Infectious causes of cancer and their detection (2009)
Dalton-Griffin, Lucy, Kellam, Paul
Abstract Molecular techniques for identifying pathogens associated with cancer continue to be developed, including one reported recently in BMC Medical Genomics . Identifying a causal infectious...
Strath, Janet, Georgopoulos, Lindsay J, Kellam, Paul, Blair, G Eric
Abstract Background Cells transformed by human adenoviruses (Ad) exhibit differential capacities to induce tumours in immunocompetent rodents; for example, Ad12-transformed rodent cells are oncogenic...
PREDICTING HIV-1 DRUG RESISTANCE PHENOTYPE FROM GENOTYPE (APRIL 2005) (2008)
Paul Kellam, Yasu Takeuchi, Deenan Pillay, Xiaohui Liu
The global pandemic of Human Immunodeficiency Virus (HIV) is one of the largest causes of infection acquired morbidity and mortality. The impact of HIV infection in countries where antiretroviral...
316 316 316 Increasing and Unusual Genetic Diversity of HIV-1 in the UK (2008)
Robert Gifford, Tulio De Oliveira, Andrew Rambaut, Richard E. Myers, Catherine V. Gale, David Dunn, ...
Phylogenetic analysis of human immunodeficiency type 1 (HIV-1) isolates from around the world reveals three major groups, M, O and N, each of which is proposed to have arisen independently via...
A Framework for Modelling Virus Gene Expression Data (2008)
Paul Kellam, Xiaohui Liu, Nigel Martin, Christine Orengo, Stephen Swift, Allan Tucker
Abstract. Short, high-dimensional, Multivariate Time Series (MTS) data are common in many fields such as medicine, finance and science, and any advance in modelling this kind of data would be...
Gene3D: comprehensive structural and functional annotation of genomes (2008)
Yeats, Corin, Lees, Jonathan, Reid, Adam, Kellam, Paul, Martin, Nigel, Liu, Xinhui, ...
Gene3D provides comprehensive structural and functional annotation of most available protein sequences, including the UniProt, RefSeq and Integr8 resources. The main structural annotation is...
De Oliveira, Tulio, Rambaut, Andrew, Pybus, Oliver G, Dunn, David, ...
With ongoing generation of viral genetic diversity and increasing levels of migration, the global human immunodeficiency virus type 1 (HIV-1) epidemic is becoming increasingly heterogeneous. In this...
De Oliveira, Tulio, Rambaut, Andrew, Myers, Richard E, Gale, Catherine V, Dunn, David, ...
BACKGROUND: The routine use of drug resistance testing provides an abundant source of HIV-1 sequence data. However, it is not clear how reliable standard genotyping of these sequences is for...
Attacking pathogens through their hosts (2006)
Abstract Through understanding the intricacies of host-pathogen interactions, it is now possible to inhibit the growth of microbes, especially viruses, by targeting host-cell proteins and functions....
Pyramidic Clustering of Large-Scale Microarray Images (2005)
O'Neill, Paul, Fraser, Karl, Wang, Zidong, Kellam, Paul, Kok, Joost N., Liu, Xiaohui
With ongoing research and development of imaging techniques such as those involved in brain MRIs, cDNA microarrays and satellite reconnaissance, the need for tools that can intelligently parse larger...
Pyramidic Clustering of Large-Scale Microarray Images (2005)
O'Neill, Paul, Fraser, Karl, Wang, Zidong, Kellam, Paul, Kok, Joost N., Liu, Xiaohui
With ongoing research and development of imaging techniques such as those involved in brain MRIs, cDNA microarrays and satellite reconnaissance, the need for tools that can intelligently parse larger...
Consensus clustering and functional interpretation of gene-expression data (2004)
Swift, Stephen, Tucker, Allan, Vinciotti, Veronica, Martin, Nigel, Orengo, Christine, Liu, Xiaohui, ...
Abstract Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of...
