Dr Quan Gu

  • Bioinformatician (Centre for Virus Research)

telephone: 01413304019
email: Quan.Gu@glasgow.ac.uk

RI of Infection, Immun & Inflam, Centre for Virus Research

ORCID iDhttps://orcid.org/0000-0002-1201-6734

Biography

I am currently a Research Bioinformatician in the MRC-University of Glasgow Centre for Virus Research. Prior to my position at Glasgow, I was a postdoctoral researcher at Imperial College London (2011-2013). I received my Ph.D. degree from Donghua University in 2011.

Research interests

CVR logo

Viral genomics & bioinformatics programme

 

I am a Research Bioinformatician in the MRC-University of Glasgow Centre for Virus Research.
My broad research interests include:
Machine learning and pattern recognition;
Transcriptomics analysis;
Nuclear magnetic resonance and mass spectrum data modelling and analysis.

Publications

List by: Type | Date

Jump to: 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2011 | 2010 | 2009 | 2008
Number of items: 30.

2021

Wickenhagen, A. et al. (2021) A prenylated dsRNA sensor protects against severe COVID-19. Science, (doi: 10.1126/science.abj3624) (PMID:34581622) (Early Online Publication)

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)

Lau, B. et al. (2021) Human cytomegalovirus RNA2.7 is required for upregulating multiple cellular genes to promote cell motility and viral spread late in lytic infection. Journal of Virology, (doi: 10.1128/JVI.00698-21) (PMID:34346763) (Early Online Publication)

Gallo, G. et al. (2021) Interactions of viral proteins from pathogenic and low or non-pathogenic orthohantaviruses with human type I interferon signaling. Viruses, 13(1), 140. (doi: 10.3390/v13010140) (PMID:33478127) (PMCID:PMC7835746)

Schultz, V. et al. (2021) Zika virus infection leads to demyelination and axonal injury in mature CNS cultures. Viruses, 13(1), 91. (doi: 10.3390/v13010091) (PMID:33440758) (PMCID:PMC7827345)

2020

Dimitrov, D. and Gu, Q. (2020) BingleSeq: A user-friendly R package for bulk and single-cell RNA-Seq data analysis. PeerJ, 8, e10469. (doi: 10.7717/peerj.10469) (PMID:33391870) (PMCID:PMC7761193)

Lau, B. , Kerr, K., Gu, Q. , Nightingale, K., Antrobus, R., Suarez, N. M., Stanton, R. J., Wang, E. C., Weekes, M. P. and Davison, A. J. (2020) Human cytomegalovirus long non-coding RNA1.2 suppresses extracellular release of the pro-inflammatory cytokine IL-6 by blocking NF-κB activation. Frontiers in Cellular and Infection Microbiology, 10, 361. (doi: 10.3389/fcimb.2020.00361) (PMID:32793512)

Sook Yuin Ho, J. et al. (2020) Hybrid gene origination creates human-virus chimeric proteins during infection. Cell, 181(7), 1502-1517.e23. (doi: 10.1016/j.cell.2020.05.035) (PMID:32559462) (PMCID:PMC7323901)

2019

McFarlane, S. et al. (2019) The histone chaperone HIRA promotes the induction of host innate immune defences in response to HSV-1 infection. PLoS Pathogens, 15(3), e1007667. (doi: 10.1371/journal.ppat.1007667) (PMID:30901352) (PMCID:PMC6472835)

2018

Gu, Q. and Veselkov, K. (2018) Bi-clustering of metabolic data using matrix factorization tools. Methods, 151, pp. 12-20. (doi: 10.1016/j.ymeth.2018.02.004) (PMID:29438828) (PMCID:PMC6297113)

Selinger, M., Wilkie, G. S., Tong, L., Gu, Q., Schnettler, E., Grubhoffer, L. and Kohl, A. (2018) Corrigendum: Analysis of tick-borne encephalitis virus-induced host responses in human cells of neuronal origin and interferon-mediated protection. Journal of General Virology, 99(8), pp. 1147-1149. (doi: 10.1099/jgv.0.001109) (PMID:30067173)

