Okamura E, Mizuno S, Matsumoto S, Murata K, Tanimoto Y, Tra D T H, Suzuki H, Kang W, Ema T, Morimoto K, Kato K, Matsumoto T, Masuyama N, Kijima Y, Morimura T, Sugiyama F, Takahashi S, Mizutani E, Woltjen K, Yachie N & Ema M

Highly efficient transgenic mouse production using piggyBac and its application to rapid phenotyping at the founder generation

bioRxiv 10.1101/2023.12.10.570953 PDF

Ishiguro S, Ishida K, Sakata R C, Mori H, Takana M, King S, Bashth O, Ichiraku M, Masuyama N, Takimoto R, Kijima Y, Adel A, Toyoshima H, Seki M, Oh J H, Archambault A-S, Nishida K, Kondo A, Kuhara S, Aburatani H, Klein Geltink R I, Takashima Y, Shakiba N & Yachie N

A multi-kingdom genetic barcoding system for precise target clone isolation

bioRxiv 10.1101/2023.01.18.524633 PDF

Baccouche A, Adel A, Yachie N, Fujii T & Genot A J

License to cut: Smart RNA guides for conditional control of CRISPR-Cas9

bioRxiv 10.1101/2022.10.26.513620 PDF

Baccouche A, Montagne K, Yachie N, Fujii T & Genot A J

Quantitative assaying of SpCas9-NG with fluorescent reporters

bioRxiv 10.1101/2022.08.04.502727 PDF

Tsubouchi A, An Y, Kawamura Y, Yanagihashi Y, Nakayama H, Murata Y, Teranishi K, Ishiguro S, Aburatani H, Yachie N & Ota S

Pooled CRISPR screening of high-content cellular phenotypes using ghost cytometry.

Cell Reports Methods 4, 100737, 2024 PubMed PDF

Kawasaki F, Mimori T, Mori Y, Aburatani H, Yachie N, Sato I, Ota S

Computational Design of Synthetic Optical Barcodes in Microdroplets.

Advanced Optical Materials 2302564, 2023 PDF

Hino T, Omura SN, Nakagawa R, Togashi T, Takeda SN, Hiramoto T, Tasaka S, Hirano H, Tokuyama T, Uosaki H, Ishiguro S, Kagieva M, Yamano H, Ozaki Y, Motooka D, Mori H, Kirita Y, Kise Y, Itoh Y, Matoba S, Aburatani H, Yachie N, Karvelis T, Siksnys V, Ohmori T, Hoshino A & Nureki O

An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis.

Cell 186, 4920-4935.e23, 2023 PubMed PDF

Yachie N* & Shakiba N*

Tenure time loopers.

Nature Biotechnology 41, 1375-1377, 2023 PubMed PDF

*Corresponding authors

Darwish M, Hattori S, Nishizono H, Miyakawa T, Yachie N & Takao K

Comprehensive behavioral analyses of mice with a glycine receptor alpha 4 deficiency.

Molecular Brain 16, 44, 2023 PubMed

Mori H & Yachie N

A framework to efficiently describe and share reproducible DNA materials and construction protocols.

Nature Communications 13, 2894, 2022 PubMed PDF

Masuyama N, Konno N & Yachie N

Molecular recorders to track cellular events.

Science 377, 469-470, 2022 PubMed PDF

Després PC, Dubé AK, Yachie N & Landry CR

High-Throughput Gene Mutagenesis Screening Using Base Editing.

Methods in Molecular Biology 2477, 331-348, 2022 PubMed

Nakagawa R, Ishiguro S, Okazaki S, Mori H, Tanaka M, Aburatani H, Yachie N, Nishimasu H & Nureki O

Engineered Campylobacter jejuni Cas9 variant with enhanced activity and broader targeting range.

Communications Biology 5, 211, 2022 PubMed

Evans-Yamamoto D, Rouleau FD, Nanda P, Makanae K, Liu Y, Després PC, Matsuo H, Seki M, Dubé AK, Ascencio D, Yachie N* & Landry CR*

Barcode fusion genetics-protein-fragment complementation assay (BFG-PCA): tools and resources that expand the potential for binary protein interaction discovery.

Nucleic Acids Research 50, e54, 2022 PubMed

*Corresponding authors

Fukushima T, Tanaka Y, Adachi K, Masuyama N, Tsuchiya A, Asada S, Ishiguro S, Mori H, Seki M, Yachie N, Goyama S & Kitamura T

CRISPR/Cas9-mediated base-editing enables a chain reaction through sequential repair of sgRNA scaffold mutations.

Scientific Reports 11, 23889, 2021 PubMed PDF

Suzuki G, Saito Y, Seki M, Evans-Yamamoto D, Negishi M, Kakoi K, Kawai H, Landry CR, Yachie N* & Mitsuyama T*

Machine learning approach for discrimination of genotypes based on bright-field cellular images.

npj Systems Biology and Applications 7, 31, 2021 PubMed PDF

*Corresponding authors

Ishiguro S & Yachie N

Highly Multiplexed Analysis of CRISPR Genome Editing Outcomes in Mammalian Cells.

