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Understanding biological functions through molecular networks
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Metabolic stability and epigenesis in randomly constructed genetic nets
inferredcites →https://doi.org/10.1016/j.tibs.2004.10.001openalex-snapshot
Hierarchical thinking in network biology: the unbiased modularization of biochemical networks
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Integrating ‘omic’ information: a bridge between genomics and systems biology
inferredcites →https://doi.org/10.1016/s0022-5193(03)00035-3openalex-snapshot
The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster
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Functional Discovery via a Compendium of Expression Profiles
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A Biological Atlas of Functional Maps
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SNP association studies in Alzheimer's disease highlight problems for complex disease analysis
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Computational genetics: finding protein function by nonhomology methods
inferredcites →https://doi.org/10.1016/s1097-2765(04)00033-4openalex-snapshot
Systematic Interactome Mapping and Genetic Perturbation Analysis of a C. elegans TGF-β Signaling Network
inferredcites →https://doi.org/10.1016/s1534-5807(02)00297-6openalex-snapshot
A Genomic Switch at the Transition from Cell Proliferation to Terminal Differentiation in the Drosophila Eye
inferredcites →https://doi.org/10.1038/30918openalex-snapshot
Collective dynamics of ‘small-world’ networks
inferredcites →https://doi.org/10.1038/35011540openalex-snapshot
From molecular to modular cell biology
inferredcites →https://doi.org/10.1038/35075138openalex-snapshot
Lethality and centrality in protein networks
inferredcites →https://doi.org/10.1038/msb4100111openalex-snapshot
Robustness and modular design of the Drosophila segment polarity network
inferredcites →https://doi.org/10.1038/nature01765openalex-snapshot
Evolutionary capacitance as a general feature of complex gene networks
inferredcites →https://doi.org/10.1038/nature02236openalex-snapshot
Functional genomic hypothesis generation and experimentation by a robot scientist
inferredcites →https://doi.org/10.1038/nature02555openalex-snapshot
Evidence for dynamically organized modularity in the yeast protein–protein interaction network
inferredcites →https://doi.org/10.1038/nature02782openalex-snapshot
Genomic analysis of regulatory network dynamics reveals large topological changes
inferredcites →https://doi.org/10.1038/nature03876openalex-snapshot
Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis
inferredcites →https://doi.org/10.1038/nature04469openalex-snapshot
Identification of pathways regulating cell size and cell-cycle progression by RNAi
inferredcites →https://doi.org/10.1038/nature04568openalex-snapshot
Chance and necessity in the evolution of minimal metabolic networks
inferredcites →https://doi.org/10.1038/nature04768openalex-snapshot
Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4
inferredcites →https://doi.org/10.1038/nature06107openalex-snapshot
Natural history and evolutionary principles of gene duplication in fungi
inferredcites →https://doi.org/10.1038/nature750openalex-snapshot
Comparative assessment of large-scale data sets of protein–protein interactions
inferredcites →https://doi.org/10.1038/nbt0606-667openalex-snapshot
Tools for kinetic modeling of biochemical networks
inferredcites →https://doi.org/10.1038/nbt1103openalex-snapshot
Probabilistic model of the human protein-protein interaction network
inferredcites →https://doi.org/10.1038/nbt1116openalex-snapshot
Effect of sampling on topology predictions of protein-protein interaction networks
inferredcites →https://doi.org/10.1038/nbt1295openalex-snapshot
A human phenome-interactome network of protein complexes implicated in genetic disorders
inferredcites →https://doi.org/10.1038/ng.2007.2openalex-snapshot
Network modeling links breast cancer susceptibility and centrosome dysfunction
inferredcites →https://doi.org/10.1038/ng1242openalex-snapshot
Evolutionary conservation of motif constituents in the yeast protein interaction network
inferredcites →https://doi.org/10.1038/ng1293openalex-snapshot
Dynamics of the p53-Mdm2 feedback loop in individual cells
inferredcites →https://doi.org/10.1038/ng1340openalex-snapshot
Gene regulatory network growth by duplication
inferredcites →https://doi.org/10.1038/ng1561openalex-snapshot
From signatures to models: understanding cancer using microarrays
inferredcites →https://doi.org/10.1038/ng1725openalex-snapshot
The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation
inferredcites →https://doi.org/10.1038/ng1747openalex-snapshot
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets
inferredcites →https://doi.org/10.1038/ng1776openalex-snapshot
Systematic identification of human mitochondrial disease genes through integrative genomics
inferredcites →https://doi.org/10.1038/nrg1272openalex-snapshot
Network biology: understanding the cell's functional organization
inferredcites →https://doi.org/10.1038/nrm1570openalex-snapshot
Reconstruction of cellular signalling networks and analysis of their properties
inferredcites →https://doi.org/10.1038/nrm1838openalex-snapshot
Cell-signalling dynamics in time and space
inferredcites →https://doi.org/10.1073/pnas.0237338100openalex-snapshot
Modular organization of cellular networks
