": "Phylogenetic tree bootstrapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://swisstree.sib.swiss/ftp/", "type": "Biological data", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1093/gbe/evv121", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream", "abstract": "Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated the congruency between existing species trees by comparing the relationships of 147 QfO reference organisms from six Tree of Life (ToL)/species tree projects: The National Center for Biotechnology Information (NCBI) taxonomy, Opentree of Life, the sequenced species/species ToL, the 16S ribosomal RNA (rRNA) database, and trees published by Ciccarelli et al. (Ciccarelli FD, et al. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287) and by Huerta-Cepas et al. (Huerta-Cepas J, Marcet-Houben M, Gabaldon T. 2014. A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life. PeerJ PrePrints 2:223) Our study reveals that each species tree suggests a different phylogeny: 87 of the 146 (60%) possible splits of a dichotomous and rooted tree are congruent, while all other splits are incongruent in at least one of the species trees. Topological differences are observed not only at deep speciation events, but also within younger clades, such as Hominidae, Rodentia, Laurasiatheria, or rosids. The evolutionary relationships of 27 archaea and bacteria are highly inconsistent. By assessing 458,108 gene trees from 65 genomes, we show that consistent species topologies are more often supported by gene phylogenies than contradicting ones. The largest concordant species tree includes 77 of the QfO reference organisms at the most. Results are summarized in the form of a consensus ToL (http://swisstree.vital-it.ch/species-tree) that can serve different benchmarking purposes.", "date": "2015-07-01T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Boeckmann B." }, { "name": "Marcet-Houben M." }, { "name": "Rees J.A." }, { "name": "Forslund K." }, { "name": "Huerta-Cepas J." }, { "name": "Muffato M." }, { "name": "Yilmaz P." }, { "name": "Xenarios I." }, { "name": "Bork P." }, { "name": "Lewis S.E." }, { "name": "Gabaldon T." } ], "journal": "Genome Biology and Evolution" } } ], "credit": [ { "name": null, "email": "swisstree@lists.isb-sib.ch", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "SIB", "additionDate": "2017-10-18T08:45:13Z", "lastUpdate": "2023-09-14T15:13:54.070720Z", "editPermission": { "type": "group", "authors": [ "smoretti" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "JASPAR", "description": "JASPAR is a high-quality, open-access database that provides manually curated, non-redundant transcription factor (TF) binding profiles for six taxonomic groups (fungi, insecta, nematoda, plantae, urochordata, vertebrata). These profiles are stored as position frequency matrices (PFMs), which can be transformed into models to predict TF binding sites (TFBS) in DNA sequences. The database collects motifs both internally, analyzing sequences using a custom motif discovery pipeline, and externally from publications and other resources. All selected motifs are manually curated for quality and supporting evidence. JASPAR now offers a tool for TFBS enrichment analysis in user-provided genomic regions. Data is accessible through the JASPAR website, its RESTful API, Bioconductor, or the Python package pyJASPAR.", "homepage": "http://jaspar.genereg.net/", "biotoolsID": "jaspar", "biotoolsCURIE": "biotools:jaspar", "version": [], "otherID": [ { "value": "RRID:SCR_003030", "type": "rrid", "version": null } ], "relation": [ { "biotoolsID": "jaspar_api", "type": "usedBy" }, { "biotoolsID": "tfbstools", "type": "usedBy" }, { "biotoolsID": "tfmotifview", "type": "usedBy" }, { "biotoolsID": "jaspextract", "type": "usedBy" }, { "biotoolsID": "aimodules", "type": "usedBy" }, { "biotoolsID": "bioconductor", "type": "uses" }, { "biotoolsID": "biocfilecache", "type": "uses" }, { "biotoolsID": "biopython", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2755", "term": "Transcription factor name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1077", "term": "Transcription factor identifier" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1868", "term": "Taxon" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2732", "term": "Family name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1045", "term": "Species name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2291", "term": "UniProt ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3671", "term": "Text" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1119", "term": "JASPAR profile ID" }, "format": [ { "uri": "http://edamontology.org/format_1367", "term": "JASPAR format" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3750", "term": "YAML" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0445", "term": "Transcription factor binding site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1119", "term": "JASPAR profile ID" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1119", "term": "JASPAR profile ID" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" }, { "uri": "http://edamontology.org/topic_0749", "term": "Transcription factors and regulatory sites" }, { "uri": "http://edamontology.org/topic_0204", "term": "Gene regulation" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_2815", "term": "Human biology" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "CC-BY-4.0", "collectionID": [ "ELIXIR-NO", "ELIXIR-Norway", "JASPAR" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Norway" ], "elixirCommunity": [ "Federated Human Data", "Plant Sciences" ], "link": [ { "url": "https://groups.google.com/g/jaspar", "type": [ "Discussion forum" ], "note": null }, { "url": "https://bitbucket.org/CBGR/jaspar/src/master/", "type": [ "Repository" ], "note": null }, { "url": "https://elixir.no/helpdesk", "type": [ "Helpdesk" ], "note": "Helpdesk and support for ELIXIR Norway services" }, { "url": "https://doi.org/10.5281/zenodo.6860527", "type": [ "Repository" ], "note": null }, { "url": "https://doi.org/10.5281/zenodo.6860555", "type": [ "Repository" ], "note": null }, { "url": "https://bioconductor.org/packages/release/data/annotation/html/JASPAR2022.html", "type": [ "Software catalogue" ], "note": null }, { "url": "https://pypi.org/project/pyjaspar/", "type": [ "Software catalogue" ], "note": null }, { "url": "https://twitter.com/jaspar_db", "type": [ "Social media" ], "note": null } ], "download": [ { "url": "http://jaspar.genereg.net/downloads/", "type": "Downloads page", "note": null, "version": null }, { "url": "https://jaspar.genereg.net/api/", "type": "API specification", "note": null, "version": null }, { "url": "https://github.com/asntech/pyjaspar", "type": "Source code", "note": "Repository for pyJASPAR", "version": null } ], "documentation": [ { "url": "http://jaspar.genereg.net/docs/", "type": [ "General", "Governance" ], "note": null }, { "url": "http://jaspar.genereg.net/faq/", "type": [ "FAQ" ], "note": null }, { "url": "http://jaspar.genereg.net/api/v1/docs/", "type": [ "API documentation" ], "note": null }, { "url": "https://pyjaspar.readthedocs.io/en/latest/", "type": [ "Citation instructions", "Command-line options", "Installation instructions", "User manual" ], "note": "Documentation for pyJASPAR" }, { "url": "https://bioconductor.org/packages/release/data/annotation/vignettes/JASPAR2022/inst/doc/JASPAR2022.html", "type": [ "Command-line options", "User manual" ], "note": "Documentation for the Bioconductor package" } ], "publication": [ { "doi": "10.1093/nar/gkab1113", "pmid": "34850907", "pmcid": "PMC8728201", "type": [ "Primary" ], "version": "9", "note": null, "metadata": { "title": "JASPAR 2022: The 9th release of the open-access database of transcription factor binding profiles", "abstract": "JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.", "date": "2022-01-07T00:00:00Z", "citationCount": 356, "authors": [ { "name": "Castro-Mondragon J.A." }, { "name": "Riudavets-Puig R." }, { "name": "Rauluseviciute I." }, { "name": "Berhanu Lemma R." }, { "name": "Turchi L." }, { "name": "Blanc-Mathieu R." }, { "name": "Lucas J." }, { "name": "Boddie P." }, { "name": "Khan A." }, { "name": "Perez N.M." }, { "name": "Fornes O." }, { "name": "Leung T.Y." }, { "name": "Aguirre A." }, { "name": "Hammal F." }, { "name": "Schmelter D." }, { "name": "Baranasic D." }, { "name": "Ballester B." }, { "name": "Sandelin A." }, { "name": "Lenhard B." }, { "name": "Vandepoele K." }, { "name": "Wasserman W.W." }, { "name": "Parcy F." }, { "name": "Mathelier A." