Explanipedia

Leveraging metatranscriptomics for the characterisation of bovine blood viromes Open

Bárbara Brito, Matthew Z. DeMaere, I.J. Lean, M.S. Hazelton, Brendon A. O’Rourke , et al. · 2025

Leveraging metatranscriptomics for the characterisation of bovine blood viromes Open

Bárbara Brito, Matthew Z. DeMaere, I.J. Lean, M.S. Hazelton, Brendon A. O’Rourke , et al. · 2025

Understanding the diversity of the bovine virome is essential for assessing their potential impact on cattle health and transmission risks. Viruses present in the blood comprise both those that establish persistent infections in blood cell…

Assessing how metal reef restoration structures shape the functional and taxonomic profile of coral-associated bacterial communities Open

Paige Strudwick, David J. Suggett, Justin R. Seymour, Matthew Z. DeMaere, Amanda Grima , et al. · 2024

Significant threats to the long-term persistence of coral reefs have accelerated the adoption of coral propagation and out-planting approaches. However, how materials commonly used for propagation structures could potentially affect coral-…

Coral endosymbiont growth is enhanced by metabolic interactions with bacteria Open

J. L. Matthews, Abeeha Khalil, Nachshon Siboni, Jeremy Bougoure, Paul Guagliardo , et al. · 2023

Bacteria are key contributors to microalgae resource acquisition, competitive performance, and functional diversity, but their potential metabolic interactions with coral microalgal endosymbionts (Symbiodiniaceae) have been largely overloo…

Phylogenomic analysis of a global collection of <i>Escherichia coli</i> ST38: evidence of interspecies and environmental transmission? Open

Piklu Roy Chowdhury, Priyanka Hastak, Matthew Z. DeMaere, Ethan R. Wyrsch, Dmitriy Li , et al. · 2023

We performed a comprehensive phylogenomic analysis of 925 extraintestinal pathogenic Escherichia coli (ExPEC) ST38 genomes from 38 countries and diverse hosts and sources. The phylogeny resolved two broad clades: A (593 strains; 91% human)…

Rhometa: Population recombination rate estimation from metagenomic read datasets Open

Sidaswar Krishnan, Matthew Z. DeMaere, Dominik Beck, Martin Ostrowski, Justin R. Seymour , et al. · 2023

Prokaryotic evolution is influenced by the exchange of genetic information between species through a process referred to as recombination. The rate of recombination is a useful measure for the adaptive capacity of a prokaryotic population.…

Rhometa: Population recombination rate estimation from metagenomic read datasets Open

Sidaswar Krishnan, Matthew Z. DeMaere, Dominik Beck, Martin Ostrowski, Justin R. Seymour , et al. · 2023

Rhometa provides a suite of pipelines for calculating the recombination rate in metagenomic datasets. The tool is developed using Nextflow, a workflow management tool, and the Python programming language. The repository contains all result…

Rhometa: Population recombination rate estimation from metagenomic read datasets Open

Sidaswar Krishnan, Matthew Z. DeMaere, Dominik Beck, Martin Ostrowski, Justin R. Seymour , et al. · 2023

Rhometa provides a suite of pipelines for calculating the recombination rate in metagenomic datasets. The tool is developed using Nextflow, a workflow management tool, and the Python programming language. The repository contains all result…

Rhometa: Population recombination rate estimation from metagenomic read datasets Open

Sidaswar Krishnan, Matthew Z. DeMaere, Dominik Beck, Martin Ostrowski, Justin R. Seymour , et al. · 2022

Bacterial evolution is influenced by the exchange of genetic information between species through a process referred to as recombination. The rate of recombination is a useful measure for the adaptive capacity of a bacterial population. We …

Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig Open

Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, G. J. Eamens, Linda Falconer , et al. · 2022

Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in t…

qc3C: Reference-free quality control for Hi-C sequencing data Open

Matthew Z. DeMaere, Aaron E. Darling · 2021

Hi-C is a sample preparation method that enables high-throughput sequencing to capture genome-wide spatial interactions between DNA molecules. The technique has been successfully applied to solve challenging problems such as 3D structural …

Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes Open

Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, Toni A. Chapman, Steven P. Djordjevic , et al. · 2021

Using a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50 000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5 % of which were classified as >70 % complete with a <10 …

A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen Open

Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, G. J. Eamens, Michael Liu , et al. · 2021

