Towards genome-scale signalling-network reconstructions
暂无分享,去创建一个
[1] J. Monod,et al. Genetic regulatory mechanisms in the synthesis of proteins. , 1961, Journal of Molecular Biology.
[2] Tony Pawson,et al. Protein modules and signalling networks , 1995, Nature.
[3] angesichts der Corona-Pandemie,et al. UPDATE , 1973, The Lancet.
[4] U. Bhalla,et al. Emergent properties of networks of biological signaling pathways. , 1999, Science.
[5] J. Collins,et al. Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.
[6] B. Palsson,et al. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[7] M. Elowitz,et al. A synthetic oscillatory network of transcriptional regulators , 2000, Nature.
[8] S. Shen-Orr,et al. Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.
[9] T. Hunter,et al. The Protein Kinase Complement of the Human Genome , 2002, Science.
[10] Sangdun Choi,et al. Unravelling the signal-transduction network in B lymphocytes , 2002, Nature.
[11] Upinder S. Bhalla,et al. The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks , 2003, Bioinform..
[12] R. Karp,et al. Conserved pathways within bacteria and yeast as revealed by global protein network alignment , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[13] Upinder S Bhalla,et al. Understanding complex signaling networks through models and metaphors. , 2003, Progress in biophysics and molecular biology.
[14] Steven P Gygi,et al. A proteomics approach to understanding protein ubiquitination , 2003, Nature Biotechnology.
[15] B. Palsson,et al. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[16] T. Pawson,et al. Assembly of Cell Regulatory Systems Through Protein Interaction Domains , 2003, Science.
[17] Peter D. Karp,et al. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases , 2004, BMC Bioinformatics.
[18] Markus J. Herrgård,et al. Integrating high-throughput and computational data elucidates bacterial networks , 2004, Nature.
[19] Giulio Superti-Furga,et al. A physical and functional map of the human TNF-α/NF-κB signal transduction pathway , 2004, Nature Cell Biology.
[20] L. Donehower,et al. Inactivation of the Wip1 phosphatase inhibits mammary tumorigenesis through p38 MAPK–mediated activation of the p16Ink4a-p19Arf pathway , 2004, Nature Genetics.
[21] Harvey J. Greenberg,et al. Reconstruction and Functional Characterization of the Human Mitochondrial Metabolic Network Based on Proteomic and Biochemical Data* , 2004, Journal of Biological Chemistry.
[22] A. Barabasi,et al. Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.
[23] Jason A. Papin,et al. The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. , 2004, Biophysical journal.
[24] Jason A. Papin,et al. Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk. , 2004, Journal of theoretical biology.
[25] L. Cantley,et al. The Crohn's Disease Protein, NOD2, Requires RIP2 in Order to Induce Ubiquitinylation of a Novel Site on NEMO , 2004, Current Biology.
[26] Huilin Zhou,et al. Global Analyses of Sumoylated Proteins in Saccharomyces cerevisiae , 2004, Journal of Biological Chemistry.
[27] E. Dennis,et al. Handbook of cell signaling , 2004 .
[28] J. Liao,et al. Design of artificial cell-cell communication using gene and metabolic networks. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[29] René Bernards,et al. A Genomic and Functional Inventory of Deubiquitinating Enzymes , 2005, Cell.
[30] Stefan Schuster,et al. A theoretical framework for detecting signal transfer routes in signalling networks , 2005, Comput. Chem. Eng..
[31] Yoav Freund,et al. Identifying metabolic enzymes with multiple types of association evidence , 2006, BMC Bioinformatics.
[32] Z. N. Oltvai,et al. Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[33] J. Liao,et al. A synthetic gene–metabolic oscillator , 2005, Nature.
[34] R. Karp,et al. From the Cover : Conserved patterns of protein interaction in multiple species , 2005 .
[35] Shoshana J. Wodak,et al. Metabolic PathFinding: inferring relevant pathways in biochemical networks , 2005, Nucleic Acids Res..
[36] T. Ideker,et al. Systematic interpretation of genetic interactions using protein networks , 2005, Nature Biotechnology.
[37] Craig Stephens,et al. Conserved modular design of an oxygen sensory/signaling network with species-specific output , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[38] D. Vitkup,et al. Influence of metabolic network structure and function on enzyme evolution , 2006, Genome Biology.
[39] Steffen Klamt,et al. A methodology for the structural and functional analysis of signaling and regulatory networks , 2006, BMC Bioinformatics.
[40] E. Klipp,et al. Integrative model of the response of yeast to osmotic shock , 2005, Nature Biotechnology.
[41] Jason A. Papin,et al. Reconstruction of cellular signalling networks and analysis of their properties , 2005, Nature Reviews Molecular Cell Biology.
[42] L. Nielsen,et al. Modeling Hybridoma Cell Metabolism Using a Generic Genome‐Scale Metabolic Model of Mus musculus , 2008, Biotechnology progress.
[43] Mirit I Aladjem,et al. Circuit diagrams for biological networks , 2006, Molecular systems biology.
