Professor David Robertson

  • Head of Viral Genomics and Bioinformatics (Centre for Virus Research)

telephone: 0141 3303923
email: David.L.Robertson@glasgow.ac.uk

Biography

  • Since 2017: Head of CVR Bioinformatics & Principal Investigator, University of Glasgow.
  • Since 2002: Principal Investigator, University of Manchester. Promoted from Lecturer to Senior Lecturer in 2007 and to research Professor in 2011.
  • 1999 – 2002: Wellcome Trust Research Fellow, Department of Zoology, University of Oxford. Sponsored by Prof. Edward Holmes.
  • 1997 – 1999: ANRS Research Fellow, CNRS, Marseilles, France. Sponsored by Prof. Jean-Michel Claverie.
  • 1996 – 1997: Postdoc, Departments of Medicine and Microbiology, University of Alabama at Birmingham, USA in Prof. Beatrice Hahn’s research group.
  • 1992 – 1996: PhD student in Genetics, University of Nottingham and Trinity College Dublin with supervisor Prof. Paul Sharp.
  • 1987 – 1991: BSc, University of Edinburgh, Scotland.

Research interests

CVR logo

Our computational virology/bioinformatics research group is interested in virus evolution and the specificity of virus-host relationships. We study virus-host interactions and change in viral genomes in order to analyse and model in silico the nature of species ‘choice’ in infection, virus life cycles and determinants of cross-species transmission/host-switching. Studying these processes in eukaryotes is important for understanding acute versus persistent infection, pathogenicity, transmission success and for predicting the emergence of new human or animal pathogens. In prokaryotes both bacterial viruses (bacteriophage/phage) and archaeal viruses are important components and regulators of the microbiome. In the case of phage, virus destruction of host bacteria can be harnessed as a safe therapeutic replacement for antibiotics. A key to successful prediction of virus-host interactions and potential for host-switching will be to understand how virus populations interact with and exploit host systems. 

Outside of cells viruses are mostly inert as they are entirely dependent on a host cell for replication. This use of host cells (eukaryotic, bacterium or archaeon) results in the need for highly specific molecular interactions in order to ‘target’ the appropriate cell type to infect (e.g., recognition of specific host cell surface receptors) and subsequently to interact, and intricately control host-cellular ‘machinery’. Hosts of course respond to viruses and have evolved molecular (immune) systems to counteract infection. This can range from clearing the infection, ignoring it, or in some cases co-opting the virus. Leading to symbiotic, usually parasitic, but in some cases mutualistic relationships. 

The key to understanding viruses and moderating the degree of harm they cause (virulence) is thus to take a molecular evolutionary perspective and combine this with systems biology/‘omics data to model the workings of the host cell, the viruses usurping of the host cell, and responses by the host system to infection. This aim of our research group focuses the study of viruses on BOTH their own and their host’s genome/proteome and the combined molecular interactions involved in the intracellular dynamics of infection, in the context of the entangled co-evolution of viruses and host species. In the case of the virome (the full set of eukaryote and prokaryote viruses in an individual) our research also requires an ecological perspective to understand co-occurrence networks and the role of both direct and indirect species interactions, including how these cycle through time and associate with disease states. 

If you'd like to work with us and have experience in virology, bioinformatics, computer science, evolutionary, computational and/or systems biology, biostatistics and/or machine learning we welcome applications for PhD and postdoctoral positions at any time. Examples of projects include the computational study of: virus diversity & evolution, virus-host molecular interaction networks, predicting virus evolution and host responses, metagenomics, the virome and bacteriophage therapy. We can also host independent research fellowships. If you have any questions please e-mail: david.l.robertson@glasgow.ac.uk.

Grants

Grants and Awards listed are those received whilst working with the University of Glasgow.

  • Nasopharyngeal virome sequencing to determine the impact of respiratory viral interference with live attenuated influenza vaccine immunogenicity in Gambian children
    Wellcome Trust
    2017 - 2018
     

Publications

List by: Type | Date

Jump to: 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001
Number of items: 100.

2017

Jiang, X., Feyertag, F. and Robertson, D. L. (2017) Protein structural disorder of the envelope V3 loop contributes to the switch in human immunodeficiency virus type 1 cell tropism. PLoS ONE, 12(10), e0185790. (doi:10.1371/journal.pone.0185790) (PMID:29049306) (PMCID:PMC5648111)

Olabode, A. S., Kandathil, S. M., Lovell, S. C. and Robertson, D. L. (2017) Adaptive HIV-1 evolutionary trajectories are constrained by protein stability. Virus Evolution, 3(2), vex019. (doi:10.1093/ve/vex019) (PMID:28852572) (PMCID:PMC5570062)

Tsimpidis, M., Bachoumis, G., Mimouli, K., Kyriakopoulou, Z., Robertson, D. L., Markoulatos, P. and Amoutzias, G. D. (2017) T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes. BMC Bioinformatics, 18, 13. (doi:10.1186/s12859-016-1420-z) (PMID:28056784) (PMCID:PMC5216575)

Kouchaki, S., Tirunagari, S., Tapinos, A. and Robertson, D. L. (2017) Local Binary Patterns as a Feature Descriptor in Alignment-free Visualisation of Metagenomic Data. In: 2016 IEEE Symposium Series on Computational Intelligence (SSCI), Athens, Greece, 06-09 Dec 2016, ISBN 9781509042401 (doi:10.1109/SSCI.2016.7849955)

Kouchaki, S., Tirunagari, S., Tapinos, A. and Robertson, D. L. (2017) Marginalised Stack Denoising Autoencoders for Metagenomic Data Binning. In: 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), Manchester, UK, 23-25 Aug 2017, ISBN 9781467389884 (doi:10.1109/CIBCB.2017.8058552)

Tapinos, A. and Robertson, D. L. (2017) De Novo Assembly of Nucleotide Sequences in a Compressed Feature Space. In: 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), Manchester, UK, 23-25 Aug 2017, ISBN 9781467389884 (doi:10.1109/CIBCB.2017.8058556)

2016

Duck, G., Nenadic, G., Filannino, M., Brass, A., Robertson, D. L. and Stevens, R. (2016) A survey of bioinformatics database and software usage through mining the literature. PLoS ONE, 11(6), e0157989. (doi:10.1371/journal.pone.0157989) (PMID:27331905) (PMCID:PMC4917176)

Ames, R. M., Talavera, D., Williams, S. G., Robertson, D. L. and Lovell, S. C. (2016) Binding interface change and cryptic variation in the evolution of protein-protein interactions. BMC Evolutionary Biology, 16, 40. (doi:10.1186/s12862-016-0608-1) (PMID:26892785) (PMCID:PMC4758157)

2015

Stoney, R. A., Ames, R. M., Nenadic, G., Robertson, D. L. and Schwartz, J.-M. (2015) Disentangling the multigenic and pleiotropic nature of molecular function. BMC Systems Biology, 9(Suppl6), S3. (doi:10.1186/1752-0509-9-S6-S3) (PMID:26678917) (PMCID:PMC4674882)

Jiang, X., Feyertag, F., Meehan, C. J., McCormack, G. P., Travers, S. A., Craig, C., Westby, M., Lewis, M. and Robertson, D. L. (2015) Characterizing the diverse mutational pathways associated with R5-tropic maraviroc resistance: HIV-1 that uses the drug-bound CCR5 coreceptor. Journal of Virology, 89(22), pp. 11457-11472. (doi:10.1128/JVI.01384-15) (PMID:26339063) (PMCID:PMC4645647)

Leoz, M. et al. (2015) The two-phase emergence of non pandemic HIV-1 group O in Cameroon. PLoS Pathogens, 11(8), e1005029. (doi:10.1371/journal.ppat.1005029) (PMID:26241860) (PMCID:PMC4524642)

Olabode, A. S., Jiang, X., Robertson, D. L. and Lovell, S. C. (2015) Ebolavirus is evolving but not changing: No evidence for functional change in EBOV from 1976 to the 2014 outbreak. Virology, 482, pp. 202-207. (doi:10.1016/j.virol.2015.03.029) (PMID:25880111) (PMCID:PMC4503884)

Duck, G., Kovacevic, A., Robertson, D. L., Stevens, R. and Nenadic, G. (2015) Ambiguity and variability of database and software names in bioinformatics. Journal of Biomedical Semantics, 6, 29. (doi:10.1186/s13326-015-0026-0) (PMID:26131352) (PMCID:PMC4485340)

Oyeyemi, O. J., Davies, O., Robertson, D. L. and Schwartz, J.-M. (2015) A logical model of HIV-1 interactions with the T-cell activation signalling pathway. Bioinformatics, 31(7), pp. 1075-1083. (doi:10.1093/bioinformatics/btu787) (PMID:25431332)

