Literature DB >> 19576841

Virus-host interactions: from systems biology to translational research.

Xinxia Peng1, Eric Y Chan, Yu Li, Deborah L Diamond, Marcus J Korth, Michael G Katze.   

Abstract

Research embracing systems biology approaches and careful analysis of the critical host response has greatly expanded our understanding of infectious diseases. First-generation studies based on genomics and proteomics have made significant progress in establishing the foundation for network-based investigations on virus-host interactions. More recently, data from complementary high-throughput technologies, such as siRNA and microRNA screens and next-generation sequencing, are augmenting systems level analyses and are providing a more detailed and insightful multidimensional view of virus-host networks. Together with advances in data integration, systems biology approaches now have the potential to provide profound impacts on translational research, leading to the more rapid development of new therapeutics and vaccines for infectious diseases. In this review, we highlight new high-throughput technologies, a new philosophy for studying virus-host interactions, and discuss the potential of systems biology to facilitate bench-to-bedside research and create novel strategies to combat disease. Can we save the world using these approaches? Read on.

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Year:  2009        PMID: 19576841      PMCID: PMC2742299          DOI: 10.1016/j.mib.2009.06.003

Source DB:  PubMed          Journal:  Curr Opin Microbiol        ISSN: 1369-5274            Impact factor:   7.934


  31 in total

1.  Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Authors:  A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

2.  Epstein-Barr virus and virus human protein interaction maps.

Authors:  Michael A Calderwood; Kavitha Venkatesan; Li Xing; Michael R Chase; Alexei Vazquez; Amy M Holthaus; Alexandra E Ewence; Ning Li; Tomoko Hirozane-Kishikawa; David E Hill; Marc Vidal; Elliott Kieff; Eric Johannsen
Journal:  Proc Natl Acad Sci U S A       Date:  2007-04-19       Impact factor: 11.205

3.  HHMI's Med Into Grad Initiative expands.

Authors:  Stu Hutson
Journal:  Nat Med       Date:  2009-02       Impact factor: 53.440

Review 4.  The art and design of genetic screens: RNA interference.

Authors:  Michael Boutros; Julie Ahringer
Journal:  Nat Rev Genet       Date:  2008-06-03       Impact factor: 53.242

5.  Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Authors:  Ali Mortazavi; Brian A Williams; Kenneth McCue; Lorian Schaeffer; Barbara Wold
Journal:  Nat Methods       Date:  2008-05-30       Impact factor: 28.547

6.  Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis.

Authors:  Kristin C Gunsalus; Hui Ge; Aaron J Schetter; Debra S Goldberg; Jing-Dong J Han; Tong Hao; Gabriel F Berriz; Nicolas Bertin; Jerry Huang; Ling-Shiang Chuang; Ning Li; Ramamurthy Mani; Anthony A Hyman; Birte Sönnichsen; Christophe J Echeverri; Frederick P Roth; Marc Vidal; Fabio Piano
Journal:  Nature       Date:  2005-08-11       Impact factor: 49.962

7.  A dynamical model of human immune response to influenza A virus infection.

Authors:  Baris Hancioglu; David Swigon; Gilles Clermont
Journal:  J Theor Biol       Date:  2006-12-19       Impact factor: 2.691

8.  Network modeling links breast cancer susceptibility and centrosome dysfunction.

Authors:  Miguel Angel Pujana; Jing-Dong J Han; Lea M Starita; Kristen N Stevens; Muneesh Tewari; Jin Sook Ahn; Gad Rennert; Víctor Moreno; Tomas Kirchhoff; Bert Gold; Volker Assmann; Wael M Elshamy; Jean-François Rual; Douglas Levine; Laura S Rozek; Rebecca S Gelman; Kristin C Gunsalus; Roger A Greenberg; Bijan Sobhian; Nicolas Bertin; Kavitha Venkatesan; Nono Ayivi-Guedehoussou; Xavier Solé; Pilar Hernández; Conxi Lázaro; Katherine L Nathanson; Barbara L Weber; Michael E Cusick; David E Hill; Kenneth Offit; David M Livingston; Stephen B Gruber; Jeffrey D Parvin; Marc Vidal
Journal:  Nat Genet       Date:  2007-10-07       Impact factor: 38.330

Review 9.  Systems biology and the host response to viral infection.

Authors:  Seng-Lai Tan; Gopinath Ganji; Bryan Paeper; Sean Proll; Michael G Katze
Journal:  Nat Biotechnol       Date:  2007-12       Impact factor: 54.908

Review 10.  Virogenomics: the virus-host interaction revisited.

