Publications

  1. HOME
  2. Publications

2024

  1. Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences. Yu D, Ren Y, Uesaka M, Beavan AJS, Muffato M, Shen J, Li Y, Sato I, Wan W, Clark JW, Keating JN, Carlisle EM, Dearden RP, Giles S, Randle E, Sansom RS, Feuda R, Fleming JF, Sugahara F, Cummins C, Patricio M, Akanni W, D'Aniello S, Bertolucci C, Irie N, Alev C, Sheng G, de Mendoza A, Maeso I, Irimia M, Fromm B, Peterson KJ, Das S, Hirano M, Rast JP, Cooper MD, Paps J, Pisani D, Kuratani S, Martin FJ, Wang W, Donoghue PCJ, Zhang YE, Pascual-Anaya J. Nat Ecol Evol. 2024 Mar;8(3):519-535.Nature Ecology & Evolution
  2. Criteria for the standardization of stem-cell-based embryo models. Martinez Arias A, Rivron N, Moris N, Tam P, Alev C, Fu J, Hadjantonakis AK, Hanna JH, Minchiotti G, Pourquie O, Sheng G, Solnica Krezel L, Veenvliet JV, Warmflash A. Nat Cell Biol. 2024 Oct;26(10):1625-1628.Nature Cell Biology

2023

  1. Reconstituting human somitogenesis in vitro. Yamanaka Y, Hamidi S, Yoshioka-Kobayashi K, Munira S, Sunadome K, Zhang Y, Kurokawa Y, Ericsson R, Mieda A, Thompson JL, Kerwin J, Lisgo S, Yamamoto T, Moris N, Martinez-Arias A, Tsujimura T, Alev C. Nature. 2023 Feb;614(7948):509-520.Nature
  2. eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio-temporal architectures of cells. Mori T, Takase T, Lan KC, Yamane J, Alev C, Kimura A, Osafune K, Yamashita JK, Akutsu T, Kitano H, Fujibuchi W. BMC Bioinformatics. 2023 Jun 15;24(1):252.BMC Bioinformatics

2022

  1. In vitro models of pre- and post-gastrulation embryonic development. Hamidi S, Alev C. Curr Opin Genet Dev. 2022 Dec;77:101985.Current Opinion in Genetics & Development

2021

  1. Differentiation of Hypertrophic Chondrocytes from Human iPSCs for the In Vitro Modeling of Chondrodysplasias. Pretemer Y, Kawai S, Nagata S, Nishio M, Watanabe M, Tamaki S, Alev C, Yamanaka Y, Xue JY, Wang Z, Fukiage K, Tsukanaka M, Futami T, Ikegawa S, Toguchida J. Stem Cell Reports. 2021 Mar 9;16(3):610-625.Stem Cell Reports
  2. Organoids: ready for the revolution? Koo BK, Bartfeld S, Alev C. J Mol Med (Berl). 2021 Apr;99(4):441-442.Springer Nature
  3. Biomedical and societal impacts of in vitro embryo models of mammalian development. Moris N, Alev C, Pera M, Martinez Arias A. Stem Cell Reports. 2021 May 11;16(5):1021-1030. Stem Cell Reports
  4. Japan: prize diversity, not conformity, to boost research. Sheng G, Carninci P, Siomi MC, Suda T, Alev C. Nature. 2021 Nov;599(7884):201. Nature

2020

  1. Mesenchymal-epithelial transition regulates initiation of pluripotency exit before gastrulation. Hamidi S, Nakaya Y, Nagai H, Alev C, Kasukawa T, Chhabra S, Lee R, Niwa H, Warmflash A, Shibata T, Sheng G. Development. 2020 Feb 3;147(3):dev184960.Development
  2. Overview of Basic Mechanisms of Notch Signaling in Development and Disease. McIntyre B, Asahara T, Alev C. Adv Exp Med Biol. 2020;1227:9-27.Springer Nature
  3. Recapitulating the human segmentation clock with pluripotent stem cells. Matsuda M, Yamanaka Y, Uemura M, Osawa M, Saito MK, Nagahashi A, Nishio M, Guo L, Ikegawa S, Sakurai S, Kihara S, Maurissen TL, Nakamura M, Matsumoto T, Yoshitomi H, Ikeya M, Kawakami N, Yamamoto T, Woltjen K, Ebisuya M, Toguchida J, Alev C. Nature. 2020 Apr;580(7801):124-129.Nature
  4. Bidirectional Wnt signaling between endoderm and mesoderm confers tracheal identity in mouse and human cells. Kishimoto K, Furukawa KT, Luz-Madrigal A, Yamaoka A, Matsuoka C, Habu M, Alev C, Zorn AM, Morimoto M. Nat Commun. 2020 Aug 27;11(1):4159.Nature Communications
  5. Species-specific segmentation clock periods are due to differential biochemical reaction speeds. Matsuda M, Hayashi H, Garcia-Ojalvo J, Yoshioka-Kobayashi K, Kageyama R, Yamanaka Y, Ikeya M, Toguchida J, Alev C, Ebisuya M. Science. 2020 Sep 18;369(6510):1450-1455. Science

2019

  1. Biomechanical regulation of EMT and epithelial morphogenesis in amniote epiblast. Hamidi S, Nakaya Y, Nagai H, Alev C, Shibata T, Sheng G. Phys Biol. 2019 Apr 23;16(4):041002.Physical Biology
  2. Bi-allelic loss of function variants of TBX6 causes a spectrum of malformation of spine and rib including congenital scoliosis and spondylocostal dysostosis. Otomo N, Takeda K, Kawai S, Kou I, Guo L, Osawa M, Alev C, Kawakami N, Miyake N, Matsumoto N, Yasuhiko Y, Kotani T, Suzuki T, Uno K, Sudo H, Inami S, Taneichi H, Shigematsu H, Watanabe K, Yonezawa I, Sugawara R, Taniguchi Y, Minami S, Kaneko K, Nakamura M, Matsumoto M, Toguchida J, Watanabe K, Ikegawa S. J Med Genet. 2019 Sep;56(9):622-628. Journal Of Medical Genetics
  3. Twins at Conspicuously Different Developmental Stages in a Turtle Egg. Hirasawa T, Alev C, Kuratani S. Zoolog Sci. 2019 Feb 1;36(1):1-4. Zoological science
  4. In vitro bone-like nodules generated from patient-derived iPSCs recapitulate pathological bone phenotypes. Kawai S, Yoshitomi H, Sunaga J, Alev C, Nagata S, Nishio M, Hada M, Koyama Y, Uemura M, Sekiguchi K, Maekawa H, Ikeya M, Tamaki S, Jin Y, Harada Y, Fukiage K, Adachi T, Matsuda S, Toguchida J. Nat Biomed Eng. 2019 Jul;3(7):558-570.Nature Biomedical Engineering
  5. Novel computational model of gastrula morphogenesis to identify spatial discriminator genes by self-organizing map (SOM) clustering. Mori T, Takaoka H, Yamane J, Alev C, Fujibuchi W. Sci Rep. 2019 Aug 29;9(1):12597. Scientific Reports