Stephen Swift, Allan Tucker, Veronica Vinciotti, Nigel Martin, Christine Orengo, Xiaohui Liu, ...
electronic version of this article is the complete one and can be
Identification of New Herpesvirus Gene Homologs in the Human Genome (2002)
Holzerlandt, Ria, Orengo, Christine, Kellam, Paul, Albà, M. Mar
Shepherd, Adrian J., Martin, Nigel J., Johnson, Roger G., Kellam, Paul, Orengo, Christine A.
Motivation: The PFDB (Protein Family Database) is a new database designed to integrate protein family-related data with relevant functional and genomic data. It currently manages biological data for...
A report on the third Microarray Gene Expression Database group meeting (MGED3), Stanford University, Palo Alto, California, USA, 29-31 March, 2001.
VIDA: a virus database system for the organization of animal virus genome open reading frames (2001)
Albà, M. Mar, Lee, David, Pearl, Frances M. G., Shepherd, Adrian J., Martin, Nigel, Orengo, Christine A., ...
VIDA is a new virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses. Currently VIDA includes all sequences from GenBank for...
Genomewide Function Conservation and Phylogeny in the Herpesviridae (2001)
Albà, M. Mar, Das, Rhiju, Orengo, Christine A., Kellam, Paul
Host-pathogen studies in the post-genomic era (2000)
Abstract Several studies are starting to show the power of DNA microarrays to identify interactions between animal hosts and their pathogens, and have revealed interesting correlations between host...
Gene expression following HIV-1 infection (2000)
Abstract The use of cDNA arrays has allowed monitoring of the change in expression of host cell genes during HIV-1 infection.
Expressed sequence tag (EST) clustering database (2000)
Abstract The sequence tag alignment and consensus knowledgebase (STACK) is an international collaborative project on EST clustering.
Predicting protein interactions from sequence (2000)
Abstract Bioinformatic analysis has been used to identify gene-fusion events in complete genomes and thus infer protein interactions on the basis of sequence analysis alone.
Analysis of microarray expression data (2000)
Abstract Detailed descriptions of the design and information content of EBI's database ArrayExpress, which is currently under development but aims to be a public repository of gene expression data,...
Dupin, Nicolas, Fisher, Cyril, Kellam, Paul, Ariad, Sam, Tulliez, Micheline, Franck, Nathalie, ...
Human herpesvirus 8 (HHV-8, also called KSHV) is linked to the etiopathogenesis of Kaposi’s sarcoma (KS), multicentric Castleman’s disease (MCD), and primary effusion lymphoma (PEL). The...
VIDA: a virus database system for the organization of animal virus genome open reading frames
Albà, M. Mar, Lee, David, Pearl, Frances M. G., Shepherd, Adrian J., Martin, Nigel, Orengo, Christine A., ...
VIDA is a new virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses. Currently VIDA includes all sequences from GenBank for...
Kellam, Paul, Bourboulia, Dimitra, Dupin, Nicolas, Shotton, Chris, Fisher, Cyril, Talbot, Simon, ...
Human herpesvirus 8 (HHV-8; also designated Kaposi’s sarcoma-associated herpesvirus) is the likely etiological agent of Kaposi’s sarcoma (KS). HHV-8 encodes a latent nuclear antigen (LNA) which...
Kaposi's Sarcoma-Associated Herpesvirus Latent and Lytic Gene Expression as Revealed by DNA Arrays
Jenner, Richard G., Albà, M. Mar, Boshoff, Chris, Kellam, Paul
Kaposi's sarcoma-associated herpesvirus (KSHV; human herpesvirus 8) is associated with three human tumors, Kaposi's sarcoma, primary effusion lymphoma (PEL), and multicentric Castleman's disease....
Gammaherpesvirus Lytic Gene Expression as Characterized by DNA Array
Ahn, Joo Wook, Powell, Kenneth L., Kellam, Paul, Alber, Dagmar G.