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkz1001", "pmid": "31701148", "pmcid": "PMC7145627", "type": [ "Primary" ], "version": "8", "note": null, "metadata": { "title": "JASPAR 2020: Update of the open-Access database of transcription factor binding profiles", "abstract": "JASPAR (http://jaspar.genereg.net) is an open-Access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups. In this 8th release of JASPAR, the CORE collection has been expanded with 245 new PFMs (169 for vertebrates, 42 for plants, 17 for nematodes, 10 for insects, and 7 for fungi), and 156 PFMs were updated (125 for vertebrates, 28 for plants and 3 for insects). These new profiles represent an 18% expansion compared to the previous release. JASPAR 2020 comes with a novel collection of unvalidated TF-binding profiles for which our curators did not find orthogonal supporting evidence in the literature. This collection has a dedicated web form to engage the community in the curation of unvalidated TF-binding profiles. Moreover, we created a Q&A forum to ease the communication between the user community and JASPAR curators. Finally, we updated the genomic tracks, inference tool, and TF-binding profile similarity clusters. All the data is available through the JASPAR website, its associated RESTful API, and through the JASPAR2020 R/Bioconductor package.", "date": "2020-01-01T00:00:00Z", "citationCount": 996, "authors": [ { "name": "Fornes O." }, { "name": "Castro-Mondragon J.A." }, { "name": "Khan A." }, { "name": "Van Der Lee R." }, { "name": "Zhang X." }, { "name": "Richmond P.A." }, { "name": "Modi B.P." }, { "name": "Correard S." }, { "name": "Gheorghe M." }, { "name": "Baranasic D." }, { "name": "Santana-Garcia W." }, { "name": "Tan G." }, { "name": "Cheneby J." }, { "name": "Ballester B." }, { "name": "Parcy F." }, { "name": "Sandelin A." }, { "name": "Lenhard B." }, { "name": "Wasserman W.W." }, { "name": "Mathelier A." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkx1126", "pmid": "29140473", "pmcid": "PMC5753243", "type": [ "Primary" ], "version": "2018", "note": null, "metadata": { "title": "JASPAR 2018: Update of the open-access database of transcription factor binding profiles and its web framework", "abstract": "JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition, we have introduced 316 TFFMs (95 for vertebrates, 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package.", "date": "2018-01-01T00:00:00Z", "citationCount": 879, "authors": [ { "name": "Khan A." }, { "name": "Fornes O." }, { "name": "Stigliani A." }, { "name": "Gheorghe M." }, { "name": "Castro-Mondragon J.A." }, { "name": "Van Der Lee R." }, { "name": "Bessy A." }, { "name": "Cheneby J." }, { "name": "Kulkarni S.R." }, { "name": "Tan G." }, { "name": "Baranasic D." }, { "name": "Arenillas D.J." }, { "name": "Sandelin A." }, { "name": "Vandepoele K." }, { "name": "Lenhard B." }, { "name": "Ballester B." }, { "name": "Wasserman W.W." }, { "name": "Parcy F." }, { "name": "Mathelier A." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/bioinformatics/btx804", "pmid": "29253085", "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "JASPAR RESTful API: Accessing JASPAR data from any programming language", "abstract": "JASPAR is a widely used open-access database of curated, non-redundant transcription factor binding profiles. Currently, data from JASPAR can be retrieved as flat files or by using programming language-specific interfaces. Here, we present a programming language-independent application programming interface (API) to access JASPAR data using the Representational State Transfer (REST) architecture. The REST API enables programmatic access to JASPAR by most programming languages and returns data in eight widely used formats. Several endpoints are available to access the data and an endpoint is available to infer the TF binding profile(s) likely bound by a given DNA binding domain protein sequence. Additionally, it provides an interactive browsable interface for bioinformatics tool developers. Availability and implementation This REST API is implemented in Python using the Django REST Framework. It is accessible at http://jaspar.genereg.net/api/ and the source code is freely available at https://bitbucket.org/CBGR/jaspar under GPL v3 license. Contact aziz.khan@ncmm.uio.no or anthony.mathelier@ncmm.uio.no Supplementary informationSupplementary dataare available at Bioinformatics online.", "date": "2018-05-01T00:00:00Z", "citationCount": 11, "authors": [ { "name": "Khan A." }, { "name": "Mathelier A." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/nar/gkv1176", "pmid": "26531826", "pmcid": null, "type": [ "Primary" ], "version": "2016", "note": null, "metadata": { "title": "JASPAR 2016: A major expansion and update of the open-access database of transcription factor binding profiles", "abstract": "JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release.", "date": "2016-01-01T00:00:00Z", "citationCount": 717, "authors": [ { "name": "Mathelier A." }, { "name": "Fornes O." }, { "name": "Arenillas D.J." }, { "name": "Chen C.-Y." }, { "name": "Denay G." }, { "name": "Lee J." }, { "name": "Shi W." }, { "name": "Shyr C." }, { "name": "Tan G." }, { "name": "Worsley-Hunt R." }, { "name": "Zhang A.W." }, { "name": "Parcy F." }, { "name": "Lenhard B." }, { "name": "Sandelin A." }, { "name": "Wasserman W.W." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkt997", "pmid": "24194598", "pmcid": null, "type": [ "Primary" ], "version": "5.0_ALPHA", "note": null, "metadata": { "title": "JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles", "abstract": "JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly expands the heart of JASPAR - the JASPAR CORE subcollection, which contains curated, non-redundant profiles - with 135 new curated profiles (74 in vertebrates, 8 in Drosophila melanogaster, 10 in Caenorhabditis elegans and 43 in Arabidopsis thaliana; a 30% increase in total) and 43 older updated profiles (36 in vertebrates, 3 in D. melanogaster and 4 in A. thaliana; a 9% update in total). The new and updated profiles are mainly derived from published chromatin immunoprecipitation-seq experimental datasets. In addition, the web interface has been enhanced with advanced capabilities in browsing, searching and subsetting. Finally, the new JASPAR release is accompanied by a new BioPython package, a new R tool package and a new R/Bioconductor data package to facilitate access for both manual and automated methods. © 2013 The Author(s). Published by Oxford University Press.", "date": "2014-01-01T00:00:00Z", "citationCount": 789, "authors": [ { "name": "Mathelier A." }, { "name": "Zhao X." }, { "name": "Zhang A.W." }, { "name": "Parcy F." }, { "name": "Worsley-Hunt R." }, { "name": "Arenillas D.J." }, { "name": "Buchman S." }, { "name": "Chen C.-Y." }, { "name": "Chou A." }, { "name": "Ienasescu H." }, { "name": "Lim J." }, { "name": "Shyr C." }, { "name": "Tan G." }, { "name": "Zhou M." }, { "name": "Lenhard B." }, { "name": "Sandelin A." }, { "name": "Wasserman W.W." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkp950", "pmid": "19906716", "pmcid": null, "type": [ "Primary" ], "version": "4", "note": null, "metadata": { "title": "JASPAR 2010: The greatly expanded open-access database of transcription factor binding profiles", "abstract": "JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. Its fourth major release is the largest expansion of the core database to date: the database now holds 457 non-redundant, curated profiles. The new entries include the first batch of profiles derived from ChIP-seq and ChIP-chip whole-genome binding experiments, and 177 yeast TF binding profiles. The introduction of a yeast division brings the convenience of JASPAR to an active research community. As binding models are refined by newer data, the JASPAR database now uses versioning of matrices: in this release, 12% of the older models were updated to improved versions. Classification of TF families has been improved by adopting a new DNA-binding domain nomenclature. A curated catalog of mammalian TFs is provided, extending the use of the JASPAR profiles to additional TFs belonging to the same structural family. The changes in the database set the system ready for more rapid acquisition of new high-throughput data sources. Additionally, three new special collections provide matrix profile data produced by recent alternative high-throughput approaches. © The Author(s) 2009. Published by Oxford University Press.", "date": "2009-11-10T00:00:00Z", "citationCount": 478, "authors": [ { "name": "Portales-Casamar E." }, { "name": "Thongjuea S." }, { "name": "Kwon A.T." }, { "name": "Arenillas D." }, { "name": "Zhao X." }, { "name": "Valen E." }, { "name": "Yusuf D." }, { "name": "Lenhard B." }, { "name": "Wasserman W.W." }, { "name": "Sandelin A." