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{ "count": 29626, "next": "?page=2", "previous": null, "list": [ { "name": "ODAMNet", "description": "A Python package to study molecular relationship between environmental factors and rare diseases.", "homepage": "https://pypi.org/project/ODAMNet/", "biotoolsID": "odamnet", "biotoolsCURIE": "biotools:odamnet", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3927", "term": "Network analysis" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0276", "term": "Protein interaction network analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [ "Rare Diseases" ], "link": [ { "url": "https://github.com/MOohTus/ODAMNet", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://odamnet.readthedocs.io/en/latest/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.softx.2024.101701", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "ODAMNet: A Python package to identify molecular relationships between chemicals and rare diseases using overlap, active module and random walk approaches", "abstract": "Environmental factors are external conditions that can affect the health of living organisms. For a number of rare genetic diseases, an interplay between genetic and environmental factors is known or suspected. However, the studies are limited by the scarcity of patients and the difficulties in gathering reliable exposure information. In order to aid in fostering research between environmental factors and rare diseases, we propose ODAMNet, a Python package to investigate the possible relationships between chemicals, which are a subset of environmental factors, and rare diseases. ODAMNet offers three different and complementary bioinformatics approaches for the exploration of relationships: overlap analysis, active module identification and random walk with restart. ODAMNet allows systematic analysis of chemical - rare disease relationships and generation of hypotheses for further investigation of effect mechanisms.", "date": "2024-05-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Terezol M." }, { "name": "Baudot A." }, { "name": "Ozisik O." } ], "journal": "SoftwareX" } } ], "credit": [ { "name": "Morgane Térézol", "email": "morgane.terezol@univ-amu.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-4090-2573", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Anaïs Baudot", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0885-7933", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Ozan Ozisik", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-5980-8002", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "mterezol", "additionDate": "2023-03-08T09:19:09.284884Z", "lastUpdate": "2024-05-02T11:58:39.872174Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ZeroBind", "description": "Protein-specific zero-shot predictor with subgraph matching for drug-target interactions.", "homepage": "http://www.csbio.sjtu.edu.cn/bioinf/ZeroBind/", "biotoolsID": "zerobind", "biotoolsCURIE": "biotools:zerobind", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3938", "term": "Virtual screening" }, { "uri": "http://edamontology.org/operation_2492", "term": "Protein interaction prediction" }, { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_3047", "term": "Molecular biology" }, { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/myprecioushh/ZeroBind", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/S41467-023-43597-1", "pmid": "38030641", "pmcid": "PMC10687269", "type": [], "version": null, "note": null, "metadata": { "title": "ZeroBind: a protein-specific zero-shot predictor with subgraph matching for drug-target interactions", "abstract": "Existing drug-target interaction (DTI) prediction methods generally fail to generalize well to novel (unseen) proteins and drugs. In this study, we propose a protein-specific meta-learning framework ZeroBind with subgraph matching for predicting protein-drug interactions from their structures. During the meta-training process, ZeroBind formulates training a protein-specific model, which is also considered a learning task, and each task uses graph neural networks (GNNs) to learn the protein graph embedding and the molecular graph embedding. Inspired by the fact that molecules bind to a binding pocket in proteins instead of the whole protein, ZeroBind introduces a weakly supervised subgraph information bottleneck (SIB) module to recognize the maximally informative and compressive subgraphs in protein graphs as potential binding pockets. In addition, ZeroBind trains the models of individual proteins as multiple tasks, whose importance is automatically learned with a task adaptive self-attention module to make final predictions. The results show that ZeroBind achieves superior performance on DTI prediction over existing methods, especially for those unseen proteins and drugs, and performs well after fine-tuning for those proteins or drugs with a few known binding partners.", "date": "2023-12-01T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Wang Y." }, { "name": "Xia Y." }, { "name": "Yan J." }, { "name": "Yuan Y." }, { "name": "Shen H.