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Evolutionary view of pluripotency seen from early development of non-mammalian amniotes.

Nakanoh S, Agata K.

Dev Biol. 2019 Aug 15;452(2):95-103. doi: 10.1016/j.ydbio.2019.04.014. Epub 2019 Apr 25.


A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology.

Matsunami M, Suzuki M, Haramoto Y, Fukui A, Inoue T, Yamaguchi K, Uchiyama I, Mori K, Tashiro K, Ito Y, Takeuchi T, Suzuki KT, Agata K, Shigenobu S, Hayashi T.

DNA Res. 2019 Jun 1;26(3):217-229. doi: 10.1093/dnares/dsz003.


JmjC Domain-Encoding Genes Are Conserved in Highly Regenerative Metazoans and Are Associated with Planarian Whole-Body Regeneration.

Cao PL, Kumagai N, Inoue T, Agata K, Makino T.

Genome Biol Evol. 2019 Feb 1;11(2):552-564. doi: 10.1093/gbe/evz021.


Association Between Sport Participation, Body Composition, Physical Fitness, and Social Correlates Among Adolescents: The PAHL Study.

Agata K, Monyeki MA.

Int J Environ Res Public Health. 2018 Dec 9;15(12). pii: E2793. doi: 10.3390/ijerph15122793.


Correction to: A Subtractive FACS Method for Isolation of Planarian Stem Cells and Neural Cells.

Hayashi T, Agata K.

Methods Mol Biol. 2018;1774:E1. doi: 10.1007/978-1-4939-7802-1_26.


A family case of X-linked Alport syndrome patients with a novel variant in COL4A5.

Kashiwagi Y, Suzuki S, Agata K, Morishima Y, Inagaki N, Numabe H, Kawashima H.

CEN Case Rep. 2019 May;8(2):75-78. doi: 10.1007/s13730-018-0368-4. Epub 2018 Oct 6.


Coordination between binocular field and spontaneous self-motion specifies the efficiency of planarians' photo-response orientation behavior.

Akiyama Y, Agata K, Inoue T.

Commun Biol. 2018 Sep 21;1:148. doi: 10.1038/s42003-018-0151-2. eCollection 2018.


Cas9 ribonucleoprotein complex allows direct and rapid analysis of coding and noncoding regions of target genes in Pleurodeles waltl development and regeneration.

Suzuki M, Hayashi T, Inoue T, Agata K, Hirayama M, Suzuki M, Shigenobu S, Takeuchi T, Yamamoto T, Suzuki KT.

Dev Biol. 2018 Nov 15;443(2):127-136. doi: 10.1016/j.ydbio.2018.09.008. Epub 2018 Sep 10.


Clinical Usefulness of Magnetic Resonance Imaging in Four Children With Scleroderma.

Agata K, Kawashima H, Kumada A, Kashiwagi Y, Hara H.

Arch Rheumatol. 2017 Nov 2;33(2):230-235. doi: 10.5606/ArchRheumatol.2018.6498. eCollection 2018 Jun.


Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians.

An Y, Kawaguchi A, Zhao C, Toyoda A, Sharifi-Zarchi A, Mousavi SA, Bagherzadeh R, Inoue T, Ogino H, Fujiyama A, Chitsaz H, Baharvand H, Agata K.

Zoological Lett. 2018 Aug 29;4:24. doi: 10.1186/s40851-018-0102-2. eCollection 2018.


Improving the standards for gut microbiome analysis of fecal samples: insights from the field biology of Japanese macaques on Yakushima Island.

Hayakawa T, Sawada A, Tanabe AS, Fukuda S, Kishida T, Kurihara Y, Matsushima K, Liu J, Akomo-Okoue EF, Gravena W, Kashima M, Suzuki M, Kadowaki K, Suzumura T, Inoue E, Sugiura H, Hanya G, Agata K.

Primates. 2018 Sep;59(5):423-436. doi: 10.1007/s10329-018-0671-x. Epub 2018 Jun 25.


A Subtractive FACS Method for Isolation of Planarian Stem Cells and Neural Cells.

Hayashi T, Agata K.

