Dr. Wayne Xu
1. Lead a bioinformatics team for Bioinformatics Research Support
2. Research in genomics and bioinformatics for genome, transcriptome, proteomics, epigentics, genomic variations, gene regulation, trait associtation studies.
Current research and/or projects
- Targeted and useful genomics for barley and oat (TUGOAT): funded (2019-2024) by Agriculture and Agri-Food Canada (AAFC) project J-002373 in partnership with Génome Québec and the National Barley Cluster led by the Barley Council of Canada (BCC) through the Canadian Agriculture Partnership (CAP).
- Crop Rotation Affects Disease Suppressive Soil Microbiomes: funded (2021-2023) by Ag Action Manitoba Program – Research and Innovation.
Research and/or project statements
- Genome assembly: Using Illumina paired-end reads, long mate-pair reads, PacBio sequences, 10X chromium linked read libraries, and chromosome conformation capture sequencing (Hi-C) to assemble genome to chromosome pseudomolecules.
- Transcriptome differentiation studies: using RNA-seq for transcriptome differentiation analyses
- Genomic variation studies: using whole genome sequencing (WGS), genotype-by-sequencing (GBS), and whole exome capture (WEC) sequencing to analyze SNPs/INDELs.
- Genome-wise association study (GWAS): Developing AI learning models for wheat and barley GWAS to aid in genomic selection (GS) and genomic edit (GE).
- Microbiome: Using whole genome sequencing or 16S sequencing for microbiota and microbiome studies.
- Gene functional analysis and annotation: Using database and computational tools for gene, protein, and genome annotations.
Professional activities / interests
- Bioinformatics
- Journal review
- Grant review
- Teaching
Education and awards
- Ph.D. Microbiology and Immunology, Nanjing Agricultural University and Shanghai Institute of Biochemistry, CAS.
- BSc. Computer Science, University of Manitoba
Key publications
1) Xu W*, Tucker JR, Bekele W, You FM, Fu YB, Khanal R, Yao Z, Singh J, Boyle B, Beattie AD, Belzile F Mascher M, Tinker NA*, Badea A*. Genome assembly of the Canadian two-row malting barley cultivar AAC Synergy. 2021; G3: Genes, Genomes, Genetics. doi.org/10.1093/g3journal/jkab031
2) Yao Z, You FM, N'Diaye A, Knox RE, McCartney C, Hiebert CW, Pozniak C, Xu W*.Evaluation of variant calling tools for large plant genome re-sequencing. BMC Bioinformatics. 2020 Aug 17;21(1):360.
3) Borrego-Benjumea A, Carter A, Tucker JR, Yao Z, Xu W, Badea A. Genome-Wide Analysis of Gene Expression Provides New Insights into Waterlogging Responses in Barley (Hordeum vulgare L.). Plants (Basel). 2020 Feb 13;9(2):240.
4) Beacon TH, Xu W, Davie JR. Genomic landscape of transcriptionally active histone arginine methylation marks, H3R2me2s and H4R3me2a, relative to nucleosome depleted regions. Gene. 2020 Jun 5;742:144593.
5) Ren Y, Su H, She Y, Dai C, Xie D, Narrandes S, Huang S, Chen C, Xu W*. Whole genome sequencing revealed microbiome in lung adenocarcinomas presented as ground-glass nodules. Transl Lung Cancer Res 2019;8(3):235-246. doi: 10.21037/tlcr.2019.06.11
6) Jahan S, Beacon TH, Xu W, Davie JR. Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes. Biochem Cell Biol. 2019 Jul 5. doi: 10.1139/bcb-2019-0107.
7) Ren Y, Huang S, Dai C, Xie D, Zheng L, Xie H, Zheng H, She Y, Zhou F, Wang Y, Li P, Fei K, Jiang G, Zhang Y, Su B, Sweet-Cordero EA, Tran NL, Yang Y, Patel JN, Rolfo C, Rocco G, Cardona AF, Tuzi A, Suter MB, Yang P, Xu W*, Chen C*. Germline Predisposition and Copy Number Alteration in Pre-stage Lung Adenocarcinomas Presenting as Ground-Glass Nodules. Front Oncol. 2019 Apr 18;9:288. doi: 10.3389/fonc.2019.00288. eCollection 2019.
8) Huang S, Xu W, Hu P, Lakowski TM. Integrative Analysis Reveals Subtype-Specific Regulatory Determinants in Triple Negative Breast Cancer. Cancers (Basel). 2019 Apr 10;11(4). pii: E507. doi: 10.3390/cancers11040507.
9) Jahan S, Beacon TH, He S, Gonzalez C, Xu W, Delcuve GP, Jia S, Hu P, Davie JR. Chromatin organization of transcribed genes in chicken polychromatic erythrocytes. Gene. 2019 May 30;699:80-87. doi: 10.1016/j.gene.2019.03.001. Epub 2019 Mar 8.
10) Xu W, Liyanage VRB, MacAulay A, Levy RD, Curtis K, Olson CO, Zachariah RM, Amiri S, Buist M, Hicks GG, Davie JR, Rastegar M. Genome-Wide Transcriptome Landscape of Embryonic Brain-Derived Neural Stem Cells Exposed to Alcohol with Strain-Specific Cross-Examination in BL6 and CD1 Mice. Sci Rep. 2019 Jan 18;9(1):206. doi: 10.1038/s41598-018-36059-y.
33) Okagaki RJ, Cho S, Kruger WM, Xu W, Heinen S, Muehlbauer GJ. The barley UNICULM2 gene resides in a centromeric region and may be associated with signaling and stress responses. Funct Integr Genomics. 2013 13(1):33-41.
35) Li L, Petsch K, Shimizu R, Liu S, Xu W, Ying K, Yu J, Scanlon M, Schnable P, Timmermans M, Springer N, Muehlbauer G. Mendelian and non-Mendelian regulation of gene expression in the maize shoot apex. PLoS Genetics, 2012 9(1):e1003202.
42) Waters AJ, Makarevitch I, Eichten SR, Swanson-Wagner RA, Yeh CT, Xu W, Schnable PS, Vaughn MW, Gehring M, Springer NM. Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm. Plant Cell, 2011, 23(12):4221-33.
47) Xu W*, Carter CJ. Parallel multiplicity and error discovery rate (EDR) in microarray experiments. BMC Bioinformatics. 2010, 11(1):465, p1-12.
48) Jia H, Millett BP, Cho S, Bilgic H, Xu W, Smith KP, Muehlbauer GJ. Quantitative trait loci conferring resistance to Fusarium head blight in barley respond differentially to Fusarium graminearum infection. Funct Integr Genomics 2010, 11(1):95-102.
51) Severin AJ, Peiffer GA, Xu W, Hyten DL, Bucciarelli B, O'Rourke JA, Bolon YT, Grant D, Farmer AD, May GD, Vance CP, Shoemaker RC, Stupar RM. An integrative approach to genomic introgression mapping. Plant Physiol. 2010, 154(1):3-12.
55) Xu W*, Cho S, Yang SS, Bolon YT, Bilgic H, Jia H, Xiong Y, Muehlbauer G. Single-feature polymorphism discovery by computing probe affinity shape powers, BMC Genetics 2009, 10:48, p1-14.
58) Bolton MD, Kolmer JA, Xu W, Garvin DF. Lr34-mediated leaf rust resistance in wheat: transcript profiling reveals a high energetic demand supported by transient recruitment of multiple metabolic pathways. Mol Plant Microbe Interact, 2008, 21(12):1515-27.