2014

Keith, B. P., Robertson, D. L. and Hentges, K. E. (2014) Locus heterogeneity disease genes encode proteins with high interconnectivity in the human protein interaction network. Frontiers in Genetics, 5, 434. (doi:10.3389/fgene.2014.00434) (PMID:25538735) (PMCID:PMC4260505)

Jamieson, D. G., Moss, A., Kennedy, M., Jones, S., Nenadic, G., Robertson, D. L. and Sidders, B. (2014) The pain interactome: connecting pain-specific protein interactions. Pain, 155(11), pp. 2243-2252. (doi:10.1016/j.pain.2014.06.020) (PMID:24978826) (PMCID:PMC4247380)

Duck, G., Nenadic, G., Brass, A., Robertson, D. L. and Stevens, R. (2014) Extracting patterns of database and software usage from the bioinformatics literature. Bioinformatics, 30(17), i601-i608. (doi:10.1093/bioinformatics/btu471) (PMID:25161253) (PMCID:PMC4147923)

Bartlett, A. D. et al. (2014) The utility of different bioinformatics algorithms for genotypic HIV-1 tropism testing in a large clinical cohort with multiple subtypes. AIDS, 28(11), pp. 1611-1617. (doi:10.1097/QAD.0000000000000288) (PMID:24785955)

Ma, D. et al. (2014) Factors associated with siman immunodeficiency virus transmission in a natural African nonhuman primate host in the wild. Journal of Virology, 88(10), pp. 5687-5705. (doi:10.1128/JVI.03606-13) (PMID:24623416) (PMCID:PMC4019088)

Gibson, R. M., Meyer, A. M., Winner, D., Archer, J., Feyertag, F., Ruiz-Mateos, E., Leal, M., Robertson, D. L., Schmotzer, C. L. and Quiñones-Mateu, M. E. (2014) Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism. Antimicrobial Agents and Chemotherapy, 58(4), pp. 2167-2185. (doi:10.1128/AAC.02710-13) (PMID:24468782) (PMCID:PMC4023761)

Woo, J., Robertson, D. L. and Lovell, S. C. (2014) Constraints from protein structure and intra-molecular coevolution influence the fitness of HIV-1 recombinants. Virology, 454-45, pp. 34-39. (doi:10.1016/j.virol.2014.01.029) (PMID:24725929)

2013

Duck, G., Nenadic, G., Brass, A., Robertson, D. L. and Stevens, R. (2013) bioNerDS: exploring bioinformatics' database and software use through literature mining. BMC Bioinformatics, 14, 194. (doi:10.1186/1471-2105-14-194) (PMID:23768135) (PMCID:PMC3693927)

Jamieson, D. G., Roberts, P. M., Robertson, D. L., Sidders, B. and Nenadic, G. (2013) Cataloging the biomedical world of pain through semi-automated curation of molecular interactions. Database, 2013, bat033. (doi:10.1093/database/bat033) (PMID:23707966) (PMCID:PMC3662864)

Ames, R. M., Macpherson, J. I., Pinney, J. W., Lovell, S. C. and Robertson, D. L. (2013) Modular biological function is most effectively captured by combining molecular interaction data types. PLoS ONE, 8(5), e62670. (doi:10.1371/journal.pone.0062670) (PMID:23658761) (PMCID:PMC3643936)

Weber, J. et al. (2013) Sensitive cell-based assay for determination of human immunodeficiency virus type 1 coreceptor tropism. Journal of Clinical Microbiology, 51(5), pp. 1517-1527. (doi:10.1128/JCM.00092-13) (PMID:23486708) (PMCID:PMC3647936)

Talavera, D., Robertson, D. L. and Lovell, S. C. (2013) The role of protein interactions in mediating essentiality and synthetic lethality. PLoS ONE, 8(4), e62866. (doi:10.1371/journal.pone.0062866) (PMID:23638160) (PMCID:PMC3639263)

Talavera, D., Robertson, D. L. and Lovell, S. C. (2013) Alternative splicing and protein interaction data sets. Nature Biotechnology, 31(4), pp. 292-293. (doi:10.1038/nbt.2540) (PMID:23563420)

Ma, D. et al. (2013) SIVagm infection in wild African green monkeys from South Africa: epidemiology, natural history, and evolutionary considerations. PLoS Pathogens, 9(1), e1003011. (doi:10.1371/journal.ppat.1003011) (PMID:23349627) (PMCID:PMC3547836)

2012

Swapna, L. S., Srinivasan, N., Robertson, D. L. and Lovell, S. C. (2012) The origins of the evolutionary signal used to predict protein-protein interactions. BMC Evolutionary Biology, 12, 238. (doi:10.1186/1471-2148-12-238) (PMID:23217198) (PMCID:PMC3537733)

Archer, J. et al. (2012) Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism. PLoS ONE, 7(11), e49602. (doi:10.1371/journal.pone.0049602) (PMID:23166726) (PMCID:PMC3498215)

Talavera, D., Williams, S. G., Norris, M. G.S., Robertson, D. l. and Lovell, S. C. (2012) Evolvability of yeast protein-protein interaction interfaces. Journal of Molecular Biology, 419(5), pp. 387-96. (doi:10.1016/j.jmb.2012.03.021) (PMID:22472422)

Archer, J., Baillie, G., Watson, S. J., Kellam, P., Rambaut, A. and Robertson, D. L. (2012) Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. BMC Bioinformatics, 13, 47. (doi:10.1186/1471-2105-13-47) (PMID:22443413) (PMCID:PMC3359224)

Dickerson, J. E. and Robertson, D. L. (2012) On the origins of Mendelian disease genes in man: the impact of gene duplication. Molecular Biology and Evolution, 29(1), pp. 61-69. (doi:10.1093/molbev/msr111) (PMID:21705381) (PMCID:PMC3709195)

Jamieson, D. G., Gerner, M., Sarafraz, F., Nenadic, G. and Robertson, D. L. (2012) Towards semi-automated curation: using text mining to recreate the HIV-1, human protein interaction database. Database, 2012, bas023. (doi:10.1093/database/bas023) (PMID:22529179) (PMCID:PMC3332570)

2011

Dickerson, J. E., Zhu, A., Robertson, D. L. and Hentges, K. E. (2011) Defining the role of essential genes in human disease. PLoS ONE, 6(11), e27368. (doi:10.1371/journal.pone.0027368) (PMID:22096564) (PMCID:PMC3214036)

MacPherson, J. I. et al. (2011) An integrated transcriptomic and meta-analysis of hepatoma cells reveals factors that influence susceptibility to HCV infection. PLoS ONE, 6(10), e25584. (doi:10.1371/journal.pone.0025584) (PMID:22046242) (PMCID:PMC3201949)

Williams, S. G., Madan, R., Norris, M. G.S., Archer, J., Mizuguchi, K., Robertson, D. L. and Lovell, S. C. (2011) Using knowledge of protein structural constraints to predict the evolution of HIV-1. Journal of Molecular Biology, 410(5), pp. 1023-1034. (doi:10.1016/j.jmb.2011.04.037) (PMID:21763504)

Talavera, D., Robertson, D. L. and Lovell, S. C. (2011) Characterization of protein-protein interaction interfaces from a single species. PLoS ONE, 6(6), e21053. (doi:10.1371/journal.pone.0021053) (PMID:21738603) (PMCID:PMC3124478)

Heyes, D. J., Levy, C., Sakuma, M., Robertson, D. L. and Scrutton, N. S. (2011) A twin-track approach has optimized proton and hydride transfer by dynamically coupled tunneling during the evolution of protochlorophyllide oxidoreductase. Journal of Biological Chemistry, 286(13), pp. 11849-11854. (doi:10.1074/jbc.M111.219626) (PMID:21317291) (PMCID:PMC3064235)

2010

Archer, J., Rambaut, A., Taillon, B. E., Harrigan, P. R., Lewis, M. and Robertson, D. L. (2010) The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time--an ultra-deep approach. PLoS Computational Biology, 6(12), e1001022. (doi:10.1371/journal.pcbi.1001022) (PMID:21187908) (PMCID:PMC3002995)

Meehan, C. J., Hedge, J. A., Robertson, D. L., McCormack, G. P. and Travers, S. A.A. (2010) Emergence, dominance, and possible decline of CXCR4 chemokine receptor usage during the course of HIV infection. Journal of Medical Virology, 82(12), pp. 2004-2012. (doi:10.1002/jmv.21922) (PMID:20981786)

Woo, J., Robertson, D. L. and Lovell, S. C. (2010) Constraints on HIV-1 diversity from protein structure. Journal of Virology, 84(24), pp. 12995-13003. (doi:10.1128/JVI.00702-10) (PMID:20881050) (PMCID:PMC3004343)

