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MAPKDB: A MAP kinase database for signal transduction element identification.

Alshehri HA, Alkharouf NW, Darwish O, McNeece BT, Klink VP.

Bioinformation. 2018 May 15;15(5):338-341. doi: 10.6026/97320630015338. eCollection 2019.


LUX ARRHYTHMO mediates crosstalk between the circadian clock and defense in Arabidopsis.

Zhang C, Gao M, Seitz NC, Angel W, Hallworth A, Wiratan L, Darwish O, Alkharouf N, Dawit T, Lin D, Egoshi R, Wang X, McClung CR, Lu H.

Nat Commun. 2019 Jun 11;10(1):2543. doi: 10.1038/s41467-019-10485-6.


Analysis of the genome sequence of Phomopsis longicolla: a fungal pathogen causing Phomopsis seed decay in soybean.

Li S, Darwish O, Alkharouf NW, Musungu B, Matthews BF.

BMC Genomics. 2017 Sep 5;18(1):688. doi: 10.1186/s12864-017-4075-x.


An eFP browser for visualizing strawberry fruit and flower transcriptomes.

Hawkins C, Caruana J, Li J, Zawora C, Darwish O, Wu J, Alkharouf N, Liu Z.

Hortic Res. 2017 Jun 21;4:17029. doi: 10.1038/hortres.2017.29. eCollection 2017.


A searchable database for the genome of Phomopsis longicolla (isolate MSPL 10-6).

Darwish O, Li S, May Z, Matthews B, Alkharouf NW.

Bioinformation. 2016 Jul 26;12(4):233-236. doi: 10.6026/97320630012233. eCollection 2016.


Genome-wide functional annotation of Phomopsis longicolla isolate MSPL 10-6.

Darwish O, Li S, Matthews B, Alkharouf N.

Genom Data. 2016 Apr 6;8:67-9. doi: 10.1016/j.gdata.2016.03.006. eCollection 2016 Jun.


Proteomic Investigation of Rhizoctonia solani AG 4 Identifies Secretome and Mycelial Proteins with Roles in Plant Cell Wall Degradation and Virulence.

Lakshman DK, Roberts DP, Garrett WM, Natarajan SS, Darwish O, Alkharouf N, Pain A, Khan F, Jambhulkar PP, Mitra A.

J Agric Food Chem. 2016 Apr 20;64(15):3101-10. doi: 10.1021/acs.jafc.5b05735. Epub 2016 Apr 6.


Draft genome sequence of Phomopsis longicolla isolate MSPL 10-6.

Li S, Darwish O, Alkharouf N, Matthews B, Ji P, Domier LL, Zhang N, Bluhm BH.

Genom Data. 2014 Nov 20;3:55-6. doi: 10.1016/j.gdata.2014.11.007. eCollection 2015 Mar.


Re-annotation of the woodland strawberry (Fragaria vesca) genome.

Darwish O, Shahan R, Liu Z, Slovin JP, Alkharouf NW.

BMC Genomics. 2015 Jan 27;16:29. doi: 10.1186/s12864-015-1221-1.


SoyProLow: A protein database enriched in low abundant soybean proteins.

Tavakolan M, Alkharouf NW, Matthews BF, Natarajan SS.

Bioinformation. 2014 Sep 30;10(9):599-601. doi: 10.6026/97320630010599. eCollection 2014.


SCNProDB: A database for the identification of soybean cyst nematode proteins.

Natarajan S, Tavakolan M, Alkharouf NW, Matthews BF.

Bioinformation. 2014 Jun 30;10(6):387-9. doi: 10.6026/97320630010387. eCollection 2014.


Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks.

Hollender CA, Kang C, Darwish O, Geretz A, Matthews BF, Slovin J, Alkharouf N, Liu Z.

Plant Physiol. 2014 Jul;165(3):1062-1075. Epub 2014 May 14.


SGR: an online genomic resource for the woodland strawberry.

Darwish O, Slovin JP, Kang C, Hollender CA, Geretz A, Houston S, Liu Z, Alkharouf NW.

BMC Plant Biol. 2013 Dec 23;13:223. doi: 10.1186/1471-2229-13-223.


BBGD454: A database for transcriptome analysis of blueberry using 454 sequences.

Darwish O, Rowland LJ, Alkharouf NW.

Bioinformation. 2013 Oct 16;9(17):883-6. doi: 10.6026/97320630009883. eCollection 2013.


