matrix factorization

Deciphering the global genomic landscape of C. neoformans: Population dynamics, molecular epidemiology and genomic signatures of pathogenicity

The paper analyzes the global genomic diversity of C. neoformans over three decades, identifying key genetic features, lineage divergence, and resistance mechanisms.

Transcriptomic analysis of the human habenula in schizophrenia

The paper performs transcriptomic analysis of the human habenula and identifies molecular changes associated with schizophrenia risk and illness state.

Genetic dissection of tissue composition in genetically diverse mouse populations

The paper uses single-cell RNAseq data to analyze genetic factors influencing cell-type composition in mouse tissues, identifying heritability and QTLs associated with cell-type abundance.

Tissue-Specific Regulatory and Expression Patterns of CDG-causative genes account to Phenotypic Variability

The paper analyzes the expression and regulatory patterns of CDG-causative genes across tissues to explain phenotypic variability in congenital disorders of glycosylation.

On ARGs, pedigrees, and genetic relatedness matrices

This paper introduces branch relatedness and efficient algorithms for computing branch GRMs using tree sequences, enabling large-scale genomic analysis.

ComplexMatrixComb: Predicting Drug Combination IC50 Doses via Complex Numbers and Matrix Factorization

ComplexMatrixComb predicts drug combination IC50 doses using complex numbers and matrix factorization, outperforming traditional methods and validating with experimental assays.

Uncovering the Genetic Blueprint of the UAE's National Tree: Genomic Evidence to Guide Prosopis cineraria (L.) Druce Conservation

This study presents the first population genomics analysis of Prosopis cineraria in the UAE, identifying genetic clusters and diversity patterns to inform conservation strategies.

Exponential Map Models as an Interpretable Framework for Generating Neural Spatial Representations

This paper introduces an exponential map framework to generate interpretable neural spatial representations, showing how algebraic conditions enable path and translational invariance and biologically relevant spatial tuning.

Single nucleus multi-omic atlas of human dorsal root ganglia reveals the contribution of nonneuronal cell types to pain

This study creates a single-nucleus multi-omic atlas of human dorsal root ganglia, identifying novel regulatory mechanisms and therapeutic targets for pain.

LieOTMap-FFT: A Differentiable Fitting Framework Combining Lie Algebra and FFT-accelerated Optimal Transport for Cryo-EM Maps

LieOTMap-FFT aligns cryo-EM maps with atomic models using Lie algebra and FFT-accelerated optimal transport, achieving high accuracy in rigid body fitting.

The role of structural connectivity on brain function through a Markov model of signal transmission

The paper links brain structure to function by showing that commute time, derived from diffusion MRI, correlates better with functional MRI data than other measures.

Integrative Gene-Centric Analysis of Breast Cancer: High-Confidence Germline Predisposition Genes from Population-Scale Cohorts

The paper identifies high-confidence breast cancer predisposition genes using multi-ethnic genomic data and integrates GWAS, TWAS, and PWAS to refine the genetic architecture of heritable breast cancer.

Integrated transcriptomic analysis reveals a metabolically quiescent state and gene expression networks related to intermediate and mature human 8-cell stage embryo resembling cells in vitro

The paper integrates scRNA-seq data to identify metabolically quiescent 8CLCs resembling human 8-cell stage embryos and characterizes their gene expression networks.

Microbiome Data Integration via Shared Dictionary Learning

This paper introduces MetaDICT, a method for integrating microbiome data that reduces batch effects and preserves biological variation, improving analysis of microbial interactions and outcome prediction.

Evaluating the Effectiveness of Data Reduction Techniques in QTL Mapping

The paper compares PCA-based QTL mapping with individual trait hotspots in metabolomic and transcriptomic data from a recombinant inbred line, finding they identify different genomic regions and genetic architectures.

Beyond the Shared Inflammatory Axis: Differentiating Molecular Signatures in Psoriatic Arthritis and Ankylosing Spondylitis through Integrated Omics

This study compares transcriptomic signatures of psoriatic arthritis and ankylosing spondylitis to identify shared and distinct molecular features using integrative omics approaches.

Agnostic Tools for Life Detection: A Multiscale Approach to Biological and Chemical Reaction Networks

The paper evaluates macroscale and microscale metrics to distinguish biotic from abiotic chemical reaction networks and proposes an agnostic toolset for life detection.

Nanoparticle enriched mass spectrometry proteomics in British South Asians identifies novel variant-protein-disease mechanisms

The paper uses nanoparticle enriched mass spectrometry proteomics in British South Asians to identify novel variant-protein-disease mechanisms through integrative analysis of exome sequencing and proteomic data.

Vaccination with mRNA-encoded membrane-bound HIV Envelope trimer induces neutralizing antibodies in animal models

Membrane-bound BG505 MD39.3 Env trimer delivered as mRNA-LNP reduced base-directed antibody responses in rabbits and macaques and elicited neutralizing antibodies, with memory B cell responses documented in macaques.

Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes

The paper analyzes insertion sequences (ISs) in prokaryotic genomes using transposon ecology to uncover general principles and niche specificities shaping their distribution and activity.

Whole-Brain Cell-Cell Interaction Axes Explaining Tissue Vulnerability Across the Neurodegenerative Spectrum

The paper maps whole-brain cell-cell interactions across neurodegenerative diseases and identifies communication axes linked to regional brain vulnerability.

Procrastination partly reflects an evolutionary byproduct of non-planning impulsivity

The paper shows non-planning impulsivity predicts procrastination and shares genetic overlap, with DLPFC deviations partially explaining this link.

skDER & CiDDER: two scalable approaches for microbial genome dereplication

The paper introduces two tools, skDER and CiDDER, for microbial genome dereplication to select representative genomes for comparative genomic studies.

Emotion Regulation in the Gradient Framework: Large-Scale Brain Organization Shapes Individual Differences in Reappraisal Success

The paper uses gradient-based brain organization to predict individual differences in emotion regulation success across two fMRI datasets.

Brain transcriptomic signatures for mood disorders and suicide phenotypes: an anterior insula and subgenual ACC network postmortem study

The paper identifies molecular signatures in the anterior insula and subgenual ACC brain network associated with mood disorders and suicide outcomes using postmortem RNA-sequencing data.

Facilitate integrated analysis of single cell multiomic data by binarizing gene expression values

This paper shows that binarizing scRNA-seq data and integrating it with scATAC-seq data using TF-IDF and LSI improves clustering for multiomic analysis.

An integrated single-cell atlas of the limb skeleton from development through adulthood

The paper integrates ten scRNA-seq datasets to create a limb skeletal cell atlas covering development to adulthood, identifying 39 cell states and enabling cell-cell communication and perturbation studies.

Multi-omics comparative analyses of synucleinopathy models reveal distinct targets and relevance for drug development

The paper compares two rat synucleinopathy models using multi-omics data to identify disease mechanisms and drug targets relevant to Parkinson's disease.

CagY sequence and structural motifs are associated with ancestry and 1 disease in world-wide Helicobacter pylori strains

The paper analyzes cagY sequences from Helicobacter pylori strains to identify ancestry and disease associations, finding specific motifs and structural changes linked to gastric cancer.

The synergistic interactions of low-dimensional brain modes

The paper examines how dimensionality reduction techniques preserve synergistic interactions in brain dynamics using resting-state fMRI data from 100 healthy participants.