Nadim Alkharouf

Education

Ph.D. Computational Sciences and Informatics, George Mason University, VA. May 2004

M.S. Biological Sciences, Yarmouk University, Irbid, Jordan. August 1998

B.Sc. Biological Sciences, Yarmouk University, Irbid, Jordan. June 1996

Areas of Expertise

Bioinformatics, Analysis of high throughout experiments (next generation sequencing, Illumina and 454), Database design and development, Data mining, Web development.

Scholarly Papers | Synopsis:  Google Scholar Profile 

Selected Publications and Presentations, 2013 – present:

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Research:

Dr. Alkharouf’s area of research is computational biology\Bioinformatics. His lab works on the design and development of databases for high throughput biological experiments. His lab also works on the analysis of data from genome sequencing projects, gene expression and proteomics experiments. Dr. Alkharouf is also very interested in data mining and web development.

Example projects in his lab include building a database and analyzing gene expression data (Microarry and RNA-Seq) from experiments on soybean, dealing with the identification of resistance genes in soybean against devastating parasites and fungal infections. And working with strawberry genomic data (Illumina RNA-Seq) to elucidate the molecular function of flower and fruit development in strawberry. His lab has also assembled and re-annotated a number of genomes, the most recent was the complete re-annotation of the strawberry genome.

Service:

  • Member of the FSCM Undergraduate Research Committee (2006 – present)
  • Member of the FSCM STEM committee (2013-present)
  • Member of the MB3 Committee (2006 – present)
  • Member of the CS Curriculum Committee (2012 – present)
  • Member of the FCSM College Council Executive Committee (recording secretary) (2012-2013)
  • Member of the FCSM College Council (2010-2013)
  • Member of the CS Graduate Committee (2009 – 2014)
  • Member of a number of Faculty Hiring Committees in MB3 and AIT