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1

Generating Genomic Tools for Blueberry Improvement

Rowland, Lisa J., Bell, Daniel J., Alkharouf, Nadim, Bassil, Nahla V., Drummond, Francis A., Beers, Lee, Buck, Emily J., Finn, Chad E., Graham, Julie, McCallum, Susan, Hancock, James F., Polashock, Ja

Journal:

International Journal of Fruit Science

Année:

2012

Langue:

english

Fichier:

PDF, 358 KB

english, 2012

2

Mapping cell fate decisions that occur during soybean defense responses

Prachi D. Matsye, Ranjit Kumar, Parsa Hosseini, Christina M. Jones, Arianne Tremblay, Nadim W. Alkharouf, Benjamin F. Matthews, Vincent P. Klink

Journal:

Plant Molecular Biology

Année:

2011

Langue:

english

Fichier:

PDF, 2.27 MB

english, 2011

3

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

Darwish, Omar, Shahan, Rachel, Liu, Zhongchi, Slovin, Janet P, Alkharouf, Nadim W

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 1.71 MB

english, 2015

4

Genome-Scale Transcriptomic Insights into Early-Stage Fruit Development in Woodland Strawberry Fragaria vesca

Chunying Kang, Omar Darwish, Aviva Geretz, Rachel Shahan, Nadim Alkharouf and Zhongchi Liu

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 4.53 MB

english, 2013

5

An eFP browser for visualizing strawberry fruit and flower transcriptomes

Hawkins, Charles, Caruana, Julie, Li, Jiaming, Zawora, Chris, Darwish, Omar, Wu, Jun, Alkharouf, Nadim, Liu, Zhongchi

Journal:

Horticulture Research

Année:

2017

Langue:

english

Fichier:

PDF, 2.47 MB

english, 2017

6

Transcriptome analysis identifies genes related to the waxy coating on blueberry fruit in two northern-adapted rabbiteye breeding populations

Qi, Xinpeng, Ogden, Elizabeth L., Die, Jose V., Ehlenfeldt, Mark K., Polashock, James J., Darwish, Omar, Alkharouf, Nadim, Rowland, L. Jeannine

Journal:

BMC Plant Biology

Année:

2019

Langue:

english

Fichier:

PDF, 5.91 MB

english, 2019

7

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

Vincent P. Klink, Parsa Hosseini, Prachi D. Matsye, Nadim W. Alkharouf, Benjamin F. Matthews

Journal:

Plant Physiology and Biochemistry

Année:

2010

Langue:

english

Fichier:

PDF, 1.36 MB

english, 2010

8

A decline in transcript abundance forHeterodera glycineshomologs ofCaenorhabditis elegans uncoordinatedgenes accompanies its sedentary parasitic phase

Vincent P Klink, Veronica E Martins, Nadim W Alkharouf, Christopher C Overall, Margaret H MacDonald, Benjamin F Matthews

Journal:

BMC Developmental Biology

Année:

2007

Langue:

english

Fichier:

PDF, 649 KB

english, 2007

9

Analysis of Gene expression in soybean (Glycine max) roots in response to the root knot nematodeMeloidogyne incognitausing microarrays and KEGG pathways

Heba MM Ibrahim, Parsa Hosseini, Nadim W Alkharouf, Ebtissam HA Hussein, Abd El Kader Y Gamal El-Din, Mohammed AM Aly, Benjamin F Matthews

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 5.65 MB

english, 2011

10

Timecourse microarray analyses reveal global changes in gene expression of susceptibleGlycine max(soybean) roots during infection byHeterodera glycines(soybean cyst nematode)

Nadim W. Alkharouf, Vincent P. Klink, Imed B. Chouikha, Hunter S. Beard, Margaret H. MacDonald, Susan Meyer, Halina T. Knap, Rana Khan, Benjamin F. Matthews

Journal:

Année:

2006

Langue:

english

Fichier:

PDF, 793 KB

english, 2006

11

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

Anik L. Dhanaraj, Nadim W. Alkharouf, Hunter S. Beard, Imed B. Chouikha, Benjamin F. Matthews, Hui Wei, Rajeev Arora, Lisa J. Rowland

