Systems-level analysis of innate immunity.
暂无分享,去创建一个
Daniel E. Zak | D. Zak | A. Aderem | V. Tam
[1] Suzanne M. Paley,et al. Browsing metabolic and regulatory networks with BioCyc. , 2012, Methods in molecular biology.
[2] Xinxia Peng,et al. MicroRNA Expression and Virulence in Pandemic Influenza Virus-Infected Mice , 2010, Journal of Virology.
[3] Virginia Pascual,et al. An Interferon-Inducible Neutrophil-Driven Blood Transcriptional Signature in Human Tuberculosis , 2010, Nature.
[4] A. Bowie,et al. Immune sensing of DNA. , 2013, Immunity.
[5] J. Blattman,et al. Retinoic Acid as a Vaccine Adjuvant Enhances CD8+ T Cell Response and Mucosal Protection from Viral Challenge , 2011, Journal of Virology.
[6] Karin Breuer,et al. InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation , 2012, Nucleic Acids Res..
[7] Peter B. Gilbert,et al. Genetic impact of vaccination on breakthrough HIV-1 sequences from the Step trial , 2011, Nature Medicine.
[8] Zachary D. Smith,et al. Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses , 2009 .
[9] Trey Ideker,et al. Cytoscape 2.8: new features for data integration and network visualization , 2010, Bioinform..
[10] M. McElrath,et al. Profiling immunity to HIV vaccines with systems biology. , 2012, Current opinion in HIV and AIDS.
[11] B. Beutler,et al. The forward genetic dissection of afferent innate immunity. , 2008, Current topics in microbiology and immunology.
[12] Richard Bonneau,et al. Integrated inference and analysis of regulatory networks from multi-level measurements. , 2012, Methods in cell biology.
[13] Yang Liu,et al. VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies , 2013, Nucleic Acids Res..
[14] Charles M. Rice,et al. Corrigendum: A diverse range of gene products are effectors of the type I interferon antiviral response , 2015, Nature.
[15] Minoru Kanehisa,et al. Molecular network analysis of diseases and drugs in KEGG. , 2013, Methods in molecular biology.
[16] Donald K Carter,et al. HIV-1 vaccine-induced immunity in the test-of-concept Step Study: a case–cohort analysis , 2008, The Lancet.
[17] Theo M Bestebroer,et al. Airborne Transmission of Influenza A/H5N1 Virus Between Ferrets , 2012, Science.
[18] K. Walters,et al. An Overlapping Protein-Coding Region in Influenza A Virus Segment 3 Modulates the Host Response , 2012, Science.
[19] D. Fuller,et al. 'Omics investigations of HIV and SIV pathogenesis and innate immunity. , 2013, Current topics in microbiology and immunology.
[20] S. McWeeney,et al. Systems immunogenetics of vaccines. , 2013, Seminars in immunology.
[21] A. Aderem,et al. Bacterial lipopolysaccharides prime macrophages for enhanced release of arachidonic acid metabolites , 1986, The Journal of experimental medicine.
[22] Livia Perfetto,et al. MINT, the molecular interaction database: 2012 update , 2011, Nucleic Acids Res..
[23] Maria Keays,et al. ArrayExpress update—trends in database growth and links to data analysis tools , 2012, Nucleic Acids Res..
[24] Alistair G. Rust,et al. A FOXO3/IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses , 2012, Nature.
[25] Bastian R. Angermann,et al. Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses , 2008, The Journal of experimental medicine.
[26] Mark M. Davis,et al. Cell type–specific gene expression differences in complex tissues , 2010, Nature Methods.
[27] Nir Friedman,et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. , 2012, Molecular cell.
[28] Garnet Navarro,et al. miR-451 Regulates Dendritic Cell Cytokine Responses to Influenza Infection , 2012, The Journal of Immunology.
[29] T. Lawrence,et al. Anti-inflammatory lipid mediators and insights into the resolution of inflammation , 2002, Nature Reviews Immunology.
[30] B. Beutler,et al. A mutation of Ikbkg causes immune deficiency without impairing degradation of IκBα , 2010, Proceedings of the National Academy of Sciences.
[31] A. Bowie,et al. The family of five: TIR-domain-containing adaptors in Toll-like receptor signalling , 2007, Nature Reviews Immunology.
[32] U. Alon. Network motifs: theory and experimental approaches , 2007, Nature Reviews Genetics.
[33] Rules to 'prime' by , 2009, Nature Immunology.
