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Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves.

Moran Lauter AN, Peiffer GA, Yin T, Whitham SA, Cook D, Shoemaker RC, Graham MA.

BMC Genomics. 2014 Aug 22;15:702. doi: 10.1186/1471-2164-15-702.


Structural brain abnormalities in patients with inflammatory illness acquired following exposure to water-damaged buildings: a volumetric MRI study using NeuroQuant®.

Shoemaker RC, House D, Ryan JC.

Neurotoxicol Teratol. 2014 Sep-Oct;45:18-26. doi: 10.1016/ Epub 2014 Jun 17.


Replication protein A subunit 3 and the iron efficiency response in soybean.

Atwood SE, O'Rourke JA, Peiffer GA, Yin T, Majumder M, Zhang C, Cianzio SR, Hill JH, Cook D, Whitham SA, Shoemaker RC, Graham MA.

Plant Cell Environ. 2014 Jan;37(1):213-34. doi: 10.1111/pce.12147. Epub 2013 Jul 22.


Genomic heterogeneity and structural variation in soybean near isogenic lines.

Stec AO, Bhaskar PB, Bolon YT, Nolan R, Shoemaker RC, Vance CP, Stupar RM.

Front Plant Sci. 2013 Apr 24;4:104. doi: 10.3389/fpls.2013.00104. eCollection 2013.


Evolutionary and comparative analyses of the soybean genome.

Cannon SB, Shoemaker RC.

Breed Sci. 2012 Jan;61(5):437-44. doi: 10.1270/jsbbs.61.437. Epub 2012 Feb 4.


Large homogeneous genome regions (isochores) in soybean [glycine max (L.) merr].

Woody JL, Beavis W, Shoemaker RC.

Front Genet. 2012 Jun 1;3:98. doi: 10.3389/fgene.2012.00098. eCollection 2012.


Integration of the Draft Sequence and Physical Map as a Framework for Genomic Research in Soybean (Glycine max (L.) Merr.) and Wild Soybean (Glycine soja Sieb. and Zucc.).

Ha J, Abernathy B, Nelson W, Grant D, Wu X, Nguyen HT, Stacey G, Yu Y, Wing RA, Shoemaker RC, Jackson SA.

G3 (Bethesda). 2012 Mar;2(3):321-9. doi: 10.1534/g3.111.001834. Epub 2012 Mar 1.


Identification of candidate genes underlying an iron efficiency quantitative trait locus in soybean.

Peiffer GA, King KE, Severin AJ, May GD, Cianzio SR, Lin SF, Lauter NC, Shoemaker RC.

Plant Physiol. 2012 Apr;158(4):1745-54. doi: 10.1104/pp.111.189860. Epub 2012 Feb 7.


Gene expression: sizing it all up.

Woody JL, Shoemaker RC.

Front Genet. 2011 Oct 17;2:70. doi: 10.3389/fgene.2011.00070. eCollection 2011.


Changes in twelve homoeologous genomic regions in soybean following three rounds of polyploidy.

Severin AJ, Cannon SB, Graham MM, Grant D, Shoemaker RC.

Plant Cell. 2011 Sep;23(9):3129-36. doi: 10.1105/tpc.111.089573. Epub 2011 Sep 13.


Gene expression patterns are correlated with genomic and genic structure in soybean.

Woody JL, Severin AJ, Bolon YT, Joseph B, Diers BW, Farmer AD, Weeks N, Muehlbauer GJ, Nelson RT, Grant D, Specht JE, Graham MA, Cannon SB, May GD, Vance CP, Shoemaker RC.

Genome. 2011 Jan;54(1):10-8. doi: 10.1139/G10-090.


There is still so much work to do.

Shoemaker RC.

Md Med. 2011;12(4):22. No abstract available.


Applying small-scale DNA signatures as an aid in assembling soybean chromosome sequences.

Peto M, Grant DM, Shoemaker RC, Cannon SB.

Adv Bioinformatics. 2010. pii: 976792. doi: 10.1155/2010/976792. Epub 2010 Aug 19.


RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome.

Severin AJ, Woody JL, Bolon YT, Joseph B, Diers BW, Farmer AD, Muehlbauer GJ, Nelson RT, Grant D, Specht JE, Graham MA, Cannon SB, May GD, Vance CP, Shoemaker RC.

BMC Plant Biol. 2010 Aug 5;10:160. doi: 10.1186/1471-2229-10-160.


Defining the neurotoxin derived illness chronic ciguatera using markers of chronic systemic inflammatory disturbances: a case/control study.

Shoemaker RC, House D, Ryan JC.

Neurotoxicol Teratol. 2010 Nov-Dec;32(6):633-9. doi: 10.1016/ Epub 2010 Jun 4.


An integrative approach to genomic introgression mapping.

Severin AJ, Peiffer GA, Xu WW, Hyten DL, Bucciarelli B, O'Rourke JA, Bolon YT, Grant D, Farmer AD, May GD, Vance CP, Shoemaker RC, Stupar RM.

