Literature DB >> 24655298

Systems-level analysis of innate immunity.

Daniel E Zak1, Vincent C Tam, Alan Aderem.   

Abstract

Systems-level analysis of biological processes strives to comprehensively and quantitatively evaluate the interactions between the relevant molecular components over time, thereby enabling development of models that can be employed to ultimately predict behavior. Rapid development in measurement technologies (omics), when combined with the accessible nature of the cellular constituents themselves, is allowing the field of innate immunity to take significant strides toward this lofty goal. In this review, we survey exciting results derived from systems biology analyses of the immune system, ranging from gene regulatory networks to influenza pathogenesis and systems vaccinology.

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Year:  2014        PMID: 24655298      PMCID: PMC4084718          DOI: 10.1146/annurev-immunol-032713-120254

Source DB:  PubMed          Journal:  Annu Rev Immunol        ISSN: 0732-0582            Impact factor:   28.527


  157 in total

1.  Transcriptional response in the peripheral blood of patients infected with Salmonella enterica serovar Typhi.

Authors:  Lucinda J Thompson; Sarah J Dunstan; Christiane Dolecek; Tim Perkins; Deborah House; Gordon Dougan; Thi Hue Nguyen; Thi Phi La Tran; Cong Du Doan; Thi Phuong Le; Thi Dung Nguyen; Tinh Hien Tran; Jeremy J Farrar; Denise Monack; David J Lynn; Stephen J Popper; Stanley Falkow
Journal:  Proc Natl Acad Sci U S A       Date:  2009-12-11       Impact factor: 11.205

2.  Expression of genes associated with immunoproteasome processing of major histocompatibility complex peptides is indicative of protection with adjuvanted RTS,S malaria vaccine.

Authors:  Maryanne T Vahey; Zhining Wang; Kent E Kester; James Cummings; D Gray Heppner; Martin E Nau; Opokua Ofori-Anyinam; Joe Cohen; Thierry Coche; W Ripley Ballou; Christian F Ockenhouse
Journal:  J Infect Dis       Date:  2010-02-15       Impact factor: 5.226

3.  Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand.

Authors:  Supachai Rerks-Ngarm; Punnee Pitisuttithum; Sorachai Nitayaphan; Jaranit Kaewkungwal; Joseph Chiu; Robert Paris; Nakorn Premsri; Chawetsan Namwat; Mark de Souza; Elizabeth Adams; Michael Benenson; Sanjay Gurunathan; Jim Tartaglia; John G McNeil; Donald P Francis; Donald Stablein; Deborah L Birx; Supamit Chunsuttiwat; Chirasak Khamboonruang; Prasert Thongcharoen; Merlin L Robb; Nelson L Michael; Prayura Kunasol; Jerome H Kim
Journal:  N Engl J Med       Date:  2009-10-20       Impact factor: 91.245

4.  A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection.

Authors:  Sagi D Shapira; Irit Gat-Viks; Bennett O V Shum; Amelie Dricot; Marciela M de Grace; Liguo Wu; Piyush B Gupta; Tong Hao; Serena J Silver; David E Root; David E Hill; Aviv Regev; Nir Hacohen
Journal:  Cell       Date:  2009-12-24       Impact factor: 41.582

Review 5.  Thematic Review Series: Proteomics. An integrated omics analysis of eicosanoid biology.

Authors:  Matthew W Buczynski; Darren S Dumlao; Edward A Dennis
Journal:  J Lipid Res       Date:  2009-02-24       Impact factor: 5.922

6.  mTOR regulates memory CD8 T-cell differentiation.

Authors:  Koichi Araki; Alexandra P Turner; Virginia Oliva Shaffer; Shivaprakash Gangappa; Susanne A Keller; Martin F Bachmann; Christian P Larsen; Rafi Ahmed
Journal:  Nature       Date:  2009-06-21       Impact factor: 49.962

7.  Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals.

Authors:  Vladimir Litvak; Stephen A Ramsey; Alistair G Rust; Daniel E Zak; Kathleen A Kennedy; Aaron E Lampano; Matti Nykter; Ilya Shmulevich; Alan Aderem
Journal:  Nat Immunol       Date:  2009-03-08       Impact factor: 25.606

8.  Lethal influenza virus infection in macaques is associated with early dysregulation of inflammatory related genes.

Authors:  Cristian Cillóniz; Kyoko Shinya; Xinxia Peng; Marcus J Korth; Sean C Proll; Lauri D Aicher; Victoria S Carter; Jean H Chang; Darwyn Kobasa; Friedericke Feldmann; James E Strong; Heinz Feldmann; Yoshihiro Kawaoka; Michael G Katze
Journal:  PLoS Pathog       Date:  2009-10-02       Impact factor: 6.823

9.  Innate immune sensing of modified vaccinia virus Ankara (MVA) is mediated by TLR2-TLR6, MDA-5 and the NALP3 inflammasome.

Authors:  Julie Delaloye; Thierry Roger; Quynh-Giao Steiner-Tardivel; Didier Le Roy; Marlies Knaup Reymond; Shizuo Akira; Virginie Petrilli; Carmen E Gomez; Beatriz Perdiguero; Jürg Tschopp; Giuseppe Pantaleo; Mariano Esteban; Thierry Calandra
Journal:  PLoS Pathog       Date:  2009-06-19       Impact factor: 6.823

10.  Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses.

