Computational Biology: The Role of Non-Coding RNAs in Disease

Publications 2024

Shultes PV, Tadele DS, Durmaz A, Weaver DT, Barker-Clarke R, Dinh MN, Liu S, Alemu EA, Rayner S, Scott JG (2024)
Cell-Cell Fusion in NSCLC Confers a Fitness Benefit Under Drug Selection
bioRxiv
DOI 10.1101/2024.12.02.626399, PubMed 39677818

Publications 2023

Frerker N, Karlsen TA, Stensland M, Nyman TA, Rayner S, Brinchmann JE (2023)
Comparison between articular chondrocytes and mesenchymal stromal cells for the production of articular cartilage implants
Front Bioeng Biotechnol, 11, 1116513
DOI 10.3389/fbioe.2023.1116513, PubMed 36896010

Jiang X, Liu S, Fu YR, Liu XJ, Li XJ, Yang B, Jiang HF, Shen ZZ, Alemu EA, Vazquez P, Tang Y, Kaarbø M, McVoy MA, Rayner S, Luo MH (2023)
Human cytomegalovirus infection perturbs neural progenitor cell fate via the expression of viral microRNAs
J Med Virol, 95 (2), e28574
DOI 10.1002/jmv.28574, PubMed 36772841

Tsagakis I, Rayner S (2023)
An open chat with…Simon Rayner
FEBS Open Bio, 13 (2), 214-216
DOI 10.1002/2211-5463.13543, PubMed 36562681

Wen L, Wang XZ, Qiu Y, Zhou YP, Zhang QY, Cheng S, Sun JY, Jiang XJ, Rayner S, Britt WJ, Chen J, Hu F, Li FC, Luo MH, Cheng H (2023)
SOX2 downregulation of PML increases HCMV gene expression and growth of glioma cells
PLoS Pathog, 19 (4), e1011316
DOI 10.1371/journal.ppat.1011316, PubMed 37058447

Publications 2022

Vazquez P, Hirayama-Shoji K, Novik S, Krauss S, Rayner S (2022)
Globally Accessible Distributed Data Sharing (GADDS): a decentralized FAIR platform to facilitate data sharing in the life sciences
Bioinformatics, 38 (15), 3812-3817
DOI 10.1093/bioinformatics/btac362, PubMed 35639939

Zhou YP, Mei MJ, Wang XZ, Huang SN, Chen L, Zhang M, Li XY, Qin HB, Dong X, Cheng S, Wen L, Yang B, An XF, He AD, Zhang B, Zeng WB, Li XJ, Lu Y, Li HC, Li H, Zou WG, Redwood AJ, Rayner S, Cheng H, McVoy MA et al. (2022)
A congenital CMV infection model for follow-up studies of neurodevelopmental disorders, neuroimaging abnormalities, and treatment
JCI Insight, 7 (1)
DOI 10.1172/jci.insight.152551, PubMed 35014624

Publications 2021

Guderud K, Sunde LH, Flåm ST, Mæhlen MT, Mjaavatten MD, Norli ES, Evenrød IM, Andreassen BK, Franzenburg S, Franke A, Rayner S, Gervin K, Lie BA (2021)
Methotrexate Treatment of Newly Diagnosed RA Patients Is Associated With DNA Methylation Differences at Genes Relevant for Disease Pathogenesis and Pharmacological Action
Front Immunol, 12, 713611
DOI 10.3389/fimmu.2021.713611, PubMed 34867944

Heinicke F, Zhong X, Flåm ST, Breidenbach J, Leithaug M, Mæhlen MT, Lillegraven S, Aga AB, Norli ES, Mjaavatten MD, Haavardsholm EA, Zucknick M, Rayner S, Lie BA (2021)
MicroRNA Expression Differences in Blood-Derived CD19+ B Cells of Methotrexate Treated Rheumatoid Arthritis Patients
Front Immunol, 12, 663736
DOI 10.3389/fimmu.2021.663736, PubMed 33897713

