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William Hsiao

Senior Scientist

Education

Affiliations

Projects

Papers

Eisler D, Fornika D, Tindale LC, Chan T, Sabaiduc S, Hickman R, Chambers C, Krajden M, Skowronski DM, Jassem A, Hsiao W. (2020). Influenza Classification Suite: An automated Galaxy workflow for rapid influenza sequence analysis. Influenza and other respiratory viruses, 14(3)

Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen AV, Cheng AA, Liu S, Min SY, Miroshnichenko A, Tran HK, Werfalli RE, Nasir JA, Oloni M, Speicher DJ, Florescu A, Singh B, Faltyn M, Hernandez-Koutoucheva A, Sharma AN, Bordeleau E, Pawlowski AC, Zubyk HL, Dooley D, Griffiths E, Maguire F, Winsor GL, Beiko RG, Brinkman FSL, Hsiao WWL, Domselaar GV, McArthur AG. (2020). CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic acids research, 48(D1)

Himsworth CG, Duan J, Prystajecky N, Coombe M, Baticados W, Jassem AN, Tang P, Sanders E, Hsiao W. (2020). TARGETED RESEQUENCING OF WETLAND SEDIMENT AS A TOOL FOR AVIAN INFLUENZA VIRUS SURVEILLANCE. Journal of wildlife diseases, 56(2)

Tyson S, Peterson CL, Olson A, Tyler S, Knox N, Griffiths E, Dooley D, Hsiao W, Cabral J, Johnson RP, Laing C, Gannon V, Lynch T, Van Domselaar G, Brinkman F, Graham M. (2019). 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. Microbiology resource announcements, 8(41)

Tsui CK, Miller R, Uyaguari-Diaz M, Tang P, Chauve C, Hsiao W, Isaac-Renton J, Prystajecky N. (2018). Beaver Fever: Whole-Genome Characterization of Waterborne Outbreak and Sporadic Isolates To Study the Zoonotic Transmission of Giardiasis. mSphere, 3(2)

Dooley DM, Griffiths EJ, Gosal GS, Buttigieg PL, Hoehndorf R, Lange MC, Schriml LM, Brinkman FSL, Hsiao WWL. (2018). FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration. NPJ science of food, (2)

Britton AP, Trapp M, Sabaiduc S, Hsiao W, Joseph T, Schwantje H. (2019). Probable reverse zoonosis of influenza A(H1N1)pdm 09 in a striped skunk (Mephitis mephitis). Zoonoses and public health, 66(4)

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. (2018). Human Activity Determines the Presence of Integron-Associated and Antibiotic Resistance Genes in Southwestern British Columbia. Frontiers in microbiology, (9)

Petkau A, Mabon P, Sieffert C, Knox NC, Cabral J, Iskander M, Iskander M, Weedmark K, Zaheer R, Katz LS, Nadon C, Reimer A, Taboada E, Beiko RG, Hsiao W, Brinkman F, Graham M, Van Domselaar G. (2017). SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. Microbial genomics, 3(6)

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

Tang P, Croxen MA, Hasan MR, Hsiao WW, Hoang LM. (2017). Infection control in the new age of genomic epidemiology. American journal of infection control, 45(2)

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

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

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. (2015). Year-Long Metagenomic Study of River Microbiomes Across Land Use and Water Quality. Frontiers in microbiology, (6)

Dooley DM, Petkau AJ, Van Domselaar G, Hsiao WW. (2016). Sequence database versioning for command line and Galaxy bioinformatics servers. Bioinformatics (Oxford, England), 32(8)

Prystajecky N, Tsui CK, Hsiao WW, Uyaguari-Diaz MI, Ho J, Tang P, Isaac-Renton J. (2015). Giardia spp. Are Commonly Found in Mixed Assemblages in Surface Water, as Revealed by Molecular and Whole-Genome Characterization. Applied and environmental microbiology, 81(14)

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

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. (2013). Genotyping of human neutrophil antigens (HNA) from whole genome sequencing data. BMC medical genomics, (6)

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

Hsiao WW, Li KL, Liu Z, Jones C, Fraser-Liggett CM, Fouad AF. (2012). Microbial transformation from normal oral microbiota to acute endodontic infections. BMC genomics, (13)

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. (2012). Quantitative assessment of mitochondrial DNA copies from whole genome sequencing. BMC genomics, (13 Suppl 7)

Langille MG, Laird MR, Hsiao WW, Chiu TA, Eisen JA, Brinkman FS. (2012). MicrobeDB: a locally maintainable database of microbial genomic sequences. Bioinformatics (Oxford, England), 28(14)

Thom KA, Hsiao WW, Harris AD, Stine OC, Rasko DA, Johnson JK. (2010). Patients with Acinetobacter baumannii bloodstream infections are colonized in the gastrointestinal tract with identical strains. American journal of infection control, 38(9)

Langille MG, Hsiao WW, Brinkman FS. (2010). Detecting genomic islands using bioinformatics approaches. Nature reviews. Microbiology, 8(5)

Ho Sui SJ, Fedynak A, Hsiao WW, Langille MG, Brinkman FS. (2009). The association of virulence factors with genomic islands. PloS one, 4(12)

Hsiao WW, Fraser-Liggett CM. (2009). Human Microbiome Project--paving the way to a better understanding of ourselves and our microbes. Drug discovery today, 14(7-8)

Hsiao WW, Metz C, Singh DP, Roth J. (2008). The microbes of the intestine: an introduction to their metabolic and signaling capabilities. Endocrinology and metabolism clinics of North America, 37(4)

Langille MG, Hsiao WW, Brinkman FS. (2008). Evaluation of genomic island predictors using a comparative genomics approach. BMC bioinformatics, (9)

McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE, Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJ, Holt R, Brinkman FS, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD. (2006). The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proceedings of the National Academy of Sciences of the United States of America, 103(42)

Coombes BK, Wickham ME, Brown NF, Lemire S, Bossi L, Hsiao WW, Brinkman FS, Finlay BB. (2005). Genetic and molecular analysis of GogB, a phage-encoded type III-secreted substrate in Salmonella enterica serovar typhimurium with autonomous expression from its associated phage. Journal of molecular biology, 348(4)

Hsiao WW, Ung K, Aeschliman D, Bryan J, Finlay BB, Brinkman FS. (2005). Evidence of a large novel gene pool associated with prokaryotic genomic islands. PLoS genetics, 1(5)

Warren R, Hsiao WW, Kudo H, Myhre M, Dosanjh M, Petrescu A, Kobayashi H, Shimizu S, Miyauchi K, Masai E, Yang G, Stott JM, Schein JE, Shin H, Khattra J, Smailus D, Butterfield YS, Siddiqui A, Holt R, Marra MA, Jones SJ, Mohn WW, Brinkman FS, Fukuda M, Davies J, Eltis LD. (2004). Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1. Journal of bacteriology, 186(22)

Hsiao W, Wan I, Jones SJ, Brinkman FS. (2003). IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics (Oxford, England), 19(3)

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