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Items: 1 to 50 of 100

1.

Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?

Kadota M, Nishimura O, Miura H, Tanaka K, Hiratani I, Kuraku S.

Gigascience. 2020 Jan 1;9(1). pii: giz158. doi: 10.1093/gigascience/giz158.

2.

Nodal paralogues underlie distinct mechanisms for visceral left-right asymmetry in reptiles and mammals.

Kajikawa E, Horo U, Ide T, Mizuno K, Minegishi K, Hara Y, Ikawa Y, Nishimura H, Uchikawa M, Kiyonari H, Kuraku S, Hamada H.

Nat Ecol Evol. 2020 Jan 6. doi: 10.1038/s41559-019-1072-2. [Epub ahead of print]

PMID:
31907383
3.

Loss of olfaction in sea snakes provides new perspectives on the aquatic adaptation of amniotes.

Kishida T, Go Y, Tatsumoto S, Tatsumi K, Kuraku S, Toda M.

Proc Biol Sci. 2019 Sep 11;286(1910):20191828. doi: 10.1098/rspb.2019.1828. Epub 2019 Sep 11.

PMID:
31506057
4.

Evolution of nodal and nodal-related genes and the putative composition of the heterodimers that trigger the nodal pathway in vertebrates.

Opazo JC, Kuraku S, Zavala K, Toloza-Villalobos J, Hoffmann FG.

Evol Dev. 2019 Jul;21(4):205-217. doi: 10.1111/ede.12292. Epub 2019 Jun 17.

PMID:
31210006
5.

Comprehensive analysis of genes contributing to euryhalinity in the bull shark, Carcharhinus leucas; Na+-Cl- co-transporter is one of the key renal factors upregulated in acclimation to low-salinity environment.

Imaseki I, Wakabayashi M, Hara Y, Watanabe T, Takabe S, Kakumura K, Honda Y, Ueda K, Murakumo K, Matsumoto R, Matsumoto Y, Nakamura M, Takagi W, Kuraku S, Hyodo S.

J Exp Biol. 2019 Jun 27;222(Pt 12). pii: jeb201780. doi: 10.1242/jeb.201780.

6.

Evaluating Genome Assemblies and Gene Models Using gVolante.

Nishimura O, Hara Y, Kuraku S.

Methods Mol Biol. 2019;1962:247-256. doi: 10.1007/978-1-4939-9173-0_15.

PMID:
31020565
7.

Asymmetric paralog evolution between the "cryptic" gene Bmp16 and its well-studied sister genes Bmp2 and Bmp4.

Feiner N, Motone F, Meyer A, Kuraku S.

Sci Rep. 2019 Feb 28;9(1):3136. doi: 10.1038/s41598-019-40055-1.

8.

Involvement of HGF/MET signaling in appendicular muscle development in cartilaginous fish.

Okamoto E, Moriyama Y, Kuraku S, Kai KI, Tanaka M.

Dev Growth Differ. 2019 Jan;61(1):97-103. doi: 10.1111/dgd.12591.

PMID:
30644548
9.

Co-option of the PRDM14-CBFA2T complex from motor neurons to pluripotent cells during vertebrate evolution.

Kawaguchi M, Sugiyama K, Matsubara K, Lin CY, Kuraku S, Hashimoto S, Suwa Y, Yong LW, Takino K, Higashida S, Kawamura D, Yu JK, Seki Y.

Development. 2019 Jan 28;146(2). pii: dev168633. doi: 10.1242/dev.168633.

10.

Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates.

Hara Y, Yamaguchi K, Onimaru K, Kadota M, Koyanagi M, Keeley SD, Tatsumi K, Tanaka K, Motone F, Kageyama Y, Nozu R, Adachi N, Nishimura O, Nakagawa R, Tanegashima C, Kiyatake I, Matsumoto R, Murakumo K, Nishida K, Terakita A, Kuratani S, Sato K, Hyodo S, Kuraku S.

Nat Ecol Evol. 2018 Nov;2(11):1761-1771. doi: 10.1038/s41559-018-0673-5. Epub 2018 Oct 8.

PMID:
30297745
11.

Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei.

Tanegashima C, Nishimura O, Motone F, Tatsumi K, Kadota M, Kuraku S.

Sci Data. 2018 Oct 8;5:180200. doi: 10.1038/sdata.2018.200.

12.

A de novo transcriptome assembly of the zebra bullhead shark, Heterodontus zebra.