Wen L, Zhao F, Qiu Y, Cheng S, Sun JY, Fang W, Rayner S, McVoy MA, Jiang XJ, Tang Q, Li FC, Hu F, Luo MH (2021)
Correction to: Human cytomegalovirus DNA and immediate early protein 1/2 are highly associated with glioma and prognosis
Protein Cell, 12 (4), 313
DOI 10.1007/s13238-020-00787-7, PubMed 32929699

Publications 2020

Guderud K, Sunde LH, Flåm ST, Mæhlen MT, Mjaavatten MD, Lillegraven S, Aga AB, Evenrød IM, Norli ES, Andreassen BK, Franzenburg S, Franke A, Haavardsholm EA, Rayner S, Gervin K, Lie BA (2020)
Rheumatoid Arthritis Patients, Both Newly Diagnosed and Methotrexate Treated, Show More DNA Methylation Differences in CD4⁺ Memory Than in CD4⁺ Naïve T Cells
Front Immunol, 11, 194
DOI 10.3389/fimmu.2020.00194, PubMed 32117312

Heinicke F, Zhong X, Zucknick M, Breidenbach J, Sundaram AYM, T Flåm S, Leithaug M, Dalland M, Rayner S, Lie BA, Gilfillan GD (2020)
An extension to: Systematic assessment of commercially available low-input miRNA library preparation kits
RNA Biol, 17 (9), 1284-1292
DOI 10.1080/15476286.2020.1761081, PubMed 32436772

Jiang X, Rayner S, Luo MH (2020)
Does SARS-CoV-2 has a longer incubation period than SARS and MERS?
J Med Virol, 92 (5), 476-478
DOI 10.1002/jmv.25708, PubMed 32056235

Wen L, Zhao F, Qiu Y, Cheng S, Sun JY, Fang W, Rayner S, McVoy MA, Jiang XJ, Tang Q, Li FC, Hu F, Luo MH (2020)
Human cytomegalovirus DNA and immediate early protein 1/2 are highly associated with glioma and prognosis
Protein Cell, 11 (7), 525-533
DOI 10.1007/s13238-020-00696-9, PubMed 32189197

Publications 2019

Heinicke F, Zhong X, Zucknick M, Breidenbach J, Sundaram AYM, T Flåm S, Leithaug M, Dalland M, Farmer A, Henderson JM, Hussong MA, Moll P, Nguyen L, McNulty A, Shaffer JM, Shore S, Yip HK, Vitkovska J, Rayner S, Lie BA, Gilfillan GD (2019)
Systematic assessment of commercially available low-input miRNA library preparation kits
RNA Biol, 17 (1), 75-86
DOI 10.1080/15476286.2019.1667741, PubMed 31559901

Liang F, Lv K, Wang Y, Yuan Y, Lu L, Feng Q, Jing X, Wang H, Liu C, Rayner S, Ling S, Chen H, Wan Y, Zhou W, He L, Wu B, Qu L, Chen S, Xiong J, Li Y (2019)
Personalized Epigenome Remodeling Under Biochemical and Psychological Changes During Long-Term Isolation Environment
Front Physiol, 10, 932
DOI 10.3389/fphys.2019.00932, PubMed 31417412

Lin A, Sved Skottvoll F, Rayner S, Pedersen-Bjergaard S, Sullivan G, Krauss S, Ray Wilson S, Harrison S (2019)
3D cell culture models and organ-on-a-chip: Meet separation science and mass spectrometry
Electrophoresis, 41 (1-2), 56-64
DOI 10.1002/elps.201900170, PubMed 31544246

Tao XY, Li ML, Wang Q, Baima C, Hong M, Li W, Wu YB, Li YR, Zhao YM, Rayner S, Zhu WY (2019)
The reemergence of human rabies and emergence of an Indian subcontinent lineage in Tibet, China
PLoS Negl Trop Dis, 13 (1), e0007036
DOI 10.1371/journal.pntd.0007036, PubMed 30640911

Zhong X, Heinicke F, Lie BA, Rayner S (2019)
Accurate Adapter Information Is Crucial for Reproducibility and Reusability in Small RNA Seq Studies
Noncoding RNA, 5 (4)
DOI 10.3390/ncrna5040049, PubMed 31661777

