Simon Rayner

Bilde av Simon Rayner
English version of this page
Mobiltelefon +47 23 02 63 79
Besøksadresse Kirkeveien 166 Laboratoriebygget 0450 OSLO
Postadresse Postboks 4956 Nydalen 0424 OSLO


Forskningsgruppen er en del av seksjon for forskning og utvikling, avdeling for medisinsk genetikk ved Oslo universitetssykehus (OUS).


Jeg har jobbet med bioinformatikk både i praksis og akademisk. Min forskning fokuserer på utvikling av metoder for datautvinning og visualisering av store data. Jeg er spesielt interessert i genomevolusjon på molekylært nivå og påfølgende innvirkning på funksjonelt nivå; til dette formålet, har jeg for tiden arbeidet med Whole Genome Sequence, Whole Exome Sequence, RNA Seq og smallRNA NGS datasett. Imidlertid, mens "tradisjonelle" genetiske metoder fokuserer på den samlede effekten av punktmutasjoner innenfor kodende områder og deres rolle i sykdommen, undersøker jeg rollen til ikke-kodende RNA i sykdommen og hvordan mutasjoner i disse regionene kan være assosiert med sykdommen.

Vitenskapelige stillinger

  • 1989 - 1993 - Lecturer. Dept of Physics, University of Texas.
  • 1995 - 1997 - Research Fellow McDermott Centre for Human Growth and Development,
                          University of Texas Southwestern Medical Centre at Dallas (UTSW)
  • 1997 - 1999 - Assistant Professor, Depts of Biochemistry & Internal Medicine, UTSW
  • 1999 - 2004 - BioAutomation inc. Co-founder and developer of DNA & RNA synthesis technology
  • 2005 - 2006 - Professor of Bioinformatics Chinese Agricultural University, Beijing
  • 2006 - 2015 - Professor / Principal Investigator, Wuhan Institute of Virology (WIV), Chinese Academy of Sciences
  • 2015 -  t.d.   - Department of Medical Genetics, UiO/Oslo University Hospital (OUS).



Utvalgte publikasjoner (siden 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.