Plant Physiol. 2010 Sep;154(1):3-12. doi: 10.1104/pp.110.158949. Epub 2010 Jul 23.


Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration.

Nelson RT, Avraham S, Shoemaker RC, May GD, Ware D, Gessler DD.

BioData Min. 2010 Jun 4;3(1):3. doi: 10.1186/1756-0381-3-3.


Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison.

Du J, Tian Z, Hans CS, Laten HM, Cannon SB, Jackson SA, Shoemaker RC, Ma J.

Plant J. 2010 Aug;63(4):584-98. doi: 10.1111/j.1365-313X.2010.04263.x.


Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean.

Bolon YT, Joseph B, Cannon SB, Graham MA, Diers BW, Farmer AD, May GD, Muehlbauer GJ, Specht JE, Tu ZJ, Weeks N, Xu WW, Shoemaker RC, Vance CP.

BMC Plant Biol. 2010 Mar 3;10:41. doi: 10.1186/1471-2229-10-41.


SoyTEdb: a comprehensive database of transposable elements in the soybean genome.

Du J, Grant D, Tian Z, Nelson RT, Zhu L, Shoemaker RC, Ma J.

BMC Genomics. 2010 Feb 17;11:113. doi: 10.1186/1471-2164-11-113.


Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR Swapping in soybean.

Du J, Tian Z, Bowen NJ, Schmutz J, Shoemaker RC, Ma J.

Plant Cell. 2010 Jan;22(1):48-61. doi: 10.1105/tpc.109.068775. Epub 2010 Jan 15.


High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence.

Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW, Shoemaker RC, Specht JE, Farmer AD, May GD, Cregan PB.

BMC Genomics. 2010 Jan 15;11:38. doi: 10.1186/1471-2164-11-38.


Genome sequence of the palaeopolyploid soybean.

Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA.

Nature. 2010 Jan 14;463(7278):178-83. doi: 10.1038/nature08670. Erratum in: Nature. 2010 May 6;465(7294):120.


SoyBase, the USDA-ARS soybean genetics and genomics database.

Grant D, Nelson RT, Cannon SB, Shoemaker RC.

Nucleic Acids Res. 2010 Jan;38(Database issue):D843-6. doi: 10.1093/nar/gkp798. Epub 2009 Dec 14.


Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response.

O'Rourke JA, Nelson RT, Grant D, Schmutz J, Grimwood J, Cannon S, Vance CP, Graham MA, Shoemaker RC.

BMC Genomics. 2009 Aug 13;10:376. doi: 10.1186/1471-2164-10-376.


Identification and analyses of candidate genes for rpp4-mediated resistance to Asian soybean rust in soybean.

Meyer JD, Silva DC, Yang C, Pedley KF, Zhang C, van de Mortel M, Hill JH, Shoemaker RC, Abdelnoor RV, Whitham SA, Graham MA.

Plant Physiol. 2009 May;150(1):295-307. doi: 10.1104/pp.108.134551. Epub 2009 Feb 27.


Establishment of a soybean (Glycine max Merr. L) transposon-based mutagenesis repository.

Mathieu M, Winters EK, Kong F, Wan J, Wang S, Eckert H, Luth D, Paz M, Donovan C, Zhang Z, Somers D, Wang K, Nguyen H, Shoemaker RC, Stacey G, Clemente T.

Planta. 2009 Jan;229(2):279-89. doi: 10.1007/s00425-008-0827-9. Epub 2008 Oct 15.


Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps.

Shoemaker RC, Grant D, Olson T, Warren WC, Wing R, Yu Y, Kim H, Cregan P, Joseph B, Futrell-Griggs M, Nelson W, Davito J, Walker J, Wallis J, Kremitski C, Scheer D, Clifton SW, Graves T, Nguyen H, Wu X, Luo M, Dvorak J, Nelson R, Cannon S, Tomkins J, Schmutz J, Stacey G, Jackson S.

Genome. 2008 Apr;51(4):294-302. doi: 10.1139/G08-010.


Sequence level analysis of recently duplicated regions in soybean [Glycine max (L.) Merr.] genome.

Van K, Kim DH, Cai CM, Kim MY, Shin JH, Graham MA, Shoemaker RC, Choi BS, Yang TJ, Lee SH.

DNA Res. 2008 Apr 30;15(2):93-102. doi: 10.1093/dnares/dsn001. Epub 2008 Mar 11.


Fractionation of synteny in a genomic region containing tandemly duplicated genes across glycine max, Medicago truncatula, and Arabidopsis thaliana.

Schlueter JA, Scheffler BE, Jackson S, Shoemaker RC.

J Hered. 2008 Jul-Aug;99(4):390-5. doi: 10.1093/jhered/esn010. Epub 2008 Mar 2.


High-throughput genotyping with the GoldenGate assay in the complex genome of soybean.

Hyten DL, Song Q, Choi IY, Yoon MS, Specht JE, Matukumalli LK, Nelson RL, Shoemaker RC, Young ND, Cregan PB.

Theor Appl Genet. 2008 May;116(7):945-52. doi: 10.1007/s00122-008-0726-2. Epub 2008 Feb 16.


