Wayne Xu
Xu's Lab
Bioinformatics Makes Better Life!

Dr Wayne Xu

Bioinformatics

Wayne Xu

Assistant Professor
Department of Biochemistry and Medical Genetics
Rady Faculty of Health Sciences, University of Manitoba

Senior Scientist
Research Institute of Oncology and Hematology, CancerCare Manitoba

Adjunct Professor
College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba

Research Interests:

I joined the Research Institute of Oncology and Hematology (RIOH) after working as a bioinformatician at the Supercomputing Institute of the University of Minnesota and the NGS platform at the University of Manitoba. I have previously collaborated on a variety of projects ranging from mammalian cancer genomics to plant genomes and microorganism genomes. My expertise is applying Bioinformatics approaches to solve biological problems, particularly to unveil the genomic and epigenomic regimes using large high throughput data including DNA-seq, RNA-seq, ChIP-seq, Methyl-seq, as well as microarray data. My current research focuses are:

1. Discovering gene signatures and targets for precision medicine of cancer therapy

Even being the same type of cancers, each cancer patient is different in terms of tumor initiation factors and the response to drug treatments. With the advancement in Next-Generation Sequencing (NGS) technology, multiple international consortia have made numerous large genomic and epigenomic data of various cancer types publicly accessible. Our lab develops new bioinformatics models and uses these large data to discover new gene signatures and gene targets aiming to aid tailoring for patient therapies.

2. Investigating tumorigenesis beyond driver gene mutations

It is generally accepted that driver gene mutations initialize the tumorigenesis. However, very few driver mutations are shared among cancers and even in the same patient with multiple tumors of the same types, there are few or none common drivers. Our lab works with an international collaborator group on targeted, whole exome, and whole genome sequencing data. We investigate SNV, CNV, SV, INDEL, LOH, cellular clonal structure in order to uncover new tumorigenesis factors in lung cancer.

3. Developing new algorithms and tools for large sequencing data analysis

The next-generation sequencing (NGS) technologies have produced large amount of various genomic data for a variety of experiments which had a tremendous impact on life science research. RNA-seq uses the large amount of short sequence reads to interrogate the transcriptome, the existence and level of RNAs. How to accurately quantify the RNAs' level without much computational cost has been one of the focuses for NGS bioinformatics research. Our lab designs an alternative RNA-seq estimate method called Feature Structure (FEST) method. In contrast to current RNA-seq expression estimation methods that do not account for GC bias and RNA degradation, FEST will handle read redundant, GC bias probability, and degradation rate in each read to estimate the expression level.

GROUP MEMBERS (current&past)



Group memebers in the lab
  • Shujun Huang, Ph.D graduate student
  • Shavira Narrandes, M.Sc, graduate student
  • Yang Zhang, Research Assistant
  • Gaofeng Jia, Ph.D, Research Associate
  • Nilubon Kurubanjerdjit, Ph.D, Post-doctoral fellow
  • Nianguang Cai, M.Sc, Research Assistant
  • Shavira Narrandes, B.Sc, Honours project student
  • Pedro Penzuti Pacheco, Summer researcher student
  • Damien Cote, MSc graduate student, Co-supervision
  • Harrison Deng, Summer project student
  • Larry Zheng, Summer project student

Trainees' award:

  • 2016 CIHR Travel Award: Shujun Huang, "Gene Functional Analysis of Breast Cancer Multi-gene Signatures", 8th International Conference on Biomarkers & Clinical Research, December 05-07, 2016 Philadelphia, Pennsylvania, USA
  • 2nd place winner, 2016 University of Manitoba Undergraduate Research Poster Competition: Pedro Pacheco, "Identifying Methylation Patterns in Young Women Breast Cancer with Machine Learning"

