title Publication list

We list only those publications that member(s) of our unit have conducted or contributed to;
for publications by current members that were published before joining our unit, go to the Member page.


20142017

Migratory appendicular muscles precursor cells in the common ancestor to all vertebrates
Eri Okamoto, Rie Kusakabe, Shigehiro Kuraku, Susumu Hyodo, Alexandre Robert-Moreno, Koh Onimaru, James Sharpe, Shigeru Kuratani & Mikiko Tanaka
Nature Ecology & Evolution 2017. doi:10.1038/s41559-017-0330-4 [ Press release: Japanese ]

gVolante for standardizing completeness assessment of genome and transcriptome assemblies
Osamu Nishimura, Yuichiro Hara, Shigehiro Kuraku
Bioinformatics 2017. doi: 10.1093/bioinformatics/btx445 [ gVolante Server ]

CTCF binding landscape in jawless fish with reference to Hox cluster evolution
Mitsutaka Kadota, Yuichiro Hara, Kaori Tanaka, Wataru Takagi, Chiharu Tanegashima, Osamu Nishimura, Shigehiro Kuraku
Scientific Reports 2017. 7, 4957. doi:10.1038/s41598-017-04506-x

Molecular cytogenetic characterization of chromosome site-specific repetitive sequences in the Arctic lamprey (Lethenteron camtschaticum, Petromyzontidae)
Junko Ishijima, Yoshinobu Uno, Mitsuo Nunome, Chizuko Nishida, Shigehiro Kuraku, Yoichi Matsuda
DNA Research 2017. 24(1): 93-101

円口類ヌタウナギとヤツメウナギの分子進化学
工樂 樹洋
月刊海洋 Vol.49, No.5, 2017


20142016

PRDM14 drives OCT3/4 recruitment via active demethylation in the transition from primed to naive pluripotency
Naoki Okashita, Yoshiaki Suwa, Osamu Nishimura, Nao Sakashita, Mitsutaka Kadota, Go Nagamatsu, Masanori Kawaguchi, Hiroki Kashida, Ayaka Nakajima, Makoto Tachibana, Yoshiyuki Seki
Stem Cell Reports 2016. 7: 1072-1086

ChIP-seq実験を成功に導くための秘訣:ChIP条件の最適化とサンプルQCについて
田中かおり、門田満隆
実 験医学 2016年10月号 Vol.34 No.16.

Gene expression profiling of granule cells and Purkinje cells in the zebrafish cerebellum
Miki Takeuchi, Shingo Yamaguchi, Masayoshi Sakakibara, Takuto Hayashi, Koji Matsuda, Yuichiro Hara, Chiharu Tanegashima, Takashi Shimizu, Shigehiro Kuraku and Masahiko Hibi
Journal of Comparative Neurology, doi: 10.1002/cne.24114

Molecular evolution in the lamprey genomes and its relevance to the timing of whole genome duplications
Tereza Manousaki, Huan Qiu, Miyuki Noro, Falk Hildebrand, Axel Meyer & Shigehiro Kuraku
in 'Jawless Fishes of the World, Volume 1', Cambridge Scholars Publishing

Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization
Jason A. West, Mari Mito, Satoshi Kurosaka, Toru Takumi, Chiharu Tanegashima, Takeshi Chujo, Kaori Yanaka, Robert E. Kingston, Tetsuro Hirose, Charles Bond, Archa Fox, Shinichi Nakagawa
The Journal of Cell Biology 2016 214: 817

The evolutionally-conserved function of group B1 Sox family members confers the unique role of Sox2 in mouse ES cells
Hitoshi Niwa, Akira Nakamura, Makoto Urata, Maki Shirae-Kurabayashi, Shigehiro Kuraku, Steven Russell and Satoshi Ohtsuka
BMC Evolutionary Biology 2016 16:173

Evolutionary diversification of retinoic acid receptor (RAR) ligand-binding pocket structure by molecular tinkering
Juliana Gutierrez-Mazariegos, Eswar Kumar Nadendla, Romain A. Studer, Susana Alvarez, Angel R. de Lera, Shigehiro Kuraku, William Bourguet, Michael Schubert & Vincent Laudet
Royal Society Open Science 2016, http://dx.doi.org/10.1098/rsos.150484