Complement split products C3a and C4a are early markers of acute lyme disease in tick bite patients in the United States.

Shoemaker RC, Giclas PC, Crowder C, House D, Glovsky MM.

Int Arch Allergy Immunol. 2008;146(3):255-61. doi: 10.1159/000116362. Epub 2008 Feb 13.


Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines.

O'Rourke JA, Charlson DV, Gonzalez DO, Vodkin LO, Graham MA, Cianzio SR, Grusak MA, Shoemaker RC.

BMC Genomics. 2007 Dec 21;8:476.


Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing.

Schlueter JA, Lin JY, Schlueter SD, Vasylenko-Sanders IF, Deshpande S, Yi J, O'Bleness M, Roe BA, Nelson RT, Scheffler BE, Jackson SA, Shoemaker RC.

BMC Genomics. 2007 Sep 19;8:330.


Recovering from iron deficiency chlorosis in near-isogenic soybeans: a microarray study.

O'Rourke JA, Graham MA, Vodkin L, Gonzalez DO, Cianzio SR, Shoemaker RC.

Plant Physiol Biochem. 2007 May;45(5):287-92. Epub 2007 Mar 14.


Pfiesteria in estuarine waters: the question of health risks.

Shoemaker RC, Lawson W.

Environ Health Perspect. 2007 Mar;115(3):A126-7. No abstract available.


A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis.

Choi IY, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon MS, Hwang EY, Yi SI, Young ND, Shoemaker RC, van Tassell CP, Specht JE, Cregan PB.

Genetics. 2007 May;176(1):685-96. Epub 2007 Mar 4.


Highly variable patterns of linkage disequilibrium in multiple soybean populations.

Hyten DL, Choi IY, Song Q, Shoemaker RC, Nelson RL, Costa JM, Specht JE, Cregan PB.

Genetics. 2007 Apr;175(4):1937-44. Epub 2007 Feb 7.


Impacts of genetic bottlenecks on soybean genome diversity.

Hyten DL, Song Q, Zhu Y, Choi IY, Nelson RL, Costa JM, Specht JE, Shoemaker RC, Cregan PB.

Proc Natl Acad Sci U S A. 2006 Nov 7;103(45):16666-71. Epub 2006 Oct 26.


Sick building syndrome (SBS) and exposure to water-damaged buildings: time series study, clinical trial and mechanisms.

Shoemaker RC, House DE.

Neurotoxicol Teratol. 2006 Sep-Oct;28(5):573-88. Epub 2006 Aug 7.


Rigor, transparency, and disclosure needed in mold position paper.

Shoemaker RC, Ammann H, Lipsey R, Montz E.

J Allergy Clin Immunol. 2006 Sep;118(3):764-6; author reply 767-8. No abstract available.


Sequence conservation of homeologous bacterial artificial chromosomes and transcription of homeologous genes in soybean (Glycine max L. Merr.).

Schlueter JA, Scheffler BE, Schlueter SD, Shoemaker RC.

Genetics. 2006 Oct;174(2):1017-28. Epub 2006 Aug 3.


Atovaquone plus cholestyramine in patients coinfected with Babesia microti and Borrelia burgdorferi refractory to other treatment.

Shoemaker RC, Hudnell HK, House DE, Van Kempen A, Pakes GE; COL40155 Study Team.

Adv Ther. 2006 Jan-Feb;23(1):1-11.


Genome studies and molecular genetics. Part 1: Model legumes. Exploring the structure, function and evolution of legume genomes.

Young ND, Shoemaker RC.

Curr Opin Plant Biol. 2006 Apr;9(2):95-8. Epub 2006 Feb 10. No abstract available.


Paleopolyploidy and gene duplication in soybean and other legumes.

Shoemaker RC, Schlueter J, Doyle JJ.

Curr Opin Plant Biol. 2006 Apr;9(2):104-9. Epub 2006 Feb 2. Review.


Placing paleopolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families.

Pfeil BE, Schlueter JA, Shoemaker RC, Doyle JJ.

Syst Biol. 2005 Jun;54(3):441-54.


Pericentromeric regions of soybean (Glycine max L. Merr.) chromosomes consist of retroelements and tandemly repeated DNA and are structurally and evolutionarily labile.

Lin JY, Jacobus BH, SanMiguel P, Walling JG, Yuan Y, Shoemaker RC, Young ND, Jackson SA.

Genetics. 2005 Jul;170(3):1221-30. Epub 2005 May 6.


Legumes as a model plant family. Genomics for food and feed report of the Cross-Legume Advances Through Genomics Conference.

Gepts P, Beavis WD, Brummer EC, Shoemaker RC, Stalker HT, Weeden NF, Young ND.

Plant Physiol. 2005 Apr;137(4):1228-35. No abstract available.


Bridging model and crop legumes through comparative genomics.

Zhu H, Choi HK, Cook DR, Shoemaker RC.

Plant Physiol. 2005 Apr;137(4):1189-96. Review. No abstract available.

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