Construction of a large scale integrated map of macrophage pathogen recognition and effector systems

[1]  Tom C. Freeman,et al.  The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways , 2010, BMC Systems Biology.

[2]  M. Kwiatkowska,et al.  Biological pathways as communicating computer systems , 2009, Journal of Cell Science.

[3]  P. Ghazal,et al.  Combined genome-wide expression profiling and targeted RNA interference in primary mouse macrophages reveals perturbation of transcriptional networks associated with interferon signalling , 2009, BMC Genomics.

[4]  Tero Aittokallio,et al.  Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks , 2009, Bioinform..

[5]  Sarala M. Wimalaratne,et al.  The Systems Biology Graphical Notation , 2009, Nature Biotechnology.

[6]  R. Medzhitov,et al.  Targeting of immune signalling networks by bacterial pathogens , 2009, Nature Cell Biology.

[7]  M. Karin,et al.  Regulation and function of NF-kappaB transcription factors in the immune system. , 2009, Annual review of immunology.

[8]  G. Superti-Furga,et al.  An orthogonal proteomic-genomic screen identifies AIM2 as a cytoplasmic DNA sensor for the inflammasome , 2009, Nature Immunology.

[9]  Jasmyn A. Dunn,et al.  HIN-200 Proteins Regulate Caspase Activation in Response to Foreign Cytoplasmic DNA , 2009, Science.

[10]  Keiji Tanaka,et al.  Molecular mechanisms of proteasome assembly , 2009, Nature Reviews Molecular Cell Biology.

[11]  E. Alnemri,et al.  AIM2 activates the inflammasome and cell death in response to cytoplasmic DNA , 2009, Nature.

[12]  Daniel R. Caffrey,et al.  AIM2 recognizes cytosolic dsDNA and forms a caspase-1 activating inflammasome with ASC , 2009, Nature.

[13]  Keiji Tanaka The proteasome: Overview of structure and functions , 2009, Proceedings of the Japan Academy. Series B, Physical and biological sciences.

[14]  Christian von Mering,et al.  STRING 8—a global view on proteins and their functional interactions in 630 organisms , 2008, Nucleic Acids Res..

[15]  Kenneth H. Buetow,et al.  PID: the Pathway Interaction Database , 2008, Nucleic Acids Res..

[16]  Anton J. Enright,et al.  Network visualization and analysis of gene expression data using BioLayout Express3D , 2009, Nature Protocols.

[17]  Andreas Zell,et al.  BowTieBuilder: modeling signal transduction pathways , 2009, BMC Systems Biology.

[18]  Richard Orton,et al.  Version control of pathway models using XML patches , 2009, BMC Systems Biology.

[19]  H. Mewes,et al.  KEGG spider: interpretation of genomics data in the context of the global gene metabolic network , 2008, Genome Biology.

[20]  P. Privalov,et al.  Assembling the human IFN-beta enhanceosome in solution. , 2008, Journal of molecular biology.

[21]  A. Bowie,et al.  Viral evasion and subversion of pattern-recognition receptor signalling , 2008, Nature Reviews Immunology.

[22]  R. Schumann,et al.  Genetic influence on bloodstream infections and sepsis. , 2008, International journal of antimicrobial agents.

[23]  M. Petroski,et al.  The ubiquitin system, disease, and drug discovery , 2008, BMC Biochemistry.

[24]  J. Devincenzo,et al.  Human Genetic Factors and Respiratory Syncytial Virus Disease Severity , 2008, Clinical Microbiology Reviews.

[25]  N. Kikuchi,et al.  CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks , 2008, Proceedings of the IEEE.

[26]  Alexander R. Pico,et al.  WikiPathways: Pathway Editing for the People , 2008, PLoS biology.

[27]  Ugur Dogrusoz,et al.  PATIKAmad: Putting microarray data into pathway context , 2008, Proteomics.

[28]  Scott M. Williams,et al.  Genetic studies of African populations: an overview on disease susceptibility and response to vaccines and therapeutics , 2008, Human Genetics.

[29]  P. Ghazal,et al.  Logic models of pathway biology. , 2008, Drug discovery today.

[30]  A. Takaoka,et al.  Cytosolic DNA recognition for triggering innate immune responses. , 2008, Advanced drug delivery reviews.

[31]  Anton J. Enright,et al.  A logic-based diagram of signalling pathways central to macrophage activation , 2008, BMC Systems Biology.

[32]  E. Barillot,et al.  A comprehensive modular map of molecular interactions in RB/E2F pathway , 2008, Molecular systems biology.

[33]  Alexander Hoffmann,et al.  Generation and Activation of Multiple Dimeric Transcription Factors within the NF-κB Signaling System , 2008, Molecular and Cellular Biology.

[34]  Luay Nakhleh,et al.  The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks , 2008, PLoS Comput. Biol..

[35]  A. Zaas,et al.  The effect of toll-like receptors and toll-like receptor genetics in human disease. , 2008, Annual review of medicine.

