Bioinformatics and Genomic Networks

GeneCodis 4: Expanding the modular enrichment analysis to regulatory elements

GeneCodis 4 extends functional enrichment analysis to regulatory elements like transcription factors, CpG sites, and miRNAs, with new databases and visualizations.

Automated, Reproducible Investigation of gene set Differential Enrichment via the AUTO-go framework

The paper introduces the AUTO-go framework to standardize and automate gene set enrichment analysis with reproducible visualizations in genomics research.

Functional network motifs defined through integrationof protein-protein and genetic interactions

The paper defines functional network motifs by integrating genetic interaction data to identify biologically relevant feedback circuits in yeast.

TWO-SIGMA-G: A New Competitive Gene Set Testing Framework for scRNA-seq Data Accounting for Inter-Gene and Cell-Cell Correlation

TWO-SIGMA-G tests gene sets in scRNA-seq data by accounting for gene and cell correlations, showing improved power and error control in simulations and real datasets.

csdR, an R package for differential co-expression analysis

The paper introduces csdR, an R package for differential co-expression analysis, which improves performance and usability compared to existing implementations.

HyMM: Hybrid method for disease-gene prediction by integrating multiscale module structures

This paper introduces HyMM, a hybrid method for disease-gene prediction that integrates multiscale module structures, showing improved performance through cross-validation and independent testing.

Identifying robust functional modules using three-body correlations in Escherichia coli

The paper identifies robust functional gene modules in Escherichia coli using three-body correlations and community detection in gene co-expression networks.

MonaGO: a novel Gene Ontology enrichment analysis visualisation system

MonaGO provides an interactive web-based visualization system for gene ontology enrichment analysis, offering dynamic clustering and customizable outputs to improve interpretation of results.

Gaining confidence in inferred networks

The paper introduces a method to assess network inference reliability by measuring functional assortativity in biological networks.

A systems biology approach to elucidate the post-translational regulome of coronary artery disease

This paper identifies serine phosphorylation as a key post-translational modification in coronary artery disease and highlights GSK3B as a master regulator with significant predictive power.

Pitfalls of machine learning models for protein-protein interactions

The paper benchmarks machine learning models for predicting protein-protein interactions, showing that functional genomics models outperform sequence-based ones and that algorithm design has little impact on performance with functional genomic data.

Statistical properties of the MetaCore network of protein-protein interactions

The paper analyzes the statistical properties of the MetaCore protein-protein interaction network using Google matrix methods to identify activation and inhibition patterns in specific protein groups.

Comparison of confound adjustment methods in the construction of gene co-expression networks

This study compares confound adjustment methods for gene co-expression network construction and finds that different methods significantly affect network architecture.

Comprehensive analysis of next-generation sequencing data in COVID-19 and its secondary complications

This study analyzes NGS data to identify differentially expressed genes and hub genes associated with COVID-19 and its secondary complications, showing diagnostic potential.

Muon: multimodal omics analysis framework

The paper introduces MUON, a framework for organizing, analyzing, and visualizing multimodal omics data, enabling flexible multi-omics analysis and interoperability with existing standards.

Leveraging gene co-regulation to identify gene sets enriched for disease heritability

The paper introduces GCSC regression to identify gene sets enriched for disease heritability by leveraging gene co-regulation in TWAS data, finding immune-related associations in Alzheimer's disease.

The DOMINO web-server for active module identification analysis

The paper introduces a web-server for the DOMINO algorithm, which identifies active modules in gene networks and provides tools for analysis and interpretation.

Gene Expression Meta-Analysis of Colon Rectal Cancer Tumour Cells Reveals Genes in Association With Tumorogenesis.

This paper performs a meta-analysis of gene expression in colon rectal cancer to identify genes associated with tumorogenesis and potential therapeutic targets.

Evaluation of critical data processing steps for reliable prediction of gene co-expression from large collections of RNA-seq data

The paper evaluates data processing steps for accurate gene co-expression prediction from RNA-seq data, finding that sample size, normalization, batch correction, and correlation measure significantly impact results.

FILER: large-scale, harmonized FunctIonaL gEnomics Repository

FILER provides a large-scale, harmonized functional genomics data catalog with streamlined access to over 50,000 datasets and efficient querying capabilities.

A biphasic Deep Semi-supervised framework for Suptype Classification and biomarker discovery

This paper introduces DeepSSC, a biphasic deep semi-supervised framework for multi-omics subtype classification and biomarker discovery, showing improved performance and novel biomarker identification.

Transcriptogram analysis reveals relationship between viral titer and gene set responses during Corona-virus infection.

The paper uses transcriptogram analysis on SARS-CoV-1 microarray data to identify gene sets and their temporal relationship with viral titer during infection.

Protein Interaction Networks Define the Genetic Architecture of Preterm Birth

The paper identifies subgroups of preterm birth patients with shared protein interaction networks and pathway enrichments using sequencing and bioinformatic analysis.

PlantNexus: A Gene Co-expression Network Database and Visualization Tool for Barley and Sorghum

The paper constructs gene co-expression networks for barley and sorghum using RNA-seq data and provides a database and visualization tool called PlantNexus.

E.PAGE: A curated database and enrichment tool to predict modules associated with gene-environment interactions

The paper curates a database and develops an R package to identify gene-environment interactions by analyzing gene modules associated with environmental factors in disease.

Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data

This study benchmarks 30 RNA-seq data processing workflows for constructing coexpression networks, finding that normalization methods significantly affect network accuracy.

NetMix2: Unifying network propagation andaltered subnetworks

NetMix2 unifies network propagation and altered subnetwork approaches to identify disease-related subnetworks, outperforming existing methods in simulated and real data.

decoupleR: Ensemble of computational methods to infer biological activities from omics data

decoupleR evaluates methods for inferring biological activities from omics data, finding simple linear models and consensus scores perform best in perturbation experiments.

HumanMine: advanced data searching, analysis and cross-species comparison.

HumanMine provides an integrated database for human genomics and proteomics data with tools for analysis and cross-species comparison.

Insights into functional connectivity in mammalian signal transduction pathways by pairwise comparison of protein interaction partners of critical signaling hubs

The paper identifies critical nodes in immune signaling pathways by analyzing shared interaction partners of transcription factors using PIC-VENN.