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Benjamin F. Matthews

Education

Ph.D. in Biology, Syracuse University

Current position

Lead Scientist, Soybean Genomics and Improvement Laboratory, USDA-ARS,  Beltsville, USA
Design and genetically engineer plants for resistance to a broad range of pests and pathogens. Identify and elucidate the biochemistry and molecular biology of useful plant genes, especially those involved in disease and pest resistance, for commercialization.

Publications (since 2005)

Over 150 peer-reviewed journal articles, books, book chapters and reviews

  1. Matthews, B. F. and Youssef, R. M. (2016). Soybean cyst nematode, hetero glycines dera, infection assay using Soybean roots. Bio-protocol 6(2): e1707.
  2. Matthews, B. F. and Youssef, R. M. (2016). Agrobacterium rhizogenes-based transformation of Soybean roots to form composite plants. Bio-protocol 6(2): e1708.
  3. Alzohairy, A. M., MacDonald, M. H., Amer, R. B. M. and Matthews, B. F. (2015). Roots of Glycine max transformed with a responsive promoter to nematodes. Egypt J Genet Cytol 44:149-164.
  4. Youssef, R. M. and Matthews, B. F. (2014). Expression of Arabidopsis genes AtNPR1 and AtTGA2 in transgenic soybean roots of composite plants confers resistance to root-knot nematode (Meloidogyne incognita). International Journal of Current Biotechnology 1:15-25.
  5. Maldonado, A., MacDonald, M. H., Brewer, E., Beard, H., Youssef, R. M. and Matthews, B. F. (2014). Overexpression of four Arabidopsis thaliana NHL genes in soybean (Glycine max) roots and their effect on resistance to the soybean cyst nematode (Heterodera glycines). Physiol Mol Plant P 86:1-10
  6. Maldonado, A., MacDonald, M. H., Brewer, E., Beard, H., Youssef, R. M. and Matthews, B. F. (2014). Modification of the expression of two NPR1 suppressors SNC1 and SNI1, in soybean (Glycine max) confers partial resistance to the soybean cyst nematode (Heterodera glycines). Funct Plant Biol 14:714-726. http://dx.doi.org/10.1071/FP13323
  7. Matthews, B. F., Beard, H., Brewer, E., Kabir, S., MacDonald, M. H. and Youssef, R. M. (2014). Arabidopsis genes, AtNPR1, AtTGA2 and AtPR-5, confer partial resistance to soybean cyst nematode (Heterodera glycines) when overexpressed in transgenic soybean roots. BMC Plant Biol 14: 96.
  8. Woo, M. O., Beard, H., MacDonald, M. H., Brewer, E. P., Youssef, R. M., Kim, H. and Matthews, B. F. (2014). Manipulation of two alpha-endo-beta-1,4-glucanase genes, AtCel6 and GmCel7, reduces susceptibility to Heterodera glycines in soybean roots. Mol Plant Pathol 15(9): 927-939.
  9. Hollender, C. A., Kang, C., Darwish, O., Geretz, A., Matthews, B. F., Slovin, J., Alkharouf, N. and Liu, Z. (2014). Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks. Plant Physiol 165(3): 1062-1075.
  10. Natarajan, S., Tavakolan, M., Alkharouf, N. W. and Matthews, B. F. (2014). SCNProDB: A database for the identification of soybean cyst nematode proteins. Bioinformation 10(6): 387-389.
  11. Hosseini, P. and Matthews, B. F. (2014). Regulatory interplay between soybean root and soybean cyst nematode during a resistant and susceptible reaction. BMC Plant Biol 14: 300.
  12. Tavakolan, M., Alkharouf, N. W., Matthews, B. F. and Natarajan, S. S. (2014). SoyProLow: A protein database enriched in low abundant soybean proteins. Bioinformation 10(9): 599-601.
  13. Li, S., Darwish, O., Alkharouf, N., Matthews, B., Ji, P., Domier, L. L., Zhang, N. and Bluhm, B. H. (2014). Draft genome sequence of Phomopsis longicolla Isolate MSPL 10-6. Genomics Data 3:55-56.
