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{ "count": 5969, "next": "?page=2", "previous": null, "list": [ { "name": "ARTEMIS", "description": "a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment", "homepage": "https://github.com/david-bogdan-r/ARTEMIS", "biotoolsID": "artemis3D", "biotoolsCURIE": "biotools:artemis3D", "version": [ "version 1.5" ], "otherID": [], "relation": [ { "biotoolsID": "artem", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0503", "term": "Pairwise structure alignment" }, { "uri": "http://edamontology.org/operation_2518", "term": "Nucleic acid structure comparison" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1459", "term": "Nucleic acid structure" }, "format": [ { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1459", "term": "Nucleic acid structure" }, "format": [ { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1482", "term": "Nucleic acid structure alignment" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0888", "term": "Structure similarity score" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1459", "term": "Nucleic acid structure" }, "format": [ { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "note": null, "cmd": "python3 artemis.py r=FILENAME q=FILENAME [OPTIONS]" } ], "toolType": [ "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_0077", "term": "Nucleic acids" }, { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_3511", "term": "Nucleic acid sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0654", "term": "DNA" }, { "uri": "http://edamontology.org/topic_0099", "term": "RNA" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "Apache-2.0", "collectionID": [ "3D-BioInfo-Structure-Function" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/david-bogdan-r/ARTEMIS", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/david-bogdan-r/ARTEMIS", "type": "Source code", "note": null, "version": "version 1.5" } ], "documentation": [ { "url": "https://github.com/david-bogdan-r/ARTEMIS/blob/main/README.md", "type": [ "Quick start guide" ], "note": "README file" } ], "publication": [ { "doi": "10.1093/nar/gkae758", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": "version 1.5", "note": null, "metadata": null }, { "doi": "10.1101/2024.04.06.588371", "pmid": null, "pmcid": null, "type": [], "version": "version 1.0", "note": null, "metadata": null } ], "credit": [ { "name": "Davyd Bohdan", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-6456-6658", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Janusz Bujnicki", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-6633-165X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Eugene Baulin", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-4694-9783", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "febos", "additionDate": "2024-09-09T07:49:35.385723Z", "lastUpdate": "2024-09-09T10:17:54.224353Z", "editPermission": { "type": "private", "authors": [ "febos" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "REPET", "description": "The REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyze transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii)\n TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files.", "homepage": "https://urgi.versailles.inrae.fr/Tools/REPET", "biotoolsID": "repet", "biotoolsCURIE": "biotools:repet", "version": [ "v3.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0379", "term": "Repeat sequence detection" }, { "uri": "http://edamontology.org/operation_0237", "term": "Repeat sequence analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "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_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_2206", "term": "Sequence feature table format (text)" } ] }, { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_1939", "term": "GFF3-seq" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0157", "term": "Sequence composition, complexity and repeats" }, { "uri": "http://edamontology.org/topic_0654", "term": "DNA" }, { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "C++", "Python" ], "license": "CECILL-2.0", "collectionID": [ "REPET", "elixir-fr-sdp-2019", "PlantBioinfoPF", "URGI" ], "maturity": "Legacy", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://urgi.versailles.inrae.fr/download/repet/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://urgi.versailles.inrae.fr/download/repet/REPET_linux-x64-3.0.tar.gz", "type": "Source code", "note": null, "version": "v3.0" } ], "documentation": [ { "url": "https://urgi.versailles.inrae.fr/Tools/REPET", "type": [ "General" ], "note": "see also https://urgi.versailles.inrae.fr/Tools/REPET/README" }, { "url": "https://urgi.versailles.inrae.fr/Tools/REPET/INSTALL", "type": [ "Installation instructions" ], "note": null }, { "url": "https://urgi.versailles.inrae.fr/Tools/REPET/TEdenovo-tuto", "type": [ "User