[34] Adolfo García-Sastre,et al. The E3-ligase TRIM family of proteins regulates signaling pathways triggered by innate immune pattern-recognition receptors. , 2013, Immunity.
[35] Jacob T. Robinson,et al. Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits , 2011, Cell.
[36] Edward A Dennis,et al. The human plasma lipidome. , 2011, The New England journal of medicine.
[37] C. Serhan,et al. Metabolomics‐Lipidomics of Eicosanoids and Docosanoids Generated by Phagocytes , 2011, Current protocols in immunology.
[38] Michael G. Katze,et al. Into the Eye of the Cytokine Storm , 2012, Microbiology and Molecular Reviews.
[39] Gabriele Neumann,et al. Experimental adaptation of an influenza H5 haemagglutinin (HA) confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets , 2012, Nature.
[40] O. Ornatsky,et al. Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. , 2009, Analytical chemistry.
[41] Amarnath Gupta,et al. BiologicalNetworks 2.0 - an integrative view of genome biology data , 2010, BMC Bioinformatics.
[42] Kevin Marsh,et al. Four-year efficacy of RTS,S/AS01E and its interaction with malaria exposure. , 2013, The New England journal of medicine.
[43] Eva K. Lee,et al. Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans , 2009, Nature Immunology.
[44] Patrick G. Shaw,et al. C9orf72 Nucleotide Repeat Structures Initiate Molecular Cascades of Disease , 2014, Nature.
[45] R. Sugrue,et al. A systems-based approach to analyse the host response in murine lung macrophages challenged with respiratory syncytial virus , 2013, BMC Genomics.
[46] D. Greiner,et al. Humanized mice for immune system investigation: progress, promise and challenges , 2012, Nature Reviews Immunology.
[47] Daniel E. Zak,et al. Merck Ad5/HIV induces broad innate immune activation that predicts CD8+ T-cell responses but is attenuated by preexisting Ad5 immunity , 2012, Proceedings of the National Academy of Sciences.
[48] A. Amalfitano,et al. Expression of the SLAM Family of Receptors Adapter EAT-2 as a Novel Strategy for Enhancing Beneficial Immune Responses to Vaccine Antigens , 2011, The Journal of Immunology.
[49] Sandra Romero-Steiner,et al. Molecular signatures of antibody responses derived from a systems biology study of five human vaccines , 2022 .
[50] Zhining Wang,et al. Expression of genes associated with immunoproteasome processing of major histocompatibility complex peptides is indicative of protection with adjuvanted RTS,S malaria vaccine. , 2010, The Journal of infectious diseases.
[51] Richard Bonneau,et al. A Validated Regulatory Network for Th17 Cell Specification , 2012, Cell.
[52] Y. Jacob,et al. Exploration of Binary Virus–Host Interactions Using an Infectious Protein Complementation Assay* , 2013, Molecular & Cellular Proteomics.
[53] Chris T. A. Evelo,et al. WikiPathways: building research communities on biological pathways , 2011, Nucleic Acids Res..
[54] D. Underhill,et al. Fungal Recognition by TLR2 and Dectin-1. , 2008, Handbook of experimental pharmacology.
[55] Mario Roederer,et al. Single-cell gene-expression profiling reveals qualitatively distinct CD8 T cells elicited by different gene-based vaccines , 2011, Proceedings of the National Academy of Sciences.
[56] Lisa E. Gralinski,et al. Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection , 2011, mBio.
[57] C. Coban,et al. Host innate immune receptors and beyond: making sense of microbial infections. , 2008, Cell host & microbe.
[58] E. Dennis,et al. An integrated omics analysis of eicosanoid biology 1 , 2009 .
[59] Kylie M. Quinn,et al. CD8+ T Cell Responses following Replication-Defective Adenovirus Serotype 5 Immunization Are Dependent on CD11c+ Dendritic Cells but Show Redundancy in Their Requirement of TLR and Nucleotide-Binding Oligomerization Domain-Like Receptor Signaling , 2010, The Journal of Immunology.
[60] C. Goodnow,et al. ENU-mutagenesis: insight into immune function and pathology. , 2006, Current opinion in immunology.
[61] M. Katze,et al. H5N1 virus causes significant perturbations in host proteome very early in influenza virus-infected primary human monocyte-derived macrophages. , 2012, The Journal of infectious diseases.
[62] R. Gamelli,et al. Genomic responses in mouse models poorly mimic human inflammatory diseases , 2013, Proceedings of the National Academy of Sciences.
[63] Daniel E. Zak,et al. Overcoming limitations in the systems vaccinology approach: a pathway for accelerated HIV vaccine development. , 2012, Current opinion in HIV and AIDS.