  14. Tremblay, A. and Matthews, B. F. (2013). Understanding the soybean rust interaction with soybean using biotechnology. In: Berhardt, L. V. (ed). Advances in Medicine and Biology. Nova Publishers 69.
  15. Matthews, B. F., Beard, H., MacDonald, M. H., Kabir, S., Youssef, R. M., Hosseini, P. and Brewer, E. (2013). Engineered resistance and hypersusceptibility through functional metabolic studies of 100 genes in soybean to its major pathogen, the soybean cyst nematode. Planta 237(5): 1337-1357.
  16. Alzohairy, A. M., MacDonald, M. H. and Matthews, B. F. (2013). The pJAN25 vector series: An enhancement of the Gateway-compatible vector pGWB533, for broader promoter testing applications. Plasmid 69:249-256.
  17. Hosseini, P., Ovcharenko, I. and Matthews, B. F. (2013). Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites. Plant Methods 9(1): 12.
  18. Youssef, R. M., Kim, K. H., Haroon, S. A. and Matthews, B. F. (2013). Post-transcriptional gene silencing of the gene encoding aldolase from soybean cyst nematode by transformed soybean roots. Exp Parasitol 134(2): 266-274.
  19. Natarajan, S. S. and Matthews, B. F. (2012). Gene expression studies of the soybean-nematode interaction. Journal of Plant Protection Sciences 4:43-45.
  20. Prince, A. M., Matthews, B. F. and Natarajan, S. S. (2013). Transcriptome and proteome alterations during the nematode-soybean interaction. Nematropica. (Accepted)
  21. Youssef, R. M., MacDonald, M. H., Brewer, E. P., Bauchan, G. R., Kim, K. H. and Matthews, B. F. (2013). Ectopic expression of AtPAD4 broadens resistance of soybean to soybean cyst and root-knot nematodes. BMC Plant Biol 13: 67.
  22. Roberts, A., Bachman, P., Grumet, R., Heck, G., Herman, E., Hokanson, K., Layton, R., Masucci, J. and Matthews, B. (2013). Transcriptome and proteome alterations during the nematode-soybean interaction Commentary: Environmental Risk Assessment for Plants with RNAi Phenotypes. Nat Biotech.
  23. Tremblay, A., Hosseini, P., Li, S., Alkharouf, N. W. and Matthews, B. F. (2013). Analysis of Phakopsora pachyrhizi transcript abundance in critical pathways at four time-points during infection of a susceptible soybean cultivar using deep sequencing. BMC Genomics 14: 614.
  24. Chen, X., MacDonald, M. H., Khan, F., Garrett, W. M., Matthews, B. F. and Natarajan, S. S. (2013). Dynamic proteome analysis of soybean roots displaying compatible and incompatible interactions to different Heterodera glycines populations. J Proteomics 10:278-291.
  25. Tremblay, A., Hosseini, P., Li, S., Alkharouf, N. and Matthews, B. F. (2012). Identification of genes expressed by Phakopsora pachyrhizi, the pathogen causing soybean rust, at a late stage of infection of susceptible soybean leaves. Plant Pathol.
  26. Tremblay, A., Hosseini, P., Alkharouf, A., Li, S. and Matthews, B. (2012). Gene expression in leaves of susceptible Glycine max during infection with Phakopsora pachyrhizi using Next-Generation sequencing. Sequencing.
  27. Hosseini, P., Tremblay, A., Matthews, B. F. and Alkharouf, N. W. (2012). MAPT and PAICE: Tools for time series and single time point transcriptionist visualization and knowledge discovery. Bioinformation 8(6): 287-289.
  28. Matsye, P. D., Lawrence, G. W., Youssef, R. M., Kim, K. H., Lawrence, K. S., Matthews, B. F. and Klink, V. P. (2012). The expression of a naturally occurring, truncated allele of an alpha-SNAP gene suppresses plant parasitic nematode infection. Plant Mol Biol 80(2): 131-155.
