GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and closely related organisms. The resource provides a portal to genome sequence and annotation data, which is primarily generated by the Pathogen Genomics group at the Wellcome Trust Sanger Institute. It combines data from completed and ongoing genome projects with curated annotation, which is readily accessible from a web based resource. The development of the database in recent years has focused on providing database-driven annotation tools and pipelines, as well as catering for increasingly frequent assembly updates. The website has been significantly redesigned to take advantage of current web technologies, and improve usability. The current release stores 41 data sets, of which 17 are manually curated and maintained by biologists, who review and incorporate data from the scientific literature, as well as other sources. GeneDB is primarily a production and annotation database for the genomes of predominantly pathogenic organisms.
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http://dx.doi.org/10.1093/nar/gkr1032 | DOI Listing |
J Cell Mol Med
January 2025
Department of Andrology, The First Hospital of Jilin University, Changchun, China.
Prostate cancer (PCa) is one of the most common cancers in men worldwide. Autophagy-related genes (ARGs) may play an important role in various biological processes of PCa. The aim of this study was to identify and evaluate autophagy-related features to predict clinical outcomes in patients with PCa.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
The accurate identification of protein-nucleotide binding residues is crucial for protein function annotation and drug discovery. Numerous computational methods have been proposed to predict these binding residues, achieving remarkable performance. However, due to the limited availability and high variability of nucleotides, predicting binding residues for diverse nucleotides remains a significant challenge.
View Article and Find Full Text PDFToxicol Appl Pharmacol
January 2025
Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia. Electronic address:
Bisphenol A (BPA), an endocrine disruptor, is linked to cancer progression in estrogen-responsive tissues, but its role in promoting colorectal cancer (CRC) progression in the context of obesity remains underexplored. This study examines BPA's influence on CRC in obese Sprague-Dawley rats using network toxicology and experimental models. Computational analysis using the Database for Annotation, Visualization, and Integrated Discovery identified pathways such as "CRC" and "chemical carcinogenesis-receptor activation", implicating the PI3K-AKT pathway in IL-1 beta upregulation and BPA's role in CRC during obesity.
View Article and Find Full Text PDFComput Methods Programs Biomed
January 2025
Laberit, Avda. de Catalunya, 9, València, 46020, Spain.
Background And Objective: Despite significant investments in the normalization and the standardization of Electronic Health Records (EHRs), free text is still the rule rather than the exception in clinical notes. The use of free text has implications in data reuse methods used for supporting clinical research since the query mechanisms used in cohort definition and patient matching are mainly based on structured data and clinical terminologies. This study aims to develop a method for the secondary use of clinical text by: (a) using Natural Language Processing (NLP) for tagging clinical notes with biomedical terminology; and (b) designing an ontology that maps and classifies all the identified tags to various terminologies and allows for running phenotyping queries.
View Article and Find Full Text PDFAnticancer Drugs
January 2025
School of Clinical Medicine, Guizhou Medical University, Guiyang City, Guizhou, China.
Eugenol, a phenolic natural product with diverse pharmacological activities, remains unexplored in liver cancer. Using network pharmacology, we investigated eugenol's therapeutic mechanisms in liver cancer. We obtained eugenol's molecular structure from PubChem and screened its targets using similarity ensemble approach in Swiss Target Predictiondatabases.
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