Professor David Robertson
- Head of CVR Bioinformatics (Virology)
telephone:
0141 3303923
email:
David.L.Robertson@glasgow.ac.uk
https://orcid.org/0000-0001-6338-0221Biography
- Since 2017: Head of CVR Bioinformatics & Principal Investigator, University of Glasgow.
- 2002 - 2017: 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
The Robertson lab is a computational biology research group focussed on understanding virus evolution and emergence, and the specificity of virus-host relationships in the context of human disease. We study virus-host interactions and change in viral genomes to analyse and model in silico the nature of species and host ‘choice’ in infection, virus life cycles and determinants of cross-species transmission/host-switching. Studying these processes in viruses is important for understanding acute versus persistent infection, pathogenicity, transmission success and for predicting the emergence of new human or animal pathogens. Since the COVID-19 2020 pandemic we’ve been heavily focussed on the origins and evolution of SARS-CoV-2.
We take a data-driven approach to our research leveraging existing public data sets or working with experimental colleagues in the CVR, or with external collaborators to help analyse their data sets. To better understand infection and how to moderate the degree of harm they cause (virulence) we take a molecular evolutionary perspective to make inferences about where they have come from, what the risks of future emergence are, what changes are taking place in the human population, eg, the evolution of novel variants, and how virus populations evolve longitudinally in infected individuals.
Publications
2025
Lytras, S., Lamb, K. D., Ito, J., Grove, J. , Yuan, K. , Sato, K., Hughes, J. and Robertson, D. L. (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99(2), e0160124. (doi: 10.1128/jvi.01601-24) (PMID:39878472) (PMCID:39878472)
Furnon, W. et al. (2025) Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic. Nature Microbiology, 10, pp. 77-93. (doi: 10.1038/s41564-024-01878-5) (PMID:39753670) (PMCID:PMC11726466)
2024
Hinsch, M., Robertson, D. L. and Silverman, E. (2024) Evolutionary rescue effect can disappear under non-neutral mutations - a reply to Zhang et al. (2022). Nature Communications, 15(1), 10676. (doi: 10.1038/s41467-024-54828-4) (PMID:39672885) (PMCID:PMC11645402)
Ruscica, V. et al. (2024) XRN1 supplies free nucleotides to feed alphavirus replication. bioRxiv, (doi: 10.1101/2024.12.09.625895)
McLachlan, I. et al. (2024) Evaluation of risk-based travel policy for the COVID-19 epidemic in Scotland: a population-based surveillance study. BMJ Open, 14(11), e085332. (doi: 10.1136/bmjopen-2024-085332) (PMID:39615890)
Liu, D., Young, F., Lamb, K. D., Claudio Quiros, A., Pancheva, A., Miller, C. , Macdonald, C. , Robertson, D. L. and Yuan, K. (2024) PLM-interact: extending protein language models to predict protein-protein interactions. bioRxiv, (doi: 10.1101/2024.11.05.622169)
Liu, D., Young, F., Lamb, K. D., Robertson, D. L. and Yuan, K. (2024) Prediction of virus-host associations using protein language models and multiple instance learning. PLoS Computational Biology, 20(11), e1012597. (doi: 10.1371/journal.pcbi.1012597) (PMID:39561204) (PMCID:PMC11614202)
Lamb, K. D., Hughes, J. , Lytras, S., Young, F., Koci, O., Herzig, J., Lovell, S. C.,, Grove, J. , Yuan, K. and Robertson, D. L. (2024) From a single sequence to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2 protein sequences. bioRxiv, (doi: 10.1101/2024.07.05.602129)
Menkir, T. F. et al. (2024) Modeling the relative influence of socio-demographic variables on post-acute COVID-19 quality of life. medXriv, (doi: 10.1101/2024.02.21.24303099)
Hinsch, M., Silverman, E. and Robertson, D. L. (2024) Whole-System Pandemic Modelling Including Pathogen Evolution. In: 18th Social Simulation Conference (SSC23), Glasgow, UK, 04-08 Sep 2023, pp. 63-71. (doi: 10.1007/978-3-031-57785-7_6)
Costa, R. L., Gadelha, L., D'arc, M., Ribeiro-Alves, M., Robertson, D. L. , Schwartz, J.-M., Soares, M. A. and Porto, F. (2024) HIHISIV: a database of gene expression in HIV and SIV host immune response. BMC Bioinformatics, 25, 125. (doi: 10.1186/s12859-024-05740-7) (PMID:38519883) (PMCID:PMC10958971)
Lamb, K. D., Luka, M. M., Saathoff, M., Orton, R. J. , Phan, M. V.T., Cotten, M. , Yuan, K. and Robertson, D. L. (2024) Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules. PLoS Computational Biology, 20(1), e1011795. (doi: 10.1371/journal.pcbi.1011795) (PMID:38271457) (PMCID:PMC10868779)
2023
Willett, B. J. et al. (2023) Omicron BA.2.86 cross-neutralising activity in community sera from the UK. Lancet, 402(10417), pp. 2075-2076. (doi: 10.1016/s0140-6736(23)02397-8) (PMID:37952549)
Swets, M. C. et al. (2023) Evaluation of pragmatic oxygenation measurement as a proxy for Covid-19 severity. Nature Communications, 14(1), 7374. (doi: 10.1038/s41467-023-42205-6) (PMID:37968269) (PMCID:PMC10651917)
Pascall, D. J. et al. (2023) Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent. Journal of Infection, 87(2), pp. 128-135. (doi: 10.1016/j.jinf.2023.05.019) (PMID:37270070) (PMCID:PMC10234362)
Hinsch, M., Silverman, E. and Robertson, D. L. (2023) Simulating the Evolutionary Response of a Viral Pandemic to Behaviour Change. In: ALIFE 2023: Ghost in the machine, Sapporo, Japan, 24-28 Jul 2023, isal_a_00691. (doi: 10.1162/isal_a_00691)
Megremis, S. et al. (2023) Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma. Scientific Reports, 13, 8319. (doi: 10.1038/s41598-023-34730-7) (PMID:37221274) (PMCID:PMC10205716)
Ho, A. et al. (2023) Adeno-associated virus 2 infection in children with non-A-E hepatitis. Nature, 617(7961), pp. 555-563. (doi: 10.1038/s41586-023-05948-2) (PMID:36996873)
Siddell, S. G. et al. (2023) Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV). Journal of General Virology, 104(5), 001840. (doi: 10.1099/jgv.0.001840) (PMID:37141106) (PMCID:PMC10227694)
Cho, S.-M. et al. (2023) Neurological manifestations of COVID-19 in adults and children. Brain, 146(4), pp. 1648-1661. (doi: 10.1093/brain/awac332) (PMID:36087305) (PMCID:PMC9494397)
Pascall, D. J. et al. (2023) The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: a genomics-based retrospective cohort analysis. PLoS ONE, 18(4), e0284187. (doi: 10.1371/journal.pone.0284187) (PMID:37053201) (PMCID:PMC10101505)
Carabelli, A. M., Peacock, T. P., Thorne, L. G., Harvey, W. T., Hughes, J. , Peacock, S. J., Barclay, W. S., de Silva, T. I., Towers, G. J. and Robertson, D. L. (2023) SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nature Reviews Microbiology, 21(3), pp. 162-177. (doi: 10.1038/s41579-022-00841-7) (PMID:36653446) (PMCID:PMC9847462)
Cox, M. et al. (2023) SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies. Nature Reviews Microbiology, 21(2), pp. 112-124. (doi: 10.1038/s41579-022-00809-7) (PMID:36307535) (PMCID:PMC9616429)
Simmonds, P. et al. (2023) Four principles to establish a universal virus taxonomy. PLoS Biology, 21(2), e3001922. (doi: 10.1371/journal.pbio.3001922) (PMID:36780432) (PMCID:PMC9925010)
Iannucci, S., Harvey, W. T., Hughes, J. , Robertson, D. L. , Poyade, M. and Hutchinson, E. (2023) The SARS-CoV-2 Spike Protein Mutation Explorer: using an interactive application to improve the public understanding of SARS-CoV-2 variants of concern. Journal of Visual Communication in Medicine, 46(3), pp. 122-132. (doi: 10.1080/17453054.2023.2237087) (PMID:37526402) (PMCID:PMC10726978)
2022
Chai, H., Gu, Q. , Robertson, D. L. and Hughes, J. (2022) Defining the characteristics of interferon-alpha–stimulated human genes: insight from expression data and machine learning. GigaScience, 11, giac103. (doi: 10.1093/gigascience/giac103) (PMID:36399061) (PMCID:PMC9673497)