Background Early weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, a…

qc3C: reference-free quality control for Hi-C sequencing data Open

Matthew Z. DeMaere, Aaron E. Darling · 2021

Hi-C is a sample preparation method that enables high-throughput sequencing to capture genome-wide spatial interactions between DNA molecules. The technique has been successfully applied to solve challenging problems such as 3D structural …

qc3C manuscript simuated sweep configuration and source code Open

Matthew Z. DeMaere, Aaron E. Darling · 2021

This is the repository of configuration details and source code necessary to reproduce the simulated sweep for the manuscript : qc3C - reference-free quality control for Hi-C sequencing data. The repository also contains the qc3C analysis …

qc3C manuscript simuated sweep configuration and source code Open

Matthew Z. DeMaere, Aaron E. Darling · 2021

This is the repository of configuration details and source code necessary to reproduce the simulated sweep for the manuscript: qc3C - reference-free quality control for Hi-C sequencing data

qc3C manuscript simuated sweep configuration and source code Open

Matthew Z. DeMaere, Aaron E. Darling · 2021

This is the repository of configuration details and source code necessary to reproduce the simulated sweep for the manuscript : qc3C - reference-free quality control for Hi-C sequencing data. The repository also contains the qc3C analysis …

qc3C manuscript simuated sweep configuration and source code Open

Matthew Z. DeMaere, Aaron E. Darling · 2021

This is the repository of configuration details and source code necessary to reproduce the simulated sweep for the manuscript : qc3C - reference-free quality control for Hi-C sequencing data. The repository also contains the qc3C analysis …

Community composition and development of the post-weaning piglet gut microbiome Open

Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, G. J. Eamens, Michael Liu , et al. · 2020

BackgroundEarly weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, an…

Post-weaning shifts in microbiome composition and metabolism revealed by over 25,000 pig gut metagenome assembled genomes Open

Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, Toni A. Chapman, Steven P. Djordjevic , et al. · 2020

Using a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50,000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5% of which were classified as >70% complete with a <10% c…

Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig Open

Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, G. J. Eamens, Tiziana Zingali , et al. · 2020

Background Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Besides leading to antimicrobial resistance (AMR), orally administered antibiotics are well known to cause dys…

Metagenomic Hi-C of a Healthy Human Fecal Microbiome Transplant Donor Open

Matthew Z. DeMaere, Michael Y. Z. Liu, Enmoore Lin, Steven P. Djordjevic, Ian G. Charles , et al. · 2020

We report the availability of a high-quality metagenomic Hi-C data set generated from a fecal sample taken from a healthy fecal microbiome transplant donor subject. We report on basic features of the data to evaluate their quality.

data for The Gene School: Metagenomics workshop Open

Aaron E. Darling, Matthew Z. DeMaere, Daniela Gaio, Kay Anantanawat · 2019

Precomputed data including a metagenomic assembly of multiple samples, reads from multiple samples mapped to the coassembly, metagenome-assembled genomes (MAGs), and anvio profiles for the MAGs. All from timeseries faecal samples of a sing…

data for The Gene School: Metagenomics workshop Open

Aaron E. Darling, Matthew Z. DeMaere, Daniela Gaio, Kay Anantanawat · 2019

Precomputed data including a metagenomic assembly of multiple samples, reads from multiple samples mapped to the coassembly, metagenome-assembled genomes (MAGs), and anvio profiles for the MAGs. All from timeseries faecal samples of a sing…

bin3C clustering result for a healthy human faecal microbiome transplant donor Open

Matthew Z. DeMaere, Michael Liu, Enmoore Lin, Steven P. Djordjevic, Ian G. Charles , et al. · 2019

bin3C clustering and checkm QC results for a metagenomic Hi-C dataset of a healthy human faecal microbiome transplant donor. bin3C version 0.3.3

Metagenomic assembly and bin3C clustering result for a healthy human faecal microbiome transplant donor Open

Matthew Z. DeMaere, Michael Liu, Enmoore Lin, Steven P. Djordjevic, Ian G. Charles , et al. · 2019

Metagenomic WGS assembly and Hi-C deconvolution of a healthy human faecal microbiome transplant donor. Metagenomic assembly was produced using Spades (v3.13.1). Extracted MAGs were produced using bin3C (v0.3.3) and QC'd using CheckM (v1.0.…

Metagenomic assembly and bin3C clustering result for a healthy human faecal microbiome transplant donor Open

Matthew Z. DeMaere, Michael Yz Liu, Enmoore Lin, Steven P. Djordjevic, Ian G. Charles , et al. · 2019

Metagenomic WGS assembly and Hi-C deconvolution of a healthy human faecal microbiome transplant donor. Metagenomic assembly was produced using Spades (v3.13.1). Extracted MAGs were produced using bin3C (v0.3.3) and QC'd using CheckM (v1.0.…

bin3C clustering result for a healthy human faecal microbiome transplant donor Open

Matthew Z. DeMaere, Michael Liu, Enmoore Lin, Steven P. Djordjevic, Ian G. Charles , et al. · 2019

bin3C clustering and checkm QC results for a metagenomic Hi-C dataset of a healthy human faecal microbiome transplant donor. bin3C version 0.3.3

Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia Open

Ethan R. Wyrsch, Cameron J. Reid, Matthew Z. DeMaere, Michael Y. Liu, Toni A. Chapman , et al. · 2019

IncHI2 ST3 plasmids are known carriers of multiple antimicrobial resistance genes. Complete plasmid sequences from multiple drug resistant Escherichia coli circulating in Australian swine is however limited. Here we sequenced two related I…

bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes Open

Matthew Z. DeMaere, Aaron E. Darling · 2019

Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon …

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