-B." }, { "name": "Pan X." } ], "journal": "Nature Communications" } } ], "credit": [ { "name": "Xiaoyong Pan", "email": "2008xypan@sjtu.edu.cn", "url": null, "orcidid": "https://orcid.org/0000-0001-5010-464X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Yuxuan Wang", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-05-02T10:02:03.465896Z", "lastUpdate": "2024-05-02T10:02:03.468091Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "COLOCdb", "description": "COLOCdb represents the most comprehensive colocalization analysis by integrating publicly available GWASs, 187 multi-omics datasets from 13 types of xQTL and three different colocalization algorithms.", "homepage": "https://ngdc.cncb.ac.cn/colocdb", "biotoolsID": "colocdb", "biotoolsCURIE": "biotools:colocdb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_3791", "term": "Collapsing methods" }, { "uri": "http://edamontology.org/operation_0282", "term": "Genetic mapping" }, { "uri": "http://edamontology.org/operation_3232", "term": "Gene expression QTL analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3517", "term": "GWAS study" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3295", "term": "Epigenetics" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" } ], "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": "10.1093/NAR/GKAD939", "pmid": "37941154", "pmcid": "PMC10767919", "type": [], "version": null, "note": null, "metadata": { "title": "COLOCdb: a comprehensive resource for multi-model colocalization of complex traits", "abstract": "Large-scale genome-wide association studies (GWAS) have provided profound insights into complex traits and diseases. Yet, deciphering the fine-scale molecular mechanisms of how genetic variants manifest to cause the phenotypes remains a daunting task. Here, we present COLOCdb (https://ngdc.cncb.ac.cn/colocdb), a comprehensive genetic colocalization database by integrating more than 3000 GWAS summary statistics and 13 types of xQTL to date. By employing two representative approaches for the colocalization analysis, COLOCdb deposits results from three key components: (i) GWAS-xQTL, pair-wise colocalization between GWAS loci and different types of xQTL, (ii) GWAS–GWAS, pair-wise colocalization between the trait-associated genetic loci from GWASs and (iii) xQTL–xQTL, pair-wise colocalization between the genetic loci associated with molecular phenotypes in xQTLs. These results together represent the most comprehensive colocalization analysis, which also greatly expands the list of shared variants with genetic pleiotropy. We expect that COLOCdb can serve as a unique and useful resource in advancing the discovery of new biological mechanisms and benefit future functional studies.", "date": "2024-01-05T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Pan S." }, { "name": "Kang H." }, { "name": "Liu X." }, { "name": "Li S." }, { "name": "Yang P." }, { "name": "Wu M." }, { "name": "Yuan N." }, { "name": "Lin S." }, { "name": "Zheng Q." }, { "name": "Jia P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Peilin Jia", "email": "pjia@big.ac.cn", "url": null, "orcidid": "https://orcid.org/0000-0003-4523-4153", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Siyu Pan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-05-02T09:56:40.263517Z", "lastUpdate": "2024-05-02T09:56:40.265959Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ZEBRA", "description": "Hierarchically integrated gene expression atlas of the murine and human brain at single-cell resolution.", "homepage": "https://www.ccb.uni-saarland.de/zebra", "biotoolsID": "zebra_ccb", "biotoolsCURIE": "biotools:zebra_ccb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression profiling" }, { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3399", "term": "Geriatric medicine" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" } ], "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": "10.1093/NAR/GKAD990", "pmid": "37941147", "pmcid": "PMC10767845", "type": [], "version": null, "note": null, "metadata": { "title": "ZEBRA: a hierarchically integrated gene