Sugrue, E. et al. (2022) The apparent interferon resistance of transmitted HIV-1 is possibly a consequence of enhanced replicative fitness. PLoS Pathogens, 18(11), e1010973. (doi: 10.1371/journal.ppat.1010973) (PMID:36399512) (PMCID:PMC9718408)
Walker, P. J. et al. (2022) Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022). Archives of Virology, 167(11), pp. 2429-2440. (doi: 10.1007/s00705-022-05516-5) (PMID:35999326)
Cantoni, D. et al. (2022) Evolutionary remodelling of N-terminal domain loops fine-tunes SARS-CoV-2 spike. EMBO Reports, 23(10), e54322. (doi: 10.15252/embr.202154322) (PMID:35999696) (PMCID:PMC9535765)
Willett, B. J. et al. (2022) Publisher Correction: SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7, 1709. (doi: 10.1038/s41564-022-01241-6) (PMID:36114232) (PMCID:PMC9483304)
Stirrup, O. et al. (2022) Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study. eLife, 11, e78427. (doi: 10.7554/elife.78427) (PMID:36098502) (PMCID:PMC9596156)
Iannucci, S., Harvey, W., Hughes, J. , Robertson, D. L. , Hutchinson, E. and Poyade, M. (2022) Using molecular visualisation techniques to explain the molecular biology of SARS-CoV-2 spike protein mutations to a general audience. In: Shapiro, Leonard and Rea, Paul M. (eds.) Biomedical Visualisation. Volume 12. Series: Advances in experimental medicine and biology (1388). Springer: Cham, pp. 129-152. ISBN 9783031108884 (doi: 10.1007/978-3-031-10889-1_6)
Willett, B. J. et al. (2022) SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7(8), pp. 1161-1179. (doi: 10.1038/s41564-022-01143-7) (PMID:35798890) (PMCID:PMC9352574)
Nickbakhsh, S. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12, 11735. (doi: 10.1038/s41598-022-15661-1) (PMID:35853960) (PMCID:PMC9296497)
Telenti, A., Hodcroft, E. B. and Robertson, D. L. (2022) The evolution and biology of SARS-CoV-2 variants. Cold Spring Harbor Perspectives in Medicine, 12(5), a041390. (doi: 10.1101/cshperspect.a041390) (PMID:35444005)
Modha, S. , Robertson, D. L. , Hughes, J. and Orton, R. J. (2022) Quantifying and cataloguing unknown sequences within human microbiomes. mSystems, 7(2), e01468-21. (doi: 10.1128/msystems.01468-21) (PMID:35258340) (PMCID:PMC9052204)
Worobey, M. et al. (2022) The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science, 377(6609), pp. 951-959. (doi: 10.1126/science.abp8715) (PMID:35881010) (PMCID:PMC9348750)
Martin, D. P. et al. (2022) Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA.1 that likely impact Spike function. Molecular Biology and Evolution, 39(4), msac061. (doi: 10.1093/molbev/msac061) (PMID:35325204) (PMCID:PMC9037384)
Zerbini, F. M. et al. (2022) Differentiating between viruses and virus species by writing their names correctly. Archives of Virology, 167(4), pp. 1231-1234. (doi: 10.1007/s00705-021-05323-4) (PMID:35043230) (PMCID:PMC9020231)
Aggarwal, D. et al. (2022) Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nature Communications, 13, 1012. (doi: 10.1038/s41467-022-28371-z) (PMID:35197443) (PMCID:PMC8866425)
Maher, M. C. et al. (2022) Predicting the mutational drivers of future SARS-CoV-2 variants of concern. Science Translational Medicine, 14(633), eabk3445. (doi: 10.1126/scitranslmed.abk3445) (PMID:35014856) (PMCID:PMC8939770)
Aggarwal, D. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13, 751. (doi: 10.1038/s41467-021-27942-w) (PMID:35136068) (PMCID:PMC8826310)
Chai, H., Gu, Q. , Hughes, J. and Robertson, D. L. (2022) In silico prediction of HIV-1-host molecular interactions and their directionality. PLoS Computational Biology, 18(2), e1009720. (doi: 10.1371/journal.pcbi.1009720) (PMID:35134057) (PMCID:PMC8856524)
Lytras, S., Hughes, J. , Martin, D., Swanepoel, P., de Klerk, A., Lourens, R., Kosakovsky Pond, S. L., Xia, W., Jiang, X. and Robertson, D. L. (2022) Exploring the natural origins of SARS-CoV-2 in the light of recombination. Genome Biology and Evolution, 14(2), evac018. (doi: 10.1093/gbe/evac018) (PMID:35137080) (PMCID:PMC8882382)
Twohig, K. A. et al. (2022) Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study. Lancet Infectious Diseases, 22(1), pp. 35-42. (doi: 10.1016/S1473-3099(21)00475-8) (PMID:34461056) (PMCID:PMC8397301)
de Klerk, A. et al. (2022) Conserved recombination patterns across coronavirus subgenera. Virus Evolution, 8(2), veac054. (doi: 10.1093/ve/veac054) (PMID:35814334) (PMCID:PMC9261289)
Hill, V. et al. (2022) The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. Virus Evolution, 8(2), veac080. (doi: 10.1093/ve/veac080) (PMID:36533153) (PMCID:PMC9752794)
Wright, D. W. et al. (2022) Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer. Virus Evolution, 8(1), veac023. (doi: 10.1093/ve/veac023) (PMID:35502202) (PMCID:PMC9037374)
2021
Niemi, M. E. K. et al. (2021) Mapping the human genetic architecture of COVID-19. Nature, 600(7889), pp. 472-477. (doi: 10.1038/s41586-021-03767-x) (PMID:34237774) (PMCID:PMC8674144)
Vöhringer, H. S. et al. (2021) Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600(7889), pp. 506-511. (doi: 10.1038/s41586-021-04069-y) (PMID:34649268) (PMCID:PMC8674138)
Davis, C. et al. (2021) Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination. PLoS Pathogens, 17(12), e1010022. (doi: 10.1371/journal.ppat.1010022) (PMID:34855916) (PMCID:PMC8639073)
Wickenhagen, A. et al. (2021) A prenylated dsRNA sensor protects against severe COVID-19. Science, 374(6567), eabj3624. (doi: 10.1126/science.abj3624) (PMID:34581622) (PMCID:PMC7612834)
Cotten, M. , Robertson, D. L. and Phan, M. V.T. (2021) Unique protein features of SARS-CoV-2 relative to other Sarbecoviruses. Virus Evolution, 7(2), veab067. (doi: 10.1093/ve/veab067) (PMID:34527286) (PMCID:PMC8385934)
Jackson, B. et al. (2021) Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell, 184(20), 5179-5188.e8. (doi: 10.1016/j.cell.2021.08.014) (PMID:34499854) (PMCID:PMC8367733)
Martin, D. P. et al. (2021) The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Cell, 184(20), 5189-5200.e7. (doi: 10.1016/j.cell.2021.09.003) (PMID:34537136) (PMCID:PMC8421097)
Holmes, E. C. et al. (2021) The origins of SARS-CoV-2: a critical review. Cell, 184(19), pp. 4848-4856. (doi: 10.1016/j.cell.2021.08.017) (PMID:34480864) (PMCID:PMC8373617)
Shaw, A. E. et al. (2021) The antiviral state has shaped the CpG composition of the vertebrate interferome to avoid self-targeting. PLoS Biology, 19(9), e3001352. (doi: 10.1371/journal.pbio.3001352) (PMID:34491982) (PMCID:PMC8423302)
Walker, P. J. et al. (2021) Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021). Archives of Virology, 166(9), pp. 2633-2648. (doi: 10.1007/s00705-021-05156-1) (PMID:34231026)
Lytras, S., Xia, W., Hughes, J. , Jiang, X. and Robertson, D. L. (2021) The animal origin of SARS-CoV-2. Science, 373(6558), pp. 968-970. (doi: 10.1126/science.abh0117) (PMID:34404734)
Russell, C. D. et al. (2021) Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study. Lancet Microbe, 2(8), e354-e365. (doi: 10.1016/S2666-5247(21)00090-2) (PMID:34100002) (PMCID:PMC8172149)
Drake, T. M. et al. (2021) Characterisation of in-hospital complications associated with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol UK: a prospective, multicentre cohort study. Lancet, 398(10296), pp. 223-237. (doi: 10.1016/S0140-6736(21)00799-6) (PMID:34274064) (PMCID:PMC8285118)
Harvey, W. T. et al. (2021) SARS-CoV-2 variants, spike mutations and immune escape. Nature Reviews Microbiology, 19(7), pp. 409-424. (doi: 10.1038/s41579-021-00573-0) (PMID:34075212) (PMCID:PMC8167834)
Li, K. K. et al. (2021) Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - a high risk community-hospital interface. Journal of Infection, 83(1), pp. 96-103. (doi: 10.1016/j.jinf.2021.04.020) (PMID:33895226) (PMCID:PMC8061788)
