Chen, Wen, Ph.D.

Research Scientist


Contact Information:

960 Carling Ave. (Room 2111)
Ottawa, Ontario K1A 0C6
Telephone: 613-759-1284
Fax: 613-759-1926
Email: wen.chen@agr.gc.ca

Areas of Expertise:

  • Metagenomics
  • Bioinformatics
  • Microbial Ecology
  • Biodiversity in relation to agro-ecosystem productivity and health.
  • Detection and identification of pathogens
  • Applied and Environmental Microbiology

Current Projects:

  • Pathogen surveillance using amplicon-based Next Generation Sequencing (NGS) technologies.
  • Development of Bioinformatics tools for improved detection accuracy of plant pathogens using NGS
  • Characterize community structure and function of epiphytic microbial populations for sustainable cereal grain production
  • Impact of agricultural practices and environmental factors on the distribution and diversity of microorganisms in agricultural value chain
  • Development of disease management technologies to improve quality and yield of malt, feed and silage barley in western Canada
  • Emerging mycotoxins to enhance food safety
  • Mycology and Bacteriology Biosystematics
  • Next generation sequencing - genomics and metagenomics of quarantine fungal and bacterial crop pathogens.
  • Monitoring an invasive bacterial pathogen (Clavibacter michiganensis subsp. nebraskensis) of corn using next-generation sequencing.
  • Dynamics of microbial population in wheat heads during Fusarium infection.
  • Detection and identification of plant pests and plant with novel traits using NGS

Affiliations:

  • Member, American Phytopathological Society (APS)
  • Member, Canadian Society of Microbiologists (CPS)

Research Publications:

The links below lead to abstracts with access to full text.

2017

2016

2015

2014

2013

2012

2011

2009

Other Science Related Publications:

2016

  • Hambleton, S., Eggertson, Q., Lévesque, C.A. Chen, W., Barasubiye, T., Redhead, S.A., and Liu, M. (2016). " DNA-barcoding the Powdery Mildews – sampling herbarium specimens in the National Mycological Herbarium (DAOM).", Canadian Phytopathological Society Annual Meeting, Delta Beausejour, Moncton, New Brunswick, Canada, June 12-15, 2016. (Poster)

2015

  • Chen, W. (2015). "Environmental metagenomics for sustainable agriculture.", Invited Oral Presentation at Biodiversity, Bioresources and Collection Science Day, Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada, December 1-2, 2015. (Presentation)
  • Chen, W., Hambleton, S., and Lévesque, C.A. (2015). "Environmental metagenomics for plant pathogen surveillance: the promise and the practice.", Invited Oral Presentation at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China, September 30, 2015. (Presentation)
  • Chen, W., Lévesque, C.A., and Sims, J.T. (2015). RAM: R for Amplicon-Sequencing-Based Microbial-Ecology. Version 1.2.1.3. (Note: available at the Comprehensive R Archive Network (CRAN) https://cran.r-project.org/web/packages/RAM/index.html; Version 1.2.1.4 is available at the https://bitbucket.org/Wen_Chen/ram_releases.).
  • Chen, W., Redhead, S.A., Seifert, K.A., Xiong, K., Hambleton, S., and Lévesque, C.A. (2015). "Fungal pathogen surveillance using metagenomics approach requires one fungus one name.", XVIII International Plant Protection Congress (IPPC), Free University Berlin, Henry Ford Building, Berlin, Germany, August 24-27, 2015.
  • Khan, I.U.H., Topp, E., Chen, W., Lapen, D.R., Lévesque, C.A., Pintar, K.D.M., Tambong, J.T., Talbot, G., and Wilkes, G.A. (2015). "Assessment of Zoonotic Pathogens in Agroecosystem.", Biodiversity, Bioresources and Collection Science Day, Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada, December 1-2, 2015. (Presentation)
  • Lévesque, C.A., Chen, W., Hambleton, S., Seifert, K.A., Adam, Z., Bilodeau, G.J., Cullis, J., Demeke, T., Dumonceaux, T.J., Gagnon, M., Graefenhan, T., Kawchuk, L.M., Khan, I.U.H., Lewis, C.T., Li, X., Links, M.G., Mimee, B., Rott, M., Tambong, J.T., Topp, E., Yu, Q., and Yuan, K. (2015). Project CRTI 09-462RD - Next generation sequencing, direct detection and genotyping of fungi, bacteria and nematodes in the agri-food system. DRDC-RDDC-2015-C148. Final Close-Out Report. (Report)
  • Lévesque, C.A., Chen, W., Hambleton, S., Seifert, K.A., Adam, Z., Bilodeau, G.J., Cullis, J., Demeke, T., Dumonceaux, T.J., Gagnon, M., Graefenhan, T., Kawchuk, L.M., Khan, I.U.H., Lewis, C.T., Li, X., Links, M.G., Mimee, B., Rott, M., Tambong, J.T., Yu, Q., and Yuan, K. (2015). Project CRTI 09-462RD - Next generation sequencing, direct detection and genotyping of fungi, bacteria and nematodes in the agri-food system. Final Report. 54. http://cradpdf.drdc-rddc.gc.ca/PDFS/unc195/p802330_A1b.pdf. (Report)
  • Lévesque, C.A., Chen, W., Hambleton, S., Seifert, K.A., and Graefenhan, T. (2015). "Environmental Sequencing – A New Frontier for Species Identification.", The First National Science Day of the Science and Technology Branch of AAFC, Horticulture Research and Development Centre (HRDC), St-Jean-sur-Richelieu, QC, Canada, July 9, 2015. (Presentation)
  • Lowe, C., Zahariev, M., Liu, M., Hambleton, S., Seifert, K.A., Lévesque, C.A., and Chen, W. (2015). "Computational pipeline to improve detection accuracy of plant pathogens from NGS datasets using signature oligonucleotides.", American Phytopathological Society Annual Meeting, Pasadena Convention Center, Pasadena, CA, USA, August 1-5, 2015. (Poster)
  • Zahariev, M., Lévesque, C.A., and Chen, W. (2015). The Automated Oligonucleotides Design Pipeline (AODP) version 2.2.3 (https://bitbucket.org/wenchen_aafc/aodp_v2.0_release.).

