David A Matthews

2025

Examining the feasibility of replacing ORF3a with fluorescent genes to construct SARS-CoV-2 reporter viruses

Webb, I., Erdmann, M. H. W., Milligan, R., Savage, M., Matthews, D. A. & Davidson, A. D., 12 Feb 2025, In: Journal of General Virology. 106, 2, 46 p., 002072.

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Using minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time

Dong, X., Matthews, D., Gallo, G., Darby, A., Donovan-Banfield, I., Goldswain, H., MacGill, T., Myers, T., Orr, R., Bailey, D., Carroll, M. & Hiscox, J., 28 Feb 2025, In: Nucleic Acids Research. 53, 4, 13 p., gkaf077.

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2022

Direct RNA sequencing of Respiratory Syncytial Virus infected human cells generates a detailed overview of RSV polycistronic mRNA and transcript abundance.

Donovan-Banfield, I., Milligan, R., Hall, S., Gao, T., Murphy, E. M. R., Li, J. B., Shalwi, G., Hiscox, J., Zhuang, X., McKeating, J., Fearns, R. & Matthews, D. A., 10 Nov 2022, In: PLoS ONE. 17, 11, p. 1-20 e0276697.

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8 Citations (Scopus)

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Nanopore ReCappable sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs

Ugolini, C., Mulroney, L., Leger, A., Castelli, M., Criscuolo, E., Kavanagh Williamson, M., Davidson, A. D., Almuqrin, A. M., Giambruno, R., Jain, M., Frige, G., Olsen, H., Tzertzinis, G., Schildkraut, I., Wulf, M. G., Corrêa Jr, I. R., Ettwiller, L., Clementi, N., Clementi, M. & Mancini, N. & 5 others, Birney, E., Akeson, M., Nicassio, F., Matthews, D. A. & Leonardi, T., 4 Mar 2022, (E-pub ahead of print) In: Nucleic Acids Research. 50, 6, p. 3475-3489 15 p., gkac144.

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11 Citations (Scopus)

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2021

Analysis of an Ebola virus disease survivor whose host and viral markers were predictive of death indicates the effectiveness of medical countermeasures and supportive care

et al., 11 Jan 2021, In: Genome Medicine. 13, 5 (2021), 18 p., 5.

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8 Citations (Scopus)

217 Downloads (Pure)

Detecting SARS-CoV-2 variants with SNP genotyping

Harper, H., Burridge, A., Winfield, M., Finn, A., Davidson, A., Matthews, D., Hutchings, S., Vipond, B., Jain, N., COVID-19 Genomics UK (COG-UK) Consortium, Edwards, K. & Barker, G., 24 Feb 2021, In: PLoS ONE. 16, 2, 12 p., e0243185.

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45 Citations (Scopus)

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SARS-CoV-2 vaccine ChAdOx1 nCoV-19 infection of human cell lines reveals low levels of viral backbone gene transcription alongside very high levels of SARS-CoV-2 S glycoprotein gene transcription

Almuqrin, A., Davidson, A. D., Kavanagh Williamson, M., Lewis, P. A., Heesom, K. J., Morris, S., Gilbert, S. C. & Matthews, D. A., 15 Mar 2021, In: Genome Medicine. 13, 1, 17 p., 43 (2021).

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38 Citations (Scopus)

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The furin cleavage site in the SARS-CoV-2 spike protein is required for transmission in ferrets

Peacock, T. P., Kavanagh Williamson, M., Davidson, A. D., Matthews, D. A., Barclay, W. S. & al., E., Jul 2021, In: Nature Microbiology. 6, 7, p. 899-909 11 p.

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494 Citations (Scopus)

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2020

Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein

Davidson, A. D., Kavanagh Williamson, M., Lewis, S. D., Shoemark, D. K., Carroll, M. W., Heesom, K. J., Zambon, M., Ellis, J., Lewis, P. A., Hiscox, J. A. & Matthews, D. A., 28 Jul 2020, In: Genome Medicine. 12, 15 p., 68.

