Nozomu YACHIE
RESEARCH DIRECTIONS
Create technologies for interrogating human biologyPROFILE
2005 B.A. from SFC, Keio University
2007 M.M.G. (Bioinformatics) from SFC, Keio University
2009 Ph.D. (Systems Biology) from SFC, Keio University
2010 Postdoctoral Fellow, Harvard Medical School and University of Toronto
2014 Associate Professor, RCAST, The University of Tokyo (-2020)
2020 Visiting Associate Professor, RCAST, The University of Tokyo (-2023)
2020 Associate Professor, School of Biomedical Engineering, The University of British Columbia (-2023)
2020 Canada Research Chair in Synthetic Biology (-Today)
2023 Research Director, School of Biomedical Engineering, The University of British Columbia (-Today)
2023 Professor, School of Biomedical Engineering, The University of British Columbia (-Today)
2023 Visiting Professor, RCAST, The University of Tokyo (-Today)
2023 Specially Appointed Professor, PRIMe, Osaka University
FIELD OF INTEREST
Starting from a fertilized egg, cells proliferate, pass their genomic information to their offspring, and dynamically change their functions to form diverse tissue structures. Throughout development, intracellular and environmental cues trigger patterns of gene expression that govern cell state transitions and produce additional cellular and environmental cues, leading cells to self-organize into functional clusters within spatially distinct areas. How can these processes be investigated? High-resolution molecular snapshots of cells can be obtained using various omics technologies, but these methods require the destruction of the sample, thereby precluding time-course analyses. Live-cell imaging with fluorescent probes can analyze time-course dynamics but this method is limited to analyzing only a small number of molecules or cells. To overcome this common obstacle in biology, our research program is pioneering two major fileds in biology: DNA event recording and retrospective clone isolation.
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