Kellam Group
Our Research and Approach
Although virus genomes are small they are incredibly diverse and subject to rapid genetic change. In addition, the host organisms viruses infected produce a wide array of defences encoded by genes that are also subjected to accelerated evolution. At the most extreme end of this evolution is the mutation and selection of unique B cells that produce antibodies to counter the diversity of virus proteins and provide immunological memory. The aim of the Virus Genomics team was to understand how genetic changes in viruses and hosts influence the biological properties of viral pathogenesis, persistence and host susceptibility to infection.
Publications
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Role of HIV-specific CD8+ T cells in pediatric HIV cure strategies after widespread early viral escape.
Journal of Experimental Medicine 2017
DOI: 10.1084/jem.20162123
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Heterogeneity of the Epstein-Barr virus major internal repeat reveals evolutionary mechanisms of EBV and a functional defect in the prototype EBV strain B95-8.
Journal of virology 2017
PUBMED: 28904201; DOI: 10.1128/JVI.00920-17
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From clinical sample to complete genome: Comparing methods for the extraction of HIV-1 RNA for high-throughput deep sequencing.
Virus research 2017;239;10-16
PUBMED: 27497916; DOI: 10.1016/j.virusres.2016.08.004
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Characterization of Posa and Posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam.
Virus evolution 2017;3;2;vex022
PUBMED: 28948041; PMC: 5597861; DOI: 10.1093/ve/vex022
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Optimisation ofex vivomemory B cell expansion/differentiation for interrogation of rare peripheral memory B cell subset responses.
Wellcome open research 2017;2;97
PUBMED: 29588920; PMC: 5843844; DOI: 10.12688/wellcomeopenres.11386.1
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Eye on the B-ALL: B-cell receptor repertoires reveal persistence of numerous B-lymphoblastic leukemia subclones from diagnosis to relapse.
Leukemia 2016;30;12;2312-2321
PUBMED: 27211266; PMC: 5155029; DOI: 10.1038/leu.2016.142
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Dynamic variation of CD5 surface expression levels within individual chronic lymphocytic leukaemia clones.
Experimental hematology 2016
PUBMED: 27693386; DOI: 10.1016/j.exphem.2016.09.010
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Resistance of Transmitted Founder HIV-1 to IFITM-Mediated Restriction.
Cell host & microbe 2016
PUBMED: 27640936; DOI: 10.1016/j.chom.2016.08.006
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Ebola virus disease cluster — Northern Sierra Leone, January 2016
Morbidity and Mortality Weekly Report 2016;65;26;681-3
DOI: 10.15585/mmwr.mm6526a4; URL: http://dx.doi.org/10.15585/mm...wr.mm6526a4.
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Alphavirus restriction by IFITM proteins.
Traffic (Copenhagen, Denmark) 2016
PUBMED: 27219333; DOI: 10.1111/tra.12416
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Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intra-Host HIV Infection.
Genetics 2016
PUBMED: 26857628; DOI: 10.1534/genetics.115.177931
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Complete Genome Characterization of Two Wild-Type Measles Viruses from Vietnamese Infants during the 2014 Outbreak.
Genome announcements 2016;4;2
PUBMED: 27081130; DOI: 10.1128/genomeA.00250-16
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Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.
Virus evolution 2016;2;1;vew016
PUBMED: 28694998; PMC: 5499387; DOI: 10.1093/ve/vew016
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The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases.
EcoHealth 2015;12;4;726-35
PUBMED: 26403795; PMC: 4700077; DOI: 10.1007/s10393-015-1061-0
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A novel genus in the order Picornavirales detected in human stool.
The Journal of general virology 2015;96;11;3440-3
PUBMED: 26354795; DOI: 10.1099/jgv.0.000279
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Molecular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013.
Journal of virology 2015;89;19;9920-31
PUBMED: 26202246; PMC: 4577897; DOI: 10.1128/JVI.00840-15
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Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management.
Science translational medicine 2015;7;307;307rv5
PUBMED: 26424572; DOI: 10.1126/scitranslmed.aab0191
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Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2015;370;1676
PUBMED: 26194755; PMC: 4528418; DOI: 10.1098/rstb.2014.0241
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Widespread Reassortment Shapes the Evolution and Epidemiology of Bluetongue Virus following European Invasion.
PLoS pathogens 2015;11;8;e1005056
PUBMED: 26252219; PMC: 4529188; DOI: 10.1371/journal.ppat.1005056
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IVA: accurate de novo assembly of RNA virus genomes.
Bioinformatics (Oxford, England) 2015;31;14;2374-6
PUBMED: 25725497; PMC: 4495290; DOI: 10.1093/bioinformatics/btv120
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Disease progression despite protective HLA expression in an HIV-infected transmission pair.
