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A General Framework for Weighted Gene Co-Expression Network Analysis

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The biology of chromatin remodeling complexes.

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The Genetic Landscape of a Cell

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High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

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A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data

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The BioGRID interaction database: 2013 update

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Evidence for Network Evolution in an Arabidopsis Interactome Map

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Exploration of the Function and Organization of the Yeast Early Secretory Pathway through an Epistatic Miniarray Profile

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The BioGRID Interaction Database: 2011 update

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Ontological analysis of gene expression data: current tools, limitations, and open problems

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Toward a Comprehensive Atlas of the Physical Interactome of Saccharomyces cerevisiae

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An in Vivo Map of the Yeast Protein Interactome

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Genomic Expression Responses to DNA-damaging Agents and the Regulatory Role of the Yeast ATR Homolog Mec1p

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A double-hexameric MCM2-7 complex is loaded onto origin DNA during licensing of eukaryotic DNA replication

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How does gene expression clustering work?

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Systematic interpretation of genetic interactions using protein networks

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Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data

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Ontology matching with semantic verification

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Judging the Quality of Gene Expression-Based Clustering Methods Using Gene AnnotationPreprint

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Recycle your receptors with retromer

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The CORVET Tethering Complex Interacts with the Yeast Rab5 Homolog Vps21 and Is Involved in Endo-Lysosomal Biogenesis

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The histone code at DNA breaks: a guide to repair?

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The National Center for Biomedical Ontology

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A critical assessment of Mus musculusgene function prediction using integrated genomic evidence

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Gene Ontology annotations at SGD: new data sources and annotation methods

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Vps-C complexes: gatekeepers of endolysosomal traffic

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Discovery of biological networks from diverse functional genomic data

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Associating Genes with Gene Ontology Codes Using a Maximum Entropy Analysis of Biomedical LiteraturePreprint

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YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface

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An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae

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Eaf1 Is the Platform for NuA4 Molecular Assembly That Evolutionarily Links Chromatin Acetylation to ATP-Dependent Exchange of Histone H2A Variants

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Telomerase, mitochondria and oxidative stress

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A probabilistic view of gene function

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Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action

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NuA4 and SWR1-C: two chromatin-modifying complexes with overlapping functions and componentsThis paper is one of a selection of papers published in this Special Issue, entitled 30th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal's usual peer review process.

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Using text to build semantic networks for pharmacogenomics

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Implementation of GenePattern within the Stanford Microarray Database

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Analysis of Biological Processes and Diseases Using Text Mining Approaches

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Quantitative Genetic Interaction Mapping Using the E-MAP Approach

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A Genomewide Suppressor and Enhancer Analysis of <i>cdc13-1</i> Reveals Varied Cellular Processes Influencing Telomere Capping in <i>Saccharomyces cerevisiae</i>

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Mercuric chloride induces apoptosis via a mitochondrial-dependent pathway in human leukemia cells

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How the gene ontology evolves

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Biological process linkage networks

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Resolving the structure of interactomes with hierarchical agglomerative clustering

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Modularity and directionality in genetic interaction maps

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Yeast Homologues of Three BLOC‐1 Subunits Highlight KxDL Proteins As Conserved Interactors of BLOC‐1

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WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

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Architecture of the human interactome defines protein communities and disease networks

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A global genetic interaction network maps a wiring diagram of cellular function

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Biological Network Exploration with Cytoscape 3

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Machine learning for integrating data in biology and medicine: principles, practice, and opportunities

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Predicting multicellular function through multi-layer tissue networks

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Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis

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Using deep learning to model the hierarchical structure and function of a cell

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Models of human core transcriptional regulatory circuitriesPreprint

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Methods for biological data integration: perspectives and challenges

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The role of ontologies in biological and biomedical research: a functional perspective

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Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63

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An interactive reference framework for modeling a dynamic immune system

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Compact integration of multi-network topology for functional analysis of genes

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Global Genetic Networks and the Genotype-to-Phenotype Relationship

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Genomics, convergent neuroscience and progress in understanding autism spectrum disorder

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Computational network biology: Data, models, and applications

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Functional landscape of SARS-CoV-2 cellular restriction

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A genome-wide atlas of co-essential modules assigns function to uncharacterized genes

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Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli

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Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations

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Genotype to phenotype via network analysis

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The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders

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Circular RNA CDR1as promotes adipogenic and suppresses osteogenic differentiation of BMSCs in steroid-induced osteonecrosis of the femoral head

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New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence

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FOXQ1/NDRG1 axis exacerbates hepatocellular carcinoma initiation via enhancing crosstalk between fibroblasts and tumor cells

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Exploiting ontology graph for predicting sparsely annotated gene function

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Genome sequence of the model rice variety KitaakeX

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Single cell proteomics in biomedicine: High‐dimensional data acquisition, visualization, and analysis

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Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems

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YeastNet v3: a public database of data-specific and integrated functional gene networks forSaccharomyces cerevisiae

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Inferring gene ontologies from pairwise similarity data

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Mapping the multiscale structure of biological systems

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Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks

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