Publications

03/08/12

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Peer Reviewed Journal Publications:

v 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.

v  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.

v 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.

v Tremblay A, Hosseini P, Alkharouf NW, Li S, Matthews BF. 2010. Transcriptome analysis of a compatible response by Glycine max to Phakopsora pachyrhiza  infection. Plant Science, Volume 179, Issue 3, September 2010, Pages 183-193.

v Ibrahim HM, Alkharouf NW, Meyer SL, Aly MA, Gamal El-Din AE, Hussein EH, Matthews BF. 2010. Post-transcriptional gene silencing of root-knot nematode in transformed soybean roots. Experimental Parasitology, Jul 3. [Epub ahead of print] PubMed PMID: 20599433.

v Hosseini P, Tremblay A, Matthews BF, Alkharouf NW. 2010. An efficient annotation and gene-expression derivation tool for Illumina Solexa datasets. BMC Research Notes, Jul 2;3(1):183.

v Klink VP, Overall C, Alkharouf NW, MacDonald M, Matthews BF. 2010. Microarray Detection Call Methodology as aMeans to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (Glycinemax) 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.

v 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.

v 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.

v 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.

v 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.

v 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.

v 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.

v 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.

v 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.

v 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.

v 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.

v 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.

v Dhanaraj AL, Alkharouf NW, Beard HS, Chouikha IB, Matthews BF, Wei H, Arora R, and LJ Rowland. 2006. Major differences observed in transcript profiles of blueberry during cold acclimation under field and cold room conditions. Planta, , 224(4):838-52.

v Alkharouf, N., V. Klink, I. Chouikha, H. Beard, M. MacDonald, S. Meyer, H. Knap, R. Khan and B.F. Matthews, 2006. Expression of soybean genes during invasion of susceptible roots by the soybean cyst nematode. Planta, 224(4):838-52.

v Klink VP, MacDonald M, Alkharouf N, 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.

v 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.

v Alkharouf, N. and B. F. Matthews, 2004. SGMD: The Soybean Genomics and Microarray Database. Nucleic Acids Research, 32: 1-3.

v 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.

v 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.

v 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.

v 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.


Conferences:

v Lisa Rowland, Nadim Alkharouf and Elizabeth Ogden. Development and Use of Genomic Tools in Blueberry Research. 18th Biennial Penn State Plant Biology Symposium, "Plant Evolutionary Genetics and Genomics". May 18-21, 2011. Poster Presentation.

v Omar Darwish, Lisa Rowland and Nadim Alkharouf. Transcriptome analysis of Blueberry using 454 EST sequencing. TU Student Research and Scholarship Expo, April 21, 2011. Poster Presentation.

v Ahmed Ismail and Nadim Alkharouf. Bioinformatics tools and analysis to identify lethal genes in Root Knot Nematode (Meloidogyne spp.). TU Student Research and Scholarship Expo, April 21, 2011. Poster Presentation. 

v Parsa Hosseini, Arianne Tremblay, Nadim Alkharouf and Benjamin Matthews. Analysis of Glycine max mRNA-Seq data upon a time-course infection with Phakospora pachyrhizi.  Twenty Seventh annual meeting of the mid-Atlantic plant molecular biology society (MAPMBS), p 30 August 12-13, 2010. Poster Presentation.  

v Nadim Alkharouf, Omar Darwish and Lisa Rowland. Transcriptome analysis of Blueberry using 454 EST sequencing. North American Blueberry Research and Extension Workers Conference, July 25-28, 2010. Poster Presentation.

v Lisa J. Rowland, Nadim Alkharouf, Nahla V. Bassil, Lee Beers, Daniel J. Bell, Emily J. Buck, Francis A. Drummond, Chad E. Finn, Julie Graham, James F. Hancock, Susan McCallum, and James W. Olmstead. Generating genomic tools for blueberry improvement. North American Blueberry Research and Extension Workers Conference, July 25-28, 2010. Talk.