2014

  • Chen, W., Lewis, C.T., Lévesque, C.A., Zhang, N., Turkington, T.K., Bamforth, J., Gaba, D., Tittlemier, S.A., MacLeod, A., and Gräfenhan, T. (2014). "454 Pyrosequencing revealed geographical distribution and ecological diversification of fungal communities on barley and malt from western Canada.", XVIth International Congress of Virology - International Union of Microbiological Societies (IUMS 2014), July 27 - August 1, 2014, Montréal, Québec, Canada, July 27-August 1, 2014.
  • Gräfenhan, T., Chen, W., Lewis, C.T., Lévesque, C.A., Zhang, N., Bamforth, J., Gaba, D., Tittlemier, S.A., MacLeod, A., and Turkington, T.K. (2014). "Composition of fungal communities on barley and malt from western Canada revealed by next generation sequencing.", 10th International Mycologists Conference, Bangkok, Thailand, August 3-8, 2014, Oral presentation, pp. 933. (Abstract)
  • Gräfenhan, T., Chen, W., Lewis, C.T., Lévesque, C.A., Zhang, N., Bamforth, J., Gaba, D., Tittlemier, S.A., MacLeod, A., and Turkington, T.K. (2014). "Composition of fungal communities on barley and malt from western Canada revealed by next generation sequencing.", 2014 North American Barley Researchers Workshop, Minneapolis, MN, USA, June 29-July 2, 2014. (Poster)
  • Gräfenhan, T., Chen, W., Lewis, C.T., Lévesque, C.A., Zhang, N., Bamforth, J., Gaba, D., Tittlemier, S.A., MacLeod, A., and Turkington, T.K. (2014). "Geographical distribution and ecological diversification of fungal communities associated with barley seeds in western Canada revealed by next generation sequencing.", 15th International Symposium on Microbial Ecology, August 24-29, 2014. (Abstract)
  • Hambleton, S., Chen, W., Chapados, J.T., Lewis, C.T., and Lévesque, C.A. (2014). "Application of NGS technology in fungal pathogen detection and challenges in identification at species level.", 10th International Mycological Conference (IMC10), Bangkok, Thailand, August 3-8, 2014, Invited oral presentation.
  • Li, X., Yuan, K., Nie, J., Adam, Z., Tambong, J.T., Chen, W., Lewis, C.T., De Boer, S.H., and Lévesque, C.A. (2014). "Comparative Genomics Approaches for Detection and Identification of Ralstonia solanacearum race 3 bv 2.", 13th International Conference of Plant Pathogenic Bacteria, Shanghai, China, June 8-13, 2014, Oral presentation. (Abstract)
  • Lowe, C., Chen, K., and Chen, W. (2014). "A Bioinformatics Pipeline for Designing Virtual DNA Arrays for Improved Species-Level Interpretation of Amplicon-Based Metagenomic Data.", 22nd Annual International Conference on Intelligent systems for Molecular Biology, Boston, MA, USA, July 11-15, 2014. (Poster)
  • Tambong, J.T., Adam, Z., Lewis, C.T., Lévesque, C.A., Chen, W., Khan, I.U.H., Bromfield, E.S.P., and Xu, R. (2014). "Comparative genomics of Pantoeastewartii subspecies and development of a TaqManReal-Time PCR assay for specific detection of P. stewartii subsp.stewartii.", 13th International Conference of Plant Pathogenic Bacteria, Shanghai, China, June 8-13, 2014, pp. 34. (Abstract)
  • Yuan, K., Li, X., Adam, Z., Tambong, J.T., Lévesque, C.A., Chen, W., Lewis, C.T., and De Boer, S.H. (2014). "Comparative genomics for re-classification of Pectobacterium wasabiae.", 3rd International Workshop on Erwinia, Shanghai, China, June 8-13, 2014, pp. 27-28. (Abstract)
  • Yuan, K., Li, X., Adam, Z., Tambong, J.T., Lévesque, C.A., Chen, W., Lewis, C.T., and De Boer, S.H. (2014). "Draft genome sequence of Pectobacterium wasabiae strain CFIA1002.", 3rd International Workshop on Erwinia, Shanghai, China, June 8-13, 2014.
  • Zhou, M., Yu, H., Yin, X., Sabour, P.M., Chen, W., and Gong, J. (2014). "Host response of Caenorhabditis elegans to enterotoxigenic Escherichia coli infection and its regulation by Lactobacillus.", 15th International symposium on microbial ecology (ISME 15), Seoul, South Korea, August 24-29, 2014.
  • Zhou, M., Zhu, J., Yu, H.H., Yin, X., Sabour, P.M., Zhao, L.H., Chen, W., and Gong, J. (2014). "Investigation into in vitro and in vivo models using intestinal epithelial IPEC-J2 cells and Caenorhabditis elegans for selecting probiotic candidates to control porcine enterotoxigenic Escherichia coli.", 9th International Symposium on lactic acid bacteria and human health, Tianjing, China, May 21-23, 2014.

