Nozomu YACHIE

LABORATORY

PROFILE

2005- B.A. from Keio University (Department of Environmental Information)
2007- M.M.G. (Bioinformatics) from Keio University (Bioinformatics Program)
2007- Resaerch Fellow (DC1), JSPS (-2009.03)
2007- Part-time Lecturer, Keio University (-March, 2009)
2009- Ph.D from Keio University (Systems Biology Program)
2009- Resaerch Fellow (PD), JSPS (-2010.03)
2010- Postdoctoral Fellow, Fritz Roth Lab, Harvard Medical School (-2010.11)
2010- Resaerch Fellow (Research Abroad), JSPS (-2012.03)
2010- Postdoctoral Fellow, Fritz Roth Lab, University of Toronto (-2014.06)
2012- Banting Postdoctoral Fellow, NSERC (-2014.03)
2014- Adjunct Assistant Professor, Keio University SFC
2014- Associate Professor, RCAST, the University of Tokyo

FIELD OF INTEREST

Our mission is developing new experiments and technologies to measure dynamics of molecules, cells and cellular developments by combining technologies in Synthetic Biology and Computational Biology to unveil new biological phenomena.

Our research topics include:

1. High-throughput screening of protein interactions by DNA barcodes and barcode fusion technologies

2. Developing of new synthetic biology circuits by engineering CRISPR/Cas9 genome editing methods

3. Single-cell tracking of evolution, cell development and cell differentiations

4. Large-scale data mining of multi omic data

PUBLICATION

DNA-GPS: A theoretical framework for optics-free spatial genomics and synthesis of current methods. Greenstreet L, Afanassiev A, Kijima Y, Heitz M, Ishiguro S, King S, Yachie N* & Schiebinger G*Cell Syst. 2023 Oct 18;14(10):844-859.e4. doi: 10.1016/j.cels.2023.08.005. Epub 2023 Sep 25. Tenure time loopers. Yachie N* & Shakiba N*Nat Biotechnol. 2023 Oct;41(10):1375-1377. doi: 10.1038/s41587-023-01924-3. A universal sequencing read interpreter. Kijima Y, Evans-Yamamoto D, Toyoshima H & Yachie NSci Adv. 2023 Jan 4;9(1):eadd2793. doi: 10.1126/sciadv.add2793. Epub 2023 Jan 4. A framework to efficiently describe and share reproducible DNA materials and construction protocols. Mori H & Yachie NNature Communications. 2022 May 24;13(1):2894. doi: 10.1038/s41467-022-30588-x. Deep distributed computing to reconstruct extremely large lineage trees. Konno N, Kijima Y, Watano K, Ishiguro S, Ono K, Tanaka M, Mori H, Masuyama N, Pratt D, Ideker T, Iwasaki W & Yachie NNature Biotechnology. 2022 Apr;40(4):566-575. doi: 10.1038/s41587-021-01111-2. Epub 2022 Jan 6. Base editors for simultaneous introduction of C-to-T and A-to-G mutations Sakata RC, Ishiguro S, Mori H, Tanaka M, Tatsuno K, Ueda H, Yamamoto S, Seki M, Masuyama N, Nishida K, Nishimasu H, Arakawa K, Kondo A, Nureki O, Tomita M, Aburatani H, Yachie N.Nat Biotechnol. 2020 Jun 2. doi: 10.1038/s41587-020-0509-0. Perturbing proteomes at single residue resolution using base editing. Després PC, Dubé AK, Seki M, Yachie N, Landry CR.Nat Commun. 2020 Apr 20;11(1):1871. doi: 10.1038/s41467-020-15796-7 DNA barcodes evolve for high-resolution cell lineage tracing. Masuyama N, Mori H, Yachie N.Curr Opin Chem Biol. 2019 10;52:63-71. doi: 10.1016/j.cbpa.2019.05.014 DNA event recorders send past information of cells to the time of observation. Ishiguro S, Mori H, Yachie N.Curr Opin Chem Biol. 2019 10;52:54-62. doi: 10.1016/j.cbpa.2019.05.009 Fast and global detection of periodic sequence repeats in large genomic resources. Mori H, Evans-Yamamoto D, Ishiguro S, Tomita M, Yachie N.Nucleic Acids Res. 2019 01 25;47(2):e8. doi: 10.1093/nar/gky890 Engineered CRISPR-Cas9 nuclease with expanded targeting space Nishimasu H, Shi X, Ishiguro S, Gao L, Hirano S, Okazaki S, Noda T, Abudayyeh OO, Gootenberg JS, Mori H, Oura S, Holmes B, Tanaka M, Seki M, Hirano H, Aburatani H, Ishitani R, Ikawa M, Yachie N, Zhang F, Nureki O.Science. 2018 09 21;361(6408):1259-1262. doi: 10.1126/science.aas9129 Robotic crowd biology with Maholo LabDroids. Yachie N, , Natsume T.Nat. Biotechnol. 2017 04 11;35(4):310-312. doi: 10.1038/nbt.3758 Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Nishida K, Arazoe T, Yachie N, Banno S, Kakimoto M, Tabata M, Mochizuki M, Miyabe A, Araki M, Hara KY, Shimatani Z, Kondo A.Science. 2016 09 16;353(6305). doi: 10.1126/science.aaf8729 Pooled-matrix protein interaction screens using Barcode Fusion Genetics. Yachie N, Petsalaki E, Mellor JC, Weile J, Jacob Y, Verby M, Ozturk SB, Li S, Cote AG, Mosca R, Knapp JJ, Ko M, Yu A, Gebbia M, Sahni N, Yi S, Tyagi T, Sheykhkarimli D, Roth JF, Wong C, Musa L, Snider J, Liu YC, Yu H, Braun P, Stagljar I, Hao T, Calderwood MA, Pelletier L, Aloy P, Hill DE, Vidal M, Roth FP.Mol. Syst. Biol. 2016 Apr 22;12(4):863. doi: 10.15252/msb.20156660 Widespread macromolecular interaction perturbations in human genetic disorders. Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, Khurana V, Sharma A, Liu YY, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási AL, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJM, Lindquist S, Vidal M.Cell. 2015 Apr 23;161(3):647-660. doi: 10.1016/j.cell.2015.04.013