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| Metabolic network topology reveals transcriptional regulatory signatures of type 2 diabetes | Q33549712 | ||
| Incomplete and noisy network data as a percolation process | Q33551129 | ||
| PuTmiR: a database for extracting neighboring transcription factors of human microRNAs | Q33557592 | ||
| Module network inference from a cancer gene expression data set identifies microRNA regulated modules | Q33564117 | ||
| Visual integration of quantitative proteomic data, pathways, and protein interactions | Q33577792 | ||
| A human functional protein interaction network and its application to cancer data analysis | Q33581341 | ||
| Network systems biology for drug discovery | Q33592795 | ||
| An interaction-motif-based scoring function for protein-ligand docking | Q33594934 | ||
| Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework | Q33597328 | ||
| TransmiR: a transcription factor-microRNA regulation database | Q33600597 | ||
| BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome | Q33600965 | ||
| Data structures and computational tools for the extraction of SAR information from large compound sets | Q33603920 | ||
| Systematic interpretation of genetic interactions using protein networks | Q33622989 | ||
| A quantitative approach to study indirect effects among disease proteins in the human protein interaction network | Q33644962 | ||
| Extracting the abstraction pyramid from complex networks | Q33648558 | ||
| A systems biology approach identifies inflammatory abnormalities between mouse strains prior to development of metabolic disease. | Q34237786 | ||
| RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations. | Q34244343 | ||
| Frequent deregulations in the hedgehog signaling network and cross-talks with the epidermal growth factor receptor pathway involved in cancer progression and targeted therapies | Q34244929 | ||
| Metabolic network alignment in large scale by network compression | Q34247874 | ||
| FluxMap: A VANTED add-on for the visual exploration of flux distributions in biological networks | Q34252886 | ||
| Diagnosing the decline in pharmaceutical R&D efficiency | Q34257771 | ||
| Drug repositioning through incomplete bi-cliques in an integrated drug–target–disease network | Q34271192 | ||
| Exploring drug combinations in genetic interaction network | Q34272629 | ||
| Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. | Q34274373 | ||
| Large-scale functional organization of long-range chromatin interaction networks | Q34275017 | ||
| Identification of high-quality cancer prognostic markers and metastasis network modules | Q34275507 | ||
| Multiplex assay for condition-dependent changes in protein–protein interactions | Q34276880 | ||
| Probing molecular mechanisms of the Hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics | Q34280087 | ||
| SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways. | Q34283765 | ||
| In silico multicellular systems biology and minimal genomes | Q34284164 | ||
| Protein-protein Interactions: Network Analysis and Applications in Drug Discovery | Q34287856 | ||
| Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks | Q34288079 | ||
| Biomine: predicting links between biological entities using network models of heterogeneous databases. | Q34294520 | ||
| Inferring cellular networks using probabilistic graphical models | Q34295031 | ||
| Network context and selection in the evolution to enzyme specificity. | Q34296873 | ||
| A 61-million-person experiment in social influence and political mobilization. | Q34299416 | ||
| Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase | Q34299819 | ||
| Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs | Q34303213 | ||
| Drug-induced liver disorders: implications for drug development and regulation | Q34303460 | ||
| Exploring the human diseasome: the human disease network | Q34305958 | ||
| AlignNemo: a local network alignment method to integrate homology and topology | Q34311823 | ||
| Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities | Q34314615 | ||
| The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells: what we (need to) know and how we can do so. | Q34315247 | ||
| Effect of correlations on network controllability | Q34322899 | ||
| Nodal dynamics, not degree distributions, determine the structural controllability of complex networks | Q34325719 | ||
| Constructing a gene semantic similarity network for the inference of disease genes | Q34333432 | ||
| Exploring virus relationships based on virus-host protein-protein interaction network | Q34333531 | ||
| Efficient reverse-engineering of a developmental gene regulatory network | Q34341320 | ||
| Relating three-dimensional structures to protein networks provides evolutionary insights | Q34593972 | ||
| The modular nature of genetic diseases. | Q34597943 | ||
| Lovastatin and extended-release niacin combination product: the first drug combination for the management of hyperlipidemia | Q34614205 | ||
| Mediators of vascular remodelling co-opted for sequential steps in lung metastasis. | Q34618411 | ||
| Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery | Q34627247 | ||
| Network analysis of FDA approved drugs and their targets | Q34630429 | ||
| Mitigation of malicious attacks on networks | Q34652315 | ||
| New uses for old drugs | Q34661227 | ||
| A computational framework for the topological analysis and targeted disruption of signal transduction networks. | Q34680360 | ||
| Proof of Concept: Network and Systems Biology Approaches Aid in the Discovery of Potent Anticancer Drug Combinations | Q34684352 | ||
| Predicting synthetic rescues in metabolic networks | Q34750436 | ||
| Structure-based systems biology for analyzing off-target binding | Q34761978 | ||
| Closed-loop control of cellular functions using combinatory drugs guided by a stochastic search algorithm | Q34763799 | ||
| Connectedness of PPI network neighborhoods identifies regulatory hub proteins. | Q34771449 | ||
| Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth | Q34779291 | ||
| Yeast and drug discovery | Q34794228 | ||
| Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes | Q34860078 | ||
| Dynamic modularity in protein interaction networks predicts breast cancer outcome | Q34934057 | ||
| Improving the prediction of pharmacogenes using text-derived drug-gene relationships | Q34974251 | ||
| Dynamical networks in tRNA:protein complexes | Q34974676 | ||
| Analysis of multiple compound–protein interactions reveals novel bioactive molecules | Q34979708 | ||
| Topological structure analysis of the protein-protein interaction network in budding yeast | Q34980439 | ||
| The NCGC pharmaceutical collection: a comprehensive resource of clinically approved drugs enabling repurposing and chemical genomics | Q34992596 | ||
| Network analyses in systems pharmacology | Q34995155 | ||
| Early-warning signals for critical transitions | Q35001007 | ||
| HBVPathDB: a database of HBV infection-related molecular interaction network | Q35011414 | ||
| Hypergraph topological quantities for tagged social networks. | Q35012344 | ||
| Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling | Q35022482 | ||
| Do cancer proteins really interact strongly in the human protein-protein interaction network? | Q35034277 | ||
| SubMAP: aligning metabolic pathways with subnetwork mappings | Q35070376 | ||
| Building protein-protein interaction networks with proteomics and informatics tools. | Q35084958 | ||
| Discovering the targets of drugs via computational systems biology | Q35084961 | ||
| Systematic approaches towards the development of host-directed antiviral therapeutics | Q35091855 | ||
| ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality. | Q30418313 | ||
| Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design | Q30431598 | ||
| Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection | Q30432839 | ||
| Network analysis of oncogenic Ras activation in cancer | Q30444797 | ||
| Functional cartography of complex metabolic networks | Q30481006 | ||
| ENDEAVOUR update: a web resource for gene prioritization in multiple species | Q30482616 | ||
| PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation | Q30483578 | ||
| Drug discovery in the age of systems biology: the rise of computational approaches for data integration. | Q30485238 | ||
| Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug | Q30485564 | ||
| HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions | Q30485647 | ||
| SePreSA: a server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical-protein interactome | Q30488528 | ||
| Protein pockets: inventory, shape, and comparison | Q30494235 | ||
| Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence | Q30495567 | ||
| Molecular mechanistic associations of human diseases | Q30496754 | ||
| Mining and integration of pathway diagrams from imaging data | Q30506021 | ||
| Arena3D: visualizing time-driven phenotypic differences in biological systems | Q30515043 | ||
| TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks | Q30520094 | ||
| Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease | Q30526431 | ||
| Automated design of ligands to polypharmacological profiles. | Q30539786 | ||
| Integrating external biological knowledge in the construction of regulatory networks from time-series expression data | Q30557880 | ||
| CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms | Q30573980 | ||
| DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data. | Q30576319 | ||
| Construction of regulatory networks using expression time-series data of a genotyped population | Q34074655 | ||
| Dynamical and Structural Analysis of a T Cell Survival Network Identifies Novel Candidate Therapeutic Targets for Large Granular Lymphocyte Leukemia | Q34079139 | ||
| Discovery of drug mode of action and drug repositioning from transcriptional responses | Q34093341 | ||
| Feedback control of intercellular signalling in development | Q34094396 | ||
| Expander: from expression microarrays to networks and functions | Q34097128 | ||
| Discovery of mutated subnetworks associated with clinical data in cancer | Q34102554 | ||
| Community structure in time-dependent, multiscale, and multiplex networks | Q34115260 | ||
| A Network-Based Approach on Elucidating the Multi-Faceted Nature of Chronological Aging in S. cerevisiae | Q34117425 | ||
| A network flow approach to predict drug targets from microarray data, disease genes and interactome network - case study on prostate cancer | Q34125720 | ||
| Plasma microRNA profiling reveals loss of endothelial miR-126 and other microRNAs in type 2 diabetes | Q34127486 | ||
| Identifying co-targets to fight drug resistance based on a random walk model | Q34132379 | ||
| Role of systems pharmacology in understanding drug adverse events | Q34134791 | ||
| Versatile Applications of microRNA in Anti-Cancer Drug Discovery: From Therapeutics to Biomarkers | Q34137643 | ||
| DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks | Q34139480 | ||
| Phosphoproteomics for the discovery of kinases as cancer biomarkers and drug targets | Q34153602 | ||
| Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast | Q34156122 | ||
| Novel insights through the integration of structural and functional genomics data with protein networks | Q34161379 | ||
| A novel framework for the comparative analysis of biological networks | Q34170651 | ||
| Discovery of intramolecular signal transduction network based on a new protein dynamics model of energy dissipation | Q34171039 | ||
| Principles for the buffering of genetic variation | Q34171380 | ||
| Principles and strategies for developing network models in cancer | Q34171479 | ||