Makalatia, K. et al. (2021) Investigation of Salmonella phage–bacteria infection profiles: network structure reveals a gradient of target-range from generalist to specialist phage clones in nested subsets. Viruses, 13(7), 1261. (doi: 10.3390/v13071261) (PMID:34203492) (PMCID:PMC8310288)
Meng, B. et al. (2021) Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the variant of concern lineage B.1.1.7. Cell Reports, 35(13), 109292. (doi: 10.1016/j.celrep.2021.109292) (PMID:34166617) (PMCID:PMC8185188)
Goettsch, W. et al. (2021) ITN—VIROINF: understanding (harmful) virus-host interactions by linking virology and bioinformatics. Viruses, 13(5), 766. (doi: 10.3390/v13050766) (PMID:33925452) (PMCID:PMC8145447)
Graham, M. S. et al. (2021) Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study. Lancet Public Health, 6(5), e335-e345. (doi: 10.1016/S2468-2667(21)00055-4)
Volz, E. et al. (2021) Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593(7858), pp. 266-269. (doi: 10.1038/s41586-021-03470-x) (PMID:33767447)
Hosie, M. J. et al. (2021) Detection of SARS-CoV-2 in respiratory samples from cats in the UK associated with human-to-cat transmission. Veterinary Record, 188(8), e247. (doi: 10.1002/vetr.247) (PMID:33890314) (PMCID:PMC8251078)
Thomson, E. C. et al. (2021) Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell, 184(5), 1171-1187.e20. (doi: 10.1016/j.cell.2021.01.037) (PMID:33621484) (PMCID:PMC7843029)
Hufsky, F. et al. (2021) Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings in Bioinformatics, 22(2), pp. 642-663. (doi: 10.1093/bib/bbaa232) (PMID:33147627) (PMCID:PMC7665365)
MacLean, O. A. , Lytras, S., Weaver, S., Singer, J. B., Boni, M. F., Lemey, P., Kosakovsky Pond, S. L. and Robertson, D. L. (2021) Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen. PLoS Biology, 19(3), e3001115. (doi: 10.1371/journal.pbio.3001115) (PMID:33711012) (PMCID:PMC7990310)
Rihn, S. J. et al. (2021) A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. PLoS Biology, 19(2), e3001091. (doi: 10.1371/journal.pbio.3001091) (PMID:33630831) (PMCID:PMC7906417)
Volz, E. et al. (2021) Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity. Cell, 184(1), 64-75.e11. (doi: 10.1016/j.cell.2020.11.020) (PMID:33275900) (PMCID:PMC7674007)
Da Silva Filipe, A. et al. (2021) Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology, 6(1), pp. 112-122. (doi: 10.1038/s41564-020-00838-z) (PMID:33349681)
2020
Sellers, R. A., Robertson, D. L. and Tassabehji, M. (2020) Ancestry of the AUTS2 family–a novel group of polycomb-complex proteins involved in human neurological disease. PLoS ONE, 15(12), e0232101. (doi: 10.1371/journal.pone.0232101) (PMID:33306672) (PMCID:PMC7732068)
Boni, M. F., Lemey, P., Jiang, X., Lam, T. T.-Y., Perry, B. W., Castoe, T. A., Rambaut, A. and Robertson, D. L. (2020) Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nature Microbiology, 5(11), pp. 1408-1417. (doi: 10.1038/s41564-020-0771-4) (PMID:32724171)
Pollock, D. D. et al. (2020) Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2. Molecular Biology and Evolution, 37(9), pp. 2706-2710. (doi: 10.1093/molbev/msaa178) (PMID:32658964) (PMCID:PMC7454803)
Masembe, C. , Phan, M. V.T., Robertson, D. L. and Cotten, M. (2020) Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains. Virus Evolution, 6(2), veaa044. (doi: 10.1093/ve/veaa044) (PMID:32913663) (PMCID:PMC7474929)
Murcia, P. , Streiker, D. , Da Silva Filipe, A. , Robertson, D. , Jarrett, R. , Willett, B. , Hosie, M. , Biek, R. , Allan, K. and Weir, W. (2020) Send cat and dog samples to test for SARS-CoV-2. Veterinary Record, 186(17), p. 571. (doi: 10.1136/vr.m2019) (PMID:32451348)
Young, F., Rogers, S. and Robertson, D. L. (2020) Predicting host taxonomic information from viral genomes: a comparison of feature representations. PLoS Computational Biology, 16(5), e1007894. (doi: 10.1371/journal.pcbi.1007894) (PMID:32453718) (PMCID:PMC7307784)
Grant, H. E. et al. (2020) Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evolution, 6(1), veaa004. (doi: 10.1093/ve/veaa004) (PMID:32395255) (PMCID:PMC7204518)
MacLean, O. A. , Orton, R. J. , Singer, J. B. and Robertson, D. L. (2020) No evidence for distinct types in the evolution of SARS-CoV-2. Virus Evolution, 6(1), veaa034. (doi: 10.1093/ve/veaa034) (PMID:32817804) (PMCID:PMC7197565)
2019
Fotiou, E., Williams, S., Martin-Geary, A., Robertson, D. , Tenin, G., Hentges, K. E. and Keavney, B. (2019) Integration of large-scale genomic data sources with evolutionary history reveals novel genetic loci for congenital heart disease. Circulation: Genomic and Precision Medicine, 12(10), pp. 442-451. (doi: 10.1161/CIRCGEN.119.002694) (PMID:31613678)
Hufsky, F. et al. (2019) The Third Annual Meeting of the European Virus Bioinformatics Center. Viruses, 11(5), 420. (doi: 10.3390/v11050420) (PMID:31060321) (PMCID:PMC6563321)
Tapinos, A., Constantinides, B., Phan, M. V. T., Kouchaki, S., Cotten, M. and Robertson, D. L. (2019) The utility of data transformation for alignment, de novo assembly and classification of short read virus sequences. Viruses, 11(5), 394. (doi: 10.3390/v11050394) (PMID:31035503) (PMCID:PMC6563281)
Singer, J. B. et al. (2019) Interpreting viral deep sequencing data with GLUE. Viruses, 11(4), 323. (doi: 10.3390/v11040323) (PMID:30987147) (PMCID:PMC6520954)
Kouchaki, S., Tapinos, A. and Robertson, D. (2019) A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns. Scientific Reports, 9, 2159. (doi: 10.1038/s41598-018-38197-9) (PMID:30770850) (PMCID:PMC6377666)
Ravindran, V., Nacher, J. C., Akutsu, T., Ishitsuka, M., Osadcenco, A., Sunitha, V., Bagler, G., Schwartz, J.-M. and Robertson, D. L. (2019) Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems. Scientific Reports, 9, 2066. (doi: 10.1038/s41598-018-38224-9) (PMID:30765882) (PMCID:PMC6375943)
2018
Lewis, M. et al. (2018) Clonal analysis of HIV-1 genotype and function associated with virologic failure in treatment-experienced persons receiving maraviroc: Results from the MOTIVATE phase 3 randomized, placebo-controlled trials. PLoS ONE, 13(12), e0204099. (doi: 10.1371/journal.pone.0204099) (PMID:30586365) (PMCID:PMC6306210)
Stoney, R. A., Schwartz, J.-M., Robertson, D. L. and Nenadic, G. (2018) Using set theory to reduce redundancy in pathway sets. BMC Bioinformatics, 19, 386. (doi: 10.1186/s12859-018-2355-3) (PMID:30340461) (PMCID:PMC6194563)
Stoney, R., Robertson, D. L. , Nenadic, G. and Schwartz, J.-M. (2018) Mapping biological process relationships and disease perturbations within a pathway network. npj Systems Biology and Applications, 4, 22. (doi: 10.1038/s41540-018-0055-2) (PMID:29900005) (PMCID:PMC5995814)
Alessandri-Gradt, E., De Oliveira, F., Leoz, M., Lemee, V., Robertson, D. L. , Feyertag, F., Ngoupo, P.-A., Mauclere, P., Simon, F. and Plantier, J.-C. (2018) HIV-1 group P infection: towards a dead-end infection? AIDS, 32(10), pp. 1317-1322. (doi: 10.1097/QAD.0000000000001791) (PMID:29547436)
Ibrahim, B. et al. (2018) Bioinformatics meets virology: the European virus bioinformatics center's second annual meeting. Viruses, 10(5), 256. (doi: 10.3390/v10050256) (PMID:29757994) (PMCID:PMC5977249)
Rivers-Auty, J., Daniels, M. J.D., Colliver, I., Robertson, D. L. and Brough, D. (2018) Redefining the ancestral origins of the interleukin-1 superfamily. Nature Communications, 9, 1156. (doi: 10.1038/s41467-018-03362-1) (PMID:29559685) (PMCID:PMC5861070)
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)
Rambaut, A., Robertson, D.L. , Pybus, O.G., Peeters, M. and Holmes, E.C. (2001) Human immunodeficiency virus. Phylogeny and the origin of HIV-1. Nature, 410(6832), pp. 1047-1048. (doi: 10.1038/35074179) (PMID:11323659)
