Literature DB >> 32060427

A systems approach to infectious disease.

Manon Eckhardt1,2,3, Judd F Hultquist4,5,6,7, Robyn M Kaake1,2,3, Ruth Hüttenhain1,2,3, Nevan J Krogan8,9,10.   

Abstract

Ongoing social, political and ecological changes in the 21st century have placed more people at risk of life-threatening acute and chronic infections than ever before. The development of new diagnostic, prophylactic, therapeutic and curative strategies is critical to address this burden but is predicated on a detailed understanding of the immensely complex relationship between pathogens and their hosts. Traditional, reductionist approaches to investigate this dynamic often lack the scale and/or scope to faithfully model the dual and co-dependent nature of this relationship, limiting the success of translational efforts. With recent advances in large-scale, quantitative omics methods as well as in integrative analytical strategies, systems biology approaches for the study of infectious disease are quickly forming a new paradigm for how we understand and model host-pathogen relationships for translational applications. Here, we delineate a framework for a systems biology approach to infectious disease in three parts: discovery - the design, collection and analysis of omics data; representation - the iterative modelling, integration and visualization of complex data sets; and application - the interpretation and hypothesis-based inquiry towards translational outcomes.

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Year:  2020        PMID: 32060427      PMCID: PMC7839161          DOI: 10.1038/s41576-020-0212-5

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  140 in total

Review 1.  Systems biology: a brief overview.

Authors:  Hiroaki Kitano
Journal:  Science       Date:  2002-03-01       Impact factor: 47.728

Review 2.  Can laboratory reference strains mirror "real-world" pathogenesis?

Authors:  C A Fux; M Shirtliff; P Stoodley; J W Costerton
Journal:  Trends Microbiol       Date:  2005-02       Impact factor: 17.079

3.  Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis.

Authors:  Priya S Shah; Nichole Link; Gwendolyn M Jang; Phillip P Sharp; Tongtong Zhu; Danielle L Swaney; Jeffrey R Johnson; John Von Dollen; Holly R Ramage; Laura Satkamp; Billy Newton; Ruth Hüttenhain; Marine J Petit; Tierney Baum; Amanda Everitt; Orly Laufman; Michel Tassetto; Michael Shales; Erica Stevenson; Gabriel N Iglesias; Leila Shokat; Shashank Tripathi; Vinod Balasubramaniam; Laurence G Webb; Sebastian Aguirre; A Jeremy Willsey; Adolfo Garcia-Sastre; Katherine S Pollard; Sara Cherry; Andrea V Gamarnik; Ivan Marazzi; Jack Taunton; Ana Fernandez-Sesma; Hugo J Bellen; Raul Andino; Nevan J Krogan
Journal:  Cell       Date:  2018-12-13       Impact factor: 41.582

4.  The human proteome project: Current state and future direction.

Authors:  Pierre Legrain; Ruedi Aebersold; Alexander Archakov; Amos Bairoch; Kumar Bala; Laura Beretta; John Bergeron; Christoph Borchers; Garry L Corthals; Catherine E Costello; Eric W Deutsch; Bruno Domon; William Hancock; Fuchu He; Denis Hochstrasser; Gyorgy Marko-Varga; Ghasem Hosseini Salekdeh; Salvatore Sechi; Michael Snyder; Sudhir Srivastava; Mathias Uhlen; Cathy H Hu; Tadashi Yamamoto; Young-Ki Paik; Gilbert S Omenn
Journal:  Mol Cell Proteomics       Date:  2011-04-29       Impact factor: 5.911

5.  Quantitative Yeast Genetic Interaction Profiling of Bacterial Effector Proteins Uncovers a Role for the Human Retromer in Salmonella Infection.

Authors:  Kristin L Patrick; Jason A Wojcechowskyj; Samantha L Bell; Morgan N Riba; Tao Jing; Sara Talmage; Pengbiao Xu; Ana L Cabello; Jiewei Xu; Michael Shales; David Jimenez-Morales; Thomas A Ficht; Paul de Figueiredo; James E Samuel; Pingwei Li; Nevan J Krogan; Robert O Watson
Journal:  Cell Syst       Date:  2018-08-01       Impact factor: 10.304

6.  Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding.

Authors:  Shashank Tripathi; Marie O Pohl; Yingyao Zhou; Ariel Rodriguez-Frandsen; Guojun Wang; David A Stein; Hong M Moulton; Paul DeJesus; Jianwei Che; Lubbertus C F Mulder; Emilio Yángüez; Dario Andenmatten; Lars Pache; Balaji Manicassamy; Randy A Albrecht; Maria G Gonzalez; Quy Nguyen; Abraham Brass; Stephen Elledge; Michael White; Sagi Shapira; Nir Hacohen; Alexander Karlas; Thomas F Meyer; Michael Shales; Andre Gatorano; Jeffrey R Johnson; Gwen Jang; Tasha Johnson; Erik Verschueren; Doug Sanders; Nevan Krogan; Megan Shaw; Renate König; Silke Stertz; Adolfo García-Sastre; Sumit K Chanda
Journal:  Cell Host Microbe       Date:  2015-12-09       Impact factor: 21.023

7.  Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells.

