Publications

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

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.

Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15582-7.

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

Hsiao WW, Metz C, Singh DP, Roth J.

Endocrinol Metab Clin North Am. 2008 Dec;37(4):857-71.

The role of patient-to-patient transmission in the acquisition of imipenem-resistant Pseudomonas aeruginosa colonization in the intensive care unit.

Johnson JK, Smith G, Lee MS, Venezia RA, Stine OC, Nataro JP, Hsiao W, Harris AD.

J Infect Dis. 2009 Sep 15;200(6):900-5. doi: 10.1086/605408

Human Microbiome Project–paving the way to a better understanding of ourselves and our microbes.

Hsiao WW, Fraser-Liggett CM.

Drug Discov Today. 2009 Apr;14(7-8):331-3.

Analyzing endodontic infections by deep coverage pyrosequencing.

Li L, Hsiao WW, Nandakumar R, Barbuto SM, Mongodin EF, Paster BJ, Fraser-Liggett CM.

Fouad AF.J Dent Res. 2010 Sep;89(9):980-4.

Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data.

Liu Z, Hsiao W, Cantarel BL, Drábek EF, Fraser-Liggett C.

Bioinformatics. 2011 Dec 1;27(23):3242-9.

Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut.

Shulzhenko N, Morgun A, Hsiao W, Battle M, Yao M, Gavrilova O, Orandle M, Mayer L, Macpherson AJ, McCoy KD, Fraser-Liggett C, Matzinger P.

Nat Med. 2011 Nov 20;17(12):1585-93.

Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity.

Sahl JW, Johnson JK, Harris AD, Phillippy AM, Hsiao WW, Thom KA, Rasko DA.

BMC Genomics. 2011 Jun 4;12:291. doi: 10.1186/1471-2164-12-291.

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.

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

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.

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

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.

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

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.

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

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.

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.

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).

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

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

The genomic epidemiology ontology and GEEM ontology reusability platform.

Dooley, D., Griffiths, E., Gosal, G., Brinkman, F., Hsiao, W.

2017 CEUR workshop Proceedings

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

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.