| Identification of an Allosteric Signaling Network within Tec Family Kinases | Q34172793 | ||
| Dynamic reconfiguration of human brain networks during learning | Q34179257 | ||
| CentiLib: comprehensive analysis and exploration of network centralities | Q34185036 | ||
| GPCR drug discovery through the exploitation of allosteric drug binding sites | Q34190091 | ||
| Untangling the wires: a strategy to trace functional interactions in signaling and gene networks | Q34190157 | ||
| Crosstalk between transcription factors and microRNAs in human protein interaction network | Q34194215 | ||
| Towards a network theory of the immune system. | Q34202813 | ||
| Conedy: A scientific tool to investigate complex network dynamics | Q34214607 | ||
| Hierarchy measure for complex networks | Q34217534 | ||
| MINT, the molecular interaction database: 2012 update | Q34233947 | ||
| Protein-protein interaction networks suggest different targets have different propensities for triggering drug resistance | Q34237349 | ||
| Stability indicators in network reconstruction | Q35108162 | ||
| Stategic trends in the drug industry | Q35111514 | ||
| DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization | Q35126543 | ||
| Genome-wide identification of genes likely to be involved in human genetic disease | Q35130251 | ||
| Building with a scaffold: emerging strategies for high- to low-level cellular modeling | Q35146255 | ||
| Systematic discovery of multicomponent therapeutics | Q35147474 | ||
| InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes | Q35158913 | ||
| Network-based prediction for sources of transcriptional dysregulation using latent pathway identification analysis | Q35164684 | ||
| Predicting selective drug targets in cancer through metabolic networks. | Q35176392 | ||
| Residues crucial for maintaining short paths in network communication mediate signaling in proteins | Q35193500 | ||
| Principles of microRNA regulation of a human cellular signaling network | Q35193525 | ||
| Pharmacophylogenomics: genes, evolution and drug targets | Q35194747 | ||
| Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation | Q35339906 | ||
| Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble | Q35367681 | ||
| Heat shock proteins as emerging therapeutic targets | Q35545091 | ||
| Vavien: An Algorithm for Prioritizing Candidate Disease Genes Based on Topological Similarity of Proteins in Interaction Networks | Q35550142 | ||
| Drug-target network in myocardial infarction reveals multiple side effects of unrelated drugs | Q35551379 | ||
| PathBLAST: a tool for alignment of protein interaction networks | Q35556674 | ||
| Autophagy as a therapeutic target in cancer. | Q35591562 | ||
| The cognitive paradigm and the immunological homunculus | Q35592137 | ||
| Neuroscience Networking: Linking Discovery to Drugs | Q35614087 | ||
| Rediscovering the sweet spot in drug discovery. | Q35615371 | ||
| Mechanisms for the inheritance of chromatin states | Q35630158 | ||
| PINA v2.0: mining interactome modules. | Q35630696 | ||
| TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support | Q35631073 | ||
| IPAVS: Integrated Pathway Resources, Analysis and Visualization System | Q35631078 | ||
| Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery | Q35631111 | ||
| dbDEPC 2.0: updated database of differentially expressed proteins in human cancers | Q35631138 | ||
| A Novel Method of Transcriptional Response Analysis to Facilitate Drug Repositioning for Cancer Therapy | Q35652903 | ||
| Mutual exclusivity analysis identifies oncogenic network modules | Q35694424 | ||
| Associating Drugs, Targets and Clinical Outcomes into an Integrated Network Affords a New Platform for Computer-Aided Drug Repurposing. | Q35694643 | ||
| Predicting protein-protein interactions based only on sequences information | Q35721356 | ||
| Complex-disease networks of trait-associated single-nucleotide polymorphisms (SNPs) unveiled by information theory. | Q35751212 | ||
| The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics | Q35753717 | ||
| Conserved patterns of protein interaction in multiple species | Q33837704 | ||
| Elementary signaling modes predict the essentiality of signal transduction network components | Q33852639 | ||
| Local Structural Changes, Global Data Views: Graphical Substructure−Activity Relationship Trailing | Q33857007 | ||
| Increasing the flux in metabolic pathways: A metabolic control analysis perspective | Q33857812 | ||
| Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels | Q33859210 | ||
| Bayesian approach to transforming public gene expression repositories into disease diagnosis databases | Q33859264 | ||
| Building the process-drug–side effect network to discover the relationship between biological Processes and side effects | Q33871546 | ||
| Multilevel compression of random walks on networks reveals hierarchical organization in large integrated systems | Q33873691 | ||
| Network Archaeology: Uncovering Ancient Networks from Present-Day Interactions | Q33886696 | ||
| From isotropic to anisotropic side chain representations: comparison of three models for residue contact estimation | Q33892544 | ||
| DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical–protein interactome | Q33894409 | ||
| Implication of microRNAs in drug resistance for designing novel cancer therapy | Q33903223 | ||
| Subnets of scale-free networks are not scale-free: sampling properties of networks | Q33934431 | ||
| Cell illustrator 4.0: a computational platform for systems biology | Q33936234 | ||
| Network target for screening synergistic drug combinations with application to traditional Chinese medicine | Q33937467 | ||
| GeneNetWeaver:in silicobenchmark generation and performance profiling of network inference methods | Q33940337 | ||
| Are splicing mutations the most frequent cause of hereditary disease? | Q33985993 | ||
| Chance and necessity in the evolution of minimal metabolic networks | Q33994506 | ||
| Discovery and preclinical validation of drug indications using compendia of public gene expression data | Q33995422 | ||
| A Computer Program for Classifying Plants | Q34006445 | ||
| Characterizing genetic interactions in human disease association studies using statistical epistasis networks | Q34017084 | ||
| A Computational Method Based on the Integration of Heterogeneous Networks for Predicting Disease-Gene Associations | Q34017854 | ||
| Epigenetic side-effects of common pharmaceuticals: a potential new field in medicine and pharmacology | Q34017909 | ||
| A network-based approach to prioritize results from genome-wide association studies | Q34018953 | ||
| Reverse engineering gene networks using singular value decomposition and robust regression | Q34028331 | ||
| Prediction of protein-binding areas by small-world residue networks and application to docking | Q34029424 | ||
| iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks | Q34029521 | ||
| Timescale analysis of rule‐based biochemical reaction networks | Q34033527 | ||
| The BioAssay network and its implications to future therapeutic discovery | Q34046379 | ||
| PRINCIPLE: a tool for associating genes with diseases via network propagation | Q34053140 | ||
| Stability of graph communities across time scales. | Q34059106 | ||
| Inferring pleiotropy by network analysis: linked diseases in the human PPI network | Q34060723 | ||
| A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology | Q34063123 | ||
| Serine Biosynthesis with One Carbon Catabolism and the Glycine Cleavage System Represents a Novel Pathway for ATP Generation | Q34071505 | ||
| Conformational spread: the propagation of allosteric states in large multiprotein complexes | Q35771546 | ||
| Genomic analysis of essentiality within protein networks | Q35774496 | ||
| IMID: integrated molecular interaction database | Q35789049 | ||
| Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics | Q35790255 | ||
| Inferring domain-domain interactions from protein-protein interactions | Q35806010 | ||
| Molecular concepts analysis links tumors, pathways, mechanisms, and drugs | Q35812701 | ||
| Pyruvate Kinase M2 Regulates Gene Transcription by Acting as a Protein Kinase | Q35822985 | ||
| Strong links are important, but weak links stabilize them | Q35827594 | ||
| CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED. | Q35838429 | ||
| Thematic review series: The pathogenesis of atherosclerosis. Toward a biological network for atherosclerosis | Q35855112 | ||
| Probing genetic overlap among complex human phenotypes. | Q35868799 | ||
| Alzheimer disease susceptibility loci: evidence for a protein network under natural selection | Q35877845 | ||
| Complexity in the signaling network: insights from the use of targeted inhibitors in cancer therapy | Q35882137 | ||
| Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages | Q35906481 | ||
| PINALOG: a novel approach to align protein interaction networks--implications for complex detection and function prediction. | Q35916743 | ||
| Superessential reactions in metabolic networks | Q35935855 | ||
| Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. | Q35950686 | ||
| Propagation of large concentration changes in reversible protein-binding networks | Q35962966 | ||
| Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. | Q35972950 | ||
| Signalling by protein phosphatases and drug development: a systems-centred view. | Q36012977 | ||
| Approaches to the analysis of cell signaling networks and their application in drug discovery. | Q36023359 | ||
| A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis | Q36023760 | ||
| The Edinburgh human metabolic network reconstruction and its functional analysis | Q36052649 | ||
| Assembling global maps of cellular function through integrative analysis of physical and genetic networks | Q36057839 | ||
| Large-scale prediction and testing of drug activity on side-effect targets | Q36059863 | ||
| Oncogene-mediated alterations in chromatin conformation | Q36061468 | ||
| Molecular signaling network complexity is correlated with cancer patient survivability | Q36061531 | ||
| Interfacial inhibition of macromolecular interactions: nature's paradigm for drug discovery | Q36062585 | ||
| microRNA Dysregulation in Prostate Cancer: Network Analysis Reveals Preferential Regulation of Highly Connected Nodes | Q36068215 | ||
| Genome semantics, in silico multicellular systems and the Central Dogma | Q36069193 | ||
| Illuminating drug discovery with biological pathways | Q36069246 | ||
| The efficiency of multi-target drugs: the network approach might help drug design | Q36088532 | ||
| Application of GQSAR for Scaffold Hopping and Lead Optimization in Multitarget Inhibitors | Q36091289 | ||
| Architecture of the human regulatory network derived from ENCODE data | Q29617046 | ||
| The Impact of the Gut Microbiota on Human Health: An Integrative View | Q29617446 | ||
| Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles | Q29617464 | ||
| Biological robustness | Q29617468 | ||
| Relating protein pharmacology by ligand chemistry | Q29617492 | ||
| Small-molecule inhibitors of protein-protein interactions: progressing towards the dream | Q29617758 | ||
| The chemical genomic portrait of yeast: uncovering a phenotype for all genes | Q29617970 | ||
| Hierarchical organization of modularity in metabolic networks | Q29618451 | ||
| Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data | Q29618517 | ||
| Causal protein-signaling networks derived from multiparameter single-cell data | Q29619136 | ||
| JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles | Q29619342 | ||
| A census of human transcription factors: function, expression and evolution | Q29622841 | ||
