8 papers · ranked by Valyu relevance
Laha Ale, Robert Gentleman, Christopher Endres, Sam Pullman + 3 more
The National Health and Nutrition Examination Survey (NHANES) provides extensive public data on demographics, health, and nutrition, collected in 2-year cycles since 1999. Although invaluable for epidemiological and health-related research, the complexity of NHANES data, involving numerous files and disjoint metadata…
Rodolfo S Allendes Osorio, Yi-An Chen, Kenji Mizuguchi
Here, we introduce SEND (Share Easily bioiNformatics Data), a suite of tools that allow users to share heterogeneous and linked biological data, in an easy and highly customizable way. The code for SEND is freely available on GitHub ([https://github.com/targetmine]()). Also, docker images of all different components of…
Gang Wang, Zhe Sun, Shiou Yih Lee, Mingyu Lai + 3 more
Simple Summary Gastric diseases, including gastric cancer, gastritis and gastric ulcers, pose significant threats to global health. However, the study of their complex causes and the development of improved diagnostic and therapeutic strategies are hindered by a lack of integrated, multi-type biological data. Here, we…
Wim L Cuypers, Halil Ceylan, Eline Turcksin, Laura Raes + 11 more
Nucleotide sequences in the FASTQ or BAM format are widely shared, yet derived from platform-specific raw data outputs that differ across sequencing platforms. In Oxford Nanopore Technologies (ONT) sequencing, raw signal data contain valuable biological information and enable basecaller optimization and modification…
Anthony Huffman, Feng-Yu Yeh, Junguk Hur, Jie Zheng + 5 more
With the increasing volume of biomedical experimental data, standardizing, sharing, and integrating heterogeneous experimental data across domains has become a major challenge. To address this challenge, we have developed an ontology-supported Study-Experiment-Assay (SEA) common data model (CDM), which includes 10 core…
Clémentine Battistel, Jean-Christophe Mouren, Benjamin Morga, Camille Pelletier + 8 more
Sequencing technologies continue to evolve, providing novel opportunities for disease surveillance and control. These advancements are crucial for diagnosing diseases and identifying genetically distinct variants with diverse host reservoir species and geographical distributions. Recent progress in sequencing-based…
Daniel J Rigden, Xosé M Fernández
The 2026 Nucleic Acids Research database issue has 182 papers from across biology and neighbouring fields. Eighty-four of these papers describe new databases, while 86 are updates on databases that have previously appeared here. Twelve more papers cover databases most recently published elsewhere. New nucleic acid…
Hao Jiang, Zhicheng Xu, Tong Li, Ji Wang + 1 more
The regulation of messenger mRNA turnover is a critical cellular process that dictates gene expression levels. High-throughput sequencing technologies have enabled the measurement of mRNA decay rates on a transcriptome-wide scale. However, this vast amount of data is dispersed across numerous publications, and it is…