Scott A Jackson

Scott A Jackson

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Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean.

Plant Cell 2019 Oct 22;31(10):2315-2331. Epub 2019 Aug 22.

Department of Genetics, University of Georgia, Athens, Georgia 30602

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http://dx.doi.org/10.1105/tpc.19.00255DOI Listing
October 2019

Breeding crops to feed 10 billion.

Nat Biotechnol 2019 Jul 17;37(7):744-754. Epub 2019 Jun 17.

John Innes Centre, Norwich Research Park, Norwich, UK.

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http://dx.doi.org/10.1038/s41587-019-0152-9DOI Listing
July 2019

Heterochromatin evolution in Arachis investigated through genome-wide analysis of repetitive DNA.

Planta 2019 May 24;249(5):1405-1415. Epub 2019 Jan 24.

Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (UNNE-CONICET), Corrientes, Argentina.

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http://dx.doi.org/10.1007/s00425-019-03096-4DOI Listing
May 2019

Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution.

Genes (Basel) 2019 04 1;10(4). Epub 2019 Apr 1.

Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.

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http://dx.doi.org/10.3390/genes10040259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6523792PMC
April 2019

Machine learning and complex biological data.

Genome Biol 2019 04 16;20(1):76. Epub 2019 Apr 16.

Center for Applied Genetic Technologies, Institute for Plant Breeding, Genetics and Genomics, The University of Georgia, 111 Riverbend Rd, Athens, GA, 30602, USA.

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-019-1689-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469083PMC
April 2019

Improving End-User Trust in the Quality of Commercial Probiotic Products.

Front Microbiol 2019 17;10:739. Epub 2019 Apr 17.

International Scientific Association for Probiotics and Prebiotics, Sacramento, CA, United States.

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http://dx.doi.org/10.3389/fmicb.2019.00739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499161PMC
April 2019

Draft Genome Sequences of 72 Isolates from All Four Species of .

Microbiol Resour Announc 2018 Nov 29;7(21). Epub 2018 Nov 29.

Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA.

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http://dx.doi.org/10.1128/MRA.01399-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6284731PMC
November 2018

Parallel selection on a dormancy gene during domestication of crops from multiple families.

Nat Genet 2018 10 24;50(10):1435-1441. Epub 2018 Sep 24.

State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.

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http://dx.doi.org/10.1038/s41588-018-0229-2DOI Listing
October 2018

Genetic and epigenetic divergence of duplicate genes in two legume species.

Plant Cell Environ 2018 09 4;41(9):2033-2044. Epub 2018 Mar 4.

Center for Applied Genetic Technologies, University of Georgia, Athens, 30602, GA, USA.

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http://dx.doi.org/10.1111/pce.13127DOI Listing
September 2018

Segmental allopolyploidy in action: Increasing diversity through polyploid hybridization and homoeologous recombination.

Am J Bot 2018 06 9;105(6):1053-1066. Epub 2018 Jul 9.

University of Georgia, Center for Applied Genetic Technologies, 111 Riverbend Road, Athens, GA, 30602-6810, USA.

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http://dx.doi.org/10.1002/ajb2.1112DOI Listing
June 2018

Genomic and epigenomic immunity in common bean: the unusual features of NB-LRR gene family.

DNA Res 2018 Apr;25(2):161-172

Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France.

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http://dx.doi.org/10.1093/dnares/dsx046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909424PMC
April 2018

Genic C-Methylation in Soybean Is Associated with Gene Paralogs Relocated to Transposable Element-Rich Pericentromeres.

Mol Plant 2018 03 21;11(3):485-495. Epub 2018 Feb 21.

Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S16742052183005
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http://dx.doi.org/10.1016/j.molp.2018.02.006DOI Listing
March 2018

Epigenomics: dissecting hybridization and polyploidization.

Authors:
Scott A Jackson

Genome Biol 2017 06 19;18(1):117. Epub 2017 Jun 19.

Center for Applied Genetic Technologies, University of Georgia, Riverbend Drive, Athens, GA, 30602, USA.

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http://dx.doi.org/10.1186/s13059-017-1254-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5474866PMC
June 2017

Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs.

