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Items: 1 to 50 of 160

1.

FAIR: A Call to Make the Published Data More Findable, Accessible, Interoperable and Reusable.

Reiser L, Harper L, Freeling M, Han B, Luan S.

Mol Plant. 2018 Aug 1. pii: S1674-2052(18)30239-9. doi: 10.1016/j.molp.2018.07.005. [Epub ahead of print] No abstract available.

PMID:
30076986
2.

Gene retention, fractionation and subgenome differences in polyploid plants.

Cheng F, Wu J, Cai X, Liang J, Freeling M, Wang X.

Nat Plants. 2018 May;4(5):258-268. doi: 10.1038/s41477-018-0136-7. Epub 2018 Apr 30. Review.

PMID:
29725103
3.

Maternal components of RNA-directed DNA methylation are required for seed development in Brassica rapa.

Grover JW, Kendall T, Baten A, Burgess D, Freeling M, King GJ, Mosher RA.

Plant J. 2018 May;94(4):575-582. doi: 10.1111/tpj.13910. Epub 2018 Apr 23.

PMID:
29569777
4.

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure.

Gordon SP, Contreras-Moreira B, Woods DP, Des Marais DL, Burgess D, Shu S, Stritt C, Roulin AC, Schackwitz W, Tyler L, Martin J, Lipzen A, Dochy N, Phillips J, Barry K, Geuten K, Budak H, Juenger TE, Amasino R, Caicedo AL, Goodstein D, Davidson P, Mur LAJ, Figueroa M, Freeling M, Catalan P, Vogel JP.

Nat Commun. 2017 Dec 19;8(1):2184. doi: 10.1038/s41467-017-02292-8.

5.

Picking up the Ball at the K/Pg Boundary: The Distribution of Ancient Polyploidies in the Plant Phylogenetic Tree as a Spandrel of Asexuality with Occasional Sex.

Freeling M.

Plant Cell. 2017 Feb;29(2):202-206. doi: 10.1105/tpc.16.00836. Epub 2017 Feb 17. No abstract available.

6.

Natural antisense transcripts are significantly involved in regulation of drought stress in maize.

Xu J, Wang Q, Freeling M, Zhang X, Xu Y, Mao Y, Tang X, Wu F, Lan H, Cao M, Rong T, Lisch D, Lu Y.

Nucleic Acids Res. 2017 May 19;45(9):5126-5141. doi: 10.1093/nar/gkx085.

7.

Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea.

Cheng F, Sun R, Hou X, Zheng H, Zhang F, Zhang Y, Liu B, Liang J, Zhuang M, Liu Y, Liu D, Wang X, Li P, Liu Y, Lin K, Bucher J, Zhang N, Wang Y, Wang H, Deng J, Liao Y, Wei K, Zhang X, Fu L, Hu Y, Liu J, Cai C, Zhang S, Zhang S, Li F, Zhang H, Zhang J, Guo N, Liu Z, Liu J, Sun C, Ma Y, Zhang H, Cui Y, Freeling MR, Borm T, Bonnema G, Wu J, Wang X.

Nat Genet. 2016 Oct;48(10):1218-24. doi: 10.1038/ng.3634. Epub 2016 Aug 15.

PMID:
27526322
8.

Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa.

Cheng F, Sun C, Wu J, Schnable J, Woodhouse MR, Liang J, Cai C, Freeling M, Wang X.

New Phytol. 2016 Jul;211(1):288-99. doi: 10.1111/nph.13884. Epub 2016 Feb 12.

9.

Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences.

Freeling M, Scanlon MJ, Fowler JE.

Curr Opin Genet Dev. 2015 Dec;35:110-8. doi: 10.1016/j.gde.2015.11.002. Epub 2015 Dec 4. Review.

PMID:
26657818
10.

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum.

VanBuren R, Bryant D, Edger PP, Tang H, Burgess D, Challabathula D, Spittle K, Hall R, Gu J, Lyons E, Freeling M, Bartels D, Ten Hallers B, Hastie A, Michael TP, Mockler TC.

Nature. 2015 Nov 26;527(7579):508-11. doi: 10.1038/nature15714. Epub 2015 Nov 11.

PMID:
26560029
11.

The pineapple genome and the evolution of CAM photosynthesis.

Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang ML, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo HB, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen LY, Shirley N, Lin YR, Liu LY, Hernandez AG, Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X, Yang X, Smith JA, Cushman JC, Paull RE, Yu Q.

Nat Genet. 2015 Dec;47(12):1435-42. doi: 10.1038/ng.3435. Epub 2015 Nov 2.

12.

Advances in understanding cis regulation of the plant gene with an emphasis on comparative genomics.

Burgess DG, Xu J, Freeling M.

Curr Opin Plant Biol. 2015 Oct;27:141-7. doi: 10.1016/j.pbi.2015.07.001. Epub 2015 Aug 3. Review.