Retrovirology 2015;12;55
PUBMED: 26123575; PMC: 4487201; DOI: 10.1186/s12977-015-0179-z
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Discovery of a polyomavirus in European badgers (Meles meles) and the evolution of host range in the family Polyomaviridae.
The Journal of general virology 2015;96;Pt 6;1411-22
PUBMED: 25626684; PMC: 4635489; DOI: 10.1099/vir.0.000071
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Bat and pig IFN-induced transmembrane protein 3 restrict cell entry by influenza virus and lyssaviruses.
The Journal of general virology 2015;96;Pt 5;991-1005
PUBMED: 25614588; PMC: 4631062; DOI: 10.1099/vir.0.000058
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Genome diversity of Epstein-Barr virus from multiple tumor types and normal infection.
Journal of virology 2015;89;10;5222-37
PUBMED: 25787276; PMC: 4442510; DOI: 10.1128/JVI.03614-14
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A novel X-linked trichothiodystrophy associated with a nonsense mutation in RNF113A.
Journal of medical genetics 2015;52;4;269-74
PUBMED: 25612912; DOI: 10.1136/jmedgenet-2014-102418
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Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing.
Journal of virology 2015;89;7;3444-54
PUBMED: 25609811; PMC: 4403408; DOI: 10.1128/JVI.03391-14
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Host genetics of Epstein-Barr virus infection, latency and disease.
Reviews in medical virology 2015;25;2;71-84
PUBMED: 25430668; PMC: 4407908; DOI: 10.1002/rmv.1816
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Identification of a novel human rhinovirus C type by antibody capture VIDISCA-454.
Viruses 2015;7;1;239-51
PUBMED: 25606972; PMC: 4306836; DOI: 10.3390/v7010239
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Novel porcine-like human G26P[19] rotavirus identified in hospitalized paediatric diarrhoea patients in Ho Chi Minh City, Vietnam.
The Journal of general virology 2014;95;Pt 12;2727-33
PUBMED: 25121549; PMC: 4233630; DOI: 10.1099/vir.0.068403-0
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Molecular evolution of broadly neutralizing Llama antibodies to the CD4-binding site of HIV-1.
PLoS pathogens 2014;10;12;e1004552
PUBMED: 25522326; PMC: 4270772; DOI: 10.1371/journal.ppat.1004552
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Respiratory tract samples, viral load, and genome fraction yield in patients with Middle East respiratory syndrome.
The Journal of infectious diseases 2014;210;10;1590-4
PUBMED: 24837403; DOI: 10.1093/infdis/jiu292
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Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom.
Journal of virology 2014;88;22;13269-83
PUBMED: 25210166; PMC: 4249111; DOI: 10.1128/JVI.01636-14
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Evidence for camel-to-human transmission of MERS coronavirus.
The New England journal of medicine 2014;371;14;1360
PUBMED: 25271614; DOI: 10.1056/NEJMc1409847
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Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting.
Journal of virology 2014;88;19;11056-69
PUBMED: 25056894; PMC: 4178781; DOI: 10.1128/JVI.01333-14
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Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest?
Journal of acquired immune deficiency syndromes (1999) 2014;67;2;181-95
PUBMED: 24977473; PMC: 4304655; DOI: 10.1097/QAI.0000000000000271
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Genomic diversity of Epstein-Barr virus genomes isolated from primary nasopharyngeal carcinoma biopsy samples.
Journal of virology 2014;88;18;10662-72
PUBMED: 24991008; PMC: 4178900; DOI: 10.1128/JVI.01665-14
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Community case clusters of Middle East respiratory syndrome coronavirus in Hafr Al-Batin, Kingdom of Saudi Arabia: a descriptive genomic study.
International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2014;23;63-8
PUBMED: 24699184; PMC: 4441753; DOI: 10.1016/j.ijid.2014.03.1372
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Human infection with MERS coronavirus after exposure to infected camels, Saudi Arabia, 2013.
Emerging infectious diseases 2014;20;6;1012-5
PUBMED: 24857749; PMC: 4036761; DOI: 10.3201/eid2006.140402
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Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus.
mBio 2014;5;1
PUBMED: 24549846; PMC: 3944817; DOI: 10.1128/mBio.01062-13
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Complete Genome Sequence of the WHO International Standard for HIV-1 RNA Determined by Deep Sequencing.
Genome announcements 2014;2;1
PUBMED: 24503998; PMC: 3916492; DOI: 10.1128/genomeA.01254-13
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IFITM proteins-cellular inhibitors of viral entry.
