Publications
Current and former members are highlighted. Our work can also be found via PubMed and bioRxiv.
Preprints
Tsubouchi A, An Y, Kawamura Y, Yanagihashi Y, Murata Y, Teranishi K, Ishiguro S, Aburatani H, Yachie N & Ota S.
Pooled CRISPR screening of high-content cellular phenotypes by ghost cytometry.
bioRxiv 2023.01.26.525784 PDF
Ishiguro S+, Ishida K+, Sakata RC+, Mori H, Tanaka M, King S, Bashth O, Ichiraku M, Masuyama N, Takimoto R, Kijima Y, Adel A, Toyoshima H, Seki M, Oh JH, Archambault A-S, Nishida K, Kondo A, Kuhara S, Aburatani H, Klein Geltink RI, Takashima Y, Shakiba N & Yachie N.
A multi-kingdom genetic barcoding system for precise target clone isolation.
bioRxiv 2023.01.18.524633 PDF
Baccouche A, Adel A, Yachie N, Fujii T & Genot AJ
License to cut: Smart RNA guides for conditional control of CRISPR-Cas9.
bioRxiv 2022.10.26.513620
Baccouche A, Montagne K, Yachie N, Fujii T & Genot AJ
Quantitative assaying of SpCas9-NG with fluorescent reporters.
bioRxiv 2022.08.04.502727
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 2022.03.22.485380
+Equally contributed
*Corresponding authors
2023
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
Kijima Y, Evans-Yamamoto D, Toyoshima H & Yachie N
A universal sequencing read interpreter.
Science Advances 9, add2793, 2023 PubMed PDF
Martin Krzywinski's website on his thoughts and process of the cover production
2022
Masuyama N+, Konno N+ & Yachie N
Molecular recorders to track cellular events.
Science 377, 469-470, 2022 PubMed e-print PDF
+Equally contributed
Mori H & Yachie N
A framework to efficiently describe and share reproducible DNA materials and construction protocols.
Nature Communications 13, 2894, 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 gkac045, 2022 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.
Nature Biotechnology 40, 566-575, 2022 PubMed PDF Supplementary Materials GIFtorial
+Equally contributed
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.
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
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.
Journal of Biological Chemistry 295, 16906-16919, 2020 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.
Nature Biotechnology 38, 865-869, 2020 PubMed PDF Addgene
+Equally contributed
Related Article:
Burgess DJ Multitasking for base editors. Nature Reviews Genetics, 21, 445, 2020 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.
Cells 9, 1156, 2020 PubMed PDF
Després PC, Dubé AK, Seki M, Yachie N* & Landry CR*
Systematic perturbation of yeast essential genes 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 158, e60808, 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, e00291-20, 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, 2020 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.
Scientific Reports 9, 19188, 2019 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.
eLife 8, e46754, 2019 PubMed PDF
Masuyama M+, Mori H+ & Yachie N
DNA barcodes evolve for high-resolution cell lineage tracing.
Current Opinion in Chemical Biology 52, 63-71, 2019 PubMed PDF
+Equally contributed
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, e00326-19, 2019 PubMed
Dandage R, Despres PC, Yachie N & Landry CR
beditor: A computational workflow for designing libraries of guide RNAs for CRISPR base editing.
Genetics published online PubMed 212, 377-385, 2019
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
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.
Science 361, 1259-1262, 2018 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.
G3: Genes, Genomes, Genetics 8, 3163-3171, 2018 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.
Genome Research 27, 1487-1500, 2017 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.
Molecular Biology of the Cell 28, 3415-3427, 2017 PubMed
Yachie N, Robotic Biology Consortium* & Natsume T
Robotic crowd biology with Maholo LabDroids.
Nature Biotechnology 35, 310, 2017 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.
Science 353, aaf8729, 2016 PubMed PDF
Related Article:
Conticello SG & Rada C Harnessing mutation: The best of two worlds. Science 353, 1206-1207, 2016 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.
Molecular Systems Biology 12, 863, 2016 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.
Genetics 203, 191-202, 2016 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.
Cell 3, 647-660, 2015 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.
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 70, 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, 10-14, 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, 1061-1071, 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, 2709-2716, 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, 450-453, 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, 4603-4610, 2007 PubMed PDF
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, 4184-4188, 2007 PubMed PDF
Negishi Y, Nakamura H, Yachie N, Saito R & Tomita M
eXpanda: an integrated platform for network analysis and visualization.
In Silico Biology 7, 141-144, 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, 671-681, 2007 PubMed PDF
Yachie N, Sekiyama K, Sugahara J, Ohashi Y & Tomita M
Alignment-based approach for durable data storage into living organisms.
Biotechnology Progress 23, 501-505, 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, 6909-6914, 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 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.
Journal of Proteome Research 5, 3312-3317, 2006 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.
In Silico Biology 6, 411-418, 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, 171-181, 2006 PubMed PDF
Watanabe Y, Yachie N, Numata K, Saito R, Kanai A & Tomita M
Computational analysis of microRNA target recognition in Caenorhabditis elegans.
Gene 365, 2-10, 2006 PubMed PDF
Review Articles
Arakawa K, Yachie N & Tomita M
Visualizing complex omics information.
BIOforum Europe 6, 27-29, 2008