Damond, F., Apetrei, C., Robertson, D.L. , Souquière, S., Leprêtre, A., Matheron, S., Plantier, J.C., Brun-Vézinet, F. and Simon, F. (2001) Variability of human immunodeficiency virus type 2 (hiv-2) infecting patients living in France. Virology, 280(1), pp. 19-30. (doi: 10.1006/viro.2000.0685) (PMID:11162815)
Rodenburg, C.M. et al. (2001) Near full-length clones and reference sequences for subtype C isolates of HIV type 1 from three different continents. AIDS Research and Human Retroviruses, 17(2), pp. 161-168. (doi: 10.1089/08892220150217247) (PMID:11177395)
2000
Robertson, D.L. et al. (2000) HIV-1 nomenclature proposal. Science, 288(5463), pp. 55-56. (doi: 10.1126/science.288.5463.55d) (PMID:10766634)
1999
Sharp, P.M., Bailes, E., Robertson, D.L. , Gao, F. and Hahn, B.H. (1999) Origins and evolution of AIDS viruses. Biological Bulletin, 196(3), pp. 338-342. (doi: 10.2307/1542965) (PMID:10390833)
Gao, F. et al. (1999) Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature, 397(6718), pp. 436-441. (doi: 10.1038/17130) (PMID:9989410)
Abergel, C., Robertson, D.L. and Claverie, J.M. (1999) "Hidden" dUTPase sequence in human immunodeficiency virus type 1 gp120. Journal of Virology, 73(1), pp. 751-753. (PMID:9847382) (PMCID:PMC103883)
1998
Gao, F. et al. (1998) An isolate of human immunodeficiency virus type 1 originally classified as subtype I represents a complex mosaic comprising three different group M subtypes (A, G, and I). Journal of Virology, 72(12), pp. 10234-10241. (PMID:9811767) (PMCID:PMC110605)
Gao, F. et al. (1998) A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1. Journal of Virology, 72(7), pp. 5680-5698. (PMID:9621027) (PMCID:PMC110237)
1997
Salminen, M.O. et al. (1997) Evolution and probable transmission of intersubtype recombinant human immunodeficiency virus type 1 in a Zambian couple. Journal of Virology, 71(4), pp. 2647-2655. (PMID:9060617) (PMCID:PMC191386)
Soares, M.A., Robertson, D.L. , Hui, H., Allan, J.S., Shaw, G.M. and Hahn, B.H. (1997) A full-length and replication-competent proviral clone of SIVAGM from tantalus monkeys. Virology, 228(2), pp. 394-399. (doi: 10.1006/viro.1996.8387) (PMID:9123848)
1996
Gao, F. et al. (1996) The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin. Journal of Virology, 70(10), pp. 7013-7029. (PMID:8794346) (PMCID:PMC190752)
Gao, F. et al. (1996) Molecular cloning and analysis of functional envelope genes from human immunodeficiency virus type 1 sequence subtypes A through G. The WHO and NIAID networks for HIV isolation and characterization. Journal of Virology, 70(3), pp. 1651-1667. (PMID:8627686) (PMCID:PMC189989)
1995
Sharp, P. M., Robertson, D. L. and Hahn, B. H. (1995) Cross-species transmission and recombination of 'AIDS' viruses. Philosophical Transactions of the Royal Society B: Biological Sciences, 349(1327), pp. 41-47. (doi: 10.1098/rstb.1995.0089) (PMID:8748018)
Robertson, D. L. , Sharp, P. M., McCutchan, F. E. and Hahn, B. H. (1995) Recombination in HIV-1. Nature, 374(6518), pp. 124-126. (doi: 10.1038/374124b0) (PMID:7877682)
Robertson, D. L. , Hahn, B. H. and Sharp, P. M. (1995) Recombination in AIDS viruses. Journal of Molecular Evolution, 40(3), pp. 249-259. (doi: 10.1007/BF00163230) (PMID:7723052)
1994
Gao, F., Yue, L., Robertson, D.L. , Hill, S.C., Hui, H., Biggar, R.J., Neequaye, A.E., Whelan, T.M., Ho, D.D. and Shaw, G.M. (1994) Genetic diversity of human immunodeficiency virus type 2: evidence for distinct sequence subtypes with differences in virus biology. Journal of Virology, 68(11), pp. 7433-7447. (PMID:7933127) (PMCID:PMC237186)
Gao, F., Yue, L., Craig, S., Thornton, C. L., Robertson, D. L. , McCutchan, F. E., Bradac, J. A., Sharp, P. M. and Hahn, B. H. (1994) Genetic variation of HIV type 1 in four World Health Organization-sponsored vaccine evaluation sites: generation of functional envelope (glycoprotein 160) clones representative of sequence subtypes A, B, C. AIDS Research and Human Retroviruses, 10(11), pp. 1359-1368. (doi: 10.1089/aid.1994.10.1359) (PMID:7888189)
Jin, M.J., Hui, H., Robertson, D.L. , Müller, M.C., Barré-Sinoussi, F., Hirsch, V.M., Allan, J.S., Shaw, G.M., Sharp, P.M. and Hahn, B.H. (1994) Mosaic genome structure of simian immunodeficiency virus from west African green monkeys. EMBO Journal, 13(12), pp. 2935-2947. (PMID:8026477) (PMCID:PMC395175)
Gao, F., Yue, L., Hill, S. C., Robertson, D. L. , Graves, A. H., Saag, M. S., Shaw, G. M., Sharp, P. M. and Hahn, B. H. (1994) HIV-1 sequence subtype D in the United States. AIDS Research and Human Retroviruses, 10(5), pp. 625-627. (doi: 10.1089/aid.1994.10.625) (PMID:7917525)
Articles
Lytras, S., Lamb, K. D., Ito, J., Grove, J. , Yuan, K. , Sato, K., Hughes, J. and Robertson, D. L. (2025) Pathogen genomic surveillance and the AI revolution. Journal of Virology, 99(2), e0160124. (doi: 10.1128/jvi.01601-24) (PMID:39878472) (PMCID:39878472)
Furnon, W. et al. (2025) Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic. Nature Microbiology, 10, pp. 77-93. (doi: 10.1038/s41564-024-01878-5) (PMID:39753670) (PMCID:PMC11726466)
Hinsch, M., Robertson, D. L. and Silverman, E. (2024) Evolutionary rescue effect can disappear under non-neutral mutations - a reply to Zhang et al. (2022). Nature Communications, 15(1), 10676. (doi: 10.1038/s41467-024-54828-4) (PMID:39672885) (PMCID:PMC11645402)
Ruscica, V. et al. (2024) XRN1 supplies free nucleotides to feed alphavirus replication. bioRxiv, (doi: 10.1101/2024.12.09.625895)
McLachlan, I. et al. (2024) Evaluation of risk-based travel policy for the COVID-19 epidemic in Scotland: a population-based surveillance study. BMJ Open, 14(11), e085332. (doi: 10.1136/bmjopen-2024-085332) (PMID:39615890)
Liu, D., Young, F., Lamb, K. D., Claudio Quiros, A., Pancheva, A., Miller, C. , Macdonald, C. , Robertson, D. L. and Yuan, K. (2024) PLM-interact: extending protein language models to predict protein-protein interactions. bioRxiv, (doi: 10.1101/2024.11.05.622169)
Liu, D., Young, F., Lamb, K. D., Robertson, D. L. and Yuan, K. (2024) Prediction of virus-host associations using protein language models and multiple instance learning. PLoS Computational Biology, 20(11), e1012597. (doi: 10.1371/journal.pcbi.1012597) (PMID:39561204) (PMCID:PMC11614202)
Lamb, K. D., Hughes, J. , Lytras, S., Young, F., Koci, O., Herzig, J., Lovell, S. C.,, Grove, J. , Yuan, K. and Robertson, D. L. (2024) From a single sequence to evolutionary trajectories: protein language models capture the evolutionary potential of SARS-CoV-2 protein sequences. bioRxiv, (doi: 10.1101/2024.07.05.602129)
Menkir, T. F. et al. (2024) Modeling the relative influence of socio-demographic variables on post-acute COVID-19 quality of life. medXriv, (doi: 10.1101/2024.02.21.24303099)
Costa, R. L., Gadelha, L., D'arc, M., Ribeiro-Alves, M., Robertson, D. L. , Schwartz, J.-M., Soares, M. A. and Porto, F. (2024) HIHISIV: a database of gene expression in HIV and SIV host immune response. BMC Bioinformatics, 25, 125. (doi: 10.1186/s12859-024-05740-7) (PMID:38519883) (PMCID:PMC10958971)
Lamb, K. D., Luka, M. M., Saathoff, M., Orton, R. J. , Phan, M. V.T., Cotten, M. , Yuan, K. and Robertson, D. L. (2024) Mutational signature dynamics indicate SARS-CoV-2's evolutionary capacity is driven by host antiviral molecules. PLoS Computational Biology, 20(1), e1011795. (doi: 10.1371/journal.pcbi.1011795) (PMID:38271457) (PMCID:PMC10868779)
Willett, B. J. et al. (2023) Omicron BA.2.86 cross-neutralising activity in community sera from the UK. Lancet, 402(10417), pp. 2075-2076. (doi: 10.1016/s0140-6736(23)02397-8) (PMID:37952549)
Swets, M. C. et al. (2023) Evaluation of pragmatic oxygenation measurement as a proxy for Covid-19 severity. Nature Communications, 14(1), 7374. (doi: 10.1038/s41467-023-42205-6) (PMID:37968269) (PMCID:PMC10651917)