Zhong X, Heinicke F, Rayner S (2019)
miRBaseMiner, a tool for investigating miRBase content
RNA Biol, 16 (11), 1534-1546
DOI 10.1080/15476286.2019.1637680, PubMed 31251108

Zhong X, Pla A, Rayner S (2019)
Jasmine: a Java pipeline for isomiR characterization in miRNA-Seq Data
Bioinformatics, 36 (6), 1933-1936
DOI 10.1093/bioinformatics/btz806, PubMed 31681943

Publications 2018

Jiang X, Dong X, Li SH, Zhou YP, Rayner S, Xia HM, Gao GF, Yuan H, Tang YP, Luo MH (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
Front Microbiol, 9, 1067
DOI 10.3389/fmicb.2018.01067, PubMed 29922247

Pla A, Zhong X, Rayner S (2018)
miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts
PLoS Comput Biol, 14 (7), e1006185
DOI 10.1371/journal.pcbi.1006185, PubMed 30005074

Yang B, Liu XJ, Yao Y, Jiang X, Wang XZ, Yang H, Sun JY, Miao Y, Wang W, Huang ZL, Wang Y, Tang Q, Rayner S, Britt WJ, McVoy MA, Luo MH, Zhao F (2018)
WDR5 Facilitates Human Cytomegalovirus Replication by Promoting Capsid Nuclear Egress
J Virol, 92 (9)
DOI 10.1128/JVI.00207-18, PubMed 29437978

Publications 2017

Cheng S, Jiang X, Yang B, Wen L, Zhao F, Zeng WB, Liu XJ, Dong X, Sun JY, Ming YZ, Zhu H, Rayner S, Tang Q, Fortunato E, Luo MH (2017)
Infected T98G glioblastoma cells support human cytomegalovirus reactivation from latency
Virology, 510, 205-215
DOI 10.1016/j.virol.2017.07.023, PubMed 28750324

Jiang HF, Wang W, Jiang X, Zeng WB, Shen ZZ, Song YG, Yang H, Liu XJ, Dong X, Zhou J, Sun JY, Yu FL, Guo L, Cheng T, Rayner S, Zhao F, Zhu H, Luo MH (2017)
ORF7 of Varicella-Zoster Virus Is Required for Viral Cytoplasmic Envelopment in Differentiated Neuronal Cells
J Virol, 91 (12)
DOI 10.1128/JVI.00127-17, PubMed 28356523

Liu XJ, Yang B, Huang SN, Wu CC, Li XJ, Cheng S, Jiang X, Hu F, Ming YZ, Nevels M, Britt WJ, Rayner S, Tang Q, Zeng WB, Zhao F, Luo MH (2017)
Human cytomegalovirus IE1 downregulates Hes1 in neural progenitor cells as a potential E3 ubiquitin ligase
PLoS Pathog, 13 (7), e1006542
DOI 10.1371/journal.ppat.1006542, PubMed 28750047

Rayner S, Bruhn S, Vallhov H, Andersson A, Billmyre RB, Scheynius A (2017)
Identification of small RNAs in extracellular vesicles from the commensal yeast Malassezia sympodialis
Sci Rep, 7, 39742
DOI 10.1038/srep39742, PubMed 28051166

Publications 2016

Pan X, Li XJ, Liu XJ, Yuan H, Li JF, Duan YL, Ye HQ, Fu YR, Qiao GH, Wu CC, Yang B, Tian XH, Hu KH, Miao LF, Chen XL, Zheng J, Rayner S, Schwartz PH, Britt WJ, Xu J, Luo MH (2016)
Correction for Pan et al., Later Passages of Neural Progenitor Cells from Neonatal Brain Are More Permissive for Human Cytomegalovirus Infection
J Virol, 90 (22), 10431-10433
DOI 10.1128/JVI.01780-16, PubMed 27794070

