Jiming Jiang

Jiming Jiang

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Jiming Jiang

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Fluorescence in situ hybridization in plants: recent developments and future applications.

Authors:
Jiming Jiang

Chromosome Res 2019 Sep 9;27(3):153-165. Epub 2019 Mar 9.

Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.

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http://dx.doi.org/10.1007/s10577-019-09607-zDOI Listing
September 2019

Dual-color oligo-FISH can reveal chromosomal variations and evolution in Oryza species.

Plant J 2019 Sep 8. Epub 2019 Sep 8.

Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China.

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http://dx.doi.org/10.1111/tpj.14522DOI Listing
September 2019

Cold stress induces enhanced chromatin accessibility and bivalent histone modifications H3K4me3 and H3K27me3 of active genes in potato.

Genome Biol 2019 06 17;20(1):123. Epub 2019 Jun 17.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.

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http://dx.doi.org/10.1186/s13059-019-1731-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6580510PMC
June 2019

Application of MNase-Seq in the Global Mapping of Nucleosome Positioning in Plants.

Methods Mol Biol 2018 ;1830:353-366

Department of Horticulture, University of Wisconsin-Madison, Madison, WI, USA.

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http://dx.doi.org/10.1007/978-1-4939-8657-6_21DOI Listing
April 2019

Historical Meiotic Crossover Hotspots Fueled Patterns of Evolutionary Divergence in Rice.

Plant Cell 2019 Mar 31;31(3):645-662. Epub 2019 Jan 31.

Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706

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http://dx.doi.org/10.1105/tpc.18.00750DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6482639PMC
March 2019

Rapid validation of transcriptional enhancers using agrobacterium-mediated transient assay.

Plant Methods 2019 6;15:21. Epub 2019 Mar 6.

1Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA.

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http://dx.doi.org/10.1186/s13007-019-0407-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6402126PMC
March 2019

Chromosome painting in meiosis reveals pairing of specific chromosomes in polyploid Solanum species.

Chromosoma 2018 12 21;127(4):505-513. Epub 2018 Sep 21.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.

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http://link.springer.com/10.1007/s00412-018-0682-9
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http://dx.doi.org/10.1007/s00412-018-0682-9DOI Listing
December 2018

Chromosome painting and comparative physical mapping of the sex chromosomes in Populus tomentosa and Populus deltoides.

Chromosoma 2018 09 8;127(3):313-321. Epub 2018 Mar 8.

Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.

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http://dx.doi.org/10.1007/s00412-018-0664-yDOI Listing
September 2018

Comparison of and Genomes Reveals Selection-Driven Gene Escape from the Centromeric Regions.

Plant Cell 2018 08 2;30(8):1729-1744. Epub 2018 Jul 2.

State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

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http://dx.doi.org/10.1105/tpc.18.00163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6139686PMC
August 2018

Single molecule mtDNA fiber FISH for analyzing numtogenesis.

Anal Biochem 2018 07 18;552:45-49. Epub 2017 Mar 18.

Departments of Genetics, Pathology, Environmental Health, Center for Free Radical Biology, Center for Aging, UAB Comprehensive Cancer Center, University of Alabama at Birmingham, AL 35294, United States; Birmingham Veterans Affairs Medical Center, Birmingham, AL 35294, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ab.2017.03.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5814351PMC
July 2018

Amplification and adaptation of centromeric repeats in polyploid switchgrass species.

New Phytol 2018 06 25;218(4):1645-1657. Epub 2018 Mar 25.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.

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http://dx.doi.org/10.1111/nph.15098DOI Listing
June 2018

Transcriptional and epigenetic adaptation of maize chromosomes in Oat-Maize addition lines.

Nucleic Acids Res 2018 06;46(10):5012-5028

National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, Key Laboratory of Crop Genetic Improvement, Beijing Municipality, Center for Crop Functional Genomics and Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 10093, P. R. China.

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http://dx.doi.org/10.1093/nar/gky209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007749PMC
June 2018

Chromosome painting and its applications in cultivated and wild rice.

BMC Plant Biol 2018 Jun 7;18(1):110. Epub 2018 Jun 7.

Key Laboratory of Plant Functional Genomics of Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.

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https://bmcplantbiol.biomedcentral.com/articles/10.1186/s128
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http://dx.doi.org/10.1186/s12870-018-1325-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991451PMC
June 2018

Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome.