Pascall, D. J. et al. (2023) Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent. Journal of Infection, 87(2), pp. 128-135. (doi: 10.1016/j.jinf.2023.05.019) (PMID:37270070) (PMCID:PMC10234362)
Megremis, S. et al. (2023) Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma. Scientific Reports, 13, 8319. (doi: 10.1038/s41598-023-34730-7) (PMID:37221274) (PMCID:PMC10205716)
Ho, A. et al. (2023) Adeno-associated virus 2 infection in children with non-A-E hepatitis. Nature, 617(7961), pp. 555-563. (doi: 10.1038/s41586-023-05948-2) (PMID:36996873)
Siddell, S. G. et al. (2023) Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV). Journal of General Virology, 104(5), 001840. (doi: 10.1099/jgv.0.001840) (PMID:37141106) (PMCID:PMC10227694)
Cho, S.-M. et al. (2023) Neurological manifestations of COVID-19 in adults and children. Brain, 146(4), pp. 1648-1661. (doi: 10.1093/brain/awac332) (PMID:36087305) (PMCID:PMC9494397)
Pascall, D. J. et al. (2023) The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: a genomics-based retrospective cohort analysis. PLoS ONE, 18(4), e0284187. (doi: 10.1371/journal.pone.0284187) (PMID:37053201) (PMCID:PMC10101505)
Carabelli, A. M., Peacock, T. P., Thorne, L. G., Harvey, W. T., Hughes, J. , Peacock, S. J., Barclay, W. S., de Silva, T. I., Towers, G. J. and Robertson, D. L. (2023) SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nature Reviews Microbiology, 21(3), pp. 162-177. (doi: 10.1038/s41579-022-00841-7) (PMID:36653446) (PMCID:PMC9847462)
Cox, M. et al. (2023) SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies. Nature Reviews Microbiology, 21(2), pp. 112-124. (doi: 10.1038/s41579-022-00809-7) (PMID:36307535) (PMCID:PMC9616429)
Simmonds, P. et al. (2023) Four principles to establish a universal virus taxonomy. PLoS Biology, 21(2), e3001922. (doi: 10.1371/journal.pbio.3001922) (PMID:36780432) (PMCID:PMC9925010)
Iannucci, S., Harvey, W. T., Hughes, J. , Robertson, D. L. , Poyade, M. and Hutchinson, E. (2023) The SARS-CoV-2 Spike Protein Mutation Explorer: using an interactive application to improve the public understanding of SARS-CoV-2 variants of concern. Journal of Visual Communication in Medicine, 46(3), pp. 122-132. (doi: 10.1080/17453054.2023.2237087) (PMID:37526402) (PMCID:PMC10726978)
Chai, H., Gu, Q. , Robertson, D. L. and Hughes, J. (2022) Defining the characteristics of interferon-alpha–stimulated human genes: insight from expression data and machine learning. GigaScience, 11, giac103. (doi: 10.1093/gigascience/giac103) (PMID:36399061) (PMCID:PMC9673497)
Sugrue, E. et al. (2022) The apparent interferon resistance of transmitted HIV-1 is possibly a consequence of enhanced replicative fitness. PLoS Pathogens, 18(11), e1010973. (doi: 10.1371/journal.ppat.1010973) (PMID:36399512) (PMCID:PMC9718408)
Walker, P. J. et al. (2022) Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022). Archives of Virology, 167(11), pp. 2429-2440. (doi: 10.1007/s00705-022-05516-5) (PMID:35999326)
Cantoni, D. et al. (2022) Evolutionary remodelling of N-terminal domain loops fine-tunes SARS-CoV-2 spike. EMBO Reports, 23(10), e54322. (doi: 10.15252/embr.202154322) (PMID:35999696) (PMCID:PMC9535765)
Willett, B. J. et al. (2022) Publisher Correction: SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7, 1709. (doi: 10.1038/s41564-022-01241-6) (PMID:36114232) (PMCID:PMC9483304)
Stirrup, O. et al. (2022) Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study. eLife, 11, e78427. (doi: 10.7554/elife.78427) (PMID:36098502) (PMCID:PMC9596156)
Willett, B. J. et al. (2022) SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7(8), pp. 1161-1179. (doi: 10.1038/s41564-022-01143-7) (PMID:35798890) (PMCID:PMC9352574)
Nickbakhsh, S. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12, 11735. (doi: 10.1038/s41598-022-15661-1) (PMID:35853960) (PMCID:PMC9296497)
Telenti, A., Hodcroft, E. B. and Robertson, D. L. (2022) The evolution and biology of SARS-CoV-2 variants. Cold Spring Harbor Perspectives in Medicine, 12(5), a041390. (doi: 10.1101/cshperspect.a041390) (PMID:35444005)
Modha, S. , Robertson, D. L. , Hughes, J. and Orton, R. J. (2022) Quantifying and cataloguing unknown sequences within human microbiomes. mSystems, 7(2), e01468-21. (doi: 10.1128/msystems.01468-21) (PMID:35258340) (PMCID:PMC9052204)
Worobey, M. et al. (2022) The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science, 377(6609), pp. 951-959. (doi: 10.1126/science.abp8715) (PMID:35881010) (PMCID:PMC9348750)
Martin, D. P. et al. (2022) Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA.1 that likely impact Spike function. Molecular Biology and Evolution, 39(4), msac061. (doi: 10.1093/molbev/msac061) (PMID:35325204) (PMCID:PMC9037384)
Zerbini, F. M. et al. (2022) Differentiating between viruses and virus species by writing their names correctly. Archives of Virology, 167(4), pp. 1231-1234. (doi: 10.1007/s00705-021-05323-4) (PMID:35043230) (PMCID:PMC9020231)
Aggarwal, D. et al. (2022) Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nature Communications, 13, 1012. (doi: 10.1038/s41467-022-28371-z) (PMID:35197443) (PMCID:PMC8866425)
Maher, M. C. et al. (2022) Predicting the mutational drivers of future SARS-CoV-2 variants of concern. Science Translational Medicine, 14(633), eabk3445. (doi: 10.1126/scitranslmed.abk3445) (PMID:35014856) (PMCID:PMC8939770)
Aggarwal, D. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13, 751. (doi: 10.1038/s41467-021-27942-w) (PMID:35136068) (PMCID:PMC8826310)
Chai, H., Gu, Q. , Hughes, J. and Robertson, D. L. (2022) In silico prediction of HIV-1-host molecular interactions and their directionality. PLoS Computational Biology, 18(2), e1009720. (doi: 10.1371/journal.pcbi.1009720) (PMID:35134057) (PMCID:PMC8856524)
Lytras, S., Hughes, J. , Martin, D., Swanepoel, P., de Klerk, A., Lourens, R., Kosakovsky Pond, S. L., Xia, W., Jiang, X. and Robertson, D. L. (2022) Exploring the natural origins of SARS-CoV-2 in the light of recombination. Genome Biology and Evolution, 14(2), evac018. (doi: 10.1093/gbe/evac018) (PMID:35137080) (PMCID:PMC8882382)
Twohig, K. A. et al. (2022) Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study. Lancet Infectious Diseases, 22(1), pp. 35-42. (doi: 10.1016/S1473-3099(21)00475-8) (PMID:34461056) (PMCID:PMC8397301)
de Klerk, A. et al. (2022) Conserved recombination patterns across coronavirus subgenera. Virus Evolution, 8(2), veac054. (doi: 10.1093/ve/veac054) (PMID:35814334) (PMCID:PMC9261289)
Hill, V. et al. (2022) The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. Virus Evolution, 8(2), veac080. (doi: 10.1093/ve/veac080) (PMID:36533153) (PMCID:PMC9752794)
Wright, D. W. et al. (2022) Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer. Virus Evolution, 8(1), veac023. (doi: 10.1093/ve/veac023) (PMID:35502202) (PMCID:PMC9037374)
Niemi, M. E. K. et al. (2021) Mapping the human genetic architecture of COVID-19. Nature, 600(7889), pp. 472-477. (doi: 10.1038/s41586-021-03767-x) (PMID:34237774) (PMCID:PMC8674144)
Vöhringer, H. S. et al. (2021) Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600(7889), pp. 506-511. (doi: 10.1038/s41586-021-04069-y) (PMID:34649268) (PMCID:PMC8674138)
Davis, C. et al. (2021) Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination. PLoS Pathogens, 17(12), e1010022. (doi: 10.1371/journal.ppat.1010022) (PMID:34855916) (PMCID:PMC8639073)
Wickenhagen, A. et al. (2021) A prenylated dsRNA sensor protects against severe COVID-19. Science, 374(6567), eabj3624. (doi: 10.1126/science.abj3624) (PMID:34581622) (PMCID:PMC7612834)
Cotten, M. , Robertson, D. L. and Phan, M. V.T. (2021) Unique protein features of SARS-CoV-2 relative to other Sarbecoviruses. Virus Evolution, 7(2), veab067. (doi: 10.1093/ve/veab067) (PMID:34527286) (PMCID:PMC8385934)
