Literature DB >> 27986392

Solving Immunology?

Yoram Vodovotz1, Ashley Xia2, Elizabeth L Read3, Josep Bassaganya-Riera4, David A Hafler5, Eduardo Sontag6, Jin Wang7, John S Tsang8, Judy D Day9, Steven H Kleinstein10, Atul J Butte11, Matthew C Altman12, Ross Hammond13, Stuart C Sealfon14.   

Abstract

Emergent responses of the immune system result from the integration of molecular and cellular networks over time and across multiple organs. High-content and high-throughput analysis technologies, concomitantly with data-driven and mechanistic modeling, hold promise for the systematic interrogation of these complex pathways. However, connecting genetic variation and molecular mechanisms to individual phenotypes and health outcomes has proven elusive. Gaps remain in data, and disagreements persist about the value of mechanistic modeling for immunology. Here, we present the perspectives that emerged from the National Institute of Allergy and Infectious Disease (NIAID) workshop 'Complex Systems Science, Modeling and Immunity' and subsequent discussions regarding the potential synergy of high-throughput data acquisition, data-driven modeling, and mechanistic modeling to define new mechanisms of immunological disease and to accelerate the translation of these insights into therapies.
Copyright © 2016 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  autoimmune disease; conference; mathematical modeling; personalized medicine; translation

Mesh:

Year:  2016        PMID: 27986392      PMCID: PMC5695553          DOI: 10.1016/j.it.2016.11.006

Source DB:  PubMed          Journal:  Trends Immunol        ISSN: 1471-4906            Impact factor:   16.687


  73 in total

Review 1.  Systems immunology: a survey of modeling formalisms, applications and simulation tools.

Authors:  Vipin Narang; James Decraene; Shek-Yoon Wong; Bindu S Aiswarya; Andrew R Wasem; Shiang Rong Leong; Alexandre Gouaillard
Journal:  Immunol Res       Date:  2012-09       Impact factor: 2.829

2.  In silico experiments of existing and hypothetical cytokine-directed clinical trials using agent-based modeling.

Authors:  Gary An
Journal:  Crit Care Med       Date:  2004-10       Impact factor: 7.598

3.  An integrative genomics approach to infer causal associations between gene expression and disease.

Authors:  Eric E Schadt; John Lamb; Xia Yang; Jun Zhu; Steve Edwards; Debraj Guhathakurta; Solveig K Sieberts; Stephanie Monks; Marc Reitman; Chunsheng Zhang; Pek Yee Lum; Amy Leonardson; Rolf Thieringer; Joseph M Metzger; Liming Yang; John Castle; Haoyuan Zhu; Shera F Kash; Thomas A Drake; Alan Sachs; Aldons J Lusis
Journal:  Nat Genet       Date:  2005-06-19       Impact factor: 38.330

4.  Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes.

Authors:  Evan W Newell; Natalia Sigal; Sean C Bendall; Garry P Nolan; Mark M Davis
Journal:  Immunity       Date:  2012-01-27       Impact factor: 31.745

5.  A mathematical simulation of the inflammatory response to anthrax infection.

Authors:  Rukmini Kumar; Carson C Chow; John D Bartels; Gilles Clermont; Yoram Vodovotz
Journal:  Shock       Date:  2008-01       Impact factor: 3.454

6.  Computational Analysis Supports an Early, Type 17 Cell-Associated Divergence of Blunt Trauma Survival and Mortality.

Authors:  Andrew Abboud; Rami A Namas; Mostafa Ramadan; Qi Mi; Khalid Almahmoud; Othman Abdul-Malak; Nabil Azhar; Akram Zaaqoq; Rajaie Namas; Derek A Barclay; Jinling Yin; Jason Sperry; Andrew Peitzman; Ruben Zamora; Richard L Simmons; Timothy R Billiar; Yoram Vodovotz
Journal:  Crit Care Med       Date:  2016-11       Impact factor: 7.598

7.  High production rates sustain in vivo levels of PD-1high simian immunodeficiency virus-specific CD8 T cells in the face of rapid clearance.

