matrix factorization

Ultra-fast and Efficient Network Embedding for Gigascale Biological Datasets

The paper introduces GraphEmbed, a scalable network embedding tool that efficiently handles large biological datasets with speed and accuracy improvements over existing methods.

Growth vs. Diversity: A Time-Evolution Analysis of the Chemical Space

The paper analyzes the time evolution of chemical library diversity using molecular fingerprints and finds that increased molecule count does not necessarily equate to increased diversity.

Multiplexed perturbation of yew reveals cryptic proteins that enable a total biosynthesis of baccatin III and Taxol precursors

A multiplexed perturbation and single-nucleus RNA-seq screen of Taxus needles found eight new Taxol pathway genes, including FoTO1, enabling baccatin III and a late Taxol precursor in N. benthamiana.

Estimating recent and historical effective population size of marine and freshwater sticklebacks

The paper estimates recent and historical effective population sizes of sticklebacks using genomic data and multiple methods, finding marine populations have the highest Ne values.

Efficient construction of Markov state models for stochastic gene regulatory networks by domain decomposition

The paper introduces a domain decomposition approach to efficiently compute Markov State Models for stochastic gene regulatory networks with uncertainty quantification.

The Neuromusculoskeletal Modeling Pipeline: MATLAB-based Model Personalization and Treatment Optimization Functionality for OpenSim

MATLAB toolsets add joint, muscle, synergy, and foot-contact personalization and optimal-control treatment design to OpenSim; one post-stroke case predicted 60% faster walking at equal metabolic cost.

Clinicogenomic characterization of inflammatory breast cancer

This study analyzes genomic alterations in a large IBC cohort, finding high TP53 mutation frequency and NOTCH pathway enrichment, but no major genomic differences compared to non-IBC cases.

Integrative, high-resolution analysis of single cell gene expression across experimental conditions with PARAFAC2-RISE

RISE, an adaptation of PARAFAC2, enables dimensionality reduction and analysis of single-cell RNA-seq data across experimental conditions by separating condition-specific effects from cell-to-cell variation.

Genomic and Behavioral Signatures of Selection for Ethanol Preference from the Heterogeneous Stock Collaborative Cross Mice: The Central Nucleus of the Amygdala

The paper uses RNA sequencing in mice to identify transcriptome differences associated with ethanol preference, finding reduced gene-gene correlation in high-preferring mice.

Genetic diversity and population structure of soybean (Glycine max (L.) Merril) germplasm.

This study evaluates genetic diversity and population structure of 147 soybean accessions using SNP analysis to inform breeding strategies.

TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila

TF2TG integrates TF-DNA binding, protein-protein interactions, and transcriptomic data to identify and rank potential target genes for Drosophila transcription factors.

Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data

The paper evaluates discrepancies in dimensionality reduction techniques for time-series scRNA-seq data using synthetic data and finds that different methods may not reliably represent dynamics when used alone.

Frequency Chaos Game Representation - Singular Value Decomposition for Alignment-Free Phylogenetic Analysis

This paper introduces SVD-FCGR, an alignment-free phylogenetic analysis method using SVD on FCGR, showing improved resolution and scalability over MEGA for viral datasets.

Insights into the Biocontrol Mechanisms of a Paenibacilluspeoriae Strain on Maize Seedling Blight through Multi-Omics Analysis

This study identifies the biocontrol mechanisms of Paenibacillus peoriae 3-B4 against Fusarium verticillioides using multi-omics analysis, showing synergistic effects between host gene expression and microbial community shifts.

Missing cell types in single-cell references impact deconvolution of bulk data but are detectable

The paper examines how missing cell types in single-cell references affect deconvolution of bulk data and shows that missing cell-type profiles can be detected using non-negative matrix factorization.

Intratumor Heterogeneity Through the Lens of Gene Regulatory Networks

The paper analyzes scRNA-seq data to infer clone-specific gene regulatory networks in tumors and shows distinct network architectures and treatment-induced rewiring across cancer types.

Uncovering Latent Biological Function Associations through Gene Set Embeddings

This study uses gene set embeddings to uncover biological function associations across species by integrating node2vec with MSigDB data.

omicsGMF: a multi-tool for dimensionality reduction, batch correction and imputation applied to bulk- and single cell proteomics data.

omicsGMF integrates dimensionality reduction, batch correction, and imputation for bulk and single-cell proteomics data, improving statistical power for differential abundance detection.

Clustering individuals using INMTD: a novel versatile multi-view embedding framework integrating omics and imaging data

INMTD integrates omics and 3D imaging data to produce unconfounded individual subgroups with biologically meaningful embeddings.

Genotype-Epigenome-Phenotype Integration Reveals the Contributions of Peripheral Immune Cells to Bipolar Disorder Pathogenesis, Phenotypic Heterogeneity, and Therapy

This study integrates genotype, epigenome, and phenotype data to show immune cells contribute to bipolar disorder pathogenesis, heterogeneity, and therapy through epigenomic and genetic mechanisms.

Deciphering lung adenocarcinoma evolution and the role of LINE-1 retrotransposition

This study analyzes 1024 lung adenocarcinomas to identify evolutionary patterns and mutational mechanisms, revealing distinct trajectories linked to smoking, ancestry, and retrotransposition.

Novel Parkinson's Disease Genetic Risk Factors Within and Across European Populations

A cross-European Parkinson's disease GWAS meta-analysis of 63,555 cases, 17,700 proxy cases and 1,746,386 controls finds 134 risk loci (59 novel), 157 independent signals, and brain-enriched risk genes.

Diabetes mellitus and tuberculosis comorbidity induce unique microbial gut dysbiosis and associated metabolome.

This study investigates gut microbiome and metabolome changes in diabetic mice co-infected with tuberculosis, identifying dysbiosis and metabolic alterations associated with comorbidity.

DySCo: a general framework for dynamic Functional Connectivity

DySCo introduces a framework for dynamic functional connectivity analysis, providing a unified theoretical approach and efficient algorithms for processing high-dimensional brain data.

Transcriptome-wide analyses delineate the genetic architecture of expression variation in atopic dermatitis

This study identifies 176 gene-tissue associations in atopic dermatitis using transcriptome-wide association analysis, highlighting novel genes involved in allergic reactions, skin barrier integrity, and inflammation.

IFNγ activates an immune-like regulatory network in the cardiac vascular endothelium

This study investigates how IFNγ affects cardiac vascular endothelium by analyzing RNA-seq and ATAC-seq data from iPSC-derived cells, revealing immune-like regulatory changes and GWAS variant overlaps.

Compression-enabled interpretability of voxel-wise encoding models

This study shows that model compression improves the interpretability and stability of voxel-wise CNN models for brain activity prediction without sacrificing accuracy.

Conservation and discovery of regulatory motifs across oomycetes through comparative genomic analysis

This study identifies conserved transcription factor binding motifs in oomycetes using comparative genomics, revealing key regulatory mechanisms and evolutionary conservation.

A neuro-immune axis of transcriptomic dysregulation within the subgenual anterior cingulate cortex in schizophrenia

The paper identifies a schizophrenia-specific gene expression pattern in the subgenual anterior cingulate cortex using multivariate analysis, highlighting neuro-immune pathways and GWAS-implicated genes.

A single low-dimensional neural component of motor unit activity explains force generation across repetitive isometric tasks

The paper uses PCA and FA to show a single low-dimensional motor unit component explains most force oscillations during repetitive isometric tasks.