Analysis of Phakopsora pachyrhizi transcript abundance in critical pathways at four time-points during infection of a susceptible soybean cultivar using deep sequencing.

Tremblay A, Hosseini P, Li S, Alkharouf NW, Matthews BF.

BMC Genomics. 2013 Sep 11;14:614. doi: 10.1186/1471-2164-14-614.


Genome-scale transcriptomic insights into early-stage fruit development in woodland strawberry Fragaria vesca.

Kang C, Darwish O, Geretz A, Shahan R, Alkharouf N, Liu Z.

Plant Cell. 2013 Jun;25(6):1960-78. doi: 10.1105/tpc.113.111732. Epub 2013 Jun 28.


SoyProDB: A database for the identification of soybean seed proteins.

Tavakolan M, Alkharouf NW, Khan FH, Natarajan S.

Bioinformation. 2013;9(3):165-7. doi: 10.6026/97320630009165. Epub 2013 Feb 6.


RKN Lethal DB: A database for the identification of Root Knot Nematode (Meloidogyne spp.) candidate lethal genes.

Ismail A, Matthews BF, Alkharouf NW.

Bioinformation. 2012;8(19):950-2. doi: 10.6026/97320630008950. Epub 2012 Oct 1.


Gene expression profiling of the plant pathogenic basidiomycetous fungus Rhizoctonia solani AG 4 reveals putative virulence factors.

Lakshman DK, Alkharouf N, Roberts DP, Natarajan SS, Mitra A.

Mycologia. 2012 Sep-Oct;104(5):1020-35. doi: 10.3852/11-226. Epub 2012 Jul 9.


MAPT and PAICE: Tools for time series and single time point transcriptionist visualization and knowledge discovery.

Hosseini P, Tremblay A, Matthews BF, Alkharouf NW.

Bioinformation. 2012;8(6):287-9. doi: 10.6026/97320630008287. Epub 2012 Mar 31.


Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation.

Rowland LJ, Alkharouf N, Darwish O, Ogden EL, Polashock JJ, Bassil NV, Main D.

BMC Plant Biol. 2012 Apr 2;12:46. doi: 10.1186/1471-2229-12-46.


Mapping cell fate decisions that occur during soybean defense responses.

Matsye PD, Kumar R, Hosseini P, Jones CM, Tremblay A, Alkharouf NW, Matthews BF, Klink VP.

Plant Mol Biol. 2011 Nov;77(4-5):513-28. doi: 10.1007/s11103-011-9828-3. Epub 2011 Oct 11.


Analysis of gene expression in soybean (Glycine max) roots in response to the root knot nematode Meloidogyne incognita using microarrays and KEGG pathways.

Ibrahim HM, Hosseini P, Alkharouf NW, Hussein EH, Gamal El-Din Ael K, Aly MA, Matthews BF.

BMC Genomics. 2011 May 10;12:220. doi: 10.1186/1471-2164-12-220.


Post-transcriptional gene silencing of root-knot nematode in transformed soybean roots.

Ibrahim HM, Alkharouf NW, Meyer SL, Aly MA, Gamal El-Din Ael K, Hussein EH, Matthews BF.

Exp Parasitol. 2011 Jan;127(1):90-9. doi: 10.1016/j.exppara.2010.06.037. Epub 2010 Jul 3.


An efficient annotation and gene-expression derivation tool for Illumina Solexa datasets.

Hosseini P, Tremblay A, Matthews BF, Alkharouf NW.

BMC Res Notes. 2010 Jul 2;3:183. doi: 10.1186/1756-0500-3-183.


Syncytium gene expression in Glycine max([PI 88788]) roots undergoing a resistant reaction to the parasitic nematode Heterodera glycines.

Klink VP, Hosseini P, Matsye PD, Alkharouf NW, Matthews BF.

Plant Physiol Biochem. 2010 Feb-Mar;48(2-3):176-93. doi: 10.1016/j.plaphy.2009.12.003. Epub 2010 Jan 4.


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).

Klink VP, Hosseini P, Matsye P, Alkharouf NW, Matthews BF.

Plant Mol Biol. 2009 Dec;71(6):525-67. doi: 10.1007/s11103-009-9539-1. Epub 2009 Sep 29.


The mRNA-destabilizing protein tristetraprolin is suppressed in many cancers, altering tumorigenic phenotypes and patient prognosis.

