Publications

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

Preprint

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. bioRxiv 564401 PDF

2019

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 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

2018

Mori H, Evans-Yamamoto D, Ishiguro S, Tomita M & Yachie N. Fast and global detection of periodic sequence repeats in large genomic resources. (2018) Nucleic Acids Research gky890 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. (2018) Science 361, 1259-1262 PubMed

Despres PC, Dube 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. The Effects of Cis-Regulatory Mutations in the SUL1 Gene on Sulfate-Limited Fitness in Yeast. (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