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkm955", "pmid": "18006571", "pmcid": null, "type": [ "Primary" ], "version": "3", "note": null, "metadata": { "title": "JASPAR, the open access database of transcription factor-binding profiles: New content and tools in the 2008 update", "abstract": "JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with additional functions aimed at both casual and power users. The heart of the JASPAR database - the JASPAR CORE sub-database - has increased by 12% in size, and three new specialized sub-databases have been added. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval. JASPAR is available at http://jaspar.genereg.net. © 2007 The Author(s).", "date": "2008-01-01T00:00:00Z", "citationCount": 550, "authors": [ { "name": "Bryne J.C." }, { "name": "Valen E." }, { "name": "Tang M.-H.E." }, { "name": "Marstrand T." }, { "name": "Winther O." }, { "name": "Da piedade I." }, { "name": "Krogh A." }, { "name": "Lenhard B." }, { "name": "Sandelin A." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkj115", "pmid": "16381983", "pmcid": null, "type": [ "Primary" ], "version": "2", "note": null, "metadata": null }, { "doi": "10.1093/nar/gkh012", "pmid": "14681366", "pmcid": null, "type": [ "Primary" ], "version": "1", "note": null, "metadata": null } ], "credit": [ { "name": "Albin Sandelin", "email": "albin@binf.ku.dk", "url": "https://albinsandelin.wixsite.com/sandelinlab", "orcidid": "http://orcid.org/0000-0002-7109-7378", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null 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"note": null }, { "name": "Jérémy Lucas", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-2252-4732", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Nicolás Manosalva Pérez", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-1559-7802", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Ieva Rauluseviciute", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-9253-8825", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Rafael Riudavets-Puig", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-2855-9952", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Daniel Schmelter", "email": null, 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It is a complete upgrade and rewrite of earlier Clustal programs. This unit describes how to run Clustal Omega interactively from a command line, although it can also be run online from several sites. The unit describes a basic protocol for taking a set of unaligned sequences and producing a full alignment. There are also protocols for using an external HMM or iteration to help improve an alignment.", "date": "2014-01-01T00:00:00Z", "citationCount": 323, "authors": [ { "name": "Sievers F." }, { "name": "Higgins D.G." } ], "journal": "Current Protocols in Bioinformatics" } }, { "doi": "10.1093/nar/gkac240", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Search and sequence analysis tools services from EMBL-EBI in 2022", "abstract": "The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. 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The capacity of machine learning (ML) to identify complex discriminative sequence patterns renders it an ideal approach for AIRR-based diagnostic and therapeutic discovery. So far, widespread adoption of AIRR ML has been inhibited by a lack of reproducibility, transparency and interoperability. immuneML (immuneml.uio.no) addresses these concerns by implementing each step of the AIRR ML process in an extensible, open-source software ecosystem that is based on fully specified and shareable workflows. To facilitate widespread user adoption, immuneML is available as a command-line tool and through an intuitive Galaxy web interface, and extensive documentation of workflows is provided. We demonstrate the broad applicability of immuneML by (1) reproducing a large-scale study on immune state prediction, (2) developing, integrating and applying a novel deep learning method for antigen specificity prediction and (3) showcasing streamlined interpretability-focused benchmarking of AIRR ML.", "date": "2021-11-01T00:00:00Z", "citationCount": 17, "authors": [ { "name": "Pavlovic M." }, { "name": "Scheffer L." }, { "name": "Motwani K." }, { "name": "Kanduri C." }, { "name": "Kompova R." }, { "name": "Vazov N." }, { "name": "Waagan K." }, { "name": "Bernal F.L.M." }, { "name": "Costa A.A." }, { "name": "Corrie B." }, { "name": "Akbar R." }, { "name": "Al Hajj G.S." }, { "name": "Balaban G." }, { "name": "Brusko T.M." }, { "name": "Chernigovskaya M." }, { "name": "Christley S." }, { "name": "Cowell L.G." }, { "name": "Frank R." }, { "name": "Grytten I." }, { "name": "Gundersen S." }, { "name": "Haff I.H." }, { "name": "Hovig E." }, { "name": "Hsieh P.-H." }, { "name": "Klambauer G." }, { "name": "Kuijjer M.L." }, { "name": "Lund-Andersen C." }, { "name": "Martini A." }, { "name": "Minotto T." }, { "name": "Pensar J." }, { "name": "Rand K." }, { "name": "Riccardi E." }, { "name": "Robert P.A." }, { "name": "Rocha A." }, { "name": "Slabodkin A." }, { "name": "Snapkov I." }, { "name": "Sollid L.M." }, { "name": "Titov D." }, { "name": "Weber C.R." }, { "name": "Widrich M." }, { "name": "Yaari G." }, { "name": "Greiff V." }, { "name": "Sandve G.K." } ], "journal": "Nature Machine Intelligence" } } ], "credit": [ { "name": "Sandve Research Group for Biomedical Informatics", "email": "contact@immuneml.uio.no", "url": "https://sandvelab.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer", "Support" ], "note": null }, { "name": "Geir Kjetil Sandve", "email": "geirksa@ifi.uio.no", "url": "https://www.mn.uio.no/sbi/english/groups/sandve-group/", "orcidid": "https://orcid.org/0000-0002-4959-1409", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer", "Support" ], "note": null }, { "name": "Milena Pavlović", "email": "contact@immuneml.uio.no", "url": null, "orcidid": "https://orcid.org/0000-0002-2484-3868", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Documentor" ], "note": null }, { "name": "Lonneke Scheffer", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-8900-075X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Documentor" ], "note": null }, { "name": "Keshav Motwani", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-1457-2731", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "University of Oslo", "email": null, "url": null, "orcidid": null, "gridid": "grid.55325.34", "rorid": "00j9c2840", "fundrefid": "10.13039/501100005366", "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk", "email": "support@elixir.no", "url": "https://elixir.no/helpdesk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Support" ], "note": null }, { "name": "Victor Greiff", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-2622-5032", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Rahmad Akbar", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-6692-0876", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Ghadi S. Al Hajj", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-1639-1424", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Alexandre Almeida Costa", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Gabriel Balaban", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-6794-9611", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Fabian L. M. 