[64] Sean C. Bendall,et al. From single cells to deep phenotypes in cancer , 2012, Nature Biotechnology.
[65] Garnet Navarro,et al. Differential Host Response, Rather Than Early Viral Replication Efficiency, Correlates with Pathogenicity Caused by Influenza Viruses , 2013, PloS one.
[66] S. Lockhart,et al. Safety and efficacy of MVA85A, a new tuberculosis vaccine, in infants previously vaccinated with BCG: a randomised, placebo-controlled phase 2b trial , 2013, The Lancet.
[67] Daniel Becker,et al. Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication , 2010, Nature.
[68] Kelly Domico,et al. Systems scale interactive exploration reveals quantitative and qualitative differences in response to influenza and pneumococcal vaccines. , 2013, Immunity.
[69] Eva K. Lee,et al. Systems Biology of Seasonal Influenza Vaccination in Humans , 2011, Nature Immunology.
[70] J. Sundberg,et al. Spontaneous mutations in the mouse Sharpin gene result in multiorgan inflammation, immune system dysregulation and dermatitis , 2007, Genes and Immunity.
[71] Ron Edgar,et al. Gene Expression Omnibus ( GEO ) : Microarray data storage , submission , retrieval , and analysis , 2008 .
[72] Joseph N. Brown,et al. Macaque Proteome Response to Highly Pathogenic Avian Influenza and 1918 Reassortant Influenza Virus Infections , 2010, Journal of Virology.
[73] Gary D. Bader,et al. Pathway Commons, a web resource for biological pathway data , 2010, Nucleic Acids Res..
[74] N. Hacohen,et al. A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection , 2009, Cell.
[75] B. Williams,et al. Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity , 2012, Cell.
[76] J. Kublin,et al. Safety and efficacy of the HVTN 503/Phambili study of a clade-B-based HIV-1 vaccine in South Africa: a double-blind, randomised, placebo-controlled test-of-concept phase 2b study. , 2011, The Lancet. Infectious diseases.
[77] Alan Aderem,et al. A microfluidic device for multiplexed protein detection in nano-liter volumes. , 2009, Analytical biochemistry.
[78] E. Davidson,et al. Transcriptional regulatory cascades in development: Initial rates, not steady state, determine network kinetics , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[79] Daniel E. Zak,et al. Systems analysis identifies an essential role for SHANK-associated RH domain-interacting protein (SHARPIN) in macrophage Toll-like receptor 2 (TLR2) responses , 2011, Proceedings of the National Academy of Sciences.
[80] J. Stender,et al. Epigenomic control of the innate immune response. , 2013, Current opinion in pharmacology.
[81] R. Sékaly,et al. Dissecting the HIV-specific immune response: a systems biology approach. , 2012, Current opinion in HIV and AIDS.
[82] C. Serhan,et al. Novel anti-inflammatory--pro-resolving mediators and their receptors. , 2011, Current topics in medicinal chemistry.
[83] Ernesto S. Nakayasu,et al. Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation , 2012, Molecular systems biology.
[84] Xinxia Peng,et al. Lethal Influenza Virus Infection in Macaques Is Associated with Early Dysregulation of Inflammatory Related Genes , 2009, PLoS pathogens.
[85] S. Plotkin,et al. Vaccines: correlates of vaccine-induced immunity. , 2008, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.
[86] Julian Parkhill,et al. Single-cell genomics , 2008, Nature Reviews Microbiology.
[87] Riet De Smet,et al. Advantages and limitations of current network inference methods , 2010, Nature Reviews Microbiology.
[88] Tamara Munzner,et al. Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation , 2007, Bioinform..
[89] Eoin Fahy,et al. LIPID MAPS online tools for lipid research , 2007, Nucleic Acids Res..
[90] L. Baum. Role of Humoral Immunity in Host Defense Against HIV , 2010, Current HIV/AIDS reports.
[91] K. Walters,et al. Francisella tularensis subsp. tularensis Induces a Unique Pulmonary Inflammatory Response: Role of Bacterial Gene Expression in Temporal Regulation of Host Defense Responses , 2013, PloS one.
[92] A. Halayko,et al. Response of Primary Human Airway Epithelial Cells to Influenza Infection: A Quantitative Proteomic Study , 2012, Journal of proteome research.
[93] J. Farrar,et al. Transcriptional response in the peripheral blood of patients infected with Salmonella enterica serovar Typhi , 2009, Proceedings of the National Academy of Sciences.