| Linear Motif Atlas for Phosphorylation-Dependent Signaling | Q30002322 | ||
| STITCH 3: zooming in on protein-chemical interactions | Q30002340 | ||
| NetworKIN: a resource for exploring cellular phosphorylation networks | Q30002344 | ||
| Systematic Discovery of In Vivo Phosphorylation Networks | Q30002403 | ||
| Reverse engineering of regulatory networks in human B cells | Q30004211 | ||
| Hierarchical structure and the prediction of missing links in networks | Q30050098 | ||
| Identification of side-chain clusters in protein structures by a graph spectral method. | Q30322969 | ||
| Prediction of protein-protein interactions by docking methods. | Q30329611 | ||
| Improving the performance of DomainParser for structural domain partition using neural network | Q30332457 | ||
| Uncovering network systems within protein structures. | Q30336273 | ||
| A network representation of protein structures: implications for protein stability. | Q30351373 | ||
| System level mechanisms of adaptation, learning, memory formation and evolvability: the role of chaperone and other networks. | Q30360926 | ||
| Markov methods for hierarchical coarse-graining of large protein dynamics. | Q30363380 | ||
| Allosteric regulation and catalysis emerge via a common route. | Q30370820 | ||
| Variations in clique and community patterns in protein structures during allosteric communication: investigation of dynamically equilibrated structures of methionyl tRNA synthetase complexes. | Q30372499 | ||
| Comparative analysis of the packing topology of structurally important residues in helical membrane and soluble proteins. | Q30373704 | ||
| Intra and inter-molecular communications through protein structure network. | Q30376051 | ||
| HAPPI: an online database of comprehensive human annotated and predicted protein interactions | Q30378866 | ||
| The protein meta-structure: a novel concept for chemical and molecular biology. | Q30379937 | ||
| SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison | Q30389394 | ||
| Predicting disease-associated substitution of a single amino acid by analyzing residue interactions | Q30398465 | ||
| Modeling allosteric signal propagation using protein structure networks | Q30399957 | ||
| RING: networking interacting residues, evolutionary information and energetics in protein structures. | Q30401853 | ||
| Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function: hypotheses and a comprehensive review | Q30408830 | ||
| Topological analysis and interactive visualization of biological networks and protein structures | Q30414346 | ||
| Strategies for optimizing combinations of molecularly targeted anticancer agents | Q36554418 | ||
| A global analysis of genetic interactions in Caenorhabditis elegans | Q36640170 | ||
| Perturbations to uncover gene networks | Q36650695 | ||
| Longevity network: construction and implications | Q36658302 | ||
| Systems biology, metabolic modelling and metabolomics in drug discovery and development | Q36665669 | ||
| Network properties of genes harboring inherited disease mutations | Q36670355 | ||
| Multi-target therapeutics: when the whole is greater than the sum of the parts | Q36697412 | ||
| Network-based global inference of human disease genes | Q36713985 | ||
| Chemotherapy: induction of stress responses | Q36720676 | ||
| Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology | Q36749291 | ||
| The power and promise of "rewiring" the mitogen-activated protein kinase network in prostate cancer therapeutics | Q36760971 | ||
| Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network | Q36804762 | ||
| Getting connected: analysis and principles of biological networks | Q36808436 | ||
| Network analysis of protein dynamics | Q36833030 | ||
| Multi-drug strategies are necessary to inhibit the synergistic mechanism causing tissue damage and organ failure in post infectious sequelae | Q36885542 | ||
| Accelerated evolution of resistance in multidrug environments | Q36893628 | ||
| Tools for visually exploring biological networks. | Q36919741 | ||
| Models from experiments: combinatorial drug perturbations of cancer cells | Q36930517 | ||
| Human protein-protein interaction networks and the value for drug discovery | Q36934800 | ||
| Quantitative phosphoproteomic analysis of signaling network dynamics. | Q36936477 | ||
| Endoplasmic reticulum stress signaling in pancreatic beta-cells | Q36951237 | ||
| A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes | Q37023137 | ||
| Neural network dysfunction in Alzheimer's disease: a drug development perspective | Q37051100 | ||
| A network biology approach to aging in yeast | Q37069115 | ||
| Signaling networks in aging | Q37078776 | ||
| Membranes: a meeting point for lipids, proteins and therapies | Q37081783 | ||
| A survey of visualization tools for biological network analysis | Q37085586 | ||
| Network medicine | Q37087536 | ||
| Some new trends in chemical graph theory | Q37095488 | ||
| Differential dependency network analysis to identify condition-specific topological changes in biological networks | Q37097107 | ||
| Proteins as networks: usefulness of graph theory in protein science | Q37108560 | ||
| A systems biology approach to drug discovery | Q37115945 | ||
| Specific synthetic lethal killing of RAD54B-deficient human colorectal cancer cells by FEN1 silencing. | Q37117721 | ||
| The impact of natural products upon modern drug discovery. | Q37142509 | ||
| Human metabolic network reconstruction and its impact on drug discovery and development | Q37158701 | ||
| Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions | Q34344292 | ||
| Concerted perturbation observed in a hub network in Alzheimer's disease | Q34344867 | ||
| atBioNet– an integrated network analysis tool for genomics and biomarker discovery | Q34346335 | ||
| Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes | Q34354173 | ||
| Genomics, complexity and drug discovery: insights from Boolean network models of cellular regulation | Q34355237 | ||
| HINT: High-quality protein interactomes and their applications in understanding human disease | Q34356822 | ||
| The chemical basis of pharmacology | Q34363831 | ||
| Alternative protein-protein interfaces are frequent exceptions | Q34372281 | ||
| DTome: a web-based tool for drug-target interactome construction | Q34383264 | ||
| Reconstruction of cellular signalling networks and analysis of their properties | Q34385115 | ||
| Random Boolean network models and the yeast transcriptional network | Q34385495 | ||
| Multicomponent therapeutics for networked systems | Q34390417 | ||
| Tackling antibiotic resistance | Q34390844 | ||
| The mutation rate and cancer | Q34410886 | ||
| Phylogenies reveal predictive power of traditional medicine in bioprospecting | Q34415770 | ||
| Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses | Q34421346 | ||
| What evidence is there for the homology of protein-protein interactions? | Q34426308 | ||
| Systematic differences in signal emitting and receiving revealed by PageRank analysis of a human protein interactome. | Q34427564 | ||
| PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries. | Q34436628 | ||
| miRandola: extracellular circulating microRNAs database | Q34456543 | ||
| Induced fit, conformational selection and independent dynamic segments: an extended view of binding events | Q34479883 | ||
| Efficient estimation of graphlet frequency distributions in protein-protein interaction networks | Q34490501 | ||
| On the nature of cavities on protein surfaces: application to the identification of drug-binding sites | Q34494450 | ||
| Cell-signalling dynamics in time and space | Q34495098 | ||
| Robust Salmonella metabolism limits possibilities for new antimicrobials. | Q34502598 | ||
| Chapter 4: Protein Interactions and Disease | Q34539656 | ||
| Chapter 5: Network biology approach to complex diseases. | Q34539662 | ||
| Identifying Ligand Binding Conformations of the β2-Adrenergic Receptor by Using Its Agonists as Computational Probes | Q34540011 | ||
| Metabolic control analysis in drug discovery and disease | Q34550535 | ||
| Temporal dynamics of tyrosine phosphorylation in insulin signaling. | Q34551910 | ||
| SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks | Q34554087 | ||
| GraphCrunch 2: Software tool for network modeling, alignment and clustering | Q34564378 | ||
| Selective optimization of side activities: the SOSA approach | Q34565597 | ||
| Resampling effects on significance analysis of network clustering and ranking | Q34570987 | ||
| A systematic prediction of multiple drug-target interactions from chemical, genomic, and pharmacological data | Q28484011 | ||
| Promiscuous drugs compared to selective drugs (promiscuity can be a virtue) | Q24799034 | ||
| Ranking candidate disease genes from gene expression and protein interaction: a Katz-centrality based approach | Q24810350 | ||
| The activity reaction core and plasticity of metabolic networks | Q24811413 | ||
| Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast | Q24812466 | ||
| ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics | Q24813006 | ||
| Detection of compound mode of action by computational integration of whole-genome measurements and genetic perturbations | Q25255700 | ||
| Pathguide: a pathway resource list | Q25256662 | ||
| Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action | Q26824166 | ||
| Aggregating data for computational toxicology applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System | Q26829544 | ||
| Systems genetics for drug target discovery | Q27012769 | ||
| A metabolic network approach for the identification and prioritization of antimicrobial drug targets | Q27014752 | ||
| Emergence of Scaling in Random Networks | Q27037290 | ||
| Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data | Q27136634 | ||
| SuperTarget and Matador: resources for exploring drug-target relationships | Q27136964 | ||
| PREDICT: a method for inferring novel drug indications with application to personalized medicine | Q27137071 | ||
| Dynamic prestress in a globular protein | Q27330899 | ||
| Designing transient binding drugs: a new concept for drug discovery | Q37158710 | ||
| Finding multiple target optimal intervention in disease-related molecular network. | Q37170511 | ||
| Predicting metabolic biomarkers of human inborn errors of metabolism | Q37196179 | ||
| PIPs: human protein-protein interaction prediction database | Q37202592 | ||
| IsoRankN: spectral methods for global alignment of multiple protein networks | Q37206322 | ||
| A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery | Q37206373 | ||
| PPISearch: a web server for searching homologous protein-protein interactions across multiple species. | Q37245673 | ||
| VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. | Q37245690 | ||
| Recovering time-varying networks of dependencies in social and biological studies | Q37248135 | ||
| The signaling hubs at the crossroad of longevity and age-related disease networks | Q37269782 | ||
| Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. | Q37283297 | ||
| Quantifying the relationships among drug classes | Q37294973 | ||
| Generating genome-scale candidate gene lists for pharmacogenomics | Q37311193 | ||
| Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia | Q37319585 | ||
| Supervised prediction of drug-target interactions using bipartite local models | Q37327753 | ||
| Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture | Q37330215 | ||
| The double-edged sword of autophagy modulation in cancer | Q37331327 | ||
| Interaction networks: from protein functions to drug discovery. A review | Q37345607 | ||
