Prof Paul Kellam

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Personal Profile

Name: Paul Kellam Email: p.kellam@ucl.ac.uk
Title: Prof Tel: 020 7679 9559
Department: Div of Infection & Immunity Fax: 020 7679 9555
Position: Honorary Professor of Viral Pathogenesis Address: Windeyer Institute, 46 Cleveland Street, London, W1T 4JF
Research Domain: Cancer, Global Health, Infection, Immunology & Inflammation, Personalised Medicine Web Page: Personal Web Page

Profile

Research Description

The aim of our research group is to explore how host and pathogen gene functions and gene expression programs are integrated during disease processes and during effective host responses to infection. The focused use of molecular, genome scale and computational methods are essential to understand the co-ordinated effects of infections on the host. The Centre for Post Genomic Virology in the Division of Infection & Immunity was established to enable the integration of computational biology and high throughput post genomic biology, with existing molecular and clinical virology. This work is within the MRC/UCL Centre for Medical Molecular Virology. Our research interests focus on two medically important groups of viruses, the herpesviruses especially the beta and gamma herpesviruses and the retroviruses, especially HIV. We are using whole genome microarrays and molecular virology to understand how human herpesviruses such as Kaposi's sarcoma associated herpesvirus (KSHV) establish a latent infection and reactivate into the lytic cycle of replication. In this context we are particularly interested in how different pathogens manipulate host gene expression programmes in lymphoid and myeloid cells. To enable this work we collaborate and produce specialist databases and tools such as the virus database VIDA, the microarray annotation database Gene3D together with our own microarray production and analysis. Our HIV research, in collaboration with Deenan Pillay, focuses on using computational biology to classify HIV sequence variation with our method STAR and determining HIV drug resistance phenotypes from genotypes.

Research Activities

Bioinformatics - prediction of protein functions and functional networks

CMV Pathogenesis and Development of Vaccines

Host and Pathogen Genomics

Humoral immunity to HIV, emerging infections

Immunopathogenesis of hepatitis B virus infection

Retrovirus in gene therapy and xenotransplantation

Education Description

UCL Collaborators

Dr Ariberto Fassati; Prof Paul Griffiths; Prof William Rosenberg; Prof David Jones; Prof Anthony Dickenson; Dr Mike Hubank; Prof Peter Coveney; Prof Mala Maini; Dr Michael Jacobs; Prof Richard Tedder; Prof Robin Weiss; Prof Arne Akbar; Prof Geoffrey Dusheiko; Dr Richard Gilson; Dr Andrew Martin; Prof Mary Collins; Dr Yasu Takeuchi; Prof Deenan Pillay; Prof Chris Boshoff; Dr Richard Milne; Prof Caroline Sabin; Prof Christine Orengo; Prof Greg Towers

External Collaborators

Publications

    2013

    • Smith SE, Wash RS, Kellam P, Gibson MS, Fife M, Ferrara F, Temperton N, Wright E (2013). Chicken interferon-inducible transmembrane protein 3 restricts influenza viruses and lyssaviruses in vitro. Journal of Virology, 87(23), 12957 - 12966. doi:10.1128/JVI.01443-13

    2009

    • Noursadeghi M, Tsang J, Miller RF, Straschewski S, Kellam P, Chain BM, Katz DR (2009). Genome wide innate immune responses in HIV 1 infected macrophages are preserved despite attenuation of the NF-κappa B activation pathway.. The Journal of Immunology, 182(1), 319 - 328.
    • Rasaiyaah J, Noursadeghi M, Kellam PACBM (2009). Transcriptional and functional defects of dendritic cells derived from the MUTZ-3 leukaemia line.. Immunology, , - .