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261 Citations (Scopus)

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Deep splicing plasticity of the human adenovirus type 5 transcriptome drives virus evolution

Donovan-Banfield, I., Turnell, A. S., Hiscox, J. A., Leppard, K. N. & Matthews, D. A., 13 Mar 2020, In: Communications Biology. 3, 14 p., 124 (2020).

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38 Citations (Scopus)

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Neuropilin-1 is a host factor for SARS-CoV-2 infection

Daly, J., Simonetti, B., Klein, K., Kavanagh Williamson, M., Anton Plagaro, C., Shoemark, D. K., Sessions, R. B., Matthews, D. A., Davidson, A. D., Cullen , P. J. & Yamauchi, Y., 13 Nov 2020, In: Science. 370, 6518, p. 861-865 5 p., eabd3072.

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933 Citations (Scopus)

257 Downloads (Pure)

2019

High Resolution Analysis of Respiratory Syncytial Virus Infection In Vivo

Aljabr, W., Armstrong, S., Rickett, N. Y., Pollakis, G., Touzelet, O., Cloutman-Green, E., Matthews, D. A. & Hiscox, J. A., 10 Oct 2019, In: Viruses. 11, 10, 16 p., 926.

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9 Citations (Scopus)

184 Downloads (Pure)

2018

High throughput discovery of protein variants using proteomics informed by transcriptomics

Matthews, D., Bessant, C. & Saha, S., 30 Apr 2018, (E-pub ahead of print) In: Nucleic Acids Research.

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8 Citations (Scopus)

305 Downloads (Pure)

PITDB: a database of translated genomic elements

Saha, S., Chatzimichali, E. A., Matthews, D. A. & Bessant, C., 4 Jan 2018, In: Nucleic Acids Research. 46, D1, p. D1223-D1228 6 p., gkx906.

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1 Citation (Scopus)

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Zika virus infection preferentially counterbalances human peripheral monocyte and/or NK cell activity

Lum, F. M., Lee, D., Chua, T. K., Tan, J. J. L., Lee, C. Y. P., Liu, X., Fang, Y., Lee, B., Yee, W. X., Rickett, N. Y., Chia, P. Y., Lim, V., Leo, Y. S., Matthews, D. A., Hiscox, J. A. & Nga, L. F. P., 28 Mar 2018, In: mSphere. 3, 2, e00120-18.

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29 Citations (Scopus)

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2017

A comparison of host gene expression signatures associated with infection in vitro by the Markona and Ecran (Mayinga) varients of Ebola virus

Bosworth, A., Dowall, S. D., Garcia-Dorival, I., Rickett, N. Y., Bruce, C. B., Matthews, D., Fang, Y., Aljabr, W., Kenny, J., Nelson, C., Laws, T. R., Williamson, E. D., Stewart, J. P., Carroll, M. W., Hewson, R. & Hiscox, J. A., 27 Feb 2017, In: Scientific Reports. 7, 43144.

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21 Citations (Scopus)

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Comparison of protein expression during wild-type, and E1B-55k-deletion, adenovirus infection using quantitative time-course proteomics

Fu, Y. R., Turnell, A. S., Davis, S., Heesom, K. J., Evans, V. C. & Matthews, D. A., 20 Jun 2017, In: Journal of General Virology. 98, 6, p. 1377-1388 12 p.

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10 Citations (Scopus)

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Deep sequencing of RNA from blood and oral swab samples reveals the presence of nucleic acid from a number of pathogens in patients with acute Ebola virus disease and is consistent with bacterial translocation across the gut

Carroll, M. W., Haldenby, S., Rickett, N. Y., Pályi, B., Garcia-Dorival, I., Liu, X., Barker, G., Bore, J. A., Koundouno, F. R., Williamson, E. D., Laws, T. R., Kerber, R., Sissoko, D., Magyar, N., Di Caro, A., Biava, M., Fletcher, T. E., Sprecher, A., Ng, L. F. P. & Rénia, L. & 6 others, Magassouba, N., Günther, S., Wölfel, R., Stoecker, K., Matthews, D. A. & Hiscox, J. A., 23 Aug 2017, In: mSphere. 2, 4, 19 p., e00325-17.

