Modeling of Protein Interaction Networks

We introduce a graph-generating model aimed at representing the evolution of protein interaction networks. The model is based on the hypothesis of evolution by duplication and divergence of the genes which produce proteins. The obtained graphs have multifractal properties recovering the absence of a characteristic connectivity as found in real data of protein interaction networks. The error tolerance of the model to random or targeted damage is in very good agreement with the behavior obtained in real protein network analyses. The proposed model is a first step in the identification of the evolutionary dynamics leading to the development of protein functions and interactions.

• Publication year

  2001

• Venue

  ComPlexUs

• Publication date

  2001-08-02

• Fields of study

  Biology, Physics, Computer Science

• Identifiers
  DOI 10.1159/000067642arXiv cond-mat/0108043
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Science of Science

  2018cited by this paper
• Functional and topological characterization of protein interaction networks

  2004cited by this paper
• Comparative assessment of large-scale data sets of protein–protein interactions

  2002cited by this paper
• A Model of Large-Scale proteome Evolution

  2002cited by this paper
• The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes.

  2001cited by this paper
• Lethality and centrality in protein networks

  2001cited by this paper
• Exploring complex networks

  2001cited by this paper
• Evolution of networks

  2001cited by this paper
• Statistical mechanics of complex networks

  2001cited by this paper
• Multifractal properties of growing networks

  2001cited by this paper
• The probability of duplicate gene preservation by subfunctionalization.

  2000cited by this paper
• Connectivity of growing random networks.

  2000cited by this paper
• Random graphs with arbitrary degree distributions and their applications.

  2000cited by this paper
• Error and attack tolerance of complex networks

  2000cited by this paper
• Network robustness and fragility: percolation on random graphs.

  2000cited by this paper
• Topology of evolving networks: local events and universality

  2000cited by this paper
• Breakdown of the internet under intentional attack.

  2000cited by this paper
• A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

  2000cited by this paper
• Evolution of networks with aging of sites

  2000cited by this paper
• Scaling behaviour of developing and decaying networks

  2000cited by this paper
• Organization of growing random networks.

  2000cited by this paper
• Emergence of scaling in random networks

  1999cited by this paper
• Emergence of Scaling in Random Networks

  1999cited by this paper
• Preservation of duplicate genes by complementary, degenerative mutations.

  1999cited by this paper
• Measuring genome evolution.

  1998cited by this paper
• Collective dynamics of ‘small-world’ networks

  1998cited by this paper
• Gene families: the taxonomy of protein paralogs and chimeras.

  1997cited by this paper
• A genomic perspective on protein families.

  1997cited by this paper
• Protein-protein interactions: methods for detection and analysis

  1995cited by this paper
• Evolution by Gene Duplication

  1970cited by this paper
• Emergence of Scaling in Random Networks

  year unknowncited by this paper
• Error and attack tolerance of complex networks

  year unknowncited by this paper

• Duplication-divergence growing graph models

  2025influential citation
• Computational interference of gene regulatory networks on the growth and development of millets

  2025cites this paper
• Divergence asymmetry and connected components in a general duplication-divergence graph model.

  2025cites this paper
• Copula Approximate Bayesian Computation Using Distribution Random Forests

  2024cites this paper
• Emergence of graph theory-based biomedical signal analysis

  2024cites this paper
• Properties of the 'friend of a friend' model for network generation

  2024cites this paper
• Information Transmission in a Drone Swarm: A Temporal Network Analysis

  2024cites this paper
• Normalized L3-based link prediction in protein–protein interaction networks

  2023cites this paper
• EgoDist: Comparing networks via distributions of egonet features

  2023cites this paper
• Growing hypergraphs with preferential linking

  2023cites this paper
• Assessment of community efforts to advance network-based prediction of protein–protein interactions

  2023cites this paper
• Metrics for network comparison using egonet feature distributions

  2023cites this paper
• Parameter estimation for connectome generative models: Accuracy, reliability, and a fast parameter fitting method

  2023cites this paper
• Comprehensive Evaluation of Algorithms for Unrestricted Graph Alignment

  2023cites this paper
• Manageable to unmanageable transition in a fractal model of project networks

  2023cites this paper
• Modeling the Evolution of Biological Neural Networks Based on Caenorhabditis elegans Connectomes across Development

  2022cites this paper
• Comparing directed networks via denoising graphlet distributions

  2022cites this paper
• Network location and clustering of genetic mutations determine chronicity in a stylized model of genetic diseases

  2022cites this paper
• Activity networks determine project performance

  2022cites this paper
• Heterogeneous graph neural networks analysis: a survey of techniques, evaluations and applications

  2022cites this paper
• MFF-Net: A multi-feature fusion network for community detection in complex network

  2022cites this paper
• Rare event ABC-SMC$^{2}$

  2022cites this paper
• A Data-dependent Approach for High-dimensional (Robust) Wasserstein Alignment

  2022cites this paper
• Network biology: Recent advances and challenges

  2022cites this paper
• Hyperbolic Graph Neural Networks: A Review of Methods and Applications

  2022cites this paper
• BioCode: A Data-Driven Procedure to Learn the Growth of Biological Networks

  2021cites this paper
• Heterogeneous node copying from hidden network structure

  2021cites this paper
• Maximum likelihood estimation for reversible mechanistic network models.

  2021cites this paper
• Genetic Networks Encode Secrets of Their Past.