expression atlas of the murine and human brain at single-cell resolution", "abstract": "The molecular causes and mechanisms of neurodegenerative diseases remain poorly understood. A growing number of single-cell studies have implicated various neural, glial, and immune cell subtypes to affect the mammalian central nervous system in many age-related disorders. Integrating this body of transcriptomic evidence into a comprehensive and reproducible framework poses several computational challenges. Here, we introduce ZEBRA, a large single-cell and single-nucleus RNA-seq database. ZEBRA integrates and normalizes gene expression and metadata from 33 studies, encompassing 4.2 million human and mouse brain cells sampled from 39 brain regions. It incorporates samples from patients with neurodegenerative diseases like Alzheimer’s disease, Parkinson’s disease, and Multiple sclerosis, as well as samples from relevant mouse models. We employed scVI, a deep probabilistic auto-encoder model, to integrate the samples and curated both cell and sample metadata for downstream analysis. ZEBRA allows for cell-type and disease-specific markers to be explored and compared between sample conditions and brain regions, a cell composition analysis, and gene-wise feature mappings. Our comprehensive molecular database facilitates the generation of data-driven hypotheses, enhancing our understanding of mammalian brain function during aging and disease. The data sets, along with an interactive database are freely available at https://www.ccb.uni-saarland.de/zebra. Graphical abstract", "date": "2024-01-05T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Flotho M." }, { "name": "Amand J." }, { "name": "Hirsch P." }, { "name": "Grandke F." }, { "name": "Wyss-Coray T." }, { "name": "Keller A." }, { "name": "Kern F." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Fabian Kern", "email": "fabianmichael.kern@helmholtz-hips.de", "url": null, "orcidid": "https://orcid.org/0000-0002-8223-3750", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Matthias Flotho", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-05-02T09:52:28.384050Z", "lastUpdate": "2024-05-02T09:52:28.386397Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "trRosettaRNA", "description": "Automated prediction of RNA 3D structure with transformer network.", "homepage": "https://yanglab.qd.sdu.edu.cn/trRosettaRNA", "biotoolsID": "trrosettarna", "biotoolsCURIE": "biotools:trrosettarna", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2441", "term": "RNA structure prediction" }, { "uri": "http://edamontology.org/operation_0278", "term": "RNA secondary structure prediction" }, { "uri": "http://edamontology.org/operation_0474", "term": "Protein structure prediction" }, { "uri": "http://edamontology.org/operation_0303", "term": "Fold recognition" }, { "uri": "http://edamontology.org/operation_3927", "term": "Network analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" }, { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" }, { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "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": "10.1038/S41467-023-42528-4", "pmid": "37945552", "pmcid": "PMC10636060", "type": [], "version": null, "note": null, "metadata": { "title": "trRosettaRNA: automated prediction of RNA 3D structure with transformer network", "abstract": "RNA 3D structure prediction is a long-standing challenge. Inspired by the recent breakthrough in protein structure prediction, we developed trRosettaRNA, an automated deep learning-based approach to RNA 3D structure prediction. The trRosettaRNA pipeline comprises two major steps: 1D and 2D geometries prediction by a transformer network; and 3D structure folding by energy minimization. Benchmark tests suggest that trRosettaRNA outperforms traditional automated methods. In the blind tests of the 15th Critical Assessment of Structure Prediction (CASP15) and the RNA-Puzzles experiments, the automated trRosettaRNA predictions for the natural RNAs are competitive with the top human predictions. trRosettaRNA also outperforms other deep learning-based methods in CASP15 when measured by the Z-score of the Root-Mean-Square Deviation. Nevertheless, it remains challenging to predict accurate structures for synthetic RNAs with an automated approach. We hope this work could be a good start toward solving the hard problem of RNA structure prediction with deep learning.", "date": "2023-12-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Wang W." }, { "name": "Feng C." }, { "name": "Han R." }, { "name": "Wang Z." }, { "name": "Ye L." }, { "name": "Du