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Robert", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-1345-5015", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Andrei Slabodkin", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9320-1666", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Dmytro Titov", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-1607-5405", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Nikolay Vazov", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Knut Waagan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Cédric R. Weber", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-4802-8996", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Michael Widrich", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-5721-0135", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Erin Calhoun", "email": "erin.calhoun@uit.no", "url": null, "orcidid": "https://orcid.org/0009-0003-3752-7156", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": "Curation of bio.tools profile - please contact me with updates/corrections" } ], "community": null, "owner": "Kigaard", "additionDate": "2021-09-27T08:24:14.939476Z", "lastUpdate": "2023-08-04T08:01:14.040850Z", "editPermission": { "type": "group", "authors": [ "eca008" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "CHOPCHOP", "description": "CHOPCHOP is a versatile tool for selecting target sites for CRISPR (Cas9, Cas9 nickase, Cas13, Cpf1/CasX) or TALEN-directed mutagenesis. The latest release of CHOPCHOP (version 3) includes many new features and visualization options, supporting over 200 genomes with whole-gene targeting and versatile search modes. The tool now enables precise RNA targeting with Cas13, supporting alternative transcript isoforms and predicting RNA accessibility using ViennaRNA's RNAfold. The update also introduces new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes. For larger queries or handling unsupported genomes, a command-line version is available with additional functionalities. CHOPCHOP v3 is user-friendly and well-equipped to support diverse targeting applications, facilitating effective experimental design.", "homepage": "http://chopchop.cbu.uib.no/", "biotoolsID": "chopchop", "biotoolsCURIE": "biotools:chopchop", "version": [ "1", "2", "3" ], "otherID": [ { "value": "RRID:SCR_015723", "type": "rrid", "version": "3" } ], "relation": [ { "biotoolsID": "blat", "type": "uses" }, { "biotoolsID": "bowtie", "type": "includes" }, { "biotoolsID": "primer3", "type": "includes" }, { "biotoolsID": "vienna_rna_package", "type": "uses" }, { "biotoolsID": "biopython", "type": "uses" }, { "biotoolsID": "pandas", "type": "uses" }, { "biotoolsID": "numpy", "type": "uses" }, { "biotoolsID": "scikit-learn", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" }, { "uri": "http://edamontology.org/operation_2419", "term": "Primer and probe design" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3497", "term": "DNA sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_2031", "term": "Gene annotation format" }, { "uri": "http://edamontology.org/format_2078", "term": "Sequence range format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2295", "term": "Gene ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1190", "term": "Tool name" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [] } ], "note": "Input target can be specified using gene IDs that are retrieved from the ENSEMBL (ensGene) and RefSeq (refGene) tables from the UCSC genome browser or FASTA file with target sequence of interest. Also we allow input to be specific coordinates e.g. chr1:3000-4000.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0925", "term": "Sequence assembly" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_1975", "term": "GFF3" } ] }, { "data": { "uri": "http://edamontology.org/data_1045", "term": "Species name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2295", "term": "Gene ID" }, "format": [] } ], "output": [], "note": "For adding a new genome to CHOPCHOP by email", "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3912", "term": "Genetic engineering" }, { "uri": "http://edamontology.org/topic_3511", "term": "Nucleic acid sites, features and motifs" }, { "uri": "http://edamontology.org/topic_3678", "term": "Experimental design and studies" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "ELIXIR-NO", "ELIXIR-Norway", "UiB tools" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Norway" ], "elixirCommunity": [ "Federated Human Data", "Plant Sciences", "Rare Diseases" ], "link": [ { "url": "https://bitbucket.org/valenlab/chopchop/", "type": [ "Repository", "Issue tracker" ], "note": "Command-line tool for running CHOPCHOP locally." }, { "url": "https://elixir.no/helpdesk", "type": [ "Helpdesk" ], "note": "Helpdesk and support for ELIXIR Norway services" } ], "download": [ { "url": "https://bitbucket.org/valenlab/chopchop/downloads/", "type": "Downloads page", "note": "Download repository", "version": null }, { "url": "https://bitbucket.org/valenlab/chopchop/src/master/", "type": "Source code", "note": "Latest release as of 3 August 2023", "version": "3" }, { "url": "https://bitbucket.org/valenlab/chopchop/src/CHOPCHOPv2/", "type": "Source code", "note": null, "version": "2" }, { "url": "https://bitbucket.org/valenlab/chopchop/src/develop/", "type": "Source code", "note": null, "version": "1" } ], "documentation": [ { "url": "http://chopchop.cbu.uib.no/instructions", "type": [ "User manual" ], "note": null }, { "url": "https://bitbucket.org/valenlab/chopchop/src/master/README.md", "type": [ "Command-line options" ], "note": null }, { "url": "http://chopchop.cbu.uib.no/faq", "type": [ "Citation instructions", "FAQ" ], "note": null }, { "url": "https://developer.atlassian.com/cloud/bitbucket/rest/api-group-downloads/#api-group-downloads", "type": [ "API documentation" ], "note": "Bitbucket REST API documentation" } ], "publication": [ { "doi": "10.1093/nar/gkz365", "pmid": "31106371", "pmcid": "PMC6602426", "type": [ "Primary" ], "version": "3", "note": null, "metadata": { "title": "CHOPCHOP v3: Expanding the CRISPR web toolbox beyond genome editing", "abstract": "The CRISPR-Cas system is a powerful genome editing tool that functions in a diverse array of organisms and cell types. The technology was initially developed to induce targeted mutations in DNA, but CRISPR-Cas has now been adapted to target nucleic acids for a range of purposes. CHOPCHOP is a web tool for identifying CRISPR-Cas single guide RNA (sgRNA) targets. In this major update of CHOPCHOP, we expand our toolbox beyond knockouts. We introduce functionality for targeting RNA with Cas13, which includes support for alternative transcript isoforms and RNA accessibility predictions. We incorporate new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes. Finally, we expand our results page visualization to reveal alternative isoforms and downstream ATG sites, which will aid users in avoiding the expression of truncated proteins. The CHOPCHOP web tool now supports over 200 genomes and we have released a command-line script for running larger jobs and handling unsupported genomes. CHOPCHOP v3 can be found at https://chopchop.cbu.uib.no", "date": "2019-07-01T00:00:00Z", "citationCount": 600, "authors": [ { "name": "Labun K." }, { "name": "Montague T.G." }, { "name": "Krause M." }, { "name": "Torres Cleuren Y.N." }, { "name": "Tjeldnes H." }, { "name": "Valen E." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1002/cpz1.46", "pmid": "33905612", "pmcid": null, "type": [ "Usage" ], "version": "3", "note": null, "metadata": { "title": "CRISPR Genome Editing Made Easy Through the CHOPCHOP Website", "abstract": "The design of optimal guide RNA (gRNA) sequences for CRISPR systems is challenged by the need to achieve highly efficient editing at the desired location (on-target editing) with minimal editing at unintended locations (off-target editing). Although laboratory validation should ideally be used to detect off-target activity, computational predictions are almost always preferred in practice due to their speed and low cost. Several studies have therefore explored gRNA-DNA interactions in order to understand how CRISPR complexes select their genomic targets. CHOPCHOP (https://chopchop.cbu.uib.no/) leverages these developments to build a user-friendly web interface that helps users design optimal gRNAs. CHOPCHOP supports a wide range of CRISPR applications, including gene knock-out, sequence knock-in, and RNA knock-down. Furthermore, CHOPCHOP offers visualization that enables an informed choice of gRNAs and supports experimental validation. In these protocols, we describe the best practices for gRNA design using CHOPCHOP. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Design of gRNAs for gene knock-out. Alternate Protocol 1: Design of gRNAs for dCas9 fusion/effector targeting. Support Protocol: Design of gRNAs for targeting transgenic or plasmid sequences. Basic Protocol 2: Design of gRNAs for RNA targeting. Basic Protocol 3: Design of gRNAs for sequence knock-in. Alternate Protocol 2: Design of gRNAs for knock-in using non-homologous end joining. Basic Protocol 4: Design of gRNAs for knock-in using Cas9 nickases.", "date": "2021-04-01T00:00:00Z", "citationCount": 12, "authors": [ { "name": "Labun K." }, { "name": "Krause M." }, { "name": "Torres Cleuren Y." }, { "name": "Valen E." } ], "journal": "Current Protocols" } }, { "doi": "10.1093/nar/gkw398", "pmid": "27185894", "pmcid": "PMC4987937", "type": [ "Primary" ], "version": "2", "note": null, "metadata": { "title": "CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering", "abstract": "In just 3 years CRISPR genome editing has transformed biology, and its popularity and potency continue to grow. New CRISPR effectors and rules for locating optimum targets continue to be reported, highlighting the need for computational CRISPR targeting tools to compile these rules and facilitate target selection and design. CHOPCHOP is one of the most widely used web tools for CRISPR- and TALEN-based genome editing. Its overarching principle is to provide an intuitive and powerful tool that can serve both novice and experienced users. In this major update we introduce tools for the next generation of CRISPR advances, including Cpf1 and Cas9 nickases. We support a number of new features that improve the targeting power, usability and efficiency of CHOPCHOP. To increase targeting range and specificity we provide support for custom length sgRNAs, and we evaluate the sequence composition of the whole sgRNA and its surrounding region using models compiled from multiple large-scale studies. These and other new features, coupled with an updated interface for increased usability and support for a continually growing list of organisms, maintain CHOPCHOP as one of the leading tools for CRISPR genome editing. CHOPCHOP v2 can be found at http://chopchop.cbu.uib.no.", "date": "2016-07-08T00:00:00Z", "citationCount": 552, "authors": [ { "name": "Labun K." }, { "name": "Montague T.G." }, { "name": "Gagnon J.A." }, { "name": "Thyme S.B." }, { "name": "Valen E." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gku410", "pmid": "24861617", "pmcid": "PMC4086086", "type": [ "Primary" ], "version": "1", "note": null, "metadata": { "title": "CHOPCHOP: A CRISPR/Cas9 and TALEN web tool for genome editing", "abstract": "Major advances in genome editing have recently been made possible with the development of the TALEN and CRISPR/Cas9 methods. The speed and ease of implementing these technologies has led to an explosion of mutant and transgenic organisms. A rate-limiting step in efficiently applying TALEN and CRISPR/Cas9 methods is the selection and design of targeting constructs. We have developed an online tool, CHOPCHOP (https://chopchop.rc.fas.harvard.edu), to expedite the design process. CHOPCHOP accepts a wide range of inputs (gene identifiers, genomic regions or pasted sequences) and provides an array of advanced options for target selection. It uses efficient sequence alignment algorithms to minimize search times, and rigorously predicts off-target binding of single-guide RNAs (sgRNAs) and TALENs. Each query produces an interactive visualization of the gene with candidate target sites displayed at their genomic positions and color-coded according to quality scores. In addition, for each possible target site, restriction sites and primer candidates are visualized, facilitating a streamlined pipeline of mutant generation and validation. The ease-of-use and speed of CHOPCHOP make it a valuable tool for genome engineering. © 2014 The Author(s).", "date": "2014-07-01T00:00:00Z", "citationCount": 736, "authors": [ { "name": "Montague T.G." }, { "name": "Cruz J.M." }, { "name": "Gagnon J.A." }, { "name": "Church G.M." }, { "name": "Valen E." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Kornel Labun", "email": "kornel.labun@uib.no", "url": null, "orcidid": "https://orcid.org/0000-0002-1262-2611", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer", "Support" ], "note": null }, { "name": "Tessa Montague", "email": "tessa.chopchop@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0002-5918-6327", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Contributor", "Support" ], "note": null }, { "name": "Valen Group (Computational Biology Unit)", "email": null, "url": "https://www.cbu.uib.no/valen/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Developer", "Maintainer", "Support" ], "note": null }, { "name": "The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk", "email": "support@elixir.no", "url": "https://elixir.no/helpdesk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Support" ], "note": "Helpdesk and support for ELIXIR Norway services" }, { "name": "University of Bergen", "email": null, "url": "https://www.uib.no/en", "orcidid": null, "gridid": "grid.7914.b", "rorid": "03zga2b32", "fundrefid": "10.13039/501100005036", "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "James Graham", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-8639-7592", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "Recommendations on the long-read enrichment mode" }, { "name": "Bergen Research Foundation", "email": null, "url": "https://mohnfoundation.no/en/about/", "orcidid": null, "gridid": "grid.478482.5", "rorid": "04efaep75", "fundrefid": "10.13039/501100006475", "typeEntity": "Funding agency", "typeRole": [], "note": "Now part of the Trond Mohn Foundation" }, { "name": "University of Bergen", "email": null, "url": "https://www.uib.no/en", "orcidid": null, "gridid": "grid.7914.b", "rorid": "03zga2b32", "fundrefid": "10.13039/501100005036", "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "The Research Council of Norway", "email": null, "url": "http://www.forskningsradet.no/en/Home_page/1177315753906", "orcidid": null, "gridid": "grid.13985.36", "rorid": "00epmv149", "fundrefid": "10.13039/501100005416", "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "Erin Calhoun", "email": "erin.calhoun@uit.no", "url": null, "orcidid": "https://orcid.org/0009-0003-3752-7156", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": "Curation of bio.tools profile - contact me with updates/corrections." } ], "community": null, "owner": "edv", "additionDate": "2016-03-11T10:35:00Z", "lastUpdate": "2023-08-03T13:19:40.201053Z", "editPermission": { "type": "group", "authors": [ "eca008" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NeLS", "description": "Norwegian e-Infrastructure for Life Sciences enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their omics-scale data. NeLS is developed by ELIXIR Norway and funded by the Research Council of Norway. It can be accessed via a web application, web API, and SSH. Online analysis of data is enabled by integrated instances of Galaxy, including a set of pre-defined workflows.", "homepage": "https://nels.bioinfo.no", "biotoolsID": "nels", "biotoolsCURIE": "biotools:nels", "version": [ "2018-05-16" ], "otherID": [ { "value": "RRID:SCR_016301", "type": "rrid", "version": null }, { "value": "DOI:10.5281/zenodo.1251639", "type": "doi", "version": "2018-05-16" } ], "relation": [ { "biotoolsID": "galaxy", "type": "includes" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [], "output": [], "note": "NeLS enables storing, sharing, archiving, and analysis of life scientific data.