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Items: 32

1.

Patterns of genomic differentiation between two Lake Victoria cichlid species, Haplochromis pyrrhocephalus and H. sp. 'macula'.

Takuno S, Miyagi R, Onami JI, Takahashi-Kariyazono S, Sato A, Tichy H, Nikaido M, Aibara M, Mizoiri S, Mrosso HDJ, Mzighani SI, Okada N, Terai Y.

BMC Evol Biol. 2019 Mar 4;19(1):68. doi: 10.1186/s12862-019-1387-2.

2.

Single-cell expression noise and gene-body methylation in Arabidopsis thaliana.

Horvath R, Laenen B, Takuno S, Slotte T.

Heredity (Edinb). 2019 Jan 16. doi: 10.1038/s41437-018-0181-z. [Epub ahead of print]

PMID:
30651589
3.

Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.

Takahashi S, Osabe K, Fukushima N, Takuno S, Miyaji N, Shimizu M, Takasaki-Yasuda T, Suzuki Y, Dennis ES, Seki M, Fujimoto R.

DNA Res. 2018 Oct 1;25(5):511-520. doi: 10.1093/dnares/dsy021.

4.

Coalescent framework for prokaryotes undergoing interspecific homologous recombination.

Akita T, Takuno S, Innan H.

Heredity (Edinb). 2018 May;120(5):474-484. doi: 10.1038/s41437-017-0034-1. Epub 2018 Jan 23.

5.

The Evolutionary Dynamics of Orthologs That Shift in Gene Body Methylation between Arabidopsis Species.

Takuno S, Seymour DK, Gaut BS.

Mol Biol Evol. 2017 Jun 1;34(6):1479-1491. doi: 10.1093/molbev/msx099.

PMID:
28333248
6.

Evolutionary patterns of genic DNA methylation vary across land plants.

Takuno S, Ran JH, Gaut BS.

Nat Plants. 2016 Jan 25;2:15222. doi: 10.1038/nplants.2015.222.

PMID:
27249194
7.

CG Methylation Covaries with Differential Gene Expression between Leaf and Floral Bud Tissues of Brachypodium distachyon.

Roessler K, Takuno S, Gaut BS.

PLoS One. 2016 Mar 7;11(3):e0150002. doi: 10.1371/journal.pone.0150002. eCollection 2016.

8.

A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response.

Bousios A, Diez CM, Takuno S, Bystry V, Darzentas N, Gaut BS.

Genome Res. 2016 Feb;26(2):226-37. doi: 10.1101/gr.193763.115. Epub 2015 Dec 2.

9.

Independent Molecular Basis of Convergent Highland Adaptation in Maize.

Takuno S, Ralph P, Swarts K, Elshire RJ, Glaubitz JC, Buckler ES, Hufford MB, Ross-Ibarra J.

Genetics. 2015 Aug;200(4):1297-312. doi: 10.1534/genetics.115.178327. Epub 2015 Jun 15.

10.

Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana.

Le TN, Miyazaki Y, Takuno S, Saze H.

Nucleic Acids Res. 2015 Apr 30;43(8):3911-21. doi: 10.1093/nar/gkv258. Epub 2015 Mar 26.

11.

Population genomics of the fission yeast Schizosaccharomyces pombe.

Fawcett JA, Iida T, Takuno S, Sugino RP, Kado T, Kugou K, Mura S, Kobayashi T, Ohta K, Nakayama J, Innan H.

PLoS One. 2014 Aug 11;9(8):e104241. doi: 10.1371/journal.pone.0104241. eCollection 2014.

12.

QTL map meets population genomics: an application to rice.

Fawcett JA, Kado T, Sasaki E, Takuno S, Yoshida K, Sugino RP, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Takagi H, Abe A, Ishii T, Terauchi R, Innan H.

PLoS One. 2013 Dec 23;8(12):e83720. doi: 10.1371/journal.pone.0083720. eCollection 2013.

13.

Identical sets of methylated and nonmethylated genes in Ciona intestinalis sperm and muscle cells.

Suzuki MM, Yoshinari A, Obara M, Takuno S, Shigenobu S, Sasakura Y, Kerr AR, Webb S, Bird A, Nakayama A.

Epigenetics Chromatin. 2013 Nov 11;6(1):38. doi: 10.1186/1756-8935-6-38.

14.

Comparative analyses identify the contributions of exotic donors to disease resistance in a barley experimental population.

Fang Z, Eule-Nashoba A, Powers C, Kono TY, Takuno S, Morrell PL, Smith KP.

G3 (Bethesda). 2013 Nov 6;3(11):1945-53. doi: 10.1534/g3.113.007294.

15.

From many, one: genetic control of prolificacy during maize domestication.

Wills DM, Whipple CJ, Takuno S, Kursel LE, Shannon LM, Ross-Ibarra J, Doebley JF.

PLoS Genet. 2013 Jun;9(6):e1003604. doi: 10.1371/journal.pgen.1003604. Epub 2013 Jun 27.

16.