Z." }, { "name": "Wei H." }, { "name": "Zhang F." }, { "name": "Peng Z." }, { "name": "Yang J." } ], "journal": "Nature Communications" } } ], "credit": [ { "name": "Fa Zhang", "email": "zhangfa@ict.ac.cn", "url": null, "orcidid": "https://orcid.org/0000-0002-2081-9369", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Zhenling Peng", "email": "zhenling@email.sdu.edu.cn", "url": null, "orcidid": "https://orcid.org/0000-0003-0303-6693", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Jianyi Yang", "email": "yangjy@sdu.edu.cn", "url": null, "orcidid": "https://orcid.org/0000-0003-2912-7737", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-05-02T09:47:32.738021Z", "lastUpdate": "2024-05-02T09:47:32.740447Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "scMuffin", "description": "R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis.", "homepage": "https://emosca-cnr.github.io/scMuffin", "biotoolsID": "scmuffin", "biotoolsCURIE": "biotools:scmuffin", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2495", "term": "Expression analysis" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" }, { "uri": "http://edamontology.org/operation_3799", "term": "Quantification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_2229", "term": "Cell biology" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/emosca-cnr/scMuffin", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/S12859-023-05563-Y", "pmid": "38012590", "pmcid": "PMC10680269", "type": [], "version": null, "note": null, "metadata": { "title": "scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis", "abstract": "Introduction: Single-cell (SC) gene expression analysis is crucial to dissect the complex cellular heterogeneity of solid tumors, which is one of the main obstacles for the development of effective cancer treatments. Such tumors typically contain a mixture of cells with aberrant genomic and transcriptomic profiles affecting specific sub-populations that might have a pivotal role in cancer progression, whose identification eludes bulk RNA-sequencing approaches. We present scMuffin, an R package that enables the characterization of cell identity in solid tumors on the basis of a various and complementary analyses on SC gene expression data. Results: scMuffin provides a series of functions to calculate qualitative and quantitative scores, such as: expression of marker sets for normal and tumor conditions, pathway activity, cell state trajectories, Copy Number Variations, transcriptional complexity and proliferation state. Thus, scMuffin facilitates the combination of various evidences that can be used to distinguish normal and tumoral cells, define cell identities, cluster cells in different ways, link genomic aberrations to phenotypes and identify subtle differences between cell subtypes or cell states. We analysed public SC expression datasets of human high-grade gliomas as a proof-of-concept to show the value of scMuffin and illustrate its user interface. Nevertheless, these analyses lead to interesting findings, which suggest that some chromosomal amplifications might underlie the invasive tumor phenotype and the presence of cells that possess tumor initiating cells characteristics. Conclusions: The analyses offered by scMuffin and the results achieved in the case study show that our tool helps addressing the main challenges in the bioinformatics analysis of SC expression data from solid tumors.", "date": "2023-12-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Nale V." }, { "name": "Chiodi A." }, { "name": "Di Nanni N." }, { "name": "Cifola I." }, { "name": "Moscatelli M." }, { "name": "Cocola C." }, { "name": "Gnocchi M." }, { "name": "Piscitelli E." }, { "name": "Sula A." }, { "name": "Zucchi I." }, { "name": "Reinbold R." }, { "name": "Milanesi L." }, { "name": "Mezzelani A." }, { "name": "Pelucchi P." }, { "name": "Mosca E." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Paride Pelucchi", "email": "paride.pelucchi@itb.cnr.