| Identification of rare cancer driver mutations by network reconstruction | Q37363146 | ||
| Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. | Q37365634 | ||
| Cancer attractors: a systems view of tumors from a gene network dynamics and developmental perspective | Q37368971 | ||
| Knitting and untying the protein network: modulation of protein ensembles as a therapeutic strategy | Q37383647 | ||
| Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases | Q37384944 | ||
| Integrative genomics and drug development | Q37389491 | ||
| Network strategies to understand the aging process and help age-related drug design. | Q37402658 | ||
| A network medicine approach to human disease | Q37408792 | ||
| Navigating the network: signaling cross-talk in hematopoietic cells. | Q37417479 | ||
| Endoplasmic reticulum: nutrient sensor in physiology and pathology | Q37435215 | ||
| Perturbation waves in proteins and protein networks: applications of percolation and game theories in signaling and drug design. | Q37438478 | ||
| Anti- and pro-tumor functions of autophagy | Q37446106 | ||
| Anti-apoptotic mechanisms of drug resistance in cancer | Q37481512 | ||
| Ageing as a price of cooperation and complexity: self-organization of complex systems causes the gradual deterioration of constituent networks | Q37483724 | ||
| Autophagy-A double-edged sword in oncology | Q37487968 | ||
| Molecular pathways in tumor progression: from discovery to functional understanding | Q37577479 | ||
| Use of game-theoretical methods in biochemistry and biophysics | Q37577583 | ||
| Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease. | Q37585379 | ||
| Docking and chemoinformatic screens for new ligands and targets | Q37592631 | ||
| Protein-protein interaction networks: how can a hub protein bind so many different partners? | Q37616866 | ||
| Network-based drugs and biomarkers | Q37634471 | ||
| Autophagy and metastasis: another double-edged sword | Q37640885 | ||
| Cracking the phosphatase code: docking interactions determine substrate specificity | Q37649281 | ||
| Unveiling the role of network and systems biology in drug discovery | Q37684484 | ||
| A strategy based on protein-protein interface motifs may help in identifying drug off-targets | Q37691954 | ||
| The spatial architecture of protein function and adaptation | Q37710326 | ||
| Cell line-based platforms to evaluate the therapeutic efficacy of candidate anticancer agents | Q37714306 | ||
| Genetic algorithm optimization in drug design QSAR: Bayesian-regularized genetic neural networks (BRGNN) and genetic algorithm-optimized support vectors machines (GA-SVM). | Q37715779 | ||
| Review of MARCH-INSIDE & complex networks prediction of drugs: ADMET, anti-parasite activity, metabolizing enzymes and cardiotoxicity proteome biomarkers | Q37743543 | ||
| Artificial intelligence techniques for colorectal cancer drug metabolism: ontology and complex network. | Q37743545 | ||
| Genetic analysis of complex disease--a roadmap to understanding or a colossal waste of money | Q37762963 | ||
| Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery. | Q37764610 | ||
| The weirdest people in the world? | Q37765324 | ||
| Chitosan-based hydrogels for nasal drug delivery: from inserts to nanoparticles | Q37766235 | ||
| Metabolic control analysis indicates a change of strategy in the treatment of cancer | Q37769788 | ||
| Predicting drugs and proteins in parasite infections with topological indices of complex networks: theoretical backgrounds, applications, and legal issues | Q37774006 | ||
| MicroRNA and aging: a novel modulator in regulating the aging network | Q37779890 | ||
| Diseases as network perturbations | Q37779993 | ||
| Cause-effect relationships in medicine: a protein network perspective | Q37784556 | ||
| Network biology as a new approach to drug discovery | Q37784745 | ||
| Conformational ensembles, signal transduction and residue hot spots: application to drug discovery. | Q37784746 | ||
| Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework. | Q37785587 | ||
| mTORC1 signaling in energy balance and metabolic disease. | Q37793822 | ||
| Mapping the Disease Protein Interactome: Toward a Molecular Medicine GPS to Accelerate Drug and Biomarker Discovery | Q37799598 | ||
| Regulation of mammalian autophagy in physiology and pathophysiology. | Q37801517 | ||
| A comprehensive map of the mTOR signaling network | Q37823206 | ||
| The regulation of autophagy – unanswered questions | Q37824183 | ||
| Layers of epistasis: genome-wide regulatory networks and network approaches to genome-wide association studies | Q37825463 | ||
| Computational biology approaches for selecting host–pathogen drug targets | Q37833286 | ||
| Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks | Q36092552 | ||
| The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer | Q36093876 | ||
| Multifactorial optimization of endothelial cell growth using modular synthetic extracellular matrices | Q36106091 | ||
| Integrative analysis of the cancer transcriptome | Q36141641 | ||
| Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers | Q36171138 | ||
| Cytoskeletal integrity as a drug target | Q36172704 | ||
| Systems modeling: a pathway to drug discovery | Q36188268 | ||
| Drug target prediction using adverse event report systems: a pharmacogenomic approach. | Q36218106 | ||
| Pancreatic β cell dedifferentiation as a mechanism of diabetic β cell failure | Q36241895 | ||
| Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues | Q36244121 | ||
| Predicting allosteric communication in myosin via a pathway of conserved residues | Q36247779 | ||
| Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression | Q36286867 | ||
| Crowdsourcing network inference: the DREAM predictive signaling network challenge | Q36300033 | ||
| A modular network model of aging | Q36327182 | ||
| A map of human cancer signaling | Q36327214 | ||
| Finding new drug targets in the 21st century | Q36352938 | ||
| Discovering the first microRNA-targeted drug | Q36353486 | ||
| Cancer: a Systems Biology disease | Q36373713 | ||
| Differential network entropy reveals cancer system hallmarks. | Q36393280 | ||
| SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets | Q36408631 | ||
| Array-based proteomics: mapping of protein circuitries for diagnostics, prognostics, and therapy guidance in cancer. | Q36414618 | ||
| Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network | Q36424477 | ||
| Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets | Q36424741 | ||
| The proteomics big challenge for biomarkers and new drug-targets discovery | Q36432402 | ||
| Predictive energy landscapes for protein-protein association | Q36436864 | ||
| Modeling cellular machinery through biological network comparison | Q36443509 | ||
| Towards a pathway definition of Parkinson's disease: a complex disorder with links to cancer, diabetes and inflammation | Q36453886 | ||
| Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design | Q36458965 | ||
| A CXCL1 paracrine network links cancer chemoresistance and metastasis | Q36482032 | ||
| A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas | Q36496243 | ||
| Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. | Q36498348 | ||
| Aging cellular networks: chaperones as major participants | Q36524800 | ||
| Defining principles of combination drug mechanisms of action | Q36535401 | ||
| The sociobiology of molecular systems. | Q37837472 | ||
| Chemical-protein interactome and its application in off-target identification | Q37849214 | ||
| Protein Tyrosine Phosphatases as Drug Targets: Strategies and Challenges of Inhibitor Development | Q37855897 | ||
| Dynamic modeling and analysis of cancer cellular network motifs | Q37889673 | ||
| Network-based methods for human disease gene prediction | Q37901985 | ||
| The therapeutic potential of microRNAs: disease modulators and drug targets. | Q37912078 | ||
| Targeting microRNAs involved in human diseases: a novel approach for modification of gene expression and drug development | Q37921863 | ||
| Microgels and microcapsules in peptide and protein drug delivery | Q37931483 | ||
| Molecular network of microRNA targets in Alzheimer's disease brains | Q37938224 | ||
| 14-3-3 proteins as signaling integration points for cell cycle control and apoptosis | Q37938398 | ||
| Systems biology impact on antiepileptic drug discovery | Q37953017 | ||
| Metabolic network modeling and simulation for drug targeting and discovery | Q37962486 | ||
| Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. | Q37967156 | ||
| The current Salmonella‐host interactome | Q37972868 | ||
| Differential network biology | Q37976573 | ||
| Tools for protein-protein interaction network analysis in cancer research. | Q37977413 | ||
| Systems biology tools for toxicology | Q38008573 | ||
| Functional Genomics- and Network-driven Systems Biology Approaches for Pharmacogenomics and Toxicogenomics | Q38010493 | ||
| Visualization of the interactome: what are we looking at? | Q38011629 | ||
| Network analysis has diverse roles in drug discovery. | Q38012955 | ||
| Recent advances in protein–protein interaction prediction: experimental and computational methods | Q38014488 | ||
| Modular pharmacology: the next paradigm in drug discovery | Q38017212 | ||
| Recent approaches to the prioritization of candidate disease genes | Q38018005 | ||
| Beyond ‘furballs’ and ‘dumpling soups’ – towards a molecular architecture of signaling complexes and networks | Q38019703 | ||
| Clinical utility of neuroprotective agents in neurodegenerative diseases: current status of drug development for Alzheimer's, Parkinson's and Huntington's diseases, and amyotrophic lateral sclerosis. | Q38022265 | ||
| Opportunities in systems biology to discover mechanisms and repurpose drugs for CNS diseases | Q38023097 | ||
| Network Interventions | Q38024340 | ||
| Endosomal crosstalk: meeting points for signaling pathways. | Q38026339 | ||
| Understanding cancer mechanisms through network dynamics | Q38027492 | ||
| Protein interactions: mapping interactome networks to support drug target discovery and selection | Q38028416 | ||
| Towards a bioinformatics analysis of anti-Alzheimer's herbal medicines from a target network perspective. | Q38034180 | ||
| Protein-protein interaction networks: unraveling the wiring of molecular machines within the cell. | Q38036242 | ||
| Hydroximic acid derivatives: pleiotropic HSP co-inducers restoring homeostasis and robustness. | Q38037746 | ||
| Biological network analysis: insights into structure and functions | Q38062889 | ||
| Protein contact networks: an emerging paradigm in chemistry | Q38062944 | ||
| Genetics and iron in the systems biology of Parkinson's disease and some related disorders | Q38065668 | ||
| Allo-network drugs: extension of the allosteric drug concept to protein- protein interaction and signaling networks | Q38081491 | ||
| How to design multi-target drugs. | Q38089151 | ||
| A survey of computational methods for protein complex prediction from protein interaction networks | Q38100240 | ||
| Semantic web for integrated network analysis in biomedicine | Q38382895 | ||
| Identifying disease-causal genes using Semantic Web-based representation of integrated genomic and phenomic knowledge | Q38387590 | ||
| Mapping various information sources to a semantic network. | Q38420255 | ||
| Coordinated and uncoordinated optimization of networks | Q38427318 | ||
| NAViGaTOR: Network Analysis, Visualization and Graphing Toronto | Q38433769 | ||
| Architecture of basic building blocks in protein and domain structural interaction networks | Q38448307 | ||
| Relating drug–protein interaction network with drug side effects | Q38495130 | ||
