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Items: 1 to 50 of 93

1.

Horizontal Gene Transfer in Five Parasite Plant Species in Orobanchaceae.

Kado T, Innan H.

Genome Biol Evol. 2018 Nov 8. doi: 10.1093/gbe/evy219. [Epub ahead of print]

PMID:
30407540
2.

Neutral Theory in Cancer Cell Population Genetics.

Niida A, Iwasaki WM, Innan H.

Mol Biol Evol. 2018 Jun 1;35(6):1316-1321. doi: 10.1093/molbev/msy091.

PMID:
29718454
3.

Replication stress induces accumulation of FANCD2 at central region of large fragile genes.

Okamoto Y, Iwasaki WM, Kugou K, Takahashi KK, Oda A, Sato K, Kobayashi W, Kawai H, Sakasai R, Takaori-Kondo A, Yamamoto T, Kanemaki MT, Taoka M, Isobe T, Kurumizaka H, Innan H, Ohta K, Ishiai M, Takata M.

Nucleic Acids Res. 2018 Apr 6;46(6):2932-2944. doi: 10.1093/nar/gky058.

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.

PMID:
29358726
5.

Simulation framework for generating intratumor heterogeneity patterns in a cancer cell population.

Iwasaki WM, Innan H.

PLoS One. 2017 Sep 6;12(9):e0184229. doi: 10.1371/journal.pone.0184229. eCollection 2017.

6.

Forward and backward evolutionary processes and allele frequency spectrum in a cancer cell population.

Ohtsuki H, Innan H.

Theor Popul Biol. 2017 Oct;117:43-50. doi: 10.1016/j.tpb.2017.08.006. Epub 2017 Sep 1.

PMID:
28866007
7.

Evaluating the potential roles of the Gray and Extension loci in the coat coloration of Thoroughbred racing horses.

Sakamoto T, Fawcett JA, Innan H.

J Equine Sci. 2017;28(2):61-65. doi: 10.1294/jes.28.61. Epub 2017 Jul 6.

8.

varver: a database of microsatellite variation in vertebrates.

Yashima AS, Innan H.

Mol Ecol Resour. 2017 Jul;17(4):824-833. doi: 10.1111/1755-0998.12625. Epub 2016 Nov 21.

PMID:
27796069
9.

High Similarity between Distantly Related Species of a Plant SINE Family Is Consistent with a Scenario of Vertical Transmission without Horizontal Transfers.

Fawcett JA, Innan H.

Mol Biol Evol. 2016 Oct;33(10):2593-604. doi: 10.1093/molbev/msw130. Epub 2016 Jul 19.

PMID:
27436006
10.

Spreading good news.

Fawcett JA, Innan H.

Elife. 2015 Apr 2;4. doi: 10.7554/eLife.07108. No abstract available.

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.

Divergent selection for opsin gene variation in guppy (Poecilia reticulata) populations of Trinidad and Tobago.

Tezuka A, Kasagi S, van Oosterhout C, McMullan M, Iwasaki WM, Kasai D, Yamamichi M, Innan H, Kawamura S, Kawata M.

Heredity (Edinb). 2014 Nov;113(5):381-9. doi: 10.1038/hdy.2014.35. Epub 2014 Apr 2.

13.

Meiotic recombination cold spots in chromosomal cohesion sites.

Ito M, Kugou K, Fawcett JA, Mura S, Ikeda S, Innan H, Ohta K.

Genes Cells. 2014 May;19(5):359-73. doi: 10.1111/gtc.12138. Epub 2014 Mar 17.

14.

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.

15.

Population genetics and molecular evolution of DNA sequences in transposable elements. I. A simulation framework.

Kijima TE, Innan H.

Genetics. 2013 Nov;195(3):957-67. doi: 10.1534/genetics.113.150292. Epub 2013 Sep 3.

16.

Theoretical framework of population genetics with somatic mutations taken into account: application to copy number variations in humans.

Ezawa K, Innan H.

Heredity (Edinb). 2013 Nov;111(5):364-74. doi: 10.1038/hdy.2013.59. Epub 2013 Aug 28.

17.

The role of gene conversion in preserving rearrangement hotspots in the human genome.

Fawcett JA, Innan H.

Trends Genet. 2013 Oct;29(10):561-8. doi: 10.1016/j.tig.2013.07.002. Epub 2013 Aug 13.

PMID:
23953668
18.

The linkage method: a novel approach for SNP detection and haplotype reconstruction from a single diploid individual using next-generation sequence data.

Sasaki E, Sugino RP, Innan H.

Mol Biol Evol. 2013 Sep;30(9):2187-96. doi: 10.1093/molbev/mst103. Epub 2013 May 31.

PMID:
23728796
19.

Competition between the sperm of a single male can increase the evolutionary rate of haploid expressed genes.

Ezawa K, Innan H.

Genetics. 2013 Jul;194(3):709-19. doi: 10.1534/genetics.113.152066. Epub 2013 May 11.

20.

Simulation-based likelihood approach for evolutionary models of phenotypic traits on phylogeny.

Kutsukake N, Innan H.

Evolution. 2013 Feb;67(2):355-67. doi: 10.1111/j.1558-5646.2012.01775.x. Epub 2012 Sep 17.

PMID:
23356609
21.

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.

22.

Molecular evolutionary routes that lead to innovations.

Brunet F, Innan H, Liao BY, Wang W.

Int J Evol Biol. 2012;2012:483176. doi: 10.1155/2012/483176. Epub 2012 Oct 4. No abstract available.

23.

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.