  • Guderud, Kari; Sunde, Line Hagen; Flåm, Siri Tennebø; Mæhlen, Marthe Thoresen; Mjaavatten, Maria Dahl; Lillegraven, Siri; Aga, Anna-Birgitte; Evenrød, Ida Marie; Norli, Ellen Sauar; Andreassen, Bettina Kulle; Franzenburg, Sören; Franke, Andre; Haavardsholm, Espen Andre; Rayner, Simon; Gervin, Kristina & Lie, Benedicte Alexandra (2020). Rheumatoid Arthritis Patients, Both Newly Diagnosed and Methotrexate Treated, Show More DNA Methylation Differences in CD4+ Memory Than in CD4+ Naïve T Cells. Frontiers in Immunology.  ISSN 1664-3224.  11 . doi: 10.3389/fimmu.2020.00194
  • Heinicke, Fatima; Zhong, Xiangfu; Zucknick, Manuela; Breidenbach, Johannes; Sundaram, Arvind Yegambaram Meenakshi; Flåm, Siri Tennebø; Leithaug, Magnus; Dalland, Marianne; Farmer, Andrew; Henderson, Jordana M.; Hussong, Melanie A.; Moll, Pamela; Nguyen, Loan; McNulty, Amanda; Shaffer, Jonathan M.; Shore, Sabrina; Yip, Hoichong Karen; Vitkovska, Jana; Rayner, Simon; Lie, Benedicte Alexandra & Gilfillan, Gregor Duncan (2019). Systematic assessment of commercially available low-input miRNA library preparation kits. RNA Biology.  ISSN 1547-6286.  17(1), s 75- 86 . doi: 10.1080/15476286.2019.1667741 Fulltekst i vitenarkiv. Vis sammendrag
  • Liang, Fengji; Lv, Ke; Wang, Yue; Yuan, Yanhong; Lu, Liang; Feng, Qiang; Jing, Xiaolu; Wang, Honghui; Liu, Changning; Rayner, Simon; Ling, Shukuan; Chen, Hailong; Wan, Yumin; Zhou, Wanlong; He, Li; Wu, Bin; Qu, Lina; Chen, Shanguang; Xiong, Jianghui & Li, Yinghui (2019). Personalized epigenome remodeling under biochemical and psychological changes during long-term isolation environment. Frontiers in Physiology.  ISSN 1664-042X.  10(932) . doi: 10.3389/fphys.2019.00932 Fulltekst i vitenarkiv. Vis sammendrag
  • Lin, Ann; Skottvoll, Frøydis Sved; Rayner, Simon; Pedersen-Bjergaard, Stig; Sullivan, Gareth; Krauss, Stefan; Wilson, Steven Ray Haakon & Harrison, Sean (2019). 3D cell culture models and organ-on-a-chip: Meet separation science and mass spectrometry. Electrophoresis.  ISSN 0173-0835.  41, s 56- 64 . doi: 10.1002/elps.201900170
  • Tao, Xiao-Yan; Li, Mu-Li; Wang, Qian; Baima, Ciwang; Hong, Mei; Li, Wei; Wu, Yong-Biao; Li, Yan-Rong; Zhao, Yu-Min; Rayner, Simon & Zhu, Wu-Yang (2019). The reemergence of human rabies and emergence of an Indian subcontinent lineage in Tibet, China. PLoS Neglected Tropical Diseases.  ISSN 1935-2727.  13(1) . doi: 10.1371/journal.pntd.0007036 Fulltekst i vitenarkiv. Vis sammendrag
  • Zhong, Xiangfu; Heinicke, Fatima; Lie, Benedicte Alexandra & Rayner, Simon (2019). Accurate Adapter Information Is Crucial for Reproducibility and Reusability in Small RNA Seq Studies. Non-coding RNA.  ISSN 2311-553X. . doi: 10.3390/ncrna5040049 Fulltekst i vitenarkiv.
  • Zhong, Xiangfu; Heinicke, Fatima & Rayner, Simon (2019). miRBaseMiner, a tool for investigating miRBase content. RNA Biology.  ISSN 1547-6286.  16(11), s 1534- 1546 . doi: 10.1080/15476286.2019.1637680 Fulltekst i vitenarkiv. Vis sammendrag
  • Zhong, Xiangfu; Planas, Albert Pla & Rayner, Simon (2019). Jasmine: a Java pipeline for isomiR characterization in miRNA-Seq data. Bioinformatics.  ISSN 1367-4803. . doi: 10.1093/bioinformatics/btz806 Fulltekst i vitenarkiv. Vis sammendrag
  • Jiang, Xuan; Dong, Xiao; Li, Shi-Hua; Zhou, Yue-Peng; Rayner, Simon; Xia, Hui-Min; Gao, George F.; Yuan, Hui; Tang, Ya-Ping & Luo, Min-Hua (2018). Proteomic analysis of Zika virus infected primary human fetal neural progenitors suggests a role for doublecortin in the pathological consequences of infection in the cortex. Frontiers in Microbiology.  ISSN 1664-302X.  9(1067), s 1- 15 . doi: 10.3389/fmicb.2018.01067 Fulltekst i vitenarkiv.
  • Planas, Albert Pla; Zhong, Xiangfu & Rayner, Simon (2018). miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts. PLoS Computational Biology.  ISSN 1553-734X.  14:e1006185(7), s 1- 32 . doi: 10.1371/journal.pcbi.1006185 Fulltekst i vitenarkiv. Vis sammendrag
  • Yang, Bo; Liu, Xi-Juan; Yao, Yongxuan; Jiang, Xuan; Wang, Xian-Zhang; Yang, Hong; Sun, Jin-Yan; Miao, Yun; Wang, Wei; Huang, Zhen-Li; Wang, Yanyi; Tang, Qiyi; Rayner, Simon; Britt, William J.; McVoy, Michael A.; Luo, Min-Hua & Zhao, Fei (2018). WDR5 facilitates human cytomegalovirus replication by promoting capsid nuclear egress. Journal of Virology.  ISSN 0022-538X.  92(9) . doi: 10.1128/JVI.00207-18
  • Cheng, Shuang; Jiang, Xuan; Yang, Bo; Wen, Le; Zhao, Fei; Zeng, Wen-Bo; Liu, Xi-Juan; Dong, Xiao; Sun, Jin-Yan; Ming, Ying-Zi; Zhu, Hua; Rayner, Simon; Tang, Qiyi; Fortunato, Elizabeth & Luo, Min-Hua (2017). Infected T98G glioblastoma cells support human cytomegalovirus reactivation from latency. Virology.  ISSN 0042-6822.  510, s 205- 215 . doi: 10.1016/j.virol.2017.07.023
  • Jiang, Hai-Fei; Wang, Wei; Jiang, Xuan; Zeng, Wen-Bo; Shen, Zhang-Zhou; Song, Yi-Ge; Yang, Hong; Liu, Xi-Juan; Dong, Xiao; Zhou, Jing; Sun, Jin-Yan; Yu, Fei-Long; Guo, Lin; Cheng, Tong; Rayner, Simon; Zhao, Fei; Zhu, Hua & Luo, Min-Hua (2017). ORF7 of varicella-zoster virus is required for viral cytoplasmic envelopment in differentiated neuronal cells. Journal of Virology.  ISSN 0022-538X.  91:e0012717(12), s 1- 17 . doi: 10.1128/JVI.00127-17
  • Liu, Xi-Juan; Yang, Bo; Huang, Sheng-Nan; Wu, Cong-Cong; Li, Xiao-Jun; Cheng, Shuang; Jiang, Xuan; Hu, Fei; Ming, Ying-Zi; Nevels, Michael; Britt, William J; Rayner, Simon; Tang, Qiyi; Zeng, Wen-Bo; Zhao, Fei & Luo, Min-Hua (2017). Human cytomegalovirus IE1 downregulates Hes1 in neural progenitor cells as a potential E3 ubiquitin ligase. PLoS Pathogens.  ISSN 1553-7366.  13(7) . doi: 10.1371/journal.ppat.1006542
  • Rayner, Simon; Bruhn, Sören; Vallhov, Helen; Andersson, Anna; Billmyre, R. Blake & Scheynius, Annika (2017). Identification of small RNAs in extracellular vesicles from the commensal yeast Malassezia sympodialis. Scientific Reports.  ISSN 2045-2322.  7:39742, s 1- 9 . doi: 10.1038/srep39742
  • Han, Na; Adams, James; Fang, Wei; Liu, Si-Qing & Rayner, Simon (2015). Investigation of the genotype III to genotype I shift in Japanese encephalitis virus and the impact on human cases. Virologica Sinica.  ISSN 1674-0769.  30(4), s 277- 289 . doi: 10.1007/s12250-015-3621-4
  • Tao, Xiao-Yan; Guo, Zhen-Yang; Li, Hao; Jiao, Wen-Tao; Shen, Xin-Xin; Zhu, Wu-Yang; Rayner, Simon & Tang, Qing (2015). Rabies cases in the west of China have two distinct origins. PLoS Neglected Tropical Diseases.  ISSN 1935-2727.  9:e0004140(10) . doi: 10.1371/journal.pntd.0004140

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Publisert 23. apr. 2015 13:23 - Sist endret 17. aug. 2018 09:01