Onimaru K, Tatsumi K, Shibagaki K, Kuraku S.

Sci Data. 2018 Oct 8;5:180197. doi: 10.1038/sdata.2018.197.

13.

Loss of Fam60a, a Sin3a subunit, results in embryonic lethality and is associated with aberrant methylation at a subset of gene promoters.

Nabeshima R, Nishimura O, Maeda T, Shimizu N, Ide T, Yashiro K, Sakai Y, Meno C, Kadota M, Shiratori H, Kuraku S, Hamada H.

Elife. 2018 Aug 2;7. pii: e36435. doi: 10.7554/eLife.36435.

14.

Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes.

Hara Y, Takeuchi M, Kageyama Y, Tatsumi K, Hibi M, Kiyonari H, Kuraku S.

BMC Biol. 2018 Apr 16;16(1):40. doi: 10.1186/s12915-018-0509-4.

15.

Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications.

Onimaru K, Kuraku S.

Brief Funct Genomics. 2018 Sep 27;17(5):352-361. doi: 10.1093/bfgp/ely008. Review.

16.

A staging table for the embryonic development of the brownbanded bamboo shark (Chiloscyllium punctatum).

Onimaru K, Motone F, Kiyatake I, Nishida K, Kuraku S.

Dev Dyn. 2018 May;247(5):712-723. doi: 10.1002/dvdy.24623. Epub 2018 Mar 10.

17.

Publisher Correction: Migratory appendicular muscles precursor cells in the common ancestor to all vertebrates.

Okamoto E, Kusakabe R, Kuraku S, Hyodo S, Robert-Moreno A, Onimaru K, Sharpe J, Kuratani S, Tanaka M.

Nat Ecol Evol. 2017 Nov;1(11):1784. doi: 10.1038/s41559-017-0374-5.

PMID:
29042579
18.

gVolante for standardizing completeness assessment of genome and transcriptome assemblies.

Nishimura O, Hara Y, Kuraku S.

Bioinformatics. 2017 Nov 15;33(22):3635-3637. doi: 10.1093/bioinformatics/btx445.

19.

Migratory appendicular muscles precursor cells in the common ancestor to all vertebrates.

Okamoto E, Kusakabe R, Kuraku S, Hyodo S, Robert-Moreno A, Onimaru K, Sharpe J, Kuratani S, Tanaka M.

Nat Ecol Evol. 2017 Nov;1(11):1731-1736. doi: 10.1038/s41559-017-0330-4. Epub 2017 Oct 2. Erratum in: Nat Ecol Evol. 2017 Nov;1(11):1784.

PMID:
28970537
20.

CTCF binding landscape in jawless fish with reference to Hox cluster evolution.

Kadota M, Hara Y, Tanaka K, Takagi W, Tanegashima C, Nishimura O, Kuraku S.

Sci Rep. 2017 Jul 10;7(1):4957. doi: 10.1038/s41598-017-04506-x.

21.

Correction to 'Evolutionary diversification of retinoic acid receptor ligand-binding pocket structure by molecular tinkering'.

Gutierrez-Mazariegos J, Nadendla EK, Studer RA, Alvarez S, de Lera AR, Kuraku S, Bourguet W, Schubert M, Laudet V.

R Soc Open Sci. 2016 Dec 14;3(12):160895. doi: 10.1098/rsos.160895. eCollection 2016 Dec.

22.

Molecular cytogenetic characterization of chromosome site-specific repetitive sequences in the Arctic lamprey (Lethenteron camtschaticum, Petromyzontidae).

Ishijima J, Uno Y, Nunome M, Nishida C, Kuraku S, Matsuda Y.

DNA Res. 2017 Feb 1;24(1):93-101. doi: 10.1093/dnares/dsw053.

23.

Gene expression profiling of granule cells and Purkinje cells in the zebrafish cerebellum.

Takeuchi M, Yamaguchi S, Sakakibara Y, Hayashi T, Matsuda K, Hara Y, Tanegashima C, Shimizu T, Kuraku S, Hibi M.

J Comp Neurol. 2017 May 1;525(7):1558-1585. doi: 10.1002/cne.24114. Epub 2016 Oct 25.

PMID:
27615194
24.

The evolutionally-conserved function of group B1 Sox family members confers the unique role of Sox2 in mouse ES cells.

Niwa H, Nakamura A, Urata M, Shirae-Kurabayashi M, Kuraku S, Russell S, Ohtsuka S.