Methods Mol Biol. 2018;1774:467-478. doi: 10.1007/978-1-4939-7802-1_19. Erratum in: Methods Mol Biol. 2018;1774:E1.


RNA Interference in Planarians: Feeding and Injection of Synthetic dsRNA.

Shibata N, Agata K.

Methods Mol Biol. 2018;1774:455-466. doi: 10.1007/978-1-4939-7802-1_18.


Spatio-temporal neural stem cell behavior leads to both perfect and imperfect structural brain regeneration in adult newts.

Urata Y, Yamashita W, Inoue T, Agata K.

Biol Open. 2018 Jun 25;7(6). pii: bio033142. doi: 10.1242/bio.033142.


Role of MEKK1 in the anterior-posterior patterning during planarian regeneration.

Hosoda K, Motoishi M, Kunimoto T, Nishimura O, Hwang B, Kobayashi S, Yazawa S, Mochii M, Agata K, Umesono Y.

Dev Growth Differ. 2018 Aug;60(6):341-353. doi: 10.1111/dgd.12541. Epub 2018 Jun 13.


Searching for non-transposable targets of planarian nuclear PIWI in pluripotent stem cells and differentiated cells.

Kashima M, Agata K, Shibata N.

Dev Growth Differ. 2018 Jun;60(5):260-277. doi: 10.1111/dgd.12536. Epub 2018 May 23.


Clinical features of solitary functioning kidney.

Kashiwagi Y, Agata K, Go S, Nishimata S, Kawashima H.

CEN Case Rep. 2018 May;7(1):185-186. doi: 10.1007/s13730-018-0314-5. Epub 2018 Feb 5. No abstract available.


Direct estimation of de novo mutation rates in a chimpanzee parent-offspring trio by ultra-deep whole genome sequencing.

Tatsumoto S, Go Y, Fukuta K, Noguchi H, Hayakawa T, Tomonaga M, Hirai H, Matsuzawa T, Agata K, Fujiyama A.

Sci Rep. 2017 Nov 1;7(1):13561. doi: 10.1038/s41598-017-13919-7.


Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals.

Uesaka M, Agata K, Oishi T, Nakashima K, Imamura T.

BMC Genomics. 2017 Apr 7;18(1):285. doi: 10.1186/s12864-017-3662-1.


Pupal development and pigmentation process of a polka-dotted fruit fly, Drosophila guttifera (Insecta, Diptera).

Fukutomi Y, Matsumoto K, Agata K, Funayama N, Koshikawa S.

Dev Genes Evol. 2017 Jun;227(3):171-180. doi: 10.1007/s00427-017-0578-3. Epub 2017 Mar 9.


Inactivation of Sonic Hedgehog Signaling and Polydactyly in Limbs of Hereditary Multiple Malformation, a Novel Type of Talpid Mutant.

Matsubara Y, Nakano M, Kawamura K, Tsudzuki M, Funahashi JI, Agata K, Matsuda Y, Kuroiwa A, Suzuki T.

Front Cell Dev Biol. 2016 Dec 27;4:149. doi: 10.3389/fcell.2016.00149. eCollection 2016.


Analyzing pERK Activation During Planarian Regeneration.

Fraguas S, Umesono Y, Agata K, Cebrià F.

Methods Mol Biol. 2017;1487:303-315.


Jak1/Stat3 signaling acts as a positive regulator of pluripotency in chicken pre-gastrula embryos.

Nakanoh S, Fuse N, Tadokoro R, Takahashi Y, Agata K.

Dev Biol. 2017 Jan 1;421(1):43-51. doi: 10.1016/j.ydbio.2016.11.001. Epub 2016 Nov 3.


Molecular markers for X-ray-insensitive differentiated cells in the Inner and outer regions of the mesenchymal space in planarian Dugesia japonica.

Teramoto M, Kudome-Takamatsu T, Nishimura O, An Y, Kashima M, Shibata N, Agata K.

Dev Growth Differ. 2016 Sep;58(7):609-19. doi: 10.1111/dgd.12309. Epub 2016 Aug 17.


Functional joint regeneration is achieved using reintegration mechanism in Xenopus laevis.

Tsutsumi R, Yamada S, Agata K.