Lovell, S. C. and Robertson, D. L. (2010) An integrated view of molecular coevolution in protein-protein interactions. Molecular Biology and Evolution, 27(11), pp. 2567-2575. (doi:10.1093/molbev/msq144) (PMID:20551042)

MacPherson, J. I., Dickerson, J. E., Pinney, J. W. and Robertson, D. L. (2010) Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems. PLoS Computational Biology, 6(7), e1000863. (doi:10.1371/journal.pcbi.1000863) (PMID:20686668) (PMCID:PMC2912648)

Carretero-Paulet, L., Galstyan, A., Roig-Villanova, I., Martínez-García, J. F., Bilbao-Castro, J. R. and Robertson, D. L. (2010) Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae. Plant Physiology, 153(3), pp. 1398-1412. (doi:10.1104/pp.110.153593) (PMID:20472752)

Dickerson, J. E., Pinney, J. W. and Robertson, D. L. (2010) The biological context of HIV-1 host interactions reveals subtle insights into a system hijack. BMC Systems Biology, 4, 80. (doi:10.1186/1752-0509-4-80) (PMID:20529270) (PMCID:PMC2897785)

Ames, R. M., Rash, B. M., Hentges, K. E., Robertson, D. L., Delneri, D. and Lovell, S. C. (2010) Gene duplication and environmental adaptation within yeast populations. Genome Biology and Evolution, 2, pp. 591-601. (doi:10.1093/gbe/evq043) (PMID:20660110) (PMCID:PMC2997561)

2009

Robertson, D. L. and Lovell, S. C. (2009) Evolution in protein interaction networks: co-evolution, rewiring and the role of duplication. Biochemical Society Transactions, 37(4), pp. 768-771. (doi:10.1042/BST0370768) (PMID:19614591)

Plantier, J.-C., Leoz, M., Dickerson, J. E., De Oliveira, F., Cordonnier, F., Lemée, V., Damond, F., Robertson, D. L. and Simon, F. (2009) A new human immunodeficiency virus derived from gorillas. Nature Medicine, 15(8), pp. 871-872. (doi:10.1038/nm.2016) (PMID:19648927)

Archer, J., Braverman, M. S., Taillon, B. E., Desany, B., James, I., Harrigan, P. R., Lewis, M. and Robertson, D. L. (2009) Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing. AIDS, 23(10), pp. 1209-1218. (doi:10.1097/QAD.0b013e32832b4399) (PMID:19424056) (PMCID:PMC2857961)

Simon-Loriere, E., Galetto, R., Hamoudi, M., Archer, J., Lefeuvre, P., Martin, D. P., Robertson, D. L. and Negroni, M. (2009) Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus. PLoS Pathogens, 5(5), e1000418. (doi:10.1371/journal.ppat.1000418) (PMID:19424420) (PMCID:PMC2671596)

Huxley-Jones, J., Pinney, J. W., Archer, J., Robertson, D. L. and Boot-Handford, R. P. (2009) Back to basics--how the evolution of the extracellular matrix underpinned vertebrate evolution. International Journal of Experimental Pathology, 90(2), pp. 95-100. (doi:10.1111/j.1365-2613.2008.00637.x) (PMID:19335547)

MacPherson, J. I., Pinney, J. W. and Robertson, D. L. (2009) JNets: exploring networks by integrating annotation. BMC Bioinformatics, 10, 95. (doi:10.1186/1471-2105-10-95) (PMID:19323810) (PMCID:PMC2674432)

Pinney, J. W., Dickerson, J. E., Fu, W., Sanders-Beer, B. E., Ptak, R. G. and Robertson, D. L. (2009) HIV-host interactions: a map of viral perturbation of the host system. AIDS, 23(5), pp. 549-554. (doi:10.1097/QAD.0b013e328325a495) (PMID:19262354)

2008

Ptak, R. G. et al. (2008) Cataloguing the HIV type 1 human protein interaction network. AIDS Research and Human Retroviruses, 24(12), pp. 1497-1502. (doi:10.1089/aid.2008.0113) (PMID:19025396) (PMCID:PMC2655106)

Archer, J., Pinney, J. W., Fan, J., Simon-Loriere, E., Arts, E. J., Negroni, M. and Robertson, D. L. (2008) Identifying the important HIV-1 recombination breakpoints. PLoS Computational Biology, 4(9), e1000178. (doi:10.1371/journal.pcbi.1000178) (PMID:18787691) (PMCID:PMC2522274)

Eales, J. M., Pinney, J. W., Stevens, R. D. and Robertson, D. L. (2008) Methodology capture: discriminating between the "best" and the rest of community practice. BMC Bioinformatics, 9, 359. (doi:10.1186/1471-2105-9-359) (PMID:18761740) (PMCID:PMC2553348)

Amoutzias, G. D., Robertson, D. L., Van de Peer, Y. and Oliver, S. G. (2008) Choose your partners: dimerization in eukaryotic transcription factors. Trends in Biochemical Sciences, 33(5), pp. 220-229. (doi:10.1016/j.tibs.2008.02.002) (PMID:18406148)

Hakes, L., Pinney, J. W., Robertson, D. L. and Lovell, S. C. (2008) Protein-protein interaction networks and biology--what's the connection? Nature Biotechnology, 26(1), pp. 69-72. (doi:10.1038/nbt0108-69) (PMID:18183023)

2007

Pinney, J. W., Amoutzias, G. D., Rattray, M. and Robertson, D. L. (2007) Reconstruction of ancestral protein interaction networks for the bZIP transcription factors. Proceedings of the National Academy of Sciences of the United States of America, 104(51), pp. 20449-20453. (doi:10.1073/pnas.0706339104) (PMID:18077348) (PMCID:PMC2154451)

Fan, J., Negroni, M. and Robertson, D. L. (2007) The distribution of HIV-1 recombination breakpoints. Infection, Genetics and Evolution, 7(6), pp. 717-723. (doi:10.1016/j.meegid.2007.07.012) (PMID:17851137)

Archer, J. and Robertson, D. L. (2007) CTree: comparison of clusters between phylogenetic trees made easy. Bioinformatics, 23(21), pp. 2952-2953. (doi:10.1093/bioinformatics/btm410) (PMID:17717036)

Hakes, L., Pinney, J. W., Lovell, S. C., Oliver, S. G. and Robertson, D. L. (2007) All duplicates are not equal: the difference between small-scale and genome duplication. Genome Biology, 8(10), R209. (doi:10.1186/gb-2007-8-10-r209) (PMID:17916239) (PMCID:PMC2246283)

Archer, J. and Robertson, D. L. (2007) Understanding the diversification of HIV-1 groups M and O. AIDS, 21(13), pp. 1693-1700. (doi:10.1097/QAD.0b013e32825eabd0) (PMID:17690566)

Holden, B. J., Pinney, J. W., Lovell, S. C., Amoutzias, G. D. and Robertson, D. L. (2007) An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network. BMC Bioinformatics, 8, 289. (doi:10.1186/1471-2105-8-289) (PMID:17683601) (PMCID:PMC1963338)

Amoutzias, G. D., Pichler, E. E., Mian, N., De Graaf, D., Imsiridou, A., Robinson-Rechavi, M., Bornberg-Bauer, E., Robertson, D. L. and Oliver, S. G. (2007) A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. BMC Systems Biology, 1, 34. (doi:10.1186/1752-0509-1-34) (PMID:17672894) (PMCID:PMC1971058)

Hakes, L., Lovell, S. C., Oliver, S. G. and Robertson, D. L. (2007) Specificity in protein interactions and its relationship with sequence diversity and coevolution. Proceedings of the National Academy of Sciences of the United States of America, 104(19), pp. 7999-8004. (doi:10.1073/pnas.0609962104) (PMID:17468399) (PMCID:PMC1876561)

Huxley-Jones, J., Clarke, T.-K., Beck, C., Toubaris, G., Robertson, D. L. and Boot-Handford, R. P. (2007) The evolution of the vertebrate metzincins; insights from Ciona intestinalis and Danio rerio. BMC Evolutionary Biology, 7, 63. (doi:10.1186/1471-2148-7-63) (PMID:17439641) (PMCID:PMC1867822)

Zhang, X., Boot-Handford, R. P., Huxley-Jones, J., Forse, L. N., Mould, A. P., Robertson, D. L., Li, L., Athiyal, M. and Sarras, M. P. (2007) The collagens of hydra provide insight into the evolution of metazoan extracellular matrices. Journal of Biological Chemistry, 282(9), pp. 6792-802. (doi:10.1074/jbc.M607528200) (PMID:17204477)

