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Items: 1 to 50 of 113

1.

Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. II. Accumulation of Variation and Evolution of a New Subfamily.

Iwasaki WM, Kijima TE, Innan H.

Mol Biol Evol. 2019 Oct 3. pii: msz220. doi: 10.1093/molbev/msz220. [Epub ahead of print]

PMID:
31580443
2.

A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators.

Needham DM, Yoshizawa S, Hosaka T, Poirier C, Choi CJ, Hehenberger E, Irwin NAT, Wilken S, Yung CM, Bachy C, Kurihara R, Nakajima Y, Kojima K, Kimura-Someya T, Leonard G, Malmstrom RR, Mende DR, Olson DK, Sudo Y, Sudek S, Richards TA, DeLong EF, Keeling PJ, Santoro AE, Shirouzu M, Iwasaki W, Worden AZ.

Proc Natl Acad Sci U S A. 2019 Oct 8;116(41):20574-20583. doi: 10.1073/pnas.1907517116. Epub 2019 Sep 23.

3.

Functional D-box sequences reset the circadian clock and drive mRNA rhythms.

Yoshitane H, Asano Y, Sagami A, Sakai S, Suzuki Y, Okamura H, Iwasaki W, Ozaki H, Fukada Y.

Commun Biol. 2019 Aug 8;2:300. doi: 10.1038/s42003-019-0522-3. eCollection 2019.

4.

Graph Splitting: A Graph-Based Approach for Superfamily-scale Phylogenetic Tree Reconstruction.

Matsui Su M, Iwasaki W.

Syst Biol. 2019 Jul 31. pii: syz049. doi: 10.1093/sysbio/syz049. [Epub ahead of print]

PMID:
31364707
5.

Genome and transcriptome evolve separately in recently hybridized Trichosporon fungi.

Sriswasdi S, Takashima M, Manabe RI, Ohkuma M, Iwasaki W.

Commun Biol. 2019 Jul 19;2:263. doi: 10.1038/s42003-019-0515-2. eCollection 2019.

6.

Genome-wide SNP analysis of Japanese Thoroughbred racehorses.

Fawcett JA, Sato F, Sakamoto T, Iwasaki WM, Tozaki T, Innan H.

PLoS One. 2019 Jul 24;14(7):e0218407. doi: 10.1371/journal.pone.0218407. eCollection 2019.

7.

A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios.

Ishikawa SA, Zhukova A, Iwasaki W, Gascuel O.

Mol Biol Evol. 2019 Sep 1;36(9):2069-2085. doi: 10.1093/molbev/msz131.

8.

HCV IRES Captures an Actively Translating 80S Ribosome.

Yokoyama T, Machida K, Iwasaki W, Shigeta T, Nishimoto M, Takahashi M, Sakamoto A, Yonemochi M, Harada Y, Shigematsu H, Shirouzu M, Tadakuma H, Imataka H, Ito T.

Mol Cell. 2019 Jun 20;74(6):1205-1214.e8. doi: 10.1016/j.molcel.2019.04.022. Epub 2019 May 9.

PMID:
31080011
9.

Recognition and delineation of yeast genera based on genomic data: Lessons from Trichosporonales.

Takashima M, Manabe RI, Nishimura Y, Endoh R, Ohkuma M, Sriswasdi S, Sugita T, Iwasaki W.

Fungal Genet Biol. 2019 Sep;130:31-42. doi: 10.1016/j.fgb.2019.04.013. Epub 2019 Apr 23.

PMID:
31026590
10.

Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8.

Takeuchi M, Ozaki H, Hiraoka S, Kamagata Y, Sakata S, Yoshioka H, Iwasaki W.

PLoS One. 2019 Mar 14;14(3):e0213535. doi: 10.1371/journal.pone.0213535. eCollection 2019.

11.

Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community.

Hiraoka S, Okazaki Y, Anda M, Toyoda A, Nakano SI, Iwasaki W.

Nat Commun. 2019 Jan 11;10(1):159. doi: 10.1038/s41467-018-08103-y.

12.

The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA.

Iwasaki S, Iwasaki W, Takahashi M, Sakamoto A, Watanabe C, Shichino Y, Floor SN, Fujiwara K, Mito M, Dodo K, Sodeoka M, Imataka H, Honma T, Fukuzawa K, Ito T, Ingolia NT.

Mol Cell. 2019 Feb 21;73(4):738-748.e9. doi: 10.1016/j.molcel.2018.11.026. Epub 2018 Dec 27.

PMID:
30595437
13.

Simple separation of good quality bovine oocytes using a microfluidic device.

Iwasaki W, Yamanaka K, Sugiyama D, Teshima Y, Briones-Nagata MP, Maeki M, Yamashita K, Takahashi M, Miyazaki M.

Sci Rep. 2018 Sep 24;8(1):14273. doi: 10.1038/s41598-018-32687-6.

14.

Corrigendum to: Contribution of histone N-terminal tails to the structure and stability of nucleosomes.

Iwasaki W, Miya Y, Horikoshi N, Osakabe A, Taguchi H, Tachiwana H, Shibata T, Kagawa W, Kurumizaka H.

FEBS Open Bio. 2018 Aug 23;8(9):1567. doi: 10.1002/2211-5463.12508. eCollection 2018 Sep.

15.

SonicParanoid: fast, accurate and easy orthology inference.

Cosentino S, Iwasaki W.

Bioinformatics. 2019 Jan 1;35(1):149-151. doi: 10.1093/bioinformatics/bty631.