Regeneration (Oxf). 2016 Jan 6;3(1):26-38. doi: 10.1002/reg2.49. eCollection 2016 Feb.


Multiple Neuropeptide-Coding Genes Involved in Planarian Pharynx Extension.

Shimoyama S, Inoue T, Kashima M, Agata K.

Zoolog Sci. 2016 Jun;33(3):311-9. doi: 10.2108/zs150170.


Inheritance of a Nuclear PIWI from Pluripotent Stem Cells by Somatic Descendants Ensures Differentiation by Silencing Transposons in Planarian.

Shibata N, Kashima M, Ishiko T, Nishimura O, Rouhana L, Misaki K, Yonemura S, Saito K, Siomi H, Siomi MC, Agata K.

Dev Cell. 2016 May 9;37(3):226-37. doi: 10.1016/j.devcel.2016.04.009.


Simple blood-feeding method for live imaging of gut tube remodeling in regenerating planarians.

Hosoda K, Morimoto M, Motoishi M, Nishimura O, Agata K, Umesono Y.

Dev Growth Differ. 2016 Apr;58(3):260-9. doi: 10.1111/dgd.12270. Epub 2016 Mar 7.


Bidirectional promoters link cAMP signaling with irreversible differentiation through promoter-associated non-coding RNA (pancRNA) expression in PC12 cells.

Yamamoto N, Agata K, Nakashima K, Imamura T.

Nucleic Acids Res. 2016 Jun 20;44(11):5105-22. doi: 10.1093/nar/gkw113. Epub 2016 Mar 4.


Legionella thermalis sp. nov., isolated from hot spring water in Tokyo, Japan.

Ishizaki N, Sogawa K, Inoue H, Agata K, Edagawa A, Miyamoto H, Fukuyama M, Furuhata K.

Microbiol Immunol. 2016 Mar;60(3):203-8. doi: 10.1111/1348-0421.12366.


Heterogeneity of chromatoid bodies in adult pluripotent stem cells of planarian Dugesia japonica.

Kashima M, Kumagai N, Agata K, Shibata N.

Dev Growth Differ. 2016 Feb;58(2):225-37. doi: 10.1111/dgd.12268. Epub 2016 Feb 9.


The ancestral gene repertoire of animal stem cells.

Alié A, Hayashi T, Sugimura I, Manuel M, Sugano W, Mano A, Satoh N, Agata K, Funayama N.

Proc Natl Acad Sci U S A. 2015 Dec 22;112(51):E7093-100. doi: 10.1073/pnas.1514789112. Epub 2015 Dec 7.


Dynamics of Dark-Fly Genome Under Environmental Selections.

Izutsu M, Toyoda A, Fujiyama A, Agata K, Fuse N.

G3 (Bethesda). 2015 Dec 4;6(2):365-76. doi: 10.1534/g3.115.023549.


Control of Maintenance and Regeneration of Planarian Eyes by ovo.

Cross SD, Johnson AA, Gilles BJ, Bachman LA, Inoue T, Agata K, Marmorstein LY, Marmorstein AD.

Invest Ophthalmol Vis Sci. 2015 Nov;56(12):7604-10. doi: 10.1167/iovs.15-17458.


Aquatic adaptation and the evolution of smell and taste in whales.

Kishida T, Thewissen J, Hayakawa T, Imai H, Agata K.

Zoological Lett. 2015 Feb 13;1:9. doi: 10.1186/s40851-014-0002-z. eCollection 2015.


Planarian shows decision-making behavior in response to multiple stimuli by integrative brain function.

Inoue T, Hoshino H, Yamashita T, Shimoyama S, Agata K.

Zoological Lett. 2015 Feb 1;1:7. doi: 10.1186/s40851-014-0010-z. eCollection 2015.


Unusually Large Number of Mutations in Asexually Reproducing Clonal Planarian Dugesia japonica.

Nishimura O, Hosoda K, Kawaguchi E, Yazawa S, Hayashi T, Inoue T, Umesono Y, Agata K.

PLoS One. 2015 Nov 20;10(11):e0143525. doi: 10.1371/journal.pone.0143525. eCollection 2015.


Spontaneous Behaviors and Wall-Curvature Lead to Apparent Wall Preference in Planarian.