BMC Evol Biol. 2016 Aug 31;16:173. doi: 10.1186/s12862-016-0755-4.

25.

Evolutionary diversification of retinoic acid receptor ligand-binding pocket structure by molecular tinkering.

Gutierrez-Mazariegos J, Nadendla EK, Studer RA, Alvarez S, de Lera AR, Kuraku S, Bourguet W, Schubert M, Laudet V.

R Soc Open Sci. 2016 Mar 16;3(3):150484. doi: 10.1098/rsos.150484. eCollection 2016 Mar. Erratum in: R Soc Open Sci. 2016 Dec 14;3(12 ):160895.

26.

Evidence from cyclostomes for complex regionalization of the ancestral vertebrate brain.

Sugahara F, Pascual-Anaya J, Oisi Y, Kuraku S, Aota S, Adachi N, Takagi W, Hirai T, Sato N, Murakami Y, Kuratani S.

Nature. 2016 Mar 3;531(7592):97-100. doi: 10.1038/nature16518. Epub 2016 Feb 15.

PMID:
26878236
27.

Incorporating tree-thinking and evolutionary time scale into developmental biology.

Kuraku S, Feiner N, Keeley SD, Hara Y.

Dev Growth Differ. 2016 Jan;58(1):131-42. doi: 10.1111/dgd.12258. Epub 2016 Jan 5. Review.

PMID:
26818824
28.

Evolution of the fish heart by sub/neofunctionalization of an elastin gene.

Moriyama Y, Ito F, Takeda H, Yano T, Okabe M, Kuraku S, Keeley FW, Koshiba-Takeuchi K.

Nat Commun. 2016 Jan 19;7:10397. doi: 10.1038/ncomms10397.

29.

Mammalian Reverse Genetics without Crossing Reveals Nr3a as a Short-Sleeper Gene.

Sunagawa GA, Sumiyama K, Ukai-Tadenuma M, Perrin D, Fujishima H, Ukai H, Nishimura O, Shi S, Ohno RI, Narumi R, Shimizu Y, Tone D, Ode KL, Kuraku S, Ueda HR.

Cell Rep. 2016 Jan 26;14(3):662-677. doi: 10.1016/j.celrep.2015.12.052. Epub 2016 Jan 7.

30.

Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation.

Hara Y, Tatsumi K, Yoshida M, Kajikawa E, Kiyonari H, Kuraku S.

BMC Genomics. 2015 Nov 18;16:977. doi: 10.1186/s12864-015-2007-1.

31.

Neofunctionalization of Androgen Receptor by Gain-of-Function Mutations in Teleost Fish Lineage.

Ogino Y, Kuraku S, Ishibashi H, Miyakawa H, Sumiya E, Miyagawa S, Matsubara H, Yamada G, Baker ME, Iguchi T.

Mol Biol Evol. 2016 Jan;33(1):228-44. doi: 10.1093/molbev/msv218. Epub 2015 Oct 27.

PMID:
26507457
32.

Diversification of non-visual photopigment parapinopsin in spectral sensitivity for diverse pineal functions.

Koyanagi M, Wada S, Kawano-Yamashita E, Hara Y, Kuraku S, Kosaka S, Kawakami K, Tamotsu S, Tsukamoto H, Shichida Y, Terakita A.

BMC Biol. 2015 Sep 15;13:73. doi: 10.1186/s12915-015-0174-9.

33.

Discovery of conventional prolactin from the holocephalan elephant fish, Callorhinchus milii.

Yamaguchi Y, Takagi W, Kuraku S, Moriyama S, Bell JD, Seale AP, Lerner DT, Grau EG, Hyodo S.

Gen Comp Endocrinol. 2015 Dec 1;224:216-27. doi: 10.1016/j.ygcen.2015.08.020. Epub 2015 Aug 29.

PMID:
26320855
34.

A shift in anterior-posterior positional information underlies the fin-to-limb evolution.

Onimaru K, Kuraku S, Takagi W, Hyodo S, Sharpe J, Tanaka M.

Elife. 2015 Aug 18;4. doi: 10.7554/eLife.07048.

35.

Comparative, transcriptome analysis of self-organizing optic tissues.

Andrabi M, Kuraku S, Takata N, Sasai Y, Love NR.

Sci Data. 2015 Jun 23;2:150030. doi: 10.1038/sdata.2015.30. eCollection 2015.