Methods in Molecular Biology 2312, 193-223, 2021 PubMed PDF

Kim JH, Seo Y, Jo M, Jeon H, Kim YS, Kim EJ, Seo D, Lee WH, Kim SR, Yachie N, Zhong Q, Vidal M, Roth FP & Suk K

Interrogation of kinase genetic interactions provides a global view of PAK1-mediated signal transduction pathways.

Journal of Biological Chemistry 295, 16906-16919, 2020 PubMed

Kim JH, Seo Y, Jo M, Jeon H, Lee WH, Yachie N, Zhong Q, Vidal M, Roth FP & Suk K

Yeast-Based Genetic Interaction Analysis of Human Kinome.

Cells (MDPI) 9, undefined, 2020 PubMed

Després PC, Dubé AK, Seki M, Yachie N* & Landry CR*

Perturbing proteomes at single residue resolution using base editing.

Nature Communications 11, 1871, 2020 PubMed PDF

*Corresponding authors

Nishizono H+, Darwish M, Uosaki H, Masuyama N, Seki M, Abe H, Yachie N & Yasuda R

Use of Freeze-thawed Embryos for High-efficiency Production of Genetically Modified Mice.

Journal of Visualized Experiments undefined, undefined, 2020 PubMed

+Equally contributed

Murai Y, Masuda T, Onuma Y, Evans-Yamamoto D, Takeuchi N, Mori H, Masuyama N, Ishiguro S, Yachie N & Arakawa K

Complete Genome Sequence of Bacillus sp. Strain KH172YL63, Isolated from Deep-Sea Sediment.

Microbiology Resource Announcements 9, undefined, 2020 PubMed

Celaj A, Gebbia M, Musa L, Cote AG, Snider J, Wong V, Ko M, Fong T, Bansal P, Mellor JC, Seesankar G, Nguyen M, Zhou S, Wang L, Kishore N, Stagljar I, Suzuki Y, Yachie N* & Roth FP*

Highly Combinatorial Genetic Interaction Analysis Reveals a Multi-Drug Transporter Influence Network.

Cell Systems 10, 25-38.e10, 2020 PubMed PDF

*Corresponding authors

Masoudi M, Seki M, Yazdanparast R, Yachie N & Aburatani H

A genome-scale CRISPR/Cas9 knockout screening reveals SH3D21 as a sensitizer for gemcitabine.

Scientific Reports 9, 19188, 2019 PubMed

Marchant A, Cisneros AF, Dubé AK, Gagnon-Arsenault I, Ascencio D, Jain H, Aubé S, Eberlein C, Evans-Yamamoto D, Yachie N & Landry CR

The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs.

eLife 8, undefined, 2019 PubMed PDF

Masuyama N, Mori H & Yachie N

DNA barcodes evolve for high-resolution cell lineage tracing.

Current Opinion in Chemical Biology 52, 63-71, 2019 PubMed PDF

Ishiguro S, Mori H & Yachie N

DNA event recorders send past information of cells to the time of observation.

Current Opinion in Chemical Biology 52, 54-62, 2019 PubMed PDF

Evans-Yamamoto D, Takeuchi N, Masuda T, Murai Y, Onuma Y, Mori H, Masuyama N, Ishiguro S, Yachie N & Arakawa K

Complete Genome Sequence of Psychrobacter sp. Strain KH172YL61, Isolated from Deep-Sea Sediments in the Nankai Trough, Japan.

Microbiology Resource Announcements 8, undefined, 2019 PubMed

Dandage R, Després PC, Yachie N & Landry CR

beditor: A Computational Workflow for Designing Libraries of Guide RNAs for CRISPR-Mediated Base Editing.

Genetics 212, 377-385, 2019 PubMed

Mori H, Evans-Yamamoto D, Ishiguro S, Tomita M & Yachie N

Fast and global detection of periodic sequence repeats in large genomic resources.

Nucleic Acids Research 47, e8, 2019 PubMed PDF

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

Engineered CRISPR-Cas9 nuclease with expanded targeting space.

Science 361, 1259-1262, 2018 PubMed PDF

Després PC, Dubé AK, Nielly-Thibault L, Yachie N & Landry CR

Double Selection Enhances the Efficiency of Target-AID and Cas9-Based Genome Editing in Yeast.

G3: Genes, Genomes, Genetics 8, 3163-3171, 2018 PubMed

Jo M, Chung AY, Yachie N, Seo M, Jeon H, Nam Y, Seo Y, Kim E, Zhong Q, Vidal M, Park HC, Roth FP & Suk K

Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target.

Genome Research 27, 1487-1500, 2017 PubMed

Ghanegolmohammadi F, Yoshida M, Ohnuki S, Sukegawa Y, Okada H, Obara K, Kihara A, Suzuki K, Kojima T, Yachie N, Hirata D & Ohya Y

Systematic analysis of Ca(2+) homeostasis in Saccharomyces cerevisiae based on chemical-genetic interaction profiles.

