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A computational method for predicting regulation of human microRNAs on the influenza virus genome

Hao Zhang, Zhi Li, Yanpu Li, Yuanning Liu, Junxin Liu, Xin Li, Tingjie Shen, Yunna Duan, Minggang Hu, Dong Xu
2013 BMC Systems Biology  
While it has been suggested that host microRNAs (miRNAs) may downregulate viral gene expression as an antiviral defense mechanism, such a mechanism has not been explored in the influenza virus for human  ...  Although many computational tools have been designed for miRNA target prediction, there is a need for cross-species prediction, especially for predicting viral targets of human miRNAs.  ...  Acknowledgements "Human encoded miRNAs that regulate the influenza virus genome" A preliminary version of this paper was published in the proceedings of Proceedings of 2012 IEEE 6th International Conference  ... 
doi:10.1186/1752-0509-7-s2-s3 pmid:24565017 pmcid:PMC3851852 fatcat:n5w2grc5m5as3mixbg77eostay

Prediction of Site Directed miRNAs as Key Players of Transcriptional Regulators Against Influenza C Virus Infection Through Computational Approaches

Mubashir Hassan, Muhammad Shahzad Iqbal, Sawaira Naqvi, Hany Alashwal, Ahmed A. Moustafa, Andrzej Kloczkowski
2022 Frontiers in Molecular Biosciences  
Further steps to use these microRNAs may lead to new therapeutic insights on fighting influenza virus infection.  ...  In this study, we have used the computational tools, RNA22, RNAhybrid, and miRanda, to predict the microRNA-mRNA binding sites to find the putative microRNAs playing role in the host response to influenza  ...  AUTHOR CONTRIBUTIONS MH and MSI were performed experiments and wrote the initial draft of the manuscript. SN collected data. HA, AM, and AK edited the manuscript and compiled it into final format.  ... 
doi:10.3389/fmolb.2022.866072 pmid:35463952 pmcid:PMC9023806 fatcat:df5nsjotorcunho3qgfeoqieze

Prediction of Ebolavirus Genomes Encoded MicroRNA-Like Small RNAs Using Bioinformatics Approaches [chapter]

Yue Teng, Zhe Xu, Jin Yuan, Xiaoping An, Jiangman Song, Dan Feng
2016 Ebola  
In this chapter, the negative-sense RNA genome of Ebola virus (EBOV) was scanned using bioinformatics tools to predict the EBOV-encoded microRNA-like small RNAs.  ...  In conclusion, systematic investigation of microRNA-like small RNAs in EBOV genome may shed light on the underlying molecular mechanisms of the pathological process of Ebola virus disease (EVD).  ...  Acknowledgements This work was supported by a grant from the State Key Laboratory of Pathogen and BioSecurity Program (No. SKLPBS1408 and No. SKLPBS1451).  ... 
doi:10.5772/62944 fatcat:jgpkegx7x5aspn3ijj5mlzij3e

Host-virus interaction: a new role for microRNAs

Vinod Scaria, Manoj Hariharan, Souvik Maiti, Beena Pillai, Samir K Brahmachari
2006 Retrovirology  
The exclusive dependence of viruses on the host cellular machinery for their propagation and survival also make them highly susceptible to the vagaries of the cellular environment like small RNA mediated  ...  MicroRNAs (miRNAs) are a new class of 18-23 nucleotide long non-coding RNAs that play critical roles in a wide spectrum of biological processes.  ...  Authors also acknowledge the Council of Scientific and Industrial Research (CSIR), India for funding through Task Force Project CMM0017. VS acknowledges the Senior Research Fellowship from CSIR.  ... 
doi:10.1186/1742-4690-3-68 pmid:17032463 pmcid:PMC1626483 fatcat:wqtrioybwnhw5ctfygjukhnpte

Virus–host interactions: from systems biology to translational research

Xinxia Peng, Eric Y Chan, Yu Li, Deborah L Diamond, Marcus J Korth, Michael G Katze
2009 Current Opinion in Microbiology  
First-generation studies based on genomics and proteomics have made significant progress in establishing the foundation for networkbased investigations on virus-host interactions.  ...  In this review, we highlight new high-throughput technologies, a new philosophy for studying virushost interactions, and discuss the potential of systems biology to facilitate bench-to-bedside research  ...  We thank Matt Dyer for insightful suggestions and assistance with the preparation of the manuscript.  ... 
doi:10.1016/j.mib.2009.06.003 pmid:19576841 pmcid:PMC2742299 fatcat:ylka32m3ezdypov3gcem2q2gde