24.

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
25.

Genome sequencing reveals agronomically important loci in rice using MutMap.

Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R.

Nat Biotechnol. 2012 Jan 22;30(2):174-8. doi: 10.1038/nbt.2095.

PMID:
22267009
26.

The coalescent with selection on copy number variants.

Teshima KM, Innan H.

Genetics. 2012 Mar;190(3):1077-86. doi: 10.1534/genetics.111.135343. Epub 2011 Dec 14.

27.

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.

28.

Estimating the migration rate from genetic variation data.

Yamamichi M, Innan H.

Heredity (Edinb). 2012 Apr;108(4):362-3. doi: 10.1038/hdy.2011.83. Epub 2011 Sep 21. No abstract available.

29.

An autosomal analysis gives no genetic evidence for complex speciation of humans and chimpanzees.

Yamamichi M, Gojobori J, Innan H.

Mol Biol Evol. 2012 Jan;29(1):145-56. doi: 10.1093/molbev/msr172. Epub 2011 Sep 8.

30.

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.

31.

FancJ/Brip1 helicase protects against genomic losses and gains in vertebrate cells.

Kitao H, Nanda I, Sugino RP, Kinomura A, Yamazoe M, Arakawa H, Schmid M, Innan H, Hiom K, Takata M.

Genes Cells. 2011 Jun;16(6):714-27. doi: 10.1111/j.1365-2443.2011.01523.x.

32.

Natural selection on gene order in the genome reorganization process after whole-genome duplication of yeast.

Sugino RP, Innan H.

Mol Biol Evol. 2012 Jan;29(1):71-9. doi: 10.1093/molbev/msr118. Epub 2011 May 5.

PMID:
21546358
33.

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
34.

Special Issue: Gene Conversion in Duplicated Genes.

Innan H.

Genes (Basel). 2011 Jun 17;2(2):394-6. doi: 10.3390/genes2020394.

35.

The Rate and Tract Length of Gene Conversion between Duplicated Genes.

Mansai SP, Kado T, Innan H.

Genes (Basel). 2011 Mar 25;2(2):313-31. doi: 10.3390/genes2020313.

36.

Neutral and non-neutral evolution of duplicated genes with gene conversion.

Fawcett JA, Innan H.

Genes (Basel). 2011 Feb 18;2(1):191-209. doi: 10.3390/genes2010191.

37.

The evolution of gene duplications: classifying and distinguishing between models.

Innan H, Kondrashov F.

Nat Rev Genet. 2010 Feb;11(2):97-108. doi: 10.1038/nrg2689. Epub 2010 Jan 6. Review.

PMID:
20051986
38.

Recombination yet inefficient selection along the Drosophila melanogaster subgroup's fourth chromosome.

Arguello JR, Zhang Y, Kado T, Fan C, Zhao R, Innan H, Wang W, Long M.

Mol Biol Evol. 2010 Apr;27(4):848-61. doi: 10.1093/molbev/msp291. Epub 2009 Dec 14.

39.

On the estimation of the insertion time of LTR retrotransposable elements.

Kijima TE, Innan H.

Mol Biol Evol. 2010 Apr;27(4):896-904. doi: 10.1093/molbev/msp295. Epub 2009 Dec 2.

PMID:
19955475
40.

The power of the methods for detecting interlocus gene conversion.

Mansai SP, Innan H.

Genetics. 2010 Feb;184(2):517-27. doi: 10.1534/genetics.109.111161. Epub 2009 Nov 30.

41.

An explicit signature of balancing selection for color-vision variation in new world monkeys.

Hiwatashi T, Okabe Y, Tsutsui T, Hiramatsu C, Melin AD, Oota H, Schaffner CM, Aureli F, Fedigan LM, Innan H, Kawamura S.

Mol Biol Evol. 2010 Feb;27(2):453-64. doi: 10.1093/molbev/msp262. Epub 2009 Oct 27.

PMID:
19861643
42.

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
43.

mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection.

Teshima KM, Innan H.

BMC Bioinformatics. 2009 May 30;10:166. doi: 10.1186/1471-2105-10-166.

44.

Potential of fish opsin gene duplications to evolve new adaptive functions.

Gojobori J, Innan H.

Trends Genet. 2009 May;25(5):198-202. doi: 10.1016/j.tig.2009.03.008. Epub 2009 Apr 11.

PMID:
19362746
45.

Population genetic models of duplicated genes.

Innan H.

Genetica. 2009 Sep;137(1):19-37. doi: 10.1007/s10709-009-9355-1. Epub 2009 Mar 6. Review.

PMID:
19266289
46.

Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice.

Takahashi Y, Teshima KM, Yokoi S, Innan H, Shimamoto K.

Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4555-60. doi: 10.1073/pnas.0812092106. Epub 2009 Feb 25.

47.

Duplication and gene conversion in the Drosophila melanogaster genome.

Osada N, Innan H.

PLoS Genet. 2008 Dec;4(12):e1000305. doi: 10.1371/journal.pgen.1000305. Epub 2008 Dec 12.

48.

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.

49.

The evolutionary rate of duplicated genes under concerted evolution.

Mano S, Innan H.

Genetics. 2008 Sep;180(1):493-505. doi: 10.1534/genetics.108.087676. Epub 2008 Aug 30.

50.

Efficient inference of bacterial strain trees from genome-scale multilocus data.

Than C, Sugino R, Innan H, Nakhleh L.

Bioinformatics. 2008 Jul 1;24(13):i123-31. doi: 10.1093/bioinformatics/btn149.

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