matrix factorization

Genome-wide reconstruction of rediploidization following autopolyploidizationacross one hundred million years of salmonid evolution

This study reconstructs genome-wide rediploidization after autopolyploidization in salmonids over 100 million years, showing two waves of rediploidization and lineage-specific ohnologue divergence.

Genome sequencing and comparative analysis of Ficus benghalensis and Ficus religiosa trees reveal evolutionary mechanisms of longevity

This study sequenced and compared the genomes of two long-lived Ficus species to identify evolutionary mechanisms associated with their longevity.

A global atlas of genetic associations of 220 deep phenotypes

Cross-population GWAS of 220 phenotypes in BioBank Japan, UK Biobank, and FinnGen (n=628,000) identifies 5,343 previously unreported loci and decomposes summary statistics into latent genetic components for disease subtyping.

Tensor-decomposition--based unsupervised feature extraction in single-cell multiomics data analysis

This study applies tensor-decomposition-based unsupervised feature extraction to integrate single-cell multiomics data without filling missing values, producing biologically relevant embeddings.

High Dimensionality Reduction by Matrix Factorization for Systems Pharmacology

The paper applies matrix factorization methods to reduce high-dimensional multi-omic data in systems pharmacology, identifying predictive gene signatures for drug response.

Scallop2 enables accurate assembly of multiple-end RNA-seq data

Scallop2 improves transcript assembly accuracy for multiple-end RNA-seq data by efficiently bridging gaps and reducing false positives.

Chromosomal-level genome assembly of the bioluminescent cardinalfishSiphamia tubifer, an emerging model for symbiosis research

This paper presents a chromosomal-level genome assembly of the bioluminescent cardinalfish Siphamia tubifer, revealing unique genomic features and potential genes involved in symbiosis.

Enhancer-priming in ageing human bone marrow mesenchymal stromal cells contributes to immune traits

This study uses multiomics analysis of BMSCs to show age-related changes in enhancer activity and gene regulation contribute to immune traits and tissue-specific disorders.

Learning to embed lifetime social behavior from interaction dynamics

The paper introduces a temporal matrix factorization model to learn temporally consistent functional roles from social interaction networks in honey bees, enabling comparison of individual roles across time and colonies.

Harnessing Matrix Completion to Unify and Extend Viral Serology Studies

This paper applies matrix completion to predict antibody-virus interactions in influenza and HIV-1 studies, reducing the number of required experiments while improving data integration across studies.

Interpretable, scalable, and transferrable functional projection of large-scale transcriptome data using constrained matrix decomposition

This study introduces gsPCA and gsNMF for analyzing transcriptome data, showing they provide interpretable, transferrable, and gene-specific functional insights comparable to existing methods.

Predicting the effects of drug combinations using probabilistic matrix factorization

This paper uses probabilistic matrix factorization to predict synergistic drug combinations from partial data, showing high accuracy and proposing an efficient experimental design.

High-fidelity, high-spatial-resolution diffusion MRI of the ex-vivo whole human brain on the 3T Connectom scanner using structured low-rank EPI ghost correction

This paper introduces a structured low-rank matrix modeling method to correct ghosting in ex vivo dMRI, improving accuracy and reliability of diffusion metrics.

Cell type-specific meQTL extends melanoma GWAS annotation beyond eQTL and informs melanocyte gene regulatory mechanisms

The paper identifies cell-type-specific meQTLs in melanocytes and melanomas, enhancing GWAS annotation and revealing regulatory mechanisms involving IRF4.

Dimensionality reduction by UMAP reinforces sample heterogeneity analysis in bulk transcriptomic data

This study compares dimensionality reduction methods for bulk transcriptomic data, finding UMAP better preserves sample neighbourhood and clustering accuracy than PCA, MDS, and t-SNE.

Accurate estimation of cell-type resolution transcriptome in bulk tissue through matrix completion

ENIGMA deconvolutes bulk RNA-seq into single-cell-type resolution using matrix completion, validated on simulated and disease-related datasets.

Targeting CoV-2 Spike RBD and ACE-2 Interaction with Flavonoids of Anatolian Propolis by in silico and in vitro Studies in terms of possible COVID-19 therapeutics

This study evaluates the anti-SARS-CoV-2 potential of Anatolian propolis polyphenols through in silico and in vitro methods, finding pinocembrin as the strongest inhibitor.

Gene regulatory networks underlying human microglia maturation

This study defines age-specific brain environmental factors driving microglia phenotypes through transcriptomic and epigenomic analysis of human fetal and postnatal microglia.

A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants

The paper develops a multiple genome alignment workflow for plants, showing that k-mer masking and parameter tuning improve alignment of functional regions.

Revision of the genus Dichaetophora Duda (Diptera: Drosophilidae), part I: DNA bar-coding and molecular phylogenetic reconstruction

This study uses DNA barcoding and molecular phylogenetics to revise the genus Dichaetophora, identifying cryptic species and taxonomic issues within the group.

Unsupervised tensor decomposition-based method to extract candidate transcription factors as histone modification bookmarks in post-mitotic transcriptional reactivation

Simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization

GRiNCH identifies and smooths topological units from sparse chromatin contact data, improving TAD detection and structural recovery across different sequencing depths.

Rapid Estimation of SNP Heritability using Predictive Process approximation in Large scale Cohort Studies

This paper introduces PredLMM, a method for rapidly estimating SNP heritability in large cohorts by approximating linear mixed models using predictive process techniques.

Topology-based Sparsification of Graph Annotations

The paper introduces RowDiff, a method to compactly store graph labels by exploiting annotation similarities, achieving significant space reductions when combined with compression techniques.

Genomic prediction of arsenic tolerance and grain yield in rice. Contribution of trait-specific markers and multi environment models

This study evaluates genomic prediction models for arsenic tolerance and grain yield in rice using multi-environment and multi-trait approaches, finding improved predictive accuracy with advanced models.

A novel framework for single-cell Hi-C clustering based on graph-convolution-based imputation and two-phase-based feature extraction

This paper introduces ScHiC-Rep, a framework for single-cell Hi-C clustering that improves imputation and feature extraction, outperforming existing methods on human and mouse datasets.

Phylogenomics Sheds Light on the population structure of Mycobacterium bovis from a Multi-Host Tuberculosis System

The paper uses whole genome sequencing to analyze M. bovis isolates from Portugal, revealing genetic clades and transmission networks in a multi-host tuberculosis system.

A chromosome-scale strawberry genome assembly of a Japanese variety, Reikou

This study presents a chromosome-scale genome assembly for the Japanese strawberry variety Reikou and identifies its likely progenitors as F. vesca and F. iinumae.

Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels

The paper presents whole-genome comparisons of Symbiodiniaceae isolates, revealing extensive sequence divergence but conserved gene functions across species and genera.

Imputation of Spatially-resolved Transcriptomes by Graph-regularized Tensor Completion

This paper introduces FIST, a graph-regularized tensor completion model for imputing missing mRNA expressions in spatial transcriptomics data, showing improved performance over existing methods.