Akiyama Y, Agata K, Inoue T.

PLoS One. 2015 Nov 5;10(11):e0142214. doi: 10.1371/journal.pone.0142214. eCollection 2015.


Dynamic Transport and Cementation of Skeletal Elements Build Up the Pole-and-Beam Structured Skeleton of Sponges.

Nakayama S, Arima K, Kawai K, Mohri K, Inui C, Sugano W, Koba H, Tamada K, Nakata YJ, Kishimoto K, Arai-Shindo M, Kojima C, Matsumoto T, Fujimori T, Agata K, Funayama N.

Curr Biol. 2015 Oct 5;25(19):2549-54. doi: 10.1016/j.cub.2015.08.023. Epub 2015 Sep 17.


Genetic basis of keloid formation in wounds after cardiac surgery.

Kulawczuk P, Czapla N, Bińczak-Kuleta A, Safranow K, Jaworska-Kulawczuk A, Gajewska D, Agata K, Brykczyński M, Bargiel P.

Kardiochir Torakochirurgia Pol. 2014 Sep;11(3):273-7. doi: 10.5114/kitp.2014.45676. Epub 2014 Sep 28.


Epigenetic modification maintains intrinsic limb-cell identity in Xenopus limb bud regeneration.

Hayashi S, Kawaguchi A, Uchiyama I, Kawasumi-Kita A, Kobayashi T, Nishide H, Tsutsumi R, Tsuru K, Inoue T, Ogino H, Agata K, Tamura K, Yokoyama H.

Dev Biol. 2015 Oct 15;406(2):271-82. doi: 10.1016/j.ydbio.2015.08.013. Epub 2015 Aug 14.


Verification of chicken Nanog as an epiblast marker and identification of chicken PouV as Pou5f3 by newly raised antibodies.

Nakanoh S, Fuse N, Takahashi Y, Agata K.

Dev Growth Differ. 2015 Apr;57(3):251-63. doi: 10.1111/dgd.12205. Epub 2015 Apr 1.


Detection of Legionella species in environmental water by the quantitative PCR method in combination with ethidium monoazide treatment.

Inoue H, Takama T, Yoshizaki M, Agata K.

Biocontrol Sci. 2015;20(1):71-4. doi: 10.4265/bio.20.71.


Molecular characterization of viable Legionella spp. in cooling tower water samples by combined use of ethidium monoazide and PCR.

Inoue H, Fujimura R, Agata K, Ohta H.

Microbes Environ. 2015;30(1):108-12. doi: 10.1264/jsme2.ME14115. Epub 2015 Jan 16.


Two distinct roles of the yorkie/yap gene during homeostasis in the planarian Dugesia japonica.

Hwang B, An Y, Agata K, Umesono Y.

Dev Growth Differ. 2015 Apr;57(3):209-17. doi: 10.1111/dgd.12195. Epub 2015 Feb 24.


A colony multiplex quantitative PCR-Based 3S3DBC method and variations of it for screening DNA libraries.

An Y, Toyoda A, Zhao C, Fujiyama A, Agata K.

PLoS One. 2015 Feb 3;10(2):e0116997. doi: 10.1371/journal.pone.0116997. eCollection 2015.


Reintegration of the regenerated and the remaining tissues during joint regeneration in the newt Cynops pyrrhogaster.

Tsutsumi R, Inoue T, Yamada S, Agata K.

Regeneration (Oxf). 2015 Apr 8;2(1):26-36. doi: 10.1002/reg2.28. eCollection 2015 Feb.


Gene activation-associated long noncoding RNAs function in mouse preimplantation development.

Hamazaki N, Uesaka M, Nakashima K, Agata K, Imamura T.

Development. 2015 Mar 1;142(5):910-20. doi: 10.1242/dev.116996. Epub 2015 Jan 29.


Sequential actions of β-catenin and Bmp pattern the oral nerve net in Nematostella vectensis.

Watanabe H, Kuhn A, Fushiki M, Agata K, Özbek S, Fujisawa T, Holstein TW.

Nat Commun. 2014 Dec 23;5:5536. doi: 10.1038/ncomms6536.

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