Evo-Devo: Are there any general rules between ontogeny (embryogenesis) and phylogeny (evolution)? Some say that we passed through fish-like stage when we were fetus, but does this have
something to do with our evolutionary history?
Evolvability: Bodyplan evolution seems to be very conservative when compared to other features (e.g. size, coat color), but why? Can we quantitate which animals, phenotypes, or developmental system tends to evolve more? Is it possible that we quantitate evolvability (or constrained status) of animal features?
Evolvedness: Which developmental systems of animal species are more evolved? Can we say tadpole stage of frogs are more ancestral, and later stages (e.g., adult) are more evolved?
Microchimerism: We are chimera by nature, having maternal cells in our body, but what are the roles of these microchimeric cells? Is there a possibility that maternal cess are involved in an onset/progress of fetal disease?
We study whatever we feel it interesting, and we welcome students with strong curiosity. We are waiting for your contact.
The publication list here is not to flaunt my modest achievements, but to obtrain scientific feedbacks (preferably constructive criticism) from you.
I'm wanting to explore an exciting scientific adventure over the discussions. Thank you :)
*: corresponding author
The Developmental Transcriptome for Lytechinus variegatus Exhibits Temporally Punctuated Gene Expression Changes
John D. Hogan, Jessica L. Keenan, Lingqi Luo, Dakota Y. Hawkins, Jonas Ibn-Salem, Arjun Lamba, Daphne Schatzberg, Michael L. Piacentino, Daniel T. Zuch, Amanda B. Core, Carolyn Blumberg, Bernd Timmermann, José Horacio Grau, Emily Speranza, Miguel A. Andrade-Narravo, Naoki Irie, Albert J. Poustka, Cynthia A. Bradham
bioRxiv (non peer-reviewd article) https://doi.org/10.1101/481309 (2019)
Evolutionary transition in accessible chromatin landscapes during vertebrate embryogenesis
Masahiro Uesaka*, Shigeru Kuratani, Hiroyuki Takeda, Naoki Irie
bioRxiv 481309 (non peer-reviewd article) https://doi.org/10.1101/481309 (2019)
Centromere evolution and CpG methylation during vertebrate speciation
Kazuki Ichikawa, Shingo Tomioka, Yuta Suzuki, Ryohei Nakamura, Koichiro Doi, Jun Yoshimura, Masahiko Kumagai, Yusuke Inoue, Yui Uchida, Naoki Irie, Hiroyuki Takeda* & Shinich Morishita*
Nature Communications 1833 (2017)
Weighted gene co-expression network analysis reveals potential genes involved in early metamorphosis process in sea cucumber Apostichopus japonicus
Yongxin Li, Mani Kikuchi, Xueyan Li, Qionghua Gao, Zijun Xiong, Yandong Ren, Ruoping Zhao, Bingyu Mao, Mariko Kondo, Naoki Irie, Wen Wang*
Biochemical and Biophysical Research Communications (2017)
Constrained vertebrate evolution by pleiotropic genes
Haiyang Hu, Masahiro Uesaka, Song Guo, Kotaro Shimai, Tsai-Ming Lu, Fang Li, Satoko Fujimoto, Masato Ishikawa, Shiping Liu, Yohei Sasagawa, Guojie Zhang, Shigeru Kuratani, Jr-Kai Yu, Takehiro G. Kusakabe, Philipp Khaitovich, Naoki Irie*; the EXPANDE Consortium
Nature Ecology & Evolution,1, 1722–1730 (2017)
Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features
Ryohei Seki, Cai Li, Qi Fang, Shinichi Hayashi, Shiro Egawa, Jiang Hu, Luohao Xu, Hailin Pan, Mao Kondo, Tomohiko Sato, Haruka Matsubara, Namiko Kamiyama, Keiichi Kitajima, Daisuke Saito, Yang Liu, M. Thomas P. Gilbert, Qi Zhou, Xing Xu, Toshihiko Shiroishi, Naoki Irie*, Koji Tamura* & Guojie Zhang*
Nature Communications, 14229, (2017)