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Ettore Mosca", "email": "ettore.mosca@itb.cnr.it", "url": null, "orcidid": "https://orcid.org/0000-0002-3102-5150", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-05-02T09:45:52.183190Z", "lastUpdate": "2024-05-02T09:45:52.185902Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "VEuPathDB", "description": "VEuPathDB is packed with data, tools and visualizations that can help answer your research questions. We gather data from many sources, analyze according to standard workflows, and present the results for you to mine in a point and click interface. The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Resource Center funded by the National Institutes of Health with additional funding from the Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts.", "homepage": "https://veupathdb.org", "biotoolsID": "veupathdb", "biotoolsCURIE": "biotools:veupathdb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3663", "term": "Homology-based gene prediction" }, { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/VEuPathDB", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/NAR/GKAD1003", "pmid": "37953350", "pmcid": "PMC10767879", "type": [], "version": null, "note": null, "metadata": { "title": "VEuPathDB: the eukaryotic pathogen, vectorãnd host bioinf ormatics resour ce cent er in 2023", "abstract": "T he Eukary otic Pathogen, Vectorãnd Host Inf ormatics R esource (VEuPathDB, https://v eupathdb.org ) isã Bioinf ormatics R esource Center funded by the National Institutes of Health withãdditional funding from the Wellcome Trust. VEuPathDB supports > 600 organisms that comprise in v er- tebrate v ectors, eukary otic pathogens (protistsãnd fungi)ãnd rele vãnt free-living or non-pathogenic species or hosts. Since 2004, VEuPathDB hasãnalyzed omics data from the public domain using contemporary bioinformatic workflows, including orthology predictions via OrthoMCL,ãnd integrated theãnalysis results withãnalysis tools, visualizations,ãndãdvanced search capabilities. The unique data mining platform coupled with > 30 0 0 pre-analyzed datã sets facilitãtes the exploration of pertinent omics datã in support of h ypothesis driv en research. Comparisonsãre easily madeãcross data sets, data typesãnd organisms. A Galaxy workspace offers the opportunity for theãnalysis of private large-scale datasetsãnd for porting to VEuPathDB for comparisons with integrated data. The MapVEu tool providesã platform for exploration of spatially resolved data suchãs vector surveillanceãnd insecticide resistance monitoring. Toãddress the growing body of omics dataãndãdvances in laboratory techniques, VEuPathDB hasãdded se v eral ne w datã t ypes, searchesãnd features, impro v ed the Galaxy w orkspace en vironment, redesigned the MapVEu interfaceãnd updated the infrastr uct ure toãccommodate these changes.", "date": "2024-01-05T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Alvarez-Jarreta J." }, { "name": "Amos B." }, { "name": "Aurrecoechea C." }, { "name": "Bah S." }, { "name": "Barba M." }, { "name": "Barreto A." }, { "name": "Basenko E.Y." }, { "name": "Belnap R." }, { "name": "Blevins A." }, { "name": "Bohme U." }, { "name": "Brestelli J." }, { "name": "Brown S." }, { "name": "Callan D." }, { "name": "Campbell L.I." }, { "name": "Christophides G.K." }, { "name": "Crouch K." }, { "name": "Davison H.R." }, { "name": "DeBarry J.D." }, { "name": "Demko R." }, { "name": "Doherty R." }, { "name": "Duan Y." }, { "name": "Dundore W." }, { "name": "Dyer S." }, { "name": "Falke D." }, { "name": "Fischer S." }, { "name": "Gajria B." }, { "name": "Galdi D." }, { "name": "Giraldo-Calderon G.I." }, { "name": "Harb O.S." }, { "name": "Harper E." }, { "name": "Helb D." }, { "name": "Howington C." }, { "name": "Hu S." }, { "name": "Humphrey J." }, { "name": "Iodice J." }, { "name": "Jones A." }, { "name": "Judkins J." }, { "name": "Kelly S.A." }, { "name": "Kissinger J.C." }, { "name": "Kittur N." }, { "name": "Kwon D.K." }, { "name": "Lamoureux K." }, { "name": "Li W." }, { "name": "Lodha D." }, { "name": "MacCallum R.M." }, { "name": "Maslen G." }, { "name": "McDowell M.A." }, { "name": "Myers J." }, { "name": "Nural M.V." }, { "name": "Roos D.S." }, { "name": "Rund S.S.C." }, { "name": "Shanmugasundram A." }, { "name": "Sitnik V." }, { "name": "Spruill D." }, { "name": "Starns D." }, { "name": "Tomko S.S." }, { "name": "Wang H." }, { "name": "Warrenfeltz S." }, { "name": "Wieck R." }, { "name": "Wilkinson P.A." }, { "name": "Zheng J." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Omar S Harb", "email": "oharb@sas.upenn.edu", "url": null, "orcidid": "https://orcid.org/0000-0003-4446-6200", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Jorge Alvarez-Jarreta", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-05-02T09:43:00.475332Z", "lastUpdate": "2024-05-02T09:43:00.477868Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "DeepFold", "description": "Enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function.", "homepage": "https://github.com/newtonjoo/deepfold", "biotoolsID": "deepfold", "biotoolsCURIE": "biotools:deepfold", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0474", "term": "Protein structure prediction" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" }, { "uri": "http://edamontology.org/operation_1777", "term": "Protein function prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" }, { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" }, { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" } ], "operatingSystem": [], "language": [ "C", "C++", "Python" ], "license": "Apache-2.