[44] B. Palsson,et al. Systems approach to refining genome annotation , 2006, Proceedings of the National Academy of Sciences.
[45] W. Lim,et al. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. , 2006, Annual review of biochemistry.
[46] Sourav Bandyopadhyay,et al. Systematic identification of functional orthologs based on protein network comparison. , 2006, Genome research.
[47] Bernhard O. Palsson,et al. Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems , 2006, PLoS Comput. Biol..
[48] O. Myklebost,et al. Small-molecule MDM2 antagonists reveal aberrant p53 signaling in cancer: implications for therapy. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[49] H. Kitano,et al. A comprehensive map of the toll-like receptor signaling network , 2006, Molecular systems biology.
[50] Bas Teusink,et al. Accelerating the reconstruction of genome-scale metabolic networks , 2006, BMC Bioinformatics.
[51] M. Mann,et al. Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks , 2006, Cell.
[52] B. Palsson. Systems Biology: Properties of Reconstructed Networks , 2006 .
[53] Madhukar S. Dasika,et al. A computational framework for the topological analysis and targeted disruption of signal transduction networks. , 2006, Biophysical journal.
[54] P. Bork,et al. Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.
[55] Neema Jamshidi,et al. Systems biology of SNPs , 2006, Molecular systems biology.
[56] Markus J. Herrgård,et al. Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. , 2006, Genome research.
[57] Chemical combination effects predict connectivity in biological systems , 2007, Molecular systems biology.
[58] Adam M. Feist,et al. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information , 2007, Molecular systems biology.
[59] Jens Nielsen,et al. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks , 2008, BMC Systems Biology.
[60] Adam A. Friedman,et al. Genetic Screening for Signal Transduction in the Era of Network Biology , 2007, Cell.
[61] Vesteinn Thorsson,et al. Prediction of phenotype and gene expression for combinations of mutations , 2007, Molecular systems biology.
[62] James E. Ferrell,et al. Mechanisms of specificity in protein phosphorylation , 2007, Nature Reviews Molecular Cell Biology.
[63] James C Liao,et al. Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli , 2007, Proceedings of the National Academy of Sciences.
[64] Andrei L Osterman,et al. A subsystems-based approach to the identification of drug targets in bacterial pathogens. , 2007, Progress in drug research. Fortschritte der Arzneimittelforschung. Progres des recherches pharmaceutiques.
[65] Steffen Klamt,et al. Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction , 2008, BMC Systems Biology.
[66] Stefan Wiemann,et al. Combinatorial RNAi for quantitative protein network analysis , 2007, Proceedings of the National Academy of Sciences.
[67] Jong Myoung Park,et al. Genome-scale analysis of Mannheimia succiniciproducens metabolism. , 2007, Biotechnology and bioengineering.
[68] Monica L. Mo,et al. Global reconstruction of the human metabolic network based on genomic and bibliomic data , 2007, Proceedings of the National Academy of Sciences.
[69] Geoffrey J. Barton,et al. SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions , 2007, Nucleic Acids Res..
[70] Martin Fussenegger,et al. Synthetic ecosystems based on airborne inter- and intrakingdom communication , 2007, Proceedings of the National Academy of Sciences.
[71] Steffen Klamt,et al. A Logical Model Provides Insights into T Cell Receptor Signaling , 2007, PLoS Comput. Biol..
[72] Feng Luo,et al. Modular organization of protein interaction networks , 2007, Bioinform..
[73] Igor Goryanin,et al. A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola , 2009, BMC Systems Biology.
[74] N. D. Clarke,et al. Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells , 2008, Cell.
[75] Jason A. Papin,et al. Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major , 2008, Molecular systems biology.
[76] Julio Collado-Vides,et al. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation , 2007, Nucleic Acids Res..
[77] A. Fraser,et al. A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans , 2008, Nature Genetics.
[78] Robert P. St.Onge,et al. Defining genetic interaction , 2008, Proceedings of the National Academy of Sciences.
[79] Eric H Davidson,et al. Properties of developmental gene regulatory networks , 2008, Proceedings of the National Academy of Sciences.
[80] B. Andrews,et al. Linking the kinome and phosphorylome--a comprehensive review of approaches to find kinase targets. , 2008, Molecular bioSystems.
[81] Kara Dolinski,et al. The BioGRID Interaction Database: 2008 update , 2008, Nucleic Acids Res..
[82] Chung-Yen Lin,et al. Hubba: hub objects analyzer—a framework of interactome hubs identification for network biology , 2008, Nucleic Acids Res..
[83] Markus J. Herrgård,et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology , 2008, Nature Biotechnology.
[84] Trey Ideker,et al. Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data , 2008, PLoS Comput. Biol..
[85] L. Aravind,et al. Reconstructing the ubiquitin network - cross-talk with other systems and identification of novel functions , 2009, Genome Biology.
[86] R. Germain,et al. Variability and Robustness in T Cell Activation from Regulated Heterogeneity in Protein Levels , 2008, Science.