Plant Physiol 2018 04 20;176(4):2789-2803. Epub 2018 Feb 20.

Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706

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http://dx.doi.org/10.1104/pp.17.01467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5884613PMC
April 2018

Extrachromosomal circular DNA-based amplification and transmission of herbicide resistance in crop weed .

Proc Natl Acad Sci U S A 2018 03 12;115(13):3332-3337. Epub 2018 Mar 12.

Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506;

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http://dx.doi.org/10.1073/pnas.1719354115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5879691PMC
March 2018

Recurrent establishment of de novo centromeres in the pericentromeric region of maize chromosome 3.

Chromosome Res 2017 10 22;25(3-4):299-311. Epub 2017 Aug 22.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.

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http://dx.doi.org/10.1007/s10577-017-9564-xDOI Listing
October 2017

Etiolated Stem Branching Is a Result of Systemic Signaling Associated with Sucrose Level.

Plant Physiol 2017 Oct 31;175(2):734-745. Epub 2017 Aug 31.

Department of Postharvest Science of Fresh Produce, The Volcani Center, Agricultural Research Organization, Rishon LeZion 7528809, Israel

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http://dx.doi.org/10.1104/pp.17.00995DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5619910PMC
October 2017

Overexpression of StNF-YB3.1 reduces photosynthetic capacity and tuber production, and promotes ABA-mediated stomatal closure in potato (Solanum tuberosum L.).

Plant Sci 2017 Aug 4;261:50-59. Epub 2017 May 4.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address:

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http://dx.doi.org/10.1016/j.plantsci.2017.04.015DOI Listing
August 2017

Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness.

Sci Rep 2017 06 22;7(1):4093. Epub 2017 Jun 22.

College of Biological Sciences, China Agricultural University, State key Laboratory of Plant Physiology and Biochemistry, Beijing, China.

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http://dx.doi.org/10.1038/s41598-017-04524-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5481438PMC
June 2017

Towards genome-wide prediction and characterization of enhancers in plants.

Biochim Biophys Acta Gene Regul Mech 2017 Jan 16;1860(1):131-139. Epub 2016 Jun 16.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bbagrm.2016.06.006DOI Listing
January 2017

Chromatin-associated transcripts of tandemly repetitive DNA sequences revealed by RNA-FISH.

Chromosome Res 2016 12 2;24(4):467-480. Epub 2016 Sep 2.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.

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http://dx.doi.org/10.1007/s10577-016-9537-5DOI Listing
December 2016

Isolation and Proteomics Analysis of Barley Centromeric Chromatin Using PICh.

J Proteome Res 2016 06 10;15(6):1875-82. Epub 2016 May 10.

Department of Horticulture, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States.

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http://pubs.acs.org/doi/10.1021/acs.jproteome.6b00063
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http://dx.doi.org/10.1021/acs.jproteome.6b00063DOI Listing
June 2016

High-resolution tyramide-FISH mapping of markers tightly linked to the male-fertility restoration (Ms) locus of onion.

Theor Appl Genet 2016 Mar 24;129(3):535-45. Epub 2015 Dec 24.

USDA-ARS and Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA.

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http://dx.doi.org/10.1007/s00122-015-2646-2DOI Listing
March 2016

Silencing of vacuolar invertase and asparagine synthetase genes and its impact on acrylamide formation of fried potato products.

Plant Biotechnol J 2016 Feb 16;14(2):709-18. Epub 2015 Jun 16.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI, USA.

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http://dx.doi.org/10.1111/pbi.12421DOI Listing
February 2016

PlantDHS: a database for DNase I hypersensitive sites in plants.

Nucleic Acids Res 2016 Jan 22;44(D1):D1148-53. Epub 2015 Sep 22.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA

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http://dx.doi.org/10.1093/nar/gkv962DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702941PMC
January 2016

Genome-wide mapping of DNase I hypersensitive sites in plants.

Methods Mol Biol 2015 ;1284:71-89

Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706-1580, USA.

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http://dx.doi.org/10.1007/978-1-4939-2444-8_4DOI Listing
November 2015

Gene Expression and Chromatin Modifications Associated with Maize Centromeres.

G3 (Bethesda) 2015 Nov 12;6(1):183-92. Epub 2015 Nov 12.

Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706

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http://dx.doi.org/10.1534/g3.115.022764DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704717PMC
November 2015

Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures.

Plant Cell 2015 Sep 15;27(9):2415-26. Epub 2015 Sep 15.

Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706

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http://dx.doi.org/10.1105/tpc.15.00537DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815101PMC
September 2015

Stable Patterns of CENH3 Occupancy Through Maize Lineages Containing Genetically Similar Centromeres.

Genetics 2015 Aug 10;200(4):1105-16. Epub 2015 Jun 10.

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

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http://www.genetics.org/lookup/doi/10.1534/genetics.115.1773
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http://dx.doi.org/10.1534/genetics.115.177360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574241PMC
August 2015

Genome-Wide Nucleosome Occupancy and Positioning and Their Impact on Gene Expression and Evolution in Plants.

Plant Physiol 2015 Aug 4;168(4):1406-16. Epub 2015 Jul 4.

Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706 (T.Z., W.Z., J.J.); andNational Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China (W.Z.)

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http://www.plantphysiol.org/lookup/doi/10.1104/pp.15.00125
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http://dx.doi.org/10.1104/pp.15.00125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528733PMC
August 2015

Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides.

Genetics 2015 Jul 13;200(3):771-9. Epub 2015 May 13.

Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706

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http://dx.doi.org/10.1534/genetics.115.177642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4512542PMC
July 2015

The 'dark matter' in the plant genomes: non-coding and unannotated DNA sequences associated with open chromatin.

Authors:
Jiming Jiang

Curr Opin Plant Biol 2015 Apr 24;24:17-23. Epub 2015 Jan 24.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address:

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http://dx.doi.org/10.1016/j.pbi.2015.01.005DOI Listing
April 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

The E-MS Algorithm: Model Selection with Incomplete Data.

J Am Stat Assoc 2015 Apr 15;110(511):1136-1147. Epub 2014 Aug 15.

University of California, Davis, Oregon Health and Science University and University of Miami.

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http://dx.doi.org/10.1080/01621459.2014.948545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4714800PMC
April 2015

Vacuolar invertase gene silencing in potato (Solanum tuberosum L.) improves processing quality by decreasing the frequency of sugar-end defects.

PLoS One 2014 2;9(4):e93381. Epub 2014 Apr 2.

Department of Horticulture, University of Wisconsin, Madison, Wisconsin, United States of America; Vegetable Crops Research Unit, United States Department of Agriculture, Madison, Wisconsin, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0093381PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973568PMC
January 2015

Sugar metabolism, chip color, invertase activity, and gene expression during long-term cold storage of potato (Solanum tuberosum) tubers from wild-type and vacuolar invertase silencing lines of Katahdin.

BMC Res Notes 2014 Nov 16;7:801. Epub 2014 Nov 16.

United States Department of Agriculture - Agricultural Research Service, Vegetable Crops Research Unit, 1575 Linden Dr,, Madison, WI 53706, USA.

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http://dx.doi.org/10.1186/1756-0500-7-801DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239387PMC
November 2014

Open chromatin in plant genomes.

Cytogenet Genome Res 2014 6;143(1-3):18-27. Epub 2014 Jun 6.

Department of Horticulture, University of Wisconsin-Madison, Madison, Wis., USA.

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http://dx.doi.org/10.1159/000362827DOI Listing
October 2014

Distinct Copy Number, Coding Sequence, and Locus Methylation Patterns Underlie Rhg1-Mediated Soybean Resistance to Soybean Cyst Nematode.

Plant Physiol 2014 Jun 14;165(2):630-647. Epub 2014 Apr 14.

Department of Plant Pathology (D.E.C., A.M.B., X.G., A.F.B.) and Department of Horticulture (K.W., J.J.), University of Wisconsin, Madison, Wisconsin 53706; andSoybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland 20705 (Q.S.)

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http://dx.doi.org/10.1104/pp.114.235952DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4044848PMC
June 2014

Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice.

PLoS Genet 2014 May 22;10(5):e1004378. Epub 2014 May 22.

Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4031139PMC
May 2014

Three potato centromeres are associated with distinct haplotypes with or without megabase-sized satellite repeat arrays.

Genetics 2014 Feb 6;196(2):397-401. Epub 2013 Dec 6.

Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706.

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http://dx.doi.org/10.1534/genetics.113.160135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3914613PMC
February 2014

Reliability of environmental sampling culture results using the negative binomial intraclass correlation coefficient.

Springerplus 2014 22;3:40. Epub 2014 Jan 22.

Department of Statistics, University of California, Davis, CA 95616 USA.