Amoutzias, G.D., Veron, A.S., Weiner, J., Robinson-Rechavi, M., Bornberg-Bauer, E., Oliver, S.G. and Robertson, D.L. (2007) One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity. Molecular Biology and Evolution, 24(3), pp. 827-835. (doi:10.1093/molbev/msl211) (PMID:17194801)

Huxley-Jones, J., Robertson, D. L. and Boot-Handford, R. P. (2007) On the origins of the extracellular matrix in vertebrates. Matrix Biology, 26(1), pp. 2-11. (doi:10.1016/j.matbio.2006.09.008) (PMID:17055232)

Hakes, L., Robertson, D. L., Oliver, S. G. and Lovell, S. C. (2007) Protein interactions from complexes: a structural perspective. Comparative and Functional Genomics, 2007, 49356. (doi:10.1155/2007/49356) (PMID:17538689) (PMCID:PMC1838958)

2006

Baird, H. A., Galetto, R., Gao, Y., Simon-Loriere, E., Abreha, M., Archer, J., Fan, J., Robertson, D. L., Arts, E. J. and Negroni, M. (2006) Sequence determinants of breakpoint location during HIV-1 intersubtype recombination. Nucleic Acids Research, 34(18), pp. 5203-5216. (doi:10.1093/nar/gkl669) (PMID:17003055) (PMCID:PMC1636437)

Amoutzias, G. D., Bornberg-Bauer, E., Oliver, S. G. and Robertson, D. L. (2006) Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network. BMC Genomics, 7, 107. (doi:10.1186/1471-2164-7-107) (PMID:16674813) (PMCID:PMC1479340)

Apetrei, C., Lerche, N. W., Pandrea, I., Gormus, B., Silvestri, G., Kaur, A., Robertson, D. L., Hardcastle, J., Lackner, A. A. and Marx, P. A. (2006) Kuru experiments triggered the emergence of pathogenic SIVmac. AIDS, 20(3), pp. 317-321. (doi:10.1097/01.aids.0000206498.71041.0e) (PMID:16439864)

2005

Hakes, L., Robertson, D. L. and Oliver, S. G. (2005) Effect of dataset selection on the topological interpretation of protein interaction networks. BMC Genomics, 6, 131. (doi:10.1186/1471-2164-6-131) (PMID:16174296) (PMCID:PMC1249571)

Huxley-Jones, J., Apte, S. S., Robertson, D. L. and Boot-Handford, R. P. (2005) The characterisation of six ADAMTS proteases in the basal chordate Ciona intestinalis provides new insights into the vertebrate ADAMTS family. International Journal of Biochemistry and Cell Biology, 37(9), pp. 1838-1845. (doi:10.1016/j.biocel.2005.03.009) (PMID:15899586)

Apetrei, C. et al. (2005) Molecular epidemiology of simian immunodeficiency virus SIVsm in U.S. primate centers unravels the origin of SIVmac and SIVstm. Journal of Virology, 79(14), pp. 8991-9005. (doi:10.1128/JVI.79.14.8991-9005.2005) (PMID:15994793) (PMCID:PMC1168739)

van Cuyck, H., Fan, J., Robertson, D. L. and Roques, P. (2005) Evidence of recombination between divergent hepatitis E viruses. Journal of Virology, 79(14), pp. 9306-9314. (doi:10.1128/JVI.79.14.9306-9314.2005) (PMID:15994825) (PMCID:PMC1168788)

Pandrea, I., Mittleider, D., Brindley, P. J., Didier, E. S. and Robertson, D. L. (2005) Phylogenetic relationships of methionine aminopeptidase 2 among Encephalitozoon species and genotypes of microsporidia. Molecular and Biochemical Parasitology, 140(2), pp. 141-152. (doi:10.1016/j.molbiopara.2004.12.006) (PMID:15760654)

Apetrei, C., Metzger, M. J., Richardson, D., Ling, B., Telfer, P. T., Reed, P., Robertson, D. L. and Marx, P. A. (2005) Detection and partial characterization of simian immunodeficiency virus SIVsm strains from bush meat samples from rural Sierra Leone. Journal of Virology, 79(4), pp. 2631-2636. (doi:10.1128/JVI.79.4.2631-2636.2005) (PMID:15681464) (PMCID:PMC546599)

Traina-Dorge, V. L., Lorino, R., Gormus, B. J., Metzger, M., Telfer, P., Richardson, D., Robertson, D. L., Marx, P. A. and Apetrei, C. (2005) Molecular epidemiology of simian T-cell lymphotropic virus type 1 in wild and captive sooty mangabeys. Journal of Virology, 79(4), pp. 2541-2548. (doi:10.1128/JVI.79.4.2541-2548.2005) (PMID:15681454) (PMCID:PMC546543)

2004

Ling, B., Telfer, P., Reed, P., Robertson, D. L. and Marx, P. A. (2004) A link between SIVsm in sooty mangabeys (SM) in wild-living monkeys in Sierra Leone and SIVsm in an American-based SM colony. AIDS Research and Human Retroviruses, 20(12), pp. 1348-1351. (doi:10.1089/aid.2004.20.1348) (PMID:15650427)

Roques, P., Robertson, D. L., Souquière, S., Apetrei, C., Nerrienet, E., Barré-Sinoussi, F., Müller-Trutwin, M. and Simon, F. (2004) Phylogenetic characteristics of three new HIV-1 N strains and implications for the origin of group N. AIDS, 18(10), pp. 1371-1381. (doi:10.1097/01.aids.0000125990.86904.28) (PMID:15199313)

Lemey, P., Pybus, O. G., Rambaut, A., Drummond, A. J., Robertson, D. L., Roques, P., Worobey, M. and Vandamme, A.-M. (2004) The molecular population genetics of HIV-1 group O. Genetics, 167(3), pp. 1059-1068. (doi:10.1534/genetics.104.026666) (PMID:15280223) (PMCID:PMC1470933)

Damond, F., Worobey, M., Campa, P., Farfara, I., Colin, G., Matheron, S., Brun-Vézinet, F., Robertson, D. L. and Simon, F. (2004) Identification of a highly divergent HIV type 2 and proposal for a change in HIV type 2 classification. AIDS Research and Human Retroviruses, 20(6), pp. 666-672. (doi:10.1089/0889222041217392) (PMID:15242544)

Amoutzias, G. D., Robertson, D. L., Oliver, S. G. and Bornberg-Bauer, E. (2004) Convergent evolution of gene networks by single-gene duplications in higher eukaryotes. EMBO reports, 5(3), pp. 274-279. (doi:10.1038/sj.embor.7400096) (PMID:14968135) (PMCID:PMC1299007)

Choisy, M., Woelk, C. H., Guégan, J.-F. and Robertson, D. L. (2004) Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. Journal of Virology, 78(4), pp. 1962-1970. (doi:10.1128/JVI.78.4.1962-1970.2004) (PMID:14747561) (PMCID:PMC369455)

Apetrei, C., Robertson, D. L. and Marx, P. A. (2004) The history of SIVS and AIDS: epidemiology, phylogeny and biology of isolates from naturally SIV infected non-human primates (NHP) in Africa. Frontiers in Bioscience, 9, pp. 225-254. (doi:10.2741/1154) (PMID:14766362)

Amoutzias, G. D., Robertson, D. L. and Bornberg-Bauer, E. (2004) The evolution of protein interaction networks in regulatory proteins. Comparative and Functional Genomics, 5(1), pp. 79-84. (doi:10.1002/cfg.365) (PMID:18629034) (PMCID:PMC2447317)

2003

Apetrei, C., Descamps, D., Collin, G., Robertson, D. L., Pandrea, I., Groza, P., Prisecariu, L., Teodorescu, I., Luca, V. and Brun-Vézinet, F. (2003) HIV type 1 diversity in northeastern Romania in 200-2001 based on phylogenic analysis of pol sequences from patient failing antiretroviral therapy. AIDS Research and Human Retroviruses, 19(12), pp. 1155-1161. (doi:10.1089/088922203771881266) (PMID:14714572)

Hu, J., Switzer, W. M., Foley, B. T., Robertson, D. L., Goeken, R. M., Korber, B. T., Hirsch, V. M. and Beer, B. E. (2003) Characterization and comparison of recombinant simian immunodeficiency virus from drill (Mandrillus leucophaeus) and mandrill (Mandrillus sphinx) isolates. Journal of Virology, 77(8), pp. 4867-4880. (doi:10.1128/JVI.77.8.4867-4880.2003) (PMID:12663793) (PMCID:PMC152139)

2002

Roques, P. et al. (2002) Phylogenetic analysis of 49 newly derived HIV-1 group O strains: high viral diversity but no group M-like subtype structure. Virology, 302(2), pp. 259-273. (doi:10.1006/viro.2002.1430) (PMID:12441070)

