Select Publications
Journal articles
2024, 'Deciphering Bordetella pertussis epidemiology through culture-independent multiplex amplicon and metagenomic sequencing.', J Clin Microbiol, 62, pp. e0117824, http://dx.doi.org/10.1128/jcm.01178-24
,2024, 'Profiling the colonic mucosal response to fecal microbiota transplantation identifies a role for GBP5 in colitis in humans and mice', Nature Communications, 15, http://dx.doi.org/10.1038/s41467-024-46983-5
,2024, 'Refining microbial community metabolic models derived from metagenomics using reference-based taxonomic profiling', mSystems, 9, http://dx.doi.org/10.1128/msystems.00746-24
,2024, 'Single-cell landscape revealed immune characteristics associated with disease phases in brucellosis patients', iMeta, 3, http://dx.doi.org/10.1002/imt2.226
,2024, 'HtrA, fatty acids, and membrane protein interplay in Chlamydia trachomatis to impact stress response and trigger early cellular exit', Journal of Bacteriology, 206, http://dx.doi.org/10.1128/jb.00371-23
,2023, 'Serum-integrated omics reveal the host response landscape for severe pediatric community-acquired pneumonia', Critical Care, 27, http://dx.doi.org/10.1186/s13054-023-04378-w
,2023, 'Single-cell transcriptomic analysis reveals a systemic immune dysregulation in COVID-19-associated pediatric encephalopathy', Signal Transduction and Targeted Therapy, 8, http://dx.doi.org/10.1038/s41392-023-01641-y
,2023, 'Systemic immune dysregulation in severe tuberculosis patients revealed by a single-cell transcriptome atlas', Journal of Infection, 86, pp. 421 - 438, http://dx.doi.org/10.1016/j.jinf.2023.03.020
,2023, 'Multi-omics analysis reveals underlying host responses in pediatric respiratory syncytial virus pneumonia', iScience, 26, http://dx.doi.org/10.1016/j.isci.2023.106329
,2023, 'Corrigendum: Molecular pathogenesis of Chlamydia trachomatis (Frontiers in Cellular and Infection Microbiology, (2023), 13, (1281823), 10.3389/fcimb.2023.1281823)', Frontiers in Cellular and Infection Microbiology, 13, http://dx.doi.org/10.3389/fcimb.2023.1358553
,2023, 'Genome organization and genomics in Chlamydia: whole genome sequencing increases understanding of chlamydial virulence, evolution, and phylogeny', Frontiers in Cellular and Infection Microbiology, 13, http://dx.doi.org/10.3389/fcimb.2023.1178736
,2023, 'Influenza vaccination features revealed by a single-cell transcriptome atlas', Journal of Medical Virology, 95, http://dx.doi.org/10.1002/jmv.28174
,2023, 'Integrating proteomic data with metabolic modeling provides insight into key pathways of Bordetella pertussis biofilms', Frontiers in Microbiology, 14, http://dx.doi.org/10.3389/fmicb.2023.1169870
,2023, 'Microbial determinants of effective donors in faecal microbiota transplantation for UC', Gut, 72, pp. 90 - 100, http://dx.doi.org/10.1136/gutjnl-2022-327742
,2023, 'Molecular pathogenesis of Chlamydia trachomatis', Frontiers in Cellular and Infection Microbiology, 13, http://dx.doi.org/10.3389/fcimb.2023.1281823
,2023, 'Single-cell profiling reveals distinct immune response landscapes in tuberculous pleural effusion and non-TPE', Frontiers in Immunology, 14, http://dx.doi.org/10.3389/fimmu.2023.1191357
,2022, 'Single-cell transcriptomic atlas reveals distinct immunological responses between COVID-19 vaccine and natural SARS-CoV-2 infection', Journal of Medical Virology, 94, pp. 5304 - 5324, http://dx.doi.org/10.1002/jmv.28012
,2022, 'Proteomic and Metabolomic Signatures Associated With the Immune Response in Healthy Individuals Immunized With an Inactivated SARS-CoV-2 Vaccine', Frontiers in Immunology, 13, http://dx.doi.org/10.3389/fimmu.2022.848961
,2022, 'Multi-Platform Omics Analysis Reveals Molecular Signatures for Pathogenesis and Activity of Systemic Lupus Erythematosus', Frontiers in Immunology, 13, http://dx.doi.org/10.3389/fimmu.2022.833699
,2022, 'Lyophilised oral faecal microbiota transplantation for ulcerative colitis (LOTUS): a randomised, double-blind, placebo-controlled trial', The Lancet Gastroenterology and Hepatology, 7, pp. 141 - 151, http://dx.doi.org/10.1016/S2468-1253(21)00400-3
,2022, 'Changes to the upper gastrointestinal microbiotas of children with reflux oesophagitis and oesophageal metaplasia', Microbial Genomics, 8, http://dx.doi.org/10.1099/mgen.0.000870
,2022, 'Genomic dissection of the microevolution of Australian epidemic Bordetella pertussis', Emerging Microbes and Infections, 11, pp. 1460 - 1473, http://dx.doi.org/10.1080/22221751.2022.2077129
,2022, 'Metabolomic analysis reveals potential biomarkers and the underlying pathogenesis involved in Mycoplasma pneumoniae pneumonia', Emerging Microbes and Infections, 11, pp. 593 - 605, http://dx.doi.org/10.1080/22221751.2022.2036582
,2022, 'Rapid Surface Shaving for Proteomic Identification of Novel Surface Antigens for Vaccine Development', , 2414, pp. 47 - 62, http://dx.doi.org/10.1007/978-1-0716-1900-1_4
,2022, 'The role of ATG16L2 in autophagy and disease', Autophagy, 18, pp. 2537 - 2546, http://dx.doi.org/10.1080/15548627.2022.2042783