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http://dx.doi.org/10.1186/2193-1801-3-40DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3916583PMC
February 2014

Maize centromeres expand and adopt a uniform size in the genetic background of oat.

Genome Res 2014 Jan 7;24(1):107-16. Epub 2013 Oct 7.

Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;

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http://dx.doi.org/10.1101/gr.160887.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875851PMC
January 2014

Fence Methods for Backcross Experiments.

J Stat Comput Simul 2014 ;84(3):644-662

Department of Statistics, University of California, Davis, CA 95616, U.S.A.

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http://www.tandfonline.com/doi/abs/10.1080/00949655.2012.721
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http://dx.doi.org/10.1080/00949655.2012.721885DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3891925PMC
January 2014

The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres.

Proc Natl Acad Sci U S A 2013 Dec 4;110(50):E4875-83. Epub 2013 Nov 4.

Department of Horticulture, University of Wisconsin, Madison, WI 53706.

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http://dx.doi.org/10.1073/pnas.1319548110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3864355PMC
December 2013

Insertional mutagenesis using Tnt1 retrotransposon in potato.

Plant Physiol 2013 Sep 29;163(1):21-9. Epub 2013 Jul 29.

Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1104/pp.113.221903DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762642PMC
September 2013

Copy number variation in potato - an asexually propagated autotetraploid species.

Plant J 2013 Jul 13;75(1):80-89. Epub 2013 May 13.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.

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http://dx.doi.org/10.1111/tpj.12200DOI Listing
July 2013

Fluorescence in situ hybridization techniques for cytogenetic and genomic analyses.

Methods Mol Biol 2013 ;956:13-27

Department of Horticulture, University of Wisconsin-Madison, Madison, WI, USA.

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http://link.springer.com/10.1007/978-1-62703-194-3_2
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http://dx.doi.org/10.1007/978-1-62703-194-3_2DOI Listing
April 2013

Interstitial telomeric repeats are enriched in the centromeres of chromosomes in Solanum species.

Chromosome Res 2013 Mar 19;21(1):5-13. Epub 2012 Dec 19.

Key Laboratory of Horticultural Plant Biology, Ministry of Education; National Center for Vegetable Improvement; Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.

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http://dx.doi.org/10.1007/s10577-012-9332-xDOI Listing
March 2013

Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat.

Proc Natl Acad Sci U S A 2013 Feb 11;110(9):3447-52. Epub 2013 Feb 11.

Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China.

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http://dx.doi.org/10.1073/pnas.1300153110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587266PMC
February 2013

Fixed and Random Effects Selection by REML and Pathwise Coordinate Optimization.

J Comput Graph Stat 2013 ;22(2):341-355

Department of Statistics, University of California, Davis, CA 85616.

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http://dx.doi.org/10.1080/10618600.2012.681219DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049469PMC
January 2013

Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean.

Science 2012 Nov 11;338(6111):1206-9. Epub 2012 Oct 11.

Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, USA.

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http://dx.doi.org/10.1126/science.1228746DOI Listing
November 2012

Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly.

Plant J 2012 Sep 9;71(6):895-906. Epub 2012 Jul 9.

Horticulture Department, University of Wisconsin, Madison, WI 53706, USA.

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http://dx.doi.org/10.1111/j.1365-313X.2012.05017.xDOI Listing
September 2012

Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis.

Plant Cell 2012 Jul 5;24(7):2719-31. Epub 2012 Jul 5.

Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA.

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http://dx.doi.org/10.1105/tpc.112.098061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426110PMC
July 2012

Genomic in situ hybridization reveals both auto- and allopolyploid origins of different North and Central American hexaploid potato (Solanum sect. Petota) species.

Genome 2012 Jun 17;55(6):407-15. Epub 2012 May 17.

Department of Biotechnology, N.I. Vavilov Institute of Plant Industry, Bolshaya Morskaya Street, 42-44, St. Petersburg, 190000, Russia.

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http://www.nrcresearchpress.com/doi/10.1139/g2012-027
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http://dx.doi.org/10.1139/g2012-027DOI Listing
June 2012

Restricted fence method for covariate selection in longitudinal data analysis.

Biostatistics 2012 Apr 17;13(2):303-14. Epub 2011 Dec 17.

Department of Public Health and Preventive Medicine, Oregon Health and Science University, Portland, OR 97239, USA.

