Links, Matthew, Ph.D.

Research Scientist


Contact Information:

107 Science Place
Saskatoon, Saskatchewan S7N 0X2
Telephone: 306-385-9365
Fax: 306-385-9482
Email: matthew.links@agr.gc.ca

Areas of Expertise:

  • Research in Bioinformatics
  • Genomics
  • Metagenomics
  • Computer Science

Current Projects:

  • Development of novel computational methods for metagenomics
  • Application of high performance computing (e.g. clusters, cloud) to agricultural genomics
  • Genomics of crops and crop pests
  • Development of multi-user multi-touch collaborative tools to facilitate interdisciplinary research

Affiliations:

  • Adjunct Professor, Department of Computer Science, University of Saskatchewan

Research Publications:

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

2015

2014

2013

  • Chaban, B.L., Albert, A., Links, M.G., Gardy, J., Tang, P., and Hill, J.E. (2013). "Characterization of the Upper Respiratory Tract Microbiomes of Patients with Pandemic H1N1 Influenza.", PLoS ONE, 8(7), pp. e69559. doi : 10.1371/journal.pone.0069559
  • Lazarovits, G., Turnbull, Al., Haug, B., Links, M.G., Hill, J.E., and Hemmingsen, S.M. (2013). "Unraveling the rhizosphere using the cpn60 genomic marker and pyrosequencing.", in Frans J. de Bruijn (ed.) - Molecular Microbial Ecology of the Rhizosphere, John Wiley & Sons, Ltd, Chapter 108, pp. 1129-1136.
  • Links, M.G., Chaban, B.L., Hemmingsen, S.M., Muirhead, K., and Hill, J.E. (2013). "mPUMA: a computational approach to metagenomic analysis by de novo assembly of OTUs based on protein-coding barcode sequences.", Microbiome, 1(23). doi : 10.1186/2049-2618-1-23
  • Wagner, E.C., Mahal, D., Albert, A., Chaban, B.L., Vicol, L., Links, M.G., Hill, J.E., and Money, D.M. (2013). "Metagenomic profiling demonstrates that HIV infection is associated with increased diversity and abundance of abnormal vaginal microbiota.", 40th Annual Meeting of Infectious Diseases Society for Obstetrics and Gynecology (IDSOG), Santa Ana Pueblo, NM., USA, August 8-10, 2013.