New Phytol 2017 Apr 20;214(2):808-819. Epub 2017 Jan 20.

Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.

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http://dx.doi.org/10.1111/nph.14421DOI Listing
April 2017

Performing Skin Microbiome Research: A Method to the Madness.

J Invest Dermatol 2017 03 4;137(3):561-568. Epub 2017 Jan 4.

Institute of Environmental Medicine, UNIKA-T, Technical University of Munich and Helmholtz Zentrum München-German Research Center for Environmental Health, Augsburg, Germany; Christine Kühne Center for Allergy Research and Education, Davos, Switzerland.

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http://dx.doi.org/10.1016/j.jid.2016.10.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5468751PMC
March 2017

Rice: The First Crop Genome.

Authors:
Scott A Jackson

Rice (N Y) 2016 Dec 22;9(1):14. Epub 2016 Mar 22.

Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30621, USA.

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http://thericejournal.springeropen.com/articles/10.1186/s122
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http://dx.doi.org/10.1186/s12284-016-0087-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4803718PMC
December 2016

Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris).

G3 (Bethesda) 2016 07 7;6(7):2091-101. Epub 2016 Jul 7.

Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602

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http://dx.doi.org/10.1534/g3.116.028761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4938662PMC
July 2016

FDA Escherichia coli Identification (FDA-ECID) Microarray: a Pangenome Molecular Toolbox for Serotyping, Virulence Profiling, Molecular Epidemiology, and Phylogeny.

Appl Environ Microbiol 2016 06 16;82(11):3384-3394. Epub 2016 May 16.

Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA

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http://dx.doi.org/10.1128/AEM.04077-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959244PMC
June 2016

Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis.

Chromosome Res 2016 05 12;24(2):197-216. Epub 2016 Jan 12.

Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.

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http://dx.doi.org/10.1007/s10577-015-9515-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856725PMC
May 2016

Crowdsourcing the nodulation gene network discovery environment.

BMC Bioinformatics 2016 May 26;17(1):223. Epub 2016 May 26.

Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, 30602, GA, USA.

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http://dx.doi.org/10.1186/s12859-016-1089-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4880984PMC
May 2016

PEPR: pipelines for evaluating prokaryotic references.

Anal Bioanal Chem 2016 Apr 2;408(11):2975-83. Epub 2016 Mar 2.

Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.

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http://dx.doi.org/10.1007/s00216-015-9299-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4819933PMC
April 2016

Evolution of plant genome architecture.

Genome Biol 2016 Mar 1;17:37. Epub 2016 Mar 1.

Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, Tucson, AZ, 85750, USA.

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http://dx.doi.org/10.1186/s13059-016-0908-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772531PMC
March 2016

Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes.

Genome Biol 2016 Jan 18;17. Epub 2016 Jan 18.

Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.

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http://dx.doi.org/10.1186/s13059-015-0867-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717578PMC
January 2016

Gene Networks in Plant Biology: Approaches in Reconstruction and Analysis.

Trends Plant Sci 2015 Oct;20(10):664-675

Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602; Institute of Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Road, Athens, GA 30602. Electronic address:

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http://dx.doi.org/10.1016/j.tplants.2015.06.013DOI Listing
October 2015

A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean.

Plant Physiol 2015 Aug 6;168(4):1433-47. Epub 2015 Jul 6.

Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602 (K.D.K., M.E.B., B.A., A.I.-O., C.C., M.G., S.A.J.);Department of Microbiology and Plant Biology, University of Oklahoma, Noman, Oklahoma 73019 (M.L.); andHudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806 (J.G.)

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http://www.plantphysiol.org/content/168/4/1433.full.pdf
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http://www.plantphysiol.org/lookup/doi/10.1104/pp.15.00408
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http://dx.doi.org/10.1104/pp.15.00408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528746PMC
August 2015

A new approach for annotation of transposable elements using small RNA mapping.

Nucleic Acids Res 2015 Jul 26;43(13):e84. Epub 2015 Mar 26.

Center for Applied Genetic Technologies. University of Georgia, 111, Riverbend Dr., Athens, GA 30602, USA

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http://dx.doi.org/10.1093/nar/gkv257DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4513842PMC
July 2015

Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations.