Authors:  Arno C Andeweg; Bart L Haagmans; Albert Dme Osterhaus
Journal:  Curr Opin Microbiol       Date:  2008-10-14       Impact factor: 7.934

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  28 in total

1.  The role of postmortem studies in pneumonia etiology research.

Authors:  Gareth D H Turner; Charatdao Bunthi; Chizoba B Wonodi; Susan C Morpeth; Catherine S Molyneux; Sherif R Zaki; Orin S Levine; David R Murdoch; J Anthony G Scott
Journal:  Clin Infect Dis       Date:  2012-04       Impact factor: 9.079

Review 2.  Systems immunogenetics of vaccines.

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

Review 3.  Unravelling the mechanisms of durable control of HIV-1.

Authors:  Bruce D Walker; Xu G Yu
Journal:  Nat Rev Immunol       Date:  2013-07       Impact factor: 53.106

4.  Quantitative modeling of virus evolutionary dynamics and adaptation in serial passages using empirically inferred fitness landscapes.

Authors:  Hyung Jun Woo; Jaques Reifman
Journal:  J Virol       Date:  2013-11-06       Impact factor: 5.103

5.  A comprehensive collection of systems biology data characterizing the host response to viral infection.

Authors:  Brian D Aevermann; Brett E Pickett; Sanjeev Kumar; Edward B Klem; Sudhakar Agnihothram; Peter S Askovich; Armand Bankhead; Meagen Bolles; Victoria Carter; Jean Chang; Therese R W Clauss; Pradyot Dash; Alan H Diercks; Amie J Eisfeld; Amy Ellis; Shufang Fan; Martin T Ferris; Lisa E Gralinski; Richard R Green; Marina A Gritsenko; Masato Hatta; Robert A Heegel; Jon M Jacobs; Sophia Jeng; Laurence Josset; Shari M Kaiser; Sara Kelly; G Lynn Law; Chengjun Li; Jiangning Li; Casey Long; Maria L Luna; Melissa Matzke; Jason McDermott; Vineet Menachery; Thomas O Metz; Hugh Mitchell; Matthew E Monroe; Garnet Navarro; Gabriele Neumann; Rebecca L Podyminogin; Samuel O Purvine; Carrie M Rosenberger; Catherine J Sanders; Athena A Schepmoes; Anil K Shukla; Amy Sims; Pavel Sova; Vincent C Tam; Nicolas Tchitchek; Paul G Thomas; Susan C Tilton; Allison Totura; Jing Wang; Bobbie-Jo Webb-Robertson; Ji Wen; Jeffrey M Weiss; Feng Yang; Boyd Yount; Qibin Zhang; Shannon McWeeney; Richard D Smith; Katrina M Waters; Yoshihiro Kawaoka; Ralph Baric; Alan Aderem; Michael G Katze; Richard H Scheuermann
Journal:  Sci Data       Date:  2014-10-14       Impact factor: 6.444

6.  Genomic analysis reveals pre- and postchallenge differences in a rhesus macaque AIDS vaccine trial: insights into mechanisms of vaccine efficacy.

Authors:  Robert E Palermo; L Jean Patterson; Lauri D Aicher; Marcus J Korth; Marjorie Robert-Guroff; Michael G Katze
Journal:  J Virol       Date:  2010-11-10       Impact factor: 5.103

7.  An atlas of the Epstein-Barr virus transcriptome and epigenome reveals host-virus regulatory interactions.

Authors:  Aaron Arvey; Italo Tempera; Kevin Tsai; Horng-Shen Chen; Nadezhda Tikhmyanova; Michael Klichinsky; Christina Leslie; Paul M Lieberman
Journal:  Cell Host Microbe       Date:  2012-08-16       Impact factor: 21.023

8.  Opportunities in proteomics to understand hepatitis C and HIV coinfection.

Authors:  Eric G Meissner; Anthony F Suffredini; Shyamasundaran Kottilil
Journal:  Future Virol       Date:  2012-08       Impact factor: 1.831

9.  Kaposi's sarcoma: a computational approach through protein-protein interaction and gene regulatory networks analysis.

Authors:  Aubhishek Zaman; Md Habibur Rahaman; Samsad Razzaque
Journal:  Virus Genes       Date:  2012-12-25       Impact factor: 2.332

10.  Temporal proteome and lipidome profiles reveal hepatitis C virus-associated reprogramming of hepatocellular metabolism and bioenergetics.

Authors:  Deborah L Diamond; Andrew J Syder; Jon M Jacobs; Christina M Sorensen; Kathie-Anne Walters; Sean C Proll; Jason E McDermott; Marina A Gritsenko; Qibin Zhang; Rui Zhao; Thomas O Metz; David G Camp; Katrina M Waters; Richard D Smith; Charles M Rice; Michael G Katze
Journal:  PLoS Pathog       Date:  2010-01-08       Impact factor: 6.823

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