Publications 2015

Han N, Adams J, Fang W, Liu SQ, Rayner S (2015)
Investigation of the genotype III to genotype I shift in Japanese encephalitis virus and the impact on human cases
Virol Sin, 30 (4), 277-89
DOI 10.1007/s12250-015-3621-4, PubMed 26311492

Li XJ, Liu XJ, Yang B, Fu YR, Zhao F, Shen ZZ, Miao LF, Rayner S, Chavanas S, Zhu H, Britt WJ, Tang Q, McVoy MA, Luo MH (2015)
Human Cytomegalovirus Infection Dysregulates the Localization and Stability of NICD1 and Jag1 in Neural Progenitor Cells
J Virol, 89 (13), 6792-804
DOI 10.1128/JVI.00351-15, PubMed 25903338

Liu SQ, Deng CL, Yuan ZM, Rayner S, Zhang B (2015)
Identifying the pattern of molecular evolution for Zaire ebolavirus in the 2014 outbreak in West Africa
Infect Genet Evol, 32, 51-9
DOI 10.1016/j.meegid.2015.02.024, PubMed 25745889

Liu SQ, Rayner S, Zhang B (2015)
How Ebola has been evolving in West Africa
Trends Microbiol, 23 (7), 387-8
DOI 10.1016/j.tim.2015.05.003, PubMed 25986056

Tao XY, Guo ZY, Li H, Jiao WT, Shen XX, Zhu WY, Rayner S, Tang Q (2015)
Rabies Cases in the West of China Have Two Distinct Origins
PLoS Negl Trop Dis, 9 (10), e0004140
DOI 10.1371/journal.pntd.0004140, PubMed 26484668

Xu K, Yuan Z, Rayner S, Hu X (2015)
Genome comparison provides molecular insights into the phylogeny of the reassigned new genus Lysinibacillus
BMC Genomics, 16 (1), 140
DOI 10.1186/s12864-015-1359-x, PubMed 25888315

Yin F, Wu Z, Fang W, Wu C, Rayner S, Han M, Deng F, Du R, Liu J, Wang M, Wang H, Ning Q, Hu Z (2015)
Resistant mutations and quasispecies complexity of hepatitis B virus during telbivudine treatment
J Gen Virol, 96 (11), 3302-3312
DOI 10.1099/jgv.0.000285, PubMed 26382925

Zhao F, Shen ZZ, Liu ZY, Zeng WB, Cheng S, Ma YP, Rayner S, Yang B, Qiao GH, Jiang HF, Gao S, Zhu H, Xu FQ, Ruan Q, Luo MH (2015)
Identification and BAC construction of Han, the first characterized HCMV clinical strain in China
J Med Virol, 88 (5), 859-70
DOI 10.1002/jmv.24396, PubMed 26426373

Publications 2014

Fu YR, Liu XJ, Li XJ, Shen ZZ, Yang B, Wu CC, Li JF, Miao LF, Ye HQ, Qiao GH, Rayner S, Chavanas S, Davrinche C, Britt WJ, Tang Q, McVoy M, Mocarski E, Luo MH (2014)
MicroRNA miR-21 attenuates human cytomegalovirus replication in neural cells by targeting Cdc25a
J Virol, 89 (2), 1070-82
DOI 10.1128/JVI.01740-14, PubMed 25378484

Han N, Adams J, Chen P, Guo ZY, Zhong XF, Fang W, Li N, Wen L, Tao XY, Yuan ZM, Rayner S (2014)
Comparison of genotypes I and III in Japanese encephalitis virus reveals distinct differences in their genetic and host diversity
J Virol, 88 (19), 11469-79
DOI 10.1128/JVI.02050-14, PubMed 25056890

Liu H, Han N, Fang W, Adams J, Zheng K, Li T, Hu Z, Rayner S (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
Virol Sin, 29 (2), 126-7
DOI 10.1007/s12250-014-3394-1, PubMed 24664817

Song M, Tang Q, Rayner S, Tao XY, Li H, Guo ZY, Shen XX, Jiao WT, Fang W, Wang J, Liang GD (2014)
Human rabies surveillance and control in China, 2005-2012
BMC Infect Dis, 14, 212
DOI 10.1186/1471-2334-14-212, PubMed 24742224

