Publications

Our publications can also be found via PubMed.

Current and former members are highlighted.


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
**Co-corresponding authors
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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, Kov«”cs 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, Barab«”si 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-2014

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