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/bioinformatics/btad712", "pmid": "37995286", "pmcid": "PMC10699847", "type": [], "version": null, "note": null, "metadata": { "title": "DeepFold: Enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function", "abstract": "Motivation: Predicting protein structures with high accuracy is a critical challenge for the broad community of life sciences and industry. Despite progress made by deep neural networks like AlphaFold2, there is a need for further improvements in the quality of detailed structures, such as side-chains, along with protein backbone structures. Results: Building upon the successes of AlphaFold2, the modifications we made include changing the losses of side-chain torsion angles and frame aligned point error, adding loss functions for side chain confidence and secondary structure prediction, and replacing template feature generation with a new alignment method based on conditional random fields. We also performed re-optimization by conformational space annealing using a molecular mechanics energy function which integrates the potential energies obtained from distogram and side-chain prediction. In the CASP15 blind test for single protein and domain modeling (109 domains), DeepFold ranked fourth among 132 groups with improvements in the details of the structure in terms of backbone, side-chain, and Molprobity. In terms of protein backbone accuracy, DeepFold achieved a median GDT-TS score of 88.64 compared with 85.88 of AlphaFold2. For TBM-easy/hard targets, DeepFold ranked at the top based on Z-scores for GDT-TS. This shows its practical value to the structural biology community, which demands highly accurate structures. In addition, a thorough analysis of 55 domains from 39 targets with publicly available structures indicates that DeepFold shows superior side-chain accuracy and Molprobity scores among the top-performing groups.", "date": "2023-12-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Lee J.-W." }, { "name": "Won J.-H." }, { "name": "Jeon S." }, { "name": "Choo Y." }, { "name": "Yeon Y." }, { "name": "Oh J.-S." }, { "name": "Kim M." }, { "name": "Kim S." }, { "name": "Joung I." }, { "name": "Jang C." }, { "name": "Lee S.J." }, { "name": "Kim T.H." }, { "name": "Jin K.H." }, { "name": "Song G." }, { "name": "Kim E.-S." }, { "name": "Yoo J." }, { "name": "Paek E." }, { "name": "Noh Y.-K." }, { "name": "Joo K." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Yung-Kyun Noh", "email": "nohyung@hanyang.ac.kr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Keehyoung Joo", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-4612-0927", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-05-02T09:40:27.871566Z", "lastUpdate": "2024-05-02T09:40:27.873828Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "DRMref", "description": "Comprehensive reference map of drug resistance mechanisms in human cancer.", "homepage": "https://ccsm.uth.edu/DRMref/", "biotoolsID": "drmref", "biotoolsCURIE": "biotools:drmref", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression profiling" }, { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" }, { "uri": "http://edamontology.org/operation_0463", "term": "miRNA target prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0202", "term": "Pharmacology" } ], "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": "10.1093/NAR/GKAD1087", "pmid": "37986230", "pmcid": "PMC10767840", "type": [], "version": null, "note": null, "metadata": { "title": "DRMref: compr ehensive r efer ence map of drug r esistance mechanisms in human cancer", "abstract": "Drug resistance posesã significant challenge in cancer treatment. Despite the initial effectiveness of therapies suchãs chemotherapy, targeted therapyãnd immunotherapy, many patients eventually develop resistance. To gain deep insights into the underlying mechanisms, single-cell profiling has been performed to interrogate drug resistanceãt cell le v el. Herein, w e ha v e built the DRMref database ( https://ccsm.uth.edu/ DRMref/) to provide comprehensive characterization of drug resistance using single-cell data from drug treatment settings. The current version of DRMref includes 