Authors:  Ido Amit; Manuel Garber; Nicolas Chevrier; Ana Paula Leite; Yoni Donner; Thomas Eisenhaure; Mitchell Guttman; Jennifer K Grenier; Weibo Li; Or Zuk; Lisa A Schubert; Brian Birditt; Tal Shay; Alon Goren; Xiaolan Zhang; Zachary Smith; Raquel Deering; Rebecca C McDonald; Moran Cabili; Bradley E Bernstein; John L Rinn; Alex Meissner; David E Root; Nir Hacohen; Aviv Regev
Journal:  Science       Date:  2009-09-03       Impact factor: 47.728

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  29 in total

Review 1.  Antiviral innate immunity through the lens of systems biology.

Authors:  Shashank Tripathi; Adolfo Garcia-Sastre
Journal:  Virus Res       Date:  2015-12-03       Impact factor: 3.303

2.  Systematic model of peripheral inflammation after subarachnoid hemorrhage.

Authors:  Jude P J Savarraj; Kaushik Parsha; Georgene W Hergenroeder; Liang Zhu; Suhas S Bajgur; Sungho Ahn; Kiwon Lee; Tiffany Chang; Dong H Kim; Yin Liu; H Alex Choi
Journal:  Neurology       Date:  2017-03-17       Impact factor: 9.910

3.  MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling.

Authors:  Kristin E Burnum-Johnson; Jennifer E Kyle; Amie J Eisfeld; Cameron P Casey; Kelly G Stratton; Juan F Gonzalez; Fabien Habyarimana; Nicholas M Negretti; Amy C Sims; Sadhana Chauhan; Larissa B Thackray; Peter J Halfmann; Kevin B Walters; Young-Mo Kim; Erika M Zink; Carrie D Nicora; Karl K Weitz; Bobbie-Jo M Webb-Robertson; Ernesto S Nakayasu; Brian Ahmer; Michael E Konkel; Vladimir Motin; Ralph S Baric; Michael S Diamond; Yoshihiro Kawaoka; Katrina M Waters; Richard D Smith; Thomas O Metz
Journal:  Analyst       Date:  2017-01-26       Impact factor: 4.616

4.  Transcriptional profiling of mouse B cell terminal differentiation defines a signature for antibody-secreting plasma cells.

Authors:  Wei Shi; Yang Liao; Simon N Willis; Nadine Taubenheim; Michael Inouye; David M Tarlinton; Gordon K Smyth; Philip D Hodgkin; Stephen L Nutt; Lynn M Corcoran
Journal:  Nat Immunol       Date:  2015-04-20       Impact factor: 25.606

5.  Immune promotive effect of bioactive peptides may be mediated by regulating the expression of SOCS1/miR-155.

Authors:  Caixia Chen; Xiulan Su; Zhiwei Hu
Journal:  Exp Ther Med       Date:  2019-07-05       Impact factor: 2.447

6.  Insights into archaeal chaperone machinery: a network-based approach.

Authors:  Shikha Rani; Ankush Sharma; Manisha Goel
Journal:  Cell Stress Chaperones       Date:  2018-09-03       Impact factor: 3.667

7.  PPARα exacerbates necroptosis, leading to increased mortality in postinfluenza bacterial superinfection.

Authors:  Vincent C Tam; Rosa Suen; Piper M Treuting; Aaron Armando; Ronald Lucarelli; Norma Gorrochotegui-Escalante; Alan H Diercks; Oswald Quehenberger; Edward A Dennis; Alan Aderem; Elizabeth S Gold
Journal:  Proc Natl Acad Sci U S A       Date:  2020-06-24       Impact factor: 11.205

8.  IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system.

Authors:  Matthew H Spitzer; Pier Federico Gherardini; Gabriela K Fragiadakis; Nupur Bhattacharya; Robert T Yuan; Andrew N Hotson; Rachel Finck; Yaron Carmi; Eli R Zunder; Wendy J Fantl; Sean C Bendall; Edgar G Engleman; Garry P Nolan
Journal:  Science       Date:  2015-07-10       Impact factor: 47.728

9.  Cell-type deconvolution with immune pathways identifies gene networks of host defense and immunopathology in leprosy.

Authors:  Megan S Inkeles; Rosane Mb Teles; Delila Pouldar; Priscila R Andrade; Cressida A Madigan; David Lopez; Mike Ambrose; Mahdad Noursadeghi; Euzenir N Sarno; Thomas H Rea; Maria T Ochoa; M Luisa Iruela-Arispe; William R Swindell; Tom Hm Ottenhoff; Annemieke Geluk; Barry R Bloom; Matteo Pellegrini; Robert L Modlin
Journal:  JCI Insight       Date:  2016-09-22

Review 10.  Animal Models for the Study of Nucleic Acid Immunity: Novel Tools and New Perspectives.

Authors:  Isabelle K Vila; Maxence Fretaud; Dimitrios Vlachakis; Nadine Laguette; Christelle Langevin
Journal:  J Mol Biol       Date:  2020-08-26       Impact factor: 5.469

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