  2021cites this paper
• Hidden network generating rules from partially observed complex networks

  2021cites this paper
• Opleiding Bioinformatica Network analysis of polyQ proteins in the human brain

  2021cites this paper
• The expected degree distribution in transient duplication divergence models

  2021cites this paper
• Selection of Summary Statistics for Network Model Choice with Approximate Bayesian Computation

  2021cites this paper
• Cost-based Feature Selection for Network Model Choice

  2021cites this paper
• Correlated copying in a hidden network model

  2021cites this paper
• Friend of a friend models of network growth

  2021cites this paper
• BioCode: A Data-Driven Approach for Learning How Biological Networks Grow

  2021influential citation
• Network and Sequence-Based Prediction of Protein-Protein Interactions

  2021cites this paper
• A novel network aligner for the analysis of multiple protein-protein interaction networks

  2021cites this paper
• Assessment of community efforts to advance computational prediction of protein-protein interactions

  2021cites this paper
• GraphOpt: Learning Optimization Models of Graph Formation

  2020cites this paper
• Growing Random Graphs with Quantum Rules

  2020cites this paper
• Chromatin network markers of leukemia

  2020cites this paper
• Geometry and symmetry in biochemical reaction systems

  2020cites this paper
• Reconstruction of Bio-molecular Networks

  2020cites this paper
• Introduction and Preliminaries

  2020cites this paper
• Evolutionary Mechanisms of Network Motifs in PPI Networks

  2020cites this paper
• Identifying Important Nodes in Bio-Molecular Networks

  2020cites this paper
• Generating weighted social networks using multigraph

  2020cites this paper
• A review of protein–protein interaction network alignment: From pathway comparison to global alignment

  2020cites this paper
• Common Neighbors Extension of the Sticky Model for PPI Networks Evaluated by Global and Local Graphlet Similarity

  2020cites this paper
• Scalable Approximate Bayesian Computation for Growing Network Models via Extrapolated and Sampled Summaries.

  2020cites this paper
• NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families

  2020cites this paper
• Proceedings 9th International Conference on Quantum Simulation and Quantum Walks

  2020cites this paper
• Comparing Different Graphlet Measures for Evaluating Network Model Fits to BioGRID PPI Networks

  2019cites this paper
• From conventional governance to e-democracy: Tracing the evolution of e-governance research trends using network analysis tools

  2019cites this paper
• Spectral properties and the accuracy of mean-field approaches for epidemics on correlated power-law networks

  2019cites this paper
• Towards a data-integrated cell

  2019cites this paper
• Evolving complexity: how tinkering shapes cells, software and ecological networks

  2019cites this paper
• The Euler characteristic and topological phase transitions in complex systems

  2019cites this paper
• Changing the tune: mixtures of network models that vary in time

  2019cites this paper
• Aligning Statistical Dynamics Captures Biological Network Functioning

  2019influential citation
• Discontinuous percolation transitions in growing networks

  2019cites this paper
• A novel evolutionary model for constructing gene coexpression networks with comprehensive features

  2019cites this paper
• Maximum Likelihood Reconstruction of Ancestral Networks by Integer Linear Programming

  2019cites this paper
• Spectral and Dynamic Consequences of Network Specialization

  2019cites this paper
• Network Models

  2019cites this paper
• Ju n 20 19 Flexible model selection for mechanistic network models

  2019cites this paper
• Detecting the macroevolutionary signal of species interactions

  2019cites this paper
• Information on evolutionary age in redundancy of complex network

  2019cites this paper
• Propinquity drives the emergence of network structure and density

  2019cites this paper
• Application of Evolutionary Network Concept in Structuring Mathematics Curriculum

  2018cites this paper
• GoT-WAVE: Temporal network alignment using graphlet-orbit transitions

  2018cites this paper
• Aligning dynamic networks with DynaWAVE

  2018cites this paper
• Evidence of Rentian Scaling of Functional Modules in Diverse Biological Networks

  2018cites this paper
• Assessment of model fit via network comparison methods based on subgraph counts

  2018cites this paper
• Percolation on random networks with proliferation

  2018cites this paper
• Suppression effect on the Berezinskii-Kosterlitz-Thouless transition in growing networks

  2018cites this paper
• Understanding the Emergence of Neuropsychiatric Disorders With Network Neuroscience.

  2018cites this paper
• Compression of Dynamic Graphs Generated by a Duplication Model

  2018cites this paper
• Resurrected Protein Interaction Networks Reveal the Innovation Potential of Ancient Whole-Genome Duplication

  2018cites this paper
• Modelling Self-Organization in Complex Networks Via a Brain-Inspired Network Automata Theory Improves Link Reliability in Protein Interactomes

  2018cites this paper
• Graphlet Laplacians: graphlet-based neighbourhoods highlight topology-function and topology-disease relationships

  2018influential citation
• Workload-sensitive approaches to improving graph data partitioning online

  2018cites this paper
• Network-based prediction of protein interactions

  2018cites this paper
• Flexible model selection for mechanistic network models

  2018cites this paper
• Network Design and the Brain.

  2018cites this paper
• Flexible Model Selection for Mechanistic Network Models via Super Learner

  2018cites this paper
• A Bootstrap Method for Goodness of Fit and Model Selection with a Single Observed Network

  2018cites this paper
• Master equation for the degree distribution of a Duplication and Divergence network

  2017cites this paper
• Learning the Structural Vocabulary of a Network

  2017cites this paper
• Hypothesis Testing and Model Selection for Complex Data

  2017cites this paper
• An optimization-based highway network planning procedure with link growth probabilities

  2017cites this paper
• Complex Networks: Principles, Methods and Applications

  2017cites this paper
• Generative models for network neuroscience: prospects and promise

  2017cites this paper
• Nonlinear growth: an origin of hub organization in complex networks

  2017cites this paper
• Network-level study of protein-protein interactions: analysis and prediction

  2017cites this paper
• Identifying networks with common organizational principles

  2017influential citation
• Specialization Models of Network Growth

  2017cites this paper
• DNA interaction network − neuronal protein core C . elegans Transcription factor modularity in a gene-centered Material Supplemental

  2017cites this paper