Song M, Tang Q, Rayner S, Tao XY, Shen XX, Liang GD (2014)
Factors influencing the number of rabies cases in children in China
Biomed Environ Sci, 27 (8), 627-32
DOI 10.3967/bes2014.095, PubMed 25189609

Yu F, Zhang G, Zhong X, Han N, Song Y, Zhao L, Cui M, Rayner S, Fu ZF (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
Arch Virol, 159 (7), 1593-601
DOI 10.1007/s00705-013-1966-2, PubMed 24395077

Zhu L, Liu J, Liang F, Rayner S, Xiong J (2014)
Predicting response to preoperative chemotherapy agents by identifying drug action on modeled microRNA regulation networks
PLoS One, 9 (5), e98140
DOI 10.1371/journal.pone.0098140, PubMed 24848634

Publications 2013

Chen P, Gan Y, Han N, Fang W, Li J, Zhao F, Hu K, Rayner S (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
DOI 10.1371/journal.pone.0060098, PubMed 23577084

Guo Z, Tao X, Yin C, Han N, Yu J, Li H, Liu H, Fang W, Adams J, Wang J, Liang G, Tang Q, Rayner S (2013)
National borders effectively halt the spread of rabies: the current rabies epidemic in China is dislocated from cases in neighboring countries
PLoS Negl Trop Dis, 7 (1), e2039
DOI 10.1371/journal.pntd.0002039, PubMed 23383359

Huang Y, Tang Q, Rayner S, Gong K, Song B, Liang GD (2013)
Pathogenicity of rabies viruses isolated in China: two fixed strains and a street strain
Biomed Environ Sci, 26 (7), 552-61
DOI 10.3967/0895-3988.2013.07.006, PubMed 23895700

Li L, Han N, Lu J, Li T, Zhong X, Wu H, Rayner S, Chen L, Liu Y, Wang X, Li H, Li J (2013)
Genetic characterization and transmitted drug resistance of the HIV type 1 epidemic in men who have sex with men in Beijing, China
AIDS Res Hum Retroviruses, 29 (3), 633-7
DOI 10.1089/aid.2012.0281, PubMed 23121221

Pan X, Li XJ, Liu XJ, Yuan H, Li JF, Duan YL, Ye HQ, Fu YR, Qiao GH, Wu CC, Yang B, Tian XH, Hu KH, Miao LF, Chen XL, Zheng J, Rayner S, Schwartz PH, Britt WJ, Xu J, Luo MH (2013)
Later passages of neural progenitor cells from neonatal brain are more permissive for human cytomegalovirus infection
J Virol, 87 (20), 10968-79
DOI 10.1128/JVI.01120-13, PubMed 23903847

Tao X, Han N, Guo Z, Tang Q, Rayner S, Liang G (2013)
Molecular characterization of China human rabies vaccine strains
Virol Sin, 28 (2), 116-23
DOI 10.1007/s12250-013-3314-9, PubMed 23575734

Tao XY, Tang Q, Rayner S, Guo ZY, Li H, Lang SL, Yin CP, Han N, Fang W, Adams J, Song M, Liang GD (2013)
Molecular phylodynamic analysis indicates lineage displacement occurred in Chinese rabies epidemics between 1949 to 2010
PLoS Negl Trop Dis, 7 (7), e2294
DOI 10.1371/journal.pntd.0002294, PubMed 23875035

Wang L, Wu H, Tao X, Li H, Rayner S, Liang G, Tang Q (2013)
Genetic and evolutionary characterization of RABVs from China using the phosphoprotein gene
Virol J, 10, 14
DOI 10.1186/1743-422X-10-14, PubMed 23294868

Wu H, Wang L, Tao X, Li H, Rayner S, Liang G, Tang Q (2013)
Genetic diversity and molecular evolution of the rabies virus matrix protein gene in China
Infect Genet Evol, 16, 248-53
DOI 10.1016/j.meegid.2013.02.009, PubMed 23453987