Evidence from cyclostomes for complex regionalization of the ancestral vertebrate brain
Fumiaki Sugahara, Juan Pascual-Anaya, Yasuhiro Oisi, Shigehiro Kuraku, Shin-ichi Aota, Noritaka Adachi, Wataru Takagi, Tamami Hirai, Noboru Sato, Yasunori Murakami & Shigeru Kuratani
Nature 2016, 531: 97-100 [ Press release: Japanese | English ]

Evolution of the fish heart by sub/neofunctionalization of an elastin gene
Yuuta Moriyama, Fumihiro Ito, Hiroyuki Takeda, Tohru Yano, Masataka Okabe, Shigehiro Kuraku, Fred W. Keeley & Kazuko Koshiba-Takeuchi
Nature Communications 2016, 7: 10397 [ Press release: Japanese ]

Mammalian reverse genetics without crossing reveals Nr3a as a short-sleeper gene
Genshiro A. Sunagawa, Kenta Sumiyama, Maki Ukai-Tadenuma, Dimitri Perrin, Hiroshi Fujishima, Hideki Ukai, Osamu Nishimura, Shoi Shi, Rei-ichiro Ohno, Ryohei Narumi, Yoshihiro Shimizu, Daisuke Tone, Koji L. Ode, Shigehiro Kuraku, Hiroki R. Ueda
Cell Reports 2016, DOI: 10.1016/j.celrep.2015.12.052 [ Press release: Japanese ]

Incorporating tree-thinking and evolutionary time scale into developmental biology
Shigehiro Kuraku, Nathalie Feiner, Sean D. Keeley, Yuichiro Hara
Development, Growth, and Differentiation 2016, DOI: 10.1111/dgd.12258

Neofunctionalization of androgen receptor by gain-of-function mutations in teleost fish lineage
Yukiko Ogino, Shigehiro Kuraku, Hiroshi Ishibashi, Hitoshi Miyakawa, Eri Sumiya, Shinichi Miyagawa, Hajime Matsubara, Gen Yamada, Michael E. Baker and Taisen Iguchi
Molecular Biology and Evolution 2016. 33: 228-244. [ Press release: Japanese ]

「どのアセンブリを使うか?: 分子系統学的観点に基づくアセンブリの評価」(only in Japanese)
原 雄一郎
日本進化学会ニュース 2016. 17(1): 23-29.

「脊椎動物ゲノム・トランスクリプトームアセンブリ完全度を評価する」(only in Japanese)
原 雄一郎
バイオサイエンスとインダストリー 毎日学術フォーラム 2016. 74(3): 228-230.

20142015


Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation
Yuichiro Hara; Kaori Tatsumi; Michio Yoshida; Eriko Kajikawa; Hiroshi Kiyonari; Shigehiro Kuraku
BMC Genomics 2015, 16: 977. [ Press release: Japanese | English ]

Diversification of non-visual photopigment parapinopsin in spectral sensitivity for diverse pineal functions
Mitsumasa Koyanagi, Seiji Wada, Emi Kawano-Yamashita, Yuichiro Hara, Shigehiro Kuraku, Shigeaki Kosaka, Koichi Kawakami, Satoshi Tamotsu, Hisao Tsukamoto, Yoshinori Shichida, Akihisa Terakita
BMC Biology 2015, 13: 73.{ Press release: Japanese ]

Discovery of conventional prolactin from the holocephalan elephant fish, Callorhinchus milii
Yoko Yamaguchi, Wataru Takagi, Shigehiro Kuraku, Shunsuke Moriyama, Justin D. Bell, Andre P. Seale, Darren T. Lerner, E. Gordon Grau, Susumu Hyodo
General and Comparative Endocrinology 2015, 224: 216-227.

