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{ "count": 33009, "next": "?page=2", "previous": null, "list": [ { "name": "Metastasis risk prediction in Lung cancer", "description": "Α radiomics-based machine learning model, for the prediction of the occurrence of metastasis within two years of the initial lung cancer diagnosis combining information from the tumor and the peritumoral area as well clinical information of the patient.", "homepage": "https://www.med.auth.gr/en/content/laboratory-computing-medical-informatics-and-biomedical-imaging-technologies", "biotoolsID": "metastasis_risk_prediction_in_lung_cancer", "biotoolsCURIE": "biotools:metastasis_risk_prediction_in_lung_cancer", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Command-line tool" ], "topic": [], "operatingSystem": [], "language": [ "Python", "R" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1016/j.cmpb.2025.109029", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Ioanna Chouvarda", "email": "ioannach@auth.gr", "url": "https://scholar.google.com/citations?user=QgcrIzEAAAAJ&hl=el&oi=sra", "orcidid": "https://orcid.org/0000-0001-8915-6658", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "Professor, Aristotle University of Thessaloniki" } ], "owner": "dimfilos", "additionDate": "2026-05-14T11:24:19.900801Z", "lastUpdate": "2026-05-14T11:24:19.902842Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Prostate ISUP classification", "description": "This software implements a AI pipeline for the detection of clinically significant prostate cancer (csPCa) from multiparametric MRI images combined with routine clinical data. 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A suite of four Image Quality Assessment (IQA) metrics designed to evaluate the perceptual quality of preclinical and clinical image datasets within the XNAT platform at the scan and subject levels. 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It is a combination between two filters such as the Non-Local mean filter and the Anisotropic Diffusion tensor method with an estimator of Rician noise. 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However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph. Unlike other graph-based assemblers that only aim to maintain the contiguity of one haplotype, hifiasm strives to preserve the contiguity of all haplotypes. This feature enables the development of a graph trio binning algorithm that greatly advances over standard trio binning. 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It has seen wide applications in pharmaceutical and biological researches. Previously, we proposed a blind docking server, CB-Dock, which has been under heavy use (over 200 submissions per day) by researchers worldwide since 2019. Here, we substantially improved the docking method by combining CB-Dock with our template-based docking engine to enhance the accuracy in binding site identification and binding pose prediction. In the benchmark tests, it yielded the success rate of ∼85% for binding pose prediction (RMSD < 2.0 Å), which outperformed original CB-Dock and most popular blind docking tools. This updated docking server, named CB-Dock2, reconfigured the input and output web interfaces, together with a highly automatic docking pipeline, making it a particularly efficient and easy-to-use tool for the bioinformatics and cheminformatics communities. 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First, EvolView is a phylogenetic tree viewer and customization tool; it visualizes trees in various formats, customizes them through built-in functions that can link information from external datasets, and exports the customized results to publication-ready figures. Second, EvolView is a tree and dataset management tool: users can easily organize related trees into distinct projects, add new datasets to trees and edit and manage existing trees and datasets. To make EvolView easy to use, it is equipped with an intuitive user interface. With a free account, users can save data and manipulations on the EvolView server. EvolView is freely available at: http://www.evolgenius.info/evolview.html. © 2012 The Author(s).", "date": "2012-07-01T00:00:00Z", "citationCount": 361, "authors": [ { "name": "Zhang H." }, { "name": "Gao S." }, { "name": "Lercher M.J." }, { "name": "Hu S." }, { "name": "Chen W.-H." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkw370", "pmid": "27131786", "pmcid": "PMC4987921", "type": [], "version": null, "note": null, "metadata": { "title": "Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees", "abstract": "Evolview is an online visualization and management tool for customized and annotated phylogenetic trees. It allows users to visualize phylogenetic trees in various formats, customize the trees through built-in functions and user-supplied datasets and export the customization results to publication-ready figures. Its 'dataset system' contains not only the data to be visualized on the tree, but also 'modifiers' that control various aspects of the graphical annotation. Evolview is a single-page application (like Gmail); its carefully designed interface allows users to upload, visualize, manipulate and manage trees and datasets all in a single webpage. Developments since the last public release include a modern dataset editor with keyword highlighting functionality, seven newly added types of annotation datasets, collaboration support that allows users to share their trees and datasets and various improvements of the web interface and performance. In addition, we included eleven new 'Demo' trees to demonstrate the basic functionalities of Evolview, and five new 'Showcase' trees inspired by publications to showcase the power of Evolview in producing publication-ready figures. 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