[94] D. Price,et al. Wrestling with the repertoire: The promise and perils of next generation sequencing for antigen receptors , 2012, European journal of immunology.
[95] Ron Shamir,et al. Functional genomic delineation of TLR-induced transcriptional networks , 2007, BMC Genomics.
[96] J Christopher Love,et al. A high-throughput single-cell analysis of human CD8⁺ T cell functions reveals discordance for cytokine secretion and cytolysis. , 2011, The Journal of clinical investigation.
[97] Y. Kong,et al. Mapping a dynamic innate immunity protein interaction network regulating type I interferon production. , 2011, Immunity.
[98] Eva K. Lee,et al. Analysis of the consistency of a mixed integer programming-based multi-category constrained discriminant model , 2010, Ann. Oper. Res..
[99] T. Miyakawa,et al. Genomic responses in mouse models poorly mimic human inflammatory diseases , 2013 .
[100] Rona S. Gertner,et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells , 2013, Nature.
[101] M. Katze,et al. Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Proteomics , 2006, Journal of Virology.
[102] Philip R. Johnson,et al. Accelerating Next-Generation Vaccine Development for Global Disease Prevention , 2013, Science.
[103] Y. Kawaoka,et al. The Lipid Mediator Protectin D1 Inhibits Influenza Virus Replication and Improves Severe Influenza , 2013, Cell.
[104] A. Sher,et al. Cooperation of Toll-like receptor signals in innate immune defence , 2007, Nature Reviews Immunology.
[105] Eric H Davidson,et al. A Gene Regulatory Network Subcircuit Drives a Dynamic Pattern of Gene Expression , 2007, Science.
[106] Daniel S. Chertow,et al. Lethal Synergism of 2009 Pandemic H1N1 Influenza Virus and Streptococcus pneumoniae Coinfection Is Associated with Loss of Murine Lung Repair Responses , 2011, mBio.
[107] Bin Li,et al. Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics , 2008, PLoS Comput. Biol..
[108] H. Kitano,et al. Software for systems biology: from tools to integrated platforms , 2011, Nature Reviews Genetics.
[109] A. Aderem,et al. Lipidomic Profiling of Influenza Infection Identifies Mediators that Induce and Resolve Inflammation , 2013, Cell.
[110] Rafael C. Jimenez,et al. The IntAct molecular interaction database in 2012 , 2011, Nucleic Acids Res..
[111] S. Akira,et al. Innate Immune Sensing of Modified Vaccinia Virus Ankara (MVA) Is Mediated by TLR2-TLR6, MDA-5 and the NALP3 Inflammasome , 2009, PLoS pathogens.
[112] C. Bakal,et al. Genomic screening with RNAi: results and challenges. , 2010, Annual review of biochemistry.
[113] J H Moore,et al. Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination , 2009, Genes and Immunity.
[114] Christie S. Chang,et al. The BioGRID interaction database: 2013 update , 2012, Nucleic Acids Res..
[115] A. Aderem,et al. A 2020 vision for vaccines against HIV, tuberculosis and malaria , 2011, Nature.
[116] Nir Hacohen,et al. Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach , 2012, Nature Immunology.
[117] E. Rosenberg,et al. Elite control of HIV infection: implications for vaccines , 2006, Retrovirology.
[118] Virginia Pascual,et al. A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus. , 2008, Immunity.
[119] A. O’Garra,et al. Tripartite-motif proteins and innate immune regulation. , 2011, Current opinion in immunology.
[120] Meghana Kulkarni. Digital multiplexed gene expression analysis using the NanoString nCounter system. , 2011, Current protocols in molecular biology.
[121] M. Roederer,et al. T-cell quality in memory and protection: implications for vaccine design , 2008, Nature Reviews Immunology.
[122] Charles N. Serhan,et al. Resolving inflammation: dual anti-inflammatory and pro-resolution lipid mediators , 2008, Nature Reviews Immunology.
[123] Joonsoo Kang,et al. Immunological Genome Project and systems immunology. , 2013, Trends in immunology.
[124] B. Palsson,et al. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions , 2010, Molecular systems biology.
[125] N. Friedman,et al. Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis , 2011, Cell.
[126] Rong Fan,et al. A Clinical Microchip for Evaluation of Single Immune Cells Reveals High Functional Heterogeneity in Phenotypically Similar T Cells Nih Public Access Author Manuscript Design Rationale and Detection Limit of the Scbc Online Methods Microchip Fabrication On-chip Secretion Profiling Supplementary Mater , 2022 .
[127] H. Zou,et al. Regularization and variable selection via the elastic net , 2005 .
[128] J. Schatzle,et al. Cutting Edge: The Adapters EAT-2A and -2B Are Positive Regulators of CD244- and CD84-Dependent NK Cell Functions in the C57BL/6 Mouse , 2010, The Journal of Immunology.
[129] Devan V Mehrotra,et al. Efficacy assessment of a cell-mediated immunity HIV-1 vaccine (the Step Study): a double-blind, randomised, placebo-controlled, test-of-concept trial , 2008, The Lancet.
[130] J. Stender,et al. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. , 2013, Molecular cell.
[131] V. Bajic,et al. Systems biology of innate immunity. , 2006, Cellular immunology.
[132] Adrian Ozinsky,et al. Phagocytosis of microbes: complexity in action. , 2002, Annual review of immunology.
[133] Arndt Benecke,et al. Systems biology of natural simian immunodeficiency virus infections. , 2012, Current opinion in HIV and AIDS.
[134] Mario Roederer,et al. Protection Against Malaria by Intravenous Immunization with a Nonreplicating Sporozoite Vaccine , 2013, Science.
[135] Jerome H. Kim,et al. Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand. , 2009, The New England journal of medicine.
[136] S. Kaufmann,et al. The dual role of biomarkers for understanding basic principles and devising novel intervention strategies in tuberculosis , 2013, Annals of the New York Academy of Sciences.
[137] Karen Sachs,et al. Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators , 2012, Nature Biotechnology.
[138] Bali Pulendran,et al. Yellow fever vaccine YF-17D activates multiple dendritic cell subsets via TLR2, 7, 8, and 9 to stimulate polyvalent immunity , 2006, The Journal of experimental medicine.
[139] Sean C. Bendall,et al. Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes. , 2012, Immunity.
[140] K. Ozato,et al. TRIM family proteins and their emerging roles in innate immunity , 2008, Nature Reviews Immunology.
[141] B. Autran,et al. Elite controllers as a model of functional cure , 2011, Current opinion in HIV and AIDS.
[142] B. Williams,et al. Functional classification of interferon‐stimulated genes identified using microarrays , 2001, Journal of leukocyte biology.
[143] Frederick Klauschen,et al. A Systems Analysis Identifies a Feedforward Inflammatory Circuit Leading to Lethal Influenza Infection , 2013, Cell.
[144] Anushya Muruganujan,et al. PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees , 2012, Nucleic Acids Res..
[145] Stephen R Quake,et al. Genomic analysis at the single-cell level. , 2011, Annual review of genetics.
[146] David E. Swayne,et al. Genomic analysis of increased host immune and cell death responses induced by 1918 influenza virus , 2006, Nature.
[147] E. Dennis,et al. Omega-3 fatty acids cause dramatic changes in TLR4 and purinergic eicosanoid signaling , 2012, Proceedings of the National Academy of Sciences.
[148] R. Medzhitov,et al. Toll-dependent selection of microbial antigens for presentation by dendritic cells , 2006, Nature.
[149] T. Aittokallio,et al. Quantitative Subcellular Proteome and Secretome Profiling of Influenza A Virus-Infected Human Primary Macrophages , 2011, PLoS pathogens.
[150] M. Tyers,et al. Osprey: a network visualization system , 2003, Genome Biology.
[151] Bernhard O. Palsson,et al. Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling , 2009, PLoS Comput. Biol..
[152] Kathleen A. Kennedy,et al. Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4 , 2006, Nature.
[153] Lincoln Stein,et al. Reactome: a database of reactions, pathways and biological processes , 2010, Nucleic Acids Res..
[154] R. Ahmed,et al. mTOR regulates memory CD8 T cell differentiation , 2009, Nature.
[155] Martin Meier-Schellersheim,et al. Systems biology in immunology: a computational modeling perspective. , 2011, Annual review of immunology.
[156] Stephen A Ramsey,et al. A systems biology approach to understanding atherosclerosis , 2010, EMBO molecular medicine.
[157] Alistair G. Rust,et al. Role of the transcription factor C/EBPδ in a regulatory circuit that discriminates between transient and persistent Toll-like receptor 4-induced signals , 2009, Nature Immunology.
[158] Stephen A. Ramsey,et al. Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites , 2010, Bioinform..
[159] Sandhya Rani,et al. Human Protein Reference Database—2009 update , 2008, Nucleic Acids Res..
[160] R. Germain,et al. Recent progress using systems biology approaches to better understand molecular mechanisms of immunity. , 2013, Seminars in immunology.