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Preprint

High-throughput robotic isolation of human iPS cell clones reveals frequent homozygous induction of identical genetic manipulations by CRISPR-Cas9.

Takahashi G, Maeda M, Shinozaki K, Harada G, Ito S, Miyaoka Y.

birRxiv 2024.09.18.613641; doi: https://doi.org/10.1101/2024.09.18.613641

 

Predicting Alzheimer’s Trajectory: A Multi-PRS Machine Learning Approach for Early Diagnosis and Progression Forecasting.

Mustaq M, Ahmed N, Mahbub S, Li C, Miyaoka Y, TCW J, Andrews S, Md. Bayzid SM#. the Alzheimer’s Disease Neuroimaging Initiative

medRxiv 2023.11.28.23299110; doi: https://doi.org/10.1101/2023.11.28.23299110

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2024

Fusion of histone variants to Cas9 suppresses non-homologous end joining.

Kato-Inui T, Takahashi G, Ono T, Miyaoka Y#.

PLoS One. 2024 May 13;19(5):e0288578.

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2023

 Large-scale single-cell cloning of genome-edited cultured human cells by On-chip SPiS.

Takahashi G#, Miyaoka Y#.

STAR Protocols. 2023 Jun 16;4(3):102364.

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 In Vivo Delivery of Therapeutic Molecules by Transplantation of Genome-Edited Induced Pluripotent Stem Cells.
Nakajima I, Tsukimura T, Ono T, Shiga T, Shitara H, Togawa T, Sakuraba H, Miyaoka Y#.

Cell Transplantation. 2023 Jan-Dec;32:9636897231173734.

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Granulin loss of function in human mature brain organoids implicates astrocytes in TDP-43 pathology.

de Majo M*#, Koontz M*, Marsan E, Salinas N, Ramsey A, Kuo YM, Seo K, Li H, Dräger N, Leng K, Gonzales SL, Kurnellas M, Miyaoka Y, Klim JR, Kampmann M, Ward ME, Huang EJ, Ullian EM#.

Stem Cell Reports. 2023 Feb 14:S2213-6711(23)00015-2.

2022
Genome editing is induced in a binary manner in single human cells.

Takahashi G, Kondo D, Maeda M, Morishita Y, Miyaoka Y#

iSicence. 2022 Nov 17;25(12):105619.

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Retinoids rescue ceruloplasmin secretion and alleviate oxidative stress in Wilson’s disease-specific hepatocytes.

Song D*, Takahashi G*, Zheng YW, Matsuo-Takasaki M, Li J, Takami M, An Y, Hemmi Y, Miharada N, Fujioka T, Noguchi M, Nakajima T, Saito MK, Nakamura Y, Oda T, Miyaoka Y#, Hayashi Y#.

Human Molecular Genetics. 2022 Oct 28;31(21):3652-3671.

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2021

Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies.
Fenix AM*, Miyaoka Y*, Bertero A, Blue SM, Spindler MJ, Tan KKB, Perez-Bermejo JA, Chan AH, Mayerl SJ, Nguyen TD, Russell CR, Lizarraga PP, Truong A, So PL, Kulkarni A, Chetal K, Sathe S, Sniadecki NJ, Yeo GW, Murry CE#, Conklin BR#, Salomonis N#

Nature Communications. 2021 Nov 3;12: 6324.

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2020

Rapid, precise quantification of large DNA excisions and inversions by ddPCR.
Watry HL, Feliciano CM, Gjoni K, Takahashi G, Miyaoka Y, Conklin BR#, Judge LM#.

Scientific Reports. 2020 Sep 10;10:14896.

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2018

Detection and Quantification of HDR and NHEJ Induced by Genome Editing at Endogenous Gene Loci Using Droplet Digital PCR.

Miyaoka Y, Mayerl SJ, Chan AH, Conklin BR#.

Methods Mol Biol. 2018;1768:349-362.

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Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 with improved proof-reading enhances homology-directed repair.

Kato-Inui K, Takahashi G, Hsu S, Miyaoka Y#.

Nucleic Acids Research. 2018 May 18;46(9):4677-4688.

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2017

Engineered human pluripotent stem cell-derived intestinal tissues with a functional enteric nervous system.

Workman MJ*, Mahe MM*, Trisno S, Poling HM, Watson CL, Sundaram N, Chang CF, Schiesser J, Aubert P, Stanley EG, Elefanty AG, Miyaoka Y, Mandegar MA, Conklin BR, Neunlist M, Brugmann SA, Helmrath MA, Wells JM#

Nature Medicine. 2017 Jan;23(1):49-59. 