Journal:

Année:

2007

Langue:

english

Fichier:

PDF, 700 KB

english, 2007

12

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)

Vincent P. Klink, Christopher C. Overall, Nadim W. Alkharouf, Margaret H. MacDonald, Benjamin F. Matthews

Journal:

Année:

2007

Langue:

english

Fichier:

PDF, 934 KB

english, 2007

13

A time-course comparative microarray analysis of an incompatible and compatible response byGlycine max(soybean) toHeterodera glycines(soybean cyst nematode) infection

Vincent P. Klink, Christopher C. Overall, Nadim W. Alkharouf, Margaret H. MacDonald, Benjamin F. Matthews

Journal:

Année:

2007

Langue:

english

Fichier:

PDF, 1.47 MB

english, 2007

14

Laser Capture Microdissection (LCM) and Expression Analyses ofGlycine max(Soybean) Syncytium Containing Root Regions Formed by the Plant PathogenHeterodera glycines(Soybean Cyst Nematode)

Vincent P. Klink, Nadim Alkharouf, Margaret MacDonald, Benjamin Matthews

Journal:

Plant Molecular Biology

Année:

2005

Langue:

english

Fichier:

PDF, 479 KB

english, 2005

15

A gene expression analysis of syncytia laser microdissected from the roots of theGlycine max(soybean) genotype PI 548402 (Peking) undergoing a resistant reaction after infection byHeterodera glycines(soybean cyst nematode)

Vincent P. Klink, Parsa Hosseini, Prachi Matsye, Nadim W. Alkharouf, Benjamin F. Matthews

Journal:

Plant Molecular Biology

Année:

2009

Langue:

english

Fichier:

PDF, 1.06 MB

english, 2009

16

Differences in gene expression amplitude overlie a conserved transcriptomic program occurring between the rapid and potent localized resistant reaction at the syncytium of theGlycine maxgenotype Peking (PI 548402) as compared to the prolonged and potent resistant reaction of PI 88788

Vincent P. Klink, Parsa Hosseini, Prachi D. Matsye, Nadim W. Alkharouf, Benjamin F. Matthews

Journal:

Plant Molecular Biology

Année:

2011

Langue:

english

Fichier:

PDF, 1.23 MB

english, 2011

17

A correlation between host-mediated expression of parasite genes as tandem inverted repeats and abrogation of development of femaleHeterodera glycinescyst formation during infection ofGlycine max

Vincent P. Klink, Kyung-Hwan Kim, Veronica Martins, Margaret H. MacDonald, Hunter S. Beard, Nadim W. Alkharouf, Seong-Kon Lee, Soo-Chul Park, Benjamin F. Matthews

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 505 KB

english, 2009

18

Identification of Heterodera glycines (soybean cyst nematode [SCN]) cDNA sequences with high identity to those of Caenorhabditis elegans having lethal mutant or RNAi phenotypes

Nadim W. Alkharouf, Vincent P. Klink, Benjamin F. Matthews

Journal:

Experimental Parasitology

Année:

2007

Langue:

english

Fichier:

PDF, 768 KB

english, 2007

19

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

Heba M.M. Ibrahim, Nadim W. Alkharouf, Susan L.F. Meyer, Mohammed A.M. Aly, Abd El Kader Y. Gamal El-Din, Ebtissam H.A. Hussein, Benjamin F. Matthews

Journal:

Experimental Parasitology

Année:

2011

Langue:

english

Fichier:

PDF, 971 KB

english, 2011

20

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

Motoko Morimoto, Dante Zarlenga, Hunter Beard, Nadim Alkharouf, Benjamin F. Matthews, Joseph F. Urban Jr.

