Deciphering the origin of developmental stability: The role of intracellular expression variability in evolutionary conservation.
Yui Uchida*, Masato Tsutsumi, Shunsuke Ichii, Naoki Irie, Chikara Furusawa
Evolution & Development https://doi.org/10.1111/ede.12473 (2024)
Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences.
Daqi Yu, Yandong Ren, Masahiro Uesaka, Alan J. S. Beavan, Matthieu Muffato, Jieyu Shen, Yongxin Li, Iori Sato, Wenting Wan, James W. Clark, Joseph N. Keating, Emily M. Carlisle, Richard P. Dearden, Sam Giles, Emma Randle, Robert S. Sansom, Roberto Feuda, James F. Fleming, Fumiaki Sugahara, Carla Cummins, Mateus Patricio, Wasiu Akanni, Salvatore D’Aniello, Cristiano Bertolucci, Naoki Irie, Cantas Alev, Guojun Sheng, Alex de Mendoza, Ignacio Maeso, Manuel Irimia, Bastian Fromm, Kevin J. Peterson, Sabyasachi Das, Masayuki Hirano, Jonathan P. Rast, Max D. Cooper, Jordi Paps, Davide Pisani, Shigeru Kuratani, Fergal J. Martin, Wen Wang, Philip C. J. Donoghue, Yong E. Zhang & Juan Pascual-Anaya*
Nature Ecol. Evol. (2024)
Stability in gene expression and body-plan development leads to evolutionary conservation.
Yui Uchida*, Hiroyuki Takeda, Chikara Furusawa & Naoki Irie*
EvoDevo volume 14, Article number: 4 (2023)
Emergent roles of maternal microchimerism inpostnatal development.
Alexandria Borges*, Castellan Flore, and Naoki Irie*
Development, Growth & Differentiation (2022) 1–7. DOI1:0.1111/dgd.12830
Postnatal depletion of maternal cells biases T lymphocytes and natural killer cells' profiles toward early activation in the spleen.
Castellan Flore*, and Naoki Irie*
Biology Open (2022) DOI:10.1242/bio.059334 
Whole-embryonic identification of maternal microchimeric cell types in mouse using single-cell RNA sequencing.
Kana Fujimoto*, Akira Nakajima, Shohei Hori, Yumiko Tanaka, Yoshitaka Shirasaki, Sotaro Uemura, and Naoki Irie*
Scientific Reports (2022) DOI:10.1038/s41598-022-20781-9
The pentameric hydrocoel lobes organize adult pentameral structures in a sea cucumber, Apostichopus japonicus.
Sumio Udagawa, Akiko Nagai, Mani Kikuchi, Akihito Omori, Atsushi Tajika, Mieko Saito, Toru Miura, Naoki Irie, Yasuhiro Kamei, Mariko Kondoa
Developmental Biology (2022) https://doi.org/10.1016/j.ydbio.2022.09.002
Potential contribution of intrinsic developmental stability toward body plan conservation.
Yui Uchida*, Shuji Shigenobu, Hiroyuki Takeda, Chikara Furusawa & Naoki Irie*
BMC Biology (2022) 20, 82
Distinguishing Evolutionary Conservation from Derivedness.
Jason Cheok Kuan Leong*, Masahiro Uesaka, Naoki Irie*
Life (2022) 12(3), 440.
Whole embryonic detection of maternal microchimeric cells highlights significant differences in their numbers among individuals.
Kana Fujimoto*, Akira Nakajima, Shohei Hori, Naoki Irie*
PLOS ONE (2021) 16(12): e0261357
Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms.
Jason Cheok Kuan Leong*, Yongxin Li, Masahiro Uesaka, Yui Uchida, Akihito Omori, Meng Hao, Wenting Wan, Yang Dong, Yandong RenSi Zhang, Tao Zeng, Fayou Wang6, Luonan Chen, Gary Wessel, Brian T. Livingston, Cynthia Bradham, Wen Wang, Naoki Irie*
Front. Cell Dev. Biol. (2021) https://doi.org/10.3389/fcell.2021.749963
Measuring potential effects of the developmental burden associated with the vertebrate notochord.