manual" ], "note": "See also https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tuto" }, { "url": "https://forgemia.inra.fr/urgi-anagen/wiki-repet/-/wikis/REPET-V3.0-tutorial", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0091929", "pmid": "24786468", "pmcid": "PMC4008368", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PASTEC: An automatic transposable element classification tool", "abstract": "Summary: The classification of transposable elements (TEs) is key step towards deciphering their potential impact on the genome. However, this process is often based on manual sequence inspection by TE experts. With the wealth of genomic sequences now available, this task requires automation, making it accessible to most scientists. We propose a new tool, PASTEC, which classifies TEs by searching for structural features and similarities. This tool outperforms currently available software for TE classification. The main innovation of PASTEC is the search for HMM profiles, which is useful for inferring the classification of unknown TE on the basis of conserved functional domains of the proteins. In addition, PASTEC is the only tool providing an exhaustive spectrum of possible classifications to the order level of the Wicker hierarchical TE classification system. It can also automatically classify other repeated elements, such as SSR (Simple Sequence Repeats), rDNA or potential repeated host genes. Finally, the output of this new tool is designed to facilitate manual curation by providing to biologists with all the evidence accumulated for each TE consensus. Availability: PASTEC is available as a REPET module or standalone software (http://urgi.versailles.inra.fr/download/repet/REPET-linux-x64-2.2.tar. gz). It requires a Unix-like system. There are two standalone versions: one of which is parallelized (requiring Sun grid Engine or Torque), and the other of which is not. © 2014 Hoede et al.", "date": "2014-05-02T00:00:00Z", "citationCount": 203, "authors": [ { "name": "Hoede C." }, { "name": "Arnoux S." }, { "name": "Moisset M." }, { "name": "Chaumier T." }, { "name": "Inizan O." }, { "name": "Jamilloux V." }, { "name": "Quesneville H." } ], "journal": "PLoS ONE" } }, { "doi": "10.1371/journal.pone.0016526", "pmid": "21304975", "pmcid": "PMC3031573", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Considering transposable element diversification in de novo annotation approaches", "abstract": "Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of highthroughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the Drosophila melanogaster and Arabidopsis thaliana genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination of algorithms detected TE families with good recovery of the reference sequences. We then applied a new procedure for reconciling the different clustering results and classifying TE sequences. The whole approach was implemented in a pipeline using the REPET package. Finally, we show that our combined approach highlights the dynamics of well defined TE families by making it possible to identify structural variations among their copies. This approach makes it possible to annotate TE families and to study their diversification in a single analysis, improving our understanding of TE dynamics at the whole-genome scale and for diverse species. © 2011 Flutre et al.", "date": "2011-02-09T00:00:00Z", "citationCount": 330, "authors": [ { "name": "Flutre T." }, { "name": "Duprat E." }, { "name": "Feuillet C." }, { "name": "Quesneville H." } ], "journal": "PLoS ONE" } }, { "doi": "10.1371/journal.pcbi.0010022", "pmid": "16110336", "pmcid": "PMC1185648", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Combined evidence annotation of transposable elements in genome sequences", "abstract": "Transposable elements (TEs) are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most efforts to annotate TEs in genome sequences rely on the results of a single computational program, RepeatMasker. In contrast, recent advances in gene annotation indicate that high-quality gene models can be produced from combining multiple independent sources of computational evidence. To elevate the quality of TE annotations to a level comparable to that of gene models, we have developed a combined evidence-model TE annotation pipeline, analogous to systems used for gene annotation, by integrating results from multiple homology-based and de novo TE identification methods. As proof of principle, we have annotated \"TE models\" in Drosophila melanogaster Release 4 genomic sequences using the combined computational evidence derived from RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, TE-HMM and the previous Release 3.1 annotation. Our system is designed for use with the Apollo genome annotation tool, allowing automatic results to be curated manually to produce reliable annotations. The euchromatic TE fraction of