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A multi-tissue gene expression dataset for hibernating brown bears
ObjectivesComplex physiological adaptations often involve the coordination of molecular responses across multiple tissues. Establishing...
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Dataset including whole blood gene expression profiles and matched leukocyte counts with utility for benchmarking cellular deconvolution pipelines
ObjectivesCellular deconvolution is a valuable computational process that can infer the cellular composition of heterogeneous tissue samples from...
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TBGA: a large-scale Gene-Disease Association dataset for Biomedical Relation Extraction
BackgroundDatabases are fundamental to advance biomedical science. However, most of them are populated and updated with a great deal of human effort....
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Inferring Gene Regulatory Networks and Predicting the Effect of Gene Perturbations via IQCELL
IQCELL is a platform that infers Boolean gene regulatory networks from single-cell RNA sequencing data. Boolean networks can be simulated under...
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Altered vitamin B12 metabolism in the central nervous system is associated with the modification of ribosomal gene expression: new insights from comparative RNA dataset analysis
Recent studies have confirmed the direct role of vitamin B12 (VitB12) in the central nervous system (CNS) homeostasis; nevertheless, the detailed...
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PEATmoss: A Gene Expression Atlas for Bryophytes
PEATmoss is an interactive gene expression atlas for bryophytes, which originally unified Physcomitrium patens RNA-seq and microarray expression data...
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Beyond benchmarking and towards predictive models of dataset-specific single-cell RNA-seq pipeline performance
BackgroundThe advent of single-cell RNA-sequencing (scRNA-seq) has driven significant computational methods development for all steps in the...
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Characterizing the impacts of dataset imbalance on single-cell data integration
Computational methods for integrating single-cell transcriptomic data from multiple samples and conditions do not generally account for imbalances in...
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MR-GGI: accurate inference of gene–gene interactions using Mendelian randomization
BackgroundResearchers have long studied the regulatory processes of genes to uncover their functions. Gene regulatory network analysis is one of the...
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Challenges in Eventing Horizontal Gene Transfer
Horizontal gene transfer (HGT) takes place when two organisms share their genetic material. Contrary to the ancestral transfer of genes, viz....
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Gene–gene interaction detection with deep learning
The extent to which genetic interactions affect observed phenotypes is generally unknown because current interaction detection approaches only...
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ddRAD-seq generated genomic SNP dataset of Central and Southeast European Turkey oak (Quercus cerris L.) populations
Turkey oak ( Quercus cerris L.) is one of the most ecologically and economically significant deciduous tree species in the Central and Southeast...
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The gut microbiome-metabolome dataset collection: a curated resource for integrative meta-analysis
Integrative analysis of microbiome and metabolome data obtained from human fecal samples is a promising avenue for better understanding the interplay...
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Meta-analysis of Gene Activity (MAGA) Contributions and Correlation with Gene Expression, Through GAGAM
It is well-known how sequencing technologies propelled cellular biology research in the latest years, giving an incredible insight into the basic...
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Metabolic Networks: Weighted Gene Correlation Network Analysis
Weighted Gene Correlation Network Analysis (WGCNA) is used to build weighted gene networks representing direct interconnections among genes. This...
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Novel Gene Signature for Bladder Cancer Stage Identification
This article presents a study that aimed to identify the stages of bladder cancer based on gene expression data. The dataset used in the study was...
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nRCFV: a new, dataset-size-independent metric to quantify compositional heterogeneity in nucleotide and amino acid datasets
MotivationCompositional heterogeneity—when the proportions of nucleotides and amino acids are not broadly similar across the dataset—is a cause of a...
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Bioinformatics analysis identifies a key gene HLA_DPA1 in severe influenza-associated immune infiltration
BackgroundSevere influenza is a serious global health issue that leads to prolonged hospitalization and mortality on a significant scale. The...
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RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations
Single-cell RNA-seq analysis coupled with CRISPR-based perturbation has enabled the inference of gene regulatory networks with causal relationships....
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RefEX: Reference Expression Dataset
Reference Expression dataset (RefEx) is a web tool which allows users to search by the gene name, various types of IDs, chromosomal regions in...