vStephen Neyens and  Nadim Alkharouf. 2010. The soybean genomics and microarray database, version 3.0. The Colonial Academic Alliance (CAA) Undergraduate Research Conference, April 16-17, Richmond, VA.

vLisa J. Rowland, Nadim Alkharouf, Nahla Bassil, Daniel Bell, Emily Buck, Frank Drummond, Chad Finn, Julie Graham, and Jim Hancock. 2010. GENERATING GENOMIC TOOLS FOR BLUEBERRY IMPROVEMENT—A PROGRESS UPDATE. Plant and Animal Genome XVIII Conference, January 9-13.

vStephen Neyens, Michael Matthews, Benjamin F. Matthews  and  Nadim W. Alkharouf. 2009. THE SOYBEAN GENOMICS & MICROARRAY DATABASE, AN UPDATE. Twenty Sixth annual meeting of the mid-Atlantic plant molecular biology society (MAPMBS), p 21, August 20-21, 2009. 

vHeba M. M. Ibrahim, Nadim Alkharouf, Susan L. F. Meyer, Manar Sanad, Abd El Kader Gamal El-Din, Ebtissam Hussein and Benjamin F. Matthews. 2009. POST TRANSCRIPTIONAL GENE SILENCING OF ROOT-KNOT NEMATODE IN SOYBEAN. Twenty Sixth annual meeting of the mid-Atlantic plant molecular biology society (MAPMBS), p 22, August 20-21, 2009.

v Matthews B, Klink V, Kim K, Lee S, Park S, Alkharouf N. 2009. Broadening resistance of soybean to the soybean cyst nematode using biotechnology. Plant Biology Meeting, July 18-22.

vParsa Hosseini and Nadim Alkharouf, 2009. Reassembling the Soybean genome using next-generation Solexa sequencing, and analysis of its fluxome using flux coupling analysis – a Systems Biology approach. Towson University annual student research and expo, May 5.

vRobert Riggs and Nadim Alkharouf, 2008. dbEstUMD:  Bioinformatics Tool Automates Submission of Expressed Sequence Tags to NCBI’s dbEST Database. Biotechnology symposium, Twenty Fifth annual meeting of the mid-Atlantic plant molecular biology society (MAPMBS), p 29, August 21-22, 2008.

v Khan-Dung H. Nguyen* and Nadim Alkharouf. 2007. Identification of root knot nematode genes with high identity to those of Caenorhabditis elegans having lethal mutant or RNAi phenotypes. Twenty Fourth annual meeting of the mid-Atlantic plant molecular biology society (MAPMBS), p 40, August 16-17, 2007.

vLisa J. Rowland, Anik L. Dhanaraj, Dhananjay Naik, Nadim Alkharouf, Ben Matthews, and Rajeev Arora. 2007. Understanding Cold Tolerance in Blueberry Using EST Libraries and cDNA Microarrays. American Society for Horticultural Sciences meeting (ASHS), July 2007.

v Nguyen, K.H., and N. Alkharouf. 2007. Computational Identification of Lethal Genes in Root Knot Nematode. Fifth Annual Colonial Academic Alliance Undergraduate Research Conference, Wilmington, NC, p 20.

v Nguyen, K.H. and N. Alkharouf. 2007. Computational Identification of Lethal Genes in Root Knot Nematode. Towson University Expo, Towson, MD.

v Alkharouf, N., and B. F. Matthews, 2005. Applying Online Analytical Processing (OLAP) to Mine Gene Expression Databases. 13th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), PLOS G-7.

v Alkharouf, N, Klink VP, and Matthews BF. 2005. Identification of soybean cyst nematode lethal genes using computational methods. Mid Atlantic Plant Molecular Biology Society Meeting (MAPMBS 2005).

