| scholarly article | Q13442814 |
| P8978 | DBLP publication ID | journals/ploscb/ShouBLYKSG11 |
| P356 | DOI | 10.1371/JOURNAL.PCBI.1001050 |
| P8608 | Fatcat ID | release_dzjmwqrc3nhkhpf7v2eindihde |
| P932 | PMC publication ID | 3017101 |
| P698 | PubMed publication ID | 21253555 |
| P5875 | ResearchGate publication ID | 49773081 |
| P50 | author | Mark Bender Gerstein | Q6766711 |
| Michael P. Snyder | Q28924918 | ||
| P2093 | author name string | Hugo Y K Lam | |
| Philip M Kim | |||
| Nitin Bhardwaj | |||
| Koon-Kiu Yan | |||
| Chong Shou | |||
| P2860 | cites work | Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species | Q21145819 |
| Human MicroRNA targets | Q21563637 | ||
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| Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding | Q22065896 | ||
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| Genome evolution in yeasts | Q22122491 | ||
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| A human protein-protein interaction network: a resource for annotating the proteome | Q24324450 | ||
| BioGRID: a general repository for interaction datasets | Q24538650 | ||
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| MUSCLE: multiple sequence alignment with high accuracy and high throughput | Q24613456 | ||
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| Combinatorial microRNA target predictions | Q27860510 | ||
| A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae | Q27860755 | ||
| Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets | Q27860792 | ||
| Transcriptional regulatory networks in Saccharomyces cerevisiae | Q27860846 | ||
| The evolutionary fate and consequences of duplicate genes | Q27861065 | ||
| A comprehensive two-hybrid analysis to explore the yeast protein interactome | Q27861093 | ||
| Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins | Q27861094 | ||
| Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry | Q27861116 | ||
| Transcriptional regulatory code of a eukaryotic genome | Q27933887 | ||
| Global mapping of the yeast genetic interaction network | Q27934987 | ||
| A protein interaction map of Drosophila melanogaster | Q28131783 | ||
| Evolution at two levels in humans and chimpanzees | Q28141105 | ||
| Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". | Q35037874 | ||
| Substrate specificity of the cyclic AMP-dependent protein kinase | Q35088313 | ||
| Conserved pathways within bacteria and yeast as revealed by global protein network alignment | Q36160907 | ||
| The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication | Q36458856 | ||
| Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. | Q37365634 | ||
| Evolution of the mammalian transcription factor binding repertoire via transposable elements | Q41955907 | ||
| Evolutionary dynamics of prokaryotic transcriptional regulatory networks | Q44136796 | ||
| Transposable elements have rewired the core regulatory network of human embryonic stem cells | Q45103037 | ||
| Microeconomic principles explain an optimal genome size in bacteria | Q47393743 | ||
| Automatic genome-wide reconstruction of phylogenetic gene trees. | Q51909932 | ||
| Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage | Q58485110 | ||
| Conservation of primary structure in 16S ribosomal RNA | Q59059003 | ||
| Rapid reorganization of the transcriptional regulatory network after genome duplication in yeast | Q84924071 | ||
| Protein interaction mapping in C. elegans using proteins involved in vulval development | Q28141447 | ||
| Scanning Human Gene Deserts for Long-Range Enhancers | Q28210571 | ||
| Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs | Q28264442 | ||
| Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project | Q28301622 | ||
| Developmental gene regulatory network architecture across 500 million years of echinoderm evolution | Q28776684 | ||
| Global analysis of protein phosphorylation in yeast | Q29615057 | ||
| Natural selection on protein-coding genes in the human genome | Q29615352 | ||
| Intrinsic disorder and protein function | Q29616415 | ||
| Origin of a substantial fraction of human regulatory sequences from transposable elements | Q29617225 | ||
| MOTIPS: automated motif analysis for predicting targets of modular protein domains | Q30156864 | ||
| Structural determinants of the rate of protein evolution in yeast. | Q30354999 | ||
| Testing the neutral theory of molecular evolution with genomic data from Drosophila. | Q30677368 | ||
| Large-scale turnover of functional transcription factor binding sites in Drosophila | Q33260343 | ||
| Specificity and evolvability in eukaryotic protein interaction networks | Q33274191 | ||
| Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network | Q33304212 | ||
| The evolution of combinatorial gene regulation in fungi | Q33321398 | ||
| Protein complex evolution does not involve extensive network rewiring. | Q33361269 | ||
| BioMart Central Portal--unified access to biological data | Q33440110 | ||
| Evolutionary tinkering with conserved components of a transcriptional regulatory network | Q33540999 | ||
| Ordered structure of the transcription network inherited from the yeast whole-genome duplication | Q33595119 | ||
| Posttranslational regulation impacts the fate of duplicated genes | Q33734025 | ||
| Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs | Q33757668 | ||
| A c-Myc regulatory subnetwork from human transposable element sequences. | Q33773609 | ||
| Conserved patterns of protein interaction in multiple species | Q33837704 | ||
| iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions | Q33844563 | ||
| Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species | Q33881365 | ||
| Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks | Q33927257 | ||
| Scaling laws in the functional content of genomes | Q34228161 | ||
| An integrated system for studying residue coevolution in proteins | Q34585714 | ||
| Relating three-dimensional structures to protein networks provides evolutionary insights | Q34593972 | ||
| Divergence of transcription factor binding sites across related yeast species | Q34661726 | ||
| Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes | Q34860078 | ||
| P275 | copyright license | Creative Commons Attribution 4.0 International | Q20007257 |
| P6216 | copyright status | copyrighted | Q50423863 |
| P433 | issue | 1 | |
| P304 | page(s) | e1001050 | |