Damond, F. et al. (2002) Plasma RNA viral load in human immunodeficiency virus type 2 subtype A and subtype B infections. Journal of Clinical Microbiology, 40(10), pp. 3654-3659. (doi:10.1128/JCM.40.10.3654-3659.2002) (PMID:12354861) (PMCID:PMC130845)

Pandrea, I., Robertson, D. L., Onanga, R., Gao, F., Makuwa, M., Ngari, P., Bedjabaga, I., Roques, P., Simon, F. and Apetrei, C. (2002) Analysis of partial pol and env sequences indicates a high prevalence of HIV type 1 recombinant strains circulating in Gabon. AIDS Research and Human Retroviruses, 18(15), pp. 1103-1116. (doi:10.1089/088922202320567842) (PMID:12396449)

Charleston, M.A. and Robertson, D.L. (2002) Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny. Systematic Biology, 51(3), pp. 528-535. (doi:10.1080/10635150290069940) (PMID:12079649)

Worobey, M., Rambaut, A., Pybus, O. G. and Robertson, D. L. (2002) Questioning the evidence for genetic recombination in the 1918 "Spanish flu" virus. Science, 296(5566), 211. (doi:10.1126/science.296.5566.211a) (PMID:11951002)

2001

Pandrea, I. et al. (2001) HIV type 1 genetic diversity and genotypic drug susceptibility in the Republic of Moldova. AIDS Research and Human Retroviruses, 17(13), pp. 1297-1304. (doi:10.1089/088922201750461375) (PMID:11559431)

Souquière, S. et al. (2001) Wild Mandrillus sphinx are carriers of two types of lentivirus. Journal of Virology, 75(15), pp. 7086-7096. (doi:10.1128/JVI.75.15.7086-7096.2001) (PMID:11435589) (PMCID:PMC114437)

Gao, F. et al. (2001) Evidence of two distinct subsubtypes within the HIV-1 subtype A radiation. AIDS Research and Human Retroviruses, 17(8), pp. 675-688. (doi:10.1089/088922201750236951) (PMID:11429108)

This list was generated on Mon Dec 11 10:39:14 2017 GMT.
Number of items: 100.

Articles

Jiang, X., Feyertag, F. and Robertson, D. L. (2017) Protein structural disorder of the envelope V3 loop contributes to the switch in human immunodeficiency virus type 1 cell tropism. PLoS ONE, 12(10), e0185790. (doi:10.1371/journal.pone.0185790) (PMID:29049306) (PMCID:PMC5648111)

Olabode, A. S., Kandathil, S. M., Lovell, S. C. and Robertson, D. L. (2017) Adaptive HIV-1 evolutionary trajectories are constrained by protein stability. Virus Evolution, 3(2), vex019. (doi:10.1093/ve/vex019) (PMID:28852572) (PMCID:PMC5570062)

Tsimpidis, M., Bachoumis, G., Mimouli, K., Kyriakopoulou, Z., Robertson, D. L., Markoulatos, P. and Amoutzias, G. D. (2017) T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes. BMC Bioinformatics, 18, 13. (doi:10.1186/s12859-016-1420-z) (PMID:28056784) (PMCID:PMC5216575)

Duck, G., Nenadic, G., Filannino, M., Brass, A., Robertson, D. L. and Stevens, R. (2016) A survey of bioinformatics database and software usage through mining the literature. PLoS ONE, 11(6), e0157989. (doi:10.1371/journal.pone.0157989) (PMID:27331905) (PMCID:PMC4917176)

Ames, R. M., Talavera, D., Williams, S. G., Robertson, D. L. and Lovell, S. C. (2016) Binding interface change and cryptic variation in the evolution of protein-protein interactions. BMC Evolutionary Biology, 16, 40. (doi:10.1186/s12862-016-0608-1) (PMID:26892785) (PMCID:PMC4758157)

Stoney, R. A., Ames, R. M., Nenadic, G., Robertson, D. L. and Schwartz, J.-M. (2015) Disentangling the multigenic and pleiotropic nature of molecular function. BMC Systems Biology, 9(Suppl6), S3. (doi:10.1186/1752-0509-9-S6-S3) (PMID:26678917) (PMCID:PMC4674882)

Jiang, X., Feyertag, F., Meehan, C. J., McCormack, G. P., Travers, S. A., Craig, C., Westby, M., Lewis, M. and Robertson, D. L. (2015) Characterizing the diverse mutational pathways associated with R5-tropic maraviroc resistance: HIV-1 that uses the drug-bound CCR5 coreceptor. Journal of Virology, 89(22), pp. 11457-11472. (doi:10.1128/JVI.01384-15) (PMID:26339063) (PMCID:PMC4645647)

Leoz, M. et al. (2015) The two-phase emergence of non pandemic HIV-1 group O in Cameroon. PLoS Pathogens, 11(8), e1005029. (doi:10.1371/journal.ppat.1005029) (PMID:26241860) (PMCID:PMC4524642)

Olabode, A. S., Jiang, X., Robertson, D. L. and Lovell, S. C. (2015) Ebolavirus is evolving but not changing: No evidence for functional change in EBOV from 1976 to the 2014 outbreak. Virology, 482, pp. 202-207. (doi:10.1016/j.virol.2015.03.029) (PMID:25880111) (PMCID:PMC4503884)

Duck, G., Kovacevic, A., Robertson, D. L., Stevens, R. and Nenadic, G. (2015) Ambiguity and variability of database and software names in bioinformatics. Journal of Biomedical Semantics, 6, 29. (doi:10.1186/s13326-015-0026-0) (PMID:26131352) (PMCID:PMC4485340)

Oyeyemi, O. J., Davies, O., Robertson, D. L. and Schwartz, J.-M. (2015) A logical model of HIV-1 interactions with the T-cell activation signalling pathway. Bioinformatics, 31(7), pp. 1075-1083. (doi:10.1093/bioinformatics/btu787) (PMID:25431332)

Keith, B. P., Robertson, D. L. and Hentges, K. E. (2014) Locus heterogeneity disease genes encode proteins with high interconnectivity in the human protein interaction network. Frontiers in Genetics, 5, 434. (doi:10.3389/fgene.2014.00434) (PMID:25538735) (PMCID:PMC4260505)

Jamieson, D. G., Moss, A., Kennedy, M., Jones, S., Nenadic, G., Robertson, D. L. and Sidders, B. (2014) The pain interactome: connecting pain-specific protein interactions. Pain, 155(11), pp. 2243-2252. (doi:10.1016/j.pain.2014.06.020) (PMID:24978826) (PMCID:PMC4247380)

Duck, G., Nenadic, G., Brass, A., Robertson, D. L. and Stevens, R. (2014) Extracting patterns of database and software usage from the bioinformatics literature. Bioinformatics, 30(17), i601-i608. (doi:10.1093/bioinformatics/btu471) (PMID:25161253) (PMCID:PMC4147923)

Bartlett, A. D. et al. (2014) The utility of different bioinformatics algorithms for genotypic HIV-1 tropism testing in a large clinical cohort with multiple subtypes. AIDS, 28(11), pp. 1611-1617. (doi:10.1097/QAD.0000000000000288) (PMID:24785955)

Ma, D. et al. (2014) Factors associated with siman immunodeficiency virus transmission in a natural African nonhuman primate host in the wild. Journal of Virology, 88(10), pp. 5687-5705. (doi:10.1128/JVI.03606-13) (PMID:24623416) (PMCID:PMC4019088)

Gibson, R. M., Meyer, A. M., Winner, D., Archer, J., Feyertag, F., Ruiz-Mateos, E., Leal, M., Robertson, D. L., Schmotzer, C. L. and Quiñones-Mateu, M. E. (2014) Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism. Antimicrobial Agents and Chemotherapy, 58(4), pp. 2167-2185. (doi:10.1128/AAC.02710-13) (PMID:24468782) (PMCID:PMC4023761)

Woo, J., Robertson, D. L. and Lovell, S. C. (2014) Constraints from protein structure and intra-molecular coevolution influence the fitness of HIV-1 recombinants. Virology, 454-45, pp. 34-39. (doi:10.1016/j.virol.2014.01.029) (PMID:24725929)

Duck, G., Nenadic, G., Brass, A., Robertson, D. L. and Stevens, R. (2013) bioNerDS: exploring bioinformatics' database and software use through literature mining. BMC Bioinformatics, 14, 194. (doi:10.1186/1471-2105-14-194) (PMID:23768135) (PMCID:PMC3693927)

Jamieson, D. G., Roberts, P. M., Robertson, D. L., Sidders, B. and Nenadic, G. (2013) Cataloging the biomedical world of pain through semi-automated curation of molecular interactions. Database, 2013, bat033. (doi:10.1093/database/bat033) (PMID:23707966) (PMCID:PMC3662864)

