2010 NCGR PUBLICATIONS

Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature 2010 Apr 29; cover [PMID: 20428171] [Abstract] Sergio E. Baranzini, Joann Mudge, Jennifer C. van Velkinburgh , Pouya Khankhanian, Irina Khrebtukova, Neil A. Miller , Lu Zhang, Andrew D. Farmer, Callum J. Bell, Ryan W. Kim, Gregory D. May, Jimmy E. Woodward , Stacy J. Caillier, Joseph P. McElroy, Refujia Gomez, Marcelo J. Pando, Leonda E. Clendenen, Elena E. Ganusova, Faye D. Schilkey, Thiruvarangan Ramaraj , Omar A. Khan, Jim J. Huntley, Shujun Luo, Pui-yan Kwok, Thomas D. Wu, Gary P. Schroth, Jorge R. Oksenberg, Stephen L. Hauser & Stephen F. Kingsmore

Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 2010 [PMID: 20148030] [Full Text] The International Brachypodium Initiative (May G.D. Participant and Co-Author) (2010) Genome sequence analysis of the model grass /Brachypodium distachyon/: Insights into grass genome evolution. /Nature/ 463, 763-768.

Genome sequence of the palaeopolyploid soybean. Nature 2010 [PMID: 20075913] [Full Text]
Jeremy Schmutz, Steven B. Cannon, Jessica Schlueter, Jianxin Ma, Therese Mitros, William Nelson, David L. Hyten, Qijian Song, Jay J. Thelen, Jianlin Cheng, Dong Xu1, Uffe Hellsten, Gregory D. May, Yeisoo Yu, Tetsuya Sakurai, Taishi Umezawa, Madan K. Bhattacharyya, Devinder Sandhu, Babu Valliyodan, Erika Lindquist, Myron Peto, David Grant, Shengqiang Shu, David Goodstein, Kerrie Barry, Montona Futrell-Griggs, Brian Abernathy, Jianchang Du, Zhixi Tian, Liucun Zhu, Navdeep Gill, Trupti Joshi, Marc Libault, Anand Sethuraman, Xue-Cheng Zhang, Kazuo Shinozaki, Henry T. Nguyen, Rod A. Wing, Perry Cregan, James Specht, Jane Grimwood, Dan Rokhsar, Gary Stacey, Randy C. Shoemaker & Scott A. Jackson

Multiplex PCR to diagnose bloodstream infections in patients admitted from the emergency department with sepsis. J Clin Microbiol. 2010 48:26-33. PMID: 19846634 [Abstract]
Tsalik EL, Jones D, Nicholson B, Waring L, Liesenfeld O, Park LP, Glickman SW, Caram LB, Langley RJ, van Velkinburgh JC, Cairns CB, Rivers EP, Otero RM, Kingsmore SF, Lalani T, Fowler VG, Woods CW.

Disease progression in hemodynamically stable patients presenting to the emergency department with sepsis. Acad Emerg Med. 2010 17:383-90. PMID: 20370777 [Abstract]
Glickman SW, Cairns CB, Otero RM, Woods CW, Tsalik EL, Langley RJ, van Velkinburgh JC, Park LP, Glickman LT, Fowler VG Jr, Kingsmore SF, Rivers EP.

Reaching the depth of the Chinese hamster ovary cell transcriptome. Biotechnol Bioeng. 2010 Apr 1;105(5):1002-9 [PMID: 19882695] [Abstract]
Jacob NM, Kantardjieff A, Yusufi FN, Retzel EF, Mulukutla BC, Chuah SH, Yap M, Hu WS.

