Publications

 

Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package. Emma J Griffiths, Ruth E Timme, Catarina Inês Mendes, Andrew J Page, Nabil-Fareed Alikhan, Dan Fornika, Finlay Maguire, Josefina Campos, Daniel Park, Idowu B Olawoye, Paul E Oluniyi, Dominique Anderson, Alan Christoffels, Anders Gonçalves da Silva, Rhiannon Cameron, Damion Dooley, Lee S Katz, Allison Black, Ilene Karsch-Mizrachi, Tanya Barrett, Anjanette Johnston, Thomas R Connor, Samuel M Nicholls, Adam A Witney, Gregory H Tyson, Simon H Tausch, Amogelang R Raphenya, Brian Alcock, David M Aanensen, Emma Hodcroft, William W L Hsiao, Ana Tereza R Vasconcelos, Duncan R MacCannell on behalf of the Public Health Alliance for Genomic Epidemiology (PHA4GE) consortium.  GigaScience, Volume 11, 2022, giac003.

Addressing Privacy Concerns in Sharing Viral Sequences and Minimum Contextual Data in a Public Repository During the COVID-19 Pandemic. Song Lingqiao, Liu Hanshi, Brinkman Fiona S. L, Gill Erin, Griffiths Emma J., Hsiao William W. L, Savić-Kallesøe Sarah, Moreira Sandrine, Van Domselaar Gary, Zawati Ma’n H., Joly Yann. “Front Genet 2022 Mar 24;12:716541”

Metagenomic Analysis of the Pediatric-Onset Multiple Sclerosis Gut Microbiome. Ali I. Mirza, Feng Zhu, Natalie Knox, Jessica D. Forbes, Gary Van Domselaar, Charles N. Bernstein, Morag Graham, Ruth Ann Marrie, Janace Hart, E. Ann Yeh, Douglas Arnold, Amit Bar-Or, Julia O’Mahony, Yinshan Zhao, William Hsiao, Brenda Banwell, Emmanuelle Waubant, and Helen Tremlett. Neurology. 98(10).

Whole genome sequencing of Campylobacter in agri-food surveillance. Shanwei Tong,Luyao Ma, Jennifer Ronholm, William Hsiao, Xiaonan Lu. Curr. Opin. Food Sci.39: 130-139.

A systematic review and narrative synthesis of environmental samples used for the surveillance of avian influenza viruses in wild waterbirds. Michelle Coombe; Stefan Iwasawa; Kaylee A Byers; Natalie Prystajecky; William Hsiao; David M. Patrick; Chelsea G. Himsworth. J. of Wildlife Diseases, 57(1):1-18 (2021).

Targeted Resequencing of Wetland Sediment as a Tool for Avian Influenza Virus Surveillance. Chelsea G. Himsworth, Jun Duan, Natalie Prystajecky, Michelle Coombe, Waren Baticados, Agatha N. Jassem, Patrick Tang, Eric Sanders, William Hsiao. J Wildl Dis (202056 (2): 397–408

Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada.Shari Tyson, Christy-Lynn Peterson, Adam Olson, Shaun Tyler, Natalie Knox, Emma Griffiths, Damion Dooley, William Hsiao, Jennifer Cabral, Roger P Johnson, Chad Laing, Victor Gannon, Tarah Lynch,Gary Van Domselaar, Fiona Brinkman, Morag Graham.Microbial Resource Announcements, “GENOME SEQUENCES, October 2019  Volume 8  Issue 41  e00625-19”

Influenza Classification Suite: An automated Galaxy workflow for rapid influenza sequence analysis. Diane Eisler,Dan Fornika,Lauren C. Tindale, Tracy Chan, Suzana Sabaiduc, Rebecca Hickman, Catharine Chambers, Mel Krajden, Danuta M. Skowronski, Agatha Jassem, William Hsiao. Influenza Other Respir Viruses . 2020 May;14(3):358-362

Extraction and Detection of Avian Influenza Virus From Wetland Sediment Using Enrichment-Based Targeted Resequencing.Tindale, Lauren; Baticados, Waren; Duan, Jun; Coombe, Michelle; Jassem, Agatha; Tang, Patrick; Uyaguari-Diaz, Miguel; Moore, Richard; Himsworth, Chelsea; Hsiao, William; Prystajecky, Natalie. Front. Vet. Sci., 29 May 2020

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance
database.
Brian P Alcock, Edalatmand, William Huynh, Anna-Lisa V Nguyen,, Damion Dooley, Emma Griffiths, Finlay Maguire, Geoff L Winsor, Robert G Beiko, Fiona SL Brinkman, William WL Hsiao, Gary V Domselaar, Andrew G McArthur et al.Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D517–D525

MentaLiST – A fast MLST caller for large MLST schemes. Feijao P, Yao HT, Fornika D, Gardy J, Hsiao W, Chauve C, Chindelevitch L.Microb Genom. 2018 Jan 10.

Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia. Uyaguari-Díaz MI, Croxen MA, Luo Z, Cronin KI, Chan M, Baticados WN, Nesbitt MJ, Li S, Miller KM, Dooley D, Hsiao W, Isaac-Renton JL, Tang P, Prystajecky N. Front Microbiol. 2018 May 1;9:852

The genomic epidemiology ontology and GEEM ontology reusability platform. Dooley, D., Griffiths, E., Gosal, G., Brinkman, F., Hsiao, W. 2017 CEUR workshop Proceedings

Infection control in the new age of genomic epidemiology.Tang P, Croxen MA, Hasan MR, Hsiao WW, Hoang LM.Am J Infect Control. 2017 Feb 1;45(2):170-179

Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance.Griffiths E, Dooley D, Graham M, Van Domselaar G, Brinkman FSL, Hsiao WWL.Front Microbiol. 2017 June 26;8:1068

Genome Sequences of the Mycobacterium tuberculosis H37Rv-ptkA Deletion Mutant and Its Parental Strain.Tsui CKM, Wong D, Narula G, Gardy JL, Hsiao WWH, Av-Gay Y.Genome Announc. 2017 Nov 2;5(44).

Sequence database versioning for command line and Galaxy bioinformatics servers.Dooley DM, Petkau AJ, Van Domselaar G, Hsiao WW.Bioinformatics. 2016 Apr 15;32(8):1275-7.

Metagenomic Investigation of Plasma in Individuals with ME/CFS Highlights the Importance of Technical Controls to Elucidate Contamination and Batch Effects.Miller RR, Uyaguari-Diaz M, McCabe MN, Montoya V, Gardy JL, Parker S, Steiner T, Hsiao W, Nesbitt MJ, Tang P, Patrick DM; CCD Study Group. PLoS One. 2016 Nov 2;11(11):e0165691.

Giardia spp. Are Commonly Found in Mixed Assemblages in Surface Water, as Revealed by Molecular and Whole-Genome Characterization.Prystajecky N, Tsui CK, Hsiao WW, Uyaguari-Diaz MI, Ho J, Tang P, Isaac-Renton J. Appl Environ Microbiol. 2015 Jul;81(14):4827-34

Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks. Morgun A, Dzutsev A, Dong X, Greer RL, Sexton DJ, Ravel J, Schuster M, Hsiao W, Matzinger P, Shulzhenko N.Gut. 2015 Nov;64(11):1732-43.

Year-Long Metagenomic Study of River Microbiomes Across Land Use and Water Quality.Van Rossum T, Peabody MA, Uyaguari-Diaz MI, Cronin KI, Chan M, Slobodan JR, Nesbitt MJ, Suttle CA, Hsiao WW, Tang PK, Prystajecky NA, Brinkman FS.Front Microbiol. 2015 Dec 16;6:1405

EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.Chu HT, Hsiao WW, Chen JC, Yeh TJ, Tsai MH, Lin H, Liu YW, Lee SA, Chen CC, Tsao TT, Kao CY.Bioinformatics. 2013 Apr 15;29(8):1004-10.

SeqEntropy: genome-wide assessment of repeats for short read sequencing.Chu HT, Hsiao WW, Tsao TT, Hsu DF, Chen CC, Lee SA, Kao CY. PLoS One. 2013;8(3):e59484

 Genotyping of human neutrophil antigens (HNA) from whole genome sequencing data. Chu HT, Lin H, Tsao TT, Chang CF, Hsiao WW, Yeh TJ, Chang CM, Liu YW, Wang TY, Yang KC, Chen TJ, Chen JC, Chen KC, Kao CY.BMC Med Genomics. 2013 Sep 12;6:31.

Microbial transformation from normal oral microbiota to acute endodontic infections.Hsiao WW, Li KL, Liu Z, Jones C, Fraser-Liggett CM, Fouad AF. BMC Genomics. 2012 Jul 28;13:345. doi: 10.1186/1471-2164-13-345

Quantitative assessment of mitochondrial DNA copies from whole genome sequencing. Chu HT, Hsiao WW, Tsao TT, Chang CM, Liu YW, Fan CC, Lin H, Chang HH, Yeh TJ, Chen JC, Huang DM, Chen CC, Kao CY. BMC Genomics. 2012;13 Suppl 7:S5.

Full list of publications can be found here