2013

  • Fung, S., Rempel, H., Block, G.S., Chen, W., Janzen, T., Lewis, C.T., Zhang, N., El-Kayssi, N., Bilkhu, S., Hambleton, S., Amoako, K.K., Lévesque, C.A., Bach, S.J., Delaquis, P.J., and Diarra, M.S. (2013). "Bacillus species across Canada's agriculture environment: an ecological perspective.", International conference on Bacillus antracis, B. cereus, and B. thurengiensis, Victoria, BC, Canada, September 1-5, 2013, Abstract. (Poster)
  • Lévesque, C.A., Lewis, C.T., and Chen, W. (2013 internal). "Environmental metagenomics of oomycetes and downy mildews.", 53rd Annual Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC) of American Society for Microbiology, Denver, Colorado, USA, September 10-13, 2013, Invited oral presentation at the special session entitled "Status and Challenges in Identification and Diagnosis of Graminicolous Downy Mildews", Phytopathology 103: S2.178.
  • Lewis, C.T., Chen, W., Zhang, N., El-Kayssi, N., Fung, S., Diarra, M.S., Bilkhu, S., Hambleton, S., and Lévesque, C.A. (2013). "Developing an integrated bioinformatics platform to support real-time monitoring of agricultural environments.", 21st Annual Conference of Intelligent Systems for Molecular Biology (ISMB) and European Conference on Computational Biology (ECCB), Berlin, Germany, July 19-23, 2013.
  • Lewis, C.T., Chen, W., and Lévesque, C.A. (2013). "Developing an integrated bioinformatics platform to support real-time monitoring of agricultural environments.", 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 12th European Conference on Computational Biology (ISCB), Messe Berlin, Berlin, Germany, July 21-23, 2013.

