Literature DB >> 19120490

Systems biology of innate immunity.

Daniel E Zak1, Alan Aderem.   

Abstract

Systems biology is the comprehensive and quantitative analysis of the interactions between all of the components of biological systems over time. Systems biology involves an iterative cycle, in which emerging biological problems drive the development of new technologies and computational tools. These technologies and tools then open new frontiers that revolutionize biology. Innate immunity is well suited for systems analysis, because the relevant cells can be isolated in various functional states and their interactions can be reconstituted in a biologically meaningful manner. Application of the tools of systems biology to the innate immune system will enable comprehensive analysis of the complex interactions that maintain the difficult balance between host defense and inflammatory disease. In this review, we discuss innate immunity in the context of the systems biology concepts, emergence, robustness, and modularity, and we describe emerging technologies we are applying in our systems-level analyses. These technologies include genomics, proteomics, computational analysis, forward genetics screens, and analyses that link human genetic polymorphisms to disease resistance.

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Year:  2009        PMID: 19120490      PMCID: PMC2697920          DOI: 10.1111/j.1600-065X.2008.00721.x

Source DB:  PubMed          Journal:  Immunol Rev        ISSN: 0105-2896            Impact factor:   12.988


  133 in total

1.  A20 is a negative regulator of IFN regulatory factor 3 signaling.

Authors:  Tatsuya Saitoh; Masahiro Yamamoto; Makoto Miyagishi; Kazunari Taira; Makoto Nakanishi; Takashi Fujita; Shizuo Akira; Naoki Yamamoto; Shoji Yamaoka
Journal:  J Immunol       Date:  2005-02-01       Impact factor: 5.422

2.  Phagosome maturation proceeds independently of stimulation of toll-like receptors 2 and 4.

Authors:  Robin M Yates; David G Russell
Journal:  Immunity       Date:  2005-10       Impact factor: 31.745

3.  Dizzy: stochastic simulation of large-scale genetic regulatory networks.

Authors:  Stephen Ramsey; David Orrell; Hamid Bolouri
Journal:  J Bioinform Comput Biol       Date:  2005-04       Impact factor: 1.122

Review 4.  Negative regulation of toll-like receptor-mediated immune responses.

Authors:  Foo Y Liew; Damo Xu; Elizabeth K Brint; Luke A J O'Neill
Journal:  Nat Rev Immunol       Date:  2005-06       Impact factor: 53.106

5.  Nova regulates brain-specific splicing to shape the synapse.

Authors:  Jernej Ule; Aljaz Ule; Joanna Spencer; Alan Williams; Jing-Shan Hu; Melissa Cline; Hui Wang; Tyson Clark; Claire Fraser; Matteo Ruggiu; Barry R Zeeberg; David Kane; John N Weinstein; John Blume; Robert B Darnell
Journal:  Nat Genet       Date:  2005-07-24       Impact factor: 38.330

6.  Reverse engineering of regulatory networks in human B cells.

Authors:  Katia Basso; Adam A Margolin; Gustavo Stolovitzky; Ulf Klein; Riccardo Dalla-Favera; Andrea Califano
Journal:  Nat Genet       Date:  2005-03-20       Impact factor: 38.330

7.  The evolution of vertebrate Toll-like receptors.

Authors:  Jared C Roach; Gustavo Glusman; Lee Rowen; Amardeep Kaur; Maureen K Purcell; Kelly D Smith; Leroy E Hood; Alan Aderem
Journal:  Proc Natl Acad Sci U S A       Date:  2005-06-23       Impact factor: 11.205

Review 8.  Salmonella flagellin, a microbial target of the innate and adaptive immune system.

Authors:  Rosa Maria Salazar-Gonzalez; Stephen J McSorley
Journal:  Immunol Lett       Date:  2005-06-06       Impact factor: 3.685

9.  A RING-type ubiquitin ligase family member required to repress follicular helper T cells and autoimmunity.

Authors:  Carola G Vinuesa; Matthew C Cook; Constanza Angelucci; Vicki Athanasopoulos; Lixin Rui; Kim M Hill; Di Yu; Heather Domaschenz; Belinda Whittle; Teresa Lambe; Ian S Roberts; Richard R Copley; John I Bell; Richard J Cornall; Christopher C Goodnow
Journal:  Nature       Date:  2005-05-26       Impact factor: 49.962

10.  Toll-like receptor 4 polymorphisms are associated with resistance to Legionnaires' disease.

Authors:  Thomas R Hawn; Annelies Verbon; Marta Janer; Lue Ping Zhao; Bruce Beutler; Alan Aderem
Journal:  Proc Natl Acad Sci U S A       Date:  2005-02-07       Impact factor: 11.205

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  77 in total

1.  Polyfunctional responses by human T cells result from sequential release of cytokines.

Authors:  Qing Han; Neda Bagheri; Elizabeth M Bradshaw; David A Hafler; Douglas A Lauffenburger; J Christopher Love
Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-12       Impact factor: 11.205

2.  Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients.

Authors:  Thomas Köcher; Peter Pichler; Remco Swart; Karl Mechtler
Journal:  Nat Protoc       Date:  2012-04-12       Impact factor: 13.491

Review 3.  Systems immunogenetics of vaccines.

Authors:  Michael Mooney; Shannon McWeeney; Rafick-Pierre Sékaly
Journal:  Semin Immunol       Date:  2013-07-22       Impact factor: 11.130

4.  Systemic Inflammation during the First Postnatal Month and the Risk of Attention Deficit Hyperactivity Disorder Characteristics among 10 year-old Children Born Extremely Preterm.

Authors:  Elizabeth N Allred; Olaf Dammann; Raina N Fichorova; Stephen R Hooper; Scott J Hunter; Robert M Joseph; Karl Kuban; Alan Leviton; Thomas Michael O'Shea; Megan N Scott
Journal:  J Neuroimmune Pharmacol       Date:  2017-04-12       Impact factor: 4.147

Review 5.  New approaches to design HIV-1 T-cell vaccines.

Authors:  Hélène Perrin; Glenda Canderan; Rafick-Pierre Sékaly; Lydie Trautmann
Journal:  Curr Opin HIV AIDS       Date:  2010-09       Impact factor: 4.283

Review 6.  Systems-level analysis of innate immunity.

Authors:  Daniel E Zak; Vincent C Tam; Alan Aderem
Journal:  Annu Rev Immunol       Date:  2014       Impact factor: 28.527

Review 7.  Revealing the molecular signatures of host-pathogen interactions.

Authors:  Chiea-Chuen Khor; Martin L Hibberd
Journal:  Genome Biol       Date:  2011-10-19       Impact factor: 13.583

Review 8.  The top five "game changers" in vaccinology: toward rational and directed vaccine development.

Authors:  Richard B Kennedy; Gregory A Poland
Journal:  OMICS       Date:  2011-08-04

Review 9.  Navigating the network: signaling cross-talk in hematopoietic cells.

Authors:  Iain D C Fraser; Ronald N Germain
Journal:  Nat Immunol       Date:  2009-03-19       Impact factor: 25.606

10.  Antecedents of inflammation biomarkers in preterm newborns on days 21 and 28.

Authors:  Alan Leviton; Elizabeth N Allred; Raina N Fichorova; Karl C K Kuban; T Michael O'Shea; Olaf Dammann
Journal:  Acta Paediatr       Date:  2015-12-23       Impact factor: 2.299

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