| SuperTarget goes quantitative: update on drug-target interactions | Q38499993 | ||
| Reconstruction of Protein-Protein Interaction Network of Insulin Signaling inHomo Sapiens | Q38503816 | ||
| Network and pathway analysis of compound-protein interactions | Q38509112 | ||
| A systems biology case study of ovarian cancer drug resistance | Q38516560 | ||
| Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes | Q38518470 | ||
| Multi-layered representation for cell signaling pathways. | Q38521718 | ||
| A copula method for modeling directional dependence of genes | Q38525765 | ||
| Integrating Genetic Approaches into the Discovery of Anticancer Drugs | Q38555487 | ||
| Systems biology and the future of medicine | Q38647215 | ||
| Chemoinformatics as a Theoretical Chemistry Discipline | Q38911197 | ||
| Walking the interactome for prioritization of candidate disease genes | Q39140568 | ||
| Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions | Q39171046 | ||
| Novel signatures of cancer-associated fibroblasts. | Q39210456 | ||
| Construction of cell type-specific logic models of signaling networks using CellNOpt | Q39255420 | ||
| Generic indicators for loss of resilience before a tipping point leading to population collapse | Q39294165 | ||
| Universality in protein residue networks. | Q39343534 | ||
| Extracting SAR Information from a Large Collection of Anti-Malarial Screening Hits by NSG-SPT Analysis | Q39513261 | ||
| Metformin amplifies chemotherapy-induced AMPK activation and antitumoral growth. | Q39547941 | ||
| A sub-pathway-based approach for identifying drug response principal network | Q39615546 | ||
| A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization | Q39636559 | ||
| Protein dynamics in drug combinations: a linear superposition of individual-drug responses | Q39731018 | ||
| Network-based tools for the identification of novel drug targets. | Q39749340 | ||
| Classes of complex networks defined by role-to-role connectivity profiles | Q39789937 | ||
| Fault diagnosis engineering of digital circuits can identify vulnerable molecules in complex cellular pathways | Q39859567 | ||
| Distinct biological network properties between the targets of natural products and disease genes | Q39861736 | ||
| Identifying network of drug mode of action by gene expression profiling | Q39889042 | ||
| Dynamic proteomics of individual cancer cells in response to a drug. | Q39913838 | ||
| Drug repositioning using disease associated biological processes and network analysis of drug targets | Q39929131 | ||
| The 'wired' universe of organic chemistry. | Q39991362 | ||
| Rationalizing Tight Ligand Binding through Cooperative Interaction Networks | Q39999558 | ||
| Implicit methods for qualitative modeling of gene regulatory networks | Q39999844 | ||
| Multipathway model enables prediction of kinase inhibitor cross-talk effects on migration of Her2-overexpressing mammary epithelial cells | Q40001089 | ||
| A hidden oncogenic positive feedback loop caused by crosstalk between Wnt and ERK pathways. | Q40181009 | ||
| Idiotypic networks and other preconceived ideas | Q40182559 | ||
| Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases | Q40242235 | ||
| An integrated in silico analysis of drug-binding to human serum albumin. | Q40266801 | ||
| Small-world communication of residues and significance for protein dynamics | Q40269752 | ||
| Combined antibacterial activity of amoxicillin with clavulanic acid against ampicillin-resistant strains | Q40282177 | ||
| Application of network thermodynamics to the computer modeling of the pharmacology of anticancer agents: a network model for methotrexate action as a comprehensive example | Q40333054 | ||
| Herpesviral protein networks and their interaction with the human proteome | Q40341630 | ||
| Analysis of drug-induced effect patterns to link structure and side effects of medicines | Q40363457 | ||
| The proteomes of neurotransmitter receptor complexes form modular networks with distributed functionality underlying plasticity and behaviour | Q40511054 | ||
| Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES. | Q40512092 | ||
| What you see is not what you get: how sampling affects macroscopic features of biological networks | Q40538760 | ||
| TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics | Q40695124 | ||
| High order chromatin architecture shapes the landscape of chromosomal alterations in cancer | Q40719732 | ||
| Synthetic enhancement in gene interaction: a genetic tool come of age. | Q40796844 | ||
| Integrating the Alzheimer's Disease Proteome and Transcriptome: A Comprehensive Network Model of a Complex Disease | Q40963834 | ||
| Contact rearrangements form coupled networks from local motions in allosteric proteins | Q41003317 | ||
| WebInterViewer: visualizing and analyzing molecular interaction networks | Q41011120 | ||
| Bimoclomol: A nontoxic, hydroxylamine derivative with stress protein-inducing activity and cytoprotective effects | Q41086821 | ||
| Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery | Q41276143 | ||
| Regulated Noise in the Epigenetic Landscape of Development and Disease | Q41514448 | ||
| PROMISCUOUS: a database for network-based drug-repositioning | Q41578922 | ||
| Network theory of aging | Q41604629 | ||
| NetAligner--a network alignment server to compare complexes, pathways and whole interactomes. | Q41788133 | ||
| A network-based method for target selection in metabolic networks | Q41790813 | ||
| The orphan disease networks | Q41807086 | ||
| Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers | Q41816148 | ||
| A probabilistic approach to identify putative drug targets in biochemical networks | Q41836315 | ||
| Chemical combination effects predict connectivity in biological systems | Q41851112 | ||
| A Comparative Study of Metabolic Network Topology between a Pathogenic and a Non-Pathogenic Bacterium for Potential Drug Target Identification. | Q41858708 | ||
| Revealing static and dynamic modular architecture of the eukaryotic protein interaction network | Q41895485 | ||
| iPath2.0: interactive pathway explorer | Q41933346 | ||
| Mapping of ligand-binding cavities in proteins | Q41946244 | ||
| How threshold behaviour affects the use of subgraphs for network comparison | Q41955932 | ||
| Role-similarity based functional prediction in networked systems: application to the yeast proteome | Q42012920 | ||
| SIMCOMP/SUBCOMP: chemical structure search servers for network analyses | Q42100659 | ||
| Edgetic perturbation models of human inherited disorders | Q42124353 | ||
| Molecular network analysis suggests aberrant CREB-mediated gene regulation in the Alzheimer disease hippocampus | Q42125431 | ||
| Ensemble Modeling of Cancer Metabolism | Q42126656 | ||
| Circuitry and dynamics of human transcription factor regulatory networks | Q42150273 | ||
| Network rigidity at finite temperature: relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems | Q42151001 | ||
| Systems biology. How information theory handles cell signaling and uncertainty | Q42154524 | ||
| Uncovering potential Drug Targets for Tuberculosis using Protein Networks | Q42200249 | ||
| Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress | Q42204382 | ||
| Activity driven modeling of time varying networks | Q42216161 | ||
| GENIES: gene network inference engine based on supervised analysis | Q42233064 | ||
| Sampling properties of directed networks | Q42283776 | ||
| MicroRNA regulation of human protein protein interaction network | Q42413467 | ||
| Quantifying the chemical beauty of drugs. | Q42414958 | ||
| Cytokine-associated drug toxicity in human hepatocytes is associated with signaling network dysregulation | Q42423679 | ||
| Toward understanding allosteric signaling mechanisms in the ATPase domain of molecular chaperones | Q42427794 | ||
| Dr. PIAS 2.0: an update of a database of predicted druggable protein-protein interactions | Q42430108 | ||
| Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network | Q42594704 | ||
| GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks | Q42595813 | ||
| Extracting Sets of Chemical Substructures and Protein Domains Governing Drug-Target Interactions | Q42598159 | ||
| A graph-based approach to systematically reconstruct human transcriptional regulatory modules | Q42626909 | ||
| Structural resemblance between the families of bacterial signal-transduction proteins and of G proteins revealed by graph theoretical techniques | Q42630576 | ||
| PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks. | Q42639697 | ||
| EDGE: a centralized resource for the comparison, analysis, and distribution of toxicogenomic information | Q42645749 | ||
| Pharmacogenomics and bioinformatics: PharmGKB. | Q42654621 | ||
| Protein clefts in molecular recognition and function | Q42845107 | ||
| Choke point analysis of metabolic pathways in E.histolytica: a computational approach for drug target identification | Q42918994 | ||
| Computational approaches for drug repositioning and combination therapy design. | Q43015433 | ||
| Gene set-level network analysis using a toxicogenomics database | Q43110446 | ||
| An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people | Q43136367 | ||
| Predicting disease genes using protein-protein interactions. | Q43169919 | ||
| Identification of potential targets in biological signalling systems through network perturbation analysis | Q43192617 | ||
| Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis | Q43234873 | ||
| Long-range energy transfer in proteins | Q43243126 | ||
| Protein interaction network analysis--approach for potential drug target identification in Mycobacterium tuberculosis. | Q43260725 | ||
| Integrative network alignment reveals large regions of global network similarity in yeast and human | Q43467712 | ||
| Empirically determining the sample size for large-scale gene network inference algorithms | Q43501011 | ||
| Network analysis of adverse drug interactions | Q43600416 | ||
| Protein flexibility predictions using graph theory | Q43629667 | ||
| Information filtering in complex weighted networks | Q43718645 | ||
| Topological properties of the drug targets regulated by microRNA in human protein–protein interaction network | Q43845557 | ||
| Integrated network analysis platform for protein-protein interactions | Q43961965 | ||
| NetAlign: a web-based tool for comparison of protein interaction networks | Q44070985 | ||
| Network-Based Analysis and Characterization of Adverse Drug–Drug Interactions | Q44108392 | ||
| A network view of disease and compound screening | Q44111868 | ||
| MAVisto: A Tool for Biological Network Motif Analysis | Q44119930 | ||
| A network-based method for predicting disease-causing genes. | Q44271949 | ||
| Similarity index based on local paths for link prediction of complex networks | Q44312047 | ||
| Rewiring the dynamic interactome | Q44324983 | ||
| Evaluation of linear classifiers on articles containing pharmacokinetic evidence of drug-drug interactions | Q44602645 | ||
| Interaction networks as a tool to investigate the mechanisms of aging | Q44605554 | ||
| Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network. | Q44677737 | ||
| Fuzzy communities and the concept of bridgeness in complex networks | Q44683265 | ||
| Exploration of the Topology of Chemical Spaces with Network Measures | Q44802653 | ||
| Allostery wiring diagrams in the transitions that drive the GroEL reaction cycle | Q44848940 | ||
| Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir | Q44859710 | ||
| BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge | Q44870332 | ||