D. melanogaster is now estimated at 5.3% (cf. 3.86% in Release 3.1), and we found a substantially higher number of TEs (n = 6,013) than previously identified (n = 1,572). Most of the new TEs derive from small fragments of a few hundred nucleotides long and highly abundant families not previously annotated (e.g., INE-1). We also estimated that 518 TE copies (8.6%) are inserted into at least one other TE, forming a nest of elements. The pipeline allows rapid and thorough annotation of even the most complex TE models, including highly deleted and/or nested elements such as those often found in heterochromatic sequences. Our pipeline can be easily adapted to other genome sequences, such as those of the D. melanogaster heterochromatin or other species in the genus Drosophila. © 2005 Quesneville et al.", "date": "2005-01-01T00:00:00Z", "citationCount": 262, "authors": [ { "name": "Quesneville H." }, { "name": "Bergman C.M." }, { "name": "Andrieu O." }, { "name": "Autard D." }, { "name": "Nouaud D." }, { "name": "Ashburner M." }, { "name": "Anxolabehere D." } ], "journal": "PLoS Computational Biology" } }, { "doi": "10.1007/s00239-003-0007-2", "pmid": "15008403", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Detection of New Transposable Element Families in Drosophila melanogaster and Anopheles gambiae Genomes", "abstract": "The techniques that are usually used to detect transposable elements (TEs) in nucleic acid sequences rely on sequence similarity with previously characterized elements. However, these methods are likely to miss many elements in various organisms. We tested two strategies for the detection of unknown elements. The first, which we call \"TBLASTX strategy,\" searches for TE sequences by comparing the six-frame translations of the nucleic acid sequences of known TEs with the genomic sequence of interest. The second, \"repeat-based strategy,\" searches genomic sequences for long repeats and clusters them in groups of similar sequences. TE copies from a given family are expected to cluster together. We tested the Drosophila melanogaster genomic sequence and the recently sequenced Anopheles gambiae genome in which most TEs remain unknown. We showed that the \"TBLASTX strategy\" is very efficient as it detected at least 332 new TE families in D. melanogaster and 400 in A. gambiae. This was unexpected in Drosophila as TEs of this organism have been extensively studied. The \"repeat-based strategy\" appeared to be very inefficient because of two problems: (i) TE copies are heavily deleted and few copies share homologous regions, and (ii) segmental duplications are frequent and it is not easy to distinguish them from TE copies.", "date": "2003-12-29T00:00:00Z", "citationCount": 62, "authors": [ { "name": "Quesneville H." }, { "name": "Nouaud D." }, { "name": "Anxolabehere D." } ], "journal": "Journal of Molecular Evolution" } }, { "doi": "10.1109/JPROC.2016.2590833", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue", "abstract": "Transposable elements (TEs) constitute the most dynamic and the largest component of large plant genomes: for example, 80% to 90% of the maize genome and the wheat genome may be TEs. De novo TE annotation is therefore a computational challenge, and we investigated, using current tools in the REPET package, new strategies to overcome the difficulties. We tested our methodological developments on the sequence of the chromosome 3B of the hexaploid wheat; this chromosome is ~1 Gb, one of the 'fattest' genomes ever sequenced. We successfully established various strategies for annotating TEs in such a complex dataset. Our analyses show that all of our strategies can overcome the current limitations for de novo TE discovery in large plant genomes. Relative to annotation based on a library of known TEs, our de novo approaches improved genome coverage (from 84% to 90%), and the number of full length annotated copies from 14 830 to 15 905. We also developed two new metrics for qualifying TE annotation: NTE50 involves measuring the number, and LTE50 the smallest sizes of annotations that cover 50% of the genome. NTE50 decreased the number of annotations from 124 868 to 93 633 and LTE50 increased it from 1839 to 2659. This work shows how to obtain comprehensive and high-quality automatic TE annotation for a number of economically and agronomically important species.", "date": "2017-03-01T00:00:00Z", "citationCount": 15, "authors": [ { "name": "Jamilloux V." }, { "name": "Daron J." }, { "name": "Choulet F." }, { "name": "Quesneville H." } ], "journal": "Proceedings of the IEEE" } } ], "credit": [ { "name": "URGI", "email": "urgi-repet@versailles.inrae.fr", "url": "http://urgi.versailles.inrae.