The Capsella rubella genome and the genomic consequences of rapid mating system evolution.

Slotte T, Hazzouri KM, Ågren JA, Koenig D, Maumus F, Guo YL, Steige K, Platts AE, Escobar JS, Newman LK, Wang W, Mandáková T, Vello E, Smith LM, Henz SR, Steffen J, Takuno S, Brandvain Y, Coop G, Andolfatto P, Hu TT, Blanchette M, Clark RM, Quesneville H, Nordborg M, Gaut BS, Lysak MA, Jenkins J, Grimwood J, Chapman J, Prochnik S, Shu S, Rokhsar D, Schmutz J, Weigel D, Wright SI.

Nat Genet. 2013 Jul;45(7):831-5. doi: 10.1038/ng.2669. Epub 2013 Jun 9.

PMID:
23749190
17.

Gene body methylation is conserved between plant orthologs and is of evolutionary consequence.

Takuno S, Gaut BS.

Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):1797-802. doi: 10.1073/pnas.1215380110. Epub 2013 Jan 14.

18.

QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations.

Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano LM, Kamoun S, Terauchi R.

Plant J. 2013 Apr;74(1):174-83. doi: 10.1111/tpj.12105. Epub 2013 Feb 18.

19.

The power of QTL mapping with RILs.

Takuno S, Terauchi R, Innan H.

PLoS One. 2012;7(10):e46545. doi: 10.1371/journal.pone.0046545. Epub 2012 Oct 9.

20.

Modeling evolutionary growth of a microRNA-mediated regulation system.

Akita T, Takuno S, Innan H.

J Theor Biol. 2012 Oct 21;311:54-65. doi: 10.1016/j.jtbi.2012.07.011. Epub 2012 Jul 20.

PMID:
22820491
21.

Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica).

Vonholdt BM, Takuno S, Gaut BS.

Mol Biol Evol. 2012 Oct;29(10):3193-203. Epub 2012 May 15.

PMID:
22593226
22.

Population genomics in bacteria: a case study of Staphylococcus aureus.

Takuno S, Kado T, Sugino RP, Nakhleh L, Innan H.

Mol Biol Evol. 2012 Feb;29(2):797-809. doi: 10.1093/molbev/msr249. Epub 2011 Oct 17.

23.

Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly.

Takuno S, Gaut BS.

Mol Biol Evol. 2012 Jan;29(1):219-27. doi: 10.1093/molbev/msr188. Epub 2011 Aug 2.

PMID:
21813466
24.

Artificial selection for a green revolution gene during japonica rice domestication.

Asano K, Yamasaki M, Takuno S, Miura K, Katagiri S, Ito T, Doi K, Wu J, Ebana K, Matsumoto T, Innan H, Kitano H, Ashikari M, Matsuoka M.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11034-9. doi: 10.1073/pnas.1019490108. Epub 2011 Jun 6.

25.

Selection fine-tunes the expression of microRNA target genes in Arabidopsis thaliana.

Takuno S, Innan H.

Mol Biol Evol. 2011 Sep;28(9):2429-34. doi: 10.1093/molbev/msr084. Epub 2011 Apr 3.

PMID:
21478371
26.

Lowly expressed genes in Arabidopsis thaliana bear the signature of possible pseudogenization by promoter degradation.

Yang L, Takuno S, Waters ER, Gaut BS.

Mol Biol Evol. 2011 Mar;28(3):1193-203. doi: 10.1093/molbev/msq298. Epub 2010 Nov 8.

PMID:
21059790
27.

Assessment of genetic diversity of accessions in Brassicaceae genetic resources by frequency distribution analysis of S haplotypes.

Takuno S, Oikawa E, Kitashiba H, Nishio T.

Theor Appl Genet. 2010 Apr;120(6):1129-38. doi: 10.1007/s00122-009-1240-x. Epub 2009 Dec 29.

PMID:
20039015
28.

Selection to maintain paralogous amino acid differences under the pressure of gene conversion in the heat-shock protein genes in yeast.

Takuno S, Innan H.

Mol Biol Evol. 2009 Dec;26(12):2655-9. doi: 10.1093/molbev/msp211. Epub 2009 Sep 10.

PMID:
19745001
29.

Preservation of a pseudogene by gene conversion and diversifying selection.

Takuno S, Nishio T, Satta Y, Innan H.

Genetics. 2008 Sep;180(1):517-31. doi: 10.1534/genetics.108.091918. Epub 2008 Aug 30.

30.
31.

Evolution of complexity in miRNA-mediated gene regulation systems.

Takuno S, Innan H.

Trends Genet. 2008 Feb;24(2):56-9. doi: 10.1016/j.tig.2007.11.002. Epub 2008 Jan 14.

PMID:
18192068
32.

Effects of recombination on hitchhiking diversity in the Brassica self-incompatibility locus complex.

Takuno S, Fujimoto R, Sugimura T, Sato K, Okamoto S, Zhang SL, Nishio T.

Genetics. 2007 Oct;177(2):949-58. Epub 2007 Aug 24.

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