2012

2011

  • Chaban, B.L., Links, M.G., and Hill, J.E. (2011). "Characterization of the intestinal microbiota of healthy and diarrheic pet dogs using cpn60 with and without molecular enrichment for Epsilon-proteobacteria.", International Human Microbiome Congress, Vancouver, BC, Canada, 2011.
  • Hill, J.E., Links, M.G., Chaban, B.L., Paramel, J.T., Fernando, C., Hemmingsen, S.M., Reid, G., van Schalkwyk, J., and Money, D.M. (2011). "High resolution profiling of the vaginal microbiome of healthy, reproductive aged Canadian women.", 38th Annual Scientific Meeting of the Infectious Diseases Society for Obstetrics and Gynecology, Chicago, IL, USA, 2011.
  • Links, M.G., Dumonceaux, T.J., and Hill, J.E. (2011). "cpn60, a target for metagenomic profiling of complex microbial communities.", International Human Microbiome Congress, Vancouver, BC, Canada, 2011.
  • Links, M.G., Holub, E.B., Jiang, R.H.Y., Sharpe, A.G., Hegedus, D.D., Beynon, E., Sillito, D., Clarke, W.E., Uzuhashi, S., and Borhan, M.H. (2011). "de novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes.", BMC Genomics, 12(503). doi : 10.1186/1471-2164-12-503
  • Money, D.M., Hemmingsen, S.M., Hill, J.E., Reid, G., van Schalkwyk, J., Links, M.G., Paramel, J.T., Wagner, E.C., and Bourque, D. (2011). "Metagenomic characterization of the core vaginal microbiome in healthy women using chaperonin-60 based methods.", International Human Microbiome Congress, Vancouver, BC, Canada, 2011.
  • Paramel, J.T., Links, M.G., Money, D.M., Hemmingsen, S.M., van Schalkwyk, J., and Hill, J.E. (2011). "Distribution of cpn60-defined subtypes of Gardnerella vaginalis in vaginal microbiomes of women with and without bacterial vaginosis.", International Human Microbiome Congress, Vancouver, BC, Canada, 2011.
  • Paramel, J.T., Links, M.G., Schellenberg, J.J., Hemmingsen, S.M., van Schalkwyk, J., Money, D.M., and Hill, J.E. (2011). "Identification and relevance of subtypes of Gardnerella vaginalis defined by cpn60 universal target sequencing.", Unknown.
  • Schellenberg, J.J., Links, M.G., Hill, J.E., Dumonceaux, T.J., Kimani, J., Jaoko, W., Wachihi, C., Mungai, J.N., Peters, G.A., Tyler, S., Graham, M., Severini, A., Fowke, K.R., Ball, T.B., and Plummer, F.A. (2011). "Molecular definition of vaginal microbiota in East African commercial sex workers.", Applied and Environmental Microbiology, 77(12), pp. 4066-4074. doi : 10.1128/AEM.02943-10
  • Schellenberg, J.J., Links, M.G., Hill, J.E., Hemmingsen, S.M., Peters, G.A., and Dumonceaux, T.J. (2011). "Pyrosequencing of chaperonin-60 (cpn60) amplicons as a means of determining microbial community composition.", Methods in Molecular Biology (Clifton, N.J.), 733(Part 3), pp. 143-158. doi : 10.1007/978-1-61779-089-8_10
  • Verbeke, T.J., Sparling, R., Hill, J.E., Links, M.G., Levin, D.B., and Dumonceaux, T.J. (2011). "Predicting relatedness of bacterial genomes using the chaperonin-60 universal target (cpn60 UT): application to Thermoanaerobacter species.", Systematic and Applied Microbiology, 34(3), pp. 171-179. doi : 10.1016/j.syapm.2010.11.019
  • Wang, X.W., Wang, H., Wang, J., Sun, R., Wu, J.J., Liu, S.Y., Bai, Y., Mun, J.H., Bancroft, I., Cheng, F., Huang, S.W., Li, X.X., Hua, W., Wang, J.Y., Wang, X.Y., Freeling, M., Pires, J.C., Paterson, A.H., Chalhoub, B.A., Wang, B., Hayward, A., Sharpe, A.G., Park, B.S., Weisshaar, B., Liu, B.H., Li, B., Liu, B., Tong, C., Song, C., Duran, C., Peng, C., Geng, C., Koh, C., Lin, C., Edwards, D.J., Mu, D., Shen, D., Soumpourou, E., Li, F., Fraser, F.C., Conant, G.C., Lassalle, G., King, G.J., Bonnema, G.B., Tang, H., Wang, H., Belcram, H., Zhou, H., Hirakawa, H., Abe, H., Guo, H., Wang, H., Jin, H., Parkin, I.A.P., Batley, J., Kim, J.S., Just, J., Li, J.W., Xu, J., Deng, J., Kim, J.A., Li, J., Yu, J., Meng, J., Wang, J., Min, J., Poulain, J., Hatakeyama, K., Wu, K., Wang, L., Fang, L., Trick, M., Links, M.G., and others (2011). "The genome of the mesopolyploid crop species Brassica rapa.", Nature Genetics, 43(10), pp. 1035-1040. doi : 10.1038/ng.919

2010

  • Bourque, D., Paramel, J.T., Wagner, E.C., Hemmingsen, S.M., Links, M.G., Reid, G., van Schalkwyk, J., Hill, J.E., and Money, D.M. (2010). "Preliminary characterization of core vaginal microbiome in healthy women using culture independent methods.", 37th Annual Meeting of Infectious Diseases Society for Obstetrics and Gynecology (IDSOG), Santa Fe, NM, USA, 2010.
  • Kagale, S., Links, M.G., and Rozwadowski, K. (2010). "Genome-wide analysis of Ethylene responsive element binding factor-associated Amphiphilic Repression (EAR) motif-containing transcriptional regulators in Arabidopsis.", Plant Physiology, 152(3), pp. 1109-1134. doi : 10.1104/pp.109.151704
  • Li, X.L., Westcott, N.D., Links, M.G., and Gruber, M.Y. (2010). "Seed Coat Phenolics and the Developing Silique Transcriptome of Brassica carinata.", Journal of Agricultural and Food Chemistry, 58(20), pp. 10918-10928. doi : 10.1021/jf102208a
  • Links, M.G., Dumonceaux, T.J., and Hill, J.E. (2010). "Exploiting the chaperonin-60 universal target sequence in metagenomics.", 13th International Symposium on Microbial Ecology (ISME13), Seattle, WA, USA, August 22-27, 2010.
  • Parkin, I.A.P., Bekkaoui, F., Links, M.G., Nowak, J.J., Wood, R., Gilkinson, C., and Sharpe, A.G. (2010). "Beyond Brassica rapa: facilitating Brassica research through whole genome sequencing.", Plant & Animal Genome XVIII Conference, Town & Country Convention Center, San Diego, CA, USA, January 9-13, 2010.
  • Parkin, I.A.P., Clarke, W.E., Sidebottom, C., Zhang, W., Robinson, S.J., Links, M.G., Karcz, S.R., Higgins, E.E., Fobert, P., and Sharpe, A.G. (2010). "Towards unambiguous transcript mapping in the allotetraploid Brassica napus.", Genome, 53(11), pp. 929-938. doi : 10.1139/G10-053
  • Schellenberg, J.J., Links, M.G., Dumonceaux, T.J., Hill, J.E., Kimani, J., Jaoko, W., Peters, G.A., Ball, T.B., and Plummer, F.A. (2010). "Deep sequencing chaperonin-60 universal target (cpn60 UT) to define composition and structure of vaginal microbiota and bacterial vaginosis in HIV-resistant commercial sex workers from Nairobi.", 60th Annual General Meeting of Canadian Society of Microbiologists, Hamilton, ON, Canada, 2010.