| The prediction of ADMET properties using structure information representations | Q44925810 | ||
| From molecular to biological structure and back | Q44928351 | ||
| A novel approach to predict protein-protein interactions related to Alzheimer's disease based on complex network | Q44935051 | ||
| Robust classification of salient links in complex networks | Q45043914 | ||
| Inferring disease and gene set associations with rank coherence in networks | Q45358428 | ||
| Identification of potential host proteins for influenza A virus based on topological and biological characteristics by proteome-wide network approach | Q45358984 | ||
| Drug-target interaction prediction by learning from local information and neighbors | Q45371331 | ||
| A systems pharmacology analysis of major chemotherapy combination regimens used in gastric cancer treatment: predicting potential new protein targets and drugs | Q45749371 | ||
| Biological function through network topology: a survey of the human diseasome | Q45847143 | ||
| Unified QSAR approach to antimicrobials. Part 3: first multi-tasking QSAR model for input-coded prediction, structural back-projection, and complex networks clustering of antiprotozoal compounds. | Q45855420 | ||
| Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo | Q45876108 | ||
| Alignment of metabolic pathways. | Q45904398 | ||
| Gaussian interaction profile kernels for predicting drug-target interaction | Q45961548 | ||
| structureViz: linking Cytoscape and UCSF Chimera. | Q45962594 | ||
| Conserved network motifs allow protein-protein interaction prediction. | Q45966736 | ||
| A CitationRank algorithm inheriting Google technology designed to highlight genes responsible for serious adverse drug reaction. | Q45994408 | ||
| NetMatch: a Cytoscape plugin for searching biological networks | Q46078746 | ||
| Turning down, but not off. | Q46122166 | ||
| A network solution | Q53527430 | ||
| Computational simulation of multi-target research on the material basis of Caulis sinomenii in treating osteoarthritis | Q53977726 | ||
| Rationalizing three-dimensional activity landscapes and the influence of molecular representations on landscape topology and the formation of activity cliffs | Q53990515 | ||
| Metabolic network analysis revealed distinct routes of deletion effects between essential and non-essential genes. | Q54343586 | ||
| Functional classification of drugs by properties of their pairwise interactions. | Q54468515 | ||
| Essentiality and damage in metabolic networks. | Q54513267 | ||
| Identification of key residues for protein conformational transition using elastic network model. | Q54551159 | ||
| The small world inside large metabolic networks. | Q55016270 | ||
| Protein networks, pleiotropy and the evolution of senescence. | Q55287052 | ||
| Activities and sensitivities in boolean network models. | Q55524631 | ||
| Protein cavity clustering based on community structure of pocket similarity network | Q46123315 | ||
| C-GRAAL: common-neighbors-based global GRAph ALignment of biological networks | Q46143407 | ||
| How similar are similarity searching methods? A principal component analysis of molecular descriptor space | Q46174895 | ||
| Dynamical properties of a boolean model of gene regulatory network with memory | Q46190364 | ||
| QSAR and complex network study of the chiral HMGR inhibitor structural diversity. | Q46233283 | ||
| Identification of information flow-modulating drug targets: a novel bridging paradigm for drug discovery | Q46260661 | ||
| Global snapshot of a protein interaction network-a percolation based approach | Q46266078 | ||
| Unified QSAR & network-based computational chemistry approach to antimicrobials. II. Multiple distance and triadic census analysis of antiparasitic drugs complex networks. | Q46479027 | ||
| Estimating novel potential drug targets of Plasmodium falciparum by analysing the metabolic network of knock-out strains in silico | Q46551696 | ||
| Double iterative optimisation for metabolic network-based drug target identification | Q46558372 | ||
| Robustness analysis of the Escherichia coli metabolic network | Q46731594 | ||
| The influence of drug-like concepts on decision-making in medicinal chemistry | Q46922861 | ||
| PIVOT: protein interacions visualizatiOn tool | Q47207869 | ||
| Reverse engineering intracellular biochemical networks. | Q47286146 | ||
| Size estimation of chemical space: how big is it? | Q47321477 | ||
| Self-similar community structure in a network of human interactions. | Q47357648 | ||
| Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast | Q47363112 | ||
| The different ways through which specificity works in orthosteric and allosteric drugs | Q47577552 | ||
| Top-k similar graph matching using TraM in biological networks. | Q47578446 | ||
| Allo-network drugs: harnessing allostery in cellular networks | Q47579306 | ||
| Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL. | Q47594992 | ||
| Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues | Q47608015 | ||
| Aging defined by a chronologic-replicative protein network in Saccharomyces cerevisiae: an interactome analysis. | Q47827478 | ||
| Drug–target interaction prediction by random walk on the heterogeneous network | Q47845354 | ||
| Residue network in protein native structure belongs to the universality class of a three-dimensional critical percolation cluster | Q47948528 | ||
| Mining metabolic networks for optimal drug targets | Q47954463 | ||
| Protein multi-scale organization through graph partitioning and robustness analysis: application to the myosin-myosin light chain interaction | Q47987970 | ||
| Align human interactome with phenome to identify causative genes and networks underlying disease families. | Q48315327 | ||
| Alignment of molecular networks by integer quadratic programming | Q48403322 | ||
| DITOP: drug-induced toxicity related protein database | Q48403527 | ||
| Systems biology. Modular biological complexity | Q48420215 | ||
| Dynamic exploration and editing of KEGG pathway diagrams | Q48422297 | ||
| Discovering disease-genes by topological features in human protein-protein interaction network | Q48432576 | ||
| A grid layout algorithm for automatic drawing of biochemical networks | Q48500935 | ||
| A more efficient search strategy for aging genes based on connectivity | Q48525795 | ||
| CREDO: a protein-ligand interaction database for drug discovery | Q48537603 | ||
| A call to reform the taxonomy of human disease | Q48646649 | ||
| A graph layout algorithm for drawing metabolic pathways | Q48678928 | ||
| Protein domain decomposition using a graph-theoretic approach | Q48691334 | ||
| New Markov-Shannon Entropy models to assess connectivity quality in complex networks: from molecular to cellular pathway, Parasite-Host, Neural, Industry, and Legal-Social networks. | Q48808016 | ||
| The integration and annotation of the human interactome in the UniHI Database | Q50147724 | ||
| Binding similarity network of ligand | Q50862492 | ||
| An iterative algorithm for metabolic network-based drug target identification. | Q50868686 | ||
| Quantifying social group evolution | Q50905096 | ||
| Robustness analysis of a Boolean model of gene regulatory network with memory | Q51016389 | ||
| The mode-of-action by network identification (MNI) algorithm: a network biology approach for molecular target identification | Q51032367 | ||
| A robustness-based approach to systems-oriented drug design | Q51062307 | ||
| The core and most useful molecules in organic chemistry | Q51165267 | ||
| Rigidity and flexibility of biological networks | Q51298649 | ||
| Architecture and evolution of organic chemistry | Q51323964 | ||
| Analyzing and visualizing residue networks of protein structures | Q56664440 | ||
| Comparing metabolic network models based on genomic and automatically inferred enzyme information from Plasmodium and its human host to define drug targets in silico | Q56770530 | ||
| Chemical Chaperones: Mechanisms of Action and Potential Use | Q56864470 | ||
| SnapShot: Protein-Protein Interaction Networks | Q56989191 | ||
| Use of genome-wide association studies for drug repositioning | Q57338671 | ||
| Emergence of the silicon human and network targeting drugs | Q57393826 | ||
| Link communities reveal multiscale complexity in networks | Q57405864 | ||
| Exploring the Mode-of-Action of Bioactive Compounds by Chemical-Genetic Profiling in Yeast | Q57734375 | ||
| Effect of sampling on topology predictions of protein-protein interaction networks | Q58067825 | ||
| Network Medicine Strikes a Blow against Breast Cancer | Q59304980 | ||
| Small-world behavior in time-varying graphs | Q59393052 | ||
| Modularity in the genetic disease-phenotype network | Q60370295 | ||
| Employing functional interactions for characterisation and detection of sparse complexes from yeast PPI networks. | Q51325312 | ||
| Topac: alignment of gene regulatory networks using topology-aware coloring | Q51342636 | ||
| Rewiring chemistry: algorithmic discovery and experimental validation of one-pot reactions in the network of organic chemistry. | Q51342920 | ||
| Multiple weak hits confuse complex systems: a transcriptional regulatory network as an example | Q51374935 | ||
| Deconvolution of mTORC2 “in Silico” | Q51393332 | ||
| GPEC: A Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection | Q51398877 | ||
| Hive plots--rational approach to visualizing networks. | Q51478033 | ||
| Onion structure and network robustness. | Q51531089 | ||
| Transferring network topological knowledge for predicting protein-protein interactions | Q51546978 | ||
| Early warning signals and the prosecutor's fallacy | Q51548187 | ||
| A local average connectivity-based method for identifying essential proteins from the network level | Q51554307 | ||
| PocketAlign a novel algorithm for aligning binding sites in protein structures. | Q51559401 | ||
| Controllability of complex networks | Q51569838 | ||
| An Algorithmic Framework for Predicting Side Effects of Drugs | Q51594993 | ||
| Discrete breathers at the interface between a diatomic and a monoatomic granular chain | Q51614168 | ||
| Characterization of drug efficacy regions based on dosage and frequency schedules | Q51634419 | ||
| Minimal cut sets in biochemical reaction networks | Q51637467 | ||
| Self-organizing fuzzy graphs for structure-based comparison of protein pockets | Q51652977 | ||
| The network as the target | Q51661893 | ||
| Protein-protein interaction network evaluation for identifying potential drug targets | Q51694945 | ||
| Antibiotic interactions that select against resistance | Q51710862 | ||
| Architectural repertoire of ligand-binding pockets on protein surfaces | Q51729594 | ||
| Comparative study of computational methods to detect the correlated reaction sets in biochemical networks | Q51758941 | ||
| Alignment-free prediction of a drug-target complex network based on parameters of drug connectivity and protein sequence of receptors. | Q51772250 | ||
| A network model of successive partitioning-limited solute diffusion through the stratum corneum | Q51784429 | ||
| A network-based approach for resistance transmission in bacterial populations | Q51793791 | ||
| Merging chemical and biological space: Structural mapping of enzyme binding pocket space | Q51853796 | ||
| Combining the interactome and deleterious SNP predictions to improve disease gene identification | Q51855746 | ||
| Unified QSAR approach to antimicrobials. 4. Multi-target QSAR modeling and comparative multi-distance study of the giant components of antiviral drug-drug complex networks. | Q51858888 | ||
| Network Analysis Tools: from biological networks to clusters and pathways | Q51868865 | ||
| Integrating systems approaches into pharmaceutical sciences | Q51873591 | ||
