Peer Review Journal Publications

  1. Li S, Darwish O, Alkharouf N, Matthews B, Ji P, Domier L, Zhang N, Bluhm B. Draft genome sequence of Phomopsis longicolla isolate MSPL 10-6. Genomics Data, Volume 3, March 2015, Pages 55-56.
  2. Darwish O, Shahan R, Liu Z, Slovin JP, Alkharouf NW. Re-annotation of the woodland strawberry (Fragaria vesca) genome. BMC Genomics. 2015 Jan 27;16:29. doi: 10.1186/s12864-015-1221-1. PubMed PMID: 25623424; PubMed Central PMCID:PMC4318131.
  3. Tavakolan M, Alkharouf NW, Matthews BF, Natarajan SS. SoyProLow: A protein database enriched in low abundant soybean proteins. Bioinformation. 2014 Sep 30;10(9):599-601. doi: 10.6026/97320630010599. eCollection 2014. PubMed PMID: 25352730; PubMed Central PMCID: PMC4209371.
  4. Natarajan S, Tavakolan M, Alkharouf NW, Matthews BF. SCNProDB: A database for the identification of soybean cyst nematode proteins. Bioinformation. 2014 Jun 30;10(6):387-9. doi: 10.6026/97320630010387. eCollection 2014. PubMed PMID:25097385; PubMed Central PMCID: PMC4110433.
  5. Hollender CA, Kang C, Darwish O, Geretz A, Matthews BF, Slovin J, Alkharouf N, Liu Z. Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks. Plant Physiol. 2014 May 14;165(3):1062-1075. [Epub ahead of print] PubMed PMID: 24828307; PubMed Central PMCID: PMC4081322.
  6. Darwish O, Slovin JP, Kang C, Hollender CA, Geretz A, Houston S, Liu Z, Alkharouf NW. SGR: an online genomic resource for the woodland strawberry. BMC Plant Biol. 2013 Dec 23;13:223. doi: 10.1186/1471-2229-13-223. PubMed PMID: 24364888; PubMed Central PMCID: PMC3878773.
  7. Darwish O, Rowland LJ, Alkharouf NW. BBGD454: A database for transcriptome analysis of blueberry using 454 sequences. Bioinformation. 2013 Oct 16;9(17):883-6. doi: 10.6026/97320630009883. eCollection 2013. PubMed PMID: 24250117; PubMed Central PMCID: PMC3819576.
  8. Tremblay A, Hosseini P, Li S, Alkharouf NW, Matthews BF. 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. 2013 Sep 11;14:614. doi: 10.1186/1471-2164-14-614. PubMed PMID: 24025037; PubMed Central PMCID: PMC3847679.
  9. Kang C, Darwish O, Geretz A, Shahan R, Alkharouf N, Liu Z. Genome-scale transcriptomic insights into early-stage fruit development in woodland strawberry Fragaria vesca. Plant Cell. 2013 Jun;25(6):1960-78. doi: 10.1105/tpc.113.111732. Epub 2013 Jun 28. PubMed PMID: 23898027; PubMed Central PMCID: PMC3723606.
  10. Tavakolan M, Alkharouf NW, Khan FH, Natarajan S. SoyProDB: A database for the identification of soybean seed proteins. Bioinformation. 2013;9(3):165-7. doi: 10.6026/97320630009165. Epub 2013 Feb 6. PubMed PMID: 23423175; PubMed Central PMCID: PMC3569605.
  11. Ismail A, Matthews BF, Alkharouf NW. RKN Lethal DB: A database for the identification of Root Knot Nematode (Meloidogyne spp.) candidate lethal genes. Bioinformation. 2012;8(19):950-2. doi: 10.6026/97320630008950. Epub 2012 Oct 1. PubMed PMID: 23144556; PubMed Central PMCID: PMC3488838.
  12. A. Tremblay, P. Hosseini, S. Li, N. W. Alkharouf and B. F. Matthews. Identification of genes expressed by Phakopsora pachyrhizi, the pathogen causing soybean rust, at a late stage of infection of susceptible soybean leaves. Plant Pathology, Volume 61, Issue 4, August 2012, Pages: 773–786.