Systems virology: host-directed approaches to viral pathogenesis and drug targeting

G. Lynn Law, Marcus J. Korth, Arndt G. Benecke, Michael G. Katze
2013 Nature Reviews Microbiology  
Here, we provide a snapshot of the evolution of systems virology, from global gene expression profiling and signatures of disease outcome, to geometry-based computational methods that promise to yield  ...  In the past decade, tools have become available to chart a new course, one directed at obtaining comprehensive systems-level views of the host response and the interplay between virus and host.  ...  Acknowledgements The authors thank L. Josset for generating the networks in figure 3 , and M. Heise and M. Ferris for providing the data used in box 3.  ... 
doi:10.1038/nrmicro3036 pmid:23728212 pmcid:PMC4028060 fatcat:yk674zd7hzevladttnwmdgrjdi

High-Throughput MicroRNA Profiles of Permissive Madin-Darby Canine Kidney Cell Line Infected with Influenza B Viruses

Saengchoowong, Khongnomnan, Poomipak, Praianantathavorn, Poovorawan, Zhang, Payungporn
2019 Viruses  
This study provides canine microRNA responses to seasonal influenza B viruses, suggesting that virus-mediated microRNAs might play crucial roles in host gene regulation.  ...  Therefore, the present study aims at high-throughput analysis of canine microRNA profile upon infection of influenza B viruses.  ...  In the previous years, microRNAs' response to infection of influenza A viruses has been extensively studied in human cells.  ... 
doi:10.3390/v11110986 pmid:31717720 pmcid:PMC6893747 fatcat:jfhlctwio5euvlkk5amvze5oa4

microRNAs in Circulation Are Altered in Response to Influenza A Virus Infection in Humans

Paul A. Tambyah, Sugunavathi Sepramaniam, Jaminah Mohamed Ali, Siaw Ching Chai, Priyadharshini Swaminathan, Arunmozhiarasi Armugam, Kandiah Jeyaseelan, Danny Barash
2013 PLoS ONE  
Potential host and viral gene targets were identified and the impact of microRNA dysregulation on the host proteome was studied.  ...  signature microRNAs to better understand the gene regulation involved and possibly improve diagnosis.  ...  Introduction Influenza A viruses cause disease in birds and a number of mammalian species including humans.  ... 
doi:10.1371/journal.pone.0076811 pmid:24116168 pmcid:PMC3792094 fatcat:qcnlzsavqffcth4djbrsbaf74q

Small RNA Profiling of Influenza A Virus-Infected Cells Identifies miR-449b as a Regulator of Histone Deacetylase 1 and Interferon Beta

William A. Buggele, Katherine E. Krause, Curt M. Horvath, Andrew Pekosz
2013 PLoS ONE  
These findings demonstrate miRNA induction by influenza A virus infection and elucidate an example of miRNA control of antiviral gene expression in human cells, defining a role for miR-449b in regulation  ...  To determine the potential for miRNA regulation of cellular responses to influenza A virus infection, small RNA profiling was carried out using next generation sequencing.  ...  Acknowledgements We would like to thank members of the Horvath lab for critical and helpful discussions, Dr. Robert A. Lamb for the generous gift of influenza virus strains, Dr.  ... 
doi:10.1371/journal.pone.0076560 pmid:24086750 pmcid:PMC3784411 fatcat:aqgqy74m7bc73phpfogt3we3wa

Human encoded miRNAs that regulate the inflenenza virus genome

Hao Zhang, Xin Li, Yuaning Liu, Zhi Li, Minggang Hu, Dong Xu
2012 2012 IEEE 6th International Conference on Systems Biology (ISB)  
Methods: We propose a new method based on scoring to discover human encoded miRNAs that regulate the influenza virus genome.  ...  Discovering human encoded miRNAs that regulate the influenza virus genome is important for molecular targets for drug development, and it also plays positive role in influenza control and prevention.  ...  Consequently, it is of great significance to study on host-virus interactions. Here we propose a method based on scoring to discover human encoded miRNAs which have targets in influenza virus genome.  ... 
doi:10.1109/isb.2012.6314107 dblp:conf/isb/ZhangLLLHX12 fatcat:i7h4db4lubh4zjmakshrxffbi4