inferredcites →https://doi.org/10.1073/pnas.0305937101openalex-snapshot
The yeast cell-cycle network is robustly designed
inferredcites →https://doi.org/10.1073/pnas.0405996101openalex-snapshot
Global network analysis of phenotypic effects: Protein networks and toxicity modulation in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1073/pnas.0406707102openalex-snapshot
Dynamics of cellular level function and regulation derived from murine expression array data
inferredcites →https://doi.org/10.1073/pnas.0409522102openalex-snapshot
Conserved patterns of protein interaction in multiple species
inferredcites →https://doi.org/10.1073/pnas.0735871100openalex-snapshot
Assessing experimentally derived interactions in a small world
inferredcites →https://doi.org/10.1073/pnas.122653799openalex-snapshot
Community structure in social and biological networks
inferredcites →https://doi.org/10.1073/pnas.2235812100openalex-snapshot
Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network
inferredcites →https://doi.org/10.1073/pnas.242716699openalex-snapshot
Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics
inferredcites →https://doi.org/10.1073/pnas.95.25.14863openalex-snapshot
Cluster analysis and display of genome-wide expression patterns
inferredcites →https://doi.org/10.1093/bioinformatics/18.suppl_2.s202openalex-snapshot
Building and analysing genome-wide gene disruption networks
inferredcites →https://doi.org/10.1093/bioinformatics/btl038openalex-snapshot
FANMOD: a tool for fast network motif detection
inferredcites →https://doi.org/10.1093/hmg/ddi335openalex-snapshot
Interactome: gateway into systems biology
inferredcites →https://doi.org/10.1093/nar/gkh070openalex-snapshot
Human protein reference database as a discovery resource for proteomics
inferredcites →https://doi.org/10.1093/nar/gkh164openalex-snapshot
TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics
inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1101/gr.1774904openalex-snapshot
Annotation Transfer Between Genomes: Protein–Protein Interologs and Protein–DNA Regulogs
inferredcites →https://doi.org/10.1101/gr.205301openalex-snapshot
Identification of Potential Interaction Networks Using Sequence-Based Searches for Conserved Protein-Protein Interactions or “Interologs”
inferredcites →https://doi.org/10.1103/physrevlett.94.128701openalex-snapshot
Cell Fates as High-Dimensional Attractor States of a Complex Gene Regulatory Network
inferredcites →https://doi.org/10.1126/science.1065810openalex-snapshot
Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants
inferredcites →https://doi.org/10.1126/science.1068696openalex-snapshot
Evolutionary Rate in the Protein Interaction Network
inferredcites →https://doi.org/10.1126/science.1068873openalex-snapshot
MAP Kinase Phosphatase As a Locus of Flexibility in a Mitogen-Activated Protein Kinase Signaling Network
inferredcites →https://doi.org/10.1126/science.1081900openalex-snapshot
Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling
inferredcites →https://doi.org/10.1126/science.1087361openalex-snapshot
A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data
inferredcites →https://doi.org/10.1126/science.1089167openalex-snapshot
Superfamilies of Evolved and Designed Networks
inferredcites →https://doi.org/10.1126/science.1091317openalex-snapshot
Global Mapping of the Yeast Genetic Interaction Network
inferredcites →https://doi.org/10.1126/science.1099511openalex-snapshot
A Probabilistic Functional Network of Yeast Genes
inferredcites →https://doi.org/10.1126/science.1105103openalex-snapshot
Dynamic Complex Formation During the Yeast Cell Cycle
inferredcites →https://doi.org/10.1126/science.1105776openalex-snapshot
High-Throughput Mapping of a Dynamic Signaling Network in Mammalian Cells
inferredcites →https://doi.org/10.1126/science.1105809openalex-snapshot
Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data
inferredcites →https://doi.org/10.1126/science.1108876openalex-snapshot
Formation of Regulatory Patterns During Signal Propagation in a Mammalian Cellular Network
inferredcites →https://doi.org/10.1126/science.1120499openalex-snapshot
Logic of the Yeast Metabolic Cycle: Temporal Compartmentalization of Cellular Processes
inferredcites →https://doi.org/10.1126/science.1123287openalex-snapshot
Genome-Wide Prediction of C. elegans Genetic Interactions
inferredcites →https://doi.org/10.1126/science.292.5518.929openalex-snapshot
Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network
inferredcites →https://doi.org/10.1126/science.298.5594.824openalex-snapshot
Network Motifs: Simple Building Blocks of Complex Networks
inferredcites →https://doi.org/10.1142/s0219720005001144openalex-snapshot
DIZZY: STOCHASTIC SIMULATION OF LARGE-SCALE GENETIC REGULATORY NETWORKS (SUPPLEMENTARY MATERIAL)
inferredcites →https://doi.org/10.1186/1471-2105-4-2openalex-snapshot
An automated method for finding molecular complexes in large protein interaction networks
inferredcites →https://doi.org/10.1186/1471-2105-5-154openalex-snapshot
Information assessment on predicting protein-protein interactions
inferredcites →https://doi.org/10.1186/1471-2105-5-24openalex-snapshot
Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks
inferredcites →https://doi.org/10.1186/1471-2105-7-508openalex-snapshot
IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model
inferredcites →https://doi.org/10.1186/1752-0509-1-22openalex-snapshot
RMBNToolbox: random models for biochemical networks
inferredcites →https://doi.org/10.1371/journal.pbio.0040109openalex-snapshot