| P577 | publication date | 2011-01-06 | |
| P1433 | published in | PLOS Computational Biology | Q2635829 |
| P1476 | title | Measuring the evolutionary rewiring of biological networks | |
| P478 | volume | 7 |
| Q28661011 | A maximum entropy framework for nonexponential distributions |
| Q42207412 | A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq. |
| Q34103155 | Alignment-free protein interaction network comparison |
| Q34466180 | An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors |
| Q47657183 | Analysis of protein targets in pathogen-host interaction in infectious diseases: a case study on Plasmodium falciparum and Homo sapiens interaction network |
| Q38252509 | Asthma and obesity in children: current evidence and potential systems biology approaches. |
| Q92697422 | Attenuating the emergence of anti-fungal drug resistance by harnessing synthetic lethal interactions in a model organism |
| Q35927979 | Binding interface change and cryptic variation in the evolution of protein-protein interactions. |
| Q41958807 | ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa |
| Q38028400 | Comparative interaction networks: bridging genotype to phenotype. |
| Q34794119 | Complementing the Eukaryotic Protein Interactome |
| Q36022309 | Conserved Units of Co-Expression in Bacterial Genomes: An Evolutionary Insight into Transcriptional Regulation |
| Q39768567 | Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs |
| Q37184407 | Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways |
| Q27686946 | Dissecting phosphorylation networks: lessons learned from yeast |
| Q34674915 | Does habitat variability really promote metabolic network modularity? |
| Q90391311 | Dynamics of genetic variation in transcription factors and its implications for the evolution of regulatory networks in Bacteria |
| Q35198773 | Elucidation of the evolutionary expansion of phosphorylation signaling networks using comparative phosphomotif analysis |
| Q41769887 | Evaluation and properties of the budding yeast phosphoproteome |
| Q38367823 | Evidence for network evolution in an Arabidopsis interactome map. |
| Q26823238 | Evolution and functional cross-talk of protein post-translational modifications |
| Q28730461 | Evolution of biological interaction networks: from models to real data |
| Q89505435 | Evolutionary dynamics of microRNA target sites across vertebrate evolution |
| Q38814045 | Exploring the interactions of the RAS family in the human protein network and their potential implications in RAS-directed therapies. |
| Q28550898 | Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma |
| Q34202222 | Identification of novel phosphorylation modification sites in human proteins that originated after the human-chimpanzee divergence. |
| Q36008410 | Identifying Network Perturbation in Cancer |
| Q26824897 | Integrative approaches for finding modular structure in biological networks |
| Q33811809 | Interplay between chaperones and protein disorder promotes the evolution of protein networks |
| Q41840973 | Laboratory evolution of Geobacter sulfurreducens for enhanced growth on lactate via a single-base-pair substitution in a transcriptional regulator |
| Q92719182 | Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes |
| Q47563790 | Metabolic network modularity arising from simple growth processes |
| Q35176401 | Microbial laboratory evolution in the era of genome-scale science |
| Q45689907 | Mutational activation of the RocR activator and of a cryptic rocDEF promoter bypass loss of the initial steps of proline biosynthesis in Bacillus subtilis |
| Q21560876 | Mutational robustness of gene regulatory networks |
| Q36238554 | Network Centrality Analysis in Fungi Reveals Complex Regulation of Lost and Gained Genes. |
| Q89206108 | Network Modeling Unravels Mechanisms of Crosstalk between Ethylene and Salicylate Signaling in Potato |
| Q29091067 | Network biology concepts in complex disease comorbidities |
| Q30010152 | Network evolution: rewiring and signatures of conservation in signaling |
| Q41821042 | Networks of bZIP protein-protein interactions diversified over a billion years of evolution |
| Q26315280 | Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process |
| Q34161379 | Novel insights through the integration of structural and functional genomics data with protein networks |
| Q30854754 | OrthoClust: an orthology-based network framework for clustering data across multiple species |
| Q38115523 | Pathways to decoding the clinical potential of stress response FOXO-interaction networks for Huntington's disease: of gene prioritization and context dependence |
| Q28074488 | Phylogenetic Profiling for Probing the Modular Architecture of the Human Genome |
| Q30378436 | Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. |
| Q51375253 | Rewiring and dosing of systems modules as a design approach for synthetic mammalian signaling networks. |
| Q36179851 | Rewiring of posttranscriptional RNA regulons: Puf4p in fungi as an example |
| Q44324983 | Rewiring the dynamic interactome |
| Q96576700 | Robustness to extinction and plasticity derived from mutualistic bipartite ecological networks |
| Q46193293 | SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation |
| Q34017079 | Selection of organisms for the co-evolution-based study of protein interactions |
| Q36096866 | State of the art in silico tools for the study of signaling pathways in cancer |
| Q45548621 | Structural comparison of biological networks based on dominant vertices |
| Q34552419 | The Pivotal Role of Protein Phosphorylation in the Control of Yeast Central Metabolism |
| Q34308157 | The application of modular protein domains in proteomics |
| Q44777782 | The origins and evolution of ubiquitination sites |
| Q36437984 | The propagation of perturbations in rewired bacterial gene networks |
| Q41969384 | The role of structural disorder in the rewiring of protein interactions through evolution. |
| Q97542442 | TopicNet: a framework for measuring transcriptional regulatory network change |
| Q27005781 | Using biological networks to improve our understanding of infectious diseases |
| Q40425532 | Utilising established SDL-screening methods as a tool for the functional genomic characterisation of model and non-model organisms |
| Q28728252 | What is comparable in comparative cognition? |
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