Current opinion in virology 2014;4;71-7
PUBMED: 24480526; DOI: 10.1016/j.coviro.2013.11.004
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A systematic review of definitions of extreme phenotypes of HIV control and progression.
AIDS (London, England) 2014;28;2;149-62
PUBMED: 24149086; PMC: 3882304; DOI: 10.1097/QAD.0000000000000049
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A membrane topology model for human interferon inducible transmembrane protein 1.
PloS one 2014;9;8;e104341
PUBMED: 25105503; PMC: 4126714; DOI: 10.1371/journal.pone.0104341
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European surveillance network for influenza in pigs: surveillance programs, diagnostic tools and Swine influenza virus subtypes identified in 14 European countries from 2010 to 2013.
PloS one 2014;9;12;e115815
PUBMED: 25542013; PMC: 4277368; DOI: 10.1371/journal.pone.0115815
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Host genetic variants and gene expression patterns associated with Epstein-Barr virus copy number in lymphoblastoid cell lines.
PloS one 2014;9;10;e108384
PUBMED: 25290448; PMC: 4188571; DOI: 10.1371/journal.pone.0108384
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Chicken interferon-inducible transmembrane protein 3 restricts influenza viruses and lyssaviruses in vitro.
Journal of virology 2013;87;23;12957-66
PUBMED: 24067955; PMC: 3838109; DOI: 10.1128/JVI.01443-13
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Amphotericin B increases influenza A virus infection by preventing IFITM3-mediated restriction.
Cell reports 2013;5;4;895-908
PUBMED: 24268777; PMC: 3898084; DOI: 10.1016/j.celrep.2013.10.033
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Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations.
Genome research 2013;23;11;1874-84
PUBMED: 23742949; PMC: 3814887; DOI: 10.1101/gr.154815.113
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Persistence of HIV-1 transmitted drug resistance mutations.
The Journal of infectious diseases 2013;208;9;1459-63
PUBMED: 23904291; PMC: 3789571; DOI: 10.1093/infdis/jit345
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Modeling the association of space, time, and host species with variation of the HA, NA, and NS genes of H5N1 highly pathogenic avian influenza viruses isolated from birds in Romania in 2005-2007.
Avian diseases 2013;57;3;612-21
PUBMED: 24283126; PMC: 3980047; DOI: 10.1637/10494-011713-Reg.1
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Hospital outbreak of Middle East respiratory syndrome coronavirus.
The New England journal of medicine 2013;369;5;407-16
PUBMED: 23782161; PMC: 4029105; DOI: 10.1056/NEJMoa1306742
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Metagenomic study of the viruses of African straw-coloured fruit bats: detection of a chiropteran poxvirus and isolation of a novel adenovirus.
Virology 2013;441;2;95-106
PUBMED: 23562481; PMC: 3667569; DOI: 10.1016/j.virol.2013.03.014
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The CD225 domain of IFITM3 is required for both IFITM protein association and inhibition of influenza A virus and dengue virus replication.
Journal of virology 2013;87;14;7837-52
PUBMED: 23658454; PMC: 3700195; DOI: 10.1128/JVI.00481-13
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Activation of the B cell antigen receptor triggers reactivation of latent Kaposi's sarcoma-associated herpesvirus in B cells.
Journal of virology 2013;87;14;8004-16
PUBMED: 23678173; PMC: 3700181; DOI: 10.1128/JVI.00506-13
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Population genomics of post-vaccine changes in pneumococcal epidemiology.
Nature genetics 2013;45;6;656-63
PUBMED: 23644493; PMC: 3725542; DOI: 10.1038/ng.2625
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Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus.
Emerging infectious diseases 2013;19;5;736-42B
PUBMED: 23693015; PMC: 3647518; DOI: 10.3201/eid1905.130057
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Evolution of equine influenza virus in vaccinated horses.
Journal of virology 2013;87;8;4768-71
PUBMED: 23388708; PMC: 3624384; DOI: 10.1128/JVI.03379-12
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The evolutionary dynamics of influenza A virus adaptation to mammalian hosts.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013;368;1614;20120382
PUBMED: 23382435; PMC: 3678336; DOI: 10.1098/rstb.2012.0382
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Viral population analysis and minority-variant detection using short read next-generation sequencing.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013;368;1614;20120205
PUBMED: 23382427; PMC: 3678329; DOI: 10.1098/rstb.2012.0205
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Different patterns of Epstein-Barr virus latency in endemic Burkitt lymphoma (BL) lead to distinct variants within the BL-associated gene expression signature.
Journal of virology 2013;87;5;2882-94
PUBMED: 23269792; PMC: 3571367; DOI: 10.1128/JVI.03003-12
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Restriction of V3 region sequence divergence in the HIV-1 envelope gene during antiretroviral treatment in a cohort of recent seroconverters.