Mol Plant 2015 Jun 10;8(6):831-46. Epub 2015 Feb 10.

Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molp.2015.02.002DOI Listing
June 2015

Transposons play an important role in the evolution and diversification of centromeres among closely related species.

Front Plant Sci 2015 7;6:216. Epub 2015 Apr 7.

Center for Applied Genetic Technologies, University of Georgia Athens, GA, USA.

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http://dx.doi.org/10.3389/fpls.2015.00216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4387472PMC
April 2015

Gene Network Reconstruction by Integration of Prior Biological Knowledge.

G3 (Bethesda) 2015 Mar 30;5(6):1075-9. Epub 2015 Mar 30.

Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia

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http://dx.doi.org/10.1534/g3.115.018127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4478538PMC
March 2015

Transcriptomic changes due to water deficit define a general soybean response and accession-specific pathways for drought avoidance.

BMC Plant Biol 2015 Feb 3;15:26. Epub 2015 Feb 3.

Center for Applied Genetic Technologies & Department of Crop and Soil Science, University of Georgia, Athens, GA, 30602, USA.

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http://www.biomedcentral.com/1471-2229/15/26
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http://dx.doi.org/10.1186/s12870-015-0422-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4322458PMC
February 2015

The soybean (Glycine max) nodulation-suppressive CLE peptide, GmRIC1, functions interspecifically in common white bean (Phaseolus vulgaris), but not in a supernodulating line mutated in the receptor PvNARK.

Plant Biotechnol J 2014 Oct 12;12(8):1085-97. Epub 2014 Jul 12.

Centre for Integrative Legume Research, School of Agricultural and Food Sciences, The University of Queensland, St. Lucia, Brisbane, Qld, Australia.

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http://dx.doi.org/10.1111/pbi.12216DOI Listing
October 2014

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.

Nat Biotechnol 2014 Oct 14;32(10):1045-52. Epub 2014 Sep 14.

1] The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [2] Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China. [3] Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.

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http://dx.doi.org/10.1038/nbt.2979DOI Listing
October 2014

Accessing epigenetic variation in the plant methylome.

Brief Funct Genomics 2014 Jul 20;13(4):318-27. Epub 2014 Feb 20.

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http://dx.doi.org/10.1093/bfgp/elu003DOI Listing
July 2014

Fine mapping of Co-x, an anthracnose resistance gene to a highly virulent strain of Colletotrichum lindemuthianum in common bean.

Theor Appl Genet 2014 Jul 25;127(7):1653-66. Epub 2014 May 25.

CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), Rue Noetzlin, 91405, Orsay, France.

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http://dx.doi.org/10.1007/s00122-014-2328-5DOI Listing
July 2014

Annotation and sequence diversity of transposable elements in common bean (Phaseolus vulgaris).

Front Plant Sci 2014 11;5:339. Epub 2014 Jul 11.

Center for Applied Genetic Technologies, University of Georgia Athens, GA, USA.

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http://dx.doi.org/10.3389/fpls.2014.00339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4093653PMC
July 2014

Widespread and frequent horizontal transfers of transposable elements in plants.

Genome Res 2014 May 11;24(5):831-8. Epub 2014 Feb 11.

Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096 CNRS/UPVD, 66860 Perpignan Cedex, France;

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http://dx.doi.org/10.1101/gr.164400.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009612PMC
May 2014

Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean.

Plant Cell 2014 May 21;26(5):1901-1912. Epub 2014 May 21.

Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy Consiglio per la Ricerca e Sperimentazione in Agricoltura, Cereal Research Centre (CRA-CER), 71122 Foggia, Italy

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http://dx.doi.org/10.1105/tpc.114.124040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079357PMC
May 2014

Drivers and dynamics of diversity in plant genomes.

New Phytol 2014 Apr;202(1):15-8

Université de Perpignan, UMR 5096 CNRS - IRD - UPVD, Perpignan, France.

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http://dx.doi.org/10.1111/nph.12633DOI Listing
April 2014

Concerted evolution of D1 and D2 to regulate chlorophyll degradation in soybean.

Plant J 2014 Mar 4;77(5):700-12. Epub 2014 Feb 4.