v Klink VP, MacDonald M, Alkharouf N, and Matthews BF. 2005. Laser capture microdissection (LCM) and gene expression analysis of cDNAs isolated from soybean syncytial cells formed by the soybean cyst nematode Heterodera glycines,  abstract 76. 22nd Annual Missouri Symposium; Genomics and Beyond:  Frontiers in Plant Biology.

v Alkharouf, N., I. Chouikha, H. Beard, M. MacDonald, and B. F. Matthews, 2004. The use of data warehousing and Online Analytical Processing (OLAP) to identify resistance genes and pathways in a resistant soybean cultivar (Peking) against the cyst nematode. MAPMBS 2004, p30.

v Dhanaraj, A. L., Alkharouf, N., H. S. Beard, I. B. Chouikha, B. F. Matthews and L. J. Rowland. 2004. Preliminary studies on microarray analysis of gene expression during cold acclimation in blueberry. MAPMBS 2004, p32.

v Klink, V. P., M. MacDonald, N. Alkharouf and B. F. Matthews, 2004. Laser capture microdissection (LCM) and expressed sequence tag analysis of the syncytium formed by the soybean cyst nematode Heterodera glycines in Glycine max (soybean). MAPMBS 2004, p29.

v Alkharouf, N., N. Alkharouf, I. Chouikha, C. Jamison, and B.F. Matthews, 2003. Effects of normalization methods on the reproducibility of Microarray data. Pacific Symposium on Biocomputing (PSB) 2003, poster session.

v Alkharouf, N. and B.F. Matthews, 2002. Recent updates to the Soybean Genomics and Microarray Database (SGMD). MAPMBS 2002, p33.

v Alkharouf, N. and B. Matthews, 2002. SGMD: An Integrated Microarray Database. MGED IV, p3.

v Alkharouf, N., I.B. Chouikha and B.F. Matthews, 2002. Analysis of DNA Microarray Data. BARC Poster day, p36.

v Matthews, B.F., R. Khan, N. Alkharouf, H. Beard, H. MacDonald and H. Knap, 2002. Microarray analysis of gene expression in soybean resistant or susceptible to soybean cyst nematode. Plant & Animal Genome IX.

v Matthews, B.F., R. Khan, N. Alkharouf, H. Beard, H. MacDonald and H. Knap, 2002.  Microarray analysis of gene expression in soybean roots attacked by the soybean cyst nematode. 10th IAPTC&B Conference.

v Alkharouf, N. and B.F. Matthews, 2001. SMGD: The Soybean Genomics and Microarray Database. MAPMBS. p32.

v Khan, R. N. Alkharouf, H. Beard, M. MacDonald, H. Knap and B. Matthews. 2001. Genomic expression profiling in soybean plants resistant or susceptible to soybean cyst nematode (SCN). Plant Biology Proceedings. p158.

v Matthews, B.F., H.S. Beard, M.H. MacDonald and N. Alkharouf, 2000. Expression of genes involved in the resistance of soybean to the soybean cyst nematode. 6th International Congress of Plant Molecular Biology. S22 – 70.

Patents:

v Wilson G, Brennan S, Alkharouf N, Kuwano Y, Blackshear P, Gorospe M. Compositions and Methods for Diagnosing and Treating Cancer. United States Patent Office, Pub No. US2010/0055705 A1. Pub date: March 4, 2010.


Invited Talks and Workshop Presentations:

v Presented a workshop titled: “Practical approaches to DNA sequencing and Bioinformatics”, from January 9-11, 2007 at Munifeya University, Sadaat City, Egypt.

v Presented a workshop titled: “Advanced molecular techniques and practical approaches to DNA analysis”, from January 14-16, 2007 at Munifeya University, Sadaat City, Egypt.

v Presented a workshop titled: “Introduction to Bioinformatics” on January 17, 2007 at Fayoum University, Fayoum, Egypt.

v Key note speaker at the fourth annual conference of Biological Sciences titled “Biological Sciences and Society: Services and Obstacles”, October 12-14, 2004, Yarmouk University, Irbid, Jordan.

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This site was last updated 01/18/12