Select Publications
Journal articles
2023, 'What is the climate footprint of therapeutic diets for people with chronic kidney disease? Results from an Australian analysis', Journal of Human Nutrition and Dietetics, 36, pp. 2246 - 2255, http://dx.doi.org/10.1111/jhn.13204
,2023, 'ARGs-OAP v3.0: Antibiotic-Resistance Gene Database Curation and Analysis Pipeline Optimization', Engineering, 27, pp. 234 - 241, http://dx.doi.org/10.1016/j.eng.2022.10.011
,2023, 'Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples', Environmental Science and Technology, 57, pp. 9713 - 9721, http://dx.doi.org/10.1021/acs.est.3c00159
,2023, 'Second-line levofloxacin-based quadruple therapy versus bismuth-based quadruple therapy for Helicobacter pylori eradication and long-term changes to the gut microbiota and antibiotic resistome: a multicentre, open-label, randomised controlled trial', The Lancet Gastroenterology and Hepatology, 8, pp. 228 - 241, http://dx.doi.org/10.1016/S2468-1253(22)00384-3
,2023, 'Critical Assessment of Whole Genome and Viral Enrichment Shotgun Metagenome on the Characterization of Stool Total Virome in Hepatocellular Carcinoma Patients', Viruses, 15, http://dx.doi.org/10.3390/v15010053
,2022, 'The role of the microbiome in the metabolic health of people with schizophrenia and related psychoses: cross-sectional and pre-post lifestyle intervention analyses', Pathogens, 11, pp. 1279, http://dx.doi.org/10.3390/pathogens11111279
,2022, 'Nationwide biogeography and health implications of bacterial communities in household drinking water', Water Research, 215, http://dx.doi.org/10.1016/j.watres.2022.118238
,2022, 'Fecal DNA Virome Is Associated with the Development of Colorectal Neoplasia in a Murine Model of Colorectal Cancer', Pathogens, 11, http://dx.doi.org/10.3390/pathogens11040457
,2022, 'Corrigendum: The P4 Study: Postpartum Maternal and Infant Faecal Microbiome 6 Months After Hypertensive Versus Normotensive Pregnancy(Front. Cell. Infect. Microbiol., (2022), 12, (646165), 10.3389/fcimb.2022.646165)', Frontiers in Cellular and Infection Microbiology, 12, pp. 895332, http://dx.doi.org/10.3389/fcimb.2022.895332
,2022, 'The P4 Study: Postpartum Maternal and Infant Faecal Microbiome 6 Months After Hypertensive Versus Normotensive Pregnancy', Frontiers in Cellular and Infection Microbiology, 12, pp. 646165, http://dx.doi.org/10.3389/fcimb.2022.646165
,2021, 'Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma', Nature Communications, 12, pp. 187, http://dx.doi.org/10.1038/s41467-020-20422-7
,2021, 'Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years', Microbiome, 9, http://dx.doi.org/10.1186/s40168-021-01151-5
,2021, 'Seasonal prevalence of ammonia-oxidizing archaea in a full-scale municipal wastewater treatment plant treating saline wastewater revealed by a 6-year time-series analysis', Environmental Science and Technology, 55, pp. 2662 - 2673, http://dx.doi.org/10.1021/acs.est.0c07703
,2019, 'Passage and community changes of filterable bacteria during microfiltration of a surface water supply', Environment International, 131, http://dx.doi.org/10.1016/j.envint.2019.104998
,2019, 'Metagenomic and resistome analysis of a full-scale municipal wastewater treatment plant in Singapore containing membrane bioreactors', Frontiers in Microbiology, 10, http://dx.doi.org/10.3389/fmicb.2019.00172
,2018, 'The bacterial community significantly promotes cast iron corrosion in reclaimed wastewater distribution systems', Microbiome, 6, http://dx.doi.org/10.1186/s40168-018-0610-5
,2018, 'Temporal dynamics of activated sludge bacterial communities in two diversity variant full-scale sewage treatment plants', Applied Microbiology and Biotechnology, 102, pp. 9379 - 9388, http://dx.doi.org/10.1007/s00253-018-9287-8
,2018, 'ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes', Bioinformatics, 34, pp. 2263 - 2270, http://dx.doi.org/10.1093/bioinformatics/bty053
,2018, 'Antibiotic resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses', Environmental microbiology, 20, pp. 355 - 368
,2018, 'Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes', Microbiome, 6, pp. 34 - 34
,2018, 'High-Resolution Temporal and Spatial Patterns of Virome in Wastewater Treatment Systems', Environmental science & technology
,2018, 'Integrated biogeography of planktonic and sedimentary bacterial communities in the Yangtze River', Microbiome, 6, pp. 16 - 16
,2018, 'Toward an Intensive Longitudinal Understanding of Activated Sludge Bacterial Assembly and Dynamics', Environmental Science & Technology, 52, pp. 8224 - 8232
,2017, 'Cultivation-dependent and high-throughput sequencing approaches studying the co-occurrence of antibiotic resistance genes in municipal sewage system', Applied Microbiology and Biotechnology, 101, pp. 8197 - 8207, http://dx.doi.org/10.1007/s00253-017-8573-1
,2017, 'MinION Nanopore sequencing enables correlation between resistome phenotype and genotype of coliform bacteria in municipal sewage', Frontiers in Microbiology, 8, http://dx.doi.org/10.3389/fmicb.2017.02105
,2017, 'Comammox in drinking water systems', Water Research, 116, pp. 332 - 341, http://dx.doi.org/10.1016/j.watres.2017.03.042
,2017, 'Effects of endocrine disrupting chemicals (EDCs) on bacterial communities in mangrove sediments', Marine Pollution Bulletin, 122, pp. 122 - 128, http://dx.doi.org/10.1016/j.marpolbul.2017.06.035
,2017, 'Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey', Microbiome, 5, pp. 154 - 154
,2016, 'ARGs-OAP: Online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database', Bioinformatics, 32, pp. 2346 - 2351, http://dx.doi.org/10.1093/bioinformatics/btw136
,2016, 'Exploring the shift in structure and function of microbial communities performing biological phosphorus removal', PLoS ONE, 11, http://dx.doi.org/10.1371/journal.pone.0161506
,2016, 'Population dynamics of bulking and foaming bacteria in a full-scale wastewater treatment plant over five years', Scientific Reports, 6, http://dx.doi.org/10.1038/srep24180
,2015, 'Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity', MICROBIOME, 3, http://dx.doi.org/10.1186/s40168-015-0081-x
,2014, 'Evaluation of a hybrid approach using UBLAST and BLASTX for metagenomic sequences annotation of specific functional genes', PLoS ONE, 9, http://dx.doi.org/10.1371/journal.pone.0110947
,2013, 'Comparison of microbial diversity determined with the same variable tag sequence extracted from two different PCR amplicons', BMC Microbiology, 13, http://dx.doi.org/10.1186/1471-2180-13-208
,2013, 'Illumina Sequencing of 16S rRNA Tag Revealed Spatial Variations of Bacterial Communities in a Mangrove Wetland', Microbial Ecology, 66, pp. 96 - 104, http://dx.doi.org/10.1007/s00248-013-0238-8
,2012, 'Two-stage clustering (TSC): A pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons', PLoS ONE, 7, http://dx.doi.org/10.1371/journal.pone.0030230
,2011, 'BIPES, a cost-effective high-throughput method for assessing microbial diversity', ISME Journal, 5, pp. 741 - 749, http://dx.doi.org/10.1038/ismej.2010.160
,2010, 'Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method', BMC Microbiology, 10, http://dx.doi.org/10.1186/1471-2180-10-255
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