Bioinformatic Evaluation of the miRNAs Targeting ACE2 Gene in COVID-19

Milad Rafat, Aida Roshan, Mahya Abyar, Saba Keramati, Amin Reza Nikpoor
2021 Disease and Diagnosis  
Then, a score table was prepared from the candidate microRNAs, based on the affinity of the seed region of microRNAs and the 3'-UTR region of the ACE2 gene.  ...  ACE2 is abundantly expressed in different cells of different human organs. In human physiology, ACE2 is a major player in the renin-angiotensin-aldosterone (RAAS) system by degrading angiotensin II.  ...  We thank our colleagues from the Student Research Committee for providing insight and expertise that greatly assisted the research although they may not agree with all the  ... 
doi:10.34172/ddj.2021.26 fatcat:eifpxv5x6rgw5c63hw5uoxjh4q

The role of microRNAs in respiratory viral infection: friend or foe?

Alireza Tahamtan, Christopher S. Inchley, Mona Marzban, Masoumeh Tavakoli-Yaraki, Majid Teymoori-Rad, Britt Nakstad, Vahid Salimi
2016 Reviews in Medical Virology  
Our review supports the emerging concept that cellular and viral-encoded miRNAs might be broadly implicated in human respiratory viral infections, with either positive or negative effects on virus life  ...  factors for respiratory viral infectious disease caused by a variety of agents.  ...  ACKNOWLEDGEMENTS This work was supported by Iran University of Medical Sciences Grant (28601).  ... 
doi:10.1002/rmv.1894 pmid:27373545 fatcat:aq5ahwdwujealoigejcwuymfwu

The roles of microRNAs in mammalian virus infection

2008 Biochimica et Biophysica Acta. Gene Regulatory Mechanisms  
MicroRNAs (miRNAs) are post transcriptional regulators of gene expression that are important for the control of a multitude of critical processes in mammalian cells.  ...  Expression of miRNAs has been reported for various groups of viruses including herpesviruses, small DNA viruses and retroviruses.  ...  Work in KTJ's laboratory is supported by intramural funding from NIAID, NIH; and by the Intramural AIDS Targeted Antiviral Program from the Office of the Director, NIH.  ... 
doi:10.1016/j.bbagrm.2008.05.005 pmid:18549828 pmcid:PMC2641032 fatcat:4n7swcw3dndq3jsfl6c3757xqu

Identification of homologous human miRNAs as antivirals towards COVID‐19 genome

Jitender Singh, Ashvinder Raina, Namrata Sangwan, Arushi Chauhan, K. L. Khanduja, Pramod K. Avti
2021 Advances in Cell and Gene Therapy  
Computational techniques were used to predict the hairpin precursor miRNA (pre-miRNAs) of COVID-19 genome with high homology towards human (host) miRNA.  ...  The COVID-19 fatality rate is ~57% worldwide. The investigation of possible antiviral therapy using host microRNA (miRNA) to inhibit viral replication and transmission is the need of the hour.  ...  coronavirus, there is still a significant gap in our knowledge of SARS-CoV-2/COVID-19 pathology. 8 One of the recent emerging areas for effective treatment strategies for COVID-19 is the field of microRNAs  ... 
doi:10.1002/acg2.114 pmid:34901760 pmcid:PMC8646656 fatcat:qcpdaukdi5fopns7hq4y2zciqq

MicroRNA-34/449 family and viral infections

Jianliang Lv, Zhongwang Zhang, Li Pan, Yongguang Zhang
2019 Virus Research  
A growing subset of the literature reports that the miR-34/449 family is involved in the regulation of immune responses and viral infections, and data suggest the potential for miR-34/446 as a diagnostic  ...  MicroRNAs are short, endogenous, nonprotein-coding RNAs that are essential for regulation of cellular processes through gene silencing.  ...  The first human miRNA of the miR-34/449 family to be identified was miR-34a, which was predicted by computational methods (Lim et al., 2003) and validated by microRNP immunoprecipitation from the human  ... 
doi:10.1016/j.virusres.2018.11.001 pmid:30412711 pmcid:PMC7114830 fatcat:7p7hkcxhlvhmfkt54hrpjtzu3a
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