matrix factorization

PyMSQ: a python package for fast Mendelian sampling (co)variance and haplotype-based similarity in genomic selection

PyMSQ provides a fast Python package for computing Mendelian sampling variance, covariance, and haplotype-based similarity in genomic selection, enhancing haplotype diversity management.

Spatiotemporal cell type deconvolution leveraging tissue structure

SpaDecoder improves cell type deconvolution in spatial transcriptomics by leveraging 3D tissue structure and single-cell reference profiles.

The genomic basis of heat stress adaptation in indigenous Ethiopian cattle from arid and hot-humid climates

This study identifies genomic adaptation mechanisms in Ethiopian zebu cattle to arid and hot-humid climates through whole-genome sequencing and selection scans.

A multi-omics atlas of human hindbrain development

This paper creates a multi-omics atlas of human hindbrain development, revealing cellular diversity, regulatory programs, and disease relevance.

A reference panel for linkage disequilibrium and genotype imputation using whole-genome sequencing data from 2,680 participants across India

The paper constructs a large-scale LD and genotype imputation reference panel using whole-genome sequencing data from 2,680 Indian participants, improving imputation accuracy and polygenic risk score performance.

Multiscale RNA editing analysis reveals cell type specific regulatory programs across disease states in acute myeloid leukemia

The paper identifies cell type-specific RNA editing patterns in AML across disease states using single-cell and pseudo-bulk analyses, revealing condition-specific regulatory programs.

A multi-ancestry genetic reference for the Quebec population

The paper constructs a genetic reference panel for the Quebec population using whole-genome sequencing and GWAS to improve phenotype-genotype association discovery.

in silico analysis and comparison of the metabolic capabilities of different organisms by reducing metabolic complexity

This paper introduces NIS, a method to simplify genome-scale metabolic models for comparing metabolic capabilities across organisms, revealing conserved and divergent patterns in metabolism.

Expanded Chromatin Accessibility Mapping Explains Genetic Variation Associated with Complex Traits in Liver

The paper integrates chromatin accessibility data with GWAS to identify regulatory mechanisms underlying blood lipid traits, finding 20% of signals lack proposed mechanisms.

Matching Heterogeneous Cohorts by Projected Principal Components Reveals Two Novel Alzheimer's Disease-Associated Genes in the Hispanic Population

Targeting Modulated Vascular Smooth Muscle Cells in Atherosclerosis via FAP-Directed Immunotherapy

Single-cell and spatial maps of human coronary arteries identify FAP as a marker of SMC-derived modulated cells; an anti-FAP BiTE reduced plaque burden in mouse models.

Genomic Disaggregation Reveals Distinct Admixture Patterns and Cardiometabolic Risk Loci in Black Hawaiians

This study analyzes the genomic structure and cardiometabolic risks of Black Hawaiians using whole-genome sequencing and EHR data, revealing distinct admixture patterns and risk loci.

Multi-tissue Transcriptomic and Pan-genomic Analyses Reveal Reciprocal Selective Retention Drives the Phenotypic Trade-off in Gossypium hirsutum and Gossypium barbadense

This study identifies reciprocal selective retention of transcription factors in Upland and Sea Island cotton, explaining the yield-quality trade-off through genomic and transcriptomic analyses.

SparseAEH: Scalable autoregressive expression histology discovery in spatial transcriptomics via sparse Gaussian kernels

SparseAEH accelerates spatial transcriptomics analysis by using sparse Gaussian kernels, achieving faster computation with accuracy comparable to existing methods.

Substance use disorders exhibit unique and disorder specific genetic associations with externalizing and internalizing psychopathology

This study identifies genetic relationships between substance use disorders and externalizing/internalizing psychopathology, finding that internalizing contributes uniquely to SUD risk.

Fast barcode calling based on k-mer distances

The paper introduces a fast and accurate barcode calling method using k-mer filtering, achieving higher accuracy and speed than existing methods.

FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors

FEDRANN improves long-read overlap detection using dimensionality reduction and approximate nearest neighbors, outperforming existing methods on real data.

Meditation as a Bioactive Intervention: Molecular and Neurophysiological Mechanisms Revealed by Connectivity Mapping

This study uses connectivity mapping to show meditation shares molecular signatures with drugs targeting neuroactive pathways, suggesting it modulates brain excitation-inhibition balance.

Interaction of lncRNA LENT with DHX36 regulates translation and suppresses autophagy in melanoma.

This study identifies LENT, a lncRNA regulated by MITF, which interacts with DHX36 to modulate translation and suppress autophagy in melanoma cells.

Cross-species consensus atlas of the primate basal ganglia

The paper creates a cross-species consensus atlas of primate basal ganglia cell types using multiomic data from human, macaque, and marmoset, identifying 61 conserved cell types and a novel hybrid medium spiny neuron type.

Large-scale integration of omics and electronic health records to identify potential risk protein biomarkers and therapeutic drugs for cancer prevention

This study integrates large-scale omics and electronic health records to identify risk proteins and drugs for cancer prevention, finding 101 novel proteins and three drugs associated with reduced colorectal cancer risk.

Comparative genomics reveals multipartite genomes undergoing loss in the fungal endosymbiotic genus Mycetohabitans

The paper analyzes the genomes of Mycetohabitans species to reveal evolutionary trends in endofungal bacteria, showing genome reduction, multipartite structure, and dynamic genetic elements.

Error Correction Algorithms for Efficient Gene ExpressionQuantification in Single Cell Transcriptomics

This paper introduces an algorithm for error correction in scRNA-seq data, improving gene expression quantification efficiency and accuracy.

Transcriptional Profiling and Co-expression Integration for the Filtering of Relevant Bacterial sRNA-mRNA Interactions: Application to Staphylococcus aureus Biofilm

The paper integrates RNA-seq data to identify sRNA-mRNA interactions in S. aureus biofilms, prioritizing candidates through differential expression and co-expression analysis.

LCSKPOA: Enabling banded semi-global partial order alignments via efficient and accurate backbone generation through extended lcsk++

The paper introduces an extended LCSk++ algorithm for graph-based alignment, improving memory and runtime efficiency for local and semi-global POA while maintaining alignment quality.

Spatiotemporal-multimodal integration reveals BCG-induced skin-blood crosstalk

This study integrates spatiotemporal data from skin and blood to reveal BCG-induced molecular networks and predictive biomarkers of vaccine response.

The Rayleigh Quotient and Principal Component Analysis I

This paper introduces rho PCA, a method that improves upon contrastive PCA by approximating the Rayleigh quotient, offering better accuracy and efficiency for dimension reduction in genomics data.

Dynamic transcriptional and epigenetic changes define postnatal tendon growth

The paper identifies transcriptional and epigenetic changes during postnatal tendon growth and highlights Yap1's role in ECM maturation.

Metabolic Reprogramming and Therapeutic Vulnerabilities in the Tumor Microenvironment Revealed by Multi-scale Network Geometry

The paper uses multi-scale network geometry to analyze metabolic reprogramming in colorectal cancer, identifying therapeutic vulnerabilities and architectural changes in metabolic networks.

Capturing changes to animal complexity from quantifiable patterns in genomic data

The paper analyzes genomic data from 32 animal species to explore how changes in regulatory genes and microRNAs relate to morphological complexity and disparity, finding no link between genome size and disparity but strong associations between gene loss and parasitism, and microRNA increases and complexity.