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30 Citations (Scopus)

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Proteomics Informed by Transcriptomics for Characterising Active Transposable Elements and Genome Annotation in Aedes Aegypti

Maringer, K., Yousuf, A., Heesom, K., Fan, J., Lee, D., Fernandez-Sesma, A., Bessant, C., Matthews, D. & Davidson, A., 19 Jan 2017, In: BMC Genomics. 18, 18 p., 101.

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37 Citations (Scopus)

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Proteomics informed by transcriptomics for characterising differential cellular susceptibility to Nelson Bay orthoreovirus infection

Mok, L., Wynne, J. W., Tachedjian, M., Shiell, B. J., Ford, K., Matthews, D., Bacic, A. & Michalski, W. P., 14 Aug 2017, In: BMC Genomics. 18, 615, 17 p.

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7 Citations (Scopus)

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Proteomics technique opens new frontiers in mobilome research

Davidson, A., Matthews, D. & Maringer, K., 2017, In: Mobile Genetic Elements. 7, 4, p. 1-9 9 p.

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Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus

Liu, X., Matthews, D., Connor, J. H., Carroll, M. W. & Hiscox, J. A., 19 Jan 2017, In: Genome Biology. 18, 17 p., 4.

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103 Citations (Scopus)

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Virus genomes reveal factors that spread and sustained the Ebola epidemic

Dudas, G. & et al., 20 Apr 2017, In: Nature. 544, 7650, p. 309-315 7 p.

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287 Citations (Scopus)

454 Downloads (Pure)

2016

Investigating the Influence of Ribavirin on Human Respiratory Syncytial Virus RNA Synthesis by Using a High-Resolution Transcriptome Sequencing Approach

Aljabr, W., Touzelet, O., Pollakis, G., Wu, W., Munday, D. C., Hughes, M., Hertz-Fowler, C., Kenny, J., Fearns, R., Barr, J. N., Matthews, D. A. & Hiscox, J. A., 15 May 2016, In: Journal of Virology. 90, 10, p. 4876-4888 13 p.

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33 Citations (Scopus)

392 Downloads (Pure)

Real-time, portable genome sequencing for Ebola surveillance

Quick, J., Loman, N. J., Duraffour, S., Simpson, J. T., Severi, E., Cowley, L., Bore, J. A., Koundouno, R., Dudas, G., Mikhail, A., Ouédraogo, N., Afrough, B., Bah, A., Baum, J. H. J., Becker-Ziaja, B., Boettcher, J. P., Cabeza-Cabrerizo, M., Camino-Sánchez, Á., Carter, L. L. & Doerrbecker, J. & 82 others, Enkirch, T., García-Dorival, I., Hetzelt, N., Hinzmann, J., Holm, T., Kafetzopoulou, L. E., Koropogui, M., Kosgey, A., Kuisma, E., Logue, C. H., Mazzarelli, A., Meisel, S., Mertens, M., Michel, J., Ngabo, D., Nitzsche, K., Pallasch, E., Patrono, L. V., Portmann, J., Repits, J. G., Rickett, N. Y., Sachse, A., Singethan, K., Vitoriano, I., Yemanaberhan, R. L., Zekeng, E. G., Racine, T., Bello, A., Sall, A. A., Faye, O., Faye, O., Magassouba, N., Williams, C. V., Amburgey, V., Winona, L., Davis, E., Gerlach, J., Washington, F., Monteil, V., Jourdain, M., Bererd, M., Camara, A., Somlare, H., Camara, A., Gerard, M., Bado, G., Baillet, B., Delaune, D., Nebie, K. Y., Diarra, A., Savane, Y., Pallawo, R. B., Gutierrez, G. J., Milhano, N., Roger, I., Williams, C. J., Yattara, F., Lewandowski, K., Taylor, J., Rachwal, P., Turner, D. J., Pollakis, G., Hiscox, J. A., Matthews, D. A., O'Shea, M. K., Johnston, A. M., Wilson, D., Hutley, E., Smit, E., Di Caro, A., Wölfel, R., Stoecker, K., Fleischmann, E., Gabriel, M., Weller, S. A., Koivogui, L., Diallo, B., Keïta, S., Rambaut, A., Formenty, P., Günther, S. & Carroll, M. W., 11 Feb 2016, In: Nature. 530, 7589, p. 228-232 5 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