Molecular Biology of the Cell 28, 3415-3427, 2017 PubMed

Yachie N & Natsume T

Robotic crowd biology with Maholo LabDroids.

Nature Biotechnology 35, 310-312, 2017 PubMed PDF

Nishida K, Arazoe T, Yachie N, Banno S, Kakimoto M, Tabata M, Mochizuki M, Miyabe A, Araki M, Hara KY, Shimatani Z & Kondo A

Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems.

Science 353, undefined, 2016 PubMed PDF

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Comprehensive Analysis of the SUL1 Promoter of Saccharomyces cerevisiae.

Genetics 203, 191-202, 2016 PubMed PDF

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

Widespread macromolecular interaction perturbations in human genetic disorders.

Cell 161, 647-660, 2015 PubMed PDF

Soma A, Sugahara J, Onodera A, Yachie N, Kanai A, Watanabe S, Yoshikawa H, Ohnuma M, Kuroiwa H, Kuroiwa T & Sekine Y

Identification of highly-disrupted tRNA genes in nuclear genome of the red alga, Cyanidioschyzon merolae 10D.

Scientific Reports 3, 2321, 2013 PubMed PDF

Suzuki Y, Stam J, Novotny M, Yachie N, Lasken RS & Roth FP

The green monster process for the generation of yeast strains carrying multiple gene deletions.

Journal of Visualized Experiments undefined, e4072, 2012 PubMed PDF

Nozaki T, Yachie N, Ogawa R, Kratz A, Saito R & Tomita M

Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification.

BMC Genomics 12, 416, 2011 PubMed PDF

Nozaki T, Yachie N, Ogawa R, Saito R & Tomita M

Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA.

Gene 476, 10-4, 2011 PubMed PDF

Yachie N, Saito R, Sugiyama N, Tomita M & Ishihama Y

Integrative features of the yeast phosphoproteome and protein-protein interaction map.

PLOS Computational Biology 7, e1001064, 2011 PubMed PDF

Imamura H, Yachie N, Saito R, Ishihama Y & Tomita M

Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data.

BMC Bioinformatics 11, 232, 2010 PubMed PDF

Yachie N, Saito R, Sugahara J, Tomita M & Ishihama Y

In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution.

Molecular and Cellular Proteomics 8, 1061-71, 2009 PubMed PDF

Yachie N, Ohashi Y & Tomita M

Stabilizing synthetic data in the DNA of living organisms.

Systems and Synthetic Biology 2, 19-25, 2008 PubMed PDF

Sugahara J, Kikuta K, Fujishima K, Yachie N, Tomita M & Kanai A

Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales.

Molecular Biology and Evolution 25, 2709-16, 2008 PubMed PDF

Soma A, Onodera A, Sugahara J, Kanai A, Yachie N, Tomita M, Kawamura F & Sekine Y

Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae.

Science 318, 450-3, 2007 PubMed PDF

Watanabe Y, Kishi A, Yachie N, Kanai A & Tomita M

Computational analysis of microRNA-mediated antiviral defense in humans.

FEBS letters 581, 4603-10, 2007 PubMed

Matsui M, Yachie N, Okada Y, Saito R & Tomita M

Bioinformatic analysis of post-transcriptional regulation by uORF in human and mouse.

FEBS letters 581, 4184-8, 2007 PubMed

Negishi Y, Nakamura H, Yachie N, Saito R & Tomita M

eXpanda: an integrated platform for network analysis and visualization.

In Silico Biology 7, 141-4, 2007 PubMed

Sugahara J, Yachie N, Arakawa K & Tomita M

In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs.

RNA 13, 671-81, 2007 PubMed

Yachie N, Sekiyama K, Sugahara J, Ohashi Y & Tomita M

Alignment-based approach for durable data storage into living organisms.

Biotechnology Progress 23, 501-5, 2007 PubMed PDF

Yachie N, Arakawa K & Tomita M

On the interplay of gene positioning and the role of rho-independent terminators in Escherichia coli.

FEBS letters 580, 6909-14, 2006 PubMed PDF

Shinoda K, Yachie N, Masuda T, Sugiyama N, Sugimoto M, Soga T & Tomita M

HybGFS: a hybrid method for genome-fingerprint scanning.

BMC Bioinformatics 7, 479, 2006 PubMed

Shinoda K, Sugimoto M, Yachie N, Sugiyama N, Masuda T, Robert M, Soga T & Tomita M

Prediction of liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome using artificial neural networks.

Journal of Proteome Research 5, 3312-7, 2006 PubMed

Sugahara J, Yachie N, Sekine Y, Soma A, Matsui M, Tomita M & Kanai A

SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level.

In Silico Biology 6, 411-8, 2006 PubMed

Yachie N, Numata K, Saito R, Kanai A & Tomita M

Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model.

Gene 372, 171-81, 2006 PubMed PDF

Watanabe Y, Yachie N, Numata K, Saito R, Kanai A & Tomita M

Computational analysis of microRNA targets in Caenorhabditis elegans.

Gene 365, 2-10, 2006 PubMed