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2945", "term": "Analysis" } ], "input": [], "output": [], "note": "NeLS enables analysis of life scientific data via integrated instances of Galaxy.", "cmd": null } ], "toolType": [ "Command-line tool", "Web service", "Web API", "Workbench" ], "topic": [ { "uri": "http://edamontology.org/topic_3071", "term": "Data management" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Apache-2.0", "collectionID": [ "UiT", "CBU tools", "UiO tools", "UiB tools", "NMBU", "ELIXIR-NO", "NTNU tools" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [ "Norway" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/elixir-no-nels/nels-core", "type": [ "Repository" ], "note": "Source code repo of the core modules" }, { "url": "https://doi.org/10.5281/zenodo.1251638", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/elixir-no-nels/nels-core", "type": "Source code", "note": "Source code repo with NeLS core modules", "version": null }, { "url": "https://doi.org/10.5281/zenodo.1251639", "type": "Source code", "note": "Archived source code version 2018-05-16", "version": null } ], "documentation": [ { "url": "https://nels-docs.readthedocs.io/en/v0.1-beta/", "type": [ "Citation instructions", "Command-line options", "General", "User manual" ], "note": null } ], "publication": [ { "doi": "10.12688/f1000research.15119.1", "pmid": "30271575", "pmcid": "PMC6137412", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Norwegian e-Infrastructure for Life Sciences (NeLS)", "abstract": "The Norwegian e-Infrastructure for Life Sciences (NeLS) has been developed by ELIXIR Norway to provide its users with a system enabling data storage, sharing, and analysis in a project-oriented fashion. The system is available through easy-to-use web interfaces, including the Galaxy workbench for data analysis and workflow execution. Users confident with a command-line interface and programming may also access it through Secure Shell (SSH) and application programming interfaces (APIs). NeLS has been in production since 2015, with training and support provided by the help desk of ELIXIR Norway. Through collaboration with NorSeq, the national consortium for high-throughput sequencing, an integrated service is offered so that sequencing data generated in a research project is provided to the involved researchers through NeLS. Sensitive data, such as individual genomic sequencing data, are handled using the TSD (Services for Sensitive Data) platform provided by Sigma2 and the University of Oslo. NeLS integrates national e-infrastructure storage and computing resources, and is also integrated with the SEEK platform in order to store large data files produced by experiments described in SEEK. In this article, we outline the architecture of NeLS and discuss possible directions for further development.", "date": "2018-01-01T00:00:00Z", "citationCount": 4, "authors": [ { "name": "Tekle K.M." }, { "name": "Gundersen S." }, { "name": "Klepper K." }, { "name": "Bongo L.A." }, { "name": "Raknes I.A." }, { "name": "Li X." }, { "name": "Zhang W." }, { "name": "Andreetta C." }, { "name": "Mulugeta T.D." }, { "name": "Kalas M." }, { "name": "Rye M.B." }, { "name": "Hjerde E." }, { "name": "Antony Samy J.K." }, { "name": "Fornous G." }, { "name": "Azab A." }, { "name": "Vage D.I." }, { "name": "Hovig E." }, { "name": "Willassen N.P." }, { "name": "Drablos F." }, { "name": "Nygard S." }, { "name": "Petersen K." }, { "name": "Jonassen I." } ], "journal": "F1000Research" } } ], "credit": [ { "name": "ELIXIR Norway", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Provider", "Primary contact", "Developer", "Maintainer", "Support" ], "note": null }, { "name": "The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk", "email": "support@elixir.no", "url": "https://elixir.no/helpdesk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Support" ], "note": null } ], "community": null, "owner": "ELIXIR-NO", "additionDate": "2018-05-22T19:50:52Z", "lastUpdate": "2023-08-01T10:18:47.390174Z", "editPermission": { "type": "group", "authors": [ "UiB", "UiO", "UiT", "NMBU", "NTNU", "ELIXIR-NO", "matus.kalas@uib.no", "eca008" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GeneWise (EBI)", "description": "Compare a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.", "homepage": "http://www.ebi.ac.uk/Tools/psa/genewise/", "biotoolsID": "genewise", "biotoolsCURIE": "biotools:genewise", "version": [ "1" ], "otherID": [ { "value": "RRID:SCR_015054", "type": "rrid", "version": null } ], "relation": [ { "biotoolsID": "wise", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0491", "term": "Pairwise sequence alignment" }, { "uri": "http://edamontology.org/operation_0495", "term": "Local alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1381", "term": "Sequence alignment (pair)" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "EBI Tools", "Job Dispatcher Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.ebi.ac.uk/support/", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "https://www.ebi.ac.uk/~birney/wise2/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://www.ebi.ac.uk/Tools/psa/genewise/", "type": [ "General" ], "note": null }, { "url": "https://www.ebi.ac.uk/~birney/wise2/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1101/gr.10.4.547", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Using GeneWise in the Drosophila annotation experiment", "abstract": "The GeneWise method for combining gene prediction and homology searches was applied to the 2.9-Mb region from Drosophila melanogaster. The results from the Genome Annotation Assessment Project (GASP) showed that GeneWise provided reasonably accurate gene predictions. Further investigation indicates that many of the incorrect gene predictions from GeneWise were due to transposons with valid protein-coding genes and the remaining cases are pseudogenes or possible annotation oversights.", "date": "2000-04-01T00:00:00Z", "citationCount": 277, "authors": [ { "name": "Birney E." }, { "name": "Durbin R." } ], "journal": "Genome Research" } }, { "doi": "10.1093/nar/gkac240", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Search and sequence analysis tools services from EMBL-EBI in 2022", "abstract": "The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.", "date": "2022-07-05T00:00:00Z", "citationCount": 362, "authors": [ { "name": "Madeira F." }, { "name": "Pearce M." }, { "name": "Tivey A.R.N." }, { "name": "Basutkar P." }, { "name": "Lee J." }, { "name": "Edbali O." }, { "name": "Madhusoodanan N." }, { "name": "Kolesnikov A." }, { "name": "Lopez R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Ewan Birney", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Job Dispatcher", "email": null, "url": "https://www.ebi.ac.uk/Tools/jdispatcher", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "jdispatcher", "additionDate": "2015-01-29T15:47:36Z", "lastUpdate": "2023-07-25T15:25:32.224835Z", "editPermission": { "type": "group", "authors": [ "nandana", "biomadeira" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Training Infrastructure as a Service (TIaaS)", "description": "Originally developed by Galaxy Europe and the Gallantries project, together with the Galaxy community we have created \"Training Infrastructure-as-a-Service\" (TIaaS), aimed at providing user-friendly training infrastructure to the global training community. TIaaS provides dedicated training resources for Galaxy-based courses and events. Event organisers register their course, after which trainees are transparently placed in a private queue on the compute infrastructure, which ensures jobs complete quickly, even when the main queue is experiencing high wait times. A built-in dashboard allows instructors to monitor student progress.\n\nTraining Infrastructure as a Service (TIaaS) has been in development since 21 June 2018, and three days later became a production service at Galaxy Europe on 24 June. As of June 7th, 2023 is has supported 504 training events with over 24000 learners have used this infrastructure for Galaxy training.", "homepage": "https://github.com/galaxyproject/tiaas2", "biotoolsID": "tiaas", "biotoolsCURIE": "biotools:tiaas", "version": [ "2.1.0" ], "otherID": [ { "value": "RRID:SCR_023200", "type": "rrid", "version": null } ], "relation": [ { "biotoolsID": "galaxy", "type": "uses" }, { "biotoolsID": "galaxy", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3760", "term": "Service management" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0605", "term": "Informatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "AGPL-3.0", "collectionID": [ "Galaxy" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Training", "Compute" ], "elixirNode": [ "Netherlands", "Germany", "France" ], "elixirCommunity": [ "Galaxy" ], "link": [ { "url": "https://github.com/galaxyproject/tiaas2/", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/galaxyproject/ansible-tiaas2", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/galaxyproject/tiaas2/issues/", "type": [ "Issue tracker", "Helpdesk" ], "note": null }, { "url": "https://usegalaxy.eu/tiaas/", "type": [ "Service" ], "note": null }, { "url": "https://usegalaxy.org.au/tiaas/", "type": [ "Service" ], "note": null }, { "url": "https://usegalaxy.org/tiaas/", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://github.com/galaxyproject/tiaas2/archive/refs/tags/2.1.0", "type": "Software