Jackson, B. et al. (2021) Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell, 184(20), 5179-5188.e8. (doi: 10.1016/j.cell.2021.08.014) (PMID:34499854) (PMCID:PMC8367733)
Martin, D. P. et al. (2021) The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Cell, 184(20), 5189-5200.e7. (doi: 10.1016/j.cell.2021.09.003) (PMID:34537136) (PMCID:PMC8421097)
Holmes, E. C. et al. (2021) The origins of SARS-CoV-2: a critical review. Cell, 184(19), pp. 4848-4856. (doi: 10.1016/j.cell.2021.08.017) (PMID:34480864) (PMCID:PMC8373617)
Shaw, A. E. et al. (2021) The antiviral state has shaped the CpG composition of the vertebrate interferome to avoid self-targeting. PLoS Biology, 19(9), e3001352. (doi: 10.1371/journal.pbio.3001352) (PMID:34491982) (PMCID:PMC8423302)
Walker, P. J. et al. (2021) Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021). Archives of Virology, 166(9), pp. 2633-2648. (doi: 10.1007/s00705-021-05156-1) (PMID:34231026)
Lytras, S., Xia, W., Hughes, J. , Jiang, X. and Robertson, D. L. (2021) The animal origin of SARS-CoV-2. Science, 373(6558), pp. 968-970. (doi: 10.1126/science.abh0117) (PMID:34404734)
Russell, C. D. et al. (2021) Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study. Lancet Microbe, 2(8), e354-e365. (doi: 10.1016/S2666-5247(21)00090-2) (PMID:34100002) (PMCID:PMC8172149)
Drake, T. M. et al. (2021) Characterisation of in-hospital complications associated with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol UK: a prospective, multicentre cohort study. Lancet, 398(10296), pp. 223-237. (doi: 10.1016/S0140-6736(21)00799-6) (PMID:34274064) (PMCID:PMC8285118)
Harvey, W. T. et al. (2021) SARS-CoV-2 variants, spike mutations and immune escape. Nature Reviews Microbiology, 19(7), pp. 409-424. (doi: 10.1038/s41579-021-00573-0) (PMID:34075212) (PMCID:PMC8167834)
Li, K. K. et al. (2021) Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - a high risk community-hospital interface. Journal of Infection, 83(1), pp. 96-103. (doi: 10.1016/j.jinf.2021.04.020) (PMID:33895226) (PMCID:PMC8061788)
Makalatia, K. et al. (2021) Investigation of Salmonella phage–bacteria infection profiles: network structure reveals a gradient of target-range from generalist to specialist phage clones in nested subsets. Viruses, 13(7), 1261. (doi: 10.3390/v13071261) (PMID:34203492) (PMCID:PMC8310288)
Meng, B. et al. (2021) Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the variant of concern lineage B.1.1.7. Cell Reports, 35(13), 109292. (doi: 10.1016/j.celrep.2021.109292) (PMID:34166617) (PMCID:PMC8185188)
Goettsch, W. et al. (2021) ITN—VIROINF: understanding (harmful) virus-host interactions by linking virology and bioinformatics. Viruses, 13(5), 766. (doi: 10.3390/v13050766) (PMID:33925452) (PMCID:PMC8145447)
Graham, M. S. et al. (2021) Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study. Lancet Public Health, 6(5), e335-e345. (doi: 10.1016/S2468-2667(21)00055-4)
Volz, E. et al. (2021) Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593(7858), pp. 266-269. (doi: 10.1038/s41586-021-03470-x) (PMID:33767447)
Hosie, M. J. et al. (2021) Detection of SARS-CoV-2 in respiratory samples from cats in the UK associated with human-to-cat transmission. Veterinary Record, 188(8), e247. (doi: 10.1002/vetr.247) (PMID:33890314) (PMCID:PMC8251078)
Thomson, E. C. et al. (2021) Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell, 184(5), 1171-1187.e20. (doi: 10.1016/j.cell.2021.01.037) (PMID:33621484) (PMCID:PMC7843029)
Hufsky, F. et al. (2021) Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings in Bioinformatics, 22(2), pp. 642-663. (doi: 10.1093/bib/bbaa232) (PMID:33147627) (PMCID:PMC7665365)
MacLean, O. A. , Lytras, S., Weaver, S., Singer, J. B., Boni, M. F., Lemey, P., Kosakovsky Pond, S. L. and Robertson, D. L. (2021) Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen. PLoS Biology, 19(3), e3001115. (doi: 10.1371/journal.pbio.3001115) (PMID:33711012) (PMCID:PMC7990310)
Rihn, S. J. et al. (2021) A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. PLoS Biology, 19(2), e3001091. (doi: 10.1371/journal.pbio.3001091) (PMID:33630831) (PMCID:PMC7906417)
Volz, E. et al. (2021) Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity. Cell, 184(1), 64-75.e11. (doi: 10.1016/j.cell.2020.11.020) (PMID:33275900) (PMCID:PMC7674007)
Da Silva Filipe, A. et al. (2021) Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology, 6(1), pp. 112-122. (doi: 10.1038/s41564-020-00838-z) (PMID:33349681)
Sellers, R. A., Robertson, D. L. and Tassabehji, M. (2020) Ancestry of the AUTS2 family–a novel group of polycomb-complex proteins involved in human neurological disease. PLoS ONE, 15(12), e0232101. (doi: 10.1371/journal.pone.0232101) (PMID:33306672) (PMCID:PMC7732068)
Boni, M. F., Lemey, P., Jiang, X., Lam, T. T.-Y., Perry, B. W., Castoe, T. A., Rambaut, A. and Robertson, D. L. (2020) Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nature Microbiology, 5(11), pp. 1408-1417. (doi: 10.1038/s41564-020-0771-4) (PMID:32724171)
Pollock, D. D. et al. (2020) Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2. Molecular Biology and Evolution, 37(9), pp. 2706-2710. (doi: 10.1093/molbev/msaa178) (PMID:32658964) (PMCID:PMC7454803)
Masembe, C. , Phan, M. V.T., Robertson, D. L. and Cotten, M. (2020) Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains. Virus Evolution, 6(2), veaa044. (doi: 10.1093/ve/veaa044) (PMID:32913663) (PMCID:PMC7474929)
Murcia, P. , Streiker, D. , Da Silva Filipe, A. , Robertson, D. , Jarrett, R. , Willett, B. , Hosie, M. , Biek, R. , Allan, K. and Weir, W. (2020) Send cat and dog samples to test for SARS-CoV-2. Veterinary Record, 186(17), p. 571. (doi: 10.1136/vr.m2019) (PMID:32451348)
Young, F., Rogers, S. and Robertson, D. L. (2020) Predicting host taxonomic information from viral genomes: a comparison of feature representations. PLoS Computational Biology, 16(5), e1007894. (doi: 10.1371/journal.pcbi.1007894) (PMID:32453718) (PMCID:PMC7307784)
Grant, H. E. et al. (2020) Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evolution, 6(1), veaa004. (doi: 10.1093/ve/veaa004) (PMID:32395255) (PMCID:PMC7204518)
MacLean, O. A. , Orton, R. J. , Singer, J. B. and Robertson, D. L. (2020) No evidence for distinct types in the evolution of SARS-CoV-2. Virus Evolution, 6(1), veaa034. (doi: 10.1093/ve/veaa034) (PMID:32817804) (PMCID:PMC7197565)
Fotiou, E., Williams, S., Martin-Geary, A., Robertson, D. , Tenin, G., Hentges, K. E. and Keavney, B. (2019) Integration of large-scale genomic data sources with evolutionary history reveals novel genetic loci for congenital heart disease. Circulation: Genomic and Precision Medicine, 12(10), pp. 442-451. (doi: 10.1161/CIRCGEN.119.002694) (PMID:31613678)
Hufsky, F. et al. (2019) The Third Annual Meeting of the European Virus Bioinformatics Center. Viruses, 11(5), 420. (doi: 10.3390/v11050420) (PMID:31060321) (PMCID:PMC6563321)
Tapinos, A., Constantinides, B., Phan, M. V. T., Kouchaki, S., Cotten, M. and Robertson, D. L. (2019) The utility of data transformation for alignment, de novo assembly and classification of short read virus sequences. Viruses, 11(5), 394. (doi: 10.3390/v11050394) (PMID:31035503) (PMCID:PMC6563281)
Singer, J. B. et al. (2019) Interpreting viral deep sequencing data with GLUE. Viruses, 11(4), 323. (doi: 10.3390/v11040323) (PMID:30987147) (PMCID:PMC6520954)
Kouchaki, S., Tapinos, A. and Robertson, D. (2019) A signal processing method for alignment-free metagenomic binning: multi-resolution genomic binary patterns. Scientific Reports, 9, 2159. (doi: 10.1038/s41598-018-38197-9) (PMID:30770850) (PMCID:PMC6377666)