Ames, R. M., Macpherson, J. I., Pinney, J. W., Lovell, S. C. and Robertson, D. L. (2013) Modular biological function is most effectively captured by combining molecular interaction data types. PLoS ONE, 8(5), e62670. (doi:10.1371/journal.pone.0062670) (PMID:23658761) (PMCID:PMC3643936)

Weber, J. et al. (2013) Sensitive cell-based assay for determination of human immunodeficiency virus type 1 coreceptor tropism. Journal of Clinical Microbiology, 51(5), pp. 1517-1527. (doi:10.1128/JCM.00092-13) (PMID:23486708) (PMCID:PMC3647936)

Talavera, D., Robertson, D. L. and Lovell, S. C. (2013) The role of protein interactions in mediating essentiality and synthetic lethality. PLoS ONE, 8(4), e62866. (doi:10.1371/journal.pone.0062866) (PMID:23638160) (PMCID:PMC3639263)

Talavera, D., Robertson, D. L. and Lovell, S. C. (2013) Alternative splicing and protein interaction data sets. Nature Biotechnology, 31(4), pp. 292-293. (doi:10.1038/nbt.2540) (PMID:23563420)

Ma, D. et al. (2013) SIVagm infection in wild African green monkeys from South Africa: epidemiology, natural history, and evolutionary considerations. PLoS Pathogens, 9(1), e1003011. (doi:10.1371/journal.ppat.1003011) (PMID:23349627) (PMCID:PMC3547836)

Swapna, L. S., Srinivasan, N., Robertson, D. L. and Lovell, S. C. (2012) The origins of the evolutionary signal used to predict protein-protein interactions. BMC Evolutionary Biology, 12, 238. (doi:10.1186/1471-2148-12-238) (PMID:23217198) (PMCID:PMC3537733)

Archer, J. et al. (2012) Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism. PLoS ONE, 7(11), e49602. (doi:10.1371/journal.pone.0049602) (PMID:23166726) (PMCID:PMC3498215)

Talavera, D., Williams, S. G., Norris, M. G.S., Robertson, D. l. and Lovell, S. C. (2012) Evolvability of yeast protein-protein interaction interfaces. Journal of Molecular Biology, 419(5), pp. 387-96. (doi:10.1016/j.jmb.2012.03.021) (PMID:22472422)

Archer, J., Baillie, G., Watson, S. J., Kellam, P., Rambaut, A. and Robertson, D. L. (2012) Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. BMC Bioinformatics, 13, 47. (doi:10.1186/1471-2105-13-47) (PMID:22443413) (PMCID:PMC3359224)

Dickerson, J. E. and Robertson, D. L. (2012) On the origins of Mendelian disease genes in man: the impact of gene duplication. Molecular Biology and Evolution, 29(1), pp. 61-69. (doi:10.1093/molbev/msr111) (PMID:21705381) (PMCID:PMC3709195)

Jamieson, D. G., Gerner, M., Sarafraz, F., Nenadic, G. and Robertson, D. L. (2012) Towards semi-automated curation: using text mining to recreate the HIV-1, human protein interaction database. Database, 2012, bas023. (doi:10.1093/database/bas023) (PMID:22529179) (PMCID:PMC3332570)

Dickerson, J. E., Zhu, A., Robertson, D. L. and Hentges, K. E. (2011) Defining the role of essential genes in human disease. PLoS ONE, 6(11), e27368. (doi:10.1371/journal.pone.0027368) (PMID:22096564) (PMCID:PMC3214036)

MacPherson, J. I. et al. (2011) An integrated transcriptomic and meta-analysis of hepatoma cells reveals factors that influence susceptibility to HCV infection. PLoS ONE, 6(10), e25584. (doi:10.1371/journal.pone.0025584) (PMID:22046242) (PMCID:PMC3201949)

Williams, S. G., Madan, R., Norris, M. G.S., Archer, J., Mizuguchi, K., Robertson, D. L. and Lovell, S. C. (2011) Using knowledge of protein structural constraints to predict the evolution of HIV-1. Journal of Molecular Biology, 410(5), pp. 1023-1034. (doi:10.1016/j.jmb.2011.04.037) (PMID:21763504)

Talavera, D., Robertson, D. L. and Lovell, S. C. (2011) Characterization of protein-protein interaction interfaces from a single species. PLoS ONE, 6(6), e21053. (doi:10.1371/journal.pone.0021053) (PMID:21738603) (PMCID:PMC3124478)

Heyes, D. J., Levy, C., Sakuma, M., Robertson, D. L. and Scrutton, N. S. (2011) A twin-track approach has optimized proton and hydride transfer by dynamically coupled tunneling during the evolution of protochlorophyllide oxidoreductase. Journal of Biological Chemistry, 286(13), pp. 11849-11854. (doi:10.1074/jbc.M111.219626) (PMID:21317291) (PMCID:PMC3064235)

Archer, J., Rambaut, A., Taillon, B. E., Harrigan, P. R., Lewis, M. and Robertson, D. L. (2010) The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time--an ultra-deep approach. PLoS Computational Biology, 6(12), e1001022. (doi:10.1371/journal.pcbi.1001022) (PMID:21187908) (PMCID:PMC3002995)

Meehan, C. J., Hedge, J. A., Robertson, D. L., McCormack, G. P. and Travers, S. A.A. (2010) Emergence, dominance, and possible decline of CXCR4 chemokine receptor usage during the course of HIV infection. Journal of Medical Virology, 82(12), pp. 2004-2012. (doi:10.1002/jmv.21922) (PMID:20981786)

Woo, J., Robertson, D. L. and Lovell, S. C. (2010) Constraints on HIV-1 diversity from protein structure. Journal of Virology, 84(24), pp. 12995-13003. (doi:10.1128/JVI.00702-10) (PMID:20881050) (PMCID:PMC3004343)

Lovell, S. C. and Robertson, D. L. (2010) An integrated view of molecular coevolution in protein-protein interactions. Molecular Biology and Evolution, 27(11), pp. 2567-2575. (doi:10.1093/molbev/msq144) (PMID:20551042)

MacPherson, J. I., Dickerson, J. E., Pinney, J. W. and Robertson, D. L. (2010) Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems. PLoS Computational Biology, 6(7), e1000863. (doi:10.1371/journal.pcbi.1000863) (PMID:20686668) (PMCID:PMC2912648)

Carretero-Paulet, L., Galstyan, A., Roig-Villanova, I., Martínez-García, J. F., Bilbao-Castro, J. R. and Robertson, D. L. (2010) Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae. Plant Physiology, 153(3), pp. 1398-1412. (doi:10.1104/pp.110.153593) (PMID:20472752)

Dickerson, J. E., Pinney, J. W. and Robertson, D. L. (2010) The biological context of HIV-1 host interactions reveals subtle insights into a system hijack. BMC Systems Biology, 4, 80. (doi:10.1186/1752-0509-4-80) (PMID:20529270) (PMCID:PMC2897785)

Ames, R. M., Rash, B. M., Hentges, K. E., Robertson, D. L., Delneri, D. and Lovell, S. C. (2010) Gene duplication and environmental adaptation within yeast populations. Genome Biology and Evolution, 2, pp. 591-601. (doi:10.1093/gbe/evq043) (PMID:20660110) (PMCID:PMC2997561)

Robertson, D. L. and Lovell, S. C. (2009) Evolution in protein interaction networks: co-evolution, rewiring and the role of duplication. Biochemical Society Transactions, 37(4), pp. 768-771. (doi:10.1042/BST0370768) (PMID:19614591)

Plantier, J.-C., Leoz, M., Dickerson, J. E., De Oliveira, F., Cordonnier, F., Lemée, V., Damond, F., Robertson, D. L. and Simon, F. (2009) A new human immunodeficiency virus derived from gorillas. Nature Medicine, 15(8), pp. 871-872. (doi:10.1038/nm.2016) (PMID:19648927)

Archer, J., Braverman, M. S., Taillon, B. E., Desany, B., James, I., Harrigan, P. R., Lewis, M. and Robertson, D. L. (2009) Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing. AIDS, 23(10), pp. 1209-1218. (doi:10.1097/QAD.0b013e32832b4399) (PMID:19424056) (PMCID:PMC2857961)

Simon-Loriere, E., Galetto, R., Hamoudi, M., Archer, J., Lefeuvre, P., Martin, D. P., Robertson, D. L. and Negroni, M. (2009) Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus. PLoS Pathogens, 5(5), e1000418. (doi:10.1371/journal.ppat.1000418) (PMID:19424420) (PMCID:PMC2671596)

Huxley-Jones, J., Pinney, J. W., Archer, J., Robertson, D. L. and Boot-Handford, R. P. (2009) Back to basics--how the evolution of the extracellular matrix underpinned vertebrate evolution. International Journal of Experimental Pathology, 90(2), pp. 95-100. (doi:10.1111/j.1365-2613.2008.00637.x) (PMID:19335547)