1042 Citations (Scopus)

2015

Galaxy Integrated Omics: Web-based standards-compliant workflows for proteomics informed by transcriptomics

Fan, J., Saha, S., Barker, G., Heesom, K. J., Ghali, F., Jones, A. R., Matthews, D. A. & Bessant, C., 12 Aug 2015, In: Molecular and Cellular Proteomics. 14, 11, p. 3087-3093 7 p.

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31 Citations (Scopus)

353 Downloads (Pure)

Genotyping coronaviruses associated with feline infectious peritonitis

Lewis, C. S., Porter, E., Matthews, D., Kipar, A., Tasker, S., Helps, C. R. & Siddell, S. G., 1 Jun 2015, In: Journal of General Virology. 96, p. 1358-1368 11 p.

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49 Citations (Scopus)

504 Downloads (Pure)

Identification of Epstein-Barr Virus Replication Proteins in Burkitt's Lymphoma Cells

Traylen, C., Ramasubramanyan, S., Zuo, J., Rowe, M., Almohammad, R., Heesom, K., Sweet, S. M. M., Matthews, D. A. & Sinclair, A. J., 29 Oct 2015, In: Pathogens. 4, 4, p. 739-51 13 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

16 Citations (Scopus)

Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa

Carroll, M. W., Matthews, D. A., Hiscox, J. A., Elmore, M. J., Pollakis, G., Rambaut, A., Hewson, R., García-Dorival, I., Bore, J. A., Koundouno, R., Abdellati, S., Afrough, B., Aiyepada, J., Akhilomen, P., Asogun, D., Atkinson, B., Badusche, M., Bah, A., Bate, S. & Baumann, J. & 112 others, Becker, D., Becker-Ziaja, B., Bocquin, A., Borremans, B., Bosworth, A., Boettcher, J. P., Cannas, A., Carletti, F., Castilletti, C., Clark, S., Colavita, F., Diederich, S., Donatus, A., Duraffour, S., Ehichioya, D., Ellerbrok, H., Fernandez-Garcia, M. D., Fizet, A., Fleischmann, E., Gryseels, S., Hermelink, A., Hinzmann, J., Hopf-Guevara, U., Ighodalo, Y., Jameson, L., Kelterbaum, A., Kis, Z., Kloth, S., Kohl, C., Korva, M., Kraus, A., Kuisma, E., Kurth, A., Liedigk, B., Logue, C. H., Lüdtke, A., Maes, P., McCowen, J., Mély, S., Mertens, M., Meschi, S., Meyer, B., Michel, J., Molkenthin, P., Muñoz-Fontela, C., Muth, D., Newman, E. N. C., Ngabo, D., Oestereich, L., Okosun, J., Olokor, T., Omiunu, R., Omomoh, E., Pallasch, E., Pályi, B., Portmann, J., Pottage, T., Pratt, C., Priesnitz, S., Quartu, S., Rappe, J., Repits, J., Richter, M., Rudolf, M., Sachse, A., Schmidt, K. M., Schudt, G., Strecker, T., Thom, R., Thomas, S., Tobin, E., Tolley, H., Trautner, J., Vermoesen, T., Vitoriano, I., Wagner, M., Wolff, S., Yue, C., Capobianchi, M. R., Kretschmer, B., Hall, Y., Kenny, J. G., Rickett, N. Y., Dudas, G., Coltart, C. E. M., Kerber, R., Steer, D., Wright, C., Senyah, F., Keita, S., Drury, P., Diallo, B., de Clerck, H., Van Herp, M., Sprecher, A., Traore, A., Diakite, M., Konde, M. K., Koivogui, L., Magassouba, N., Avšič-Županc, T., Nitsche, A., Strasser, M., Ippolito, G., Becker, S., Stoecker, K., Gabriel, M., Raoul, H., Di Caro, A., Wölfel, R., Formenty, P. & Günther, S., 6 Aug 2015, In: Nature. 524, 7563, p. 97-101 5 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