| Analysis of protein surface patterns by pocket similarity network | Q51876241 | ||
| A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. | Q51896048 | ||
| Protein-protein interaction networks and biology--what's the connection? | Q51897141 | ||
| Computing topological parameters of biological networks | Q51900389 | ||
| Hypothesis generation in signaling networks | Q51927544 | ||
| Algorithms for network analysis in systems-ADME/Tox using the MetaCore and MetaDrug platforms | Q51928372 | ||
| Similarity networks of protein binding sites | Q51959646 | ||
| Emergent behavior of growing knowledge about molecular interactions. | Q51962700 | ||
| Discovery of regulatory interactions through perturbation: inference and experimental design | Q52076375 | ||
| Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. | Q52211190 | ||
| Reveal, a general reverse engineering algorithm for inference of genetic network architectures | Q52238235 | ||
| Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis. | Q52594611 | ||
| Atomic interactions and profile of small molecules disrupting protein-protein interfaces: the TIMBAL database. | Q52596153 | ||
| Molecular evolution of protein conformational changes revealed by a network of evolutionarily coupled residues | Q52609779 | ||
| Unfolding accessibility provides a macroscopic approach to temporal networks | Q52884597 | ||
| Drug-efficacy depends on the inhibitor type and the target position in a metabolic network--a systematic study. | Q52922420 | ||
| Assessing Relative Bioactivity of Chemical Substances Using Quantitative Molecular Network Topology Analysis | Q53175427 | ||
| Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison | Q53510397 | ||
| Identification of novel hub genes associated with liver metastasis of gastric cancer | Q84150763 | ||
| A network-QSAR model for prediction of genetic-component biomarkers in human colorectal cancer | Q84346859 | ||
| On the supertertiary structure of proteins | Q84402199 | ||
| Bacterial survival strategies suggest rethinking cancer cooperativity | Q84504964 | ||
| Pattern formation in oscillatory complex networks consisting of excitable nodes | Q84506141 | ||
| Relationships between ligand binding sites, protein architecture and correlated paths of energy and conformational fluctuations | Q84742496 | ||
| Drug effects viewed from a signal transduction network perspective | Q84852104 | ||
| Selection of reprogramming factors of induced pluripotent stem cells based on the protein interaction network and functional profiles | Q84947355 | ||
| BioTapestry: A Tool to Visualize the Dynamic Properties of Gene Regulatory Networks | Q84973212 | ||
| The relationship between rational drug design and drug side effects | Q84992161 | ||
| Betweenness preference: quantifying correlations in the topological dynamics of temporal networks | Q86850041 | ||
| Finding missing edges in networks based on their community structure | Q87361717 | ||
| Transport on Coupled Spatial Networks | Q87366378 | ||
| Parallel Optimization of Synthetic Pathways within the Network of Organic Chemistry | Q61311517 | ||
| Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE | Q61447401 | ||
| Discrete breathers in protein structures | Q61763316 | ||
| xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures | Q63214343 | ||
| Characterization of microRNA-regulated protein-protein interaction network | Q63641881 | ||
| Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry | Q63953718 | ||
| MOLGEN: Personal computer-based modeling system | Q71785929 | ||
| Network topology of a potential energy landscape: a static scale-free network | Q74278716 | ||
| Cancer as a robust system: implications for anticancer therapy | Q76394082 | ||
| Drug target validation and identification of secondary drug target effects using DNA microarrays | Q77534975 | ||
| Games network and application to PAs system | Q79312530 | ||
| Creative elements: network-based predictions of active centres in proteins and cellular and social networks | Q79688862 | ||
| Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph | Q79811403 | ||
| Essentiality is an emergent property of metabolic network wiring | Q80309384 | ||
| The protein folding network | Q80458006 | ||
| Using process diagrams for the graphical representation of biological networks | Q81010511 | ||
| PIMWalker: visualising protein interaction networks using the HUPO PSI molecular interaction format | Q81130759 | ||
| Small-world network approach to identify key residues in protein-protein interaction | Q81193331 | ||
| Regulatory network motifs and hotspots of cancer genes in a mammalian cellular signalling network | Q81378507 | ||
| Virtual identification of essential proteins within the protein interaction network of yeast | Q81466184 | ||
| PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization | Q81480709 | ||
| Unified QSAR and network-based computational chemistry approach to antimicrobials, part 1: multispecies activity models for antifungals | Q81592130 | ||
| Protein-protein interactions as new drug targets. Preface | Q81656198 | ||
| Water and molecular chaperones act as weak links of protein folding networks: energy landscape and punctuated equilibrium changes point towards a game theory of proteins | Q81679864 | ||
| Network-based prediction of human tissue-specific metabolism | Q81798711 | ||
| Structure-activity relationship anatomy by network-like similarity graphs and local structure-activity relationship indices | Q81979863 | ||
| DCDB: drug combination database | Q82329206 | ||
| Correlating allostery with rigidity | Q82370626 | ||
| iMAT: an integrative metabolic analysis tool | Q82473473 | ||
| CFinder: locating cliques and overlapping modules in biological networks | Q82534265 | ||
| Target Family-Directed Exploration of Scaffolds with Different SAR Profiles | Q82543696 | ||
| A similarity network approach for the analysis and comparison of protein sequence/structure sets | Q82627996 | ||
| Self-similarity of phase-space networks of frustrated spin models and lattice gas models | Q83021574 | ||
| Vertex similarity in networks | Q83131559 | ||
| Mechanisms of drug combinations: interaction and network perspectives | Q83265745 | ||
| Secreted microRNAs: a new form of intercellular communication | Q83285061 | ||
| Systems biology. Attractors and democratic dynamics | Q83379338 | ||
| Architecture of the drug-drug interaction network | Q83512732 | ||
| SnapShot: MicroRNAs in Cancer | Q83761139 | ||
| Carbon nanotubes in drug delivery: focus on infectious diseases | Q83766454 | ||
| Drug candidates derailed in case of mistaken identity | Q83770486 | ||
| Optimizing controllability of complex networks by minimum structural perturbations | Q83776183 | ||
| Highlights of drug package inserts and the website DailyMed: the need for further improvement in package inserts to help busy prescribers | Q83917611 | ||
| Molecular Mechanism-Based Network-like Similarity Graphs Reveal Relationships between Different Types of Receptor Ligands and Structural Changes that Determine Agonistic, Inverse-Agonistic, and Antagonistic Effects | Q84054327 | ||
| The analysis of the drug-targets based on the topological properties in the human protein-protein interaction network | Q84073874 | ||
| Correlation between EEG-EMG coherence during isometric contraction and its imaginary execution | Q84083047 | ||
| Getting pharmaceutical R&D back on target | Q84133263 | ||
| P4510 | describes a project that uses | Cytoscape | Q3699942 |
| P433 | issue | 3 | |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | drug discovery | Q1418791 |
| P304 | page(s) | 333-408 | |
| P577 | publication date | 2013-06-01 | |
| P13046 | publication type of scholarly work | review article | Q7318358 |
| P1433 | published in | Pharmacology & Therapeutics | Q3378596 |
| P1476 | title | Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review | |
| P478 | volume | 138 |
| Q46342985 | A Discrete Dynamical System Approach to Pathway Activation Profiles of Signaling Cascades. |
| Q36546500 | A Modified Amino Acid Network Model Contains Similar and Dissimilar Weight |
| Q28553224 | A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism |
| Q90716625 | A Network Pharmacology Approach to Explore the Mechanisms of Qishen Granules in Heart Failure |
| Q28554086 | A Network-Based Data Integration Approach to Support Drug Repurposing and Multi-Target Therapies in Triple Negative Breast Cancer |
| Q46734695 | A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression. |
| Q37029832 | A Perspective on Implementing a Quantitative Systems Pharmacology Platform for Drug Discovery and the Advancement of Personalized Medicine. |
| Q42083154 | A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis. |
| Q35901993 | A multiple kernel learning algorithm for drug-target interaction prediction |
| Q28543628 | A novel mathematical model describing adaptive cellular drug metabolism and toxicity in the chemoimmune system |
| Q35867650 | A novel quantitative high-throughput screen identifies drugs that both activate SUMO conjugation via the inhibition of microRNAs 182 and 183 and facilitate neuroprotection in a model of oxygen and glucose deprivation |
| Q24289222 | A scalable method for molecular network reconstruction identifies properties of targets and mutations in acute myeloid leukemia |
| Q90667792 | A systematic survey of centrality measures for protein-protein interaction networks |
| Q37598989 | A systems biology-based investigation into the therapeutic effects of Gansui Banxia Tang on reversing the imbalanced network of hepatocellular carcinoma |
| Q57451675 | Accelerating the Drug Development Pipeline with Genome-Scale Metabolic Network Reconstructions |
| Q38775661 | Advantages of Structure-Based Drug design Approaches in Neurological Disorders |
| Q98178435 | Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning |
| Q38134781 | Allosteric conformational barcodes direct signaling in the cell |
| Q35016456 | Alternative RNA structure-coupled gene regulations in tumorigenesis |
| Q41444600 | An Integrative Thrombosis Network: Visualization and Topological Analysis. |
| Q35101895 | An approach for dynamical network reconstruction of simple network motifs |
| Q30402785 | An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass |
| Q86693817 | Analysis of core-periphery organization in protein contact networks reveals groups of structurally and functionally critical residues |
| Q58743469 | Antiarrhythmic drugs for atrial fibrillation: Imminent impulses are emerging |
| Q52641243 | Apoptotic impact on Brugia malayi by sulphonamido-quinoxaline: search for a novel therapeutic rationale |
| Q55044864 | Aromatic Rings Commonly Used in Medicinal Chemistry: Force Fields Comparison and Interactions With Water Toward the Design of New Chemical Entities. |
| Q47572067 | Attractor Structures of Signaling Networks: Consequences of Different Conformational Barcode Dynamics and Their Relations to Network-Based Drug Design |
| Q100946063 | Automatic construction of molecular similarity networks for visual graph mining in chemical space of bioactive peptides: an unsupervised learning approach |
| Q35852733 | Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy. |
| Q35240181 | BalestraWeb: efficient online evaluation of drug-target interactions |
| Q34700554 | Bayesian hierarchical models for protein networks in single-cell mass cytometry |
| Q26830010 | Beyond modules and hubs: the potential of gene coexpression networks for investigating molecular mechanisms of complex brain disorders |
| Q37375683 | Bioinformatics analysis for the antirheumatic effects of huang-lian-jie-du-tang from a network perspective |