,2021, 'Development and comparison of novel multiple cross displacement amplification (MCDA) assays with other nucleic acid amplification methods for SARS-CoV-2 detection', Scientific Reports, 11, pp. 1873, http://dx.doi.org/10.1038/s41598-021-81518-8
,2021, 'A one-step, one-pot CRISPR nucleic acid detection platform (CRISPR-top): Application for the diagnosis of COVID-19', Talanta, 233, http://dx.doi.org/10.1016/j.talanta.2021.122591
,2021, 'Comparative Phosphoproteomics of Classical Bordetellae Elucidates the Potential Role of Serine, Threonine and Tyrosine Phosphorylation in Bordetella Biology and Virulence', Frontiers in Cellular and Infection Microbiology, 11, http://dx.doi.org/10.3389/fcimb.2021.660280
,2021, 'Enhancing genomics-based outbreak detection of endemic salmonella enterica serovar typhimurium using dynamic thresholds', Microbial Genomics, 7, pp. 000310, http://dx.doi.org/10.1099/MGEN.0.000310
,2021, 'Proteomic and metabolomic signatures associated with the immune response in healthy individuals immunized with an inactivated SARS-CoV-2 vaccine', , http://dx.doi.org/10.1101/2021.07.21.21260959
,2020, 'Temporal ordering of omics and multiomic events inferred from time-series data', npj Systems Biology and Applications, 6, http://dx.doi.org/10.1038/s41540-020-0141-0
,2020, 'Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis', Microbial Genomics, http://dx.doi.org/10.1099/mgen.0.000457
,2020, 'Behavioural and pharmaceutical interventions for the prevention of skin cancers in solid organ transplant recipients: A systematic review of randomised controlled trials', BMJ Open, 10, http://dx.doi.org/10.1136/bmjopen-2019-029265
,2020, 'Surfaceome analysis of Australian epidemic Bordetella pertussis reveals potential vaccine antigens', Vaccine, 38, pp. 539 - 548, http://dx.doi.org/10.1016/j.vaccine.2019.10.062
,2020, 'Development and comparison of a novel multiple cross displacement amplification (MCDA) assay with other nucleic acid amplification methods for SARS-CoV-2 detection', , http://dx.doi.org/10.1101/2020.10.03.20206193
,2020, 'Temporal ordering of omics and multiomic events inferred from time series data', , http://dx.doi.org/10.1101/2020.04.14.040527
,2019, 'Pertactin-negative and filamentous hemagglutinin-negative Bordetella pertussis, Australia, 2013-2017', Emerging Infectious Diseases, 25, pp. 1196 - 1199, http://dx.doi.org/10.3201/eid2506.180240
,2019, 'A novel multilocus variable-number tandem repeat analysis for Bordetella parapertussis', Journal of Medical Microbiology, 68, pp. 1671 - 1676, http://dx.doi.org/10.1099/jmm.0.001095
,2019, 'Pathogen adaptation to vaccination: The Australian Bordetella pertussis story', Microbiology Australia, 40, pp. 177 - 180, http://dx.doi.org/10.1071/MA19052
,2018, 'Comparison of the whole cell proteome and secretome of epidemic bordetella pertussis strains from the 2008–2012 Australian epidemic under sulfate-modulating conditions', Frontiers in Microbiology, 9, http://dx.doi.org/10.3389/fmicb.2018.02851
,2018, 'Proteomic Adaptation of Australian Epidemic Bordetella pertussis', Proteomics, 18, http://dx.doi.org/10.1002/pmic.201700237
,2017, 'Characterisation of the Bordetella pertussis secretome under different media', Journal of Proteomics, 158, pp. 43 - 51, http://dx.doi.org/10.1016/j.jprot.2017.02.010
,2016, 'Better colonisation of newly emerged Bordetella pertussis in the co-infection mouse model study', Vaccine, 34, pp. 3967 - 3971, http://dx.doi.org/10.1016/j.vaccine.2016.06.052
,2015, 'Pertactin negative Bordetella pertussis demonstrates higher fitness under vaccine selection pressure in a mixed infection model', Vaccine, 33, pp. 6277 - 6281, http://dx.doi.org/10.1016/j.vaccine.2015.09.064
,Conference Papers
2022, 'Genetic variants involved in innate immunity modulate the risk of inflammatory bowel diseases in an understudied Malaysian population', in Journal of Gastroenterology and Hepatology (Australia), pp. 342 - 351, http://dx.doi.org/10.1111/jgh.15752
,Conference Abstracts
2022, 'ENRICHMENT OF PREVOTELLA IS A CONSISTENT SIGNATURE IN THE METAPLASTIC ESOPHAGUS IN CHILDREN AND ADULTS', in GASTROENTEROLOGY, W B SAUNDERS CO-ELSEVIER INC, Vol. 162, pp. S833 - S833, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000826446203214&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
,2022, 'Mo1603: ENRICHMENT OF PREVOTELLA IS A CONSISTENT SIGNATURE IN THE METAPLASTIC ESOPHAGUS IN CHILDREN AND ADULTS', in Gastroenterology, Elsevier BV, Vol. 162, pp. S - 833, http://dx.doi.org/10.1016/s0016-5085(22)61964-4
,Preprints
2024, Proteomic comparison of epidemic AustralianBordetella pertussisbiofilm cells, http://dx.doi.org/10.1101/2024.02.19.581093
,2022, Integrating proteomic data with metabolic modelling provides insight into key pathways ofBordetella pertussisbiofilms, http://dx.doi.org/10.1101/2022.05.27.493021
,2022, Genomic dissection of the microevolution of Australian epidemic Bordetella pertussis, http://dx.doi.org/10.1101/2022.01.05.475016
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