A shift in anterior–posterior positional information underlies the fin-to-limb evolution
Koh Onimaru, Shigehiro Kuraku, Wataru Takagi, Susumu Hyodo, James Sharpe, & Mikiko Tanaka
eLife 2015, 4:e07048 [ Press release: Japanese ]

Comparative, transcriptome analysis of self-organizing optic tissues
Munazah Andrabi, Shigehiro Kuraku, Nozomu Takata, Yoshiki Sasai & Nick R. Love
Scientific Data 2015, 2. Article number: 150030

Reevaluating Emx gene phylogeny: homopolymeric amino acid tracts as a potential factor obscuring orthology signals in cyclostome genes
Miyuki Noro, Fumiaki Sugahara and Shigehiro Kuraku
BMC Evolutionary Biology, 2015 15: 78.

Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing
Kaori Tatsumi, Osamu Nishimura, Kazu Itomi, Chiharu Tanegashima, Shigehiro Kuraku
Biotechniques, 2015. 58: 253-257.

Evolution of retinoic acid receptors in chordates: insights from three lamprey species, Lampetra fluviatilis, Petromyzon marinus, and Lethenteron japonicum
Florent Campo-Paysaa, David Jandzik, Yoko Takio-Ogawa, Maria V Cattell, Haley C Neef, James A Langeland, Shigeru Kuratani, Daniel M Medeiros, Sylvie Mazan, Shigehiro Kuraku, Vincent Laudet and Michael Schubert
EvoDevo, 2015. 6: 18.

20142014

Mechanisms of endoderm formation in a cartilaginous fish reveal ancestral and homoplastic traits in jawed vertebrates Benoit G Godard, Marion Coolen, Sophie Le Panse, Aurelie Gombault, Susana Ferreiro-Galve, Laurent Laguerre, Ronan Lagadec, Patrick Wincker, Julie Poulain, Corinne Da Silva, Shigehiro Kuraku, Wilfrid Carre, Agnes Boutet, and Sylvie Mazan
Biology Open, published online. doi: 10.1242/​bio.20148037.


「ヒストン修飾や転写因子の結合領域を同定するコツやポイント」(only in Japanese)
門田満隆、蓑田亜希子
次世代シークエンス解析スタンダード
  羊土社 2014. 105-121.

20132013

Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells.
Kenjiro Adachi, Itoshi Nikaido, Hiroshi Ohta, Satoshi Ohtsuka, Hiroki Ura, Mitsutaka Kadota, Teruhiko Wakayama, Hiroki R. Ueda, & Hitoshi Niwa.
Molecular Cell
, 2013. 52: 380-392.

Homeogenetic inductive mechanism of segmentation in polychaete tail regeneration.
Nao Niwa, Ai Akimoto, Masashi Sakuma, Shigehiro Kuraku, and Shigeo Hayashi.
Developmental Biology, 2013. 381: 460-470.
 

aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.
Shigehiro Kuraku, Christian Zmasek, Osamu Nishimura, and Kazutaka Katoh.
Nucleic Acids Research, 2013. Web Server Issue. Accepted. [ aLeaves Server | MAFFT Server ]
 

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.
Zhuo Wang, et al.
Nature Genetics, 2013. 45: 701–706

Quartz-Seq: a highly reproducible and sensitive single-cell RNA-Seq reveals non-genetic gene expression heterogeneity
Yohei Sasagawa, Itoshi Nikaido, Tetsutaro Hayashi, Hiroki Danno, Kenichiro D Uno, Takeshi Imai and Hiroki R Ueda.
Genome Biology, 2013. 14: R31

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.
Jeramiah J Smith, Shigehiro Kuraku, Carson Holt, .... , Paul Flicek, Marianne E Bronner, Wesley C Warren, Sandra W Clifton, Richard K Wilson and Weiming Li.
Nature Genetics, 2013. 45: 415-421.

Non-parsimonious evolution of hagfish Dlx genes.
Satoko Fujimoto, Yasuhiro Oisi, Shigehiro Kuraku, Kinya G Ota and Shigeru Kuratani.
BMC Evolutionary Biology, 2013. 13:15.

The Dlx genes as clues to vertebrate genomics and craniofacial evolution.
Masaki Takechi, Noritaka Adachi, Tamami Hirai, Shigeru Kuratani, and Shigehiro Kuraku.
Seminars in Cell and Developmental Biology, 2013.24: 110-118.