Functional Partitioning of Yeast Co-Expression Networks after Genome Duplication
inferredcites →https://doi.org/10.1371/journal.pbio.0050153openalex-snapshot
Confirmation of Organized Modularity in the Yeast Interactome
inferredcites →https://doi.org/10.1371/journal.pcbi.0020145openalex-snapshot
Identification of the Proliferation/Differentiation Switch in the Cellular Network of Multicellular Organisms
inferredcites →https://doi.org/10.1371/journal.pcbi.0030059openalex-snapshot
The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics
inferredcites →https://doi.org/10.1371/journal.pgen.0020130openalex-snapshot
Integrating Genetic and Network Analysis to Characterize Genes Related to Mouse Weight
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Participant-invariant, evolving patterns of influence in dynamic networks
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Ectopic Expression ofAtJMTinNicotiana attenuata: Creating a Metabolic Sink Has Tissue-Specific Consequences for the Jasmonate Metabolic Network and Silences Downstream Gene Expression
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BINESA — A software tool for evolution modelling of biochemical networks' structure
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Uncovering structure dynamics of the evolving networks
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Efficient Alignments of Metabolic Networks with Bounded Treewidth
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Fixed-Parameter Tractable Combinatorial Algorithms for Metabolic Networks Alignments
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ANN-based simulation of transcriptional networks in Yeast
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Network Modeling and Control of Dynamic Disease Pathways, Review and Perspectives
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A Unified and Scalable Algorithm Framework of User-Defined Temporal (k,X)-Core Query
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Analysis of biological networks and biological pathways associated with residual feed intake in beef cattle
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Sic1 as a timer of Clb cyclin waves in the yeast cell cycle – design principle of not just an inhibitor
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Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases
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A scalable approach for inferring transcriptional regulation in the yeast cell cycle
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OMIC Technologies and Vaccine Development: From the Identification of Vulnerable Individuals to the Formulation of Invulnerable Vaccines
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Handling Noise in Protein Interaction Networks
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Tools for analysis of biochemical network topology
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Genetic profile analysis of tumor stem cells in locally advanced breast cancer
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Integrating Phylogenetic and Network Approaches to Study Gene Family Evolution: The Case of the AGAMOUS Family of Floral Genes
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Genome-wide identification of heat shock proteins (Hsps) and Hsp interactors in rice: Hsp70s as a case study
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Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods
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Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network
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RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations
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Systems medicine: the future of medical genomics and healthcare
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Topology-aware functional similarity: integrating extended neighborhoods via exponential attenuation
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Differential network analysis of bovine muscle reveals changes in gene coexpression patterns in response to changes in maternal nutrition
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Interactive molecular causal networks of hypertension using a fast machine learning algorithm MRdualPC
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New genes drive the evolution of gene interaction networks in the human and mouse genomes
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Scrutinizing neurodegenerative diseases: decoding the complex genetic architectures through a multi-omics lens
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Cancer Gene Prediction Using a Network Approach
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Network Biology, the Framework of Systems Biology
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Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability
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A Developmental Systems Perspective on Epistasis: Computational Exploration of Mutational Interactions in Model Developmental Regulatory Networks
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The Implications of Relationships between Human Diseases and Metabolic Subpathways
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A Network-Based Approach to Prioritize Results from Genome-Wide Association Studies