[87] J. Liao,et al. Determination of the Escherichia coli S-Nitrosoglutathione Response Network Using Integrated Biochemical and Systems Analysis* , 2008, Journal of Biological Chemistry.
[88] Teresa M. Przytycka,et al. DOMINE: a database of protein domain interactions , 2007, Nucleic Acids Res..
[89] Erwin P. Gianchandani,et al. Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks , 2008, PLoS Comput. Biol..
[90] Bonnie Berger,et al. Global alignment of multiple protein interaction networks with application to functional orthology detection , 2008, Proceedings of the National Academy of Sciences.
[91] Bernhard O. Palsson,et al. Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction , 2009, BMC Systems Biology.
[92] Adam M. Feist,et al. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli , 2008, Nature Biotechnology.
[93] M. Vidal,et al. Literature-curated protein interaction datasets , 2009, Nature Methods.
[94] L. Wiesmüller,et al. DNA repair, damage signaling and carcinogenesis. , 2008, DNA repair.
[95] M. Mann,et al. Dissection of the insulin signaling pathway via quantitative phosphoproteomics , 2008, Proceedings of the National Academy of Sciences.
[96] Jens Nielsen,et al. Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae , 2009, BMC Systems Biology.
[97] Sean R. Collins,et al. Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast , 2008, Science.
[98] Mark A. Ragan,et al. BMC Systems Biology BioMed Central Research article Protein-protein interaction as a predictor of subcellular location , 2008 .
[99] Adam P Arkin,et al. Modularity of stress response evolution , 2008, Proceedings of the National Academy of Sciences.
[100] M. Bennett,et al. A fast, robust, and tunable synthetic gene oscillator , 2008, Nature.
[101] Michael T. Laub,et al. Rewiring the Specificity of Two-Component Signal Transduction Systems , 2008, Cell.
[102] Martin Jones,et al. IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels , 2008, Nucleic Acids Res..
[103] Arthur Brady,et al. Fault Tolerance in Protein Interaction Networks: Stable Bipartite Subgraphs and Redundant Pathways , 2009, PloS one.
[104] P. Pryciak,et al. Designing new cellular signaling pathways. , 2009, Chemistry & biology.
[105] E. Sontheimer,et al. Origins and Mechanisms of miRNAs and siRNAs , 2009, Cell.
[106] E. Fraenkel,et al. Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks , 2009, Science Signaling.
[107] Michael C. Jewett,et al. Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p , 2009, Proceedings of the National Academy of Sciences.
[108] Ronan M. T. Fleming,et al. Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization , 2009, PLoS Comput. Biol..
[109] Hiroaki Kitano,et al. Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway , 2009, Molecular systems biology.
[110] Ali R. Zomorrodi,et al. Genome-scale gene/reaction essentiality and synthetic lethality analysis , 2009, Molecular systems biology.
[111] L. Bossi,et al. Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target. , 2009, Genes & development.
[112] Chikara Furusawa,et al. Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum , 2009, Microbial cell factories.
[113] Vinay Satish Kumar,et al. A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189 , 2009, PLoS Comput. Biol..
[114] Tony Pawson,et al. Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases , 2009, Science Signaling.
[115] Bei Wang,et al. Redefining the p53 response element , 2009, Proceedings of the National Academy of Sciences.
[116] Rick L Stevens,et al. iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations , 2009, Genome Biology.
[117] A. Barabasi,et al. Targets Drug Genomes Identify Novel Antimicrobial Staphylococcus Aureus of Multiple Reconstruction and Flux Balance Analysis Comparative Genome-scale Metabolic Supplemental Material , 2009 .
[118] M. Simon,et al. Deciphering Signaling Outcomes from a System of Complex Networks , 2009, Science Signaling.
[119] Jens Timmer,et al. Systems-level interactions between insulin–EGF networks amplify mitogenic signaling , 2009, Molecular systems biology.
[120] W. Lim,et al. Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species , 2009, PLoS biology.
[121] Homme W Hellinga,et al. Engineering key components in a synthetic eukaryotic signal transduction pathway , 2009, Molecular systems biology.
[122] Adam M. Feist,et al. Reconstruction of biochemical networks in microorganisms , 2009, Nature Reviews Microbiology.
[123] Gabriel C. Wu,et al. Synthetic protein scaffolds provide modular control over metabolic flux , 2009, Nature Biotechnology.
[124] G. Church,et al. Synthetic Gene Networks That Count , 2009, Science.
[125] Gary D Bader,et al. Rapid Evolution of Functional Complexity in a Domain Family , 2009, Science Signaling.
[126] M. Vingron,et al. Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments , 2009, Molecular systems biology.
[127] Karsten Zengler,et al. The transcription unit architecture of the Escherichia coli genome , 2009, Nature Biotechnology.
[128] Bernhard O. Palsson,et al. Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling , 2009, PLoS Comput. Biol..
[129] Feng Luo,et al. Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks , 2010, Int. J. Bioinform. Res. Appl..
[130] Adam M. Feist,et al. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. , 2010, Metabolic engineering.
[131] Jennifer M. Rust,et al. The BioGRID Interaction Database , 2011 .