Unexpected link between polyketide synthase and calcium carbonate biomineralization
Motoki Hojo, Ai Omi, Gen Hamanaka, Kazutoshi Shindo, Atsuko Shimada, Mariko Kondo, Takanori Narita, Masato Kiyomoto, Yohei Katsuyama, Yasuo Ohnishi, Naoki Irie and Hiroyuki Takeda
Zoological Letters, 1:3, (2015)
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
Richard E. Green*, Edward L. Braun, Joel Armstrong, Dent Earl, Ngan Nguyen, Glenn Hickey, Michael W. Vandewege, John A. St. John, Salvador Capella-Gutiérrez, Todd A. Castoe, Colin Kern, Matthew K. Fujita, Juan C. Opazo, Jerzy Jurka, Kenji K. Kojima, Juan Caballero, Robert M. Hubley, Arian F. Smit, Roy N. Platt, Christine A. Lavoie, Meganathan P. Ramakodi, John W. Finger Jr., Alexander Suh, Sally R. Isberg, Lee Miles, Amanda Y. Chong, Weerachai Jaratlerdsiri, Jaime Gongora, Christopher Moran, Andrés Iriarte, John McCormack, Shane C. Burgess, Scott V. Edwards, Eric Lyons, Christina Williams, Matthew Breen, Jason T. Howard, Cathy R. Gresham, Daniel G. Peterson, Jürgen Schmitz, David D. Pollock, David Haussler, Eric W. Triplett, Guojie Zhang, Naoki Irie, Erich D. Jarvis, Christopher A. Brochu, Carl J. Schmidt, Fiona M. McCarthy, Brant C. Faircloth, Federico G. Hoffmann, Travis C. Glenn, Toni Gabaldón, Benedict Paten, and David A. Ray*
Science, 12 December Vol. 346 no. 6215 (2014)
The Evolutionary Origin of the Vertebrate Body Plan: The Problem of Head Segmentation
Takayuki Onai, Naoki Irie , and Shigeru Kuratani
Annual Review of Genomics and Human Genetics, Vol. 15: 443-459 (2014)
The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan
Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis.
Naoki Irie*, Shigeru Kuratani
Nature Communications, 2 : 248., 2011 + (Erratum)
Reviews of Biliary Atresia: A New Immunological Insight on Etiopathogenesis
Toshihiro Muraji, David L. Suskind, and Naoki Irie
Expert Review of Gastroenterology & Hepatology, Dec; 3(6): 599-606. (2009)
Maternal HLA class I compatibility in patients with biliary atresia.
Naoki Irie, Toshihiro Muraji, Naoki Hosaka, Yasutsugu Takada, Seisuke Sakamoto, Kohichi Tanaka
Journal of Pediatric Gastroenterology & Nutrition, Volume 49, Issue 4, 488-492 (2009)
Maternal Microchimerism in Underlying Pathogenesis of Biliary Atresia: Quantification and Phenotypes of Maternal Cells in the Liver.
Toshihiro Muraji, Naoki Hosaka, Naoki Irie, Makiko Yoshida, Yukihiro Imai, Kohichi Tanaka, Yasutsugu Takada, Seisuke Sakamoto, Hironori Haga, Susumu Ikehara
Pediatrics, Mar 1; 121, 3 (2008)
Fused protein of PKC activation loop and PDK1-interacting fragment (AL-PIF) functions as a pseudosubstrate and an inhibitory molecule for PDK1 when expressed in cells
Takahiro Seki, Naoki Irie, Kyoko Nakamura, Hiroshi Sakaue, Wataru Ogawa, Masato Kasuga, Hideyuki Yamamoto, Shiho Ohmori, Naoaki Saito, and Norio Sakai
Genes to Cells, 11: pages 1051-1070, Sep (2006)
Essential roles of Meltrin beta (ADAM19) in heart development.
Kazuto Kurohara, Kouji Komatsu, Tomohiro Kurisaki, Aki Masuda, Naoki Irie, Masahide Asano, Katsuko Sudo, Yo-ichi Nabeshima, Yoichiro Iwakura, and Atsuko Sehara-Fujisawa
Developmental Biology, Volume 267, Issue 1, pages 14-28 (2004)
Subtype- and species-specific knockdown of PKC using short interfering RNA
Naoki Irie, Norio Sakai, Takehiko Ueyama, Taketoshi Kajimoto, Ysuhito Shirai, and Naoaki Saito
Biochem Biophys Res Commun, 298(5): pages 738-43 (2002)
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