Authors:  Bertram Bengsch; Takuya Ohtani; Omar Khan; Manu Setty; Sasikanth Manne; Shaun O'Brien; Pier Federico Gherardini; Ramin Sedaghat Herati; Alexander C Huang; Kyong-Mi Chang; Evan W Newell; Niels Bovenschen; Dana Pe'er; Steven M Albelda; E John Wherry
Journal:  Immunity       Date:  2018-05-15       Impact factor: 31.745

8.  Identification of host proteins required for HIV infection through a functional genomic screen.

Authors:  Abraham L Brass; Derek M Dykxhoorn; Yair Benita; Nan Yan; Alan Engelman; Ramnik J Xavier; Judy Lieberman; Stephen J Elledge
Journal:  Science       Date:  2008-01-10       Impact factor: 47.728

Review 9.  Multi-omics approaches to disease.

Authors:  Yehudit Hasin; Marcus Seldin; Aldons Lusis
Journal:  Genome Biol       Date:  2017-05-05       Impact factor: 13.583

10.  The variable quality of metadata about biological samples used in biomedical experiments.

Authors:  Rafael S Gonçalves; Mark A Musen
Journal:  Sci Data       Date:  2019-02-19       Impact factor: 6.444

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  34 in total

1.  Better together.

Authors: 
Journal:  Nat Rev Genet       Date:  2020-06       Impact factor: 53.242

2.  A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness.

Authors:  T J Sego; Josua O Aponte-Serrano; Juliano Ferrari Gianlupi; Samuel R Heaps; Kira Breithaupt; Lutz Brusch; Jessica Crawshaw; James M Osborne; Ellen M Quardokus; Richard K Plemper; James A Glazier
Journal:  PLoS Comput Biol       Date:  2020-12-21       Impact factor: 4.475

3.  Genetic interaction mapping informs integrative structure determination of protein complexes.

Authors:  Hannes Braberg; Ignacia Echeverria; Stefan Bohn; Peter Cimermancic; Anthony Shiver; Richard Alexander; Jiewei Xu; Michael Shales; Raghuvar Dronamraju; Shuangying Jiang; Gajendradhar Dwivedi; Derek Bogdanoff; Kaitlin K Chaung; Ruth Hüttenhain; Shuyi Wang; David Mavor; Riccardo Pellarin; Dina Schneidman; Joel S Bader; James S Fraser; John Morris; James E Haber; Brian D Strahl; Carol A Gross; Junbiao Dai; Jef D Boeke; Andrej Sali; Nevan J Krogan
Journal:  Science       Date:  2020-12-11       Impact factor: 47.728

4.  Impact of COVID-19 on paediatric admissions to a Chinese hospital: a single-centre retrospective chart review.

Authors:  Jie Zheng; Yan-Hui Chen
Journal:  BMJ Open       Date:  2022-07-04       Impact factor: 3.006

5.  RANBP2 and USP9x regulate nuclear import of adenovirus minor coat protein IIIa.

Authors:  Ashrafali M Ismail; Amrita Saha; Ji S Lee; David F Painter; Yinghua Chen; Gurdeep Singh; Gabriela N Condezo; James Chodosh; Carmen San Martín; Jaya Rajaiya
Journal:  PLoS Pathog       Date:  2022-06-16       Impact factor: 7.464

Review 6.  Application of Mathematical Modeling and Computational Tools in the Modern Drug Design and Development Process.

Authors:  Md Rifat Hasan; Ahad Amer Alsaiari; Burhan Zain Fakhurji; Mohammad Habibur Rahman Molla; Amer H Asseri; Md Afsar Ahmed Sumon; Moon Nyeo Park; Foysal Ahammad; Bonglee Kim
Journal:  Molecules       Date:  2022-06-29       Impact factor: 4.927

7.  A computational approach for detecting physiological homogeneity in the midst of genetic heterogeneity.

Authors:  Peng Zhang; Aurélie Cobat; Yoon-Seung Lee; Yiming Wu; Cigdem Sevim Bayrak; Clémentine Boccon-Gibod; Daniela Matuozzo; Lazaro Lorenzo; Aayushee Jain; Soraya Boucherit; Louis Vallée; Burkhard Stüve; Stéphane Chabrier; Jean-Laurent Casanova; Laurent Abel; Shen-Ying Zhang; Yuval Itan
Journal:  Am J Hum Genet       Date:  2021-05-19       Impact factor: 11.025

Review 8.  In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology.

Authors:  Juan D Chavez; Helisa H Wippel; Xiaoting Tang; Andrew Keller; James E Bruce
Journal:  Chem Rev       Date:  2021-07-07       Impact factor: 72.087

Review 9.  Multi-Omics Approaches in Immunological Research.

Authors:  Xiaojing Chu; Bowen Zhang; Valerie A C M Koeken; Manoj Kumar Gupta; Yang Li
Journal:  Front Immunol       Date:  2021-06-11       Impact factor: 7.561

Review 10.  Systems Biology Approaches for Therapeutics Development Against COVID-19.

Authors:  Shweta Jaiswal; Mohit Kumar; Yogendra Singh; Pratyoosh Shukla
Journal:  Front Cell Infect Microbiol       Date:  2020-10-28       Impact factor: 5.293

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