matrix factorization

Fast, accurate local ancestry inference with FLARE

FLARE infers local ancestry with high accuracy and efficiency, scaling to large datasets using advanced computational techniques.

Efficient Sequence Embedding For SARS-CoV-2 Variants Classification

This paper introduces an efficient sequence embedding method for SARS-CoV-2 variant classification, improving predictive performance and computational efficiency over existing kernel methods.

A low dimensional cognitive-network space in Alzheimer's disease and frontotemporal dementia

This study identifies cognitive components and their relationship with brain network connectivity in Alzheimer's disease and frontotemporal dementia, revealing convergent and divergent patterns.

Uncovering context-specific genetic-regulation of gene expression from single-cell RNA-sequencing using latent-factor models

This paper introduces SURGE, a method to discover context-specific eQTLs from single-cell RNA-seq data, showing its relevance in disease through colocalization analysis.

CAbiNet: Joint visualization of cells and genes based on a gene-cell graph

CAbiNet jointly visualizes cells and genes using a gene-cell graph and biMAP embedding for interactive exploration and biclustering.

M-Band Wavelet-Based Imputation of scRNA-seq Matrix and Multi-view Clustering of Cell

The paper introduces a wavelet-based method for imputing sparse scRNA-seq data and performing multi-view clustering to recover missing cell types and discover rare cell states.

Deducing ensemble dynamics and information flow from the whole-brain imaging data

The paper analyzes whole-brain imaging data of C. elegans to decompose neural dynamics and model information flow using time-delay embedding, independent component analysis, and dimensionality reduction techniques.

Multi-'Omic Integration via Similarity Network Fusion to Detect Molecular Subtypes of Aging

This paper uses multi-omic integration to identify molecular subtypes of aging in brain tissue, finding subtypes associated with cognitive decline.

Application of a Latent Trait Modeling Method for Missing Data Across Datasets: Guidance on Appropriate Factor Structure

The paper extends a latent trait modeling method to handle missing data across datasets without requiring overlapping measurement instruments, using matrix completion and evaluates its reliability through simulation.

Uncovering Cross-Cohort Molecular Features with Multi-Omics Integration Analysis

This paper improves multi-omics integration by enhancing orthogonality in canonical vectors and demonstrates transferability across cohorts for proteomics and methylomics data.

A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships

The paper creates a high-density chromatin interaction network across species by integrating 3C experiments, showing improved prediction of coexpression and eQTL for long-range and trans chromatin contacts.

Genetic associations with resistance to Meloidogyne enterolobii in guava (Psidium sp.) using cross-genera SNPs and comparative genomics to Eucalyptus highlight evolutionary conservation across the Myrtaceae

The paper identifies genomic loci associated with resistance to Meloidogyne enterolobii in guava using cross-genera SNPs and comparative genomics with Eucalyptus.

Novel estimators for family-based genome-wide association studies increase power and robustness

The paper introduces novel estimators for family-based GWAS that increase power and robustness to population structure by improving imputation of missing parent genotypes and using a linear-mixed model.

Identifying hierarchical cell states and gene signatures with deep exponential families for single-cell transcriptomics

The paper introduces scDEF, a Bayesian model for single-cell RNA-seq data that identifies hierarchical cell states and improves gene signature detection across batches.

Integrative Multi-Omics Approaches for Identifying Cervical Cancer Therapeutic Targets

This paper explores integrative multi-omics approaches to identify therapeutic targets for cervical cancer by analyzing HT data and clinical information.

A highly contiguous, scaffold-level nuclear genome assembly for the Fever tree (Cinchona pubescens Vahl) as a novel resource for research in the Rubiaceae

The paper presents the first highly contiguous nuclear and organelle genome assemblies for C. pubescens, enabling research on alkaloid biosynthesis and evolutionary relationships within the Rubiaceae family.

Functional genomics of cattle through integration of multi-omics data

The paper improves bovine genome annotation by integrating multi-omics data to identify novel transcripts and gene functions, and constructs a trait similarity network.

Projection in genomic analysis: A theoretical basis to rationalize tensor decomposition and principal component analysis as feature selection tools

This paper explains why PCA and tensor decomposition work well for feature selection in genomic data by relating them to projection pursuit and empirical P-value thresholds.

Efficient estimation of time-dependent functional connectivity using Structural Connectivity constraints

The paper introduces a model that efficiently estimates time-dependent brain connectivity using structural connectivity constraints and sparse MAR parameters.

EagleImp: Fast and Accurate Genome-wide Phasing and Imputation in a Single Tool

EagleImp provides fast and accurate genome-wide phasing and imputation, outperforming existing tools in speed while maintaining or improving accuracy.

Whole Exome Sequencing of Nigerian Prostate Tumors from the Prostate Cancer Transatlantic Consortium (CaPTC) Reveals DNA Repair Genes Associated with African Ancestry

This study analyzes whole-exome sequencing data from Nigerian prostate cancer tumors to identify germline and somatic variants associated with African ancestry and DNA repair gene mutations.

Deconvoluting complex correlates of COVID19 severity with local ancestry inference and viral phylodynamics: Results of a multiomic pandemic tracking strategy

The paper integrates multi-omic data to identify genetic and microbiome factors associated with severe COVID-19, independent of ancestry and social factors.

Revealing the molecular mechanisms underlying neural transmission of female pheromone signals in the male antennae of Antheraea pernyi by integrative proteomics and metabolomics analysis

The paper identifies differentially expressed proteins and metabolites in male moth antennae after female pheromone stimulation, revealing their roles in neural transmission of pheromone signals.

Data Fusion by Matrix Completion for Exposome Target Interaction Prediction

This study introduces a matrix completion method to predict chemical-target interactions, achieving high accuracy and demonstrating its utility for prioritizing environmental chemicals.

ERStruct: A Python Package for Inferring the Number of Top Principal Components from Whole Genome Sequencing Data

ERStruct estimates the number of top principal components from whole-genome sequencing data using parallel computing and GPU acceleration.

Regimes and mechanisms of transient amplification in abstract and biological networks

The paper explores transient amplification regimes in neuronal networks by manipulating eigenspectra and non-normality in upper triangular matrices, showing that imaginary distribution manipulation can lead to high amplification despite biological constraints.

A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids

This paper integrates GWAS data with functional genomic datasets to identify regulatory mechanisms and causal genes underlying lipid-related traits.

Phylophenomic and Phylogenomic analysis for Ovis aries reveals distinct identity of newly reported breed

The paper identifies a new sheep breed from West Bengal with distinct genetic identity using phylophenomic and phylogenomic analyses.

Exact polynomial-time isomorphism testing in directed graphs through comparison of vertex signatures in Krylov subspaces.

This paper introduces an exact polynomial-time algorithm for isomorphism testing in directed graphs using Krylov subspaces and vertex signatures, validated on enzyme structures.

Genetic variation in correlated regulatory region of Immunity

The paper identifies regulatory domains in immune cells using genomic and epigenomic data, revealing cell-type specific gene regulation and genetic control of regulatory elements.