Publications

Current and former members are highlighted. Our publications can also be found via PubMed.

Preprints

Kijima Y, Evans-Yamamoto D, Toyoshima H & Yachie N. A universal sequencing read interpreter. bioRxiv doi: 10.1101/2022.04.16.488535

Greenstreet L+, Afanassiev A+, Kijima Y+, Heitz M+, Ishiguro S, King S, Yachie N* & Schiebinger G*. The DNA-based global positioning system—a theoretical framework for large-scale spatial genomics. bioRxiv doi: 10.1101/2022.03.22.485380
+Equally contributed
*Corresponding authors

2022

Mori H & Yachie N. A universal framework to efficiently share material and process resources in the DNA construction world. (2022) Nature Communications 13, 2894 PubMed PDF

Després PC, Dubé AK, Yachie N, Landry CR. High-Throughput Gene Mutagenesis Screening Using Base Editing. (2022) Methods in Molecular Biology 2477, 331-348 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. (2022) Communications Biology 5, 211 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. (2022) Nucleic Acids Research gkac045 PubMed
*Corresponding authors

Konno N, Kijima Y, Watano K, Ishiguro S, Ono K, Tanaka M, Mori H, Masuyama N, Pratt D, Ideker T, Iwasaki W & Yachie N. Deep distributed computing to reconstruct extremely large lineage trees. (2022) Nature Biotechnology 40, 566–575 PubMed PDF Supplementary Materials GIFtorial

2021

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. (2021) Scientific Reports 11, 23889 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. (2021) npj Systems Biology and Applications 7, 31 PubMed PDF
*Corresponding authors

Ishiguro S & Yachie N. Highly Multiplexed Analysis of CRISPR Genome Editing Outcomes in Mammalian Cells. (2021) Methods in Molecular Biology 2312, 193-223 PubMed

2020

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. (2020) Journal of Biological Chemistry 295, 16906-16919 PubMed

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. Base editors for simultaneous introduction of C-to-T and A-to-G mutations. (2020) Nature Biotechnology 38, 865-869 PubMed PDF Addgene
+Equally contributed

Related Article:
Burgess DJ. Multitasking for base editors. (2020) Nature Reviews Genetics (published online)
PubMed PDF

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. (2020) Cells 9, 1156 PubMed PDF

Després PC, Dubé AK, Seki M, Yachie N* & Landry CR*. Systematic perturbation of yeast essential genes using base editing. (2020) Nature Communications 11, 1871 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. (2020) Journal of Visualized Experiments 158, e60808 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. (2020) Microbiology Resource Announcements 9, e00291-20 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. (2020) Cell Systems 10, 25-38 PubMed PDF
*Corresponding authors

2019

Masoudi M, Seki M, Yazdanparast R, Yachie N & Aburatani H. A genome-scale CRISPR/Cas9 knockout screening reveals SH3D21 as a sensitizer for gemcitabine. (2019) Scientific Reports 9, 19188 PubMed PDF

Marchant A, Cisneros AF, Dubé AK, Gagnon-Arsenault I, Ascencio D, Jain HA, 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. (2019) eLife 8, e46754 PubMed PDF

Masuyama M+, Mori H+ & Yachie N. DNA barcodes evolve for high-resolution cell lineage tracing. (2019) Current Opinion in Chemical Biology 52, 63-71 PubMed PDF
+Equally contributed

Ishiguro S, Mori H & Yachie N. DNA event recorders send past information of cells to the time of observation. (2019) Current Opinion in Chemical Biology 52, 54-62 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. (2019) Microbiology Resource Announcements 8, e00326-19 PubMed

Dandage R, Despres PC, Yachie N & Landry CR. beditor: A computational workflow for designing libraries of guide RNAs for CRISPR base editing. (2019) Genetics published online PubMed 212, 377-385

Mori H, Evans-Yamamoto D, Ishiguro S, Tomita M & Yachie N. Fast and global detection of periodic sequence repeats in large genomic resources. (2019) Nucleic Acids Research 47, e8 PubMed PDF

2018

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. (2018) Science 361, 1259-1262 PubMed

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

2017

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. (2017) Genome Research 27, 1487-1500 PubMed
+Equally contributed

Ghanegolmohammadia 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 Ca2+ homoeostasis in Saccharomyces cerevisiae based on chemical-genetic interaction profiles. (2017) Molecular Biology of the Cell 28, 3415-3427 PubMed

Yachie N, Robotic Biology Consortium* & Natsume T. Robotic crowd biology with Maholo LabDroids. (2017) Nature Biotechnology 35, 310 PubMed PDF
*Ishiguro S, Mori H, Evans-Yamamoto D and Masuyama N are members of the Robotic Biology Consortium.