  29. Ismail, A., Matthews, B. F. and Alkharouf, N. W. (2012). RKN Lethal DB; A database for the identification of root-knot nematode (Meloidogyne spp.) candidate lethal genes. Bioinformation 8:950-952.
  30. Chen, X., MacDonald, M. H., Khan, F., Garrett, W. M., Matthews, B. F. and Natarajan, S. S. (2011). Two-dimensional proteome reference maps for the soybean cyst nematode Heterodera glycines. Proteomics 11(24): 4742-4746.
  31. Natarajan, S. S. and Matthews, B. F. (2011). Proteomics: an efficient tool to analyze nematode proteins. J Plant Protection Sci 3:61-64.
  32. Ibrahim, H. M., Alkharouf, N. W., Meyer, S. L., Aly, M. A., Gamal El-Din Ael, K., Hussein, E. H. and Matthews, B. F. (2011). Post-transcriptional gene silencing of root-knot nematode in transformed soybean roots. Exp Parasitol 127(1): 90-99.
  33. Klink, V. P., Hosseini, P., Matsye, P. D., Alkharouf, N. W. and Matthews, B. F. (2011). Differences in gene expression amplitude overlie a conserved transcriptomic program occurring between the rapid and potent localized resistant reaction at the syncytium of the Glycine max genotype Peking (PI 548402) as compared to the prolonged and potent resistant reaction of PI 88788. Plant Mol Biol 75(1-2): 141-165.
  34. Ibrahim, H. M., Hosseini, P., Alkharouf, N. W., Hussein, E. H., Gamal El-Din Ael, K., Aly, M. A. and Matthews, B. F. (2011). Analysis of gene expression in soybean (Glycine max) roots in response to the root knot nematode Meloidogyne incognita using microarrays and KEGG pathways. BMC Genomics 12: 220. http://www.biomedcentral.com/1471-2164/12/220
  35. Lee, S. K., Kim, B. G., Kwon, T. R., Jeong, M. J., Park, S. R., Lee, J. W., Byun, M. O., Kwon, H. B., Matthews, B. F., Hong, C. B. and Park, S. C. (2011). Overexpression of the mitogen-activated protein kinase gene OsMAPK33 enhances sensitivity to salt stress in rice (Oryza sativa L.). J Biosci 36(1): 139-151.
  36. Matthews, B. F., Ibrahim, H. M. M. and Klink, V. P. (2011). Changes in the expression of genes in soybean roots infected by nematodes. In: Soybean. Intech.
  37. Matthews, B. F., Ibrahim, H. M. M., Hosseini, P., Alkharouf, N. and Natarajan, S. (2011). The response of soybean roots to soybean cyst nematode at the molecular level. In: The hidden half.
  38. Chen, X., MacDonald, M., Garret, W. M., Matthews, B. F. and Natarajan, S. S. (2011). Extraction and analysis of soybean cyst nematode (Heterodera glycines) proteins by two-dimensional gel electrophoresis. Nematropica 41:240-247.
  39. Matsye, P. D., Kumar, R., Hosseini, P., Jones, C. M., Tremblay, A., Alkharouf, N. W., Matthews, B. F. and Klink, V. P. (2011). Cell-type specific association mapping and gene pathway analyses of resistant reactions in Glycine max (soybean) roots reacting to infection by Heterodera glycines (soybean cyst nematode). Mapping cell fate decisions that occur during soybean defense responses. Plant Mol Biol 77: 513-528.
  40. Klink, V. P., Hosseini, P., Matsye, P., Alkharouf, N. W. and Matthews, B. F. (2010). Syncytium gene expression in Glycine max [PI88788] roots undergoing a resistant reaction to the parasitic nematode Heterodera glycines. Plant Physiol Bioch 48:176-193.
  41. Sicher, R., Bunce, J. and Matthews, B. (2010). Differing responses to carbon dioxide enrichment by a dwarf and a normal-sized soybean cultivar may depend on sink capacity. Can J Plant Sci 90:257-264.
