Publications
Selected publications
- Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and mcr-9 Genes. (Journal article - 2024)
- Whole-genome sequencing reveals widespread presence of Staphylococcus capitis NRCS-A clone in neonatal units across the United Kingdom. (Journal article - 2023)
- IS<i>1</i>-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene <i>nfsB</i> causes nitrofurantoin heteroresistance in <i>Escherichia coli</i>. (Journal article - 2023)
- Alterations in chromosomal genes <i>nfsA</i>, <i>nfsB</i>, and <i>ribE</i> are associated with nitrofurantoin resistance in <i>Escherichia coli</i> from the United Kingdom. (Journal article - 2021)
- GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure. (Journal article - 2020)
2025
Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates.
Wan, Y., Pike, R., Harley, A., Mumin, Z., Potterill, I., Meunier, D., . . . Pichon, B. (2025). Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates. . BMC genomic data, 26(1), 12. doi:10.1186/s12863-025-01303-8
2024
Queer- and trans-inclusive faculty hiring-A call for change.
Weissman, J. L., Chappell, C. R., Francesco Rodrigues de Oliveira, B., Evans, N., Fagre, A. C., Forsythe, D., . . . Advancing Queer and Trans Equity in Science (AQTES) Consortium. (2024). Queer- and trans-inclusive faculty hiring-A call for change.. PLoS biology, 22(11), e3002919. doi:10.1371/journal.pbio.3002919
Exploring real-world vancomycin target attainment in neonatal intensive care in the context of Staphylococcal infections: a retrospective observational cohort study.
Blank, M., Wilson, R. C., Wan, Y., Peters, J., Davies, F., Tyszczuk, L., . . . Rawson, T. M. (2024). Exploring real-world vancomycin target attainment in neonatal intensive care in the context of Staphylococcal infections: a retrospective observational cohort study.. The Journal of infection, 89(2), 106191. doi:10.1016/j.jinf.2024.106191
Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and mcr-9 Genes.
Wan, Y., Myall, A. C., Boonyasiri, A., Bolt, F., Ledda, A., Mookerjee, S., . . . Davies, F. (2024). Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and mcr-9 Genes.. The Journal of infectious diseases, 230(1), e159-e170. doi:10.1093/infdis/jiae019
Rapid expansion and international spread of M1<sub>UK</sub> in the post-pandemic UK upsurge of Streptococcus pyogenes.
Vieira, A., Wan, Y., Ryan, Y., Li, H. K., Guy, R. L., Papangeli, M., . . . Sriskandan, S. (2024). Rapid expansion and international spread of M1<sub>UK</sub> in the post-pandemic UK upsurge of Streptococcus pyogenes.. Nature communications, 15(1), 3916. doi:10.1038/s41467-024-47929-7
Running a queer- and trans-inclusive microbiology faculty search
Clinical outcomes of <i>Staphylococcus capitis</i> isolation from neonates, England, 2015-2021: a retrospective case-control study.
Yuan, J. -M., Nugent, C., Wilson, A., Verlander, N. Q., Alexander, E., Fleming, P., . . . Demirjian, A. (2024). Clinical outcomes of <i>Staphylococcus capitis</i> isolation from neonates, England, 2015-2021: a retrospective case-control study.. Archives of disease in childhood. Fetal and neonatal edition, 109(2), 128-134. doi:10.1136/archdischild-2023-325887
Integrated analysis of patient networks and plasmid genomes reveals a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes.
Wan, Y., Myall, A. C., Boonyasiri, A., Bolt, F., Ledda, A., Mookerjee, S., . . . Davies, F. (2024). Integrated analysis of patient networks and plasmid genomes reveals a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes.. The Journal of infectious diseases, jiae019. doi:10.1093/infdis/jiae019
2023
Building a queer- and trans-inclusive microbiology conference.
Gregor, R., Johnston, J., Coe, L. S. Y., Evans, N., Forsythe, D., Jones, R., . . . Weissman, J. L. (2023). Building a queer- and trans-inclusive microbiology conference.. mSystems, 8(5), e0043323. doi:10.1128/msystems.00433-23
Detection, survival, and persistence of Staphylococcus capitis NRCS-A in neonatal units in England.
Moore, G., Barry, A., Carter, J., Ready, J., Wan, Y., Elsayed, M., . . . UK Health Security Agency Staphylococcus capitis Environment Task and Finish Group. (2023). Detection, survival, and persistence of Staphylococcus capitis NRCS-A in neonatal units in England.. The Journal of hospital infection, 140, 8-14. doi:10.1016/j.jhin.2023.06.030
IS<i>1</i>-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene <i>nfsB</i> causes nitrofurantoin heteroresistance in <i>Escherichia coli</i>.
Wan, Y., Sabnis, A., Mumin, Z., Potterill, I., Jauneikaite, E., Brown, C. S., . . . Sriskandan, S. (2023). IS<i>1</i>-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene <i>nfsB</i> causes nitrofurantoin heteroresistance in <i>Escherichia coli</i>.. Microbial genomics, 9(9). doi:10.1099/mgen.0.001102
Whole-genome sequencing reveals widespread presence of Staphylococcus capitis NRCS-A clone in neonatal units across the United Kingdom.