Satoko Fujimoto Kaori Yamanaka Chiharu Tanegashima Osamu Nishimura Shigehiro Kuraku Shigeru Kuratani Naoki Irie*
Journal of Experimental Zoology, part B (2021) https://doi.org/10.1002/jez.b.23032
The developmental hourglass model and recapitulation: An attempt to integrate the two models
Masahiro Uesaka*, Shigeru Kuratani, Naoki Irie
Journal of Experimental Zoology, part B (2021) https://doi.org/10.1002/jez.b.23027
How can recapitulation be reconciled with modern concepts of evolution?
Shigeru Kuratani*, Masahiro Uesaka, Naoki Irie
Journal of Experimental Zoology, part B (2021) https://doi.org/10.1002/jez.b.23020
Genomic insights of body plan transitions from bilateral to pentameric symmetry in Echinoderms
Yongxin Li, Akihito Omori, Rachel Flores, Sheri Satterfield, Christine Nguyen, Tatsuya Ota, Toko Tsurugaya, Tetsuro Ikuta, Kazuho Ikeo, Mani Kikuchi,
Jason Leong, Adrian Reich, Meng Hao, Wenting Wan, Yang Dong, Yandong Ren, Si Zhang, Tao Zeng, Masahiro Uesaka, Yui Uchida, Xueyan Li, Tomoko Shibata, Takahiro Bino, Kota Ogawa,
Shuji Shigenobu, Mariko Kondo, Fayou Wang, Luonan Chen, Gary Wessel, Hidetoshi Saiga, Robert Cameron, Brian Livingston, Cynthia Bradham, Wen Wang*, Naoki Irie*
Communications Biology 3, Article number: 371 (2020)
Toward understanding of evolutionary constraints: experimental and theoretical approaches
Chikara Furusawa*, Naoki Irie*
Biophysical Reviews DOI: 10.1007/s12551-020-00708-2 (2020)
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
Developmental Biology Vol. 460, Issue 2, 139-154 (2020)
Recapitulation-like developmental transitions of chromatin accessibility in vertebrates
Masahiro Uesaka*, Shigeru Kuratani, Hiroyuki Takeda, Naoki Irie
Zoological Letters 5, Article number: 33 (2019)
The phylum Vertebrata: a case for zoological recognition
Naoki Irie*, Noriyuki Satoh, Shigeru Kuratani
Zoological Letters 4:32 (2018)
Embryonic lethality is not sufficient to explain hourglass-like conservation of vertebrate embryos
Yui Uchida*, Masahiro Uesaka, Takayoshi Yamamoto, Hiroyuki Takeda and Naoki Irie*
EvoDevo 9:7 (2018)
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)
Remaining questions related to the hourglass model in vertebrate evolution.
Naoki Irie*
Current Opinion in Genetics & Development, 45:103-107, (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 developmental hourglass model: a predictor of the basic body plan?
Naoki Irie*, and Shigeru Kuratani
Development, 141:4649-4655 (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)
Turtle ghrelin
Juan Pascual-Anaya, Amonida Zaddissa, Bronwen Aken, Guojie Zhang and Naoki Irie*
Nature Genetics, 46,526 (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
Zhuo Wang, Juan Pascual-Anaya, Amonida Zadissa, Wenqi Li, Yoshihito Niimura, Zhiyong Huang, Chunyi Li, Simon White, Zhiqiang Xiong, Dongming Fang, Bo Wang, Yao Ming, Yan Chen, Yuan Zheng, Shigehiro Kuraku, Miguel Pignatelli, Javier Herrero, Kathryn Beal, Masafumi Nozawa, Juan Wang, Hongyan Zhang, Lili Yu, Shuji Shigenobu, Junyi Wang, Jiannan Liu, Paul Flicek, Steve Searle, Jun Wang, Shigeru Kuratani, Ye Yin, Bronwen Aken, Guojie Zhang, Naoki Irie*
Nature Genetics , 45(6):701-706, 2013
Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis.
Naoki Irie*, Shigeru Kuratani
Nature Communications, 2 : 248., 2011
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)
The vertebrate phylotypic stage and an early bilaterian-related stage in mouse embryogenesis defined by genomic information
Naoki Irie and Atsuko Sehara-Fujisawa
BMC Biology, 5:1, 12 January (2007)
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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