Yang CQ, Miao LF, Pan X, Wu CC, Rayner S, Mocarski ES, Ye HQ, Luo MH (2013)
Natural antisense transcripts of UL123 packaged in human cytomegalovirus virions
Arch Virol, 159 (1), 147-51
DOI 10.1007/s00705-013-1793-5, PubMed 23884634

Ye Y, Wei B, Wen L, Rayner S (2013)
BlastGraph: a comparative genomics tool based on BLAST and graph algorithms
Bioinformatics, 29 (24), 3222-4
DOI 10.1093/bioinformatics/btt553, PubMed 24068035

Zhou Z, Deng F, Han N, Wang H, Sun S, Zhang Y, Hu Z, Rayner S (2013)
Reassortment and migration analysis of Crimean-Congo haemorrhagic fever virus
J Gen Virol, 94 (Pt 11), 2536-2548
DOI 10.1099/vir.0.056374-0, PubMed 23939975

Publications 2012

Adams JT, Gray DJ, Rayner S (2012)
Observation of non-principal plane neutral points in the upwelling polarized light field above a water surface
Appl Opt, 51 (22), 5387-91
DOI 10.1364/AO.51.005387, PubMed 22859026

Duan Y, Miao L, Ye H, Yang C, Fu B, Schwartz PH, Rayner S, Fortunato EA, Luo MH (2012)
A faster immunofluorescence assay for tracking infection progress of human cytomegalovirus
Acta Biochim Biophys Sin (Shanghai), 44 (7), 597-605
DOI 10.1093/abbs/gms041, PubMed 22659494

Hou D, Zhang L, Deng F, Fang W, Wang R, Liu X, Guo L, Rayner S, Chen X, Wang H, Hu Z (2012)
Comparative proteomics reveal fundamental structural and functional differences between the two progeny phenotypes of a baculovirus
J Virol, 87 (2), 829-39
DOI 10.1128/JVI.02329-12, PubMed 23115289

Hu C, Xiong N, Zhang Y, Rayner S, Chen S (2012)
Functional characterization of lipase in the pathogenesis of Staphylococcus aureus
Biochem Biophys Res Commun, 419 (4), 617-20
DOI 10.1016/j.bbrc.2012.02.057, PubMed 22369949

Hu Y, Feng L, Li Y, Zhang Y, Lu P, Rayner S, Chen S (2012)
Ribosomal binding site switching: an effective strategy for high-throughput cloning constructions
PLoS One, 7 (11), e50142
DOI 10.1371/journal.pone.0050142, PubMed 23185557

Huanyu W, Haiyan W, Shihong F, Guifang L, Hong L, Xiaoyan G, Lizhi S, Rayner S, Aiqiang X, Guodong L (2012)
Isolation and identification of a distinct strain of Culex Flavivirus from mosquitoes collected in Mainland China
Virol J, 9, 73
DOI 10.1186/1743-422X-9-73, PubMed 22452813

Lu P, Zhang Y, Li L, Hu Y, Huang L, Li Y, Rayner S, Chen S (2012)
Small non-coding RNA SraG regulates the operon YPK_1206-1205 in Yersinia pseudotuberculosis
FEMS Microbiol Lett, 331 (1), 37-43
DOI 10.1111/j.1574-6968.2012.02548.x, PubMed 22428705

Qin B, Budeus B, Cao L, Wu C, Wang Y, Zhang X, Rayner S, Hoffmann D, Lu M, Chen X (2012)
The amino acid substitutions rtP177G and rtF249A in the reverse transcriptase domain of hepatitis B virus polymerase reduce the susceptibility to tenofovir
Antiviral Res, 97 (2), 93-100
DOI 10.1016/j.antiviral.2012.12.007, PubMed 23261845

Wang L, Lv X, Zhai Y, Fu S, Wang D, Rayner S, Tang Q, Liang G (2012)
Genomic characterization of a novel virus of the family Tymoviridae isolated from mosquitoes
PLoS One, 7 (7), e39845
DOI 10.1371/journal.pone.0039845, PubMed 22848363