    2008

    • Hirsch M, Tucker A, Swift S, Martin N, Orengo C, Kellam PAL, X (2008). Improved robustness in time series analysis of gene expression data by polynomial model based clustering..
    • Kellam PAK, A (2008). Plasticity of dendritic cell transcriptional responses to antigen.. In Schonbach C, Ranganathan S, Brusic V (Ed.), Immunoinformatics (pp. 133 - 145). : .
    • Lopes AR, Kellam P, Das A, Dunn C, Kwan A, Turner J, Peppa D, Gilson RJ, Gehring A, Bertoletti A, Maini MK (2008). Bim-mediated deletion of antigen-specific CD8 T cells in patients unable to control HBV infection. Journal of Clinical Investigation, 118(5), 1835 - 1845. doi:10.1172/JCI33402
    • Sadiq KS, Mazzeo MD, Zasada SJ, Manos S, Stoica I, Gale CV, Watson SJ, Kellam P, Brew SAC, P V (2008). Patient-specific simulation as a basis for clinical decision-making.. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 366(1878), 3199 - 3219.
    • Fraser K, Wang Z, Li Y, Kellam PALX (2008). Can graph-cutting improve microarray gene expression reconstructions?. Pattern Recognition Letters, 29(16), 2129 - 2136.
    • Kerr JR, Petty R, Burke B, Gough J, Fear D, Sinclair LI, Mattey DL, Richards SC, Montgomery J, Baldwin DA, Kellam P, Harrison TJ, Griffin GE, Main J, Enlander D, Nutt DJ, Holgate ST (2008). Gene expression subtypes in patients with chronic fatigue syndrome/myalgic encephalomyelitis.. The Journal of Infectious Diseases, 197(8), 1171 - 1184.
    • Yeats C, Lees J, Reid A, Kellam P, Martin N, Liu X, Orengo C (2008). Gene3D: comprehensive structural and functional annotation of genomes.. Nucleic Acids Research, 36, D414 - D418.

    2007

    • Wilson SJ, Tsao EH, Webb BL, Ye H, Dalton-Griffin L, Tsantoulas C, Gale CV, Du MQ, Whitehouse A, Kellam P (2007). 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, 81(24), 13578 - 13586.
    • Ogilvie EM, Khan A, Hubank M, Kellam P, Woo P (2007). Specific gene expression profiles in systemic juvenile idiopathic arthritis. Arthritis Rheum, 56(6), 1954 - 1965.
    • Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, Vandamme AM, Kellam P, Pillay D, UK CGOHDR (2007). Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1. Journal of Virology, 81(23), 13050 - 13056.
    • Rasaiyaah J, Yong K, Katz DR, Kellam P, Chain BM (2007). Dendritic cells and myeloid leukaemias: plasticity and commitment in cell differentiation. British Journal of Haematology, 138(3), 281 - 290.
    • Kerr J, Christian P, Hodgetts A, Langford P, Devanur LD, Petty R, Burke B, Sinclair LI, Richards SCM, Montgomery J, McDermott C, Harrison TJ, Kellam P, Nutt D, Holgate S (2007). Current research priorities in chronic fatigue syndrome/myalgic encephalomyelitis: disease mechanisms, a diagnostic test and specific treatments. Journal of Clinical Pathology, 60(2), 113 - 116. doi:10.1136/jcp.2006.042374
    • Shun MC, Raghavendra NK, Vandegraaff N, Daigle JE, Hughes S, Kellam P, Cherepanov P, Engelman A (2007). LEDGF/p75 functions downstream from preintegration complex formation to effect gene-specific HIV-1 integration. Genes and Development, 21(14), 1767 - 1778.

    2006

    • Vinciotti V, Tucker A, Kellam P, Liu X (2006). Robust Selection of Predictive Genes via a Simple Classifier.. Applied Bioinformatics, 5(1), 1 - 11.
    • Kellam P (2006). Attacking pathogens through their hosts.. Genome Biology, 7(1), 201 - .
    • Hidvegi NC, Sales KM, Izadi D, Ong J, Kellam P, Eastwood D, Butler PE (2006). A low temperature method of isolating normal human articular chondrocytes. Osteoarthritis Cartilage, 14(1), 89 - 93.
    • Gifford R, Kellam P, Dunn DAP, D (2006). The impact of structural and functional constraints acting at the nucleic acid level on the evolution of drug resistance in HIV-1. Antiviral Therapy, 11(5), S57 - S58.
    • Kellam P, Weiss RA (2006). Infectogenomics: Insights from the host genome into infectious diseases.. Cell, 124, 695 - 697.
    • Myers R, Clark C, Khan A, Kellam P, Tedder R (2006). Genotyping Hepatitis B virus from whole- and sub-genomic fragments using position-specific scoring matrices in HBV STAR.. Journal of General Virology, 87(6), 1459 - 1464.
    • Gifford R, de Oliveira T, Rambaut A, Myers RE, Gale CV, Dunn D, Shafer R, Vandamme AM, Kellam P, pillay D, UK CGOHDR (2006). Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity. AIDS, 13;20(11), 1521 - 1529.