Chauché, C., Nogales, A., Zhu, H., Goldfarb, D., Shanizza A.I., A., Gu, Q. , Parrish, C.R., Martínez-Sobrido, L., Marshall, J.F. and Murcia, P.R. (2018) Mammalian adaptation of an avian influenza A virus involves stepwise changes in NS1. Journal of Virology, 92(5), e01875-17. (doi: 10.1128/JVI.01875-17) (PMID:29237841) (PMCID:PMC5809720)

2017

Shaw, A. E. et al. (2017) Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses. PLoS Biology, 15(12), e2004086. (doi: 10.1371/journal.pbio.2004086) (PMID:29253856) (PMCID:PMC574750)

Bhome, R. et al. (2017) Exosomal microRNAs derived from colorectal cancer-associated fibroblasts: role in driving cancer progression. Aging, 9(12), pp. 2666-2694. (doi: 10.18632/aging.101355) (PMID:29283887)

Klymenko, T. et al. (2017) RNA-Seq analysis of differentiated keratinocytes reveals a massive response to late events during human papillomavirus 16 infection, including loss of epithelial barrier function. Journal of Virology, 91(24), e01001-17. (doi: 10.1128/JVI.01001-17) (PMID:29021401) (PMCID:PMC5709591)

Selinger, M., Wilkie, G. S., Tong, L., Gu, Q. , Schnettler, E., Grubhoffer, L. and Kohl, A. (2017) Analysis of tick-borne encephalitis virus-induced host responses in human cells of neuronal origin and interferon-mediated protection. Journal of General Virology, 98(8), pp. 2043-2060. (doi: 10.1099/jgv.0.000853) (PMID:28786780)

Dumas, M.-E. et al. (2017) Microbial-host co-metabolites are prodromal markers predicting phenotypic heterogeneity in behavior, obesity, and impaired glucose tolerance. Cell Reports, 20(1), pp. 136-148. (doi: 10.1016/j.celrep.2017.06.039) (PMID:28683308)

2016

Dumas, M.-E. et al. (2016) Topological analysis of metabolic networks integrating co-segregating transcriptomes and metabolomes in type 2 diabetic rat congenic series. Genome Medicine, 8, 101. (doi: 10.1186/s13073-016-0352-6) (PMID:27716393) (PMCID:PMC5045612)

Ratinier, M., Shaw, A. E., Barry, G., Gu, Q., Di Gialleonardo, L., Janowicz, A., Varela, M., Randall, R. E., Caporale, M. and Palmarini, M. (2016) Bluetongue virus NS4 protein is an interferon antagonist and a determinant of virus virulence. Journal of Virology, 90(11), pp. 5427-5439. (doi: 10.1128/JVI.00422-16) (PMID:27009961) (PMCID:PMC4934764)

Orton, R.J. , Gu, Q., Hughes, J. , Maabar, M., Modha, S. , Vattipally, S. , Wilkie, G.S. and Davison, A. (2016) Bioinformatics tools for analysing viral genomic data. Revue scientifique et technique (International Office of Epizootics), 35(1), pp. 241-285. (doi: 10.20506/rst.35.1.2432) (PMID:27217183)

2015

Gu, Q., Ding, Y.-S. and Zhang, T.-L. (2015) An ensemble classifier based prediction of G-protein-coupled receptor classes in low homology. Neurocomputing, 154, pp. 110-118. (doi: 10.1016/j.neucom.2014.12.013)

Blomström, A.-L. et al. (2015) Transcriptome analysis reveals the host response to Schmallenberg virus in bovine cells and antagonistic effects of the NSs protein. BMC Genomics, 16, 324. (doi: 10.1186/s12864-015-1538-9) (PMID:25896169) (PMCID:PMC4404599)

2014

Hudson, N. J., Baker, M. L., Hart, N. S., Wynne, J. W., Gu, Q. , Huang, Z., Zhang, G., Ingham, A. B., Wang, L. and Reverter, A. (2014) Sensory rewiring in an echolocator: genome-wide modification of retinogenic and auditory genes in the bat myotis davidii. G3: Genes, Genomes, Genetics, 4(10), pp. 1825-1835. (doi: 10.1534/g3.114.011262) (PMID:25096539) (PMCID:PMC4199690)

