2024

Garge RK, Lynch V, Fields R, Casadei S, Best S, Stone J, Snyder M, McGann CD, Shendure J, Starita LM, Hamazaki N, Schweppe DK. The proteomic landscape and temporal dynamics of mammalian gastruloid development. bioRxiv. 2024 Sep 7;. doi: 10.1101/2024.09.05.609098. PubMed PMID: 39282277; PubMed Central PMCID: PMC11398484.

Deciphering the impact of genomic variation on function. Nature. 2024 Sep;633(8028):47-57. doi: 10.1038/s41586-024-07510-0. Epub 2024 Sep 4. Review. PubMed PMID: 39232149.

Hamazaki N, Yang W, Kubo CA, Qiu C, Martin BK, Garge RK, Regalado SG, Nichols EK, Pendyala S, Bradley N, Fowler DM, Lee C, Daza RM, Srivatsan S, Shendure J. Retinoic acid induces human gastruloids with posterior embryo-like structures. Nat Cell Biol. 2024 Aug 20;. doi: 10.1038/s41556-024-01487-8. [Epub ahead of print] PubMed PMID: 39164488.

Chen W, Choi J, Li X, Nathans JF, Martin B, Yang W, Hamazaki N, Qiu C, Lalanne JB, Regalado S, Kim H, Agarwal V, Nichols E, Leith A, Lee C, Shendure J. Symbolic recording of signalling and cis-regulatory element activity to DNA. Nature. 2024 Aug;632(8027):1073-1081. doi: 10.1038/s41586-024-07706-4. Epub 2024 Jul 17. PubMed PMID: 39020177; PubMed Central PMCID: PMC11357993.

Sepulveda-Rincon LP, Wang YF, Whilding C, Moyon B, Ojarikre OA, Maciulyte V, Hamazaki N, Hayashi K, Turner JMA, Leitch HG. Determining the potency of primordial germ cells by injection into early mouse embryos. Dev Cell. 2024 Mar 25;59(6):695-704.e5. doi: 10.1016/j.devcel.2024.01.022. Epub 2024 Feb 14. PubMed PMID: 38359835.

Qiu C, Martin BK, Welsh IC, Daza RM, Le TM, Huang X, Nichols EK, Taylor ML, Fulton O, O'Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, Noble WS, Hamazaki N, Moens CB, Kimelman D, Cao J, Schier AF, Spielmann M, Murray SA, Trapnell C, Shendure J. A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature. 2024 Feb;626(8001):1084-1093. doi: 10.1038/s41586-024-07069-w. Epub 2024 Feb 14. PubMed PMID: 38355799; PubMed Central PMCID: PMC10901739.

Hamazaki N, Yang W, Kubo C, Qiu C, Martin BK, Garge RK, Regalado SG, Nichols E, Lee C, Daza RM, Srivatsan S, Shendure J. Induction and in silico staging of human gastruloids with neural tube, segmented somites & advanced cell types. bioRxiv. 2024 Feb 12;. doi: 10.1101/2024.02.10.579769. PubMed PMID: 38405970; PubMed Central PMCID: PMC10888963.

2023

Weatherbee BAT, Gantner CW, Iwamoto-Stohl LK, Daza RM, Hamazaki N, Shendure J, Zernicka-Goetz M. A model of the post-implantation human embryo derived from pluripotent stem cells. Nature. 2023 Jun 27;. doi: 10.1038/s41586-023-06368-y. [Epub ahead of print] PubMed PMID: 37369347.

Qiu C, Martin BK, Welsh IC, Daza RM, Le TM, Huang X, Nichols EK, Taylor ML, Fulton O, Oâ Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, Noble WS, Hamazaki N, Moens CB, Kimelman D, Cao J, Schier AF, Spielmann M, Murray SA, Trapnell C, Shendure J. A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup. bioRxiv. 2023 Apr 5;. doi: 10.1101/2023.04.05.535726. PubMed PMID: 37066300; PubMed Central PMCID: PMC10104014.

Murakami K, Hamazaki N, Hamada N, Nagamatsu G, Okamoto I, Ohta H, Nosaka Y, Ishikura Y, Kitajima TS, Semba Y, Kunisaki Y, Arai F, Akashi K, Saitou M, Kato K, Hayashi K. Generation of functional oocytes from male mice in vitro. Nature. 2023 Mar;615(7954):900-906. doi: 10.1038/s41586-023-05834-x. Epub 2023 Mar 15. PubMed PMID: 36922585.

2022 and before

Hayashi M, Zywitza V, Naitou Y, Hamazaki N, Goeritz F, Hermes R, Holtze S, Lazzari G, Galli C, Stejskal J, Diecke S, Hildebrandt TB, Hayashi K. Robust induction of primordial germ cells of white rhinoceros on the brink of extinction. Sci Adv. 2022 Dec 9;8(49):eabp9683. doi: 10.1126/sciadv.abp9683. Epub 2022 Dec 9. PubMed PMID: 36490332; PubMed Central PMCID: PMC9733929.

Choi J, Chen W, Minkina A, Chardon FM, Suiter CC, Regalado SG, Domcke S, Hamazaki N, Lee C, Martin B, Daza RM, Shendure J. A time-resolved, multi-symbol molecular recorder via sequential genome editing. Nature. 2022 Aug;608(7921):98-107. doi: 10.1038/s41586-022-04922-8. Epub 2022 Jul 6. PubMed PMID: 35794474; PubMed Central PMCID: PMC9352581.