Gammaherpesviruses are associated with a number of diseases including lymphomas and other malignancies. Murine gammaherpesvirus 68 (MHV-68) constitutes the most amenable animal model for this family...
Host-pathogen studies in the post-genomic era
Several studies are starting to show the power of DNA microarrays to identify interactions between animal hosts and their pathogens, and have revealed interesting correlations between host responses...
A report on the third Microarray Gene Expression Database group meeting (MGED3), Stanford University, Palo Alto, California, USA, 29-31 March, 2001.
Identification of New Herpesvirus Gene Homologs in the Human Genome
Holzerlandt, Ria, Orengo, Christine, Kellam, Paul, Albà, M. Mar
Viruses are intracellular parasites that use many cellular pathways during their replication. Large DNA viruses, such as herpesviruses, have captured a repertoire of cellular genes to block or mimic...
Jenner, Richard G., Maillard, Karine, Cattini, Nicola, Weiss, Robin A., Boshoff, Chris, Wooster, Richard, ...
Kaposi's sarcoma-associated herpesvirus is associated with three human tumors: Kaposi's sarcoma, and the B cell lymphomas, plasmablastic lymphoma associated with multicentric Castleman's disease, and...
Genomewide Function Conservation and Phylogeny in the Herpesviridae
Albà, M. Mar, Das, Rhiju, Orengo, Christine A., Kellam, Paul
The Herpesviridae are a large group of well-characterized double-stranded DNA viruses for which many complete genome sequences have been determined. We have extracted protein sequences from all...
Consensus clustering and functional interpretation of gene-expression data
Swift, Stephen, Tucker, Allan, Vinciotti, Veronica, Martin, Nigel, Orengo, Christine, Liu, Xiaohui, ...
Consensus clustering, a new method for analyzing microarray data that takes a consensus set of clusters from various algorithms, is shown to perform better than individual methods alone.
Attacking pathogens through their hosts
Through understanding the intricacies of host-pathogen interactions, it is now possible to inhibit the growth of microbes, especially viruses, by targeting host-cell proteins and functions.
Dupin, Nicolas, Fisher, Cyril, Kellam, Paul, Ariad, Sam, Tulliez, Micheline, Franck, Nathalie, ...
Human herpesvirus 8 (HHV-8, also called KSHV) is linked to the etiopathogenesis of Kaposi’s sarcoma (KS), multicentric Castleman’s disease (MCD), and primary effusion lymphoma (PEL). The...
VIDA: a virus database system for the organization of animal virus genome open reading frames
Albà, M. Mar, Lee, David, Pearl, Frances M. G., Shepherd, Adrian J., Martin, Nigel, Orengo, Christine A., ...
VIDA is a new virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses. Currently VIDA includes all sequences from GenBank for...
Kellam, Paul, Bourboulia, Dimitra, Dupin, Nicolas, Shotton, Chris, Fisher, Cyril, Talbot, Simon, ...
Human herpesvirus 8 (HHV-8; also designated Kaposi’s sarcoma-associated herpesvirus) is the likely etiological agent of Kaposi’s sarcoma (KS). HHV-8 encodes a latent nuclear antigen (LNA) which...
Kaposi's Sarcoma-Associated Herpesvirus Latent and Lytic Gene Expression as Revealed by DNA Arrays
Jenner, Richard G., Albà, M. Mar, Boshoff, Chris, Kellam, Paul
Kaposi's sarcoma-associated herpesvirus (KSHV; human herpesvirus 8) is associated with three human tumors, Kaposi's sarcoma, primary effusion lymphoma (PEL), and multicentric Castleman's disease....
Gammaherpesvirus Lytic Gene Expression as Characterized by DNA Array
Ahn, Joo Wook, Powell, Kenneth L., Kellam, Paul, Alber, Dagmar G.
Gammaherpesviruses are associated with a number of diseases including lymphomas and other malignancies. Murine gammaherpesvirus 68 (MHV-68) constitutes the most amenable animal model for this family...