2011

Hudson, N. J., Gu, Q. , Nagaraj, S. H., Ding, Y.-S., Dalrymple, B. P. and Reverter, A. (2011) Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins. PLoS ONE, 6(9), e25457. (doi: 10.1371/journal.pone.0025457) (PMID:21966531) (PMCID:PMC3179510)

Gu, Q. , Nagaraj, S. H., Hudson, N. J., Dalrymple, B. P. and Reverter, A. (2011) Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscle. BMC Genomics, 12, 23. (doi: 10.1186/1471-2164-12-23) (PMID:21226902) (PMCID:PMC3025955)

2010

Gu, Q., Ding, Y.-S. and Zhang, T.-L. (2010) Prediction of G-protein-coupled receptor classes in low homology using Chou's pseudo amino acid composition with approximate entropy and hydrophobicity patterns. Protein and Peptide Letters, 17(5), pp. 559-567. (doi: 10.2174/092986610791112693)

Shen, Y.-Z., Ding, Y.-S., Gu, Q. and Chou, K.-C. (2010) Identifying the hub proteins from complicated membrane protein network systems. Medicinal Chemistry, 6(3), pp. 165-173. (doi: 10.2174/1573406411006030165) (PMID:20507268)

Gu, Q., Ding, Y.-S., Jiang, X.-Y. and Zhang, T.-L. (2010) Prediction of subcellular location apoptosis proteins with ensemble classifier and feature selection. Amino Acids, 38(4), pp. 975-983. (doi: 10.1007/s00726-008-0209-4) (PMID:19048186)

2009

Ding, Y.-S., Zhang, T.-L., Gu, Q., Zhao, P.-Y. and Chou, K.-C. (2009) Using maximum entropy model to predict protein secondary structure with single sequence. Protein and Peptide Letters, 16(5), pp. 552-560. (doi: 10.2174/092986609788167833) (PMID:19442235)

2008

Jiang, X., Wei, R., Zhang, T. and Gu, Q. (2008) Using the concept of chous pseudo amino acid composition to predict apoptosis proteins subcellular location: an approach by approximate entropy. Protein and Peptide Letters, 15(4), pp. 392-396.

This list was generated on Tue Oct 26 01:33:33 2021 BST.
Jump to: Articles
Number of items: 30.

Articles

Wickenhagen, A. et al. (2021) A prenylated dsRNA sensor protects against severe COVID-19. Science, (doi: 10.1126/science.abj3624) (PMID:34581622) (Early Online Publication)

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)

Lau, B. et al. (2021) Human cytomegalovirus RNA2.7 is required for upregulating multiple cellular genes to promote cell motility and viral spread late in lytic infection. Journal of Virology, (doi: 10.1128/JVI.00698-21) (PMID:34346763) (Early Online Publication)

Gallo, G. et al. (2021) Interactions of viral proteins from pathogenic and low or non-pathogenic orthohantaviruses with human type I interferon signaling. Viruses, 13(1), 140. (doi: 10.3390/v13010140) (PMID:33478127) (PMCID:PMC7835746)

Schultz, V. et al. (2021) Zika virus infection leads to demyelination and axonal injury in mature CNS cultures. Viruses, 13(1), 91. (doi: 10.3390/v13010091) (PMID:33440758) (PMCID:PMC7827345)

Dimitrov, D. and Gu, Q. (2020) BingleSeq: A user-friendly R package for bulk and single-cell RNA-Seq data analysis. PeerJ, 8, e10469. (doi: 10.7717/peerj.10469) (PMID:33391870) (PMCID:PMC7761193)

Lau, B. , Kerr, K., Gu, Q. , Nightingale, K., Antrobus, R., Suarez, N. M., Stanton, R. J., Wang, E. C., Weekes, M. P. and Davison, A. J. (2020) Human cytomegalovirus long non-coding RNA1.2 suppresses extracellular release of the pro-inflammatory cytokine IL-6 by blocking NF-κB activation. Frontiers in Cellular and Infection Microbiology, 10, 361. (doi: 10.3389/fcimb.2020.00361) (PMID:32793512)

Sook Yuin Ho, J. et al. (2020) Hybrid gene origination creates human-virus chimeric proteins during infection. Cell, 181(7), 1502-1517.e23. (doi: 10.1016/j.cell.2020.05.035) (PMID:32559462) (PMCID:PMC7323901)

McFarlane, S. et al. (2019) The histone chaperone HIRA promotes the induction of host innate immune defences in response to HSV-1 infection. PLoS Pathogens, 15(3), e1007667. (doi: 10.1371/journal.ppat.1007667) (PMID:30901352) (PMCID:PMC6472835)

Gu, Q. and Veselkov, K. (2018) Bi-clustering of metabolic data using matrix factorization tools. Methods, 151, pp. 12-20. (doi: 10.1016/j.ymeth.2018.02.004) (PMID:29438828) (PMCID:PMC6297113)

Selinger, M., Wilkie, G. S., Tong, L., Gu, Q., Schnettler, E., Grubhoffer, L. and Kohl, A. (2018) Corrigendum: Analysis of tick-borne encephalitis virus-induced host responses in human cells of neuronal origin and interferon-mediated protection. Journal of General Virology, 99(8), pp. 1147-1149. (doi: 10.1099/jgv.0.001109) (PMID:30067173)

Chauché, C., Nogales, A., Zhu, H., Goldfarb, D., Shanizza A.I., A., Gu, Q. , Parrish, C.R., Martínez-Sobrido, L., Marshall, J.F. and Murcia, P.R. (2018) Mammalian adaptation of an avian influenza A virus involves stepwise changes in NS1. Journal of Virology, 92(5), e01875-17. (doi: 10.1128/JVI.01875-17) (PMID:29237841) (PMCID:PMC5809720)

Shaw, A. E. et al. (2017) Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses. PLoS Biology, 15(12), e2004086. (doi: 10.1371/journal.pbio.2004086) (PMID:29253856) (PMCID:PMC574750)

Bhome, R. et al. (2017) Exosomal microRNAs derived from colorectal cancer-associated fibroblasts: role in driving cancer progression. Aging, 9(12), pp. 2666-2694. (doi: 10.18632/aging.101355) (PMID:29283887)

Klymenko, T. et al. (2017) RNA-Seq analysis of differentiated keratinocytes reveals a massive response to late events during human papillomavirus 16 infection, including loss of epithelial barrier function. Journal of Virology, 91(24), e01001-17. (doi: 10.1128/JVI.01001-17) (PMID:29021401) (PMCID:PMC5709591)

Selinger, M., Wilkie, G. S., Tong, L., Gu, Q. , Schnettler, E., Grubhoffer, L. and Kohl, A. (2017) Analysis of tick-borne encephalitis virus-induced host responses in human cells of neuronal origin and interferon-mediated protection. Journal of General Virology, 98(8), pp. 2043-2060. (doi: 10.1099/jgv.0.000853) (PMID:28786780)

Dumas, M.-E. et al. (2017) Microbial-host co-metabolites are prodromal markers predicting phenotypic heterogeneity in behavior, obesity, and impaired glucose tolerance. Cell Reports, 20(1), pp. 136-148. (doi: 10.1016/j.celrep.2017.06.039) (PMID:28683308)

Dumas, M.-E. et al. (2016) Topological analysis of metabolic networks integrating co-segregating transcriptomes and metabolomes in type 2 diabetic rat congenic series. Genome Medicine, 8, 101. (doi: 10.1186/s13073-016-0352-6) (PMID:27716393) (PMCID:PMC5045612)

Ratinier, M., Shaw, A. E., Barry, G., Gu, Q., Di Gialleonardo, L., Janowicz, A., Varela, M., Randall, R. E., Caporale, M. and Palmarini, M. (2016) Bluetongue virus NS4 protein is an interferon antagonist and a determinant of virus virulence. Journal of Virology, 90(11), pp. 5427-5439. (doi: 10.1128/JVI.00422-16) (PMID:27009961) (PMCID:PMC4934764)

Orton, R.J. , Gu, Q., Hughes, J. , Maabar, M., Modha, S. , Vattipally, S. , Wilkie, G.S. and Davison, A. (2016) Bioinformatics tools for analysing viral genomic data. Revue scientifique et technique (International Office of Epizootics), 35(1), pp. 241-285. (doi: 10.20506/rst.35.1.2432) (PMID:27217183)

Gu, Q., Ding, Y.-S. and Zhang, T.-L. (2015) An ensemble classifier based prediction of G-protein-coupled receptor classes in low homology. Neurocomputing, 154, pp. 110-118. (doi: 10.1016/j.neucom.2014.12.013)

Blomström, A.-L. et al. (2015) Transcriptome analysis reveals the host response to Schmallenberg virus in bovine cells and antagonistic effects of the NSs protein. BMC Genomics, 16, 324. (doi: 10.1186/s12864-015-1538-9) (PMID:25896169) (PMCID:PMC4404599)

Hudson, N. J., Baker, M. L., Hart, N. S., Wynne, J. W., Gu, Q. , Huang, Z., Zhang, G., Ingham, A. B., Wang, L. and Reverter, A. (2014) Sensory rewiring in an echolocator: genome-wide modification of retinogenic and auditory genes in the bat myotis davidii. G3: Genes, Genomes, Genetics, 4(10), pp. 1825-1835. (doi: 10.1534/g3.114.011262) (PMID:25096539) (PMCID:PMC4199690)

Hudson, N. J., Gu, Q. , Nagaraj, S. H., Ding, Y.-S., Dalrymple, B. P. and Reverter, A. (2011) Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins. PLoS ONE, 6(9), e25457. (doi: 10.1371/journal.pone.0025457) (PMID:21966531) (PMCID:PMC3179510)

Gu, Q. , Nagaraj, S. H., Hudson, N. J., Dalrymple, B. P. and Reverter, A. (2011) Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscle. BMC Genomics, 12, 23. (doi: 10.1186/1471-2164-12-23) (PMID:21226902) (PMCID:PMC3025955)

Gu, Q., Ding, Y.-S. and Zhang, T.-L. (2010) Prediction of G-protein-coupled receptor classes in low homology using Chou's pseudo amino acid composition with approximate entropy and hydrophobicity patterns. Protein and Peptide Letters, 17(5), pp. 559-567. (doi: 10.2174/092986610791112693)

Shen, Y.-Z., Ding, Y.-S., Gu, Q. and Chou, K.-C. (2010) Identifying the hub proteins from complicated membrane protein network systems. Medicinal Chemistry, 6(3), pp. 165-173. (doi: 10.2174/1573406411006030165) (PMID:20507268)

Gu, Q., Ding, Y.-S., Jiang, X.-Y. and Zhang, T.-L. (2010) Prediction of subcellular location apoptosis proteins with ensemble classifier and feature selection. Amino Acids, 38(4), pp. 975-983. (doi: 10.1007/s00726-008-0209-4) (PMID:19048186)

Ding, Y.-S., Zhang, T.-L., Gu, Q., Zhao, P.-Y. and Chou, K.-C. (2009) Using maximum entropy model to predict protein secondary structure with single sequence. Protein and Peptide Letters, 16(5), pp. 552-560. (doi: 10.2174/092986609788167833) (PMID:19442235)

Jiang, X., Wei, R., Zhang, T. and Gu, Q. (2008) Using the concept of chous pseudo amino acid composition to predict apoptosis proteins subcellular location: an approach by approximate entropy. Protein and Peptide Letters, 15(4), pp. 392-396.

This list was generated on Tue Oct 26 01:33:33 2021 BST.

Research datasets

Jump to: 2021
Number of items: 2.

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)

This list was generated on Tue Oct 26 11:38:53 2021 BST.