36.

Evolution of retinoic acid receptors in chordates: insights from three lamprey species, Lampetra fluviatilis, Petromyzon marinus, and Lethenteron japonicum.

Campo-Paysaa F, Jandzik D, Takio-Ogawa Y, Cattell MV, Neef HC, Langeland JA, Kuratani S, Medeiros DM, Mazan S, Kuraku S, Laudet V, Schubert M.

Evodevo. 2015 May 7;6:18. doi: 10.1186/s13227-015-0016-4. eCollection 2015.

37.
38.

Mechanisms of endoderm formation in a cartilaginous fish reveal ancestral and homoplastic traits in jawed vertebrates.

Godard BG, Coolen M, Le Panse S, Gombault A, Ferreiro-Galve S, Laguerre L, Lagadec R, Wincker P, Poulain J, Da Silva C, Kuraku S, Carre W, Boutet A, Mazan S.

Biol Open. 2014 Oct 31;3(11):1098-107. doi: 10.1242/bio.20148037.

39.

Evolution of the vertebrate Pax4/6 class of genes with focus on its novel member, the Pax10 gene.

Feiner N, Meyer A, Kuraku S.

Genome Biol Evol. 2014 Jun 19;6(7):1635-51. doi: 10.1093/gbe/evu135.

40.

Comparative analysis of pleurodiran and cryptodiran turtle embryos depicts the molecular ground pattern of the turtle carapacial ridge.

Pascual-Anaya J, Hirasawa T, Sato I, Kuraku S, Kuratani S.

Int J Dev Biol. 2014;58(10-12):743-50. doi: 10.1387/ijdb.140296jp.

41.

Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing.

Tatsumi K, Nishimura O, Itomi K, Tanegashima C, Kuraku S.

Biotechniques. 2015 May 1;58(5):253-7. doi: 10.2144/000114288. eCollection 2015 May.

42.

Saltatory evolution of the ectodermal neural cortex gene family at the vertebrate origin.

Feiner N, Murakami Y, Breithut L, Mazan S, Meyer A, Kuraku S.

Genome Biol Evol. 2013;5(8):1485-502. doi: 10.1093/gbe/evt104.

43.

Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes.

Renz AJ, Meyer A, Kuraku S.

PLoS One. 2013 Jun 25;8(6):e66400. doi: 10.1371/journal.pone.0066400. Print 2013.

44.

Developmental expression and evolution of muscle-specific microRNAs conserved in vertebrates.

Tani S, Kuraku S, Sakamoto H, Inoue K, Kusakabe R.

Evol Dev. 2013 Jul-Aug;15(4):293-304. doi: 10.1111/ede.12039.

PMID:
23809703
45.

aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.

Kuraku S, Zmasek CM, Nishimura O, Katoh K.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W22-8. doi: 10.1093/nar/gkt389. Epub 2013 May 15.

46.

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.

Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D, Wang B, Ming Y, Chen Y, Zheng Y, Kuraku S, Pignatelli M, Herrero J, Beal K, Nozawa M, Li Q, Wang J, Zhang H, Yu L, Shigenobu S, Wang J, Liu J, Flicek P, Searle S, Wang J, Kuratani S, Yin Y, Aken B, Zhang G, Irie N.

Nat Genet. 2013 Jun;45(6):701-706. doi: 10.1038/ng.2615. Epub 2013 Apr 28. Erratum in: Nat Genet. 2014 Jun;46(6):657.

47.

Homeogenetic inductive mechanism of segmentation in polychaete tail regeneration.

Niwa N, Akimoto-Kato A, Sakuma M, Kuraku S, Hayashi S.

Dev Biol. 2013 Sep 15;381(2):460-70. doi: 10.1016/j.ydbio.2013.04.010. Epub 2013 Apr 20.

48.

The African coelacanth genome provides insights into tetrapod evolution.

Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K.

Nature. 2013 Apr 18;496(7445):311-6. doi: 10.1038/nature12027.

49.

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.

Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SM, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W.

Nat Genet. 2013 Apr;45(4):415-21, 421e1-2. doi: 10.1038/ng.2568. Epub 2013 Feb 24.

50.

Non-parsimonious evolution of hagfish Dlx genes.

Fujimoto S, Oisi Y, Kuraku S, Ota KG, Kuratani S.

BMC Evol Biol. 2013 Jan 19;13:15. doi: 10.1186/1471-2148-13-15.

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