MacPherson, J. I., Pinney, J. W. and Robertson, D. L. (2009) JNets: exploring networks by integrating annotation. BMC Bioinformatics, 10, 95. (doi:10.1186/1471-2105-10-95) (PMID:19323810) (PMCID:PMC2674432)

Pinney, J. W., Dickerson, J. E., Fu, W., Sanders-Beer, B. E., Ptak, R. G. and Robertson, D. L. (2009) HIV-host interactions: a map of viral perturbation of the host system. AIDS, 23(5), pp. 549-554. (doi:10.1097/QAD.0b013e328325a495) (PMID:19262354)

Ptak, R. G. et al. (2008) Cataloguing the HIV type 1 human protein interaction network. AIDS Research and Human Retroviruses, 24(12), pp. 1497-1502. (doi:10.1089/aid.2008.0113) (PMID:19025396) (PMCID:PMC2655106)

Archer, J., Pinney, J. W., Fan, J., Simon-Loriere, E., Arts, E. J., Negroni, M. and Robertson, D. L. (2008) Identifying the important HIV-1 recombination breakpoints. PLoS Computational Biology, 4(9), e1000178. (doi:10.1371/journal.pcbi.1000178) (PMID:18787691) (PMCID:PMC2522274)

Eales, J. M., Pinney, J. W., Stevens, R. D. and Robertson, D. L. (2008) Methodology capture: discriminating between the "best" and the rest of community practice. BMC Bioinformatics, 9, 359. (doi:10.1186/1471-2105-9-359) (PMID:18761740) (PMCID:PMC2553348)

Amoutzias, G. D., Robertson, D. L., Van de Peer, Y. and Oliver, S. G. (2008) Choose your partners: dimerization in eukaryotic transcription factors. Trends in Biochemical Sciences, 33(5), pp. 220-229. (doi:10.1016/j.tibs.2008.02.002) (PMID:18406148)

Hakes, L., Pinney, J. W., Robertson, D. L. and Lovell, S. C. (2008) Protein-protein interaction networks and biology--what's the connection? Nature Biotechnology, 26(1), pp. 69-72. (doi:10.1038/nbt0108-69) (PMID:18183023)

Pinney, J. W., Amoutzias, G. D., Rattray, M. and Robertson, D. L. (2007) Reconstruction of ancestral protein interaction networks for the bZIP transcription factors. Proceedings of the National Academy of Sciences of the United States of America, 104(51), pp. 20449-20453. (doi:10.1073/pnas.0706339104) (PMID:18077348) (PMCID:PMC2154451)

Fan, J., Negroni, M. and Robertson, D. L. (2007) The distribution of HIV-1 recombination breakpoints. Infection, Genetics and Evolution, 7(6), pp. 717-723. (doi:10.1016/j.meegid.2007.07.012) (PMID:17851137)

Archer, J. and Robertson, D. L. (2007) CTree: comparison of clusters between phylogenetic trees made easy. Bioinformatics, 23(21), pp. 2952-2953. (doi:10.1093/bioinformatics/btm410) (PMID:17717036)

Hakes, L., Pinney, J. W., Lovell, S. C., Oliver, S. G. and Robertson, D. L. (2007) All duplicates are not equal: the difference between small-scale and genome duplication. Genome Biology, 8(10), R209. (doi:10.1186/gb-2007-8-10-r209) (PMID:17916239) (PMCID:PMC2246283)

Archer, J. and Robertson, D. L. (2007) Understanding the diversification of HIV-1 groups M and O. AIDS, 21(13), pp. 1693-1700. (doi:10.1097/QAD.0b013e32825eabd0) (PMID:17690566)

Holden, B. J., Pinney, J. W., Lovell, S. C., Amoutzias, G. D. and Robertson, D. L. (2007) An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network. BMC Bioinformatics, 8, 289. (doi:10.1186/1471-2105-8-289) (PMID:17683601) (PMCID:PMC1963338)

Amoutzias, G. D., Pichler, E. E., Mian, N., De Graaf, D., Imsiridou, A., Robinson-Rechavi, M., Bornberg-Bauer, E., Robertson, D. L. and Oliver, S. G. (2007) A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. BMC Systems Biology, 1, 34. (doi:10.1186/1752-0509-1-34) (PMID:17672894) (PMCID:PMC1971058)

Hakes, L., Lovell, S. C., Oliver, S. G. and Robertson, D. L. (2007) Specificity in protein interactions and its relationship with sequence diversity and coevolution. Proceedings of the National Academy of Sciences of the United States of America, 104(19), pp. 7999-8004. (doi:10.1073/pnas.0609962104) (PMID:17468399) (PMCID:PMC1876561)

Huxley-Jones, J., Clarke, T.-K., Beck, C., Toubaris, G., Robertson, D. L. and Boot-Handford, R. P. (2007) The evolution of the vertebrate metzincins; insights from Ciona intestinalis and Danio rerio. BMC Evolutionary Biology, 7, 63. (doi:10.1186/1471-2148-7-63) (PMID:17439641) (PMCID:PMC1867822)

Zhang, X., Boot-Handford, R. P., Huxley-Jones, J., Forse, L. N., Mould, A. P., Robertson, D. L., Li, L., Athiyal, M. and Sarras, M. P. (2007) The collagens of hydra provide insight into the evolution of metazoan extracellular matrices. Journal of Biological Chemistry, 282(9), pp. 6792-802. (doi:10.1074/jbc.M607528200) (PMID:17204477)

Amoutzias, G.D., Veron, A.S., Weiner, J., Robinson-Rechavi, M., Bornberg-Bauer, E., Oliver, S.G. and Robertson, D.L. (2007) One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity. Molecular Biology and Evolution, 24(3), pp. 827-835. (doi:10.1093/molbev/msl211) (PMID:17194801)

Huxley-Jones, J., Robertson, D. L. and Boot-Handford, R. P. (2007) On the origins of the extracellular matrix in vertebrates. Matrix Biology, 26(1), pp. 2-11. (doi:10.1016/j.matbio.2006.09.008) (PMID:17055232)

Hakes, L., Robertson, D. L., Oliver, S. G. and Lovell, S. C. (2007) Protein interactions from complexes: a structural perspective. Comparative and Functional Genomics, 2007, 49356. (doi:10.1155/2007/49356) (PMID:17538689) (PMCID:PMC1838958)

Baird, H. A., Galetto, R., Gao, Y., Simon-Loriere, E., Abreha, M., Archer, J., Fan, J., Robertson, D. L., Arts, E. J. and Negroni, M. (2006) Sequence determinants of breakpoint location during HIV-1 intersubtype recombination. Nucleic Acids Research, 34(18), pp. 5203-5216. (doi:10.1093/nar/gkl669) (PMID:17003055) (PMCID:PMC1636437)

Amoutzias, G. D., Bornberg-Bauer, E., Oliver, S. G. and Robertson, D. L. (2006) Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network. BMC Genomics, 7, 107. (doi:10.1186/1471-2164-7-107) (PMID:16674813) (PMCID:PMC1479340)

Apetrei, C., Lerche, N. W., Pandrea, I., Gormus, B., Silvestri, G., Kaur, A., Robertson, D. L., Hardcastle, J., Lackner, A. A. and Marx, P. A. (2006) Kuru experiments triggered the emergence of pathogenic SIVmac. AIDS, 20(3), pp. 317-321. (doi:10.1097/01.aids.0000206498.71041.0e) (PMID:16439864)

Hakes, L., Robertson, D. L. and Oliver, S. G. (2005) Effect of dataset selection on the topological interpretation of protein interaction networks. BMC Genomics, 6, 131. (doi:10.1186/1471-2164-6-131) (PMID:16174296) (PMCID:PMC1249571)

Huxley-Jones, J., Apte, S. S., Robertson, D. L. and Boot-Handford, R. P. (2005) The characterisation of six ADAMTS proteases in the basal chordate Ciona intestinalis provides new insights into the vertebrate ADAMTS family. International Journal of Biochemistry and Cell Biology, 37(9), pp. 1838-1845. (doi:10.1016/j.biocel.2005.03.009) (PMID:15899586)

Apetrei, C. et al. (2005) Molecular epidemiology of simian immunodeficiency virus SIVsm in U.S. primate centers unravels the origin of SIVmac and SIVstm. Journal of Virology, 79(14), pp. 8991-9005. (doi:10.1128/JVI.79.14.8991-9005.2005) (PMID:15994793) (PMCID:PMC1168739)

van Cuyck, H., Fan, J., Robertson, D. L. and Roques, P. (2005) Evidence of recombination between divergent hepatitis E viruses. Journal of Virology, 79(14), pp. 9306-9314. (doi:10.1128/JVI.79.14.9306-9314.2005) (PMID:15994825) (PMCID:PMC1168788)