2012

  • Chen, W., Lewis, C.T., Chapados, J.T., Hambleton, S., Seifert, K.A., Temple, K., Biernacka-Larocque, A., Robleh Djama, Z., and Lévesque, C.A. (2012). "Canada-wide spore-trapping network provides effective monitoring of microbial phytopathogens in air and rain samples.", Annual meeting of the American Phytopathological Society, Providence, RI, USA, August 4-8, 2012, In: Phytopathology 102: S4.22.
  • Lévesque, C.A., Bilkhu, S., Chapados, J.T., Chen, W., Hambleton, S., Lewis, C.T., Oliver, K., and Seifert, K.A. (2012). "AeroNet: A Canadian spore trapping network monitoring fungi and bacteria with DNA barcodes and next generation sequencing.", The Role of Genomics & Bioinformatics in Protecting Canadians from Microbial Food Safety Risks Workshop, Southway Hotel and Conference Centre, Ottawa, ON, Canada, February 21-22, 2012, Invited oral presentation.
  • Lévesque, C.A., Robideau, G.P., Chen, W., and Lewis, C.T. (2012). "Oomycete barcoding and applications.", Inoculum, 63(3), pp. 28.
  • Lewis, C.T., Chen, W., and Lévesque, C.A. (2012). "Developing a robust framework for the identification of Fungal metagenomic sequences.", 11th European Conference on Computational Biology (ECCB'12), Congress Center Basel, Basel, Switzerland, September 9-12, 2012.
  • Rintoul, T.L., Rintoul, T., Lévesque, C.A., Robideau, G.P., Eggertson, Q.A., Rodrigue, N., Chen, W., Spies, C.F.J., Bala, K., de Cock, A.W.A.M., Coffey, M.F., Hamilton, J.P., Hambleton, S., Adhikari, B., and Buell, C.R. (2012). "Molecular diagnosis, identification and phylogeny of Pythium, Phytopythium and related genera.", 4th International Workshop on Phytophthora, Pythium and Phytopythium, College Park, MD, USA, May 21-25, 2012, Invited oral presentation.
  • Seifert, K.A., Graefenhan, T., Chen, W., Lewis, C.T., Bilkhu, S., Chapados, J.T., Hambleton, S., and Lévesque, C.A. (2012). "Prospects for using quantitative PCR and metagenomics to detect mycotoxigenic fungi without culturing.", MycoRed International Conference, Carleton University, Ottawa, ON, Canada, June 2012.

2011

  • Chen, W. (2011). "Species-level interpretation of 454 pyrosequencing data.", Science Seminars on the Central Experimental Farm, AAFC, Ottawa, ON, Canada, April 14, 2011. (Presentation)
  • Chen, W., Lewis, C.T., Chapados, J.T., Bilkhu, S., Hambleton, S., Seifert, K.A., and Lévesque, C.A. (2011). "Aerobiota diversity in Canada’s air: Mining the metagenomic data.", Great Lakes - St. Lawrence Spring Workshop in Mycology, Peterborough, ON, Canada, May 7-8, 2011. (Presentation)
  • Chen, W., Robleh Djama, Z., and Lévesque, C.A. (2011). "Phytophthora under surveillance.", Science Seminars on the Central Experimental Farm, AAFC, Ottawa, ON, Canada, March 28, 2011. (Presentation)
  • Chen, W., Robleh-Djama, Z., Coffey, M.D., Martin, F.N., Sarhan, C.E., Rodríguez, C.M., Brar, A., Radmer, L., Bilodeau, G.J., Denton, G., Denton, J., Henricot, B., Waghorn, I., and Lévesque, C.A. (2011). "Phytophthora under surveillance – The development of oligonucleotide arrays from multiple gene loci for the detection of Phytophthora species.", Great Lakes - St. Lawrence Spring Workshop in Mycology, Peterborough, ON, Canada, May 7-8, 2011. (Poster)
  • Hambleton, S., Chen, W., Lewis, C.T., Bilkhu, S., Chapados, J.T., Oliver, K., Tenuta, A.U., and Lévesque, C.A. (2011). "AeroNet Canada: Profiling rust fungus diversity in spore trap samples with DNA barcoding and next generation sequencing.", North American Rust Workers Meeting (NARW), St. Paul, MN, USA, June 12, 2011. (Presentation)
  • Lévesque, C.A., Bilkhu, S., Chapados, J.T., Chen, W., Hambleton, S., Lewis, C.T., Oliver, K., and Seifert, K.A. (2011). "AeroNet: A Canadian spore trapping network monitoring fungi and bacteria with DNA barcodes and next generation sequencing.", iBOL-Canada: The future of DNA Barcoding in Canada, Beaty Biodiversity Museum, UBC, Vancouver, BC, Canada, April 29-May 1, 2011. (Presentation)
  • Lévesque, C.A., Robideau, G.P., Eggertson, Q.A., Rodrigue, N., Chen, W., Spies, C.F.J., Bala, K., de Cock, A.W.A.M., Hamilton, J., Adhikari, B., and Buell, C.R. (2011). "A case study with oomycetes on new approaches in taxonomy and ecology using next generation sequencing and comparative genomics.", The Research Horizons Seminar Series, McGill University, Macdonald Campus, Montréal, QC, Canada, October 27, 2011. (Presentation)
  • Lévesque, C.A., Robideau, G.P., Eggertson, Q.A., Rodrigue, N., Chen, W., Spies, C.F.J., de Cock, A.W.A.M., Hamilton, J., Adhikari, B., and Buell, C.R. (2011). "Comparative genomics opens up a new era for oomycete taxonomy, ecology and diagnostics.", 71th Annual Meeting Meeting of the North-East Division of the American Phytopathological Society: The Oomycetes: Current and Future Challenges, New Brunswick, NJ, USA, October 12-14, 2011.
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