State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100039, China.

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http://dx.doi.org/10.1111/tpj.12419DOI Listing
March 2014

Identification and characterization of functional centromeres of the common bean.

Plant J 2013 Oct 5;76(1):47-60. Epub 2013 Aug 5.

Center for Applied Genetic Technologies and Institute for Plant Breeding Genetics, and Genomics, University of Georgia, Athens, GA, 30602, USA.

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http://dx.doi.org/10.1111/tpj.12269DOI Listing
October 2013

A platform for soybean molecular breeding: the utilization of core collections for food security.

Plant Mol Biol 2013 Sep 25;83(1-2):41-50. Epub 2013 May 25.

The National Key Facility for Crop Gene Resources and Genetic Improvement NFCRI, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

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http://dx.doi.org/10.1007/s11103-013-0076-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3755216PMC
September 2013

A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar.

Front Plant Sci 2013 25;4:210. Epub 2013 Jun 25.

Plant Science Research Unit, USDA-Agricultural Research Service St. Paul, MN, USA ; Department of Agronomy and Plant Genetics, University of Minnesota St. Paul, MN, USA.

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http://dx.doi.org/10.3389/fpls.2013.00210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691542PMC
June 2013

Functional and structural divergence of an unusual LTR retrotransposon family in plants.

PLoS One 2012 31;7(10):e48595. Epub 2012 Oct 31.

Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048595PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3485330PMC
May 2013

The fate of duplicated genes in a polyploid plant genome.

Plant J 2013 Jan 22;73(1):143-53. Epub 2012 Oct 22.

Institute for Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.

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http://dx.doi.org/10.1111/tpj.12026DOI Listing
January 2013

Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view.

Mol Ecol 2012 Sep 30;21(18):4593-604. Epub 2012 May 30.

Department of Biology, Washington University, St. Louis, MO 63130, USA.

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http://dx.doi.org/10.1111/j.1365-294X.2012.05625.xDOI Listing
September 2012

High density microarray analysis reveals new insights into genetic footprints of Listeria monocytogenes strains involved in listeriosis outbreaks.

PLoS One 2012 21;7(3):e32896. Epub 2012 Mar 21.

Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032896PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310058PMC
August 2012

Rapid genomic-scale analysis of Escherichia coli O104:H4 by using high-resolution alternative methods to next-generation sequencing.

Appl Environ Microbiol 2012 Mar 30;78(5):1601-5. Epub 2011 Dec 30.

Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, Laurel, MD, USA.

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http://aem.asm.org/lookup/doi/10.1128/AEM.07464-11
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http://dx.doi.org/10.1128/AEM.07464-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3294476PMC
March 2012

Current state-of-art of sequencing technologies for plant genomics research.

Brief Funct Genomics 2012 Jan;11(1):3-11

Centre of Excellence in Genomics, ICRISAT, Patancheru 502 324, Greater Hyderabad, India.

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http://dx.doi.org/10.1093/bfgp/elr045DOI Listing
January 2012

Sequencing crop genomes: approaches and applications.

New Phytol 2011 Sep 27;191(4):915-25. Epub 2011 Jun 27.

Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1111/j.1469-8137.2011.03804.xDOI Listing
September 2011

Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies.

BMC Genomics 2011 Jul 6;12:349. Epub 2011 Jul 6.

Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland 20708, USA.

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http://dx.doi.org/10.1186/1471-2164-12-349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146454PMC
July 2011

Integration of physical and genetic maps of common bean through BAC-derived microsatellite markers.

BMC Genomics 2010 Jul 16;11:436. Epub 2010 Jul 16.

International Center for Tropical Agriculture (CIAT) Bean Project; A.A. 6713, Cali, Colombia.

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http://dx.doi.org/10.1186/1471-2164-11-436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091635PMC
July 2010

Three sequenced legume genomes and many crop species: rich opportunities for translational genomics.

Plant Physiol 2009 Nov 16;151(3):970-7. Epub 2009 Sep 16.

United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011, USA.

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http://www.plantphysiol.org/cgi/doi/10.1104/pp.109.144659
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http://dx.doi.org/10.1104/pp.109.144659DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773077PMC
November 2009