Pandrea, I., Mittleider, D., Brindley, P. J., Didier, E. S. and Robertson, D. L. (2005) Phylogenetic relationships of methionine aminopeptidase 2 among Encephalitozoon species and genotypes of microsporidia. Molecular and Biochemical Parasitology, 140(2), pp. 141-152. (doi:10.1016/j.molbiopara.2004.12.006) (PMID:15760654)

Apetrei, C., Metzger, M. J., Richardson, D., Ling, B., Telfer, P. T., Reed, P., Robertson, D. L. and Marx, P. A. (2005) Detection and partial characterization of simian immunodeficiency virus SIVsm strains from bush meat samples from rural Sierra Leone. Journal of Virology, 79(4), pp. 2631-2636. (doi:10.1128/JVI.79.4.2631-2636.2005) (PMID:15681464) (PMCID:PMC546599)

Traina-Dorge, V. L., Lorino, R., Gormus, B. J., Metzger, M., Telfer, P., Richardson, D., Robertson, D. L., Marx, P. A. and Apetrei, C. (2005) Molecular epidemiology of simian T-cell lymphotropic virus type 1 in wild and captive sooty mangabeys. Journal of Virology, 79(4), pp. 2541-2548. (doi:10.1128/JVI.79.4.2541-2548.2005) (PMID:15681454) (PMCID:PMC546543)

Ling, B., Telfer, P., Reed, P., Robertson, D. L. and Marx, P. A. (2004) A link between SIVsm in sooty mangabeys (SM) in wild-living monkeys in Sierra Leone and SIVsm in an American-based SM colony. AIDS Research and Human Retroviruses, 20(12), pp. 1348-1351. (doi:10.1089/aid.2004.20.1348) (PMID:15650427)

Roques, P., Robertson, D. L., Souquière, S., Apetrei, C., Nerrienet, E., Barré-Sinoussi, F., Müller-Trutwin, M. and Simon, F. (2004) Phylogenetic characteristics of three new HIV-1 N strains and implications for the origin of group N. AIDS, 18(10), pp. 1371-1381. (doi:10.1097/01.aids.0000125990.86904.28) (PMID:15199313)

Lemey, P., Pybus, O. G., Rambaut, A., Drummond, A. J., Robertson, D. L., Roques, P., Worobey, M. and Vandamme, A.-M. (2004) The molecular population genetics of HIV-1 group O. Genetics, 167(3), pp. 1059-1068. (doi:10.1534/genetics.104.026666) (PMID:15280223) (PMCID:PMC1470933)

Damond, F., Worobey, M., Campa, P., Farfara, I., Colin, G., Matheron, S., Brun-Vézinet, F., Robertson, D. L. and Simon, F. (2004) Identification of a highly divergent HIV type 2 and proposal for a change in HIV type 2 classification. AIDS Research and Human Retroviruses, 20(6), pp. 666-672. (doi:10.1089/0889222041217392) (PMID:15242544)

Amoutzias, G. D., Robertson, D. L., Oliver, S. G. and Bornberg-Bauer, E. (2004) Convergent evolution of gene networks by single-gene duplications in higher eukaryotes. EMBO reports, 5(3), pp. 274-279. (doi:10.1038/sj.embor.7400096) (PMID:14968135) (PMCID:PMC1299007)

Choisy, M., Woelk, C. H., Guégan, J.-F. and Robertson, D. L. (2004) Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. Journal of Virology, 78(4), pp. 1962-1970. (doi:10.1128/JVI.78.4.1962-1970.2004) (PMID:14747561) (PMCID:PMC369455)

Apetrei, C., Robertson, D. L. and Marx, P. A. (2004) The history of SIVS and AIDS: epidemiology, phylogeny and biology of isolates from naturally SIV infected non-human primates (NHP) in Africa. Frontiers in Bioscience, 9, pp. 225-254. (doi:10.2741/1154) (PMID:14766362)

Amoutzias, G. D., Robertson, D. L. and Bornberg-Bauer, E. (2004) The evolution of protein interaction networks in regulatory proteins. Comparative and Functional Genomics, 5(1), pp. 79-84. (doi:10.1002/cfg.365) (PMID:18629034) (PMCID:PMC2447317)

Apetrei, C., Descamps, D., Collin, G., Robertson, D. L., Pandrea, I., Groza, P., Prisecariu, L., Teodorescu, I., Luca, V. and Brun-Vézinet, F. (2003) HIV type 1 diversity in northeastern Romania in 200-2001 based on phylogenic analysis of pol sequences from patient failing antiretroviral therapy. AIDS Research and Human Retroviruses, 19(12), pp. 1155-1161. (doi:10.1089/088922203771881266) (PMID:14714572)

Hu, J., Switzer, W. M., Foley, B. T., Robertson, D. L., Goeken, R. M., Korber, B. T., Hirsch, V. M. and Beer, B. E. (2003) Characterization and comparison of recombinant simian immunodeficiency virus from drill (Mandrillus leucophaeus) and mandrill (Mandrillus sphinx) isolates. Journal of Virology, 77(8), pp. 4867-4880. (doi:10.1128/JVI.77.8.4867-4880.2003) (PMID:12663793) (PMCID:PMC152139)

Roques, P. et al. (2002) Phylogenetic analysis of 49 newly derived HIV-1 group O strains: high viral diversity but no group M-like subtype structure. Virology, 302(2), pp. 259-273. (doi:10.1006/viro.2002.1430) (PMID:12441070)

Damond, F. et al. (2002) Plasma RNA viral load in human immunodeficiency virus type 2 subtype A and subtype B infections. Journal of Clinical Microbiology, 40(10), pp. 3654-3659. (doi:10.1128/JCM.40.10.3654-3659.2002) (PMID:12354861) (PMCID:PMC130845)

Pandrea, I., Robertson, D. L., Onanga, R., Gao, F., Makuwa, M., Ngari, P., Bedjabaga, I., Roques, P., Simon, F. and Apetrei, C. (2002) Analysis of partial pol and env sequences indicates a high prevalence of HIV type 1 recombinant strains circulating in Gabon. AIDS Research and Human Retroviruses, 18(15), pp. 1103-1116. (doi:10.1089/088922202320567842) (PMID:12396449)

Charleston, M.A. and Robertson, D.L. (2002) Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny. Systematic Biology, 51(3), pp. 528-535. (doi:10.1080/10635150290069940) (PMID:12079649)

Worobey, M., Rambaut, A., Pybus, O. G. and Robertson, D. L. (2002) Questioning the evidence for genetic recombination in the 1918 "Spanish flu" virus. Science, 296(5566), 211. (doi:10.1126/science.296.5566.211a) (PMID:11951002)

Pandrea, I. et al. (2001) HIV type 1 genetic diversity and genotypic drug susceptibility in the Republic of Moldova. AIDS Research and Human Retroviruses, 17(13), pp. 1297-1304. (doi:10.1089/088922201750461375) (PMID:11559431)

Souquière, S. et al. (2001) Wild Mandrillus sphinx are carriers of two types of lentivirus. Journal of Virology, 75(15), pp. 7086-7096. (doi:10.1128/JVI.75.15.7086-7096.2001) (PMID:11435589) (PMCID:PMC114437)

Gao, F. et al. (2001) Evidence of two distinct subsubtypes within the HIV-1 subtype A radiation. AIDS Research and Human Retroviruses, 17(8), pp. 675-688. (doi:10.1089/088922201750236951) (PMID:11429108)

Conference Proceedings

Kouchaki, S., Tirunagari, S., Tapinos, A. and Robertson, D. L. (2017) Local Binary Patterns as a Feature Descriptor in Alignment-free Visualisation of Metagenomic Data. In: 2016 IEEE Symposium Series on Computational Intelligence (SSCI), Athens, Greece, 06-09 Dec 2016, ISBN 9781509042401 (doi:10.1109/SSCI.2016.7849955)

Kouchaki, S., Tirunagari, S., Tapinos, A. and Robertson, D. L. (2017) Marginalised Stack Denoising Autoencoders for Metagenomic Data Binning. In: 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), Manchester, UK, 23-25 Aug 2017, ISBN 9781467389884 (doi:10.1109/CIBCB.2017.8058552)

Tapinos, A. and Robertson, D. L. (2017) De Novo Assembly of Nucleotide Sequences in a Compressed Feature Space. In: 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), Manchester, UK, 23-25 Aug 2017, ISBN 9781467389884 (doi:10.1109/CIBCB.2017.8058556)

This list was generated on Mon Dec 11 10:39:14 2017 GMT.

 

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