Impact of asymmetric gene repertoire between cyclostomes and gnathostomes.
Shigehiro Kuraku
Seminars in Cell and Developmental Biology, 2013. 24: 119-127.

Craniofacial development of hagfishes and the evolution of vertebrates.
Yasuhiro Oisi, Kinya G. Ota, Shigehiro Kuraku, Satoko Fujimoto and Shigeru Kuratani
Nature, 2013. 493: 175-180. [ featured in News & Views ]

「aLeaves( エイリーヴズ):多様な動物群を網羅した、より簡便な分子系統解析の入り口として」(only in Japanese)
工樂樹洋
日本進化学会ニュース 2013. 14(3): 50-53.

2012 2012

Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC3 profiling in snake.
Kazumi Matsubara, Shigehiro Kuraku, Hiroshi Tarui, Osamu Nishimura, Chizuko Nishida, Kiyokazu Agata, Yoshinori Kumazawa and Yoichi Matsuda
BMC Genomics. 2012. 13: 604.

 

Pax2 modulates proliferation during specification of the otic and epibranchial placodes.
Sabine Freter, Yuko Muta, Paul O'Neill, Vassil S. Vassilev, Shigehiro Kuraku, Raj K. Ladher
Dev Dyn. 2012 In press. doi: 10.1002/dvdy.23856.

 

Genomic novelty at the vertebrate ancestor.
Shigehiro Kuraku
eLS 2012. DOI: 10.1002/9780470015902.a0024137

 

2011 2011

Overview of the transcriptome profiles identified in hagfish, shark, and bichir: current issues arising from some nonmodel vertebrate taxa.
Takechi M, Takeuchi M, Ota KG, Nishimura O, Mochii M, Itomi K, Adachi N, Takahashi M, Fujimoto S, Tarui H, Okabe M, Aizawa S, Kuratani S.
J Exp Zool B Mol Dev Evol. 2011 Nov 15;316(7):526-46. [ Vertebrate TimeCapsule Database ]

 

A LIM-homeobox gene is required for differentiation of Wnt-expressing cells at the posterior end of the planarian body.
Hayashi T, Motoishi M, Yazawa S, Itomi K, Tanegashima C, Nishimura O, Agata K, Tarui H.
Development. 2011 Sep;138(17):3679-88.

 

Etv2/ER71 induces vascular mesoderm from Flk1+PDGFR{alpha}+ primitive mesoderm.
Kataoka H, Hayashi M, Nakagawa R, Tanaka Y, Izumi N, Nishikawa S, Jakt ML, Tarui H, Nishikawa S.
Blood. 2011 Sep 12.
doi:10.1182

 

Travelling and splitting of a wave of hedgehog expression involved in spider-head segmentation.
Kanayama M, Akiyama-Oda Y, Nishimura O, Tarui H, Agata K, Oda H.
Nat Commun. 2011 Oct 11;2:500. doi: 10.1038

 

ERK signaling controls blastema cell differentiation during planarian regeneration.
Tasaki J, Shibata N, Nishimura O, Itomi K, Tabata Y, Son F, Suzuki N, Araki R, Abe M, Agata K, Umesono Y.
Development. 2011 Jun;138(12):2417-27.

 


2011 2010

Oocyte-type linker histone B4 is required for transdifferentiation of somatic cells in vivo.
Maki N, Suetsugu-Maki R, Sano S, Nakamura K, Nishimura O, Tarui H, Del Rio-Tsonis K, Ohsumi K, Agata K, Tsonis PA.
FASEB J. 2010 Sep;24(9):3462-7.

 

Single-cell gene profiling of planarian stem cells using fluorescent activated cell sorting and its "index sorting" function for stem cell research.
Hayashi T
, Shibata N, Okumura R, Kudome T, Nishimura O, Tarui H, Agata K.
Dev Growth Differ. 2010 Jan;52(1):131-44.

 

Expression profiles during dedifferentiation in newt lens regeneration revealed by expressed sequence tags.
Maki N, Martinson J, Nishimura O, Tarui H, Meller J, Tsonis PA, Agata K.
Mol Vis. 2010 Jan 18;16:72-8.

