matrix factorization

Computational prediction of Drug-Disease association based on Graph-regularized one bit Matrix completion

This paper predicts drug-disease associations using a graph-regularized one-bit matrix completion framework, showing superior performance over existing methods.

Highly perturbed genes and hub genes associated with type 2 diabetes in different tissues of adult humans: A bioinformatics analytic workflow

The paper identifies highly perturbed and hub genes associated with type 2 diabetes across human tissues using a bioinformatics workflow and meta-analysis.

Decoding gene regulation in the mouse embryo using single-cell multi-omics

A mouse embryo multiome atlas (E7.5 to E8.75) and an unsupervised transcription factor binding predictor; a Brachyury knockout supports its network predictions in neuromesodermal progenitors.

Accelerating in-silico saturation mutagenesis using compressed sensing

This paper introduces Yuzu, a method that accelerates in-silico saturation mutagenesis by using compressed sensing, reducing computation time for convolution-based models.

Deciphering Hematopoiesis at single-cell level through the lens of reduced dimensions

The paper uses matrix factorization on single-cell RNA-Seq data to uncover a tri-directional transcriptional hierarchy in hematopoiesis and improves progenitor compartment characterization with a bootstrap method.

Genome-wide SNPs of vegetable leafminer, Liriomyza sativae: insights into the recent Australian invasion

The paper uses ddRAD-seq SNP data to analyze the genetic origin and invasion history of Liriomyza sativae in Australia, finding connections to the Torres Strait, Bali, and Papua New Guinea.

Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies

The paper genotypes over 4,000 Sprague Dawley rats to characterize genetic diversity and performs GWAS on Pavlovian conditioned approach behavior, identifying 46 significant loci.

On Weighted K-Mer Dictionaries

This paper introduces an improved weighted k-mer dictionary that compresses k-mer counts more efficiently than existing methods.

scMoMaT: Mosaic integration of single cell multi-omics data using matrix trifactorization

scMoMaT integrates single-cell multi-omics data under mosaic integration using matrix tri-factorization, uncovering modality-specific biomarkers for improved cell type annotation.

Normalization for sampled count data

The paper introduces a normalization method for single-cell RNA-seq data that meets three criteria and outperforms existing methods on benchmarks.

Global genomic epidemiology, resistome, virulome and plasmidome of the Extraintestinal Pathogenic Escherichia coli (ExPEC) ST38 lineage

This study analyzes the global genomic epidemiology, resistome, virulome, and plasmidome of ExPEC ST38 lineage across multiple hosts and regions, revealing clustering patterns and pathogenic features.

Assembly and comparative analysis of the complete mitochondrial genome of three Macadamia species (M. integrifolia, M. ternifolia and M. tetraphylla)

This study assembles and compares the mitochondrial genomes of three Macadamia species, revealing gene composition, evolutionary relationships, and selection pressures.

SMURF: embedding single-cell RNA-seq data with matrix factorization preserving selfconsistency

SMURF embeds scRNA-seq data using matrix factorization with a Poisson-Gamma divergence objective, preserving self-consistency and recovering gene expression and cell cycle time courses.

A Genome-Wide Association Analysis of Happiness: Consistent Genetic Effects Across the Lifespan and Across Genetic Ancestries in Multiple Cohorts.

This paper conducts a genome-wide association study of happiness, identifying genetic loci and correlations with personality traits, and shows consistent genetic effects across age and ancestry.

Joint Gene Network Construction by Single-Cell RNA Sequencing Data

This paper introduces JGNsc, a method for constructing joint gene networks from scRNA-seq data, and applies it to cancer studies to identify novel findings.

Apolipoprotein ε4 modifies obesity-related atrophy in the hippocampal formation of cognitively healthy adults.

The paper examines how APOE ε4 modifies obesity-related atrophy in hippocampal subfields of cognitively healthy adults using neuroimaging data.

Characterization of altered molecular mechanisms in Parkinson disease through cell type-resolved multi-omics analyses

This study identifies cell-type-specific dysregulated cis-regulatory elements and target genes in Parkinson's disease using multi-omic analyses of single-cell transcriptomes and epigenomes.

Single-cell multi-region dissection of brain vasculature in Alzheimer's Disease

The paper identifies cell-type-specific molecular changes in cerebrovascular cells across brain regions in Alzheimer's Disease, linking them to genetic variants and potential therapeutic targets.

Building an atlas of transposable elements reveals the extensive roles of young SINE in gene regulation, genetic diversity, and complex traits in pigs

The paper builds a TE atlas in pigs, showing young SINEs' roles in gene regulation, genetic diversity, and complex traits through multi-omics analysis.

Comparison of Single-Trait and Multi-Trait Genome-Wide Association Models and Inclusion of Correlated Traits in the Dissection of the Genetic Architecture of a Complex Trait in a Breeding Program

This study compares single-trait and multi-trait GWAS models to dissect the genetic architecture of seedling emergence in wheat, finding that multi-trait models identify more large-effect markers.

Shared genetic influences on resting-state functional networks of the brain

This study uses a multivariate method to identify shared genetic factors influencing resting-state brain networks and finds nine replicated SNPs associated with their joint architecture.

Establishing gene regulatory networks from Parkinson's disease risk loci

This study identifies gene regulatory networks influenced by Parkinson's disease risk SNPs using eQTL and chromosomal conformation data across multiple tissues.

Mixed matrix factorization: a novel algorithm for the extraction of kinematic-muscular synergies

This paper introduces a mixed matrix factorization algorithm to extract kinematic-muscular synergies, showing improved performance over existing methods in both simulated and real data.

Core Microbiota Drive the Prevalence of Extracellular Antibiotic Resistome in the Water Compartments

The paper identifies core bacterial taxa and mobile genetic elements associated with extracellular antibiotic resistance genes in water compartments.

Integration of public DNA methylation and expression networks via eQTMs improves prediction of functional gene-gene associations

The paper integrates DNA methylation and gene expression networks to improve prediction of functional gene-gene associations using eQTMs and a novel integration pipeline.

Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution genome-wide InDels and SNPs

This paper analyzes genomic data from Sherpa people to explore their genetic origin, evolutionary history, and forensic characteristics using InDels and SNPs.

SCYN: Single cell CNV profiling method using dynamic programming

SCYN is a single-cell CNV segmentation method using dynamic programming, showing high accuracy and speed on scDNA datasets.

Weak Coupling Between Spontaneous Local Cortical Activity State Switches Under Anesthesia Leads to Strongly Correlated Global Cortical States

The paper shows that cortical state transitions under anesthesia are local and weakly coupled, not driven by subcortical inputs.

Single-cell chromatin state analysis with Signac

Signac extends Seurat with a ChromatinAssay for single-cell chromatin and multimodal analysis, adds modified TF-IDF weighting, peak-gene linkage and mitochondrial-variant clonotyping, and scales to 733,526 cells.

Genomic adaptation in the CAZyome and specialised metabolism of the plant-associated Streptomyces violaceusniger clade

This paper sequenced and analyzed the genome of Streptomyces sp. AgN23, revealing its ability to produce auxin, degrade plant cell walls, and synthesize antimicrobials, with these features conserved in the S. violaceusniger clade.