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UnknownNCMine: Core-peripheral based functional module detection using near-clique mining.

Motivation

The identification of functional modules from protein-protein interaction (PPI) networks is an important step toward understanding the biological features of PPI networks. The detection of functional modules in PPI networks is often performed by identifying internally densely conn...
S-EPMC5181566 | biostudies-literature
UnknownMatataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data.

Background

Data generated by RNA sequencing (RNA-Seq) is now accumulating in vast amounts in public repositories, especially for human and mouse genomes. Reanalyzing these data has emerged as a promising approach to identify gene modules or pathways. Although meta-analyses of gene expression...
S-EPMC6048772 | biostudies-literature
UnknownDe novo profile generation based on sequence context specificity with the long short-term memory network.

Background

Long short-term memory (LSTM) is one of the most attractive deep learning methods to learn time series or contexts of input data. Increasing studies, including biological sequence analyses in bioinformatics, utilize this architecture. Amino acid sequence profiles are widely used f...
S-EPMC6052547 | biostudies-literature
UnknownTheoretical characterisation of strand cross-correlation in ChIP-seq.

Background

Strand cross-correlation profiles are used for both peak calling pre-analysis and quality control (QC) in chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis. Despite its potential for robust and accurate assessments of signal-to-noise ratio (S/N) because of i...
S-EPMC7510163 | biostudies-literature
UnknownNLDB: a database for 3D protein-ligand interactions in enzymatic reactions.
NLDB (Natural Ligand DataBase; URL: http://nldb.hgc.jp ) is a database of automatically collected and predicted 3D protein-ligand interactions for the enzymatic reactions of metabolic pathways registered in KEGG. Structural information about these reactions is important for studying the molecular fu...
S-EPMC5274645 | biostudies-literature
UnknownDiscrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population.
The protein coding sequences of the human reference genome GRCh38, RefSeq mRNA and UniProt protein databases are sometimes inconsistent with each other, due to polymorphisms in the human population, but the overall landscape of the discordant sequences has not been clarified. In this study, we compr...
S-EPMC5009343 | biostudies-literature
UnknownTwo-stage strategy using denoising autoencoders for robust reference-free genotype imputation with missing input genotypes.
Widely used genotype imputation methods are based on the Li and Stephens model, which assumes that new haplotypes can be represented by modifying existing haplotypes in a reference panel through mutations and recombinations. These methods use genotypes from SNP arrays as inputs to estimate haplotype...
S-EPMC11422160 | biostudies-literature
UnknownIdentifying critical age and gender-based metabolomic shifts in a Japanese population of the Tohoku Medical Megabank cohort.
Understanding the physiological changes associated with aging and the associated disease risks is essential to establish biomarkers as indicators of biological aging. This study used the NMR-measured plasma metabolome to calculate age-specific metabolite indices. In doing so, the scope of the study ...
S-EPMC11231361 | biostudies-literature
UnknownDietary habits and plasma lipid concentrations in a general Japanese population.

Introduction

Accumulating data on the associations between food consumption and lipid composition in the body is essential for understanding the effects of dietary habits on health.

Objectives

As part of omics research in the Tohoku Medical Megabank Community-Based Cohort Study, this ...
S-EPMC10914877 | biostudies-literature
UnknownSimulating metabolic pathways to enhance interpretations of metabolome genome-wide association studies.
Advancements in large-scale analysis of metabolites in human peripheral blood samples revealed the links between metabolite concentrations and genetic variations. This field is known as metabolome-genome-wide association study (MGWAS). Although MGWAS is a powerful tool, it has some limitations, part...
S-EPMC12084608 | biostudies-literature
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