Lachlan Coin

Real-time resolution of short-read assembly graph using ONT long reads

Son Hoang Nguyen, Minh Duc Cao, Lachlan JM Coin

Journal article  |  2021  |  PLOS Computational Biology

A streaming assembly pipeline utilising real-time Oxford Nanopore Technology (ONT) sequencing data is important for saving sequenc..

Identification of Reduced Host Transcriptomic Signatures for Tuberculosis Disease and Digital PCR-Based Validation and Quantification.

Harriet D Gliddon, Myrsini Kaforou, Mary Alikian, Dominic Habgood-Coote, Chenxi Zhou, Tolu Oni, Suzanne T Anderson, Andrew J Brent, Amelia C Crampin, Brian Eley, Robert Heyderman, Florian Kern, Paul R Langford, Tom HM Ottenhoff, Martin L Hibberd, Neil French, Victoria J Wright, Hazel M Dockrell, Lachlan J Coin, Robert J Wilkinson, et al.

Journal article  |  2021  |  Frontiers in Immunology

Recently, host whole blood gene expression signatures have been identified for diagnosis of tuberculosis (TB). Absolute quantifica..

Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection

Jessie J-Y Chang, Daniel Rawlinson, Miranda Pitt, George Taiaroa, Josie Gleeson, Chenxi Zhou, Francesca Mordant, Ricardo De Paoli-Iseppi, Leon Caly, Damian FJ Purcell, Tim Stinear, Sarah Londrigan, Michael Clark, Deborah Williamson, Kanta Subbarao, Lachlan JM Coin

Journal article  |  2020

Summary SARS-CoV-2 uses subgenomic (sg)RNA to produce viral proteins for replication and immune evasion. We applied long-read RNA ..

Comparison of long-read methods for sequencing and assembly of a plant genome

Valentine Murigneux, Subash Kumar Rai, Agnelo Furtado, Timothy JC Bruxner, Wei Tian, Ivon Harliwong, Hanmin Wei, Bicheng Yang, Qianyu Ye, Ellis Anderson, Qing Mao, Radoje Drmanac, Ou Wang, Brock A Peters, Mengyang Xu, Pei Wu, Bruce Topp, Lachlan JM Coin, Robert J Henry

Journal article  |  2020  |  GigaScience

BACKGROUND: Sequencing technologies have advanced to the point where it is possible to generate high-accuracy, haplotype-resolved,..

Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations

Chenxi Zhou, Bode Olukolu, Dorcus C Gemenet, Shan Wu, Wolfgang Gruneberg, Minh Duc Cao, Zhangjun Fei, Zhao-Bang Zeng, Andrew W George, Awais Khan, G Craig Yencho, Lachlan JM Coin

Journal article  |  2020  |  Nature Genetics

Despite advances in sequencing technologies, assembly of complex plant genomes remains elusive due to polyploidy and high repeat c..

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

Chenxi Zhou, Tania Duarte, Rocio Silvestre, Genoveva Rossel, Robert Mwanga, Awais Khan, Andrew George, Zhangjun Fei, Craig Yencho, David Ellis, Lachlan Coin

Journal article  |  2020  |  Gates Open Research

Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp ge..

Complete Genome Sequences of Clinical Pandoraea fibrosis Isolates

Miranda E Pitt, Son H Nguyen, Tania PS Duarte, Louise F Roddam, Mark AT Blaskovich, Matthew A Cooper, Lachlan JM Coin

Journal article  |  2020  |  Microbiology Resource Announcements

Pandoraea fibrosis is a newly identified Gram-negative bacterial species that was isolated from the respiratory tract of an Austra..

Real-time resolution of short-read assembly graph using ONT long reads

Son Hoang Nguyen, Minh Duc Cao, Lachlan Coin

Journal article  |  2020

A streaming assembly pipeline utilising real-time Oxford Nanopore Technology (ONT) sequencing data is important for saving sequenc..

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

Miranda E Pitt, Son H Nguyen, Tania PS Duarte, Haotian Teng, Mark AT Blaskovich, Matthew A Cooper, Lachlan JM Coin

Journal article  |  2020  |  GigaScience

BACKGROUND: Klebsiella pneumoniae frequently harbours multidrug resistance, and current diagnostics struggle to rapidly identify a..

Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy

Ping Zhang, Devika Ganesamoorthy, Son Hoang Nguyen, Raymond Au, Lachlan J Coin, Siok-Keen Tey

Journal article  |  2020  |  Journal for ImmunoTherapy of Cancer

BACKGROUND: Analysis of vector integration sites in gene-modified cells can provide critical information on clonality and potentia..