    2005

    • Kellam PAG, C (2005). Genome scale views of host and pathogen interactions.. In (Ed.), Encyclopaedia of Genetics, Genomics, Proteomics and Bioinformatics. (pp. - ). : Wiley.
    • Vinciotti V, Khanin R, D'Alimonte D, Liu X, Cattini N, Hotchkiss G, Bucca G, de Jesus O, Rasaiyaah J, Smith CP, Kellam P, Wit E (2005). An experimental evaluation of a loop versus a reference design for two-channel microarrays.. Bioinformatics, 21(4), 492 - 501.
    • O'Niel P, Frasier K, Wang Z, Kellam P, Kok JNAL, X (2005). Pyramidic Clustering of Large Scale Microarray Imagery. The Computer Journal, 48(4), 466 - 479.
    • Kellam P, Swift S, Tucker A, Vinciotti V, Martin N, Orengo C, Liu X (2005). Consensus clustering and functional interpretation of gene expression data. Genome Biology, 5(94), - .
    • Myers RE, Gale CV, Harrison A, Takeuchi Y, Kellam P (2005). A statistical model for HIV-1 sequence, classification using the subtype analyser (STAR). Bioinformatics, 21, 3535 - 3540.
    • Kaushik NK, Fear D, Richards SCM, McDermott CR, Nuwaysir EF, Kellam P, Harrison TJ, Wilkinson RJ, Tyrrell DAJ, Holgate ST, Kerr JR (2005). Gene expression in peripheral blood mononuclear cells from patients with chronic fatigue syndrome.. Journal of Clinical Pathology, 58, 826 - 832.

    2004

    • Swift S, Tucker A, Vinciotti V, Martin N, Orengo C, Liu X, Kellam P (2004). Consensus clustering and functional interpretation of gene-expression data.. Genome Biology, 5(11), 94 - 94. doi:10.1186/gb-2004-5-11-r94
    • Gubser C, Hue S, Kellam P, Smith GL (2004). Poxvirus genomes: a phylogenetic analysis. J GEN VIROL, 85(Pt 1), 105 - 117.
    • Gale CV, Myers R, Tedder RS, Williams IG, Kellam P (2004). Development of a novel human immunodeficiency virus type 1 subtyping tool, Subtype Analyzer (STAR): analysis of subtype distribution in London. AIDS Research and Human Retroviruses, 20(5), 457 - 464.

    2003

    • Kellam P, Liu X (2003). Experimental use of DNA arrays. In Orengo CA, Jones DT, Thornton JM (Ed.), Bioinformatics: gene proteins and computers (pp. - ). : BIOS Scientific Publishers Limited.
    • Jenner RG, Maillard K, Cattini N, Weiss RA, Boshoff C, Wooster R, Kellam P (2003). Kaposi's sarcoma-associated herpes virus-infected primary effusion lymphoma has a plasma cell gene expression profile. Proceedings of the National Academy of Sciences of the United States of America, 100(18), 10399 - 10404. doi:10.1073/pnas.1630810100
    • Voisset C, Myers RE, Carne A, Kellam P, Griffiths DJ (2003). Rabbit endogenous retrovirus-H encodes a functional protease. Journal of General Virology, 84(Pt 1), 215 - 225.
    • Kellam P, Holzerlandt R, Gramastianou E, Jenner R, Kwan A (2003). Viral bioinformatics: computational views of host and pathogen. Immunoinformatics: bioinformatics strategies for better understanding of immune function, (254), 234 - 247.
    • Liu X, Kellam P (2003). Mining gene expression data. In Orengo C, Jones T (Ed.), Bioinformatics: genes proteins and computers (pp. - ). : BIOS Scientific Publishers Limited.

    2002

    • Kellam P, Mar Alba M (2002). Databases and recent applications. Applied Bioinformatics, 1(1), 37 - 42.
    • Ahn JW, Powell KL, Kellam P, Alba MM (2002). Gammaherpesvirus lytic gene expression as characterised by DNA array. Journal of Virology, 76(12), 6244 - 6256.
    • Holzerlandt R, Orengo CA, Kellam P, Mar Alba M (2002). Identification of novel herpesvirus homologues in the human genome. Genome Research, 12(11), 1739 - 1748. doi:10.1101/gr.334302
    • Shepherd AJ, Martin NJ, Johnson RG, Kellam P, Orengo CA (2002). PFDB: A generic protein family database integrating the CATH domain structure database with sequence based protein family resources. Bioinformatics, 18(12), 1666 - 1672.
    • Kellam P, Xiaohui L, Martin NJ, Orengo CA, Swift S, Tucker A (2002). A framework for modelling virus gene expression data. Intelligent Data Analysis, 5, 1 - 13.
    • Kellam P, Albà MM (2002). Virus bioinformatics: databases and recent applications.. Applied Bioinformatics, 1(1), 37 - 42.