  13. Lakshman DK, Alkharouf N, Roberts DP, Natarajan SS, Mitra A. Gene expression profiling of the plant pathogenic basidiomycetous fungus Rhizoctonia solani AG 4 reveals putative virulence factors. Mycologia. 2012 Sep-Oct;104(5):1020-35. doi: 10.3852/11-226. Epub 2012 Jul 9. PubMed PMID: 22778167.
  14. Hosseini P, Tremblay A, Matthews BF, Alkharouf NW. MAPT and PAICE: Tools for time series and single time point transcriptionist visualization and knowledge discovery. Bioinformation. 2012;8(6):287-9. Epub 2012 Mar 31. PMID:22493539.
  15. Rowland LJ, Alkharouf N, Darwish O, Ogden EL, Polashock JJ, Bassil NV, Main D. Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation. BMC Plant Biol. 2012 Apr 2;12(1):46. PMID: 22471859. Highly accessed, ranked number 1 as of May 1, 2012.
  16. Arianne Tremblay, Parsa Hosseini, Nadim W. Alkharouf, Shuxian Li, and Benjamin F. Matthews, “Gene Expression in Leaves of Susceptible Glycine max during Infection with Phakopsora pachyrhizi Using Next Generation Sequencing,” Sequencing, vol. 2011, Article ID 827250, 14 pages, 2011. doi:10.1155/2011/827250
  17. Ibrahim HM, Hosseini P, Alkharouf NW, Hussein EH, Gamal El-Din Ael K, Aly MA, Matthews BF. 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. 2011 May 10;12(1):220. PubMed PMID: 21569240.
  18. Ibrahim HM, Alkharouf NW, Meyer SL, Aly MA, Gamal El-Din Ael K, Hussein EH, Matthews BF. Post-transcriptional gene silencing of root-knot nematode in transformed soybean roots. Exp Parasitol. 2011 Jan;127(1):90-9. Epub 2010 Jul 3. PubMed PMID: 20599433.
  19. Klink VP, Hosseini P, Matsye PD, Alkharouf NW, Matthews BF. 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. 2011 Jan;75(1-2):141-65. Epub 2010 Dec 14. PubMed PMID: 21153862.
  20. Arianne Tremblay, Parsa Hosseini, Nadim W. Alkharouf, Shuxian Li, Benjamin F. Matthews, Transcriptome analysis of a compatible response by Glycine max to Phakopsora pachyrhizi infection, Plant Science, Volume 179, Issue 3, September 2010, Pages 183-193, ISSN 0168-9452, DOI: 10.1016/j.plantsci.2010.04.011.
  21. Hosseini P, Tremblay A, Matthews BF, Alkharouf NW. An efficient annotation and gene-expression derivation tool for Illumina Solexa datasets. BMC Res Notes. 2010 Jul 2;3:183. PubMed PMID: 20598141; PubMed Central PMCID: PMC2908109.
  22. Klink VP, Overall C, Alkharouf NW, MacDonald M, Matthews BF. 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). Journal of Biomedicine and Biotechnology, Volume 2010, doi:10.1155/2010/491217.
  23. Klink VP, Hosseini P, Matsye PD, Alkharouf NW and Matthews BF. 2010. Syncytium gene expression in Glycine max ([PI 88788]) roots undergoing a resistant reaction to the parasitic nematode Heterodera glycines. Plant Physiol Biochem. Feb-Mar;48(2-3):176-93. Epub 2010 Jan 4.
  24. Vincent P. Klink, Parsa Hosseini, Prachi Matsye, Nadim W. Alkharouf and Benjamin F. Matthews. 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. Dec;71(6):525-67. Epub 2009 Sep 29.
  25. Sarah E. Brennan, Yuki Kuwano, Nadim Alkharouf, Perry J. Blackshear, Myriam Gorospe and Gerald M. Wilson. 2009. The mRNA-destabilizing protein tristetraprolin is suppressed in many cancers, altering tumorigenic phenotypes and patient prognosis. Cancer Research, Jun 15; 69(12): 5168-76. Epub 2009 Jun 2.
  26. Vincent P. Klink, Kyung-Hwan Kim, Veronica Martins, Margaret H. MacDonald, Hunter S. Beard, Nadim W. Alkharouf, Soo-Chul Park, Benjamin F. Matthews. 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, Apr 4 [Epub ahead of print], DOI 10.1007/s00425-009-0926-2.
