NCGR Publications - 2014

Development of an alfalfa SNP array and its use to evaluate patterns of population structure and linkage disequilibrium.
Li, X., Han, Y., Wei, Y., Acharya, A., Farmer, A.D., Ho, J., Monteros, M.J., and Brummer, E.C.
(2014). PLoS ONE 9, e84329

Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L.) using sanger and next generation sequencing platforms: development and applications.
Kudapa, H., Azam, S., Sharpe, A.G., Taran, B., Li, R., Deonovic, B., Cameron, C., Farmer, A.D., Cannon, S.B., and Varshney, R.K.
(2014). PLoS ONE 9, e86039

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing.
Keeling, P.J., Burki, F., Wilcox, H.M., Allam, B., Allen, E.E., Amaral-Zettler, L.A., Armbrust, E.V., Archibald, J.M., Bharti, A.K., Bell, C.J., et al.
(2014). PLoS Biol. 12, e1001889.

Phase variation in Myxococcus xanthus yields cells specialized for iron sequestration.
Dziewanowska, K., Settles, M., Hunter, S., Linquist, I., Schilkey, F., and Hartzell
P.L. (2014). PLoS ONE 9, e95189

Molecular and biological characterization of a new isolate of guinea pig cytomegalovirus.
Schleiss MR1, McAllister S2, Armién AG3, Hernandez-Alvarado N4, Fernández-Alarcón C4, Zabeli JC5, Ramaraj T6, Crow JA7, McVoy MA8
Viruses. 2014 Jan 27;6(2):448-75. doi: 10.3390/v6020448.

A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement.
He R, Salvato F, Park JJ, Kim MJ, Nelson W, Balbuena TS, Willer M, Crow JA, May GD, Soderlund CA, Thelen JJ, Gang DR1.
BMC Plant Biol. 2014 Feb 12;14:46. doi: 10.1186/1471-2229-14-46.

Genome and Secretome analysis of the Hemibiotrophic Fungal Pathogen, Moniliophthora roreri, which causes Frosty Pod Rot Disease of Cacao:Mechanisms of the Biotrophic and Necrotrophic Phases.
Lyndel W Meinhardt, Gustavo G L Costa, Daniela PT Thomazella, Paulo J P L Teixeira, Marcelo F Carazzolle, Stephen C Schuster, John E Carlson, Mark J Guiltinan, Piotr Mieczkowski, Andrew Farmer, Thiruvarangan Ramaraj, Jayne Crozier, Robert E Davis, Jonathan Shao, Rachel L Melnick, Goncalo A G Pereira and Bryan A Bailey
BMC Genomics 2014, 15:164

Sequencing-based large-scale genomics approaches with small numbers of isolated maize meiocytes.
Stefanie Dukowic-Schulze, Anitha Sundararajan, Thiruvarangan Ramaraj, Joann Mudge, and Changbin Chen.
Frontiers in Plant Science 2014 Feb 05 5:57.

Improved hybrid genome assemblies of two Bacteroides xylanisolvens, SD CC 1b and SD CC 2a, obtained using Illumina and 454 sequencing technologies.
Thiruvarangan Ramaraj, Anitha Sundararajan, Faye D. Schilkey, Vito G. Delvecchio, Mildred Donlon, Cherie Ziemer, and Joann Mudge.
Genome announcements 2014 2 (2), e00237-14

Comparative transcriptomics of early meiosis in Arabidopsis and maize.
Dukowic-Schulze S, Harris A, Li J, Sundararajan A, Mudge J, Retzel EF, Pawlowski WP, Chen C
J Genet Genomics. 2014 Mar 20;41(3):139-52. doi: 10.1016/j.jgg.2013.11.007. Epub 2013 Dec 14.

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