2009

  • Borhan, M.H., Links, M.G., Utermark, J., and Sharpe, A.G. (2009). "Genomic studies of Albugo candida - Arabidopsis thaliana interactions.", 14th International Congress on Molecular Plant-Microbe Interactions, Centre des congrès de Québec, Québec City, QC, Canada, July 19-23, 2009.
  • Karcz, S.R., Links, M.G., and Parkin, I.A.P. (2009). "Development of a simple method for representation of genomics features as file system objects with extended attributes.", Canadian Plant Genomics Workshop, Saskatoon, SK, Canada, 2009.
  • Links, M.G., Sharpe, A.G., Yu, F.Q., Hill, J.E., Hemmingsen, S.M., Hegedus, D.D., Lydiate, D.J., and Borhan, H. (2009). "Bioinformatic analysis of whole genome shotgun data derived from 454 sequencing of two Leptosphaeria maculans isolates.", Canadian Plant Genomics Workshop, Saskatoon, SK, Canada, 2009.
  • Robinson, S.J., Tang, L.H., Mooney, B.G., McKay, S.J., Clarke, W.E., Links, M.G., Karcz, S.R., Regan, S., Wu, Y.-Y., Gruber, M.Y., Cui, D., Yu, M., and Parkin, I.A.P. (2009). "An archived activation tagged population of Arabidopsis thaliana to facilitate forward genetics approaches.", BMC Plant Biology, 9(101). doi : 10.1186/1471-2229-9-101
  • Schellenberg, J.J., Ball, T.B., Kimani, J., Jaoko, W., Wachihi, C., Mungai, J.N., Dumonceaux, T.J., Hill, J.E., Links, M.G., and Plummer, F.A. (2009). "Defining bacterial vaginosis through in-depth culture-based and molecular characterization of the vaginal microbiome in exposed seronegative commercial sex workers from Nairobi, Kenya.", International Symposium on Natural Immunity to HIV., Winnipeg, MB, Canada, 2009.
  • Schellenberg, J.J., Links, M.G., Hill, J.E., Dumonceaux, T.J., Peters, G.A., Tyler, S., Ball, T.B., Severini, A., and Plummer, F.A. (2009). "Pyrosequencing of the chaperonin-60 (cpn60) universal target as a tool for determining the composition of microbial communities.", Applied and Environmental Microbiology, 75(9), pp. 2889-2898. doi : 10.1128/AEM.01640-08

Other Science Related Publications:

2015

  • 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)

2013

  • Town, J.R., Links, M.G., Fonstad, T.A., and Dumonceaux, T.J. (2013). "Molecular characterization of digestate identifies microorganisms that correlate to reactor performance.", CSBE/SCGAB 2013 Annual Conference, University of Saskatechewan, Saskatoon, SK, Canada, July 7-10, 2013, Presentation, No. CSBE13-128.

2010

  • Erlandson, M.A., Links, M.G., Maghodia, A.B., Donly, B.C., Hegedus, D.D., and Theilmann, D.A. (2010). "Mamestra configurata nucleopolyhedrovirus strain variation at the genome sequence level.", Society for Invertebrate Pathology Conference 2010, Trabzon, Turkey.
  • Links, M.G. (2010). "Recognizing and exploiting meta-genomic information.", Seminar Series: Veterinary Microbiology, Saskatoon, SK, Canada, 2010.

2009

  • Borhan, M.H., Links, M.G., Utermark, J., Sharpe, A.G., Beynon, E., Clarke, W.E., Jiang, R.H.Y., Hegedus, D.D., and Rimmer, S.R. (2009). "Genomic studies of Albugo candida – Arabidopsis thaliana interactions.", Molecular Plant-Microbe Interaction Workshop, Quebec City, Canada.
  • Erlandson, M.A., Links, M.G., Ethier, S., Toprak, U., Hegedus, D.D., and Theilmann, D.A. (2009). "Baculoviruses associated with Mamestra configurata (Bertha Armyworm): Role of viral enhancing factor (VEF) in the infection process.", 8th Workshop on the Molecular Biology and Genetics of the Lepidoptera, Crete, Greece.
  • Links, M.G., Sharpe, A.G., Yu, F.Q., Hill, J., Hemmingsen, S.M., Hegedus, D.D., Lydiate, D.J., and Borhan, H. (2009). "Bioinformatic analysis of whole genome shotgun data derived from 454 sequencing of two Leptosphaeria maculans isolates.", 7th Canadian Plant Genomics Workshop, Sheraton Cavalier Hotel, Saskatoon, SK, Canada, August 24-27, 2009.
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