Wan, Y., Ganner, M., Mumin, Z., Ready, D., Moore, G., Potterill, I., . . . Pichon, B. (2023). Whole-genome sequencing reveals widespread presence of Staphylococcus capitis NRCS-A clone in neonatal units across the United Kingdom.. The Journal of infection, 87(3), 210-219. doi:10.1016/j.jinf.2023.06.020
Soft Tissue Infection of Immunocompetent Man with Cat-Derived Globicatella Species.
Jones, N. K., Coelho, J., Logan, J. M. J., Broughton, K., Hopkins, K. L., Pichon, B., . . . Gouliouris, T. (2023). Soft Tissue Infection of Immunocompetent Man with Cat-Derived Globicatella Species.. Emerging infectious diseases, 29(8), 1684-1687. doi:10.3201/eid2908.221770
Trends in coagulase-negative staphylococci (CoNS), England, 2010-2021.
Paranthaman, K., Wilson, A., Verlander, N., Rooney, G., Macdonald, N., Nsonwu, O., . . . Demirjian, A. (2023). Trends in coagulase-negative staphylococci (CoNS), England, 2010-2021.. Access microbiology, 5(6), acmi000491.v3. doi:10.1099/acmi.0.000491.v3
RECONSTRUCTING AND PREDICTING THE SPATIAL EVOLUTION OF CARBAPENEMASE-PRODUCING ENTEROBACTERIACEAE OUTBREAKS
Myall, A., Wiedermann, M., Vasikasin, P., Klamser, P., Wan, Y., Zachariae, A., . . . Brockmann, D. (2023). RECONSTRUCTING AND PREDICTING THE SPATIAL EVOLUTION OF CARBAPENEMASE-PRODUCING ENTEROBACTERIACEAE OUTBREAKS. International Journal of Infectious Diseases, 130, S65. doi:10.1016/j.ijid.2023.04.163
Need for standardized vancomycin dosing for coagulase-negative staphylococci in hospitalized infants.
Harvey, E. J., Ashiru-Oredope, D., Hill, L. F., Demirjian, A., & United Kingdom Health Security Agency Staphylococcus capitis Incident Management Team. (2023). Need for standardized vancomycin dosing for coagulase-negative staphylococci in hospitalized infants.. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, 29(1), 10-12. doi:10.1016/j.cmi.2022.09.016
2022
Improved contact tracing using network analysis and spatial-temporal proximity
Myall, A., Peach, R., Wan, Y., Mookerjee, S., Jauneikaite, E., Bolt, F., . . . Barahona, M. (2022). Improved contact tracing using network analysis and spatial-temporal proximity. International Journal of Infectious Diseases, 116, S20. doi:10.1016/j.ijid.2021.12.047
2021
Alterations in chromosomal genes <i>nfsA</i>, <i>nfsB</i>, and <i>ribE</i> are associated with nitrofurantoin resistance in <i>Escherichia coli</i> from the United Kingdom.
Wan, Y., Mills, E., Leung, R. C. Y., Vieira, A., Zhi, X., Croucher, N. J., . . . Sriskandan, S. (2021). Alterations in chromosomal genes <i>nfsA</i>, <i>nfsB</i>, and <i>ribE</i> are associated with nitrofurantoin resistance in <i>Escherichia coli</i> from the United Kingdom.. Microbial genomics, 7(12). doi:10.1099/mgen.0.000702
Characterising contact in disease outbreaks via a network model of spatial-temporal proximity
2020
GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure.
Wan, Y., Wick, R. R., Zobel, J., Ingle, D. J., Inouye, M., & Holt, K. E. (2020). GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure.. BMC genomics, 21(1), 658. doi:10.1186/s12864-020-07019-6
GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene Associations Controlled for Population Structure
2019
Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions.
Chen, Q., Zhang, X., Wan, Y., Zobel, J., & Verspoor, K. (2019). Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions.. Journal of computational biology : a journal of computational molecular cell biology, 26(6), 605-617. doi:10.1089/cmb.2018.0198
2017
Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases
Chen, Q., Wan, Y., Zhang, X., Lei, Y., Zobel, J., & Verspoor, K. (2017). Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases. Journal of Data and Information Quality, 9(3), 1-27. doi:10.1145/3131611
2016
Evaluation of CD-HIT for constructing non-redundant databases
Qingyu Chen., Yu Wan., Yang Lei., Zobel, J., & Verspoor, K. (2016). Evaluation of CD-HIT for constructing non-redundant databases. In 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE. doi:10.1109/bibm.2016.7822604
2015
Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1.
Wan, Y., Gorrie, C. L., Jenney, A., Mirceta, M., & Holt, K. E. (2015). Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1.. Genome announcements, 3(5), e01007-e01015. doi:10.1128/genomea.01007-15