matrix factorization

Highly efficient genotype compression leveraging genealogical relatedness

The paper introduces a lossless compression method for genotype data using genealogical relatedness, achieving significant size reduction and speedup in genetic analyses.

From fluke to fragment: a multifaceted method for molecular sex identification and mitochondrial haplotyping from environmental DNA samples

This paper develops a method to identify molecular sex and mitochondrial haplotypes from environmental DNA samples, achieving high concordance with tissue samples and resolving lineage-level genetic diversity.

Parallel algorithms for phylogenetic inference under a structured coalescent approximation

The paper introduces parallel algorithms to improve the computational efficiency of structured coalescent models for phylogeographic analysis, enabling faster and larger-scale studies of pathogen spread.

Coordinated Temporal Dynamics of Glucocorticoid Receptor Binding and Chromatin Landscape Drive Transcriptional Regulation

The paper defines a temporally resolved framework for GR-mediated gene regulation, identifying three binding classes and their functional links to transcriptional output.

Environment-aware genomic prediction enhances the transferability of polygenic resistance to ash dieback in Fraxinus excelsior

This study improves genomic prediction of ash dieback resistance by incorporating environmental factors, showing enhanced transferability across environments.

Hormonally responsive bovine oviductal organoids recapitulate native oviductal secretions and enhance sperm capacitation

Bovine oviductal organoids treated with estradiol or a progesterone analog reproduce follicular and luteal transcriptomes and secretomes; estradiol-stimulated secretions boost bull sperm capacitation and acrosome reaction.

Tracing cell communication programs across conditions at single cell resolution with CCC-RISE

The paper introduces CCC-RISE, a method to analyze cell-cell communication at single-cell resolution across conditions, identifying disease-relevant signaling programs and subpopulations.

CanVAS: A Harmonized and Imputed Canine Variant Atlas1

CanVAS harmonizes and imputes canine genotype data from multiple sources to create a unified resource for genetic studies.

General, orders-of-magnitude faster whole-genome analysis with genotype representation graphs

The paper introduces GRG v2 and grapp to enable faster and more efficient whole-genome analysis for large biobank datasets.

Global Signal Removal (GSR) as graph spatial filtering

This paper reframes Global Signal Removal (GSR) as graph spatial filtering, introducing variants with different effects on network connectivity.

Transcriptomic Integration Reveals a Conserved Inflammatory--Proliferative Paradox in Acquired Resistance to Immune Checkpoint Blockade

The paper integrates transcriptomic datasets to identify a conserved inflammatory-proliferative paradox in acquired resistance to immune checkpoint blockade across multiple models.

Lifestyle-associated variation in type IV secretion systems between phytopathogenic and environmental Ralstonia

This study compares T4SS diversity between phytopathogenic and environmental Ralstonia species, finding more T4SS clusters in environmental strains and identifying a specialized cluster in phytopathogens.

A diagnostic plasma omics-biomarker for Alzheimer's disease informed by microglial single-cell transcriptomics: A pilot study

The paper develops a blood-based diagnostic biomarker for Alzheimer's disease using microglial single-cell transcriptomics and validates it in plasma omics data.

Analysis of biological networks using Krylov subspace trajectories

The paper introduces a method using Krylov subspace trajectories for analyzing biological networks, demonstrating its application in community detection and perturbation analysis on the C. elegans neural network.

An atlas of genetic effects on the monocyte methylome across European and African populations

The paper constructs a multi-ancestry methylome atlas of purified monocytes, identifies population-specific methylation quantitative trait loci, and performs methylome-wide association studies for 41 traits, revealing novel associations for type 2 diabetes.

Smoothie: Efficient Inference of Spatial Co-expression Networks from Denoised Spatial Transcriptomics Data

Smoothie denoises spatial transcriptomics data and constructs co-expression networks to detect gene modules and annotate functions across tissues and conditions.

A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development

The paper compiles a large transcriptomic dataset of neocortical development and uses joint matrix decomposition to identify conserved transcriptome dynamics across mammals and developmental stages.

Gene and cell line efficiency of CRISPR computed by tensor decomposition in genome-wide CRISPR-Cas9 knockout screens

This study uses tensor decomposition to analyze CRISPR-Cas9 knockout screens, distinguishing essential from non-essential genes with performance comparable to JACKS without requiring control samples or logarithmic transformations.

A Multi-Omics Processing Pipeline (MOPP) for Extracting Taxonomic and Functional Insights from Metaribosome Profiling (metaRibo-Seq) data

The paper introduces MOPP, a pipeline for processing metaRibo-Seq data to improve taxonomic and functional analysis by reducing false positives through coverage breadth filtering.

CTFacTomo: Reconstructing 3D Spatial Structures of RNA Tomography Transcriptomes by Collapsed Tensor Factorization

CTFacTomo reconstructs 3D spatial gene expressions from RNA tomography data using tensor factorization and regularization, outperforming benchmarks on zebrafish and mouse datasets.

Shared and organ-specific gene expression programs of fibrotic diseases

This paper performs a cross-organ meta-analysis of single-cell transcriptomic data to identify shared and organ-specific gene expression programs in fibrotic diseases.

Inferring large networks with matrix factorisation to capture non-linear dependencies among genes using sparse single-cell profiles

The paper introduces NIRD, a method for inferring gene networks from sparse single-cell data, showing improved performance and consistency across datasets.

What Do Biological Foundation Models Compute? Sparse Autoencoders from Feature Recovery to Mechanistic Interpretability

This paper reviews sparse autoencoders applied to biological foundation models, finding they recover interpretable biological features but lack experimental validation of mechanistic understanding.

The Landscape of Stop Codon-Free Regions in Primates: A Reservoir of Proto-Genes

The paper identifies and characterizes stop-codon-free regions in primate genomes, suggesting they may serve as substrates for de novo gene emergence.

MetaGLIMPSE: Meta Imputation of Low Coverage Sequencing Data for Modern and Ancient Genomes

MetaGLIMPSE improves low coverage sequencing imputation by combining multiple reference panels, outperforming single-panel methods for modern and ancient DNA samples across various coverage and allele frequency ranges.

Complete chloroplast genome of African Baobab (Adansonia digitata L.): structural characterization, comparative genomics, and phylogenetic placement within Malvaceae

This paper characterizes the complete chloroplast genome of Adansonia digitata, compares it with other Adansonia species, and places it phylogenetically within Malvaceae.

KuPID: Kmer-based Upstream Preprocessing of Long Reads forIsoform Discovery

KuPID preprocesses long RNA-seq reads using kmer sketching to improve isoform discovery accuracy and reduce runtime.

Pan-cortical area sensorimotor network coordination during motor learning of forelimb-reaching task in the marmoset

The paper examines how motor learning affects cortical network coordination in marmosets using calcium imaging and analysis of activity components.

Efficient Identification of Phylogenetically Informative Alignment Sites via Sparse Learning

The paper introduces a sparse learning method to identify phylogenetically informative sites in alignments, showing it matches full alignment results and provides an objective metric for evaluating alignment filtering tools.

Analysis of Transcriptograms in Epithelial-Mesenchymal Transition (EMT)

The paper introduces a method combining PPI network topology with PCA to analyze EMT, revealing hidden functional modules and distinct cellular trajectories.