Host-pathogen studies in the post-genomic era
Several studies are starting to show the power of DNA microarrays to identify interactions between animal hosts and their pathogens, and have revealed interesting correlations between host responses...
A report on the third Microarray Gene Expression Database group meeting (MGED3), Stanford University, Palo Alto, California, USA, 29-31 March, 2001.
Identification of New Herpesvirus Gene Homologs in the Human Genome
Holzerlandt, Ria, Orengo, Christine, Kellam, Paul, Albà, M. Mar
Viruses are intracellular parasites that use many cellular pathways during their replication. Large DNA viruses, such as herpesviruses, have captured a repertoire of cellular genes to block or mimic...
Jenner, Richard G., Maillard, Karine, Cattini, Nicola, Weiss, Robin A., Boshoff, Chris, Wooster, Richard, ...
Kaposi's sarcoma-associated herpesvirus is associated with three human tumors: Kaposi's sarcoma, and the B cell lymphomas, plasmablastic lymphoma associated with multicentric Castleman's disease, and...
Genomewide Function Conservation and Phylogeny in the Herpesviridae
Albà, M. Mar, Das, Rhiju, Orengo, Christine A., Kellam, Paul
The Herpesviridae are a large group of well-characterized double-stranded DNA viruses for which many complete genome sequences have been determined. We have extracted protein sequences from all...
Consensus clustering and functional interpretation of gene-expression data
Swift, Stephen, Tucker, Allan, Vinciotti, Veronica, Martin, Nigel, Orengo, Christine, Liu, Xiaohui, ...
Consensus clustering, a new method for analyzing microarray data that takes a consensus set of clusters from various algorithms, is shown to perform better than individual methods alone.
Attacking pathogens through their hosts
Through understanding the intricacies of host-pathogen interactions, it is now possible to inhibit the growth of microbes, especially viruses, by targeting host-cell proteins and functions.
Shun, Ming-Chieh, Raghavendra, Nidhanapati K., Vandegraaff, Nick, Daigle, Janet E., Hughes, Siobhan, Kellam, Paul, ...
LEDGF/p75 directly interacts with lentiviral integrase proteins and can modulate their enzymatic activities and chromosomal association. A novel genetic knockout model was established that allowed us...
Gene3D: comprehensive structural and functional annotation of genomes
Yeats, Corin, Lees, Jonathan, Reid, Adam, Kellam, Paul, Martin, Nigel, Liu, Xinhui, ...
Gene3D provides comprehensive structural and functional annotation of most available protein sequences, including the UniProt, RefSeq and Integr8 resources. The main structural annotation is...
Wilson, Sam J., Tsao, Edward H., Webb, Benjamin L. J., Ye, Hongtao, Dalton-Griffin, Lucy, Tsantoulas, Christoforos, ...
Reactivation of lytic replication from viral latency is a defining property of all herpesviruses. Despite this, the authentic physiological cues for the latent-lytic switch are unclear. Such cues...
Gifford, Robert J., De Oliveira, Tulio, Rambaut, Andrew, Pybus, Oliver G., Dunn, David, Vandamme, Anne-Mieke, ...
With ongoing generation of viral genetic diversity and increasing levels of migration, the global human immunodeficiency virus type 1 (HIV-1) epidemic is becoming increasingly heterogeneous. In this...
Bim-mediated deletion of antigen-specific CD8+ T cells in patients unable to control HBV infection
Lopes, A. Ross, Kellam, Paul, Das, Abhishek, Dunn, Claire, Kwan, Antonia, Turner, Joanna, ...
HBV-specific CD8+ T cells are critical for a successful immune response to HBV infection. They are markedly diminished in number in patients who fail to control the virus, but the mechanisms...
Infectious causes of cancer and their detection
Dalton-Griffin, Lucy, Kellam, Paul
Molecular techniques for identifying pathogens associated with cancer continue to be developed, including one reported recently in BMC Medical Genomics. Identifying a causal infectious agent helps in...