Yin CP, Zhou H, Wu H, Tao XY, Rayner S, Wang SM, Tang Q, Liang GD (2012)
Analysis on factors related to rabies epidemic in China from 2007-2011
Virol Sin, 27 (2), 132-43
DOI 10.1007/s12250-012-3244-y, PubMed 22492004

Yu J, Li H, Tang Q, Rayner S, Han N, Guo Z, Liu H, Adams J, Fang W, Tao X, Wang S, Liang G (2012)
The spatial and temporal dynamics of rabies in China
PLoS Negl Trop Dis, 6 (5), e1640
DOI 10.1371/journal.pntd.0001640, PubMed 22563518

Yu PC, Noguchi A, Inoue S, Tang Q, Rayner S, Liang GD (2012)
Comparison of RFFIT tests with different standard sera and testing procedures
Virol Sin, 27 (3), 187-93
DOI 10.1007/s12250-012-3247-8, PubMed 22684473

Publications 2011

Chen P, Rayner S, Hu KH (2011)
Advances of bioinformatics tools applied in virus epitopes prediction
Virol Sin, 26 (1), 1-7
DOI 10.1007/s12250-011-3159-4, PubMed 21331885

Han N, Rayner S (2011)
Epidemiology and mutational analysis of global strains of Crimean-Congo haemorrhagic fever virus
Virol Sin, 26 (4), 229-44
DOI 10.1007/s12250-011-3211-z, PubMed 21847754

Pan XL, Liu H, Wang HY, Fu SH, Liu HZ, Zhang HL, Li MH, Gao XY, Wang JL, Sun XH, Lu XJ, Zhai YG, Meng WS, He Y, Wang HQ, Han N, Wei B, Wu YG, Feng Y, Yang DJ, Wang LH, Tang Q, Xia G, Kurane I, Rayner S et al. (2011)
Emergence of genotype I of Japanese encephalitis virus as the dominant genotype in Asia
J Virol, 85 (19), 9847-53
DOI 10.1128/JVI.00825-11, PubMed 21697481

Qiu J, Qin B, Rayner S, Wu CC, Pei RJ, Xu S, Wang Y, Chen XW (2011)
Novel evidence suggests Hepatitis B virus surface proteins participate in regulation of HBV genome replication
Virol Sin, 26 (2), 131-8
DOI 10.1007/s12250-011-3190-0, PubMed 21468936

Wei B, Han N, Liu HZ, Rayner A, Rayner S (2011)
Use of mutual information arrays to predict coevolving sites in the full length HIV gp120 protein for subtypes B and C
Virol Sin, 26 (2), 95-104
DOI 10.1007/s12250-011-3188-7, PubMed 21468932

Wu Y, Wei B, Liu H, Li T, Rayner S (2011)
MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences
BMC Bioinformatics, 12, 107
DOI 10.1186/1471-2105-12-107, PubMed 21504621

Zhao JR, Li YD, Pan LM, Zhu N, Ni HX, Xu GZ, Jiang YZ, Huo XX, Xu JQ, Xia H, Han N, Tang S, Zhang Z, Kou Z, Rayner S, Li TX (2011)
Genetic characteristics of 2009 pandemic H1N1 influenza a viruses isolated from Mainland China
Virol Sin, 26 (6), 418-27
DOI 10.1007/s12250-011-3228-3, PubMed 22160942

Publications 2010

Xiong J, Liu J, Rayner S, Li Y, Chen S (2010)
Protein-protein interaction reveals synergistic discrimination of cancer phenotype
Cancer Inform, 9, 61-6
DOI 10.4137/cin.s3899, PubMed 20458363

Xiong J, Liu J, Rayner S, Tian Z, Li Y, Chen S (2010)
Pre-clinical drug prioritization via prognosis-guided genetic interaction networks
PLoS One, 5 (11), e13937
DOI 10.1371/journal.pone.0013937, PubMed 21085674