High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence BMC Genomics 2010 Jan 15;11(1):38 [PMID: 20078886] [Full Text]
Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW, Shoemaker RC, Specht JE, Farmer AD, May GD, Cregan PB

Complete Transcriptome of the Soybean Root Hair Cell, a Single-Cell Model, and Its Alteration in Response to Bradyrhizobium japonicum Infection. Plant Physiol. 2010 Feb;152(2):541-52. Epub 2009 Nov 20. [PMID: 19933387]
Libault M, Farmer A , Brechenmacher L, Drnevich J, Langley RJ, Bilgin DD, Radwan O, Neece DJ, Clough SJ, May GD , Stacey G

CCL18 predicts intraventricular hemorrhage in very preterm infants. Ann Med. 2010 Sep;42(6):416-25. PubMed PMID: 20608885.
Kallankari H, Kaukola T, Ojaniemi M, Herva R, Perhomaa M, Vuolteenaho R, Kingsmore SF, Hallman M. Chemokine

Characterization of duplicate gene evolution in the recent natural allopolyploid /Tragopogon miscellus/ by next-generation sequencing and Sequenom iPLEX genotyping /Molecular Ecology/ 19, 132-146.
Buggs R.J.A., Chamala S., Wu W., Gao L., May G.D., Schnable P.S., Soltis D.E., Soltis P.S. and Barbazuk B.W. (2010)

Soybean root hairs: A valuable system to investigate plant biology at the cellular level. /Plant Signal Behav/. 19;5(4).
Libault M., Farmer A., Brechenmacher L., May G.D. and Stacey G. (2010)

RNA-Seq Atlas of /Glycine max/: A guide to the soybean transcriptome. /BMC Plant Biology/2010,*10:*160doi:10.1186/1471-2229-10-160.
Severin A.J., Woody J.L., Bolon Y.-T., Joseph B., Diers B.W., Farmer A.D., Muehlbauer G.J., Nelson R.T., Grant D., Specht J.E., Graham M.A., Cannon S.B., May G.D., Vance C.P. and Shoemaker R.C. (2010)

Prediction of novel miRNAs and associated target genes in /Glycine max/. /BMC Bioinformatics/ 11:S14.
Joshi T., Yan Z., Libault M., Findley S., Sherrier J., Farmer A., May G., Meyers B., Xu D. and Stacey G. (2010)

Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean. /BMC Plant Biology/ *10:*41.
Bolon Y.-T., Joseph B., Cannon S., Graham M., Diers B., Farmer A., May G.D., Muehlbauer G., Specht J., Tu Z.J., Weeks N., Xu W., Shoemaker R. and Vance C. (2010)

Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration. /BMC BioData Mining/ /BioData Mining/ 2010, *3:*3 doi:10.1186/1756-0381-3-3.
Nelson R.T., Avraham S., Shoemaker R.C., May G.D., Ware D. and Gessler D.D.G. (2010)

Rapid genome-wide SNP discovery in soybean and rice using the Illumina Genome Analyzer. /The Plant Genome/ 3:1.
Deschamps S., la Rota M., Ratashak J., Biddle P., Thureen D., Farmer A., Luck S., Beatty M., Nagasawa N., Michael L., Llaca V., Sakai, H., May G., Lightner J. and Campbell M.A. (2010)

Polyploidy did not predate the evolution of nodulation in all legumes. /PLoS One/. 2010 Jul 16;5(7):e11630.
Cannon S.B., Ilut D., Farmer A.D., Maki S.L., May G.D., Singer S.R. and Doyle J.J. (2010)

An integrated transcriptome atlas of the crop model /Glycine max/, and its use in comparative analyses in plants. /Plant J//./ 2010 Jul 1;63(1):86-99.
Libault M., Farmer A., Joshi T., Takahashi K., Langley R.J., Franklin L.D., He J., Xu D., May G. and Stacey G. (2010)

An integrative approach to genomic introgression mapping. /Plant Physiology/.
Severin, A.J., Peiffer G., Xu, W.W., Hyten D.L., Bucciarelli B., O’Rourke J.A., Grant D., Farmer A.D., May G.D., Vance C.P., Shoemaker, R.C. and Stupar R.M. (2010)

Gene expression patterns are correlated with genomic and genic structure in soybean./ Genome. (_In Press_)./
Woody J.L., Severin A.A., Bolon Y.-T., Joseph B., Diers B., Farmer A., Weeks N., Muehlbauer G., Nelson R., Grant D., Specht J., Graham M., Cannon S., May G., Vance C. and Shoemaker R. (2010)