[36]  Yoshihiro Yamanishi,et al.  KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[37]  G. Irwin,et al.  Modelling molecular interaction pathways using a two-stage identification algorithm , 2007, Systems and Synthetic Biology.

[38]  S. Gordon The macrophage: Past, present and future , 2007, European journal of immunology.

[39]  Stijn van Dongen,et al.  Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data , 2007, PLoS Comput. Biol..

[40]  F. Martinon,et al.  NALP Inflammasomes: a central role in innate immunity , 2007, Seminars in Immunopathology.

[41]  K. Honda,et al.  DAI (DLM-1/ZBP1) is a cytosolic DNA sensor and an activator of innate immune response , 2007, Nature.

[42]  L. O’Neill,et al.  Diversity and regulation in the NF-κB system , 2007 .

[43]  S. Harrison,et al.  An Atomic Model of the Interferon-β Enhanceosome , 2007, Cell.

[44]  M. Colonna TLR pathways and IFN‐regulatory factors: To each its own , 2007, European journal of immunology.

[45]  L. O’Neill,et al.  Diversity and regulation in the NF-kappaB system. , 2007, Trends in biochemical sciences.

[46]  Sean Ekins,et al.  Pathway mapping tools for analysis of high content data. , 2007, Methods in molecular biology.

[47]  F. Martinon,et al.  Inflammatory caspases and inflammasomes: master switches of inflammation , 2007, Cell Death and Differentiation.

[48]  BMC Systems Biology , 2007 .

[49]  Gopal R. Gopinath,et al.  Reactome: a knowledge base of biologic pathways and processes , 2007, Genome Biology.

[50]  Igor Goryanin,et al.  A Graphical Notation to describe the Logical Interactions of Biological Pathways , 2006, J. Integr. Bioinform..

[51]  Natal A. W. van Riel,et al.  Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments , 2006, Briefings Bioinform..

[52]  D. Golenbock,et al.  TLR9 and the Recognition of Self and Non‐Self Nucleic Acids , 2006, Annals of the New York Academy of Sciences.

[53]  R. Flavell,et al.  Involvement of Toll-like receptor 5 in the recognition of flagellated bacteria , 2006, Proceedings of the National Academy of Sciences.

[54]  Jing Zhao,et al.  Hierarchical modularity of nested bow-ties in metabolic networks , 2006, BMC Bioinformatics.

[55]  H. Kitano,et al.  A comprehensive map of the toll-like receptor signaling network , 2006, Molecular systems biology.

[56]  Steve Gerondakis,et al.  Diverse Toll-like receptors utilize Tpl2 to activate extracellular signal-regulated kinase (ERK) in hemopoietic cells. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[57]  H. Kitano,et al.  Robustness trade-offs and host–microbial symbiosis in the immune system , 2006, Molecular systems biology.

[58]  K. S. Deshpande,et al.  Human protein reference database—2006 update , 2005, Nucleic Acids Res..

[59]  N. V. van Riel Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments. , 2006, Briefings in bioinformatics.

[60]  A. Kupfer,et al.  Modelling and Simulation of the TLR4 Pathway with Coloured Petri Nets , 2006, 2006 International Conference of the IEEE Engineering in Medicine and Biology Society.

[61]  J. Bazan,et al.  Pathogen recognition: TLRs throw us a curve. , 2005, Immunity.

[62]  Osamu Takeuchi,et al.  IPS-1, an adaptor triggering RIG-I- and Mda5-mediated type I interferon induction , 2005, Nature Immunology.

[63]  Yukiko Matsuoka,et al.  Using process diagrams for the graphical representation of biological networks , 2005, Nature Biotechnology.

[64]  Joanne S. Luciano,et al.  PAX of mind for pathway researchers. , 2005, Drug discovery today.

[65]  D. Hume,et al.  Inflammation suppressor genes: please switch out all the lights , 2005, Journal of leukocyte biology.

[66]  H. Kitano,et al.  A comprehensive pathway map of epidermal growth factor receptor signaling , 2005, Molecular systems biology.

[67]  D. Cavalieri,et al.  Bioinformatic methods for integrating whole-genome expression results into cellular networks. , 2005, Drug discovery today.

[68]  M. Heim RIG-I: an essential regulator of virus-induced interferon production. , 2005, Journal of hepatology.

[69]  T. Seya,et al.  Surface-Expressed TLR6 Participates in the Recognition of Diacylated Lipopeptide and Peptidoglycan in Human Cells1 , 2005, The Journal of Immunology.

[70]  Ian M. Donaldson,et al.  The Biomolecular Interaction Network Database and related tools 2005 update , 2004, Nucleic Acids Res..

[71]  Masaru Tomita,et al.  KEGG-Based Pathway Visualization Tool for Complex Omics Data , 2005, Silico Biol..

[72]  Tom Maniatis,et al.  Crystal structure of ATF‐2/c‐Jun and IRF‐3 bound to the interferon‐β enhancer , 2004 .