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2016

Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity​.

Nguyen DP, Miyaoka Y, Gilbert LA, Mayerl SJ, Lee BH, Weissman JS, Conklin BR, Wells JA#.

Nature Communications. 2016 Jul 1;7:12009.

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Using Digital Polymerase Chain Reaction to Detect Single-Nucleotide Substitutions Induced by Genome Editing.

Miyaoka Y, Chan AH, Conklin BR#.

Cold Spring Harbor Protocols. 2016 Jun 1.

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Detecting Single-Nucleotide Substitutions Induced by Genome Editing. (Introduction for the protocol above)

Miyaoka Y, Chan AH, Conklin BR#.

Cold Spring Harbor Protocols. 2016 Jun 1.

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Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing.

Miyaoka Y*#, Berman JR*, Cooper SB, Mayerl SJ, Chan AH, Zhang B, Karlin-Neumann GA, Conklin BR#.

Scientific Reports. 2016 Mar 31;6:23549.

 

CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs.

Mandegar MA#, Huebsch N, Frolov EB, Shin E, Truong A, Olvera MP, Chan AH, Miyaoka Y, Holmes K, Spencer CI, Judge LM, Gordon DE, Eskildsen TV, Villalta JE, Horlbeck MA, Gilbert LA, Krogan NJ, Sheikh SP, Weissman JS, Qi LS, So PL, Conklin BR#.

Cell Stem Cell. 2016 Apr 7;18(4):541-553.

 

-2015

Detection of Genome Editing Events by Digital PCR.

Miyaoka Y.

TheScientist Webinar Series. Advancing Genomic Medicine: Exploring Applications of Digital PCR, 2015 Oct 14.

(Web seminar)

 

Oncostatin M maintains the hematopoietic microenvironment in the bone marrow by modulating adipogenesis and osteogenesis.

Sato F, Miyaoka Y, Miyajima A, Tanaka M#.

PLoS One. 2014 Dec 31;9(12):e116209.

 

Isolation of single-base genome-edited human iPS cells without antibiotic selection. (PMC Ver.)

Miyaoka Y, Chan AH, Judge LM, Yoo J, Huang M, Nguyen TD, Lizarraga PP, So PL, Conklin BR#.

Nat Methods. 2014 Mar;11(3):291-3. (Please request full-text via email)

 

To divide or not to divide: revisiting liver regeneration.

Miyaoka Y, Miyajima A#.

Cell Div. 2013 Jun 20;8(1):8.

Recommended in F1000.

 

Hypertrophy and unconventional cell division of hepatocytes underlie liver regeneration.

Miyaoka Y, Ebato K, Kato H, Arakawa S, Shimizu S, Miyajima A#.

Curr Biol. 2012 Jul 10;22(13):1166-75.

Recommended in F1000.

 

Hepatic stellate cell-derived delta-like homolog 1 (DLK1) protein in liver regeneration.

Zhu NL, Asahina K, Wang J, Ueno A, Lazaro R, Miyaoka Y, Miyajima A, Tsukamoto H#.

J Biol Chem. 2012 Mar 23;287(13):10355-67.

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Retention in the Golgi apparatus and expression on the cell surface of Cfr/Esl-1/Glg-1/MG-160 are regulated by two distinct mechanisms.

Miyaoka Y*, Kato H*, Ebato K*, Saito S, Miyata N, Imamura T, Miyajima A#.

Biochem J. 2011 Nov 15;440(1):33-41.

 

A novel regulatory mechanism for Fgf18 signaling involving cysteine-rich FGF receptor (Cfr) and delta-like protein (Dlk).

Miyaoka Y, Tanaka M, Imamura T, Takada S, Miyajima A#.

Development. 2010 Jan;137(1):159-67.

 

TRB2, a mouse Tribbles ortholog, suppresses adipocyte differentiation by inhibiting AKT and C/EBPbeta.

Naiki T, Saijou E, Miyaoka Y, Sekine K, Miyajima A#.

J Biol Chem. 2007 Aug 17;282(33):24075-82.

 

Oncostatin M inhibits adipogenesis through the RAS/ERK and STAT5 signaling pathways.

Miyaoka Y, Tanaka M, Naiki T, Miyajima A#.

J Biol Chem. 2006 Dec 8;281(49):37913-20.