 

2011 2009

Planarian Hedgehog/Patched establishes anterior-posterior polarity by regulating Wnt signaling.
Yazawa S, Umesono Y, Hayashi T, Tarui H, Agata K.
Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22329-34.

 

To be or not to be a flatworm: the acoel controversy.
Egger B, Steinke D, Tarui H, De Mulder K, Arendt D, Borgonie G, Funayama N, Gschwentner R, Hartenstein V, Hobmayer B, Hooge M, Hrouda M, Ishida S, Kobayashi C, Kuales G, Nishimura O, Pfister D, Rieger R, Salvenmoser W, Smith J, Technau U, Tyler S, Agata K, Salzburger W, Ladurner P.
PLoS One. 2009;4(5):e5502.

 

2011 2008

Promotion of spermatogonial proliferation by neuregulin 1 in newt (Cynops pyrrhogaster) testis.
Oral O, Uchida I, Eto K, Nakayama Y, Nishimura O, Hirao Y, Ueda J, Tarui H, Agata K, Abé S.
Mech Dev. 2008 Sep-Oct;125(9-10):906-17.

 

Cthrc1 selectively activates the planar cell polarity pathway of Wnt signaling by stabilizing the Wnt-receptor complex.
Yamamoto S, Nishimura O, Misaki K, Nishita M, Minami Y, Yonemura S, Tarui H, Sasaki H.
Dev Cell. 2008 Jul;15(1):23-36.

 

Expression and functional analysis of musashi-like genes in planarian CNS regeneration.
Higuchi S, Hayashi T, Tarui H, Nishimura O, Nishimura K, Shibata N, Sakamoto H, Agata K.
Mech Dev
. 2008 Jul;125(7):631-45.

 

Expression profiling of circulating non-red blood cells in embryonic blood.
McIntyre BA, Alev C, Tarui H, Jakt LM, Sheng G.
BMC Dev Biol. 2008 Feb 27;8:21.

 

2011 2007

The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons.
Sone M, Hayashi T, Tarui H, Agata K, Takeichi M, Nakagawa S.
J Cell Sci. 2007 Aug 1;120(Pt 15):2498-506.

 

Regeneration-dependent conditional gene knockdown (Readyknock) in planarian: demonstration of requirement for Djsnap-25 expression in the brain for negative phototactic behavior.
Takano T, Pulvers JN, Inoue T, Tarui H, Sakamoto H, Agata K, Umesono Y.
Dev Growth Differ. 2007 Jun;49(5):383-94.

 

Progressive activation of Delta-Notch signaling from around the blastopore is required to set up a functional caudal lobe in the spider Achaearanea tepidariorum.
Oda H, Nishimura O, Hirao Y, Tarui H, Agata K, Akiyama-Oda Y.Development.
2007 Jun;134(12):2195-205.

 

Rapid accumulation of nucleostemin in nucleolus during newt regeneration.
Maki N, Takechi K, Sano S, Tarui H, Sasai Y, Agata K.
Dev Dyn. 2007 Apr;236(4):941-50.

 

The Dugesia ryukyuensis database as a molecular resource for studying switching of the reproductive system.
Ishizuka H, Maezawa T, Kawauchi J, Nodono H, Hirao Y, Nishimura O, Nakagawa H, Sekii K, Tasaka K, Tarui H, Agata K, Hoshi M, Kobayashi K, Sakakibara Y, Matsumoto M.
Zoolog Sci. 2007 Jan;24(1):31-7.

 

2011 2006

Evidence for different origin of sex chromosomes in snakes, birds, and mammals and step-wise differentiation of snake sex chromosomes.
Matsubara K, Tarui H, Toriba M, Yamada K, Nishida-Umehara C, Agata K, Matsuda Y.
Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18190-5.

 

2011 2005

Highly conserved linkage homology between birds and turtles: bird and turtle chromosomes are precise counterparts of each other.
Matsuda Y, Nishida-Umehara C, Tarui H, Kuroiwa A, Yamada K, Isobe T, Ando J, Fujiwara A, Hirao Y, Nishimura O, Ishijima J, Hayashi A, Saito T, Murakami T, Murakami Y, Kuratani S, Agata K.
Chromosome Res. 2005;13(6):601-15.

 

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