  27. Klink VP, Hosseini P, MacDonald MH, Alkharouf N, Matthews BF. 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, Mar 16;10:111, doi:10.1186/1471-2164-10-111.
  28. Choi JJ, Alkharouf NW, Schneider KT, Matthews BF, Frederick RD. 2008. Expression patterns in soybean resistant to Phakopsora pachyrhizi reveal the importance of peroxidases and lipoxygenases. Funct Integr Genomics, Nov;8(4):341-59. Epub 2008 Apr 15.
  29. Klink VP, Overall CC, Alkharouf N, MacDonald MH, Matthews BF. 2007. A comparative microarray analysis of an incompatible and compatible disease response by soybean (Glycine max) to soybean cyst nematode (Heterodera glycines) infection. Planta. Nov;226(6):1423-47.
  30. Klink VP, Overall CC, Alkharouf N, MacDonald MH, Matthews BF. 2007. Laser capture microdissection (LCM) and comparative microarray expression analysis of syncytial cells isolated from incompatible and compatible soybean roots infected by soybean cyst nematode (Heterodera glycines). Planta. Nov;226(6):1389-409.
  31. Klink VP , Martins VE , Alkharouf NW, Overall CC, MacDonald MM and Matthews BF. 2007. A decline in transcript abundance for Heterodera glycines homologs of Caenorhabditis elegans uncoordinated genes accompanies its sedentary parasitic phase. BMC Developmental Biology, 7:35, doi:10.1186/1471-213X-7-35.
  32. Alkharouf NW, Dhanaraj AL, Naik D, Overall C, Matthews BF and Rowland LJ. 2007. BBGD: An online database for blueberry genomic data. BMC Plant Biology, 7(1):5, doi:10.1186/1471-2229-7-5.
  33. Alkharouf NW, Klink VP, and BF Matthews. 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):247-58.
  34. Dhanaraj AL, Alkharouf NW, Beard HS, Chouikha IB, Matthews BF, Wei H, Arora R, and LJ Rowland. 2007. Major differences observed in transcript profiles of blueberry during cold acclimation under field and cold room conditions. Planta, 225:735–751.
  35. Alkharouf, N., V. Klink, I. Chouikha, H. Beard, M. MacDonald, S. Meyer, H. Knap, R. Khan and B.F. Matthews, 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):838-52.
  36. Klink VP, Alkharouf N, MacDonald M and Matthews BF. 2005. Laser capture microdissection (LCM) and analysis of Glycine max (soybean) syncytial cells formed by the soybean cyst nematode Heterodera glycines. Plant Molecular Biology 59: 969-983.
  37. Alkharouf, N., C. Jamison and B. F. Matthews, 2005. Online Analytical Processing (OLAP): A fast and effective data mining tool for gene expression databases. Journal of Biomedicine and Biotechnology, 30(2):181-188.
  38. Alkharouf, N. and B. F. Matthews, 2004. SGMD: The Soybean Genomics and Microarray Database. Nucleic Acids Research, 32: 1-3.
  39. Alkharouf, N., R. Khan and B. F. Matthews, 2004. EST Analysis of gene expression in roots of soybean resistant to the soybean cyst nematode. Genome, 47: 380-388.
  40. Khan, R., N. Alkharouf, H.S. Beard, M. MacDonald, I. Chouikha, S. Meyer, J. Grefenstette, H. Knap and B.F. Matthews, 2004. Resistance mechanisms in soybean: Gene expression profile at an early stage of soybean cyst nematode invasion. J. of Nematology, 36(3): 241-248.
  41.  Min, W., Lillehoj, H.S., Kim, S., Zhu, J.J., Beard, H., Alkharouf, N., and B. F. Matthews, 2003. Profiling local gene expression changes associated with Eimeria maxima and Eimeria acervulina using cDNA microarray. Appl Microbiol Biotechnol, 62: 392-399.
  42. Morimoto, M., D. Zarlenga, H. Beard, N. Alkharouf, B. F. Matthews and J. F. Urban, 2003. Ascaris suum: cDNA Microarray Analysis of 4th stage larvae (L4) during self-cure from the intestine. Experimental Parasitology, 104: 113-121.