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Developer", "Contributor", "Maintainer", "Provider", "Support", "Documentor" ], "note": "This tool has a \"Numero de depot APP\": FR 001 480007 000 R P 2008 000 31 235" } ], "community": null, "owner": "Institut Francais de Bioinform", "additionDate": "2016-03-24T16:22:28Z", "lastUpdate": "2024-09-06T17:39:57.162017Z", "editPermission": { "type": "group", "authors": [ "vjamilloux", "johann_confais", "raphael.flores" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "DataDiscovery", "description": "DataDiscovery aims at providing researchers a simple and fast access to relevant biological data using specific keywords and easy to use filters.\n\nThis tool is expected to be easily customizable for specific filters, environments, or data schemas. Its current implementations supported by URGI are: WheatIS, Plant, RARe.", "homepage": "https://urgi.versailles.inrae.fr/data-discovery/", "biotoolsID": "DataDiscovery", "biotoolsCURIE": "biotools:DataDiscovery", "version": [], "otherID": [], "relation": [ { "biotoolsID": "wheatis", "type": "usedBy" }, { "biotoolsID": "RARe", "type": "usedBy" }, { "biotoolsID": "Plant_DataDiscovery", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3625", "term": "Relation extraction" }, { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" }, { "uri": "http://edamontology.org/operation_3908", "term": "Information retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0968", "term": "Keyword" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2353", "term": "Ontology data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2093", "term": "Data reference" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web API", "Web application", "Web service", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_0610", "term": "Ecology" }, { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3810", "term": "Agricultural science" } ], "operatingSystem": [ "Linux" ], "language": [ "JavaScript", "Java", "Bash" ], "license": "BSD-3-Clause", "collectionID": [ "elixir-fr-sdp-2019", "URGI" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Data", "Tools", "Interoperability" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://forgemia.inra.fr/urgi-is/data-discovery", "type": [ "Repository" ], "note": "GitLab code repository for DataDiscovery" }, { "url": "https://github.com/gnpis/DataDiscovery/", "type": [ "Mirror" ], "note": "Code repository mirror link for DataDiscovery" } ], "download": [], "documentation": [ { "url": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/LEGAL-MENTIONS.md", "type": [ "Terms of use" ], "note": "General terms of use" }, { "url": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/README.md#contribute", "type": [ "Contributions policy" ], "note": "How to contribute" }, { "url": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/HELP.md", "type": [ "User manual" ], "note": "How to use" }, { "url": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/README.md#setup", "type": [ "Installation instructions" ], "note": "How to install" } ], "publication": [ { "doi": "10.3835/plantgenome2015.06.0038", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": "1-\tSpannagl, M., Alaux, M., Lange, M., Bolser, D. M., Bader, K. C., Letellier, T., Kimmel, E., Flores, R.-G., Pommier, C., Kerhornou, A., Walts, B., Nussbaumer, T., Grabmuller, C., Chen, J., Colmsee, C., Beier, S., Mascher, M., Schmutzer, T., Arend, D., Thanki, A., Ramirez-Gonzalez, R., Ayling, M., Ayling, S., Caccamo, M., Mayer, K. F. X., Scholz, U., Steinbach, D., Quesneville, H., Kersey, P. (2016). TransPLANT resources for triticeae genomic data. Plant Genome, 9 (1), 13 p.", "metadata": { "title": "TransPLANT resources for triticeae genomic data", "abstract": "The genome sequences of many important Triticeae species, including bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have recently been deciphered. These efforts have generated new insights into Triticeae biology and genome organization and have important implications for downstream usage by breeders, experimental biologists, and comparative genomicists. transPLANT (http://www.transplantdb.eu) is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale research in the life sciences. Since the Triticeae data are intrinsically complex, heterogenous, and distributed, the transPLANT consortium has undertaken efforts to develop common data formats and tools that enable the exchange and integration of data from distributed resources. Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting integrated data access.", "date": "2016-03-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Spannagl M." }, { "name": "Alaux M." }, { "name": "Lange M." }, { "name": "Bolser D.M." }, { "name": "Bader K.C." }, { "name": "Letellier T." }, { "name": "Kimmel E." }, { "name": "Flores R." }, { "name": "Pommier C." }, { "name": "Kerhornou A." }, { "name": "Walts B." }, { "name": "Nussbaumer T." }, { "name": "Grabmuller C." }, { "name": "Chen J." }, { "name": "Colmsee C." }, { "name": "Beier S." }, { "name": "Mascher M." }, { "name": "Schmutzer T." }, { "name": "Arend D." }, { "name": "Thanki A." }, { "name": "Ramirez-Gonzalez R." }, { "name": "Ayling M." }, { "name": "Ayling S." }, { "name": "Caccamo M." }, { "name": "Mayer K.F.X." }, { "name": "Scholz U." }, { "name": "Steinbach D." }, { "name": "Quesneville H." }, { "name": "Kersey P.J." } ], "journal": "Plant Genome" } }, { "doi": "10.1038/hortres.2016.56", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "2-\tAdam-Blondon, A.