Ravindran, V., Nacher, J. C., Akutsu, T., Ishitsuka, M., Osadcenco, A., Sunitha, V., Bagler, G., Schwartz, J.-M. and Robertson, D. L. (2019) Network controllability analysis of intracellular signalling reveals viruses are actively controlling molecular systems. Scientific Reports, 9, 2066. (doi: 10.1038/s41598-018-38224-9) (PMID:30765882) (PMCID:PMC6375943)
Lewis, M. et al. (2018) Clonal analysis of HIV-1 genotype and function associated with virologic failure in treatment-experienced persons receiving maraviroc: Results from the MOTIVATE phase 3 randomized, placebo-controlled trials. PLoS ONE, 13(12), e0204099. (doi: 10.1371/journal.pone.0204099) (PMID:30586365) (PMCID:PMC6306210)
Stoney, R. A., Schwartz, J.-M., Robertson, D. L. and Nenadic, G. (2018) Using set theory to reduce redundancy in pathway sets. BMC Bioinformatics, 19, 386. (doi: 10.1186/s12859-018-2355-3) (PMID:30340461) (PMCID:PMC6194563)
Stoney, R., Robertson, D. L. , Nenadic, G. and Schwartz, J.-M. (2018) Mapping biological process relationships and disease perturbations within a pathway network. npj Systems Biology and Applications, 4, 22. (doi: 10.1038/s41540-018-0055-2) (PMID:29900005) (PMCID:PMC5995814)
Alessandri-Gradt, E., De Oliveira, F., Leoz, M., Lemee, V., Robertson, D. L. , Feyertag, F., Ngoupo, P.-A., Mauclere, P., Simon, F. and Plantier, J.-C. (2018) HIV-1 group P infection: towards a dead-end infection? AIDS, 32(10), pp. 1317-1322. (doi: 10.1097/QAD.0000000000001791) (PMID:29547436)
Ibrahim, B. et al. (2018) Bioinformatics meets virology: the European virus bioinformatics center's second annual meeting. Viruses, 10(5), 256. (doi: 10.3390/v10050256) (PMID:29757994) (PMCID:PMC5977249)
Rivers-Auty, J., Daniels, M. J.D., Colliver, I., Robertson, D. L. and Brough, D. (2018) Redefining the ancestral origins of the interleukin-1 superfamily. Nature Communications, 9, 1156. (doi: 10.1038/s41467-018-03362-1) (PMID:29559685) (PMCID:PMC5861070)
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)
Rambaut, A., Robertson, D.L. , Pybus, O.G., Peeters, M. and Holmes, E.C. (2001) Human immunodeficiency virus. Phylogeny and the origin of HIV-1. Nature, 410(6832), pp. 1047-1048. (doi: 10.1038/35074179) (PMID:11323659)
Damond, F., Apetrei, C., Robertson, D.L. , Souquière, S., Leprêtre, A., Matheron, S., Plantier, J.C., Brun-Vézinet, F. and Simon, F. (2001) Variability of human immunodeficiency virus type 2 (hiv-2) infecting patients living in France. Virology, 280(1), pp. 19-30. (doi: 10.1006/viro.2000.0685) (PMID:11162815)
Rodenburg, C.M. et al. (2001) Near full-length clones and reference sequences for subtype C isolates of HIV type 1 from three different continents. AIDS Research and Human Retroviruses, 17(2), pp. 161-168. (doi: 10.1089/08892220150217247) (PMID:11177395)
Robertson, D.L. et al. (2000) HIV-1 nomenclature proposal. Science, 288(5463), pp. 55-56. (doi: 10.1126/science.288.5463.55d) (PMID:10766634)
Sharp, P.M., Bailes, E., Robertson, D.L. , Gao, F. and Hahn, B.H. (1999) Origins and evolution of AIDS viruses. Biological Bulletin, 196(3), pp. 338-342. (doi: 10.2307/1542965) (PMID:10390833)
Gao, F. et al. (1999) Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature, 397(6718), pp. 436-441. (doi: 10.1038/17130) (PMID:9989410)
Abergel, C., Robertson, D.L. and Claverie, J.M. (1999) "Hidden" dUTPase sequence in human immunodeficiency virus type 1 gp120. Journal of Virology, 73(1), pp. 751-753. (PMID:9847382) (PMCID:PMC103883)
Gao, F. et al. (1998) An isolate of human immunodeficiency virus type 1 originally classified as subtype I represents a complex mosaic comprising three different group M subtypes (A, G, and I). Journal of Virology, 72(12), pp. 10234-10241. (PMID:9811767) (PMCID:PMC110605)
Gao, F. et al. (1998) A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1. Journal of Virology, 72(7), pp. 5680-5698. (PMID:9621027) (PMCID:PMC110237)
Salminen, M.O. et al. (1997) Evolution and probable transmission of intersubtype recombinant human immunodeficiency virus type 1 in a Zambian couple. Journal of Virology, 71(4), pp. 2647-2655. (PMID:9060617) (PMCID:PMC191386)
Soares, M.A., Robertson, D.L. , Hui, H., Allan, J.S., Shaw, G.M. and Hahn, B.H. (1997) A full-length and replication-competent proviral clone of SIVAGM from tantalus monkeys. Virology, 228(2), pp. 394-399. (doi: 10.1006/viro.1996.8387) (PMID:9123848)
Gao, F. et al. (1996) The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin. Journal of Virology, 70(10), pp. 7013-7029. (PMID:8794346) (PMCID:PMC190752)
Gao, F. et al. (1996) Molecular cloning and analysis of functional envelope genes from human immunodeficiency virus type 1 sequence subtypes A through G. The WHO and NIAID networks for HIV isolation and characterization. Journal of Virology, 70(3), pp. 1651-1667. (PMID:8627686) (PMCID:PMC189989)
Sharp, P. M., Robertson, D. L. and Hahn, B. H. (1995) Cross-species transmission and recombination of 'AIDS' viruses. Philosophical Transactions of the Royal Society B: Biological Sciences, 349(1327), pp. 41-47. (doi: 10.1098/rstb.1995.0089) (PMID:8748018)
Robertson, D. L. , Sharp, P. M., McCutchan, F. E. and Hahn, B. H. (1995) Recombination in HIV-1. Nature, 374(6518), pp. 124-126. (doi: 10.1038/374124b0) (PMID:7877682)
Robertson, D. L. , Hahn, B. H. and Sharp, P. M. (1995) Recombination in AIDS viruses. Journal of Molecular Evolution, 40(3), pp. 249-259. (doi: 10.1007/BF00163230) (PMID:7723052)
Gao, F., Yue, L., Robertson, D.L. , Hill, S.C., Hui, H., Biggar, R.J., Neequaye, A.E., Whelan, T.M., Ho, D.D. and Shaw, G.M. (1994) Genetic diversity of human immunodeficiency virus type 2: evidence for distinct sequence subtypes with differences in virus biology. Journal of Virology, 68(11), pp. 7433-7447. (PMID:7933127) (PMCID:PMC237186)
Gao, F., Yue, L., Craig, S., Thornton, C. L., Robertson, D. L. , McCutchan, F. E., Bradac, J. A., Sharp, P. M. and Hahn, B. H. (1994) Genetic variation of HIV type 1 in four World Health Organization-sponsored vaccine evaluation sites: generation of functional envelope (glycoprotein 160) clones representative of sequence subtypes A, B, C. AIDS Research and Human Retroviruses, 10(11), pp. 1359-1368. (doi: 10.1089/aid.1994.10.1359) (PMID:7888189)
Jin, M.J., Hui, H., Robertson, D.L. , Müller, M.C., Barré-Sinoussi, F., Hirsch, V.M., Allan, J.S., Shaw, G.M., Sharp, P.M. and Hahn, B.H. (1994) Mosaic genome structure of simian immunodeficiency virus from west African green monkeys. EMBO Journal, 13(12), pp. 2935-2947. (PMID:8026477) (PMCID:PMC395175)
Gao, F., Yue, L., Hill, S. C., Robertson, D. L. , Graves, A. H., Saag, M. S., Shaw, G. M., Sharp, P. M. and Hahn, B. H. (1994) HIV-1 sequence subtype D in the United States. AIDS Research and Human Retroviruses, 10(5), pp. 625-627. (doi: 10.1089/aid.1994.10.625) (PMID:7917525)
Book Sections
Iannucci, S., Harvey, W., Hughes, J. , Robertson, D. L. , Hutchinson, E. and Poyade, M. (2022) Using molecular visualisation techniques to explain the molecular biology of SARS-CoV-2 spike protein mutations to a general audience. In: Shapiro, Leonard and Rea, Paul M. (eds.) Biomedical Visualisation. Volume 12. Series: Advances in experimental medicine and biology (1388). Springer: Cham, pp. 129-152. ISBN 9783031108884 (doi: 10.1007/978-3-031-10889-1_6)
Conference Proceedings
Hinsch, M., Silverman, E. and Robertson, D. L. (2024) Whole-System Pandemic Modelling Including Pathogen Evolution. In: 18th Social Simulation Conference (SSC23), Glasgow, UK, 04-08 Sep 2023, pp. 63-71. (doi: 10.1007/978-3-031-57785-7_6)
Hinsch, M., Silverman, E. and Robertson, D. L. (2023) Simulating the Evolutionary Response of a Viral Pandemic to Behaviour Change. In: ALIFE 2023: Ghost in the machine, Sapporo, Japan, 24-28 Jul 2023, isal_a_00691. (doi: 10.1162/isal_a_00691)
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)
Grants
Grants and Awards listed are those received whilst working with the University of Glasgow.