Brennan SE, Kuwano Y, Alkharouf N, Blackshear PJ, Gorospe M, Wilson GM.

Cancer Res. 2009 Jun 15;69(12):5168-76. doi: 10.1158/0008-5472.CAN-08-4238. Epub 2009 Jun 2.


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.

Klink VP, Kim KH, Martins V, Macdonald MH, Beard HS, Alkharouf NW, Lee SK, Park SC, Matthews BF.

Planta. 2009 Jun;230(1):53-71. doi: 10.1007/s00425-009-0926-2. Epub 2009 Apr 4.


Expression patterns in soybean resistant to Phakopsora pachyrhizi reveal the importance of peroxidases and lipoxygenases.

Choi JJ, Alkharouf NW, Schneider KT, Matthews BF, Frederick RD.

Funct Integr Genomics. 2008 Nov;8(4):341-59. doi: 10.1007/s10142-008-0080-0. Epub 2008 Apr 15.


A time-course comparative microarray analysis of an incompatible and compatible response by Glycine max (soybean) to Heterodera glycines (soybean cyst nematode) infection.

Klink VP, Overall CC, Alkharouf NW, MacDonald MH, Matthews BF.

Planta. 2007 Nov;226(6):1423-47. Epub 2007 Jul 25.


BBGD: an online database for blueberry genomic data.

Alkharouf NW, Dhanaraj AL, Naik D, Overall C, Matthews BF, Rowland LJ.

BMC Plant Biol. 2007 Jan 30;7:5.


Major differences observed in transcript profiles of blueberry during cold acclimation under field and cold room conditions.

Dhanaraj AL, Alkharouf NW, Beard HS, Chouikha IB, Matthews BF, Wei H, Arora R, Rowland LJ.

Planta. 2007 Feb;225(3):735-51. Epub 2006 Sep 5.


Timecourse microarray analyses reveal global changes in gene expression of susceptible Glycine max (soybean) roots during infection by Heterodera glycines (soybean cyst nematode).

Alkharouf NW, Klink VP, Chouikha IB, Beard HS, MacDonald MH, Meyer S, Knap HT, Khan R, Matthews BF.

Planta. 2006 Sep;224(4):838-52. Epub 2006 Mar 31.


Online analytical processing (OLAP): a fast and effective data mining tool for gene expression databases.

Alkharouf NW, Jamison DC, Matthews BF.

J Biomed Biotechnol. 2005 Jun 30;2005(2):181-8.


Global expression profiling identifies signatures of tumor virulence in MMTV-PyMT-transgenic mice: correlation to human disease.

Qiu TH, Chandramouli GV, Hunter KW, Alkharouf NW, Green JE, Liu ET.

Cancer Res. 2004 Sep 1;64(17):5973-81.


Microarray analysis of gene expression in soybean roots susceptible to the soybean cyst nematode two days post invasion.

Khan R, Alkharouf N, Beard H, Macdonald M, Chouikha I, Meyer S, Grefenstette J, Knap H, Matthews B.

J Nematol. 2004 Sep;36(3):241-8.


Gene expression correlating with response to paclitaxel in ovarian carcinoma xenografts.

Bani MR, Nicoletti MI, Alkharouf NW, Ghilardi C, Petersen D, Erba E, Sausville EA, Liu ET, Giavazzi R.

Mol Cancer Ther. 2004 Feb;3(2):111-21.


SGMD: the Soybean Genomics and Microarray Database.

Alkharouf NW, Matthews BF.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D398-400.


Ascaris suum: cDNA microarray analysis of 4th stage larvae (L4) during self-cure from the intestine.

Morimoto M, Zarlenga D, Beard H, Alkharouf N, Matthews BF, Urban JF Jr.

Exp Parasitol. 2003 Jul-Aug;104(3-4):113-21.


Profiling local gene expression changes associated with Eimeria maxima and Eimeria acervulina using cDNA microarray.

Min W, Lillehoj HS, Kim S, Zhu JJ, Beard H, Alkharouf N, Matthews BF.

Appl Microbiol Biotechnol. 2003 Sep;62(4):392-9. Epub 2003 Apr 24.


Characterization of mice deficient in the Src family nonreceptor tyrosine kinase Frk/rak.

Chandrasekharan S, Qiu TH, Alkharouf N, Brantley K, Mitchell JB, Liu ET.

Mol Cell Biol. 2002 Jul;22(14):5235-47.

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