42 single-cell datasets from 30 studies, co v ering 382 samples, 13 major cancer types, 26 cancer subtypes, 35 treatment regimensãnd 42 drugs. All datasets in DRMrefãre browsableãnd searchable, with detailedãnnotations pro vided. Mean while, DRMref includesãnalyses of cellular composition, intratumoral heterogeneity, epithelial-mesenchymal transition, cell-cell interactionãnd differentially expressed genes in resistãnt cells. Notãbly, DRMref in v estigates the drug resistãnce mechanisms (e.g . Aberration of Drug' s Therapeutic Tãrget, Drug Inactivãtion b y Str uct ure Modification, etc.) in resistant cells. A dditional enrichmentãnaly sis of hallmark / KEGG (Ky oto Ency clopedia of Genesãnd Genomes) / GO (Gene Ontology) pathwã y s,ãs w ellãs the identification of microRNA, motifãnd transcription fãctors in v olv ed in resistant cells, is provided in DRMref for user's exploration. Overall, DRMref servesãsã unique single-cell-based resource for st udying dr ug resistance, drug combination therapyãnd discovering novel drug targets.", "date": "2024-01-05T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Liu X." }, { "name": "Yi J." }, { "name": "Li T." }, { "name": "Wen J." }, { "name": "Huang K." }, { "name": "Liu J." }, { "name": "Wang G." }, { "name": "Kim P." }, { "name": "Song Q." }, { "name": "Zhou X." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Pora Kim", "email": "Pora.Kim@uth.tmc.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-8321-6864", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Qianqian Song", "email": "qsong1@ufl.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-4455-5302", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Xiaobo Zhou", "email": "xiaobo.zhou@uth.tmc.edu", "url": null, "orcidid": "https://orcid.org/0000-0001-7191-6495", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-05-02T09:38:05.878431Z", "lastUpdate": "2024-05-02T09:38:05.880496Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "IMG PR", "description": "Database of plasmids from genomes and metagenomes with rich annotations and metadata. It provides an extensive collection of plasmids, identified across thousands of isolate genomes, SAGs, MAGs, metagenomes, and metatranscriptomes using the geNomad tool. These plasmids are presented within a structured framework encompassing functional annotation and extensive metadata, which includes host taxonomy, similarity to other plasmids, geographic coordinates, and ecosystem information, allowing users to investigate plasmid function and ecology thoroughly.", "homepage": "https://img.jgi.doe.gov/pr", "biotoolsID": "img_pr", "biotoolsCURIE": "biotools:img_pr", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" }, { "uri": "http://edamontology.org/operation_0578", "term": "Plasmid map drawing" }, { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3941", "term": "Metatranscriptomics" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_0798", "term": "Mobile genetic elements" }, { "uri": "http://edamontology.org/topic_0637", "term": "Taxonomy" } ], "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": "10.1093/NAR/GKAD964", "pmid": "37930866", "pmcid": "PMC10767988", "type": [], "version": null, "note": null, "metadata": { "title": "IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata", "abstract": "Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.", "date": "2024-01-05T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Camargo A.P." }, { "name": "Call L." }, { "name": "Roux S." }, { "name": "Nayfach S." }, { "name": "Huntemann M." }, { "name": "Palaniappan K." }, { "name": "Ratner A." }, { "name": "Chu K." }, { "name": "Mukherjeep S." }, { "name": "Reddy T.B.K." }, { "name": "Chen I.-M.A." }, { "name": "Ivanova N.N." }, { "name": "Eloe-Fadrosh E.A." }, { "name": "Woyke T." }, { "name": "Baltrus D.A." }, { "name": "Castaneda-Barba S." }, { "name": "de la Cruz F." }, { "name": "Funnell B.E." }, { "name": "Hall J.P.J." }, { "name": "Mukhopadhyay A." }, { "name": "Rocha E.P.C." }, { "name": "Stalder T." }, { "name": "Top E." }, { "name": "Kyrpides N.C." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Antonio Pedro Camargo", "email": "antoniop.camargo@lbl.gov", "url": null, "orcidid": "https://orcid.org/0000-0003-3913-2484", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Nikos C Kyrpides", "email": "nckyrpides@lbl.gov", "url": null, "orcidid": "https://orcid.org/0000-0002-6131-0462", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-05-02T09:31:27.814833Z", "lastUpdate": "2024-05-02T09:31:27.816984Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" } ] }