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Items: 36

1.

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

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

Elife. 2019 Aug 27;8. pii: e46754. doi: 10.7554/eLife.46754.

2.

DNA barcodes evolve for high-resolution cell lineage tracing.

Masuyama N, Mori H, Yachie N.

Curr Opin Chem Biol. 2019 Jun 15;52:63-71. doi: 10.1016/j.cbpa.2019.05.014. [Epub ahead of print] Review.

PMID:
31212208
3.

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

Ishiguro S, Mori H, Yachie N.

Curr Opin Chem Biol. 2019 Jun 11;52:54-62. doi: 10.1016/j.cbpa.2019.05.009. [Epub ahead of print] Review.

PMID:
31200335
4.

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

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

Microbiol Resour Announc. 2019 Apr 18;8(16). pii: e00326-19. doi: 10.1128/MRA.00326-19.

5.

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

Dandage R, Després PC, Yachie N, Landry CR.

Genetics. 2019 Jun;212(2):377-385. doi: 10.1534/genetics.119.302089. Epub 2019 Apr 1.

6.

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

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

Nucleic Acids Res. 2019 Jan 25;47(2):e8. doi: 10.1093/nar/gky890.

7.

Engineered CRISPR-Cas9 nuclease with expanded targeting space.

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.

Science. 2018 Sep 21;361(6408):1259-1262. doi: 10.1126/science.aas9129. Epub 2018 Aug 30.

8.

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

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

G3 (Bethesda). 2018 Oct 3;8(10):3163-3171. doi: 10.1534/g3.118.200461.

9.

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

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.

Genome Res. 2017 Sep;27(9):1487-1500. doi: 10.1101/gr.211649.116. Epub 2017 Jun 8.

10.

Systematic analysis of Ca2+ homeostasis in Saccharomyces cerevisiae based on chemical-genetic interaction profiles.

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

Mol Biol Cell. 2017 Nov 7;28(23):3415-3427. doi: 10.1091/mbc.E17-04-0216. Epub 2017 May 31.

11.

Robotic crowd biology with Maholo LabDroids.

Yachie N; Robotic Biology Consortium, Natsume T.

Nat Biotechnol. 2017 Apr 11;35(4):310-312. doi: 10.1038/nbt.3758. No abstract available.

PMID:
28398329
12.

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

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

Science. 2016 Sep 16;353(6305). pii: aaf8729. doi: 10.1126/science.aaf8729. Epub 2016 Aug 4.

13.

Pooled-matrix protein interaction screens using Barcode Fusion Genetics.

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 YC, Yu H, Braun P, Stagljar I, Hao T, Calderwood MA, Pelletier L, Aloy P, Hill DE, Vidal M, Roth FP.

Mol Syst Biol. 2016 Apr 22;12(4):863. doi: 10.15252/msb.20156660.

14.

Comprehensive Analysis of the SUL1 Promoter of Saccharomyces cerevisiae.

Rich MS, Payen C, Rubin AF, Ong GT, Sanchez MR, Yachie N, Dunham MJ, Fields S.

Genetics. 2016 May;203(1):191-202. doi: 10.1534/genetics.116.188037. Epub 2016 Mar 2.

15.

Widespread macromolecular interaction perturbations in human genetic disorders.

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.

Cell. 2015 Apr 23;161(3):647-660. doi: 10.1016/j.cell.2015.04.013.

16.

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

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

Sci Rep. 2013;3:2321. doi: 10.1038/srep02321.

17.

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

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

J Vis Exp. 2012 Dec 15;(70):e4072. doi: 10.3791/4072.

18.

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

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

BMC Genomics. 2011 Aug 17;12:416. doi: 10.1186/1471-2164-12-416.

19.

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

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

Gene. 2011 May 1;476(1-2):10-4. doi: 10.1016/j.gene.2011.02.004. Epub 2011 Feb 19.

PMID:
21338662
20.

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

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

PLoS Comput Biol. 2011 Jan 27;7(1):e1001064. doi: 10.1371/journal.pcbi.1001064.

21.

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

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

BMC Bioinformatics. 2010 May 7;11:232. doi: 10.1186/1471-2105-11-232.

22.

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

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

Mol Cell Proteomics. 2009 May;8(5):1061-71. doi: 10.1074/mcp.M800466-MCP200. Epub 2009 Jan 9.

23.

Stabilizing synthetic data in the DNA of living organisms.

Yachie N, Ohashi Y, Tomita M.

Syst Synth Biol. 2008 Jun;2(1-2):19-25. doi: 10.1007/s11693-008-9020-5. Epub 2008 Dec 13.

24.

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

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

Mol Biol Evol. 2008 Dec;25(12):2709-16. doi: 10.1093/molbev/msn216. Epub 2008 Oct 1.

PMID:
18832079
25.

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

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

Science. 2007 Oct 19;318(5849):450-3. Erratum in: Science. 2007 Dec 21;318(5858):1866.

26.

Computational analysis of microRNA-mediated antiviral defense in humans.

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

FEBS Lett. 2007 Oct 2;581(24):4603-10. Epub 2007 Aug 31.

27.

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

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

FEBS Lett. 2007 Sep 4;581(22):4184-8. Epub 2007 Aug 3.

28.

eXpanda: an integrated platform for network analysis and visualization.

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

In Silico Biol. 2007;7(2):141-4.

PMID:
17688438
29.

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

Sugahara J, Yachie N, Arakawa K, Tomita M.

RNA. 2007 May;13(5):671-81. Epub 2007 Mar 16.

30.

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

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

In Silico Biol. 2006;6(5):411-8.

PMID:
17274770
31.

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

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

Biotechnol Prog. 2007 Mar-Apr;23(2):501-5. Epub 2007 Jan 25.

PMID:
17253725
32.

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

Yachie N, Arakawa K, Tomita M.

FEBS Lett. 2006 Dec 22;580(30):6909-14. Epub 2006 Nov 30.

33.

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

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

J Proteome Res. 2006 Dec;5(12):3312-7.

PMID:
17137332
34.

HybGFS: a hybrid method for genome-fingerprint scanning.

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

BMC Bioinformatics. 2006 Oct 29;7:479.

35.

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

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

Gene. 2006 May 10;372:171-81. Epub 2006 Mar 24.

PMID:
16564143
36.

Computational analysis of microRNA targets in Caenorhabditis elegans.

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

Gene. 2006 Jan 3;365:2-10. Epub 2005 Dec 13.

PMID:
16356665

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