PMID:
26247124
13.

A Solution to the C-Value Paradox and the Function of Junk DNA: The Genome Balance Hypothesis.

Freeling M, Xu J, Woodhouse M, Lisch D.

Mol Plant. 2015 Jun;8(6):899-910. doi: 10.1016/j.molp.2015.02.009. Epub 2015 Mar 3.

14.

Exploring experienced nurses' attitudes, views and expectations of new graduate nurses: a critical review.

Freeling M, Parker S.

Nurse Educ Today. 2015 Feb;35(2):e42-9. doi: 10.1016/j.nedt.2014.11.011. Epub 2014 Nov 28. Review.

PMID:
25499528
15.

Co-option of the polarity gene network shapes filament morphology in angiosperms.

de Almeida AM, Yockteng R, Schnable J, Alvarez-Buylla ER, Freeling M, Specht CD.

Sci Rep. 2014 Aug 29;4:6194. doi: 10.1038/srep06194.

16.

Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids.

Woodhouse MR, Cheng F, Pires JC, Lisch D, Freeling M, Wang X.

Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5283-8. doi: 10.1073/pnas.1402475111. Epub 2014 Mar 24. Erratum in: Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6527.

17.
18.

Two evolutionarily distinct classes of paleopolyploidy.

Garsmeur O, Schnable JC, Almeida A, Jourda C, D'Hont A, Freeling M.

Mol Biol Evol. 2014 Feb;31(2):448-54. doi: 10.1093/molbev/mst230. Epub 2013 Dec 1.

PMID:
24296661
19.

Unequal redundancy in maize knotted1 homeobox genes.

Bolduc N, Tyers RG, Freeling M, Hake S.

Plant Physiol. 2014 Jan;164(1):229-38. doi: 10.1104/pp.113.228791. Epub 2013 Nov 11.

20.

Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses.

Turco G, Schnable JC, Pedersen B, Freeling M.

Front Plant Sci. 2013 Jul 2;4:170. doi: 10.3389/fpls.2013.00170. eCollection 2013.

21.

The Brassica genome.

Wang X, Freeling M.

Front Plant Sci. 2013 May 30;4:148. doi: 10.3389/fpls.2013.00148. eCollection 2013. No abstract available.

22.

The fate of Arabidopsis thaliana homeologous CNSs and their motifs in the Paleohexaploid Brassica rapa.

Subramaniam S, Wang X, Freeling M, Pires JC.

Genome Biol Evol. 2013;5(4):646-60. doi: 10.1093/gbe/evt035.

23.

Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules.

Spangler JB, Ficklin SP, Luo F, Freeling M, Feltus FA.

PLoS One. 2012;7(9):e45041. Epub 2012 Sep 14.

24.

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.

D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengellé J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, Mckain MR, Leebens-Mack J, Burgess D, Freeling M, Mbéguié-A-Mbéguié D, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci AM, Weissenbach J, Ruiz M, Glaszmann JC, Quétier F, Yahiaoui N, Wincker P.

Nature. 2012 Aug 9;488(7410):213-7. doi: 10.1038/nature11241.

PMID:
22801500
25.

Escape from preferential retention following repeated whole genome duplications in plants.

Schnable JC, Wang X, Pires JC, Freeling M.

Front Plant Sci. 2012 May 15;3:94. doi: 10.3389/fpls.2012.00094. eCollection 2012.

26.

Long identical multispecies elements in plant and animal genomes.

Reneker J, Lyons E, Conant GC, Pires JC, Freeling M, Shyu CR, Korkin D.

Proc Natl Acad Sci U S A. 2012 May 8;109(19):E1183-91. doi: 10.1073/pnas.1121356109. Epub 2012 Apr 10.

27.

Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants.

Freeling M, Woodhouse MR, Subramaniam S, Turco G, Lisch D, Schnable JC.

Curr Opin Plant Biol. 2012 Apr;15(2):131-9. doi: 10.1016/j.pbi.2012.01.015. Epub 2012 Feb 14. Review.

PMID:
22341793
28.

Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy.

Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS, Conant G, Wang X, Freeling M, Pires JC.

Genetics. 2012 Apr;190(4):1563-74. doi: 10.1534/genetics.111.137349. Epub 2012 Feb 2.

29.

Genome-wide analysis of syntenic gene deletion in the grasses.

Schnable JC, Freeling M, Lyons E.

Genome Biol Evol. 2012;4(3):265-77. doi: 10.1093/gbe/evs009. Epub 2012 Jan 23.

30.

Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids.

Woodhouse MR, Tang H, Freeling M.

Plant Cell. 2011 Dec;23(12):4241-53. doi: 10.1105/tpc.111.093567. Epub 2011 Dec 16.

31.

Heritable epigenetic variation among maize inbreds.

Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh CT, Jia Y, Gendler K, Freeling M, Schnable PS, Vaughn MW, Springer NM.

