Simon Rayner

Image of Simon Rayner
Norwegian version of this page
Mobile phone +47 23 02 63 79
Username
Visiting address Kirkeveien 166 Laboratoriebygget 0450 OSLO
Postal address Postboks 4956 Nydalen 0424 OSLO

Research environment

The research group is a part of the Research section (In Norwegian) at the Department of Medical Genetics, Oslo University Hospital (OUH).

Research Interests

I have been working in bioinformatics in both industry and academia. My research focuses on the development of methods for mining and visualizing big data. I have a particular interest in genome evolution at the molecular level and the subsequent impact at the functional level; to this end, I have currently working with Whole Genome Sequence, Whole Exome Sequence, RNA Seq and smallRNA NGS datasets. However, whereas “traditional” genetic methods are focusing on the collective effect of point mutations within coding regions and their role in disease, I am examining the role of non-coding RNAs in disease and how mutations in these regions can be associated with disease.

Scientific Appointments

1989 to 1993              Lecturer. Dept of Physics, University of Texas. .

1995 to 1997              Research Fellow McDermott Centre for Human Growth and Development, University of Texas Southwestern Medical Centre at Dallas (UTSW)

1997 to 1999              Assistant Professor, Depts of Biochemistry & Internal Medicine, UTSW

1999 to 2004              BioAutomation inc. Co-founder and developer of DNA & RNA synthesis technology

2005 to 2006              Professor of Bioinformatics Chinese Agricultural University, Beijing

2006 to 2015              Professor / Principal Investigator, Wuhan Institute of Virology (WIV), Chinese Academy of Sciences

2015 to Present          Department of Medical Genetics, UiO/Oslo University Hospital (OUS).

Tags: Bioinformatics, Evolution, NGS, Algorithm Development

Publications

Selected Publications (since 2006)

Xiong, J., S. Rayner, K. Luo, Y. Li and S. Chen (2006). "Genome wide prediction of protein function via a generic knowledge discovery approach based on evidence integration." BMC bioinformatics 7(1): 268.

Li, X., H. Jin, Z. Wu, S. Rayner, J. Yin, Y. Yu, W. Zhang, Z. He, C. Wang and B. Wang (2007). "An automated process to extract plasmid DNA by alkaline lysis." Applied microbiology and biotechnology 75(5): 1217-1223.

Deng, X., X. Deng, S. Rayner, X. Liu, Q. Zhang, Y. Yang and N. Li (2008). "DHPC: a new tool to express genome structural features." Genomics 91(5): 476-483.

Deng, X., H. Liu, Y. Shao, S. Rayner* and R. Yang (2008). "The epidemic origin and molecular properties of B′: a founder strain of the HIV-1 transmission in Asia." Aids 22(14): 1851-1858.

Li, X., H. Jin, Z. Wu, S. Rayner and B. Wang (2008). "A continuous process to extract plasmid DNA based on alkaline lysis." Nature protocols 3(2): 176-180.

Fu, B., F. Sun, B. Li, L. Yang, Y. Zeng, X. Sun, F. Xu, S. Rayner, M. Guadalupe and S. J. Gao (2009). "Seroprevalence of Kaposi's sarcoma‐associated herpesvirus and risk factors in Xinjiang, China." Journal of medical virology 81(8): 1422-1431.

Jiang, Y., F. Deng, S. Rayner, H. Wang and Z. Hu (2009). "Evidence of a major role of GP64 in group I alphabaculovirus evolution." Virus research 142(1): 85-91.

Pan, X., H. Wang, S. Fu, N. Hian, H. Liu, S. Rayner and G. Hang (2009). "[Molecular characterization of full-length genome of Japanese encephalitis virus strain patient's cerebrospinal fluid in China]." y 23(1): 26-28.

潘晓玲, 王环宇, 付士红, 韩娜, 刘海舟 and 梁国栋 (2009). "流行性乙型脑炎病毒脑脊液分离株 “47 株” 全基因组特征分析." 中华实验和临床病毒学杂志(1): 26-28.

Ming, P., J. Yan, S. Rayner, S. Meng, G. Xu, Q. Tang, J. Wu, J. Luo and X. Yang (2010). "A history estimate and evolutionary analysis of rabies virus variants in China." Journal of General Virology 91(3): 759-764.

Xiong, J., J. Liu, S. Rayner, Y. Li and S. Chen (2010). "Protein-protein interaction reveals synergistic discrimination of cancer phenotype." Cancer informatics 9: 61.