| Q38243624 | Biological networks and drug discovery--where do we stand? |
| Q49315568 | Breakthroughs in modern cancer therapy and elusive cardiotoxicity: Critical research-practice gaps, challenges, and insights |
| Q50420648 | Building protein-protein interaction networks for Leishmania species through protein structural information. |
| Q44428862 | Cancer-related networks: A help to understand, predict and change malignant transformation |
| Q41536919 | Chaperone co-inducer BGP-15 inhibits histone deacetylases and enhances the heat shock response through increased chromatin accessibility |
| Q28392590 | Characterization of Protein-Protein Interfaces through a Protein Contact Network Approach |
| Q37733252 | Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection |
| Q38232706 | Chemo- and bioinformatics resources for in silico drug discovery from medicinal plants beyond their traditional use: a critical review |
| Q37236776 | Clustering drug-drug interaction networks with energy model layouts: community analysis and drug repurposing |
| Q92711824 | Co-emergence and Collapse: The Mesoscopic Approach for Conceptualizing and Investigating the Functional Integration of Organisms |
| Q64118454 | Collective influencers in protein interaction networks |
| Q64930905 | Combining learning and constraints for genome-wide protein annotation. |
| Q34993880 | Combining small molecules for cell reprogramming through an interatomic analysis. |
| Q38907478 | Computational approaches for innovative antiepileptic drug discovery |
| Q30363516 | Computational modeling of allosteric regulation in the hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric communications. |
| Q42396552 | Computational polypharmacology comes of age. |
| Q92932799 | Conservation of Potentially Druggable Cavities in Intrinsically Disordered Proteins |
| Q36574707 | Control of Multilayer Networks |
| Q89178715 | Controllability and stability analysis of large transcriptomic dynamic systems for host response to influenza infection in human |
| Q28535399 | Controllability in cancer metabolic networks according to drug targets as driver nodes |
| Q35571951 | Convergence and divergence of genetic and modular networks between diabetes and breast cancer |
| Q38216443 | Counteracting antibiotic resistance: breaking barriers among antibacterial strategies |
| Q38733091 | Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors |
| Q44121896 | Critical controllability analysis of directed biological networks using efficient graph reduction |
| Q35655576 | DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference. |
| Q35855961 | Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins |
| Q31087381 | Data Requirements for Model-Based Cancer Prognosis Prediction |
| Q37032419 | Deciphering the genetic and modular connections between coronary heart disease, idiopathic pulmonary arterial hypertension and pulmonary heart disease |
| Q90177357 | Deep graph embedding for prioritizing synergistic anticancer drug combinations |
| Q47290651 | DeepSynergy: Predicting anti-cancer drug synergy with Deep Learning |
| Q34876386 | Detection of deregulated modules using deregulatory linked path |
| Q41866229 | Determining Associations between Human Diseases and non-coding RNAs with Critical Roles in Network Control |
| Q34572459 | Development and implementation of (Q)SAR modeling within the CHARMMing web-user interface |
| Q57314662 | Differential Network Analysis and Graph Classification: A Glocal Approach |
| Q35605218 | Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity |
| Q91869113 | Dissecting the Role of NF-κb Protein Family and Its Regulators in Rheumatoid Arthritis Using Weighted Gene Co-Expression Network |
| Q36123974 | Diverse array-designed modes of combination therapies in Fangjiomics |
| Q36104367 | Drug combinatorics and side effect estimation on the signed human drug-target network |
| Q33589478 | Drug repurposing: a better approach for infectious disease drug discovery? |
| Q38816088 | Drug target prioritization by perturbed gene expression and network information |
| Q42701435 | Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology |
| Q86513793 | Drug-target networks for Tanshinone IIA identified by data mining |
| Q38167225 | Edgotype: a fundamental link between genotype and phenotype |
| Q62457780 | Eigenvector centrality for characterization of protein allosteric pathways |
| Q59135002 | Elucidating the Interaction of CF Airway Epithelial Cells and Rhinovirus: Using the Host-Pathogen Relationship to Identify Future Therapeutic Strategies |
| Q35661742 | Emergent Self-Organized Criticality in Gene Expression Dynamics: Temporal Development of Global Phase Transition Revealed in a Cancer Cell Line |
| Q35752078 | Emerging targets in osteoarthritis therapy. |
| Q58712093 | Endogenous metabolites of vitamin E limit inflammation by targeting 5-lipoxygenase |
| Q33705752 | Epigenomic and transcriptomic approaches in the post-genomic era: path to novel targets for diagnosis and therapy of the ischaemic heart? Position Paper of the European Society of Cardiology Working Group on Cellular Biology of the Heart. |
| Q57609430 | Evolutionary Approaches to Ethnobiology |
| Q30395364 | Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways |
| Q41005963 | Exploring Wound-Healing Genomic Machinery with a Network-Based Approach. |
| Q92730841 | Exploring allosteric communication in multiple states of the bacterial ribosome using residue network analysis |
| Q28648163 | Extracting research-quality phenotypes from electronic health records to support precision medicine |
| Q33722886 | Fetal alcohol syndrome, chemo-biology and OMICS: ethanol effects on vitamin metabolism during neurodevelopment as measured by systems biology analysis |
| Q100737090 | Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method |
| Q34646772 | Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it. |
| Q34281990 | GIANT: a cytoscape plugin for modular networks |
| Q64868728 | Gene co-expression network analysis for identifying genetic markers in Parkinson's disease - a three-way comparative approach |
| Q99638192 | Genome-wide pathogenesis interpretation using a heat diffusion-based systems genetics method and implications for gene function annotation |
| Q48182249 | Heat Shock Proteins and Autophagy Pathways in Neuroprotection: from Molecular Bases to Pharmacological Interventions |
| Q52626039 | Heterogeneous network propagation for herb target identification |
| Q28087226 | How do oncoprotein mutations rewire protein-protein interaction networks? |
| Q24273350 | How drugs get into cells: tested and testable predictions to help discriminate between transporter-mediated uptake and lipoidal bilayer diffusion |
| Q38116370 | How to escape the cancer attractor: Rationale and limitations of multi-target drugs |
| Q38488857 | Human interactome resource and gene set linkage analysis for the functional interpretation of biologically meaningful gene sets |
| Q56993529 | Identification of Antifungal Targets Based on Computer Modeling |
| Q35094597 | Identification of core T cell network based on immunome interactome. |
| Q37475825 | Identification of critical paralog groups with indispensable roles in the regulation of signaling flow |
| Q47130286 | Identification of genes and critical control proteins associated with inflammatory breast cancer using network controllability. |
| Q38275632 | Identification of intrinsically disordered regions in PTEN and delineation of its function via a network approach |
| Q64098317 | Identification of key regulatory genes connected to NF-κB family of proteins in visceral adipose tissues using gene expression and weighted protein interaction network |
| Q47245987 | Identify bilayer modules via pseudo-3D clustering: applications to miRNA-gene bilayer networks |
| Q34521677 | Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation |
| Q95270414 | Identifying Drug Targets in Pancreatic Ductal Adenocarcinoma Through Machine Learning, Analyzing Biomolecular Networks, and Structural Modeling |
| Q64923346 | Identifying influential spreaders by gravity model. |
| Q51024931 | Identifying progression related disease risk modules based on the human subcellular signaling networks |
| Q36262362 | Identifying robust communities and multi-community nodes by combining top-down and bottom-up approaches to clustering |
| Q40672660 | Illuminating drug action by network integration of disease genes: a case study of myocardial infarction |
| Q35146130 | Improved multi-level protein-protein interaction prediction with semantic-based regularization |
| Q48166040 | Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks |
| Q36111892 | Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer. |
| Q34979129 | Insights from systems pharmacology into cardiovascular drug discovery and therapy |
| Q30375668 | Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity. |
| Q38709521 | Integrating personalized gene expression profiles into predictive disease-associated gene pools |
| Q33645618 | Integrating systems biology sources illuminates drug action |
| Q38802358 | Integration of Chinese medicine with Western medicine could lead to future medicine: molecular module medicine |
| Q38891078 | Intracellular and intercellular signaling networks in cancer initiation, development and precision anti-cancer therapy: RAS acts as contextual signaling hub. |
| Q40590037 | Ion Mobility-Mass Spectrometry Reveals Highly-Compact Intermediates in the Collision Induced Dissociation of Charge-Reduced Protein Complexes |
| Q47114235 | Linking physiologically-based pharmacokinetic and genome-scale metabolic networks to understand estradiol biology |
| Q36611128 | Locating influential nodes via dynamics-sensitive centrality |
| Q35962054 | Logic-Based and Cellular Pharmacodynamic Modeling of Bortezomib Responses in U266 Human Myeloma Cells |
| Q90324304 | Machine learning prediction of oncology drug targets based on protein and network properties |
| Q34235803 | Machine learning-based prediction of drug-drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties |
| Q51084127 | MaxLink: network-based prioritization of genes tightly linked to a disease seed set. |
| Q92962253 | Measuring rank robustness in scored protein interaction networks |
| Q28829555 | Metabolic profiling and in vitro assessment of anthelmintic fractions of Picria fel-terrae Lour |
| Q27144251 | Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery |
| Q38442694 | Methods for protein complex prediction and their contributions towards understanding the organisation, function and dynamics of complexes. |
| Q41013966 | Metric projection for dynamic multiplex networks |
| Q33716566 | Microbial succession in the gut: directional trends of taxonomic and functional change in a birth cohort of Spanish infants. |
| Q38698524 | Minimum dominating set-based methods for analyzing biological networks |
| Q49718973 | Mining the Synergistic Core Allosteric Modules Variation and Sequencing Pharmacological Module Driverome in a preclinical model of Ischemia |
| Q35346548 | Mining the modular structure of protein interaction networks |
| Q38254881 | Mismatch binding, ADP-ATP exchange and intramolecular signaling during mismatch repair |
| Q42043842 | Model for high-throughput screening of multitarget drugs in chemical neurosciences: synthesis, assay, and theoretic study of rasagiline carbamates. |
| Q46811191 | Modeling the mitotic regulatory network identifies highly efficient anti-cancer drug combinations. |
| Q37614684 | Modelling the yeast interactome |
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