PUBLICATIONS


  1. Narrandes S, Huang S, Murphy L, Xu W*. The Exploration of Contrasting Pathways in Triple Negative Breast Cancer (TNBC). BMC Cancer 2018,18:22.DOI 10.1186/s12885-017-3939-4.
  2. Huang S, Cai N, Pacheco PP, Narrandes S, Wang Y, Xu W*. Applications of Support Vector Machine (SVM) learning in cancer genomics. Cancer Genomics and Proteomics 2018, 15(1):41-51. PMID: 29275361.
  3. Huang S, Kurubanjerdjit N, Xu W*. Two opposing effects (Yin and Yang) determine the cancer cells' fate. Critical Review in Oncogenesis 2018, accepted in press. 22(1-2):000000. DOI: 10.1615/CritRevOncog.2017020882.
  4. Ilic A, Lu S, Bhatia V, Begum F, Klonisch T, Agarwal P, Xu W, Davie JR. Ubiquitin C-terminal hydrolase isozyme L1 is associated with shelterin complex at interstitial telomeric sites. Epigenetics & Chromatin 2017, Nov 10;10(1):54. PMID: 29126443
  5. Xu W*, Jia G, Cai N, Huang S, Davie JR, Pitz M, Banerji S, Murphy L. A 16 Yin Yang Gene Expression Ratio Signature for ER+/Node- Breast Cancer. International Journal of Cancer 2017, 140(6): 1413-1424.
  6. Ran X, Ao Z, Trajtman A, Xu W, Kobinger G, Keynan Y, Yao X. HIV-1 envelope glycoprotein stimulates viral transcription and increases the infectivity of the progeny virus through the manipulation of cellular machinery. Scientific Reports, 2017, 7(1):9487.
  7. Xu W*, Jia G, Davie JR, Murphy L, Kratzke R, Banerji S. A Ten Yin Yang Gene Expression Ratio Signature for Lung Cancer Prognosis. Journal of Thoracic Oncology 2016, 11(12): 2150-2160. PMID: 27498386.
  8. Elizabeth Hammond, Emma Shu, Karagin Sawchuk, Yvonne Myal, Afshin Raouf, Thomas Klonisch, Sabine Hombach-Klonisch, Michael Mowat, Wayne Xu, Leigh Murphy, Marshall Pitz. Population-based analysis of Breast Cancer Treatment by Intrinsic Sub-type in Manitoba, Canada. Cancer Epidemiol. 2016, 45:82-90. PMID: 27770672.
  9. Jahan S, Xu W, He S, Gonzalez C, Delcuve G, Davie JR. The chicken erythrocyte epigenome. Epigenetics and Chromatins 2016. 9:19. doi: 10.1186/s13072-016-0068-2. PMID: 27226810.
  10. Skubitz KM, Geschwind K, Xu WW, Koopmeiners JS, Skubitz AP (2016). Gene expression identifies heterogeneity of metastatic behavior among gastrointestinal stromal tumors. J Transl Med 2016 13;14(1):51. 
  11. Peng Z, Xu WW, Sham Y, Lam H, Sun D, Li C, Rasic NF, Guan Q, James AA, Simons FE (2015). Mosquito salivary allergen Aed a 3: cloning, comprehensive molecular analysis, and clinical evaluation. Allergy. 2015 Nov 26. doi: 10.1111/all.12812. [Epub ahead of print]
  12. Mahood TH, Johar DR, Iwasiow BM, Xu W, Keijzer R (2015). The transcriptome of nitrofen-induced pulmonary hypoplasia in the rat model of congenital diaphragmatic hernia. Pediatr Res. 2015 Dec 31. doi: 10.1038/pr.2015.277. PMID: 26720608.
  13. Yan Y, Cooper C, Hamedani MK, Guppy B, Xu W, Tsuyuki D, Zhang C, Nugent Z, Blanchard A, Davie JR, McManus K, Murphy LC, Myal Y, Leygue E (2015). The steroid receptor RNA activator protein (SRAP) controls cancer cell migration/motility. FEBS Lett. 2015 Dec 21;589(24 Pt B):4010-8.
  14. Davie JR, Xu W, Delcuve GP (2015). Histone H3K4 trimethylation: dynamic interplay with pre-mRNA splicing. Biochem Cell Biol. 2015 Jul 15:1-11. [Epub ahead of print]
  15. Fernando DM, Xu W, Loewen PC, Zhanel GG, Kumar A. (2014) Triclosan can select for an AdeIJK overexpressing mutant of Acinetobacter baumannii ATCC17978 that displays reduced susceptibility to multiple antibiotics. Antimicrob Agents Chemother. 2014, 58(11):6424-31