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http://dx.doi.org/10.1093/biostatistics/kxr046DOI Listing
April 2012

Stable integration of an engineered megabase repeat array into the maize genome.

Plant J 2012 Apr 10;70(2):357-65. Epub 2012 Jan 10.

Department of Genetics, University of Georgia, Athens, GA 30602, USA.

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http://dx.doi.org/10.1111/j.1365-313X.2011.04867.xDOI Listing
April 2012

High-resolution mapping of open chromatin in the rice genome.

Genome Res 2012 Jan 22;22(1):151-62. Epub 2011 Nov 22.

Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1101/gr.131342.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246202PMC
January 2012

Simple estimation of hidden correlation in repeated measures.

Stat Med 2011 Dec 14;30(29):3403-15. Epub 2011 Oct 14.

Department of Public Health and Preventive Medicine, Oregon Health and Science University, Portland, OR, USA.

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http://doi.wiley.com/10.1002/sim.4366
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http://dx.doi.org/10.1002/sim.4366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3891926PMC
December 2011

Euchromatic subdomains in rice centromeres are associated with genes and transcription.

Plant Cell 2011 Nov 11;23(11):4054-64. Epub 2011 Nov 11.

Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1105/tpc.111.090043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246336PMC
November 2011

Conservation and purifying selection of transcribed genes located in a rice centromere.

Plant Cell 2011 Aug 19;23(8):2821-30. Epub 2011 Aug 19.

Arizona Genomics Institute, School of Plant Sciences, Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.

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http://dx.doi.org/10.1105/tpc.111.085605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3180794PMC
August 2011

Genome sequence and analysis of the tuber crop potato.

Nature 2011 Jul 10;475(7355):189-95. Epub 2011 Jul 10.

BGI-Shenzhen, Chinese Ministry of Agricultural, Key Lab of Genomics, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.

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http://dx.doi.org/10.1038/nature10158DOI Listing
July 2011

Distinct DNA methylation patterns associated with active and inactive centromeres of the maize B chromosome.

Genome Res 2011 Jun 25;21(6):908-14. Epub 2011 Apr 25.

Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1101/gr.116202.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106323PMC
June 2011

Comparative FISH mapping of Daucus species (Apiaceae family).

Chromosome Res 2011 May 6;19(4):493-506. Epub 2011 May 6.

Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA.

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http://dx.doi.org/10.1007/s10577-011-9202-yDOI Listing
May 2011

Super-stretched pachytene chromosomes for plant molecular cytogenetic mapping.

Methods Mol Biol 2011 ;701:239-45

Department of Horticulture, University of Wisconsin, Madison, WI, USA.

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http://link.springer.com/10.1007/978-1-61737-957-4_13
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http://dx.doi.org/10.1007/978-1-61737-957-4_13DOI Listing
April 2011

De novo assembly of potential linear artificial chromosome constructs capped with expansive telomeric repeats.

Plant Methods 2011 Apr 15;7:10. Epub 2011 Apr 15.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA.

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http://dx.doi.org/10.1186/1746-4811-7-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3101654PMC
April 2011

Centromere inactivation and epigenetic modifications of a plant chromosome with three functional centromeres.

Chromosoma 2010 Oct 25;119(5):553-63. Epub 2010 May 25.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA.

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http://dx.doi.org/10.1007/s00412-010-0278-5DOI Listing
October 2010

Suppression of the vacuolar invertase gene prevents cold-induced sweetening in potato.

Plant Physiol 2010 Oct 24;154(2):939-48. Epub 2010 Aug 24.

Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1104/pp.110.162545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2948980PMC
October 2010

Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data.

Bioinformatics 2010 Sep 8;26(17):2101-8. Epub 2010 Jul 8.

Institute of Plant Molecular Biology, Biology Centre ASCR, Branisovska 31, CZ-37005, Ceske Budejovice, Czech Republic.

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http://dx.doi.org/10.1093/bioinformatics/btq343DOI Listing
September 2010

Evolution of chromosome 6 of Solanum species revealed by comparative fluorescence in situ hybridization mapping.

Chromosoma 2010 Aug 30;119(4):435-42. Epub 2010 Mar 30.

Department of Horticulture, University of Wisconsin-Madison, 53706, USA.

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http://dx.doi.org/10.1007/s00412-010-0269-6DOI Listing
August 2010

Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice.

Plant J 2010 Aug 6;63(3):353-65. Epub 2010 May 6.

Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USAU.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.