[73]  David W. Mount,et al.  Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data , 2004, Bioinform..

[74]  J. Doyle,et al.  Bow Ties, Metabolism and Disease , 2022 .

[75]  R. Iyengar,et al.  Modeling cell signaling networks. , 2004, Biology of the cell.

[76]  Catherine M Lloyd,et al.  CellML: its future, present and past. , 2004, Progress in biophysics and molecular biology.

[77]  A. DeFranco,et al.  Ligand-regulated Chimeric Receptor Approach Reveals Distinctive Subcellular Localization and Signaling Properties of the Toll-like Receptors* , 2004, Journal of Biological Chemistry.

[78]  Akiko Iwasaki,et al.  Recognition of single-stranded RNA viruses by Toll-like receptor 7. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[79]  Martin Vingron,et al.  IntAct: an open source molecular interaction database , 2004, Nucleic Acids Res..

[80]  Yukiko Matsuoka,et al.  Molecular Interaction Map of a Macrophage , 2004 .

[81]  S. Harrison,et al.  Crystal structure of ATF-2/c-Jun and IRF-3 bound to the interferon-beta enhancer. , 2004, The EMBO journal.

[82]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[83]  K. Honda,et al.  Essential role of IRF-3 in lipopolysaccharide-induced interferon-beta gene expression and endotoxin shock. , 2003, Biochemical and biophysical research communications.

[84]  C. Semple,et al.  The comparative proteomics of ubiquitination in mouse. , 2003, Genome research.

[85]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[86]  F. Martinon,et al.  NALPs: a novel protein family involved in inflammation , 2003, Nature Reviews Molecular Cell Biology.

[87]  S. Akira,et al.  Recognition of lipopeptides by Toll-like receptors , 2002, Journal of endotoxin research.

[88]  Govinda Rao,et al.  IRF3 mediates a TLR3/TLR4-specific antiviral gene program. , 2002, Immunity.

[89]  Eric H Davidson,et al.  New computational approaches for analysis of cis-regulatory networks. , 2002, Developmental biology.

[90]  Steven C. Lawlor,et al.  GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways , 2002, Nature Genetics.

[91]  Michael Karin,et al.  NF-κB at the crossroads of life and death , 2002, Nature Immunology.

[92]  Michael Karin,et al.  NF-kappaB at the crossroads of life and death. , 2002, Nature immunology.

[93]  Chen Dong,et al.  MAP kinases in the immune response. , 2002, Annual review of immunology.

[94]  R. Flavell,et al.  Recognition of double-stranded RNA and activation of NF-κB by Toll-like receptor 3 , 2001, Nature.

[95]  K. Ishii,et al.  Cutting Edge: Role of Toll-Like Receptor 9 in CpG DNA-Induced Activation of Human Cells1 , 2001, The Journal of Immunology.

[96]  Anton J. Enright,et al.  BioLayout-an automatic graph layout algorithm for similarity visualization , 2001, Bioinform..

[97]  S. Akira,et al.  The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5 , 2001, Nature.

[98]  Vladimir Batagelj,et al.  Pajek - Analysis and Visualization of Large Networks , 2001, Graph Drawing Software.

[99]  S. Rhee,et al.  Murine TOLL-like Receptor 4 Confers Lipopolysaccharide Responsiveness as Determined by Activation of NFκB and Expression of the Inducible Cyclooxygenase* , 2000, The Journal of Biological Chemistry.

[100]  D. Schwartz,et al.  TLR4 mutations are associated with endotoxin hyporesponsiveness in humans , 2000, Nature Genetics.

[101]  S. Dongen Graph clustering by flow simulation , 2000 .

[102]  K. Senger,et al.  Mechanism by which the IFN-beta enhanceosome activates transcription. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[103]  K. Kohn Molecular interaction map of the mammalian cell cycle control and DNA repair systems. , 1999, Molecular biology of the cell.

[104]  M. Drutskaya,et al.  The N-Terminal Domain of IκBα Masks the Nuclear Localization Signal(s) of p50 and c-Rel Homodimers , 1998, Molecular and Cellular Biology.

[105]  M. Drutskaya,et al.  The N-terminal domain of IkappaB alpha masks the nuclear localization signal(s) of p50 and c-Rel homodimers. , 1998, Molecular and cellular biology.

[106]  M. Karin,et al.  Nuclear factor-kappaB: a pivotal transcription factor in chronic inflammatory diseases. , 1997, The New England journal of medicine.

[107]  D. White,et al.  Rel/NF-kappaB/IkappaB proteins and cancer. , 1996, Oncogene.

[108]  W. Greene,et al.  I kappa B/MAD-3 masks the nuclear localization signal of NF-kappa B p65 and requires the transactivation domain to inhibit NF-kappa B p65 DNA binding. , 1992, Molecular biology of the cell.

[109]  R. van Furth The mononuclear phagocyte system. , 1980, Verhandlungen der Deutschen Gesellschaft fur Pathologie.