  16. Skubitz KM, Skubitz AP, Xu W, Luo X, Lagarde P, Coindre JM, and Chibon F (2014). Gene expression identifies heterogeneity of metastatic behavior among high-grade non-translocation associated soft tissue sarcomas. J Transl Med. 2014 12:176.
  17. Khan D, Gonzalez C, Cooper C, Sun J, Chen H, HealyS, Xu W, SmithK, Workman J, Leygue E, Davie J.(2013). RNA-Dependent Dynamic Histone Acetylation Regulates MCL1 Alternative Splicing. Nucleic Acids Research 2013, 42(3):1656-70.
  18. Lamont EA, Xu W, Sreevatsan S (2013). Host-Mycobacterium avium subsp. paratuberculosis interactome reveals a novel iron assimilation mechanism linked to nitric oxide stress during early infection. BMC Genomics. 2013, 14(1):694.
  19. Xu W, Banerji S, Davie JR, Kassie F, Yee D, Kratzke R (2013) Yin Yang gene expression ratio signature for lung cancer prognosis. PLoS One, 2013, 8(7): e68742
  20. Li L, Petsch K, Shimizu R, Liu S, Xu W, Ying K, Yu J, Scanlon M, Schnable P, Timmermans M, Springer N, Muehlbauer G. (2012) Mendelian and non-Mendelian regulation of gene expression in the maize shoot apex. PLoS Genetics, 2013, 9(1):e1003202 (Impact factor =9.543).
  21. Patterson S, Borewicz K, Johnson T, Xu W, Isaacson R. (2012) Characterization and differential gene expression between two phenotypic phase variants in Salmonella enterica serovar Typhimurium. PLoS One, 2012;7(8):e43592. PMID: 22937065.
  22. Babra B, Watson G, Xu W, Jeffrey B, Xu J, Rockey D, Rohrmann G, Jin L. (2012) Analysis of the genome of the Leporid Herpesvirus-4. Virology, 2012, 433(1):183-91.
  23. Watson G, Xu W, Reed A, Babra B, Putman T, Wick E, Wechsler SL, Rohrmann GF, Jin L. (2012) Sequence and comparative analysis of the genome of HSV-1 strain McKrae. Virology, 2012, 433(2):528-37.
  24. Lang KS, Danzeisen JL, Xu W, Johnson T. (2012) Transcriptome mapping of pAR060302, a blaCMY-2 positive, IncA/C broad host range plasmid. Applied and Environmental microbiology, 2012, 78(9):3379-86.
  25. Qu B, Qi X, Wu X, Liang M, Li C, Cardona CJ, Xu W, Tang F, et al. (2012) Suppression of the Interferon and NF-kB Responses by Severe Fever with Thrombocytopenia Syndrome Virus. Journal of Virology 2012, 86(16):8388401.
  26. Metivier K, Deitz K, Xu W, Conzemius M, Wilke V. (2012) Differential expression of osteopontin in follicular thyroid carcinomas compared to normal thyroid tissue in dogs. Veterinary and Comparative Oncology, 2012, 12(3):181-97.
  27. McHale LK, Haun WJ, Xu W, Bhaskar PB, Hyten DL, Gerhardt DJ, Jeddeloh JA, Stupar RM. (2012) Structural variants in the soybean genome localize to clusters of biotic stress response genes. Plant Physiology, 2012, 159(4):1295-308.
  28. Okagaki RJ, Cho S, Kruger WM, Xu W, Heinen S, Muehlbauer GJ (2012). The barley UNICULM2 gene resides in a centromeric region and may be associated with signaling and stress responses. Funct Integr Genomics. 2012, 13(1):33-41.
  29. Waters AJ, Makarevitch I, Eichten SR, Swanson-Wagner RA, Yeh CT, Xu W, Schnable PS, Vaughn MW, Gehring M, Springer NM. (2011) Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm. Plant Cell, 2011, 23(12):4221-33. (Impact factor =9.396).
  30. Valdes-Lopez O, Thibivilliers S, Qiu J, Xu W, Nguyen TH, Libault M, Le BH, Goldberg RB, Hill CB, Hartman GL, Diers B, Stacey G. (2011) Identification of quantitative trait loci controlling gene expression during the innate immunity response of soybean. Plant Physiol. 2011, 157(4):1975-86.
  31. Yang SS, Tu Z, Cheung F, Xu W, Lamb JFS, Jung HJG, Vance CP, Gronwald JW (2011) Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics 2011, 12(1):199. P1-75 (Impact factor = 3.76).
  32. Bolon YT, Haun WJ, Xu W, Grant D, et al, (2011) Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean. Plant Physiol. 2011, 156(1):240-53. (Impact factor = 6.928).
  33. Haun WJ, Hyten DL, Xu W, Gerhardt DJ, et al (2011). The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82. Plant Physiology 2011, 155(2):645-55. (Impact factor = 6.928).
  34. Xu W, Carter CJ (2010) Parallel multiplicity and error discovery rate (EDR) in microarray experiments. BMC Bioinformatics. 2010, 11(1):465, p1-12.
  35. Yang SS?, Xu W?, Tesfaye M, Lamb JF, Jung HJ, VandenBosch KA, Vance CP, Gronwald JW (2010) Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes. BMC Genomics, 11:323, p1-18. (Impact factor = 3.76).
  36. Janagama HK, Lamont EA, George S, Bannantine JP, Xu W, Tu Z, Wells SJ, Schefers J, Sreevatsan S. (2010) Primary transcriptomes of Mycobacterium avium subsp. paratuberculosis reveal proprietary pathways in tissue and macrophages. BMC Genomics 2010, 11:561, p1-11. (Impact factor = 3.76).
  37. Jia H, Millett BP, Cho S, Bilgic H, Xu W, Smith KP, Muehlbauer GJ. (2010) 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.
  38. 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 (2010) An integrative approach to genomic introgression mapping. Plant Physiol. 154(1):3-12.
  39. Yang SS, Valdes-Lopez O, Xu W, Bucciarelli B, Gronwald JW, Hernandez G, Vance CP (2010) Transcript profiling of common bean (Phaseolus vulgaris L.) using the GeneChip Soybean Genome Array: optimizing analysis by masking biased probes. BMC Plant Biol, 10:85, p1-15. (Impact factor = 3.77).
  40. Bolon YT, Joseph B, Cannon SB, Graham MA, Diers BW, Farmer AD, May GD, Muehlbauer GJ, Specht JE, Tu ZJ, Weeks N, Xu W, Shoemaker RC, Vance CP (2010) Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean. BMC Plant Biol. 10:41.p1-24.
  41. Hampton M, Xu W, Kram BW, Chambers EM, Ehrnriter JS, Gralewski JH, Joyal T, Carter CJ. (2010) Identification of differential gene expression in Brassica rapa nectaries through expressed sequence tag analysis. PLoS One 5(1):e8782, p1-9.
  42. Xu W, Cho S, Yang SS, Bolon YT, Bilgic H, Jia H, Xiong Y, Muehlbauer G (2009) Single-feature polymorphism discovery by computing probe affinity shape powers, BMC Genetics 10:48, p1-14. (Impact factor = 2.23).
  43. Kram BW?, Xu W?, Carter CJ (2009) Uncovering the Arabidopsis thaliana nectary transcriptome: investigation of differential gene expression in floral nectaries tissues. BMC Plant Biol. 9:92, p1-16, (Impact factor = 3.77).
  44. Yang SS, Xu W, Tesfaye M, Lamb JFS, Jung HJG, Samac DA, Vance CP, Gronwald JW* (2009) Single-feature Polymorphism Discovery in the Transcriptome of Tetraploid Alfalfa (Medicago sativa), The Plant Genome, 2(3):224-232.
  45. Zhang X, Xu W, Tan J, Zeng Y. (2009) Stripping custom microRNA microarrays and the lessons learned about probe:slide interactions. Analytical Chemistry 386(2):222-227. (Impact factor = 5.24).
  46. Hammer BE, Kidder LS, Williams PC, Xu W. (2009) Magnetic Levitation of MC3T3 Osteoblast Cells as a Ground-Based Simulation of Microgravity. Microgravity Sci Technol. 21(4):311-318.

