matrix factorization

Fast and robust ancestry prediction using principal component analysis

This paper introduces two methods to improve ancestry prediction in GWAS by reducing bias and computational cost compared to existing approaches.

Contribution of common and rare variants to bipolar disorder susceptibility in extended pedigrees from population isolates

This study examines genetic risk for bipolar disorder in extended families, finding that both common and rare variants contribute to susceptibility, with no significant segregation of large-effect variants.

Factors affecting Response to Recurrent Genomic Selection in Soybeans

This study evaluates the effects of selection methods on genetic response in soybean recurrent selection over 40 cycles, identifying interactions that influence short-term gains and long-term genetic potential.

In silico prediction of high-resolution Hi-C interaction matrices

HiC-Reg predicts high-resolution Hi-C interaction matrices from regulatory signals, identifying topologically associated domains and CTCF motifs.

Addressing dereplication crisis: Taxonomy-free reduction of massive genome collections using embeddings of protein content

The paper introduces a method to reduce large genome collections by grouping similar genomes using embeddings, improving metagenomic classification accuracy.

A murine aging cell atlas reveals cell identity and tissue-specific trajectories of aging

This study uses single-cell RNA-seq to analyze aging in mice, finding that cell identity has a greater influence on aging trajectories than tissue environment.

Predicting Synthetic Lethal Interactions usingHeterogeneous Data Sources

The paper develops a method to predict synthetic lethal interactions by integrating heterogeneous data sources, outperforming existing methods with minimal feature engineering.

Meta-analysis of Scandinavian Schizophrenia Exomes

This study performs a meta-analysis of Scandinavian schizophrenia exomes, identifying three genes associated with the disorder and highlighting shared genetic architecture with high-functioning autism.

A computational framework for systematic exploration of biosynthetic diversity from large-scale genomic data

The paper introduces two tools, BiG-SCAPE and CORASON, for analyzing biosynthetic gene clusters in large genomic datasets, demonstrating their utility through validation and discovery of new gene cluster families.

Comprehensive biological interpretation of gene signatures using semantic distributed representation

This paper introduces GsVec, a method for interpreting gene signatures using distributed representation, achieving biologically valid results comparable to traditional methods.

Transcriptomic and Cellular Decoding of Regional Brain Vulnerability to Neurodevelopmental Disorders

The paper links genetic risks to spatial brain vulnerabilities in neurodevelopmental disorders using neuroimaging and gene expression data.

Interlaboratory Data Variability Contributes to the Differential Principal Components of Human Primed and Naïve-like Pluripotent States in Multivariate Meta-Analysis

The paper performs a multivariate meta-analysis of human pluripotent stem cell datasets to assess interlaboratory variability in defining naive-like pluripotent states.

deepMc: deep Matrix Completion for imputation of single cell RNA-seq data

deepMc uses deep matrix factorization to impute missing values in single cell RNA-seq data, improving clustering, differential expression analysis, and cell type separability.

Complex evolutionary origins of specialized metabolite gene cluster diversity among the plant pathogenic fungi of the Fusarium graminearum species complex

The paper analyzes gene cluster diversity in Fusarium fungi, identifying processes like horizontal transfer and transposable element-driven rearrangements that shape specialized metabolite production.

Mechanisms of tissue-specific genetic regulation revealed by latent factors across eQTLs

The paper uses matrix factorization to analyze eQTLs across 49 human tissues, identifying tissue-specific and shared genetic regulation patterns and their potential transcription factor drivers.

Studying the drug treatment pattern based on the action of drug and multi-layer network model

This paper introduces STAM, a method using multi-layer networks to identify drug treatment patterns by analyzing tissue-specific PPI networks and drug-target modules.

Detecting task-dependent modulation of spatiotemporal module via tensor decomposition: application to kinematics and EMG data for walking and running at various speed

This paper uses tensor decomposition to quantify spatial and temporal modules and their task-dependent modulation in kinematics and EMG data for walking and running.

Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements

The paper analyzes TE transcript variation across non-tumorous tissues and identifies co-expression modules with immune genes and KZFPs.

Sex-Biased Trajectories of Amygdalo-Hippocampal Morphology Change Over Human Development

The paper analyzes longitudinal MRI data to identify sex-biased growth trajectories of the amygdala and hippocampus across human development, revealing differences in volume expansion and shape changes between males and females.

Exome sequencing of 457 autism families recruited online provides evidence for novel ASD genes

The paper reports exome sequencing of 457 ASD families, identifying 10.4% with known ASD genes and 3.4% with possibly associated variants, and provides statistical support for 34 ASD risk genes using the TADA framework.

catch22: CAnonical Time-series CHaracteristics

The paper introduces catch22, a set of 22 time-series features that balance computational efficiency and classification performance across diverse biomedical and other time-series datasets.

Genetic variation in the Major Histocompatibility Complex and association with depression

This study investigates whether genetic variation in the Major Histocompatibility Complex (MHC) is associated with depression risk, finding no significant associations at a conservative threshold.

Stochastic Lanczos estimation of genomic variance components for linear mixed-effects models

This paper introduces two new algorithms for faster REML estimation in linear mixed-effects models used in GWAS, showing they are faster and more accurate than existing methods.

Identifying Gene Expression Programs of Cell-type Identity and Cellular Activity with Single-Cell RNA-Seq

This paper introduces cNMF, a matrix factorization method to disentangle cell-type identity and activity programs from scRNA-Seq data, showing it improves cell type hierarchy and identifies novel activity programs.

Molecular Inverse Comorbidity between Alzheimer’s disease and Lung Cancer: new insights from Matrix Factorization

The paper uses matrix factorization to analyze molecular mechanisms behind the inverse comorbidity between Alzheimer’s disease and lung cancer, identifying new candidate factors and subtype-specific mechanisms.

Novel DNA methylation sites of glucose and insulin homeostasis: an integrative cross-omics analysis

This study identifies nine novel DNA methylation sites associated with fasting glucose and insulin levels by integrating cross-omics data from multiple cohorts.

The Geometric Sparse Matrix Completion Model for Predicting Drug Side effects

The paper introduces a matrix completion model to predict drug side effects using pharmacological side information, achieving better performance than existing methods with explainable predictions.

Technical Note: Efficient and accurate estimation of genotype odds ratios in biobank-based unbalanced case-control studies

The paper introduces a scalable method to accurately estimate genotype odds ratios in unbalanced biobank-based case-control studies, improving computational efficiency compared to existing methods.

Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization

This study introduces CSMF, a matrix factorization framework that combines data dimension reduction and differential analysis to reveal common and specific patterns across interrelated biological scenarios.

Ocular disease mechanisms elucidated by genetics of human fetal retinal pigment epithelium gene expression

This study identifies fRPE-specific genes and variants associated with AMD and myopia, revealing novel e/sQTL and mechanisms linking a common variant to both diseases.