Yin Y, Xiao Y, Liu HZ, Hao F, Rayner S, Tang H, Zhou NY (2010)
Characterization of catabolic meta-nitrophenol nitroreductase from Cupriavidus necator JMP134
Appl Microbiol Biotechnol, 87 (6), 2077-85
DOI 10.1007/s00253-010-2666-4, PubMed 20508930

Zhang Y, Hu Y, Yang B, Ma F, Lu P, Li L, Wan C, Rayner S, Chen S (2010)
Duckweed (Lemna minor) as a model plant system for the study of human microbial pathogenesis
PLoS One, 5 (10), e13527
DOI 10.1371/journal.pone.0013527, PubMed 21049039

Publications 2009

Fu B, Sun F, Li B, Yang L, Zeng Y, Sun X, Xu F, Rayner S, Guadalupe M, Gao SJ, Wang L (2009)
Seroprevalence of Kaposi's sarcoma-associated herpesvirus and risk factors in Xinjiang, China
J Med Virol, 81 (8), 1422-31
DOI 10.1002/jmv.21550, PubMed 19551832

Jiang Y, Deng F, Rayner S, Wang H, Hu Z (2009)
Evidence of a major role of GP64 in group I alphabaculovirus evolution
Virus Res, 142 (1-2), 85-91
DOI 10.1016/j.virusres.2009.01.015, PubMed 19428740

Ming P, Yan J, Rayner S, Meng S, Xu G, Tang Q, Wu J, Luo J, Yang X (2009)
A history estimate and evolutionary analysis of rabies virus variants in China
J Gen Virol, 91 (Pt 3), 759-64
DOI 10.1099/vir.0.016436-0, PubMed 19889927

Pan XL, Wang HY, Fu SH, Hian N, Liu HZ, Rayner S, Hang GD (2009)
[Molecular characterization of full-length genome of Japanese encephalitis virus strain patient's cerebrospinal fluid in China]
Zhonghua Shi Yan He Lin Chuang Bing Du Xue Za Zhi, 23 (1), 26-8
PubMed 19799010

Publications 2008

Deng X, Deng X, Rayner S, Liu X, Zhang Q, Yang Y, Li N (2008)
DHPC: a new tool to express genome structural features
Genomics, 91 (5), 476-83
DOI 10.1016/j.ygeno.2008.01.003, PubMed 18343093

Deng X, Liu H, Shao Y, Rayner S, Yang R (2008)
The epidemic origin and molecular properties of B': a founder strain of the HIV-1 transmission in Asia
AIDS, 22 (14), 1851-8
DOI 10.1097/QAD.0b013e32830f4c62, PubMed 18753865

Li X, Jin H, Wu Z, Rayner S, Wang B (2008)
A continuous process to extract plasmid DNA based on alkaline lysis
Nat Protoc, 3 (2), 176-80
DOI 10.1038/nprot.2007.526, PubMed 18274518

Publications 2007

Li X, Jin H, Wu Z, Rayner S, Yin J, Yu Y, Zhang W, He Z, Wang C, Wang B (2007)
An automated process to extract plasmid DNA by alkaline lysis
Appl Microbiol Biotechnol, 75 (5), 1217-23
DOI 10.1007/s00253-007-0925-9, PubMed 17387470

Publications 2006

Xiong J, Rayner S, Luo K, Li Y, Chen S (2006)
Genome wide prediction of protein function via a generic knowledge discovery approach based on evidence integration
BMC Bioinformatics, 7, 268
DOI 10.1186/1471-2105-7-268, PubMed 16725034

Publications 2002

Livesay EA, Liu YH, Luebke KJ, Irick J, Belosludtsev Y, Rayner S, Balog R, Johnston SA (2002)
A scalable high-throughput chemical synthesizer
Genome Res, 12 (12), 1950-60
DOI 10.1101/gr.359002, PubMed 12466300

Rombel IT, Sykes KF, Rayner S, Johnston SA (2002)
ORF-FINDER: a vector for high-throughput gene identification
Gene, 282 (1-2), 33-41
DOI 10.1016/s0378-1119(01)00819-8, PubMed 11814675