Xiong, J., J. Liu, S. Rayner, Z. Tian, Y. Li and S. Chen (2010). "Pre-clinical drug prioritization via prognosis-guided genetic interaction networks." PloS one 5(11): e13937.

Xiong, J., J. Liu, S. Rayner, Z. Tian, Y. Li and S. Chen (2010). "In silico Genetic Network Models for Pre-clinical Drug Prioritization."

Yin, Y., Y. Xiao, H.-Z. Liu, F. Hao, S. Rayner, H. Tang and N.-Y. Zhou (2010). "Characterization of catabolic meta-nitrophenol nitroreductase from Cupriavidus necator JMP134." Applied microbiology and biotechnology 87(6): 2077-2085.

Zhang, Y., Y. Hu, B. Yang, F. Ma, P. Lu, L. Li, C. Wan, S. Rayner and S. Chen (2010). "Duckweed (Lemna minor) as a model plant system for the study of human microbial pathogenesis." PloS one 5(10): e13527.

Chen, P., S. Rayner and K.-h. Hu (2011). "Advances of bioinformatics tools applied in virus epitopes prediction." Virologica sinica 26(1): 1-7.

Han, N. and S. Rayner* (2011). "Epidemiology and mutational analysis of global strains of Crimean-Congo haemorrhagic fever virus." Virologica Sinica 26(4): 229-244.

Pan, X.-L., H. Liu, H.-Y. Wang, S.-H. Fu, H.-Z. Liu, H.-L. Zhang, M.-H. Li, X.-Y. Gao, J.-L. Wang and X.-H. Sun, S. Rayner*, G.-DLiang (2011). "Emergence of genotype I of Japanese encephalitis virus as the dominant genotype in Asia." Journal of virology 85(19): 9847-9853.

Qiu, J., B. Qin, S. Rayner, C.-c. Wu, R.-j. Pei, S. Xu, Y. Wang and X.-W. Chen (2011). "Novel evidence suggests Hepatitis B virus surface proteins participate in regulation of HBV genome replication." Virologica Sinica 26(2): 131-138.

Wu, Y., B. Wei, H. Liu, T. Li and S. Rayner* (2011). "MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences." BMC bioinformatics 12(1): 107.

Zhao, J.-r., Y.-d. Li, L.-m. Pan, N. Zhu, H.-x. Ni, G.-z. Xu, Y.-z. Jiang, X.-x. Huo, J.-q. Xu and H. Xia (2011). "Genetic characteristics of 2009 pandemic H1N1 influenza a viruses isolated from Mainland China." Virologica Sinica 26(6): 418-427.

Zhou, X., J. Liu, C. Liu, S. Rayner, F. Liang, J. Ju, Y. Li, S. Chen and J. Xiong (2011). Context-specific miRNA regulation network predicts cancer prognosis. Systems Biology (ISB), 2011 IEEE International Conference on, IEEE.

Zhu, L., F. Liang, J. Liu, S. Rayner, Y. Li, S. Chen and J. Xiong (2011). Dynamic remodeling of context-specific miRNAs regulation networks facilitate in silico cancer drug screening. Systems Biology (ISB), 2011 IEEE International Conference on, IEEE.

Adams, J. T., D. J. Gray and S. Rayner (2012). "Observation of non-principal plane neutral points in the upwelling polarized light field above a water surface." Applied optics 51(22): 5387-5391.

Duan, Y., L. Miao, H. Ye, C. Yang, B. Fu, P. H. Schwartz, S. Rayner, E. A. Fortunato and M.-H. Luo (2012). "A faster immunofluorescence assay for tracking infection progress of human cytomegalovirus." Acta biochimica et biophysica Sinica: gms041.

Hu, C., N. Xiong, Y. Zhang, S. Rayner and S. Chen (2012). "Functional characterization of lipase in the pathogenesis of Staphylococcus aureus." Biochemical and biophysical research communications 419(4): 617-620.

Hu, Y., L. Feng, Y. Li, Y. Zhang, P. Lu, S. Rayner and S. Chen (2012). "Ribosomal Binding Site Switching: An Effective Strategy for High-Throughput Cloning Constructions." PloS one 7(11): e50142.

Huanyu, W., W. Haiyan, F. Shihong, L. Guifang, L. Hong, G. Xiaoyan, S. Lizhi, S. Rayner, X. Aiqiang and L. Guodong (2012). "Isolation and identification of a distinct strain of Culex Flavivirus from mosquitoes collected in Mainland China." Virol J 9: 73.