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http://dx.doi.org/10.1111/j.1365-313X.2010.04246.xDOI Listing
August 2010

Lineage-specific adaptive evolution of the centromeric protein CENH3 in diploid and allotetraploid Oryza species.

Mol Biol Evol 2009 Dec 9;26(12):2877-85. Epub 2009 Sep 9.

Department of Horticulture, University of Wisconsin-Madison, USA.

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http://dx.doi.org/10.1093/molbev/msp208DOI Listing
December 2009

The B73 maize genome: complexity, diversity, and dynamics.

Authors:
Patrick S Schnable Doreen Ware Robert S Fulton Joshua C Stein Fusheng Wei Shiran Pasternak Chengzhi Liang Jianwei Zhang Lucinda Fulton Tina A Graves Patrick Minx Amy Denise Reily Laura Courtney Scott S Kruchowski Chad Tomlinson Cindy Strong Kim Delehaunty Catrina Fronick Bill Courtney Susan M Rock Eddie Belter Feiyu Du Kyung Kim Rachel M Abbott Marc Cotton Andy Levy Pamela Marchetto Kerri Ochoa Stephanie M Jackson Barbara Gillam Weizu Chen Le Yan Jamey Higginbotham Marco Cardenas Jason Waligorski Elizabeth Applebaum Lindsey Phelps Jason Falcone Krishna Kanchi Thynn Thane Adam Scimone Nay Thane Jessica Henke Tom Wang Jessica Ruppert Neha Shah Kelsi Rotter Jennifer Hodges Elizabeth Ingenthron Matt Cordes Sara Kohlberg Jennifer Sgro Brandon Delgado Kelly Mead Asif Chinwalla Shawn Leonard Kevin Crouse Kristi Collura Dave Kudrna Jennifer Currie Ruifeng He Angelina Angelova Shanmugam Rajasekar Teri Mueller Rene Lomeli Gabriel Scara Ara Ko Krista Delaney Marina Wissotski Georgina Lopez David Campos Michele Braidotti Elizabeth Ashley Wolfgang Golser HyeRan Kim Seunghee Lee Jinke Lin Zeljko Dujmic Woojin Kim Jayson Talag Andrea Zuccolo Chuanzhu Fan Aswathy Sebastian Melissa Kramer Lori Spiegel Lidia Nascimento Theresa Zutavern Beth Miller Claude Ambroise Stephanie Muller Will Spooner Apurva Narechania Liya Ren Sharon Wei Sunita Kumari Ben Faga Michael J Levy Linda McMahan Peter Van Buren Matthew W Vaughn Kai Ying Cheng-Ting Yeh Scott J Emrich Yi Jia Ananth Kalyanaraman An-Ping Hsia W Brad Barbazuk Regina S Baucom Thomas P Brutnell Nicholas C Carpita Cristian Chaparro Jer-Ming Chia Jean-Marc Deragon James C Estill Yan Fu Jeffrey A Jeddeloh Yujun Han Hyeran Lee Pinghua Li Damon R Lisch Sanzhen Liu Zhijie Liu Dawn Holligan Nagel Maureen C McCann Phillip SanMiguel Alan M Myers Dan Nettleton John Nguyen Bryan W Penning Lalit Ponnala Kevin L Schneider David C Schwartz Anupma Sharma Carol Soderlund Nathan M Springer Qi Sun Hao Wang Michael Waterman Richard Westerman Thomas K Wolfgruber Lixing Yang Yeisoo Yu Lifang Zhang Shiguo Zhou Qihui Zhu Jeffrey L Bennetzen R Kelly Dawe Jiming Jiang Ning Jiang Gernot G Presting Susan R Wessler Srinivas Aluru Robert A Martienssen Sandra W Clifton W Richard McCombie Rod A Wing Richard K Wilson

Science 2009 Nov;326(5956):1112-5

Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA.

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http://www.dawelab.org/wp-content/uploads/2011/03/schnable-2
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http://www.sciencemag.org/cgi/doi/10.1126/science.1178534
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November 2009

Centromere repositioning in cucurbit species: implication of the genomic impact from centromere activation and inactivation.

Proc Natl Acad Sci U S A 2009 Sep 18;106(35):14937-41. Epub 2009 Aug 18.

National Maize Improvement Center of China, Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, China.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0904833106
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http://dx.doi.org/10.1073/pnas.0904833106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736423PMC
September 2009