15 papers · ranked by Valyu relevance
R. Balamurugan
Microarray gene expression data are high-dimensional and complex, with patterns that may appear only under specific conditions. Traditional clustering often misses these local patterns, whereas biclustering can reveal groups of genes with coordinated expression across particular conditions. In this paper, we propose a…
Simo Inkala, Antonio Federico, Angela Serra, Dario Greco
This study provides manually curated and homogenised transcriptomics data of interstitial lung disease (ILD) patients retrieved from the NCBI Gene Expression Omnibus and European Nucleotide Archive repositories. The compendium includes 30 transcriptomics datasets generated with DNA microarrays and RNA sequencing…
A S Escobedo-Muñoz, Diego Carmona-Campos, Armando G G Trapaga, Julio A Freyre-González
The Gene Expression Omnibus (GEO) is the largest functional genomics repository, including ~5 million entries related to the main transcriptomic technologies: microarrays and RNA-seq. This amount of data has the potential to be reused in large-scale meta-analysis, such as those in bacterial systems biology, where the…
Elio Nushi, François P Douillard, Katja Selby, Benjamin A Blount + 4 more
Transcriptomics experiments are often conducted to capture changes in gene expression over time. However, time annotations may be missing, imprecise, or not reflect the same physiological state of the bacterial culture between different experiments. Assigning accurate time points to these experiments using a reference…
Hung Pham, Adam P Lombroso, Esma Cansu Cevik, Hugh S Taylor + 2 more
For microarray DNAm data, we used the Gene Expression Omnibus GSE286313 DNAm data (N = 72): blood samples profiled using the EPICv2 DNAm microarrays across four cohorts of mixed sex and diverse geographical origin, spanning early to late adulthood (). For a second dataset, we used the GSE264438 data (N = 581): DNAm…
Erika Schaudy, Jory Lietard
Chemically modifying the backbone, sugar, or nucleobase moieties of nucleic acids greatly expands their functional repertoire. Nucleobase modifications have received particular attention for their proven ability to generate a greater diversity of intra- and intermolecular interactions. This broader interaction…
Santra Santhosh, Sharon Istvánffy, Omer Sabary, Eitan Yaakobi + 3 more
Large-scale de novo nucleic acid synthesis is a powerful tool enabling researchers to better understand and engineer biological systems. Fields ranging from genomics to nucleic acid therapeutics to synthetic biology make use of high-throughput experimental approaches requiring access to large pools or libraries of DNA…
Zhining Sui, Disa Yu, Arslan Erdengasileng, Jinfeng Zhang + 1 more
The immense value of public gene expression repositories is constrained by the lack of compatibility among datasets generated from diverse experimental technologies. Differences in measurement scales, probe chemistries, and signal distributions create systematic discrepancies across platforms and laboratories. These…
Hongyan Sui, Rosana Wiscovitch-Russo, Silvia Cachaco, Jun Yang + 4 more
Author “Sylvain Laverdure” was erroneously assigned to affiliation “Center for Infectious Disease Research, George Mason University, Manassas, VA, United States”. This affiliation needs to be removed for author “Sylvain Laverdure”. The Data Availability statement was erroneously given as “Publicly available datasets…
Ícaro S. Lopes, Eduardo R. Fukutani, Tiago F. Mota, Bruno B. Andrade + 3 more
The omics sciences represent a revolution for clinical studies, offering integrative approaches to analyzing biological data with unprecedented depth. From the discovery of the double-helix structure of DNA to the CRISPR-Cas9 gene editing tool, passing through the evolution of sequencing platforms and the exponential…
Dexin Li, Junhua Deng, Zenglin Wang, Yunjing Zhang + 5 more
Senecavirus A (SVA) is an emerging swine pathogen that causes vesicular disease, which presents clinically indistinguishable signs from other vesicular diseases. To enable differentiation of infected from vaccinated animals (DIVA), we developed a novel protein microarray for dual serological detection of antibodies…
Chinmay Nitin Mokal, Piyush Agrawal
Background Oral submucosal fibrosis (OSF) is a chronic and progressive disorder, caused by chewing areca nuts, affecting the oral cavity and oropharynx. OSF is characterized by severe symptoms like severe burning sensation, restricted mouth opening, etc. Given the multifactorial and poorly understood molecular basis of…
Igor Ilić, Erika Schaudy, Jory Lietard
The phosphorothioate bond (PS) is one of the most common chemical modifications of DNA and RNA and replaces one of the non-bridging oxygen atoms of the phosphodiester (PO) bond with a sulfur atom. Ubiquitous in oligonucleotide drug design, as it equips most FDA-approved therapeutics, it imparts resistance against…
Hope A. Townsend, Kimberly R. Jordan, Rebecca J. Wolsky, Lucy B. Van Kleunen + 6 more
The clinical heterogeneity of cancer poses a major challenge for precision medicine. Limited cohort sizes across evolving assay platforms impede reliable biomarker discovery. Here, we systematically evaluate how to integrate data from four transcriptomics platforms: bulk and single-cell (sc) RNA sequencing (RNA-seq)…
Jessica Kreutz, Tijana Mitić, Andrea Caporali, Luca Agnelli
The emergence of single-cell sequencing and computational analysis has dramatically improved our understanding of cellular diversity and gene expression dynamics. The rapid advancement of high-throughput omics technologies has led to an exponential growth in biological data. However, many gene regulatory processes at…