Lu, P., Y. Zhang, L. Li, Y. Hu, L. Huang, Y. Li, S. Rayner and S. Chen (2012). "Small non-coding RNA SraG regulates the operon YPK_1206-1205 in Yersinia pseudotuberculosis." FEMS microbiology letters 331(1): 37-43.

Tang, Q., J. Yu, L. Hao, S. Rayner* and G. Liang (2012). "The spatial and temporal dynamics of rabies in China." PLoS neglected tropical diseases 10(2/3): 52-53.

Wang, L., X. Lv, Y. Zhai, S. Fu, D. Wang, S. Rayner, Q. Tang and G. Liang (2012). "Genomic Characterization of a Novel Virus of the Family Tymoviridae Isolated from Mosquitoes." PloS one 7(7): e39845.

Xiong, J., S. Rayner, F. Liang and Y. Li (2012). The Principle of Rational Design of Drug Combination and Personalized Therapy Based on Network Pharmacology. Systems Biology in Cancer Research and Drug Discovery, Springer Netherlands: 325-337.

Yin, C.-p., H. Zhou, H. Wu, X.-y. Tao, S. Rayner, S.-m. Wang, Q. Tang and G.-d. Liang (2012). "Analysis on factors related to rabies epidemic in China from 2007–2011." Virologica Sinica 27(2): 132-143.

Yu, J., H. Li, Q. Tang, S. Rayner*, N. Han, Z. Guo, H. Liu, J. Adams, W. Fang and X. Tao (2012). "The spatial and temporal dynamics of rabies in China." PLoS neglected tropical diseases 6(5): e1640.

Yu, P.-c., A. Noguchi, S. Inoue, Q. Tang, S. Rayner and G.-d. Liang (2012). "Comparison of RFFIT tests with different standard sera and testing procedures." Virologica Sinica 27(3): 187-193.

Chen, P., Y. Gan, N. Han, W. Fang, J. Li, F. Zhao, K. Hu and S. Rayner* (2013). "Computational evolutionary analysis of the overlapped surface (S) and polymerase (P) region in hepatitis B virus indicates the spacer domain in P is crucial for survival." PloS one 8(4): e60098.

Guo, Z., X. Tao, C. Yin, N. Han, J. Yu, H. Li, H. Liu, W. Fang, J. Adams and S. Rayner* (2013). "National borders effectively halt the spread of rabies: the current rabies epidemic in China is dislocated from cases in neighboring countries." PLoS neglected tropical diseases 7(1): e2039.

Hou, D., L. Zhang, F. Deng, W. Fang, R. Wang, X. Liu, L. Guo, S. Rayner*, X. Chen and H. Wang (2013). "Comparative proteomics reveal fundamental structural and functional differences between the two progeny phenotypes of a baculovirus." Journal of virology 87(2): 829-839.

HUANG, Y., T. Qing, S. Rayner, G. Kai, S. Bo and G. D. LIANG (2013). "Pathogenicity of Rabies Viruses Isolated in China: Two Fixed Strains and a Street Strain." Biomedical and Environmental Sciences 26(7): 552-561.

Li, L., N. Han, J. Lu, T. Li, X. Zhong, H. Wu, S. Rayner*, L. Chen, Y. Liu and X. Wang (2013). "Genetic characterization and transmitted drug resistance of the HIV type 1 epidemic in men who have sex with men in Beijing, China." AIDS research and human retroviruses 29(3): 633-637.

Pan, X., X.-J. Li, X.-J. Liu, H. Yuan, J.-F. Li, Y.-L. Duan, H.-Q. Ye, Y.-R. Fu, G.-H. Qiao and C.-C. Wu (2013). "Later passages of neural progenitor cells from neonatal brain are more permissive for human cytomegalovirus infection." Journal of virology 87(20): 10968-10979.

Qin, B., B. Budeus, L. Cao, C. Wu, Y. Wang, X. Zhang, S. Rayner, D. Hoffmann, M. Lu and X. Chen (2013). "The amino acid substitutions rtP177G and rtF249A in the reverse transcriptase domain of hepatitis B virus polymerase reduce the susceptibility to tenofovir." Antiviral research 97(2): 93-100.

Tao, X.-Y., Q. Tang, S. Rayner*, Z.-Y. Guo, H. Li, S.-L. Lang, C.-P. Yin, N. Han, W. Fang and J. Adams (2013). "Molecular phylodynamic analysis indicates lineage displacement occurred in Chinese rabies epidemics between 1949 to 2010." PLoS neglected tropical diseases 7(7): e2294.

Tao, X., N. Han, Z. Guo, Q. Tang, S. Rayner and G. Liang (2013). "Molecular characterization of China human rabies vaccine strains." Virologica Sinica 28(2): 116-123.