PLoS Genet. 2011 Nov;7(11):e1002372. doi: 10.1371/journal.pgen.1002372. Epub 2011 Nov 17.

32.

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

Zhang W, Wu Y, Schnable JC, Zeng Z, Freeling M, Crawford GE, Jiang J.

Genome Res. 2012 Jan;22(1):151-62. doi: 10.1101/gr.131342.111. Epub 2011 Nov 22.

33.

Evidence of function for conserved noncoding sequences in Arabidopsis thaliana.

Spangler JB, Subramaniam S, Freeling M, Feltus FA.

New Phytol. 2012 Jan;193(1):241-52. doi: 10.1111/j.1469-8137.2011.03916.x. Epub 2011 Sep 28.

34.

The genome of the mesopolyploid crop species Brassica rapa.

Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z; Brassica rapa Genome Sequencing Project Consortium.

Nat Genet. 2011 Aug 28;43(10):1035-9. doi: 10.1038/ng.919.

PMID:
21873998
35.

Inna Golubovskaya: the life of a geneticist studying meiosis.

Cande WZ, Freeling M.

Genetics. 2011 Jul;188(3):491-8. doi: 10.1534/genetics.111.130039.

36.

Screening synteny blocks in pairwise genome comparisons through integer programming.

Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M.

BMC Bioinformatics. 2011 Apr 18;12:102. doi: 10.1186/1471-2105-12-102.

37.

Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize.

Schnable JC, Freeling M.

PLoS One. 2011 Mar 10;6(3):e17855. doi: 10.1371/journal.pone.0017855.

38.

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss.

Schnable JC, Springer NM, Freeling M.

Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4069-74. doi: 10.1073/pnas.1101368108. Epub 2011 Feb 22.

39.

Using genomic sequencing for classical genetics in E. coli K12.

Lyons E, Freeling M, Kustu S, Inwood W.

PLoS One. 2011 Feb 25;6(2):e16717. doi: 10.1371/journal.pone.0016717.

40.

Gobe: an interactive, web-based tool for comparative genomic visualization.

Pedersen BS, Tang H, Freeling M.

Bioinformatics. 2011 Apr 1;27(7):1015-6. doi: 10.1093/bioinformatics/btr056. Epub 2011 Feb 3.

PMID:
21296748
41.

Dose-sensitivity, conserved non-coding sequences, and duplicate gene retention through multiple tetraploidies in the grasses.

Schnable JC, Pedersen BS, Subramaniam S, Freeling M.

Front Plant Sci. 2011 Mar 10;2:2. doi: 10.3389/fpls.2011.00002. eCollection 2011.

42.

Epigenetic reprogramming during vegetative phase change in maize.

Li H, Freeling M, Lisch D.

Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22184-9. doi: 10.1073/pnas.1016884108. Epub 2010 Dec 6.

43.

A maize thiamine auxotroph is defective in shoot meristem maintenance.

Woodward JB, Abeydeera ND, Paul D, Phillips K, Rapala-Kozik M, Freeling M, Begley TP, Ealick SE, McSteen P, Scanlon MJ.

Plant Cell. 2010 Oct;22(10):3305-17. doi: 10.1105/tpc.110.077776. Epub 2010 Oct 22.

44.

Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs.

Woodhouse MR, Schnable JC, Pedersen BS, Lyons E, Lisch D, Subramaniam S, Freeling M.

PLoS Biol. 2010 Jun 29;8(6):e1000409. doi: 10.1371/journal.pbio.1000409.

45.

The evolution of a high copy gene array in Arabidopsis.

Kane J, Freeling M, Lyons E.

J Mol Evol. 2010 Jun;70(6):531-44. doi: 10.1007/s00239-010-9350-2. Epub 2010 May 22.

46.

Transposed genes in Arabidopsis are often associated with flanking repeats.

Woodhouse MR, Pedersen B, Freeling M.

PLoS Genet. 2010 May 13;6(5):e1000949. doi: 10.1371/journal.pgen.1000949.

47.

Insights from the comparison of plant genome sequences.

Paterson AH, Freeling M, Tang H, Wang X.

Annu Rev Plant Biol. 2010;61:349-72. doi: 10.1146/annurev-arplant-042809-112235. Review.

PMID:
20441528
48.

Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition.

Freeling M.

Annu Rev Plant Biol. 2009;60:433-53. doi: 10.1146/annurev.arplant.043008.092122. Review.

PMID:
19575588
49.

Conserved noncoding sequences (CNSs) in higher plants.

Freeling M, Subramaniam S.

Curr Opin Plant Biol. 2009 Apr;12(2):126-32. doi: 10.1016/j.pbi.2009.01.005. Epub 2009 Feb 25. Review.

PMID:
19249238
50.

The Sorghum bicolor genome and the diversification of grasses.

Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS.

Nature. 2009 Jan 29;457(7229):551-6. doi: 10.1038/nature07723.

PMID:
19189423

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