    2001

    • Alba MM, Das R, Orengo CA, Kellam P (2001). Genomewide function conservation and phylogeny in the Herpesviridae. Genome Research, 11(1), 43 - 54. doi:10.1101/gr.149801
    • Kellam P (2001). Microarray gene expression database: progress towards an international repository of gene expression data. Genome Biology, 2(5), 4011 - .
    • Kellam P (2001). Post-genomic virology: the impact of bioinformatics, microarrays and proteomics on investigating host and pathogen interactions. Review of Medical Virology, 11(5), 313 - 329.
    • Alba M, Lee D, Pearl F, Shepherd A, Orengo C, Kellam P (2001). VIDA: A Virus Database System for the Orgainsation of Virus Genome Open Reading Frames. Nucleic Acids Research, 29, 133 - 136.
    • Kellam P, Liu X, Martin N, Orengo C, Swift S, Tucker A (2001). Comparing, Contrasting and Combining Clusters in Viral Gene Expression. Proceedings of the Sixth Workshop on Intelligent Data Analysis in Medicine and Pharmacology, 6, 56 - 62.
    • Kellam P, Weiss RA (2001). How technology drives pathogen discovery. Microbiology Today, (28), 16 - 17.
    • Jenner RG, Alba MM, Boshoff C, Kellam P (2001). Kaposi's sarcoma-associated herpesvirus latent and lytic gene expression as revealed by DNA arrays. Journal of Virology, 75(2), 891 - 902.

    2000

    • Radkov SA, Kellam P, Boshoff C (2000). The latent nuclear antigen of Kaposi sarcoma-associated herpesvirus targets the retinoblastoma-E2F pathway and with the oncogene Hras transforms primary rat cells. Nature Medicine, 6(10), 1121 - 1127.
    • Kellam P (2000). Host-pathogen studies in the post-genomic era. Genome Biology, 1(2), 1009 - 10009.
    • Dupin N, Diss T, Kellam P, Tulliez M, Du MQ, Sicard D, Weiss RA, Isaacson PG, Boshoff C (2000). HHV-8 is associated with a plasmablastic variant of Castleman disease that is linked to HHV-8-positive plasmablastic lymphoma. BLOOD, 95(4), 1406 - 1412.

    1999

    • Talbot SJ, Weiss RA, Kellam P, Boshoff C (1999). Transcriptional analysis of human herpesvirus-8 open reading frames 71, 72, 73, K14, and 74 in a primary effusion lymphoma cell line.. Virology, 257(1), 84 - 94.
    • Kellam P, Bourboulia D, Dupin N, Shotton C, Fisher C, Talbot S, Boshoff C, Weiss RA (1999). Characterisation of monoclonal antibodies raised against against the latent nuclear antigen (LNA) of human herpesvirus 8. Journal of Virology, 73, 5149 - 5155.
    • Kellam P (1999). Emerging viruses: their diseases and identification. In (Ed.), AIDS and the New Viruses (pp. 521 - 537). : Academic Press.
    • Dupin N, Fisher C, Kellam P, Ariad S, Tulliez M, Franck N, vanMarck E, Salmon D, Gorin I, Escande JP, Weiss RA, Alitalo K, Boshoff C (1999). Distribution of human herpesvirus-8 latently infected cells in Kaposi's sarcoma, multicentric Castleman's disease, and primary effusion lymphoma. Proceedings of the National Academy of Sciences of the United States of America, 96, 4546 - 4551.

    1998

    • Thomas MC, Ballantine SP, Bethell SS, Bains S, Kellam P, Delves CJ (1998). Single amino acid substitutions disrupt tetramer formation in the dihydroneopterin aldolase enzyme of Pneumocystis carinii.. Biochemistry, 37(33), 11629 - 11636.
    • Weiss RA, Whitby D, Talbot S, Kellam P, Boshoff C (1998). Human herpesvirus Type 8 and Kaposi's sarcoma. Journal of the National Cancer Institute Monographs, 23, 51 - 54.
    • Kellam P (1998). Molecular identification of novel viruses.. Trends in Microbiology, 6(4), 160 - 165.