Authors:  Constantinos Petrovas; Takuya Yamamoto; David A Price; Srinivas S Rao; Nichole R Klatt; Jason M Brenchley; Daniel C Douek; Emma Gostick; Bastian R Angermann; Zvi Grossman; Derek C Macallan; Martin Meier-Schellersheim; Richard A Koup
Journal:  J Virol       Date:  2013-07-03       Impact factor: 5.103

8.  A global reference for human genetic variation.

Authors:  Adam Auton; Lisa D Brooks; Richard M Durbin; Erik P Garrison; Hyun Min Kang; Jan O Korbel; Jonathan L Marchini; Shane McCarthy; Gil A McVean; Gonçalo R Abecasis
Journal:  Nature       Date:  2015-10-01       Impact factor: 49.962

9.  Control of RelB during dendritic cell activation integrates canonical and noncanonical NF-κB pathways.

Authors:  Vincent F-S Shih; Jeremy Davis-Turak; Monica Macal; Jenny Q Huang; Julia Ponomarenko; Jeffrey D Kearns; Tony Yu; Riku Fagerlund; Masataka Asagiri; Elina I Zuniga; Alexander Hoffmann
Journal:  Nat Immunol       Date:  2012-10-21       Impact factor: 25.606

10.  Dynamics of immune escape during HIV/SIV infection.

Authors:  Christian L Althaus; Rob J De Boer
Journal:  PLoS Comput Biol       Date:  2008-07-18       Impact factor: 4.475

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  17 in total

Review 1.  Applications of mechanistic modelling to clinical and experimental immunology: an emerging technology to accelerate immunotherapeutic discovery and development.

Authors:  L V Brown; E A Gaffney; J Wagg; M C Coles
Journal:  Clin Exp Immunol       Date:  2018-09       Impact factor: 4.330

Review 2.  A case for the reuse and adaptation of mechanistic computational models to study transplant immunology.

Authors:  Miguel Fribourg
Journal:  Am J Transplant       Date:  2019-10-23       Impact factor: 8.086

3.  High-resolution computational modeling of immune responses in the gut.

Authors:  Meghna Verma; Josep Bassaganya-Riera; Andrew Leber; Nuria Tubau-Juni; Stefan Hoops; Vida Abedi; Xi Chen; Raquel Hontecillas
Journal:  Gigascience       Date:  2019-06-01       Impact factor: 6.524

4.  Agents and networks to model the dynamic interactions of intracellular transport.

Authors:  Luis S Mayorga; Meghna Verma; Raquel Hontecillas; Stefan Hoops; Josep Bassaganya-Riera
Journal:  Cell Logist       Date:  2017-11-29

Review 5.  Systems biology of malaria explored with nonhuman primates.

Authors:  Mary R Galinski
Journal:  Malar J       Date:  2022-06-07       Impact factor: 3.469

6.  Sepsis reconsidered: Identifying novel metrics for behavioral landscape characterization with a high-performance computing implementation of an agent-based model.

Authors:  Chase Cockrell; Gary An
Journal:  J Theor Biol       Date:  2017-07-18       Impact factor: 2.691

7.  Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria.

Authors:  Thomas J Hall; Michael P Mullen; Gillian P McHugo; Kate E Killick; Siobhán C Ring; Donagh P Berry; Carolina N Correia; John A Browne; Stephen V Gordon; David E MacHugh
Journal:  BMC Genomics       Date:  2021-05-12       Impact factor: 3.969

8.  Toll-Like Receptor 4 on both Myeloid Cells and Dendritic Cells Is Required for Systemic Inflammation and Organ Damage after Hemorrhagic Shock with Tissue Trauma in Mice.

Authors:  Kent Zettel; Sebastian Korff; Ruben Zamora; Adrian E Morelli; Sophie Darwiche; Patricia A Loughran; Greg Elson; Limin Shang; Susana Salgado-Pires; Melanie J Scott; Yoram Vodovotz; Timothy R Billiar
Journal:  Front Immunol       Date:  2017-11-28       Impact factor: 7.561

9.  Modulation of Immune Signaling and Metabolism Highlights Host and Fungal Transcriptional Responses in Mouse Models of Invasive Pulmonary Aspergillosis.

Authors:  Shiv D Kale; Tariq Ayubi; Dawoon Chung; Nuria Tubau-Juni; Andrew Leber; Ha X Dang; Saikumar Karyala; Raquel Hontecillas; Christopher B Lawrence; Robert A Cramer; Josep Bassaganya-Riera
Journal:  Sci Rep       Date:  2017-12-06       Impact factor: 4.379

10.  Molecular design of the γδT cell receptor ectodomain encodes biologically fit ligand recognition in the absence of mechanosensing.

Authors:  Robert J Mallis; Jonathan S Duke-Cohan; Dibyendu Kumar Das; Aoi Akitsu; Adrienne M Luoma; Debasis Banik; Hannah M Stephens; Paul W Tetteh; Caitlin D Castro; Sophie Krahnke; Rebecca E Hussey; Brian Lawney; Kristine N Brazin; Pedro A Reche; Wonmuk Hwang; Erin J Adams; Matthew J Lang; Ellis L Reinherz
Journal:  Proc Natl Acad Sci U S A       Date:  2021-06-29       Impact factor: 11.205

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