2016

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. (2016) Science 353, aaf8729 PubMed PDF

Related Article:
Conticello SG & Rada C. Harnessing mutation: The best of two worlds. (2016) Science 353, 1206-1207 PubMed PDF

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 Y-C, Yu H, Braun P, Stagljar I, Hao T, Calderwood MA, Pelletier L, Aloy P, Hill DE, Vidal M & Roth FP*. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. (2016) Molecular Systems Biology 12, 863 PubMed PDF Expanded View Figures Appendix
+Equally contributed
*Corresponding authors

Rich MS, Payen C, Rubin AF, Ong GT, Sanchez MR, Yachie N, Dunham MJ & Fields S. Comprehensive Analysis of the SUL1 Promoter of Saccharomyces cerevisiae. (2016) Genetics 203, 191-202 PubMed PDF

2015

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 Y-Y, 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 A-L, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJM, Lindquist S & Vidal M. Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders. (2015) Cell 3, 647-660 PubMed PDF

pre-2015

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. (2013) Scientific Reports 3, 2321 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. (2012) Journal of Visualized Experiments 70, e4072 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. (2011) BMC Genomics 12, 416 PubMed PDF

Nozaki T, Yachie N, Ogawa R, Saito R & Tomita M. Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA. (2011) Gene 476, 10-14 PubMed PDF

Yachie N, Saito R, Sugiyama N, Tomita M & Ishihama Y. Integrative features of the yeast phosphoproteome and protein-protein interaction map. (2011) PLOS Computational Biology 7, e1001064 PubMed PDF

Imamura H, Yachie N, Saito R, Ishihama Y & Tomita M. Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. (2010) BMC Bioinformatics 11, 232 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. (2009) Molecular and Cellular Proteomics 8, 1061-1071 PubMed PDF

Yachie N, Ohashi Y & Tomita M. Stabilizing synthetic data in the DNA of living organisms. (2008) Systems and Synthetic Biology 2, 19-25 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. (2008) Molecular Biology and Evolution 25, 2709-2716 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. (2007) Science 318, 450-453 PubMed PDF

Watanabe Y, Kishi A, Yachie N, Kanai A & Tomita M. Computational analysis of microRNA-mediated antiviral defense in humans. (2007) FEBS Letters 581, 4603-4610 PubMed PDF

Matsui M, Yachie N, Okada Y, Saito R & Tomita M. Bioinformatic analysis of post-transcriptional regulation by uORF in human and mouse. (2007) FEBS Letters 581, 4184-4188 PubMed PDF

Negishi Y, Nakamura H, Yachie N, Saito R & Tomita M. eXpanda: an integrated platform for network analysis and visualization. (2007) In Silico Biology 7, 141-144 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. (2007) RNA 13, 671-681 PubMed PDF

Yachie N, Sekiyama K, Sugahara J, Ohashi Y & Tomita M. Alignment-based approach for durable data storage into living organisms. (2007) Biotechnology Progress 23, 501-505 PubMed PDF

Yachie N, Arakawa K & Tomita M. On the interplay of gene positioning and the role of rho-independent terminators in Escherichia coli. (2006) FEBS Letters 580, 6909-6914 PubMed PDF

Shinoda K, Yachie N, Masuda T, Sugiyama N, Sugimoto M, Soga T & Tomita M. HybGFS: a hybrid method for genome-fingerprint scanning. (2006) BMC Bioinformatics 7, 479 PubMed PDF

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. (2006) Journal of Proteome Research 5, 3312-3317 PubMed PDF

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. (2006) In Silico Biology 6, 411-418 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. (2006) Gene 372, 171-181 PubMed PDF

Watanabe Y, Yachie N, Numata K, Saito R, Kanai A & Tomita M. Computational analysis of microRNA target recognition in Caenorhabditis elegans. (2006) Gene 365, 2-10 PubMed PDF

Review Articles

Arakawa K, Yachie N & Tomita M. Visualizing complex omics information. (2008) BIOforum Europe 6, 27-29