package", "note": null, "version": "2.1.0" }, { "url": "https://github.com/galaxyproject/ansible-tiaas2/releases/tag/2.2.0", "type": "Other", "note": "Ansible role for TIaaS installation", "version": "2.2.0 (ansible)" } ], "documentation": [ { "url": "https://training.galaxyproject.org/training-material/topics/admin/tutorials/tiaas/tutorial.html", "type": [ "Installation instructions", "Training material" ], "note": null }, { "url": "https://github.com/galaxyproject/tiaas2/blob/main/CODE_OF_CONDUCT.md", "type": [ "Code of conduct" ], "note": null }, { "url": "https://training.galaxyproject.org/training-material/topics/teaching/tutorials/setup-tiaas-for-training/tutorial.html", "type": [ "Training material", "User manual" ], "note": null }, { "url": "https://usegalaxy.eu/tiaas/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1101/2020.08.23.263509", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "This is a preprint", "metadata": null }, { "doi": "10.1093/gigascience/giad048", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Helena Rasche", "email": "helena.rasche@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0001-9760-8992", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Documentor", "Maintainer", "Support" ], "note": null }, { "name": "Bundesministerium für Bildung und Forschung", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": "10.13039/501100002347", "typeEntity": "Funding agency", "typeRole": [], "note": "grants 031 A538A/A538C RBC and 031L0101B/031L0101C de.NBI-epi" }, { "name": "National Human Genome Research Institute", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": "10.13039/100000051", "typeEntity": "Funding agency", "typeRole": [], "note": "grant 2U24HG006620" }, { "name": "Cameron Hyde", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-5913-9766", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "John Davis", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-1363-1245", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Simon Gladman", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-6100-4385", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "In loving memory of Simon Gladman (1970-2022) beloved mentor and system administrator, who was instrumental in getting the second TIaaS deployment running at Galaxy Australia, proving its generalisability." }, { "name": "Nate Coraor", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-8083-2963", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Provider" ], "note": null }, { "name": "Anthony Bretaudeau", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0914-2470", "gridid": 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"Support" ], "note": null }, { "name": "Erasmus+ Programme", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": "10.13039/100001501", "typeEntity": "Funding agency", "typeRole": [ "Support" ], "note": "Grant 2020-1-NL01-KA203-064717" } ], "community": null, "owner": "hexylena", "additionDate": "2021-01-18T10:21:30Z", "lastUpdate": "2023-07-04T13:36:19.654323Z", "editPermission": { "type": "group", "authors": [ "hexylena" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "SynergyFinder plus (SynergyFinder+)", "description": "Efficient implementations for all the popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of the synergy scores as either a two-dimensional or a three-dimensional interaction surface over the dose matrix. R package available at https://bioconductor.org/packages/release/bioc/html/synergyfinder.html. The web server is available at http://www.synergyfinder.org or http://www.synergyfinderplus.org", "homepage": "http://www.synergyfinder.org", "biotoolsID": "synergyfinder", "biotoolsCURIE": "biotools:synergyfinder", "version": [ "1.0.0" ], "otherID": [ { "value": "RRID:SCR_019318", "type": "rrid", "version": null } ], "relation": [ { "biotoolsID": "drugcomb", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "Artistic-2.0", "collectionID": [ "BioConductor" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.helsinki.fi/en/researchgroups/network-pharmacology-for-precision-medicine", "type": [ "Helpdesk" ], "note": "NETWORK PHARMACOLOGY FOR PRECISION MEDICINE, FACULTY OF MEDICINE, UNIVERSITY OF HELSINKI" }, { "url": "https://twitter.com/SynergyFinder", "type": [ "Social media" ], "note": "Twitter site" }, { "url": "https://tangsoftwarelab.shinyapps.io/synergyfinder/", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/synergyfinder_1.0.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/synergyfinder.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btx162", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "SynergyFinder: A web application for analyzing drug combination dose-response matrix data", "abstract": "Summary: Rational design of drug combinations has become a promising strategy to tackle the drug sensitivity and resistance problem in cancer treatment. To systematically evaluate the preclinical significance of pairwise drug combinations, functional screening assays that probe combination effects in a dose-response matrix assay are commonly used. To facilitate the analysis of such drug combination experiments, we implemented a web application that uses key functions of Rpackage SynergyFinder, and provides not only the flexibility of using multiple synergy scoring models, but also a user-friendly interface for visualizing the drug combination landscapes in an interactive manner.", "date": "2017-08-01T00:00:00Z", "citationCount": 277, "authors": [ { "name": "Ianevski A." }, { "name": "He L." }, { "name": "Aittokallio T." }, { "name": "Tang J." } ], "journal": "Bioinformatics" } }, { "doi": "10.1007/978-1-4939-7493-1_17", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Methods for high-throughput drug combination screening and synergy scoring", "abstract": "Gene products or pathways that are aberrantly activated in cancer but not in normal tissue hold great promises for being effective and safe anticancer therapeutic targets. Many targeted drugs have entered clinical trials but so far showed limited efficacy mostly due to variability in treatment responses and often rapidly emerging resistance. Toward more effective treatment options, we will need multi-targeted drugs or drug combinations, which selectively inhibit the viability and growth of cancer cells and block distinct escape mechanisms for the cells to become resistant. Functional profiling of drug combinations requires careful experimental design and robust data analysis approaches. At the Institute for Molecular Medicine Finland (FIMM), we have developed an experimental-computational pipeline for high-throughput screening of drug combination effects in cancer cells. The integration of automated screening techniques with advanced synergy scoring tools allows for efficient and reliable detection of synergistic drug interactions within a specific window of concentrations, hence accelerating the identification of potential drug combinations for further confirmatory studies.", "date": "2018-01-01T00:00:00Z", "citationCount": 91, "authors": [ { "name": "He L." }, { "name": "Kulesskiy E." }, { "name": "Saarela J." }, { "name": "Turunen L." }, { "name": "Wennerberg K." }, { "name": "Aittokallio T." }, { "name": "Tang J." } ], "journal": "Methods in Molecular Biology" } } ], "credit": [ { "name": "Jing Tang", "email": "jing.tang@helsinki.fi", "url": "https://scholar.google.com/citations?user=6sNdZq8AAAAJ&hl=en", "orcidid": "https://orcid.org/0000-0001-7480-7710", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "Assistant professor in statistics, Faculty of Medicine, University of Helsinki" } ], "community": null, "owner": "jtang920", "additionDate": "2017-01-17T14:57:10Z", "lastUpdate": "2023-04-21T20:55:59.813894Z", "editPermission": { "type": "group", "authors": [ "jtang920" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BioPlex", "description": "A repository of protein interaction data from mass spectrometry experiments.", "homepage": "http://bioplex.hms.harvard.edu/", "biotoolsID": "bioplex", "biotoolsCURIE": "biotools:bioplex", "version": [ "3.0" ], "otherID": [ { "value": "RRID:SCR_016144", "type": "rrid", "version": null } ], "relation": [ { "biotoolsID": "bioplex_r", "type": "usedBy" }, { "biotoolsID": "bioplexpy", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_3083", "term": "Pathway