-F., Alaux, M., Pommier, C., Cantu, D., Cheng, Z.-M., Cramer, G. R., Davies, C., Delrot, S., Deluc, L., di Gaspero, G., Grimplet, J., Fennell, A., Londo, J. P., Kersey, P., Mattivi, F., Naithani, S., Neveu, P., Nikolski, M., Pezzotti, M., Reisch, B. I., Topfer, R., Vivier, M., Ware, D., Quesneville, H. (2016). Towards an open grapevine information system. Horticulture Research, 3, 8 p. , DOI : 10.1038/hortres.2016.56", "metadata": { "title": "Towards an open grapevine information system", "abstract": "Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www.vitaceae.org), to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools. To achieve this goal, it will be critical to develop, implement and adopt appropriate standards for data annotation and formatting. The development of this system, the GrapeIS, linking genotypes to phenotypes, and scientific research to agronomical and oeneological data, should provide new insights into grape biology, and allow the development of new varieties to meet the challenges of biotic and abiotic stress, environmental change, and consumer demand.", "date": "2016-11-23T00:00:00Z", "citationCount": 37, "authors": [ { "name": "Adam-Blondon A.-F." }, { "name": "Alaux M." }, { "name": "Pommier C." }, { "name": "Cantu D." }, { "name": "Cheng Z.-M." }, { "name": "Cramer G." }, { "name": "Davies C." }, { "name": "Delrot S." }, { "name": "Deluc L." }, { "name": "Di Gaspero G." }, { "name": "Grimplet J." }, { "name": "Fennell A." }, { "name": "Londo J." }, { "name": "Kersey P." }, { "name": "Mattivi F." }, { "name": "Naithani S." }, { "name": "Neveu P." }, { "name": "Nikolski M." }, { "name": "Pezzotti M." }, { "name": "Reisch B." }, { "name": "Topfer R." }, { "name": "Vivier M." }, { "name": "Ware D." }, { "name": "Quesneville H." } ], "journal": "Horticulture Research" } }, { "doi": "10.1186/s13059-018-1491-4", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "3-\tAlaux M, Rogers J, Letellier T, Flores R, Alfama F, Pommier C, Mohellibi N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Lainé M, Steinbach D, Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, International Wheat Genome Sequencing Consortium, Paux E, Eversole K, Adam-Blondon A-F, Quesneville H (2018) Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biology, 19:111.", "metadata": { "title": "Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data", "abstract": "The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. 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Description: We present the Cellular Microscopy Phenotype Ontology (CMPO), a species neutral ontology for describing phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is compatible with related ontology efforts, allowing for future cross-species integration of phenotypic data. CMPO was developed following a curator-driven approach where phenotype data were annotated by expert biologists following the Entity-Quality (EQ) pattern. These EQs were subsequently transformed into new CMPO terms following an established post composition process. Conclusion: CMPO is currently being utilized to annotate phenotypes associated with high content screening datasets stored in several image repositories including the Image Data Repository (IDR), MitoSys project database and the Cellular Phenotype Database to facilitate data browsing and discoverability.", "date": "2016-05-18T00:00:00Z", "citationCount": 24, "authors": [ { "name": "Jupp S." }, { "name": "Malone J." }, { "name": "Burdett T." }, { "name": "Heriche J.-K." }, { "name": "Williams E." }, { "name": "Ellenberg J." }, { "name": "Parkinson H." }, { "name": "Rustici G." } ], "journal": "Journal of Biomedical Semantics" } } ], "credit": [ { "name": "Simon Jupp", "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": [ 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We present SpaceM, an open-source method for in situ single-cell metabolomics that detects >100 metabolites from >1,000 individual cells per hour, together with a fluorescence-based readout and retention of morpho-spatial features. We validated SpaceM by predicting the cell types of cocultured human epithelial cells and mouse fibroblasts. We used SpaceM to show that stimulating human hepatocytes with fatty acids leads to the emergence of two coexisting subpopulations outlined by distinct cellular metabolic states. Inducing inflammation with the cytokine interleukin-17A perturbs the balance of these states in a process dependent on NF-κB signaling. The metabolic state markers were reproduced in a murine model of nonalcoholic steatohepatitis. We anticipate SpaceM to be broadly applicable for investigations of diverse cellular models and to democratize single-cell metabolomics.", "date": "2021-07-01T00:00:00Z", "citationCount": 167, "authors": [ { "name": "Rappez L." }, { "name": "Stadler M." }, { "name": "Triana S." }, { "name": "Gathungu R.M." }, { "name": "Ovchinnikova K." }, { "name": "Phapale P." }, { "name": "Heikenwalder M." }, { "name": "Alexandrov T." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "Mathias Heikenwalder", "email": "m.heikenwaelder@dkfz-heidelberg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Theodore Alexandrov", "email": "theodore.alexandrov@embl.de", "url": null, "orcidid": "https://orcid.org/0000-0001-9464-6125", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Prasad Phapale", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9487-597X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "Jennifer", "additionDate": "2021-11-20T18:38:56.875636Z", "lastUpdate": "2024-09-03T09:20:10.636926Z", "editPermission": { "type": "group", "authors": [ "sizhengZhao" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "massPix", "description": "Processes high resolution mass spectrometry imaging data, performs multivariate statistics (PCA, clustering) and lipid identification.", "homepage": "https://github.com/hallz/massPix", "biotoolsID": "masspix", "biotoolsCURIE": "biotools:masspix", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3214", "term": "Spectral analysis" }, { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" }, { "uri": "http://edamontology.org/operation_3960", "term": "Principal component analysis" }, { "uri": "http://edamontology.org/operation_3432", "term": "Clustering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] }, { "data": { "uri": "http://edamontology.org/data_2850", "term": "Lipid structure" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3579", "term": "JPG" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" }, { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/hallz/massPix", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1007/s11306-017-1252-5", "pmid": "28989334", "pmcid": "PMC5608769", "type": [], "version": null, "note": null, "metadata": { "title": "massPix: an R package for annotation and interpretation of mass spectrometry imaging data for lipidomics", "abstract": "Introduction: Mass spectrometry imaging (MSI) experiments result in complex multi-dimensional datasets, which require specialist data analysis tools. Objectives: We have developed massPix—an R package for analysing and interpreting data from MSI of lipids in tissue. Methods: massPix produces single ion images, performs multivariate statistics and provides putative lipid annotations based on accurate mass matching against generated lipid libraries. Results: Classification of tissue regions with high spectral similarly can be carried out by principal components analysis (PCA) or k-means clustering. Conclusion: massPix is an open-source tool for the analysis and statistical interpretation of MSI data, and is particularly useful for lipidomics applications.", "date": "2017-11-01T00:00:00Z", "citationCount": 19, "authors": [ { "name": "Bond N.J." }, { "name": "Koulman A." }, { "name": "Griffin J.L." }, { "name": "Hall Z." } ], "journal": "Metabolomics" } } ], "credit": [ { "name": "Julian L. 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Genome Biology, 19:111", "metadata": { "title": "Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data", "abstract": "© 2018 The Author(s).The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.", "date": "2018-08-17T00:00:00Z", "citationCount": 88, "authors": [ { "name": "Alaux M." }, { "name": "Rogers J." }, { "name": "Letellier T." }, { "name": "Flores R." }, { "name": "Alfama F." }, { "name": "Pommier C." }, { "name": "Mohellibi N." }, { "name": "Durand S." }, { "name": "Kimmel E." }, { "name": "Michotey C." }, { "name": "Guerche C." }, { "name": "Loaec M." }, { "name": "Laine M." }, { "name": "Steinbach D." }, { "name": "Choulet F." }, { "name": "Rimbert H." }, { "name": "Leroy P." }, { "name": "Guilhot N." }, { "name": "Salse J." }, { "name": "Feuillet C." }, { "name": "Paux E." }, { "name": "Eversole K." }, { "name": "Adam-Blondon A.-F." }, { "name": "Quesneville H." } ], "journal": "Genome Biology" } } ], "credit": [ { "name": "Support service", "email": "urgi-support@inrae.