The University of Queensland

High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing

Ganesamoorthy, Devika, Yan, Mengjia, Murigneux, Valentine, Zhou, Chenxi, Cao, Minh Duc, Duarte, Tania P. S. and Coin, Lachlan J. M. (2020). High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing. F1000Research, 9, 1084. doi: 10.12688/f1000research.25693.1

Complete genome sequences of clinical Pandoraea fibrosis isolates

Pitt, Miranda E., Nguyen, Son H., Duarte, Tânia P. S., Roddam, Louise F., Blaskovich, Mark A. T., Cooper, Matthew A. and Coin, Lachlan J. M. (2020). Complete genome sequences of clinical Pandoraea fibrosis isolates. Microbiology Resource Announcements, 9 (13) e00060-20. doi: 10.1128/mra.00060-20

Evaluating the genome and resistome of extensively drug-resistant Klebsiella pneumoniae using native DNA and RNA Nanopore sequencing

Pitt, Miranda E., Nguyen, Son H., Duarte, Tânia P. S., Teng, Haotian, Blaskovich, Mark A. T., Cooper, Matthew A. and Coin, Lachlan J. M. (2020). Evaluating the genome and resistome of extensively drug-resistant Klebsiella pneumoniae using native DNA and RNA Nanopore sequencing. GigaScience, 9 (2), 1-14. doi: 10.1093/gigascience/giaa002

Retooling phage display with electrohydrodynamic nanomixing and nanopore sequencing

Raftery, Lyndon J., Howard, Christopher B., Grewal, Yadveer S., Vaidyanathan, Ramanathan, Jones, Martina L., Anderson, Will, Korbie, Darren, Duarte, Tania, Duc Cao, Minh, Nguyen, Son Hoang, Coin, Lachlan JM, Mahler, Stephen M and Trau, Matt (2019). Retooling phage display with electrohydrodynamic nanomixing and nanopore sequencing. Lab on a Chip, 19 (24), 4083-4092. doi: 10.1039/c9lc00978g

Rapid diagnosis of Capnocytophaga canimorsus septic shock in an immunocompetent individual using real-time Nanopore sequencing: a case report

Bialasiewicz, Seweryn, Duarte, Tania P. S., Nguyen, Son H., Sukumaran, Vichitra, Stewart, Alexandra, Appleton, Sally, Pitt, Miranda E., Bainomugisa, Arnold, Jennison, Amy V., Graham, Rikki, Coin, Lachlan J. M. and Hajkowicz, Krispin (2019). Rapid diagnosis of Capnocytophaga canimorsus septic shock in an immunocompetent individual using real-time Nanopore sequencing: a case report. BMC Infectious Diseases, 19 (1) 660, 1-5. doi: 10.1186/s12879-019-4173-2

Correction to: Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

Teng, Haotian, Cao, Minh Duc, Hall, Michael B., Duarte, Tania, Wang, Sheng and Coin, Lachlan J M (2019). Correction to: Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning. GigaScience, 8 (5). doi: 10.1093/gigascience/giz049

Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes

Zhou, Chenxi, Duarte, Tania, Silvestre, Rocio, Rossel, Genoveva, Mwanga, Robert O. M., Khan, Awais, George, Andrew W., Fei, Zhangjun, Yencho, G. Craig, Ellis, David and Coin, Lachlan J. M. (2018). Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes. Gates Open Research, 2 41, 41. doi: 10.12688/gatesopenres.12856.1

GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing

Ganesamoorthy, Devika, Cao, Minh Duc, Duarte, Tania, Chen, Wenhan and Coin, Lachlan (2018). GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing. BMC Bioinformatics, 19 (1) 267, 267. doi: 10.1186/s12859-018-2282-3

npInv: accurate detection and genotyping of inversions using long read sub-alignment

Shao, Haojing, Ganesamoorthy, Devika, Duarte, Tania, Cao, Minh Duc, Hoggart, Clive J. and Coin, Lachlan J. M. (2018). npInv: accurate detection and genotyping of inversions using long read sub-alignment. BMC Bioinformatics, 19 (1) 261, 261. doi: 10.1186/s12859-018-2252-9

A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions

Bainomugisa, Arnold, Duarte, Tania, Lavu, Evelyn, Pandey, Sushil, Coulter, Chris, Marais, Ben J. and Coin, Lachlan M. (2018). A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions. Microbial Genomics, 4 (7) 000188. doi: 10.1099/mgen.0.000188

Chiron: Translating nanopore raw signal directly into nucleotide sequence using deep learning

Teng, Haotian, Cao, Minh Duc, Hall, Michael B., Duarte, Tania, Wang, Sheng and Coin, Lachlan J. M. (2018). Chiron: Translating nanopore raw signal directly into nucleotide sequence using deep learning. GigaScience, 7 (5). doi: 10.1093/gigascience/giy037

Triclosan at environmentally relevant concentrations promotes horizontal transfer of multidrug resistance genes within and across bacterial genera

Lu, Ji, Wang, Yue, Li, Jie, Mao, Likai, Nguyen, Son Hoang, Duarte, Tania, Coin, Lachlan, Bond, Philip, Yuan, Zhiguo and Guo, Jianhua (2018). Triclosan at environmentally relevant concentrations promotes horizontal transfer of multidrug resistance genes within and across bacterial genera. Environment International, 121 (Pt 2), 1217-1226. doi: 10.1016/j.envint.2018.10.040

Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode

Nguyen, Son Hoang, Duarte, Tania, Coin, Lachlan and Cao, Minh Duc (2017). Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode. Bioinformatics (Oxford, England), 33 (24), 3988-3990. doi: 10.1093/bioinformatics/btx537

Genetic variants in ICAM1, PPARGC1A and MTHFR are potentially associated with different phenotypes of diabetic retinopathy

Simões, Maria José, Lobo, Conceição, Egas, Conceição, Nunes, Sandrina, Carmona, Susana, Costa, Miguel Ângelo, Duarte, Tânia, Ribeiro, Luísa, Faro, Carlos and Cunha-Vaz, José G. (2014). Genetic variants in ICAM1, PPARGC1A and MTHFR are potentially associated with different phenotypes of diabetic retinopathy. Ophthalmologica, 232 (3), 156-162. doi: 10.1159/000365229

New achievements for diagnostics of banana streak virus

Ngo, Ha, Crew, Kathy S., Vance, Megan, Thomas, John, Nguyen, Son, Duarte, Tania, Coin, Lachlan and Geering, Andrew (2019). New achievements for diagnostics of banana streak virus. Australasian Plant Pathology Society 22nd Biennial Conference, Melbourne, Australia, 26-28 November 2019. Melbourne, Australia:

Deep sequencing of microbial communities in cystic fibrosis airways

Da Silva Duarte, Tania Patricia (2022). Deep sequencing of microbial communities in cystic fibrosis airways. PhD Thesis, Institute for Molecular Bioscience, The University of Queensland. doi: 10.14264/40053f4