  42. Klink, V. P., Overall, C. C., Alkharouf, N. W., Macdonald, M. H. and Matthews, B. F. (2010). Microarray Detection Call Methodology as a Means to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (Glycine max) Roots Undergoing Resistant and Susceptible Reactions to the Soybean Cyst Nematode (Heterodera glycines). J Biomed Biotechnol 2010: 491217.
  43. Tremblay, A., Hosseini, P., Alkharouf, N. W., Li, S. and Matthews, B. F. (2010). Transcriptome analysis of a compatible response by Glycine max to Phakopsora pachyrhiza infection. Plant Sci 179:183-193.
  44. Hosseini, P., Tremblay, A., Matthews, B. F. and Alkharouf, N. W. (2010). An efficient annotation and gene-expression derivation tool for Illumina Solexa datasets. BMC Res Notes 3: 183.
  45. Klink, V. P., Kim, K. H., Martins, V., Macdonald, M. H., Beard, H. S., Alkharouf, N. W., Lee, S. K., Park, S. C. and Matthews, B. F. (2009). A correlation between host-mediated expression of parasite genes as tandem inverted repeats and abrogation of development of female Heterodera glycines cyst formation during infection of Glycine max. Planta 230(1): 53-71.
  46. Klink, V. P., Hosseini, P., MacDonald, M. H., Alkharouf, N. W. and Matthews, B. F. (2009). Population-specific gene expression in the plant pathogenic nematode Heterodera glycines exists prior to infection and during the onset of a resistant or susceptible reaction in the roots of the Glycine max genotype Peking. BMC Genomics 10: 111. http://www.biomedcentral.com/1471-2164/10/111
  47. Klink, V. P. and Matthews, B. F. (2009). Emerging approaches to broaden resistance of soybean to soybean cyst nematode as supported by gene expression studies. Plant Physiol 151(3): 1017-1022.
  48. Tremblay, A. and Matthews, B. F. (2009). Laser capture microdissection, a new technique to collect specific cells. Food and Agriculture Magazine 4: 4.
  49. Klink, V. P., Hosseini, P., Matsye, P., Alkharouf, N. W. and Matthews, B. F. (2009). A gene expression analysis of syncytia laser microdissected from the roots of the Glycine max (soybean) genotype PI 548402 (Peking) undergoing a resistant reaction after infection by Heterodera glycines (soybean cyst nematode). Plant Mol Biol 71(6): 525-567.
  50. Klink, V. P. and Matthews, B. F. (2008). The use of laser capture microdissection to study the infection of Glycine max (soybean) by Heterodera glycines (soybean cyst nematode). Plant Signal Behav 3(2): 105-107.
  51. Klink, V. P., MacDonald, M. H., Martins, V. E., Park, S. C., Kim, K. H., Baek, S. H. and Matthews, B. F. (2008). MiniMax, a new diminutive Glycine max genotype with a rapid life cycle, embryonic potential and transformation capabilities. Plant Cell Tiss Org 92:183-195
  52. Choi, J. J., Alkharouf, N. W., Schneider, K. T., Matthews, B. F., Frederick, R. D. (2008). An enriched cDNA library and microarray analysis reveal expression patterns in soybean resistant to soybean rust. Functional and Integrative Genomics 8:341-351.
  53. Rashed, N. A., Macdonald, M. H. and Matthews, B. F. (2008). Protease inhibitor expression in soybean roots exhibiting susceptible and resistant interactions with soybean cyst nematode. J Nematol 40(2): 138-146.
  54. Rowland, L. J., Dhanaraj, A. L., Naik, D., Alkharouf, N., Matthews, B. and Arora, R. (2008). Study of cold tolerance in blueberry using EST libraries, cDNA microarrays, and subtractive hybridization. Hort Sci 43:1976-1981.
  55. Tremblay, A., Li, S., Scheffler, B. E. and Matthews, B. F. (2008). Laser capture microdissection (LCM) and expressed sequence tag analysis of uredinia formed by, Phakopsora pachyrhizi, the causal agent of Asian soybean rust. Physiol Mol Plant P 73:163-174.