- Flu: TrailMap-One Health
Medical Research Council
2024 - 2025
- The G2P2 virology consortium: Keeping pace with SARS-CoV-2 variants, providing evidence to vaccine policy, and building agility for the next pandemic
UK Research and Innovation
2023 - 2027
- Virus Dashboards: Preparing for Pandemics
Medical Research Council
2023 - 2024
- CVR Preparedness compute capacity
Medical Research Council
2023 - 2024
- MonkeyPox - Rapid Response
Biotechnology and Biological Sciences Research Council
2022 - 2023
- Using national whole-genome sequence data to inform epidemiological models of COVID-19 variant emergence and outbreak risks in Scotland
Office of the Chief Scientific Adviser
2022 - 2023
- Identification of viruses causing undiagnosed febrile illness in returning travellers to the UK using enhanced NGS-based metagenomic methods
UK Research and Innovation
2022 - 2023
- Investigating Host and Viral Factors for Improved Design of Future Live Attenuated Vaccines for IBV
Biotechnology and Biological Sciences Research Council
2022 - 2025
- Using virus genomic data to inform the COVID-19 response: Risks of VOC introductions and spread
Public Health Scotland
2022 - 2022
- SARS-CoV-2 infections in cats: assessing their zoonotic potential and role in sustaining the pandemic
Biotechnology and Biological Sciences Research Council
2021 - 2022
- Genotype to Phenotype Consortium
UK Research and Innovation
2021 - 2022
- Identifying the Host and Viral Determinants of Coronavirus Emergence and Adaptation in Human Populations
Medical Research Council
2020 - 2023
- Linking virology and bioinformatics against harmful virus-host interactions
European Commission
2020 - 2024
- African COVID-19 Preparedness (AFRICO19)
Wellcome Trust
2020 - 2022
- ISARIC - Coronavirus Clinical Characterisation Consortium
Medical Research Council
2020 - 2021
- Modelling viral-host molecular interactions using control theory
The Royal Society
2018 - 2020
- Developing innovative and sustainable approaches to prevent the spread fo African swine fever in Africa (ASF-RESIST)
African Union
2018 - 2021
- Nasopharyngeal virome sequencing to determine the impact of respiratory viral interference with live attenuated influenza vaccine immunogenicity in Gambian children
Wellcome Trust
2017 - 2018
Supervision
Our computational lab investigates virus origins and evolution with particular focus on fast evolving RNA viruses. Current topics include studying SARS-CoV-2 evolution with a view to predicting virus fitness and future evolutionary trajectories based on virus genome sequence information alone, studying virus-host molecular interaction data sets with focus on better understanding of virus-host specificity and host switching potential, and computational prediction of host functions exploited by virus versus antiviral responses to infection. For example, arboviruses successfully infect both insects and mammals so present an ideal system for understanding the use of homologous host molecules versus the extent of host-specific interactions. Mechanistic insights of constraints on host specificity are a key to understanding host-switching/spillover risk and thus are important for Preparedness planning, e.g., SARS-CoV-2 has a clear generalist property that permits replication in many mammal species.
We’re a computational lab so are flexible in terms of projects. If you’re interested in collaborating or a computational PhD in the CVR please get contact. We can host PhD studentships either for self-funded projects or through the various funding schemes available at the University of Glasgow. For example, the CVR has its own MRC-funded PhD programme and we welcome applications from potential students interested in computer-based projects. We can also host computational fellowships at the CVR and are particularly interested in supporting projects applying machine learning/AI models to virology, for example, protein language models in collaboration with computer science colleagues.
Research datasets
2024
Furnon, W. , Cowton, V. M., De Lorenzo, G. , Orton, R. , Herder, V. , Cantoni, D. , Ilia, G., Correa Mendonca, D. , Kerr, K., Allan, J., Upfold, N. , Meehan, G. R. , Bakshi, S., Das, U. R., Molina Arias, S., McElwee, M., Little, S., Logan, N., Kwok, K. , Smollett, K. , Willett, B. , Da Silva Filipe, A. , Robertson, D. L. , Grove, J. , Patel, A. H. and Palmarini, M. (2024) Phenotypic evolution of SARS-CoV-2 spike throughout the COVID-19 pandemic. [Data Collection]
2022
Sugrue, E. , Wickenhagen, A., Mollentze, N. , Aziz, M. A., Sreenu, V. B., Truxa, S., Tong, L., Da Silva Filipe, A. , Robertson, D. , Hughes, J. , Rihn, S. and Wilson, S. (2022) The Interferon Resistance of Transmitted HIV-1 is Possibly a Consequence of Enhanced Replicative Fitness. [Data Collection]
2021
Wickenhagen, A., Sugrue, E. , Lytras, S., Kuchi, S., Noerenberg, M. , Turnbull, M. , Loney, C. , Herder, V., Allan, J., Jarmson, I., Cameron Ruiz, N., Varjak, M. , Pinto, R. , Lee, J. Y., Iselin, L., Palmalux, N., Stewart, D., Swingler, S., Greenwood, E. J. D., Crozier, T. W. M., Gu, Q. , Davies, E., Clohisey, S., Wang, B., Trindade Maranhã Costa, F., Santana, M. F., Carlos de Lima Ferreira, L., Murphy, L., Fawkes, A., Meynert, A., Grimes, G., ISARICC investigators, , Da Silva Filho, J. , Marti, M. , Hughes, J. , Stanton, R. J., Wang, E. C. Y., Ho, A. , Davis, I., Jarrett, R. , Castello, A. , Robertson, D. , Semple, M. G., Openshaw, P. J. M., Palmarini, M. , Lehner, P. J., Baillie, K., Rihn, S. and Wilson, S. (2021) A Prenylated dsRNA Sensor Protects Against Severe COVID-19. [Data Collection]
Shaw, A., Rihn, S. , Mollentze, N. , Wickenhagen, A., Stewart, D., Orton, R. , Kuchi, S., Bakshi, S., Collados Rodriguez, M. , Turnbull, M. , Busby, J., Gu, Q. , Smollett, K., Bamford, C., Sugrue, E. , Johnson, P. , Da Silva Filipe, A. , Castello, A. , Streicker, D. , Robertson, D. , Palmarini, M. and Wilson, S. (2021) The 'antiviral state' has shaped the CpG composition of the vertebrate interferome to avoid self-targeting. [Data Collection] (Unpublished)
Visit the Robertson Group webpage