Journal:

Experimental Parasitology

Année:

2003

Langue:

english

Fichier:

PDF, 218 KB

english, 2003

21

Population-specific gene expression in the plant pathogenic nematodeHeterodera glycinesexists prior to infection and during the onset of a resistant or susceptible reaction in the roots of theGlycine maxgenotype Peking

Vincent P Klink, Parsa Hosseini, Margaret H MacDonald, Nadim W Alkharouf, Benjamin F Matthews

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 3.66 MB

english, 2009

22

BBGD: an online database for blueberry genomic data

Nadim W Alkharouf, Anik L Dhanaraj, Dhananjay Naik, Chris Overall, Benjamin F Matthews, Lisa J Rowland

Journal:

BMC Plant Biology

Année:

2007

Langue:

english

Fichier:

PDF, 478 KB

english, 2007

23

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

Parsa Hosseini, Arianne Tremblay, Benjamin F Matthews, Nadim W Alkharouf

Journal:

BMC Research Notes

Année:

2010

Langue:

english

Fichier:

PDF, 635 KB

english, 2010

24

Transcriptome analysis of a compatible response by Glycine max to Phakopsora pachyrhizi infection

Arianne Tremblay, Parsa Hosseini, Nadim W. Alkharouf, Shuxian Li, Benjamin F. Matthews

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 1.25 MB

english, 2010

25

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

Rowland, Lisa J, Alkharouf, Nadim, Darwish, Omar, Ogden, Elizabeth L, Polashock, James J, Bassil, Nahla V, Main, Dorrie

Journal:

BMC Plant Biology

Année:

2012

Langue:

english

Fichier:

PDF, 438 KB

english, 2012

26

SGR: an online genomic resource for the woodland strawberry

Darwish, Omar, Slovin, Janet P, Kang, Chunying, Hollender, Courtney A, Geretz, Aviva, Houston, Sam, Liu, Zhongchi, Alkharouf, Nadim W

Journal:

BMC Plant Biology

Année:

2013

Langue:

english

Fichier:

PDF, 1.13 MB

english, 2013

27

Analysis ofPhakopsora pachyrhizitranscript abundance in critical pathways at four time-points during infection of a susceptible soybean cultivar using deep sequencing

Tremblay, Arianne, Hosseini, Parsa, Li, Shuxian, Alkharouf, Nadim W, Matthews, Benjamin F

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 1.52 MB

english, 2013

28

Analysis of expressed sequence tags from roots of resistant soybean infected by the soybean cyst nematode

Alkharouf, Nadim, Khan, Rana, Matthews, Benjamin

Journal:

Année:

2004

Fichier:

PDF, 1.32 MB

2004

29

Draft genome sequence of Phomopsis longicolla isolate MSPL 10-6

Li, Shuxian, Darwish, Omar, Alkharouf, Nadim, Matthews, Benjamin, Ji, Pingsheng, Domier, Leslie L., Zhang, Ning, Bluhm, Burton H.

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 205 KB

english, 2015

30

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)

Klink, Vincent P., Overall, Christopher C., Alkharouf, Nadim W., MacDonald, Margaret H., Matthews, Benjamin F.

Journal:

Journal of Biomedicine and Biotechnology

Année:

2010

Langue:

english

Fichier:

PDF, 1.98 MB

english, 2010

31

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

Dilip K. Lakshman, Nadim Alkharouf, Daniel P. Roberts, Savithiry S. Natarajan and Amitava Mitra

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 2.23 MB

english, 2012

32

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

Lakshman, Dilip, Roberts, Daniel P., Garrett, Wesley M., Natarajan, Savithiry S., Darwish, Omar, Alkharouf, Nadim, Pain, Arnab, Khan, Farooq, Jambhulkar, Prashant P., Mitra, Amitava

Journal:

Journal of Agricultural and Food Chemistry

Année:

2016

Langue:

english

Fichier:

PDF, 3.83 MB

english, 2016

33

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

Darwish, Omar, Li, Shuxian, Matthews, Benjamin, Alkharouf, Nadim

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 745 KB

english, 2016

34

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)

Vincent P. Klink, Christopher C. Overall, Nadim W. Alkharouf, Margaret H. MacDonald and Benjamin F. Matthews

Journal:

Année:

2007

Langue:

english

Fichier:

PDF, 3.83 MB

english, 2007

35

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

Vincent P. Klink, Kyung-Hwan Kim, Veronica Martins, Margaret H. MacDonald, Hunter S. Beard, Nadim W. Alkharouf, Seong-Kon Lee, Soo-Chul Park and Benjamin F. Matthews

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 3.79 MB

english, 2009

36

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

Nadim W. Alkharouf, Vincent P. Klink, Imed B. Chouikha, Hunter S. Beard, Margaret H. MacDonald, Susan Meyer, Halina T. Knap, Rana Khan and Benjamin F. Matthews

Journal:

Année:

2006

Langue:

english

Fichier:

PDF, 3.45 MB

english, 2006

37

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

Anik L. Dhanaraj, Nadim W. Alkharouf, Hunter S. Beard, Imed B. Chouikha, Benjamin F. Matthews, Hui Wei, Rajeev Arora and Lisa J. Rowland

Journal:

Année:

2007

Langue:

english

Fichier:

PDF, 3.43 MB

english, 2007

38

[IEEE 2016 IEEE 14th International Conference on Software Engineering Research, Management and Applications (SERA) - Towson, MD, USA (2016.6.8-2016.6.10)] 2016 IEEE 14th International Conference on Software Engineering Research, Management and Applications (SERA) - Data mining of genomic data generated from soybean treated with different phytohormones

Tavakolan, Mona, Alkharouf, Nadim W

Année:

2016

Langue:

english

Fichier:

PDF, 2.00 MB

english, 2016

39

Gene Expression in Leaves of Susceptible Glycine max during Infection with Phakopsora pachyrhizi Using Next Generation Sequencing

Tremblay, Arianne, Hosseini, Parsa, Alkharouf, Nadim W., Li, Shuxian, Matthews, Benjamin F.

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 3.25 MB

english, 2011

40

Online Analytical Processing (OLAP): A Fast and Effective Data Mining Tool for Gene Expression Databases

Alkharouf, Nadim W., Jamison, D. Curtis, Matthews, Benjamin F.

Journal:

Journal of Biomedicine and Biotechnology

Année:

2005

Langue:

english

Fichier:

PDF, 1.63 MB

english, 2005

41

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

Li, Shuxian, Darwish, Omar, Alkharouf, Nadim W., Musungu, Bryan, Matthews, Benjamin F.

Journal:

Année:

2017

Langue:

english

Fichier:

PDF, 1.29 MB

english, 2017

42

SoyProLow: A protein database enriched in low abundant soybean proteins

Tavakolan, Mona, Alkharouf, Nadim W., Matthews, Benjamin F., Natarajan, Savithiry S.

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 266 KB

english, 2014

43

Transcriptome analysis identifies genes related to the waxy coating on blueberry fruit in two northern-adapted rabbiteye breeding populations

Qi, Xinpeng, Ogden, Elizabeth L., Die, Jose V., Ehlenfeldt, Mark K., Polashock, James J., Darwish, Omar, Alkharouf, Nadim, Rowland, L. Jeannine

Journal:

BMC Plant Biology

Année:

2019

Fichier:

PDF, 5.91 MB

2019

44

[IEEE 2018 International Conference on Computational Science and Computational Intelligence (CSCI) - Las Vegas, NV, USA (2018.12.12-2018.12.14)] 2018 International Conference on Computational Science and Computational Intelligence (CSCI) - Compare and Contrast of Differential Gene Expression Software Packages of RNA-Seq

Alshehri, Hamdan, Alkharouf, Nadim

Année:

2018

Langue:

english

Fichier:

PDF, 252 KB

english, 2018

45

Exocyst components promote an incompatible interaction between Glycine max (soybean) and Heterodera glycines (the soybean cyst nematode)

Sharma, Keshav, Niraula, Prakash M., Troell, Hallie A., Adhikari, Mandeep, Alshehri, Hamdan Ali, Alkharouf, Nadim W., Lawrence, Kathy S., Klink, Vincent P.

Journal:

Scientific Reports

Année:

2020

Fichier:

PDF, 3.28 MB

2020