  56. Alkharouf, N. W., Klink, V. P. and Matthews, B. F. (2007). Identification of Heterodera glycines (soybean cyst nematode [SCN]) cDNA sequences with high identity to those of Caenorhabditis elegans having lethal mutant or RNAi phenotypes. Exp Parasitol 115(3): 247-258.
  57. Dhanaraj, A. L., Alkharouf, N. W., Beard, H. S., Chouikha, I. B., Matthews, B. F., Wei, H., Arora, R. and Rowland, L. J. (2007). Major differences observed in transcript profiles of blueberry during cold acclimation under field and cold room conditions. Planta 225(3): 735-751.
  58. Alkharouf, N. W., Dhanaraj, A. L., Naik, D., Overall, C., Matthews, B. F. and Rowland, L. J. (2007). BBGD: an online database for blueberry genomic data. BMC Plant Biol 7: 5.
  59. Matthews, B. F., MacDonald, M. H., Song, Q. J., Cregan, P. B. and Lewers, K. S. (2007). Registration of “MiniMax” soybean. J Plant Reg 1:1-2.
  60. Klink, V. P., Martins, V. E., Alkharouf, N. W., Overall, C. C., MacDonald, M. H. and Matthews, B. F. (2007). A decline in transcript abundance for Heterodera glycines homologs of Caenorhabditis elegans uncoordinated genes accompanies its sedentary parasitic phase. BMC Dev Biol 7: 35.
  61. Klink, V. P., Overall, C. C. and Matthews, B. F. (2007). Developing a systems biology approach to study disease progression caused by Heterodera glycines in Glycine max. Gene Regul Syst Bio 1: 17-33.
  62. Klink, V. P., Overall, C. C., Alkharouf, N. W., MacDonald, M. H. and Matthews, B. F. (2007). A time-course comparative microarray analysis of an incompatible and compatible response by Glycine max (soybean) to Heterodera glycines (soybean cyst nematode) infection. Planta 226(6): 1423-1447.
  63. Klink, V. P., Overall, C. C., Alkharouf, N. W., MacDonald, M. H. and Matthews, B. F. (2007). Laser capture microdissection (LCM) and comparative microarray expression analysis of syncytial cells isolated from incompatible and compatible soybean (Glycine max) roots infected by the soybean cyst nematode (Heterodera glycines). Planta 226(6): 1389-1409.
  64. Alkharouf, N. W., Klink, V. P., Chouikha, I. B., Beard, H. S., MacDonald, M. H., Meyer, S., Knap, H. T., Khan, R. and Matthews, B. F. (2006). Timecourse microarray analyses reveal global changes in gene expression of susceptible Glycine max (soybean) roots during infection by Heterodera glycines (soybean cyst nematode). Planta 224(4): 838-852.
  65. Matthews, B. F., Klink, V. and Alkharouf, N. (2006). Broadening resistance of soybean to the soybean cyst nematode using biotechnology. 3rd Congreso de Soja del Mercosur: 6-9.
  66. Matthews, B. F. and Lewers, K. S. (2006). Registration of “MiniMax” soybean. & Plant Variety Protection. Plant Variety Protection.
  67. Alkharouf, N. W., Jamison, D. C. and Matthews, B. F. (2005). Online analytical processing (OLAP): a fast and effective data mining tool for gene expression databases. J Biomed Biotechnol 2005(2): 181-188.
  68. Klink, V., MacDonald, M. H. and Matthews, B. F. (2005). Laser capture microdissection(LCM) and analysis of Glycine max(soybean) syncytial cells formed by the soybean cyst nematode Heterodera glycines. Plant Mol Biol 59(6):969-983.
Protocols by Benjamin F. Matthews
  1. Soybean Cyst Nematode, Heterodera glycines, Infection Assay Using Soybean Roots
  2. Agrobacterium rhizogenes-Based Transformation of Soybean Roots to Form Composite Plants