Retrovirology 2013;10;8
PUBMED: 23331949; PMC: 3605130; DOI: 10.1186/1742-4690-10-8
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Autologous antibody capture to enrich immunogenic viruses for viral discovery.
PloS one 2013;8;11;e78454
PUBMED: 24223808; PMC: 3817278; DOI: 10.1371/journal.pone.0078454
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Defining the range of pathogens susceptible to Ifitm3 restriction using a knockout mouse model.
PloS one 2013;8;11;e80723
PUBMED: 24278312; PMC: 3836756; DOI: 10.1371/journal.pone.0080723
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Interferon-induced transmembrane protein-3 genetic variant rs12252-C is associated with severe influenza in Chinese individuals.
Nature communications 2013;4;1418
PUBMED: 23361009; PMC: 3562464; DOI: 10.1038/ncomms2433
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Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes.
Journal of clinical microbiology 2012;50;12;3838-44
PUBMED: 22993180; PMC: 3502977; DOI: 10.1128/JCM.01516-12
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Estimating reassortment rates in co-circulating Eurasian swine influenza viruses.
The Journal of general virology 2012;93;Pt 11;2326-36
PUBMED: 22971819; PMC: 3542128; DOI: 10.1099/vir.0.044503-0
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Permissive and restricted virus infection of murine embryonic stem cells.
The Journal of general virology 2012;93;Pt 10;2118-30
PUBMED: 22815272; PMC: 3541792; DOI: 10.1099/vir.0.043406-0
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Evolutionary dynamics of local pandemic H1N1/2009 influenza virus lineages revealed by whole-genome analysis.
Journal of virology 2012;86;1;11-8
PUBMED: 22013031; PMC: 3255882; DOI: 10.1128/JVI.05347-11
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Metagenomics and the molecular identification of novel viruses.
Veterinary journal (London, England : 1997) 2011;190;2;191-8
PUBMED: 21111643; DOI: 10.1016/j.tvjl.2010.10.014
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Disease-associated XMRV sequences are consistent with laboratory contamination.
Retrovirology 2010;7;1;111
PUBMED: 21171979; PMC: 3018392; DOI: 10.1186/1742-4690-7-111
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The RING-CH ligase K5 antagonizes restriction of KSHV and HIV-1 particle release by mediating ubiquitin-dependent endosomal degradation of tetherin.
PLoS pathogens 2010;6;4;e1000843
PUBMED: 20419159; PMC: 2855335; DOI: 10.1371/journal.ppat.1000843
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Regulation of the Epstein-Barr virus Zp promoter in B lymphocytes during reactivation from latency.
The Journal of general virology 2010;91;Pt 3;622-9
PUBMED: 19923262; DOI: 10.1099/vir.0.017277-0
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KSHV-encoded miRNAs target MAF to induce endothelial cell reprogramming.
Genes & development 2010;24;2;195-205
PUBMED: 20080955; PMC: 2807354; DOI: 10.1101/gad.553410
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X-box binding protein 1 contributes to induction of the Kaposi's sarcoma-associated herpesvirus lytic cycle under hypoxic conditions.
Journal of virology 2009;83;14;7202-9
PUBMED: 19403667; PMC: 2704782; DOI: 10.1128/JVI.00076-09
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Genome-wide innate immune responses in HIV-1-infected macrophages are preserved despite attenuation of the NF-kappa B activation pathway.
Journal of immunology (Baltimore, Md. : 1950) 2009;182;1;319-28
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Computational inference of replication and transcription activator regulator activity in herpesvirus from gene expression data.
IET systems biology 2008;2;6;385-96
PUBMED: 19045834; DOI: 10.1049/iet-syb:20070053
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X box binding protein XBP-1s transactivates the Kaposi's sarcoma-associated herpesvirus (KSHV) ORF50 promoter, linking plasma cell differentiation to KSHV reactivation from latency.
Journal of virology 2007;81;24;13578-86
PUBMED: 17928342; PMC: 2168861; DOI: 10.1128/JVI.01663-07
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A statistical model for HIV-1 sequence classification using the subtype analyser (STAR).
Bioinformatics (Oxford, England) 2005;21;17;3535-40
PUBMED: 16046498; DOI: 10.1093/bioinformatics/bti569
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Kaposi's sarcoma-associated herpesvirus-infected primary effusion lymphoma has a plasma cell gene expression profile.
Proceedings of the National Academy of Sciences of the United States of America 2003;100;18;10399-404
PUBMED: 12925741; PMC: 193573; DOI: 10.1073/pnas.1630810100