Abstracts:

  1. Canadian Cancer Research Conference 2013: November 22-26, 2015 at Toronto. Yin Yang Gene Expression Ratio Signature for Lung Cancer Prognosis
  2. Canadian Cancer Research Conference 2015: November 8-10, 2015 at the Hôtel Bonaventure Montréal
  3. Guiding Manitoba Breast Cancer in the Clinical Setting: OncotypeDx or YMR ?
  4. IARC 50th Anniversary Conference: 7-10 JUNE 2016, Lyon, France
  5. A Ten Yin Yang Gene Expression Ratio Signature for Stage IA and IB of Non-small Cell Lung Cancer
  6. Manitoba CancerCare Research Day, May 9 2016: Exploring Yin Yang Pathways of Triple-Negative Breast Cancer
  7. Manitoba CancerCare Research Day, May 9 2016: Gene Functions of Breast Cancer Signatures

Invited / Seminars:

  1. MICB Senior presentation: Cancer Biomarker Discovery, Nov. 6, 2014
  2. Computer Science Department: Diverse Genomic Data Integration for Cancer Biomarker Discovery, Jan. 16, 2015.
  3. June 05, 2015, Breast cancer group presentation
  4. CancerCare Genomic Consortium: Next Generation Sequencing Bioinformatics. May 28, 2015.
  5. Terry Fox Conference in Winnipeg: Guiding Manitoba Breast Cancer in the Clinical Setting: OncotypeDx or YMR? June 09, 2015
  6. CCRC poster presentation: Yin Yang gene expression ratio signature YMR for breast cancer. Nov 10, 2015, Montreal
  7. Department of Biochemistry and Medical Genetics seminar: Forming and proofing an innovative idea: two opposing effects Yin and Yang in cancer. Dec 09, 2015

Other Activities:

  1. The 17th annual CancerCare Manitoba Research Day for Trainees, poster judge. May 13, 2015.
  2. Journal Reviewers: JTO, OMICS, Food Research International, Bioinformatics
  3. Journal editor board member: Medical Genomics & Biomarkers
  4. BGEN 4041 Project course PI judge
  5. Advisory Committees: Ph.D: Sanzida Jahan (2013-2016).
  6. NGS platform advisory committee (2013-2017)
  7. NGS bioinformatics Services
  8. Guest lectures for the graduate course: Gene Expression and Epigenetics, 2015.

Funding:

  1. 2014-2015: Manitoba Medical Service Foundation (MMSF) research grant. PI
  2. 2014-2015: CIHR Operating Grant. Co-Applicant
  3. 2012-2016: NIH/NIBIB, UH2 EB013647-01, Collaborator.
  4. 2014-2016: Canadian Breast Cancer Foundation (CBCF) Research Grant, PI
  5. 2015-2017: Cancer Research Society (CRS), Canada. Co-Applicant
  6. 2016-2017: Faculty of Science Interdisciplinary/New Directions Research Collaboration Initiation grant. Co-PI
  7. 2016-2021: CIHR team grant, Co-Applicant
  8. 2017-2018: CancerCare Manitoba Foundation (CCMF). PI

POSITIONS


we are recruiting graduate students in computer science/computer engineering or graduate student in statistics or biostatistics or graduate student in human genetics. All these positions are fully funded by research assistantships.