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Support" ], "note": null } ], "community": null, "owner": "jison", "additionDate": "2019-11-05T10:40:37Z", "lastUpdate": "2024-09-02T05:04:35.733493Z", "editPermission": { "type": "group", "authors": [ "nfrancillon", "raphael.flores" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "APE", "description": "APE (the Automated Pipeline Explorer) as a command-line tool and API for automated composition of scientific workflows. APE is easily configured to a new application domain by providing it with a domain ontology and semantically annotated tools. It can then be used to synthesize purpose-specific workflows based on a specification of the available workflow inputs, desired outputs and possibly additional constraints.", "homepage": "https://github.com/sanctuuary/APE/", "biotoolsID": "ape", "biotoolsCURIE": "biotools:ape", "version": [ "2.1.7" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3429", "term": "Generation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0949", "term": "Workflow metadata" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0949", "term": "Workflow metadata" }, "format": [ { "uri": "http://edamontology.org/format_3857", "term": "CWL" }, { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Java" ], "license": "Apache-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/sanctuuary/ape", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://mvnrepository.com/artifact/io.github.sanctuuary/APE/2.1.7", "type": "Software package", "note": "Download APE java library or the CLI", "version": "2.1.7" } ], "documentation": [ { "url": "https://ape-framework.readthedocs.io/", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-030-50436-6_34", "pmid": null, "pmcid": "PMC7304703", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Ape: A command-line tool and api for automated workflow composition", "abstract": "Automated workflow composition is bound to take the work with scientific workflows to the next level. On top of today’s comprehensive eScience infrastructure, it enables the automated generation of possible workflows for a given specification. However, functionality for automated workflow composition tends to be integrated with one of the many available workflow management systems, and is thus difficult or impossible to apply in other environments. Therefore we have developed APE (the Automated Pipeline Explorer) as a command-line tool and API for automated composition of scientific workflows. APE is easily configured to a new application domain by providing it with a domain ontology and semantically annotated tools. It can then be used to synthesize purpose-specific workflows based on a specification of the available workflow inputs, desired outputs and possibly additional constraints. The workflows can further be transformed into executable implementations and/or exported into standard workflow formats. In this paper we describe APE v1.0 and discuss lessons learned from applications in bioinformatics and geosciences.", "date": "2020-01-01T00:00:00Z", "citationCount": 12, "authors": [ { "name": "Kasalica V." }, { "name": "Lamprecht A.-L." } ], "journal": "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)" } }, { "doi": "10.1021/ACS.JPROTEOME.0C00983", "pmid": "33720735", "pmcid": "PMC8041394", "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "APE in the Wild: Automated Exploration of Proteomics Workflows in the bio.tools Registry", "abstract": "The bio.tools registry is a main catalogue of computational tools in the life sciences. More than 17 000 tools have been registered by the international bioinformatics community. The bio.tools metadata schema includes semantic annotations of tool functions, that is, formal descriptions of tools' data types, formats, and operations with terms from the EDAM bioinformatics ontology. Such annotations enable the automated composition of tools into multistep pipelines or workflows. In this Technical Note, we revisit a previous case study on the automated composition of proteomics workflows. We use the same four workflow scenarios but instead of using a small set of tools with carefully handcrafted annotations, we explore workflows directly on bio.tools. We use the Automated Pipeline Explorer (APE), a reimplementation and extension of the workflow composition method previously used. Moving \"into the wild\"opens up an unprecedented wealth of tools and a huge number of alternative workflows. Automated composition tools can be used to explore this space of possibilities systematically. Inevitably, the mixed quality of semantic annotations in bio.tools leads to unintended or erroneous tool combinations. However, our results also show that additional control mechanisms (tool filters, configuration options, and workflow constraints) can effectively guide the exploration toward smaller sets of more meaningful workflows.", "date": "2021-04-02T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Kasalica V." }, { "name": "Schwammle V." }, { "name": "Palmblad M." }, { "name": "Ison J." }, { "name": "Lamprecht A.-L." