Bioinformatics and Genomic Networks

Accuracy of functional gene community detection in Saccharomyces cerevisiae by maximizing Generalized Modularity Density

The paper compares twelve methods for inferring gene co-expression networks and identifying functional communities in yeast, finding that CLR followed by Generalized Modularity Density clustering performs best.

Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data

The paper introduces contrast subgraphs to compare gene and protein networks from different conditions or techniques, highlighting altered connectivity modules.

Hetnet connectivity search provides rapid insights into how two biomedical entities are related

The paper introduces hetnet connectivity search to find meaningful relationships between biomedical entities in heterogeneous networks without requiring supervised training data.

A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

The paper presents a computational framework for analyzing SARS-CoV-2-host interactions to identify drug targets and model disease mechanisms.

Phosphoproteomics data-driven signalling network inference: does it work?

This study evaluates six pairwise measures for predicting kinase-substrate and substrate-substrate associations from phosphoproteomics data, finding poor performance but improved results with sequence similarity filtering.

amica: an interactive and user-friendly web-platform for the analysis of proteomics data

amica provides a user-friendly web platform for proteomics data analysis, offering quality control, differential expression, and network analysis with minimal user input.

OmicsTIDE: Interactive Exploration of Trends in Multi-Omics Data

OmicsTIDE provides an interactive visualization tool to explore trends in multi-omics data by clustering and comparing regulatory trends across different experimental designs.

bulkAnalyseR: An accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data

bulkAnalyseR provides an interactive pipeline for analyzing and sharing bulk multi-modal sequencing data, offering quality checks, differential expression, and regulatory network analysis.

Large-scale changes of molecular network states explain complex traits

The paper identifies a central state transition in yeast molecular networks linked to PKA and TOR signaling, showing how genetic variants can cause global or local molecular changes affecting multiple cellular traits.

Beyond Pairwise Interactions: Higher-Order Dynamics in Protein Interaction Networks

The paper analyzes dynamic gene expression data using a hypergraph model to quantify network heterogeneity and identifies differences in curvature between pluripotent stem cells, cancer cells, and pathways in melanoma.

Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data

The paper introduces LINEX2, a lipid network analysis framework that identifies enzymatic dysregulation from lipidomics data by integrating metabolic networks and graph algorithms.

Optimal construction of a functional interaction network from pooled library CRISPR fitness screens

This study identifies optimal methods for constructing functional interaction networks from CRISPR knockout screens by evaluating scoring schemes and normalization techniques.

MSdb: an integrated expression atlas of human musculoskeletal system

MSdb provides an integrated expression atlas of human musculoskeletal system data with visualization, analysis tools, and curated phenotype information.

Multi-layer guilt-by-association-based drug repurposing by integrating clinical knowledge on biological heterogeneous networks

This paper introduces a multi-layer guilt-by-association approach for drug repurposing by integrating clinical knowledge into biological networks, improving drug-disease association prediction accuracy.

gtexture: novel extension of image texture analysis to graphs and its application to cancer informatics

The paper introduces graph texture features, a novel method for analyzing network structures, and applies it to cancer informatics to classify cell lines by lineage with high accuracy.

rGREAT: an R/Bioconductor package for functional enrichment on genomic regions

rGREAT is an R/Bioconductor package that provides local implementation of the GREAT algorithm for functional enrichment on genomic regions, supporting over 500 organisms and user-provided gene sets.

In silico network-based screening reveals candidates for endothelial dysfunction therapy

The paper identifies 17 candidate genes for endothelial dysfunction therapy using computational network analysis and in silico perturbation, with one target showing anti-inflammatory and antioxidant effects.

Identifying genes and pathways linking astrocyte regional specificity to Alzheimer's disease susceptibility

The paper identifies region-specific astrocyte genes and pathways linked to Alzheimer's disease susceptibility using a network-guided approach and mouse gene expression data.

Integrative network analysis interweaves the missing links in cardiomyopathy diseasome

The paper identifies candidate genes for cardiomyopathies by integrating network analysis and disease associations, highlighting key genes like NOS3, MMP2, and SIRT1.

Single sample pathway analysis in metabolomics: performance evaluation and application

This paper evaluates single-sample pathway analysis methods for metabolomics, finding that clustering-based methods offer higher precision while GSEA-based methods have better recall, and introduces two new methods with a software package.

RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from genes, proteins, and metabolites

RaMP-DB 2.0 provides an updated database and tools for functional interpretation of metabolomic and multi-omic data, with enhanced annotations and enrichment analysis capabilities.

Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners

The paper shows that protein abundance is often poorly predicted from mRNA levels and that interacting proteins' transcripts better predict protein abundance.

An improved network alignment algorithm of dynamic protein interaction networks of floral development in Arabidopsis

The paper develops an improved network alignment algorithm, NetCoffee 2+, to analyze dynamic protein interaction networks in Arabidopsis floral development and identifies key proteins and potential ABCDE-like genes.

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.

Network reconstruction for trans acting genetic loci using multi-omics data and prior information

The paper reconstructs regulatory networks underlying trans-QTL hotspots using human multi-omics data and biological priors, identifying novel networks related to schizophrenia and lean body mass.

FACTORs: a Novel R Package for Functional Data Reduction and Hypothesis Testing

FACTORs provides a method to validate differentially expressed genes across studies and reduce Type I error in functional analysis.

scHumanNet: a single-cell network analysis platform for the study of cell-type specificity of disease genes

scHumanNet identifies cell-type-specific gene functions by analyzing single-cell transcriptomes, revealing disease-related gene effects in specific cell types.

FunHoP analysis reveals upregulation of mitochondrial genes in prostate cancer

The paper uses FunHoP to analyze mitochondrial gene expression in prostate cancer, finding upregulation of mitochondrial pathways in cancerous cells compared to normal cells.

Benchmarking of protein interaction databases for integration with manually reconstructed signaling network models

The paper benchmarks protein interaction databases for their ability to recover manually curated edges from signaling network models of cardiac hypertrophy, mechano-signaling, and fibrosis.

The Molecular Signatures Database Revisited: Extending Support for Mouse Data

The paper extends the Molecular Signatures Database to support mouse gene data by adding mouse-specific gene sets and improved orthology mapping resources.