An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling.

[1]  T. Mak,et al.  Severe impairment of interleukin-1 and Toll-like receptor signalling in mice lacking IRAK-4 , 2002, Nature.

[2]  A. Al-ghonaium,et al.  Pyogenic Bacterial Infections in Humans with IRAK-4 Deficiency , 2003, Science.

[3]  G. Trinchieri,et al.  Cell proliferation and survival induced by Toll-like receptors is antagonized by type I IFNs , 2007, Proceedings of the National Academy of Sciences.

[4]  Alma L Burlingame,et al.  A semisynthetic epitope for kinase substrates , 2007, Nature Methods.

[5]  A. Yoshimura,et al.  FLN29 Deficiency Reveals Its Negative Regulatory Role in the Toll-like Receptor (TLR) and Retinoic Acid-inducible Gene I (RIG-I)-like Helicase Signaling Pathway* , 2008, Journal of Biological Chemistry.

[6]  Osamu Takeuchi,et al.  Sequential control of Toll-like receptor–dependent responses by IRAK1 and IRAK2 , 2008, Nature Immunology.

[7]  S. Akira,et al.  TRAM couples endocytosis of Toll-like receptor 4 to the induction of interferon-β , 2008, Nature Immunology.

[8]  J. Banchereau,et al.  Pyogenic Bacterial Infections in Humans with MyD88 Deficiency , 2003, Science.

[9]  Y. Mok,et al.  Dendritic cell‐derived interferon‐γ‐induced protein mediates tumor necrosis factor‐α stimulation of human lung fibroblasts , 2008, Proteomics.

[10]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[11]  Michael T. Laub,et al.  Rewiring the Specificity of Two-Component Signal Transduction Systems , 2008, Cell.

[12]  E. Fraenkel,et al.  Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks , 2009, Science Signaling.

[13]  Hiroaki Kimura,et al.  Tryptophan aspartate‐containing coat protein (CORO1A) suppresses Toll‐like receptor signalling in Mycobacterium leprae infection , 2009, Clinical and experimental immunology.

[14]  T. Maritzen,et al.  Gadkin: A novel link between endosomal vesicles and microtubule tracks. , 2010, Communicative & integrative biology.

[15]  S. Akira,et al.  Pattern Recognition Receptors and Inflammation , 2010, Cell.

[16]  Chanchal Kumar,et al.  Quantitative analysis of kinase-proximal signaling in lipopolysaccharide-induced innate immune response. , 2010, Journal of proteome research.

[17]  Patrick G. A. Pedrioli,et al.  Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast , 2010, Science Signaling.

[18]  I. Amit,et al.  The phosphoproteome of toll-like receptor-activated macrophages , 2010, Molecular systems biology.

[19]  P. Anderson.  Post-transcriptional regulons coordinate the initiation and resolution of inflammation , 2010, Nature Reviews Immunology.

[20]  Jacob T. Robinson,et al.  Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits , 2011, Cell.

[21]  W. Garrett,et al.  Severity of innate immune-mediated colitis is controlled by the cytokine deficiency-induced colitis susceptibility-1 (Cdcs1) locus , 2011, Proceedings of the National Academy of Sciences.

[22]  Y. Kong,et al.  Mapping a dynamic innate immunity protein interaction network regulating type I interferon production. , 2011, Immunity.

[23]  M. Mann,et al.  Extracting gene function from protein-protein interactions using Quantitative BAC InteraCtomics (QUBIC). , 2011, Methods.

[24]  V. Dixit,et al.  Phosphorylation of NLRC4 is critical for inflammasome activation , 2012, Nature.

[25]  R. Aebersold,et al.  Mass spectrometry-based proteomics and network biology. , 2012, Annual review of biochemistry.

[26]  Nir Friedman,et al.  A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. , 2012, Molecular cell.

[27]  Michael R. Schmidt,et al.  Gadkin negatively regulates cell spreading and motility via sequestration of the actin-nucleating ARP2/3 complex , 2012, Proceedings of the National Academy of Sciences.

[28]  Jenny Taylor,et al.  Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns. , 2012, Blood.

[29]  Steven A Carr,et al.  Integrated proteomic analysis of post-translational modifications by serial enrichment , 2013, Nature Methods.

[30]  J. Rehwinkel,et al.  SAMHD1-dependent retroviral control and escape in mice , 2013, Retrovirology.

[31]  Z. Bar-Joseph,et al.  Linking the signaling cascades and dynamic regulatory networks controlling stress responses , 2013, Genome research.

[32]  Ernest Fraenkel,et al.  Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling , 2013, PLoS Comput. Biol..

[33]  B. Clotet,et al.  Cell Cycle Control and HIV-1 Susceptibility Are Linked by CDK6-Dependent CDK2 Phosphorylation of SAMHD1 in Myeloid and Lymphoid Cells , 2014, The Journal of Immunology.

[34]  Margery G. Smelkinson,et al.  Phosphoproteome Profiling of the Macrophage Response to Different Toll-Like Receptor Ligands Identifies Differences in Global Phosphorylation Dynamics , 2014, Journal of proteome research.

[35]  Michalis K. Titsias,et al.  SAMHD1 is mutated recurrently in chronic lymphocytic leukemia and is involved in response to DNA damage. , 2014, Blood.

[36]  Tapesh Santra,et al.  Navigating the Multilayered Organization of Eukaryotic Signaling: A New Trend in Data Integration , 2014, PLoS Comput. Biol..

[37]  Jiahuai Han,et al.  The kinases Mst1 and Mst2 positively regulate phagocyte ROS induction and bactericidal activity , 2015, Nature Immunology.

[38]  Y. Crow,et al.  Aicardi–Goutières syndrome and the type I interferonopathies , 2015, Nature Reviews Immunology.

[39]  S. Michnick,et al.  A cell-signaling network temporally resolves specific versus promiscuous phosphorylation. , 2015, Cell reports.

[40]  Sharon E. Miller,et al.  CALM Regulates Clathrin-Coated Vesicle Size and Maturation by Directly Sensing and Driving Membrane Curvature , 2015, Developmental cell.

[41]  J. Saez-Rodriguez,et al.  Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data , 2015, Nature Communications.

[42]  E. Ballana,et al.  SAMHD1: at the crossroads of cell proliferation, immune responses, and virus restriction. , 2015, Trends in microbiology.

[43]  M. Torgersen,et al.  Retinoic acid-induced IgG production in TLR-activated human primary B cells involves ULK1-mediated autophagy , 2015, Autophagy.

[44]  Edward L. Huttlin,et al.  The BioPlex Network: A Systematic Exploration of the Human Interactome , 2015, Cell.

[45]  Sky W. Brubaker,et al.  Innate immune pattern recognition: a cell biological perspective. , 2015, Annual review of immunology.

[46]  Hiroyuki Kubota,et al.  Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers. , 2016, Trends in biotechnology.