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": "Vedran Kasalica", "email": "v.kasalica@esciencecenter.nl", "url": null, "orcidid": "https://orcid.org/0000-0002-0097-1056", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Anna-Lena Lamprecht", "email": "anna-lena.lamprecht@uni-potsdam.de", "url": null, "orcidid": "https://orcid.org/0000-0003-1953-5606", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "VKasalica", "additionDate": "2021-01-18T10:10:48Z", "lastUpdate": "2024-08-26T12:57:24.763845Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "FunGenES", "description": "A database and web application for analyzing embryonic stem cells differentiation process on mouse model. The data is collected by FunGenES consortium and organized into six clusters to facilitate data mining.", "homepage": "http://biit.cs.ut.ee/fungenes/", "biotoolsID": "fungenes", "biotoolsCURIE": "biotools:fungenes", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3439", "term": "Pathway or network prediction" }, { "uri": "http://edamontology.org/operation_2495", "term": "Gene expression analysis" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_3083", "term": "Pathway or network visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0928", "term": "Gene expression profile" }, "format": [ { "uri": "http://edamontology.org/format_3617", "term": "Graph format" } ] }, { "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_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_3365", "term": "Data architecture, analysis and design" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_3395", "term": "Regenerative medicine" }, { "uri": "http://edamontology.org/topic_0607", "term": "Laboratory information management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Freeware", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://biit.cs.ut.ee/fungenes/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1007/s12015-006-0001-3", "pmid": null, "pmcid": null, "type": [ "Review" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "ELIXIR-EE", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "kolde@ut.ee", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "ELIXIR-EE", "additionDate": "2015-01-22T11:13:24Z", "lastUpdate": "2024-08-21T06:17:55.305290Z", "editPermission": { "type": "group", "authors": [ "ambreen" ] }, "validated": 1, "homepage_status": 1, "elixir_badge": 0, "confidence_flag": null }, { "name": "CellPPDMod", "description": "CellPPD-Mod is an in silico method, which is developed to predict efficient modified cell penetrating peptides (CellPPD-Mods).", "homepage": "http://webs.iiitd.edu.in/raghava/cellppdmod/", "biotoolsID": "cellppdmod", "biotoolsCURIE": "biotools:cellppdmod", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0252", "term": "Peptide immunogenicity prediction" }, { "uri": "http://edamontology.org/operation_4009", "term": "Small molecule design" }, { "uri": "http://edamontology.org/operation_0418", "term": "Protein signal peptide detection" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3374", "term": "Biotherapeutics" }, { "uri": "http://edamontology.org/topic_3930", "term": "Immunogenetics" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3375", "term": "Drug metabolism" } ], "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": "10.1007/978-1-0716-1752-6_4", "pmid": "34766282", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "In Silico Design of Chemically Modified Cell-Penetrating Peptides", "abstract": "© 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.In the past few decades, a large number of cell-penetrating peptides (CPPs) have been discovered. These CPPs have a wide range of applications including drug delivery vehicles. Numerous in silico tools have been developed over the years to design and predict the cell-penetrating peptides that contain natural amino acids. The majority of natural cell-penetrating peptides have several limitations including stability, immunogenicity as well as got entrapped in the cell’s endosomes. The chemical modification is commonly used to most of these limitations. An in silico tool called CellPPDMod have been developed by our group to predict cell-penetration potential of chemically modified peptides. This chapter is dedicated for designing therapeutically important cell-penetrating peptides using CellPPDMod (http://webs.iiitd.edu.in/raghava/cellppdmod/ ).", "date": "2022-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Kumar V." }, { "name": "Raghava G.P.S." } ], "journal": "Methods in Molecular Biology" } } ], "credit": [ { "name": "Gajendra P. S. Raghava", "email": "raghava@iiitd.ac.in", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Vinod Kumar", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "raghavagps", "additionDate": "2022-04-04T09:27:41.653337Z", "lastUpdate": "2024-08-21T06:17:30.142454Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "medium" } ] }