Wang, L., H. Wu, X. Tao, H. Li, S. Rayner, G. Liang and Q. Tang (2013). "Genetic and evolutionary characterization of RABVs from China using the phosphoprotein gene." Virol J 10(1): 14-23.

Wu, H., L. Wang, X. Tao, H. Li, S. Rayner, G. Liang and Q. Tang (2013). "Genetic diversity and molecular evolution of the rabies virus matrix protein gene in China." Infection, Genetics and Evolution 16: 248-253.

Ye, Y., B. Wei, L. Wen and S. Rayner* (2013). "BlastGraph: a comparative genomics tool based on BLAST and graph algorithms." Bioinformatics 29(24): 3222-3224.

Zhou, Z., F. Deng, N. Han, H. Wang, S. Sun, Y. Zhang, Z. Hu and S. Rayner (2013). "Reassortment and migration analysis of Crimean–Congo haemorrhagic fever virus." Journal of General Virology 94(Pt 11): 2536-2548.

Han, N., J. Adams, P. Chen, Z.-y. Guo, X.-f. Zhong, W. Fang, N. Li, L. Wen, X.-y. Tao, Z.-m. Yuan and S. Rayner* (2014). "Comparison of Genotypes I and III in Japanese encephalitis virus reveal distinct differences in their genetic and host diversity." Journal of virology: JVI. 02050-02014.

Liu, H., N. Han, W. Fang, J. Adams, K. Zheng, T. Li, Z. Hu and S. Rayner* (2014). "The limited number of available nucleotide and protein sequence data from the recent H7N9 cases in China impeded investigation and characterization of the outbreak." Virologica Sinica 29(2): 126-127.

Song, M., Q. Tang, S. Rayner*, X.-Y. Tao, H. Li, Z.-Y. Guo, X.-X. Shen, W.-T. Jiao, W. Fang and J. Wang (2014). "Human rabies surveillance and control in China, 2005–2012." BMC infectious diseases 14(1): 212.

Song, M., Q. Tang, S. Rayner*, X. Y. Tao, X. X. Shen and G. D. Liang (2014). "Factors influencing the number of rabies cases in children in china." Biomedical and environmental sciences: BES 27(8): 627-632.

Yang, C.-Q., L.-F. Miao, X. Pan, C.-C. Wu, S. Rayner, E. S. Mocarski, H.-Q. Ye and M.-H. Luo (2014). "Natural antisense transcripts of UL123 packaged in human cytomegalovirus virions." Archives of virology 159(1): 147-151.

Yu, F., G. Zhang, X. Zhong, N. Han, Y. Song, L. Zhao, M. Cui, S. Rayner* and Z. F. Fu (2014). "Comparison of complete genome sequences of dog rabies viruses isolated from China and Mexico reveals key amino acid changes that may be associated with virus replication and virulence." Archives of virology 159(7): 1593-1601.

Zhu, L., J. Liu, F. Liang, S. Rayner* and J. Xiong (2014). "Predicting response to preoperative chemotherapy agents by identifying drug action on modeled microRNA regulation networks." PloS one 9(5): e98140.

Fu, Y.-R., X.-J. Liu, X.-J. Li, Z.-z. Shen, B. Yang, C.-C. Wu, J.-F. Li, L.-F. Miao, H.-Q. Ye and G.-H. Qiao (2015). "MicroRNA miR-21 Attenuates Human Cytomegalovirus Replication in Neural Cells by Targeting Cdc25a." Journal of virology 89(2): 1070-1082.

Li, X.-J., X.-J. Liu, B. Yang, Y.-r. Fu, F. Zhao, Z.-z. Shen, L.-f. Miao, S. Rayner, S. Chavanas and H. Zhu (2015). "Human Cytomegalovirus Infection Dysregulates the Localization and Stability of NICD1 and Jag1 in Neural Progenitor Cells." Journal of virology: JVI. 00351-00315.

Liu, S.-Q., C.-L. Deng, Z.-M. Yuan, S. Rayner and B. Zhang (2015). "Identifying the pattern of molecular evolution for Zaire ebolavirus in the 2014 outbreak in West Africa." Infection, Genetics and Evolution 32: 51-59.

Xu, K., Z. Yuan, S. Rayner* and X. Hu (2015). "Genome comparison provides molecular insights into the phylogeny of the reassigned new genus Lysinibacillus." BMC genomics 16(1): 140.

 

Published Apr. 23, 2015 1:26 PM - Last modified Aug. 17, 2018 9:00 AM