Topology of molecular interaction networks

Does Habitat Variability Really Promote Metabolic Network Modularity?

(2013) Kazuhiro Takemoto   PLoS One

Observability of complex systems

(2013) Y.-Y. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PINALOG: a novel approach to align protein interaction networks—implications for complex detection and function prediction

(2012) Hang T. T. Phan et al.   BIOINFORMATICS

Graphlet-based edge clustering reveals pathogen-interacting proteins

(2012) R. W. Solava et al.   BIOINFORMATICS

Global network alignment using multiscale spectral signatures

(2012) R. Patro et al.   BIOINFORMATICS

Scalable global alignment for multiple biological networks

(2012) Yu-Keng Shih et al.   BMC BIOINFORMATICS

Convergent evolution of modularity in metabolic networks through different community structures

(2012) Wanding Zhou et al.   BMC EVOLUTIONARY BIOLOGY

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

DNA–protein interactions: methods for detection and analysis

(2012) Bipasha Dey et al.   MOLECULAR AND CELLULAR BIOCHEMISTRY

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

(2012) Sandra Orchard et al.   NATURE METHODS

Molecular signaling network complexity is correlated with cancer patient survivability

(2012) D. Breitkreutz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chapter 5: Network Biology Approach to Complex Diseases

(2012) Dong-Yeon Cho et al.   PLoS Computational Biology

“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks

(2012) Jesse Gillis et al.   PLoS Computational Biology

Multifunctional proteins revealed by overlapping clustering in protein interaction network

(2011) Emmanuelle Becker et al.   BIOINFORMATICS

Mass-balanced randomization of metabolic networks

(2011) Georg Basler et al.   BIOINFORMATICS

Environmental versatility promotes modularity in genome-scale metabolic networks

(2011) Areejit Samal et al.   BMC Systems Biology

The human phosphotyrosine signaling network: Evolution and hotspots of hijacking in cancer

(2011) L. Li et al.   GENOME RESEARCH

Controllability of complex networks

(2011) Yang-Yu Liu et al.   NATURE

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Randomizing Genome-Scale Metabolic Networks

(2011) Areejit Samal et al.   PLoS One

A Toolbox Model of Evolution of Metabolic Pathways on Networks of Arbitrary Topology

(2011) Tin Yau Pang et al.   PLoS Computational Biology

Epistatic Interaction Maps Relative to Multiple Metabolic Phenotypes

(2011) Evan S. Snitkin et al.   PLoS Genetics

Using graph theory to analyze biological networks

(2011) Georgios A Pavlopoulos et al.   BioData Mining

Evolution of biological interaction networks: from models to real data

(2011) Mark GF Sun et al.   GENOME BIOLOGY

Protein-protein interactions: Making sense of networks via graph-theoretic modeling

(2010) Nataša Pržulj   BIOESSAYS

Multi-level reproducibility of signature hubs in human interactome for breast cancer metastasis

(2010) Chen Yao et al.   BMC Systems Biology

Statistical Analysis of Global Connectivity and Activity Distributions in Cellular Networks

(2010) Adrián López García De Lomana et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Topological network alignment uncovers biological function and phylogeny

(2010) O. Kuchaiev et al.   Journal of the Royal Society Interface

Link communities reveal multiscale complexity in networks

(2010) Yong-Yeol Ahn et al.   NATURE

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Protein evolution in yeast transcription factor subnetworks

(2010) Yong Wang et al.   NUCLEIC ACIDS RESEARCH

BRENDA, the enzyme information system in 2011

(2010) M. Scheer et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data

(2010) Yiannis A. I. Kourmpetis et al.   PLoS One

Biological role of noise encoded in a genetic network motif

(2010) M. Kittisopikul et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

Rewiring of Transcriptional Regulatory Networks: Hierarchy, Rather Than Connectivity, Better Reflects the Importance of Regulators

(2010) N. Bhardwaj et al.   Science Signaling

Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks

(2010) Javier De Las Rivas et al.   PLoS Computational Biology

Identifying functional modules using expression profiles and confidence-scored protein interactions

(2009) Igor Ulitsky et al.   BIOINFORMATICS

Disease candidate gene identification and prioritization using protein interaction networks

(2009) Jing Chen et al.   BMC BIOINFORMATICS

Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data

(2009) T. Milenkovic et al.   Journal of the Royal Society Interface

The powerful law of the power law and other myths in network biology

(2009) Gipsi Lima-Mendez et al.   Molecular BioSystems

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Toolbox model of evolution of prokaryotic metabolic networks and their regulation

(2009) S. Maslov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Localized network centrality and essentiality in the yeast–protein interaction network

(2009) Keunwan Park et al.   PROTEOMICS

Protein–protein interaction networks: how can a hub protein bind so many different partners?

(2009) Chung-Jung Tsai et al.   TRENDS IN BIOCHEMICAL SCIENCES

Structure of Protein Interaction Networks and Their Implications on Drug Design

(2009) Takeshi Hase et al.   PLoS Computational Biology

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

(2008) Markus W. Covert et al.   BIOINFORMATICS

Metabolic pathway alignment between species using a comprehensive and flexible similarity measure

(2008) Yunlei Li et al.   BMC Systems Biology

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions

(2008) Y. Qi et al.   GENOME RESEARCH

The evolution of modularity in bacterial metabolic networks

(2008) A. Kreimer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cascading failure and robustness in metabolic networks

(2008) A. G. Smart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optimal partition and effective dynamics of complex networks

(2008) W. E et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics

(2008) M. E. Sardiu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA