Social network architecture of human immune cells unveiled by quantitative proteomics
暂无分享,去创建一个
S. Shen-Orr | M. Mann | Daniel Hornburg | J. Rieckmann | R. Geiger | Tobias Wolf | Ksenya Kveler | D. Jarrossay | F. Sallusto | A. Lanzavecchia | F. Meissner
[1] C. Mackay,et al. Molecular cloning and characterization of a human eotaxin receptor expressed selectively on eosinophils , 1996, The Journal of experimental medicine.
[2] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[3] R. Tibshirani,et al. Significance analysis of microarrays applied to the ionizing radiation response , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[4] V. Appay. The physiological role of cytotoxic CD4+ T‐cells: the holy grail? , 2004, Clinical and experimental immunology.
[5] P. Farnham,et al. T-bet regulates the terminal maturation and homeostasis of NK and Valpha14i NKT cells. , 2004, Immunity.
[6] Jean YH Yang,et al. Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.
[7] Uri Alon,et al. The immune-body cytokine network defines a social architecture of cell interactions , 2006, Biology Direct.
[8] Eric Vivier,et al. Functions of natural killer cells , 2008, Nature Immunology.
[9] Steve Horvath,et al. WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.
[10] D. Koller,et al. The Immunological Genome Project: networks of gene expression in immune cells , 2008, Nature Immunology.
[11] Antal Rot,et al. CCR7 and its ligands: balancing immunity and tolerance , 2008, Nature Reviews Immunology.
[12] Eric E Schadt,et al. Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease. , 2009 .
[13] 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.
[14] Russ B. Altman,et al. Towards a Cytokine-Cell Interaction Knowledgebase of the Adaptive Immune System , 2008, Pacific Symposium on Biocomputing.
[15] Trevor Hastie,et al. Regularization Paths for Generalized Linear Models via Coordinate Descent. , 2010, Journal of statistical software.
[16] J. Epstein,et al. Persistence of effector memory Th1 cells is regulated by Hopx , 2010, European journal of immunology.
[17] M. Selbach,et al. Global quantification of mammalian gene expression control , 2011, Nature.
[18] Michael J. Bevan,et al. CD8+ T Cells: Foot Soldiers of the Immune System , 2011, Immunity.
[19] Sean C. Bendall,et al. Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum , 2011, Science.
[20] Michele Magrane,et al. UniProt Knowledgebase: a hub of integrated protein data , 2011, Database J. Biol. Databases Curation.
[21] N. Friedman,et al. Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis , 2011, Cell.
[22] M. Mann,et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. , 2011, Journal of proteome research.
[23] M. Mann,et al. System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap* , 2011, Molecular & Cellular Proteomics.
[24] David Z. Chen,et al. Architecture of the human regulatory network derived from ENCODE data , 2012, Nature.
[25] Charles C. Kim,et al. Molecular definition of the identity and activation of natural killer cells , 2012, Nature Immunology.
[26] Jürgen Cox,et al. 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data , 2012, BMC Bioinformatics.
[27] Sharline Madera,et al. The transcription factors T-bet and Eomes control key checkpoints of natural killer cell maturation. , 2012, Immunity.
[28] Katsuhiko Murakami,et al. PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from H-Invitational protein-protein interactions integrative dataset , 2012, BMC Systems Biology.
[29] Matthias Mann,et al. Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database , 2012, Molecular & Cellular Proteomics.
[30] Susumu Goto,et al. KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..
[31] D. Berg,et al. Stepwise isolation of human peripheral erythrocytes, T lymphocytes, and monocytes for blood cell proteomics , 2012, Proteomics. Clinical applications.
[32] Matthias Mann,et al. SprayQc: a real-time LC-MS/MS quality monitoring system to maximize uptime using off the shelf components. , 2012, Journal of proteome research.
[33] J. Thomason,et al. Ultra-pure platelet isolation from canine whole blood , 2013, BMC Veterinary Research.
[34] Johannes Griss,et al. The Proteomics Identifications (PRIDE) database and associated tools: status in 2013 , 2012, Nucleic Acids Res..
[35] Charles C. Kim,et al. Beyond the transcriptome: completion of act one of the Immunological Genome Project. , 2013, Current opinion in immunology.
[36] Or Zuk,et al. Identification of transcriptional regulators in the mouse immune system , 2013, Nature Immunology.
[37] Matthias Mann,et al. Direct Proteomic Quantification of the Secretome of Activated Immune Cells , 2013, Science.
[38] A. Heck,et al. Next-generation proteomics: towards an integrative view of proteome dynamics , 2012, Nature Reviews Genetics.
[39] M. Mann,et al. Cell-type-resolved quantitative proteomics of murine liver. , 2014, Cell metabolism.
[40] Gary D Bader,et al. A draft map of the human proteome , 2014, Nature.
[41] Roland Eils,et al. circlize implements and enhances circular visualization in R , 2014, Bioinform..
[42] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[43] Matthias Mann,et al. The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer* , 2014, Molecular & Cellular Proteomics.
[44] Marco Y. Hein,et al. A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards* , 2014, Molecular & Cellular Proteomics.
[45] Matthias Mann,et al. Quantitative shotgun proteomics: considerations for a high-quality workflow in immunology , 2014, Nature Immunology.
[46] Marco Y. Hein,et al. Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ * , 2014, Molecular & Cellular Proteomics.
[47] M. Mann,et al. Functional classification of memory CD8+ T cells by CX3CR1 expression , 2015, Nature Communications.
[48] K. Bieber,et al. Insights how monocytes and dendritic cells contribute and regulate immune defense against microbial pathogens. , 2015, Immunobiology.
[49] Z. Dembić. The cytokines of the immune system : the role of cytokines in disease related to immune response , 2015 .
[50] R. Germain,et al. Network representations of immune system complexity , 2015, Wiley interdisciplinary reviews. Systems biology and medicine.
[51] Davide Heller,et al. STRING v10: protein–protein interaction networks, integrated over the tree of life , 2014, Nucleic Acids Res..
[52] Chun Jimmie Ye,et al. A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks , 2015, Cell.
[53] Cytokines of the Immune System: Chemokines , 2015 .
[54] Matthias Mann,et al. Cell type– and brain region–resolved mouse brain proteome , 2015, Nature Neuroscience.
[55] Maxwell R. Mumbach,et al. Dynamic profiling of the protein life cycle in response to pathogens , 2015, Science.
[56] G. von Heijne,et al. Tissue-based map of the human proteome , 2015, Science.
[57] I. Amit,et al. Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors , 2015, Cell.
[58] Marco Y. Hein,et al. The Perseus computational platform for comprehensive analysis of (prote)omics data , 2016, Nature Methods.
[59] Ruedi Aebersold,et al. Mass-spectrometric exploration of proteome structure and function , 2016, Nature.
[60] G. Nolan,et al. Coordinate actions of innate immune responses oppose those of the adaptive immune system during Salmonella infection of mice , 2016, Science Signaling.
[61] Jüergen Cox,et al. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics , 2016, Nature Protocols.
[62] W. Gause,et al. Innate cell communication kick-starts pathogen-specific immunity , 2016, Nature Immunology.