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Protein Thermostability Is Owing to Their Preferences to Non-Polar Smaller Volume Amino Acids, Variations in Residual Physico-Chemical Properties and More Salt-Bridges
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Integrated Testing Strategy (ITS) – Opportunities to better use existing data and guide future testing in toxicology
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BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology
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Genetic effects on molecular network states explain complex traits
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Systems biology and modeling in neuroblastoma: practicalities and perspectives
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Systems Biology in Aging: Linking the Old and the Young
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Modular Organization in a Cell: Concepts and Applications
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BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology
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Hybrid Approach of Relation Network and Localized Graph Convolutional Filtering for Breast Cancer Subtype Classification
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Translational Systems Approaches to the Biology of Inflammation and Healing
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Novel methods and software for disease module inference
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A Machine Learning Framework Predicts the Clinical Severity of Hemophilia B Caused by Point-Mutations
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Modeling regulatory cascades using Artificial Neural Networks: the case of transcriptional regulatory networks shaped during the yeast stress response
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Applying differential network analysis to longitudinal gene expression in response to perturbations
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Robust Physiological Metrics From Sparsely Sampled Networks
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A Special Structural Based Weighted Network Approach for the Analysis of Protein Complexes
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Rumen and Urine Amine/Phenol-Metabolome of Beef Steers with Divergent Residual Feed Intake
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Knowledge-Driven, Data-Assisted Integrative Pathway Analytics
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Modules in Biological Networks
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Graphical Analysis and Visualization Tools for Protein Interaction Networks
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Knowledge-Driven, Data-Assisted Integrative Pathway Analytics
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Modules in Biological Networks
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Prioritizing Disease Genes and Understanding Disease Pathways
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Combinatorial Optimization Algorithms for Metabolic Networks Alignments and Their Applications
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Network-Based Identification of Biomarkers Coexpressed with Multiple Pathways
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Network and Pathway Analysis of Cancer Susceptibility (A)
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Construction of a Pig Physical Interactome Using Sequence Homology and a Comprehensive Reference Human Interactome
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Multiplatform Serum Metabolic Phenotyping Combined with Pathway Mapping to Identify Biochemical Differences in Smokers
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Approaches to uncovering cancer diagnostic and prognostic molecular signatures
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Network Medicine: New Paradigm in the -Omics Era
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Modular organisation of interaction networks based on asymptotic dynamics
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Utilising Graph Machine Learning within Drug Discovery and Development
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Modeling Stress-Induced Regulatory Cascades With Artificial Neural Networks
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Partitioning a PPI Network into Overlapping Modules Constrained by High-Density and Periphery Tracking
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Long Non-Coding RNAs in Kidney Injury: A Comprehensive Review
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Paradigm of Time-sequence Development of the Intestine of Suckling Piglets with Microarray
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Metabolic Network Alignments and their Applications
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An Evolutionary Biology Approach to Understanding Neurological Disorders
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QuantCell: machine learning based cell annotation integrating qualitative and quantitative imaging profiles
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Etude du rôle de la protéine CDC48 dans l'immunité des plantes
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Graphes complexes en biologie : problèmes, algorithmes et évaluations
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Network science meets respiratory medicine for OSAS phenotyping and severity prediction
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