247 Citations (Scopus)

Tumour-mediated inhibition of infiltrating CTL may occur via Downregulation of Immune Synapse Signaling Molecules: New Insights from T Cell Proteomics

Edmunds, G., Heesom, Matthews, D., Davidson, A. & Morgan, D., 2015, (In preparation) In: Cancer Research.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

2014

Analysis of purified wild type and mutant adenovirus particles by SILAC based quantitative proteomics

Alqahtani, A., Heesom, K., Bramson, J. L., Curiel, D., Ugai, H. & Matthews, D. A., Nov 2014, In: Journal of General Virology. 95, Pt 11, p. 2504-11 8 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

12 Citations (Scopus)

Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity

Dowall, S. D., Matthews, D. A., Garcia-Dorival, I., Taylor, I., Kenny, J., Hertz-Fowler, C., Hall, N., Corbin-Lickfett, K., Empig, C., Schlunegger, K., Barr, J. N., Carroll, M. W., Hewson, R. & Hiscox, J. A., 2014, In: Genome Biology. 15, 11, p. 540

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41 Citations (Scopus)

Elucidation of the Ebola virus VP24 cellular interactome and disruption of virus biology through targeted inhibition of host cell protein function

García-Dorival, I., Wu, W., Dowall, S., Armstrong, S., Touzelet, O., Wastling, J., Barr, J. N., Matthews, D., Carroll, M., Hewson, R. & Hiscox, J. A., 26 Aug 2014, In: Journal of Proteome Research.

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81 Citations (Scopus)

Factors affecting de novo RNA synthesis and back-priming by the respiratory syncytial virus polymerase

Noton, S. L., Aljabr, W., Hiscox, J. A., Matthews, D. A. & Fearns, R., Aug 2014, In: Virology. 462, p. 318-327 10 p.

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26 Citations (Scopus)

High-throughput quantitative proteomic analysis of dengue virus type 2 infected A549 cells

Chiu, H.-C., Hannemann, H., Heesom, K. J., Matthews, D. A. & Davidson, A. D., 26 Mar 2014, In: PLoS ONE. 9, 3, p. e93305 22 p., 93305.

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53 Citations (Scopus)

Proteomics informed by transcriptomics reveals Hendra virus sensitizes bat cells to TRAIL-mediated apoptosis

Wynne, J. W., Shiell, B. J., Marsh, G. A., Boyd, V., Harper, J. A., Heesom, K., Monaghan, P., Zhou, P., Payne, J., Klein, R., Todd, S., Mok, L., Green, D., Bingham, J., Tachedjian, M., Baker, M. L., Matthews, D. & Wang, L.-F., 2014, In: Genome Biology. 15, 11, p. 532

Research output: Contribution to journal › Article (Academic Journal) › peer-review

45 Citations (Scopus)

2012

Adenoviral protein V promotes a process of viral assembly through nucleophosmin 1

Ugai, H., Dobbins, G. C., Wang, M., Le, L. P., Matthews, D. A. & Curiel, D. T., 2012, In: Virology. 432, 2, p. 283-95 13 p.

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26 Citations (Scopus)

De novo derivation of proteomes from transcriptomes for transcript and protein identification

Evans, V. C., Barker, G., Heesom, K. J., Fan, J., Bessant, C. & Matthews, D. A., Dec 2012, In: Nature Methods. 9, 12, p. 1207-11 5 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

138 Citations (Scopus)

The interactome of the human respiratory syncytial virus NS1 protein highlights multiple effects on host cell biology

Wu, W., Tran, K. C., Teng, M. N., Heesom, K. J., Matthews, D. A., Barr, J. N. & Hiscox, J. A., Aug 2012, In: Journal of Virology. 86, 15, p. 7777-89 13 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

63 Citations (Scopus)

Using SILAC and quantitative proteomics to investigate the interactions between viral and host proteomes

Munday, D. C., Surtees, R., Emmott, E., Dove, B. K., Digard, P., Barr, J. N., Whitehouse, A., Matthews, D. & Hiscox, J. A., 2012, In: Proteomics. 12, 4-5, p. 666-72 7 p.

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57 Citations (Scopus)

2010

In vitro dynamic visualization analysis of fluorescently labeled minor capsid protein IX and core protein V by simultaneous detection

Ugai, H., Wang, M., Le, L. P., Matthews, D. A., Yamamoto, M. & Curiel, D. T., Jan 2010, In: Journal of Molecular Biology. 395, 1, p. 55 - 78 24 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

14 Citations (Scopus)

Nucleolar proteomics and viral infection

Hiscox, J. A., Whitehouse, A. & Matthews, D. A., Nov 2010, In: Proteomics. 10, 22, p. 4077 - 4086 10 p.

Research output: Contribution to journal › Article (Academic Journal)

58 Citations (Scopus)

Quantitative proteomics using SILAC coupled to LC-MS/MS reveals changes in the nucleolar proteome in influenza A virus-infected cells

Emmott, E., Wise, H., Loucaides, E. M., Matthews, D. A., Digard, P. & Hiscox, J. A., Sept 2010, In: Journal of Proteome Research. 9, 10, p. 5335 - 5345 10 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

72 Citations (Scopus)

2009

Upstream Binding Factor is sequestered into Herpes Simplex Virus type 1 replication compartments

Stow, N., Evans, V. & Matthews, D., Jan 2009, In: Journal of General Virology. 90, p. 69 - 73 5 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

15 Citations (Scopus)

2007

A role for transportin in the nuclear import of adenovirus core proteins and DNA

Hindley, C., Lawrence, F. & Matthews, D., Oct 2007, In: Traffic. 8 (10), p. 1313 - 1322 10 p.

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57 Citations (Scopus)

Relationship between adenovirus DNA replication proteins and nucleolar proteins B23.1 and B23.2

Hindley, C., Davidson, A. & Matthews, D., Dec 2007, In: Journal of General Virology. 88 (12), p. 3244 - 3248 5 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

23 Citations (Scopus)

2006

Novel molecular approaches to Cystic Fibrosis gene therapy

Lee, T., Matthews, D. & Blair, G., 2006, In: Biochemical Journal. 387, p. 1 - 15 15 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

76 Citations (Scopus)

Nucleolar protein upstream binding factor is sequestered into adenovirus DNA replication centres during infection without affecting RNA polymerase I location or ablating rRNA synthesis

Lawrence, F., McStay, B. & Matthews, D., Jun 2006, In: Journal of Cell Science. 119 (12), p. 2621 - 2631 12 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

36 Citations (Scopus)

1994

Adenovirus protein-protein interactions: hexon and protein VI

Matthews, D. A. & Russell, W. C., 1994, In: Journal of General Virology. 75 ( Pt 12), p. 3365-74 10 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

36 Citations (Scopus)

Analysis of respiratory syncytial virus strain variation in successive epidemics in one city

Cane, P. A., Matthews, D. A. & Pringle, C. R., 1994, In: Journal of Clinical Microbiology. 32, 1, p. 1-4 4 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

106 Citations (Scopus)

Professor David A Matthews

Research output

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