or network visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1025", "term": "Gene identifier" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [ { "uri": "http://edamontology.org/format_2060", "term": "Map format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/ccb-hms/BioPlexAnalysis", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "http://bioplex.hms.harvard.edu/downloadInteractions.php", "type": "Biological data", "note": "Link to download interactions data", "version": null }, { "url": "http://bioplex.hms.harvard.edu/downloadData.php", "type": "Biological data", "note": "Link to download MS data", "version": null } ], "documentation": [], "publication": [ { "doi": "10.1038/nature22366", "pmid": "28514442", "pmcid": "PMC5531611", "type": [], "version": null, "note": null, "metadata": { "title": "Architecture of the human interactome defines protein communities and disease networks", "abstract": "The physiology of a cell can be viewed as the product of thousands of proteins acting in concert to shape the cellular response. Coordination is achieved in part through networks of protein-protein interactions that assemble functionally related proteins into complexes, organelles, and signal transduction pathways. Understanding the architecture of the human proteome has the potential to inform cellular, structural, and evolutionary mechanisms and is critical to elucidating how genome variation contributes to disease. Here we present BioPlex 2.0 (Biophysical Interactions of ORFeome-derived complexes), which uses robust affinity purification-mass spectrometry methodology to elucidate protein interaction networks and co-complexes nucleated by more than 25% of protein-coding genes from the human genome, and constitutes, to our knowledge, the largest such network so far. With more than 56,000 candidate interactions, BioPlex 2.0 contains more than 29,000 previously unknown co-associations and provides functional insights into hundreds of poorly characterized proteins while enhancing network-based analyses of domain associations, subcellular localization, and co-complex formation. Unsupervised Markov clustering of interacting proteins identified more than 1,300 protein communities representing diverse cellular activities. Genes essential for cell fitness are enriched within 53 communities representing central cellular functions. Moreover, we identified 442 communities associated with more than 2,000 disease annotations, placing numerous candidate disease genes into a cellular framework. BioPlex 2.0 exceeds previous experimentally derived interaction networks in depth and breadth, and will be a valuable resource for exploring the biology of incompletely characterized proteins and for elucidating larger-scale patterns of proteome organization.", "date": "2017-05-25T00:00:00Z", "citationCount": 807, "authors": [ { "name": "Huttlin E.L." }, { "name": "Bruckner R.J." }, { "name": "Paulo J.A." }, { "name": "Cannon J.R." }, { "name": "Ting L." }, { "name": "Baltier K." }, { "name": "Colby G." }, { "name": "Gebreab F." }, { "name": "Gygi M.P." }, { "name": "Parzen H." }, { "name": "Szpyt J." }, { "name": "Tam S." }, { "name": "Zarraga G." }, { "name": "Pontano-Vaites L." }, { "name": "Swarup S." }, { "name": "White A.E." }, { "name": "Schweppe D.K." }, { "name": "Rad R." }, { "name": "Erickson B.K." }, { "name": "Obar R.A." }, { "name": "Guruharsha K.G." }, { "name": "Li K." }, { "name": "Artavanis-Tsakonas S." }, { "name": "Gygi S.P." }, { "name": "Wade Harper J." } ], "journal": "Nature" } }, { "doi": "10.1016/j.cell.2015.06.043", "pmid": "26186194", "pmcid": "PMC4617211", "type": [], "version": null, "note": null, "metadata": { "title": "The BioPlex Network: A Systematic Exploration of the Human Interactome", "abstract": "Summary Protein interactions form a network whose structure drives cellular function and whose organization informs biological inquiry. Using high-throughput affinity-purification mass spectrometry, we identify interacting partners for 2,594 human proteins in HEK293T cells. The resulting network (BioPlex) contains 23,744 interactions among 7,668 proteins with 86% previously undocumented. BioPlex accurately depicts known complexes, attaining 80%-100% coverage for most CORUM complexes. The network readily subdivides into communities that correspond to complexes or clusters of functionally related proteins. More generally, network architecture reflects cellular localization, biological process, and molecular function, enabling functional characterization of thousands of proteins. Network structure also reveals associations among thousands of protein domains, suggesting a basis for examining structurally related proteins. Finally, BioPlex, in combination with other approaches, can be used to reveal interactions of biological or clinical significance. For example, mutations in the membrane protein VAPB implicated in familial amyotrophic lateral sclerosis perturb a defined community of interactors.", "date": "2015-07-18T00:00:00Z", "citationCount": 864, "authors": [ { "name": "Huttlin E.L." }, { "name": "Ting L." }, { "name": "Bruckner R.J." }, { "name": "Gebreab F." }, { "name": "Gygi M.P." }, { "name": "Szpyt J." }, { "name": "Tam S." }, { "name": "Zarraga G." }, { "name": "Colby G." }, { "name": "Baltier K." }, { "name": "Dong R." }, { "name": "Guarani V." }, { "name": "Vaites L.P." }, { "name": "Ordureau A." }, { "name": "Rad R." }, { "name": "Erickson B.K." }, { "name": "Wuhr M." }, { "name": "Chick J." }, { "name": "Zhai B." }, { "name": "Kolippakkam D." }, { "name": "Mintseris J." }, { "name": "Obar R.A." }, { "name": "Harris T." }, { "name": "Artavanis-Tsakonas S." }, { "name": "Sowa M.E." }, { "name": "De Camilli P." }, { "name": "Paulo J.A." }, { "name": "Harper J.W." }, { "name": "Gygi S.P." } ], "journal": "Cell" } }, { "doi": "10.1016/j.cell.2021.04.011", "pmid": "33961781", "pmcid": "PMC8165030", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Dual proteome-scale networks reveal cell-specific remodeling of the human interactome", "abstract": "Thousands of interactions assemble proteins into modules that impart spatial and functional organization to the cellular proteome. Through affinity-purification mass spectrometry, we have created two proteome-scale, cell-line-specific interaction networks. The first, BioPlex 3.0, results from affinity purification of 10,128 human proteins—half the proteome—in 293T cells and includes 118,162 interactions among 14,586 proteins. The second results from 5,522 immunoprecipitations in HCT116 cells. These networks model the interactome whose structure encodes protein function, localization, and complex membership. Comparison across cell lines validates thousands of interactions and reveals extensive customization. Whereas shared interactions reside in core complexes and involve essential proteins, cell-specific interactions link these complexes, “rewiring” subnetworks within each cell's interactome. Interactions covary among proteins of shared function as the proteome remodels to produce each cell's phenotype. Viewable interactively online through BioPlexExplorer, these networks define principles of proteome organization and enable unknown protein characterization.", "date": "2021-05-27T00:00:00Z", "citationCount": 144, "authors": [ { "name": "Huttlin E.L." }, { "name": "Bruckner R.J." }, { "name": "Navarrete-Perea J." }, { "name": "Cannon J.R." }, { "name": "Baltier K." }, { "name": "Gebreab F." }, { "name": "Gygi M.P." }, { "name": "Thornock A." }, { "name": "Zarraga G." }, { "name": "Tam S." }, { "name": "Szpyt J." }, { "name": "Gassaway B.M." }, { "name": "Panov A." }, { "name": "Parzen H." }, { "name": "Fu S." }, { "name": "Golbazi A." }, { "name": "Maenpaa E." }, { "name": "Stricker K." }, { "name": "Guha Thakurta S." }, { "name": "Zhang T." }, { "name": "Rad R." }, { "name": "Pan J." }, { "name": "Nusinow D.P." }, { "name": "Paulo J.A." }, { "name": "Schweppe D.K." }, { "name": "Vaites L.P." }, { "name": "Harper J.W." }, { "name": "Gygi S.P." } ], "journal": "Cell" } } ], "credit": [ { "name": "Wade Harper", "email": "wade_harper@hms.harvard.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Edward L Huttlin", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "Chan019", "additionDate": "2023-03-09T08:16:32.218358Z", "lastUpdate": "2023-03-09T08:34:58.777202Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }