2024

Herder, V. et al. (2024) Correlates of disease severity in bluetongue as a model of acute arbovirus infection. PLoS Pathogens, 20(8), e1012466. (doi: 10.1371/journal.ppat.1012466) (PMID:39150989) (Early Online Publication)

Herder, V. et al. (2024) A machine learning framework to identify the correlates of disease severity in acute arbovirus infection. bioRxiv, (doi: 10.1101/2024.02.23.581333)

2023

Meehan, G. R. et al. (2023) Phenotyping the virulence of SARS-CoV-2 variants in hamsters by digital pathology and machine learning. PLoS Pathogens, 19(11), e1011589. (doi: 10.1371/journal.ppat.1011589) (PMID:37934791) (PMCID:PMC10656012)

Cao, G. et al. (2023) Single-cell dissection of cervical cancer reveals key subsets of the tumor immune microenvironment. EMBO Journal, 42(16), e110757. (doi: 10.15252/embj.2022110757) (PMID:37427448)

Pinto, R. M. et al. (2023) BTN3A3 evasion promotes the zoonotic potential of influenza A viruses. Nature, 619(7969), pp. 338-347. (doi: 10.1038/s41586-023-06261-8) (PMID:37380775)

Hardy, A. et al. (2023) The timing and magnitude of the type I interferon response are correlated with disease tolerance in arbovirus infection. mBio, 14(3), e0010123. (doi: 10.1128/mbio.00101-23) (PMID:37097030) (PMCID:PMC10294695)

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)

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)

2021

Amat, J. A.R. et al. (2021) Long-term adaptation following influenza A virus host shifts results in increased within-host viral fitness due to higher replication rates, broader dissemination within the respiratory epithelium and reduced tissue damage. PLoS Pathogens, 17(12), e1010174. (doi: 10.1371/journal.ppat.1010174) (PMID:34919598) (PMCID:PMC8735595)

Herder, V. et al. (2021) Elevated temperature inhibits SARS-CoV-2 replication in respiratory epithelium independently of IFN-mediated innate immune defences. PLoS Biology, 19(12), e3001065. (doi: 10.1371/journal.pbio.3001065) (PMID:34932557) (PMCID:PMC8765667)

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)

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, 95(20), e00698-21. (doi: 10.1128/JVI.00698-21) (PMID:34346763) (PMCID:PMC8475523)

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)

Baksmeier, C. et al. (2021) Modified recombinant human IgG1-Fc is superior to natural intravenous immunoglobulin at inhibiting immune-mediated demyelination. Immunology, 164(1), pp. 90-105. (doi: 10.1111/imm.13341) (PMID:33880776) (PMCID:PMC8358725)

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.