    1997

    • Weiss RA, Kellam P (1997). Illicit viral DNA.. Nature, 390(6657), 235 - 236.
    • Kellam P, Boshoff C, Whitby D, Matthews S, Weiss RA, Talbot SJ (1997). Identification of a major latent nuclear antigen, LNA-1, in the human herpesvirus 8 genome.. Journal of Human Virology, 1(1), 19 - 29.

    1995

    • Kellam P, Larder BA (1995). Retroviral recombination can lead to linkage of reverse transcriptase mutations that confer increased zidovudine resistance.. Journal of Virology, 69(2), 669 - 674.
    • Kellam P, Dallas WS, Ballantine SP, Delves CJ (1995). Functional cloning of the dihydropteroate synthase gene of Staphylococcus haemolyticus.. FEMS Microbiology Letters, 134(2), 165 - 169.

    1994

    • Kellam P, Larder BA (1994). Recombinant virus assay: a rapid, phenotypic assay for assessment of drug susceptibility of human immunodeficiency virus type 1 isolates.. Antimicrobial Agents and Chemotherapy, 38(1), 23 - 30.
    • Kellam P, Boucher CA, Tijnagel JM, Larder BA (1994). Zidovudine treatment results in the selection of human immunodeficiency virus type 1 variants whose genotypes confer increasing levels of drug resistance.. Journal of General Virology, 75(2), 341 - 351.

    1993

    • Larder BA, Kellam P, Kemp SD (1993). Convergent combination therapy can select viable multidrug-resistant HIV-1 in vitro.. Nature, 365(6445), 451 - 453.
    • Larder BA, Kohli A, Kellam P, Kemp SD, Kronick M, Henfrey RD (1993). Quantitative detection of HIV-1 drug resistance mutations by automated DNA sequencing.. Nature, 365(6447), 671 - 673.
    • Boucher CA, van Leeuwen R, Kellam P, Schipper P, Tijnagel J, Lange JM, Larder BA (1993). Effects of discontinuation of zidovudine treatment on zidovudine sensitivity of human immunodeficiency virus type 1 isolates.. Antimicrobial Agents and Chemotherapy, 37(7), 1525 - 1530.

    1992

    • Boucher CA, Lange JM, Miedema FF, Weverling GJ, Koot M, Mulder JW, Goudsmit J, Kellam P, Larder BA, Tersmette M (1992). HIV-1 biological phenotype and the development of zidovudine resistance in relation to disease progression in asymptomatic individuals during treatment.. AIDS, 6(11), 1259 - 1264.
    • Kellam P, Boucher CA, Larder BA (1992). Fifth mutation in human immunodeficiency virus type 1 reverse transcriptase contributes to the development of high-level resistance to zidovudine.. Proceedings of the National Academy of Sciences of the United States of America, 89(5), 1934 - 1938.
    • Boucher CA, O'Sullivan E, Mulder JW, Ramautarsing C, Kellam P, Darby G, Lange JM, Goudsmit J, Larder BA (1992). Ordered appearance of zidovudine resistance mutations during treatment of 18 human immunodeficiency virus-positive subjects.. The Journal of Infectious Diseases, 165(1), 105 - 110.

    1991

    • St CMH, Martin JL, Tudor-Williams G, Bach MC, Vavro CL, King DM, Kellam P, Kemp SD, Larder BA (1991). Resistance to ddI and sensitivity to AZT induced by a mutation in HIV-1 reverse transcriptase.. Science, 5, 137 - 144.
    • Daly A, Kellam P, Berry ST, Chojecki AJ, Barnes SR (1991). The isolation and characterisation of plant sequences homologous to human hypervariable minisatellites.. EXS, 58, 330 - 341.
    • Larder BA, Kellam P, Kemp SD (1991). Zidovudine resistance predicted by direct detection of mutations in DNA from HIV-infected lymphocytes.. AIDS, 5(2), 137 - 144.

    1990

    • Boucher CA, Tersmette M, Lange JM, Kellam P, de Goede RE, Mulder JW, Darby G, Goudsmit J, Larder BA (1990). Zidovudine sensitivity of human immunodeficiency viruses from high-risk, symptom-free individuals during therapy.. The Lancet, 336(8715), 585 - 590.

    • Recchia A, Wit E, Vinciotti VAKP (). Computational inference of replication and transcription activator regulator activity in herpesviruses from gene expression data.. IET Systems Biology, , - .