Detecting genomic islands using bioinformatics approaches

MGI Langille, WWL Hsiao, FSL Brinkman - Nature Reviews …, 2010 - nature.com
Bacterial genomes contain clusters of genes that are acquired by horizontal transfer, called
genomic islands (GIs). GIs are frequently associated with microbial adaptations that are of …

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

BP Alcock, AR Raphenya, TTY Lau… - Nucleic acids …, 2020 - academic.oup.com
Abstract The Comprehensive Antibiotic Resistance Database (CARD; https://card. mcmaster.
ca) is a curated resource providing reference DNA and protein sequences, detection models …

The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse

MP McLeod, RL Warren, WWL Hsiao… - Proceedings of the …, 2006 - National Acad Sciences
Rhodococcus sp. RHA1 (RHA1) is a potent polychlorinated biphenyl-degrading soil
actinomycete that catabolizes a wide range of compounds and represents a genus of …

[HTML][HTML] Infection control in the new age of genomic epidemiology

P Tang, MA Croxen, MR Hasan, WWL Hsiao… - American Journal of …, 2017 - Elsevier
Highlights•Advances in genome sequencing have allowed for its use in infection
control.•Genome sequencing provides higher resolution than conventional genotyping …

The microbes of the intestine: an introduction to their metabolic and signaling capabilities

WWL Hsiao, C Metz, DP Singh, J Roth - Endocrinology and metabolism …, 2008 - Elsevier
This article summarizes advances in the field of host-microbe interactions in the gut. The
human gut is home to a complex community of microbes (the microbiota) that plays a critical …

CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database

BP Alcock, W Huynh, R Chalil, KW Smith… - Nucleic acids …, 2023 - academic.oup.com
Abstract The Comprehensive Antibiotic Resistance Database (CARD; card. mcmaster. ca)
combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) …

[HTML][HTML] FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration

DM Dooley, EJ Griffiths, GS Gosal, PL Buttigieg… - npj Science of …, 2018 - nature.com
The construction of high capacity data sharing networks to support increasing government
and commercial data exchange has highlighted a key roadblock: the content of existing …

[HTML][HTML] Evidence of a large novel gene pool associated with prokaryotic genomic islands

WWL Hsiao, K Ung, D Aeschliman, J Bryan… - PLoS …, 2005 - journals.plos.org
Microbial genes that are “novel”(no detectable homologs in other species) have become of
increasing interest as environmental sampling suggests that there are many more such …

[HTML][HTML] Evaluation of genomic island predictors using a comparative genomics approach

MGI Langille, WWL Hsiao, FSL Brinkman - BMC bioinformatics, 2008 - Springer
Abstract Background Genomic islands (GIs) are clusters of genes in prokaryotic genomes of
probable horizontal origin. GIs are disproportionately associated with microbial adaptations …

[HTML][HTML] Microbial transformation from normal oral microbiota to acute endodontic infections

WWL Hsiao, KL Li, Z Liu, C Jones, CM Fraser-Liggett… - BMC genomics, 2012 - Springer
Background Endodontic infections are a leading cause of oro-facial pain and tooth loss in
western countries, and may lead to severe life-threatening infections. These infections are …