Naitou Y, Nagamatsu G, Hamazaki N, Shirane K, Hayashi M, Hayashi M, Kobayashi S, Hayashi K. Dual role of Ovol2 on the germ cell lineage segregation during gastrulation in mouse embryogenesis. Development. 2022 Feb 15;149(4). doi: 10.1242/dev.200319. Epub 2022 Feb 18. PubMed PMID: 35029669.

Hamazaki N, Kyogoku H, Araki H, Miura F, Horikawa C, Hamada N, Shimamoto S, Hikabe O, Nakashima K, Kitajima TS, Ito T, Leitch HG, Hayashi K. Reconstitution of the oocyte transcriptional network with transcription factors. Nature. 2021 Jan;589(7841):264-269. doi: 10.1038/s41586-020-3027-9. Epub 2020 Dec 16. PubMed PMID: 33328630.

Mayama S, Hamazaki N, Maruyama Y, Matsubara S, Kimura AP. Transcriptional activation of the mouse Scd2 gene by interdependent enhancers and long noncoding RNAs in ovarian granulosa cells. J Reprod Dev. 2020 Oct 13;66(5):435-444. doi: 10.1262/jrd.2019-161. Epub 2020 Jun 5. PubMed PMID: 32507774; PubMed Central PMCID: PMC7593631.

Hamada N, Hamazaki N, Shimamoto S, Hikabe O, Nagamatsu G, Takada Y, Kato K, Hayashi K. Germ cell-intrinsic effects of sex chromosomes on early oocyte differentiation in mice. PLoS Genet. 2020 Mar;16(3):e1008676. doi: 10.1371/journal.pgen.1008676. eCollection 2020 Mar. PubMed PMID: 32214314; PubMed Central PMCID: PMC7138321.

Nagamatsu G, Shimamoto S, Hamazaki N, Nishimura Y, Hayashi K. Mechanical stress accompanied with nuclear rotation is involved in the dormant state of mouse oocytes. Sci Adv. 2019 Jun;5(6):eaav9960. doi: 10.1126/sciadv.aav9960. eCollection 2019 Jun. PubMed PMID: 31249869; PubMed Central PMCID: PMC6594774.

Shimamoto S, Nishimura Y, Nagamatsu G, Hamada N, Kita H, Hikabe O, Hamazaki N, Hayashi K. Hypoxia induces the dormant state in oocytes through expression of Foxo3. Proc Natl Acad Sci U S A. 2019 Jun 18;116(25):12321-12326. doi: 10.1073/pnas.1817223116. Epub 2019 May 30. PubMed PMID: 31147464; PubMed Central PMCID: PMC7056940.

Matsuda T, Irie T, Katsurabayashi S, Hayashi Y, Nagai T, Hamazaki N, Adefuin AMD, Miura F, Ito T, Kimura H, Shirahige K, Takeda T, Iwasaki K, Imamura T, Nakashima K. Pioneer Factor NeuroD1 Rearranges Transcriptional and Epigenetic Profiles to Execute Microglia-Neuron Conversion. Neuron. 2019 Feb 6;101(3):472-485.e7. doi: 10.1016/j.neuron.2018.12.010. Epub 2019 Jan 9. PubMed PMID: 30638745.

Sanosaka T, Imamura T, Hamazaki N, Chai M, Igarashi K, Ideta-Otsuka M, Miura F, Ito T, Fujii N, Ikeo K, Nakashima K. DNA Methylome Analysis Identifies Transcription Factor-Based Epigenomic Signatures of Multilineage Competence in Neural Stem/Progenitor Cells. Cell Rep. 2017 Sep 19;20(12):2992-3003. doi: 10.1016/j.celrep.2017.08.086. PubMed PMID: 28930691.

Hamazaki N, Nakashima K, Hayashi K, Imamura T. Detection of Bidirectional Promoter-Derived lncRNAs from Small-Scale Samples Using Pre-Amplification-Free Directional RNA-seq Method. Methods Mol Biol. 2017;1605:83-103. doi: 10.1007/978-1-4939-6988-3_6. PubMed PMID: 28456959.

Hamazaki N, Nakashima K, Imamura T. Manipulation of Promoter-Associated Noncoding RNAs in Mouse Early Embryos for Controlling Sequence-Specific Epigenetic Status. Methods Mol Biol. 2017;1543:271-282. doi: 10.1007/978-1-4939-6716-2_16. PubMed PMID: 28349434.

Hikabe O, Hamazaki N, Nagamatsu G, Obata Y, Hirao Y, Hamada N, Shimamoto S, Imamura T, Nakashima K, Saitou M, Hayashi K. Reconstitution in vitro of the entire cycle of the mouse female germ line. Nature. 2016 Nov 10;539(7628):299-303. doi: 10.1038/nature20104. Epub 2016 Oct 17. PubMed PMID: 27750280.

Hamazaki N, Uesaka M, Nakashima K, Agata K, Imamura T. Gene activation-associated long noncoding RNAs function in mouse preimplantation development. Development. 2015 Mar 1;142(5):910-20. doi: 10.1242/dev.116996. Epub 2015 Jan 29. PubMed PMID: 25633350; PubMed Central PMCID: PMC4352986.