16.

Enhancement of Self-Aggregation Properties of Linear Elastin-Derived Short Peptides by Simple Cyclization: Strong Self-Aggregation Properties of Cyclo[FPGVG] n, Consisting Only of Natural Amino Acids.

Suyama K, Tatsubo D, Iwasaki W, Miyazaki M, Kiyota Y, Takahashi I, Maeda I, Nose T.

Biomacromolecules. 2018 Aug 13;19(8):3201-3211. doi: 10.1021/acs.biomac.8b00353. Epub 2018 Jul 9.

PMID:
29932654
17.

Neutral Theory in Cancer Cell Population Genetics.

Niida A, Iwasaki WM, Innan H.

Mol Biol Evol. 2018 Jun 1;35(6):1316-1321. doi: 10.1093/molbev/msy091.

PMID:
29718454
18.

MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding.

Sato Y, Miya M, Fukunaga T, Sado T, Iwasaki W.

Mol Biol Evol. 2018 Jun 1;35(6):1553-1555. doi: 10.1093/molbev/msy074.

19.

Demonstration of the potential of environmental DNA as a tool for the detection of avian species.

Ushio M, Murata K, Sado T, Nishiumi I, Takeshita M, Iwasaki W, Miya M.

Sci Rep. 2018 Mar 14;8(1):4493. doi: 10.1038/s41598-018-22817-5.

20.

Correlation between Electronic Shell Structure and Inertness of Cu n+ toward O2 Adsorption at n = 15, 21, 41, and 49.

Ohshimo K, Akimoto K, Ogawa M, Iwasaki W, Yamamoto H, Tona M, Tsukamoto K, Nakano M, Misaizu F.

J Phys Chem A. 2018 Mar 22;122(11):2927-2932. doi: 10.1021/acs.jpca.8b00246. Epub 2018 Mar 13.

PMID:
29494765
21.

Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre.

Olson DK, Yoshizawa S, Boeuf D, Iwasaki W, DeLong EF.

ISME J. 2018 Apr;12(4):1047-1060. doi: 10.1038/s41396-018-0074-4. Epub 2018 Feb 23.

22.

Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis 'Somei-yoshino' across the Japanese archipelago.

Ohta T, Kawashima T, Shinozaki NO, Dobashi A, Hiraoka S, Hoshino T, Kanno K, Kataoka T, Kawashima S, Matsui M, Nemoto W, Nishijima S, Suganuma N, Suzuki H, Taguchi YH, Takenaka Y, Tanigawa Y, Tsuneyoshi M, Yoshitake K, Sato Y, Yamashita R, Arakawa K, Iwasaki W.

J Plant Res. 2018 Jul;131(4):709-717. doi: 10.1007/s10265-018-1017-x. Epub 2018 Feb 19.

PMID:
29460198
23.

Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia.

Kumagai Y, Yoshizawa S, Nakajima Y, Watanabe M, Fukunaga T, Ogura Y, Hayashi T, Oshima K, Hattori M, Ikeuchi M, Kogure K, DeLong EF, Iwasaki W.

ISME J. 2018 May;12(5):1329-1343. doi: 10.1038/s41396-018-0058-4. Epub 2018 Feb 6.

24.

Replication stress induces accumulation of FANCD2 at central region of large fragile genes.

Okamoto Y, Iwasaki WM, Kugou K, Takahashi KK, Oda A, Sato K, Kobayashi W, Kawai H, Sakasai R, Takaori-Kondo A, Yamamoto T, Kanemaki MT, Taoka M, Isobe T, Kurumizaka H, Innan H, Ohta K, Ishiai M, Takata M.

Nucleic Acids Res. 2018 Apr 6;46(6):2932-2944. doi: 10.1093/nar/gky058.

25.

Inferring evolutionary responses of Anolis carolinensis introduced into the Ogasawara archipelago using whole genome sequence data.

Tamate S, Iwasaki WM, Krysko KL, Camposano BJ, Mori H, Funayama R, Nakayama K, Makino T, Kawata M.

Sci Rep. 2017 Dec 21;7(1):18008. doi: 10.1038/s41598-017-17852-7.

26.

A sodium binding system alleviates acute salt stress during seawater acclimation in eels.

Wong MKS, Tsukada T, Ogawa N, Pipil S, Ozaki H, Suzuki Y, Iwasaki W, Takei Y.

Zoological Lett. 2017 Dec 12;3:22. doi: 10.1186/s40851-017-0081-8. eCollection 2017.

27.

Generalist species drive microbial dispersion and evolution.

Sriswasdi S, Yang CC, Iwasaki W.

Nat Commun. 2017 Oct 27;8(1):1162. doi: 10.1038/s41467-017-01265-1.

28.

A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved 'natural' hybrid genomes.

Takashima M, Sriswasdi S, Manabe RI, Ohkuma M, Sugita T, Iwasaki W.

Yeast. 2018 Jan;35(1):99-111. doi: 10.1002/yea.3284. Epub 2017 Dec 6.

29.

Simulation framework for generating intratumor heterogeneity patterns in a cancer cell population.

Iwasaki WM, Innan H.

PLoS One. 2017 Sep 6;12(9):e0184229. doi: 10.1371/journal.pone.0184229. eCollection 2017.

30.

Seasonal Analysis of Microbial Communities in Precipitation in the Greater Tokyo Area, Japan.

Hiraoka S, Miyahara M, Fujii K, Machiyama A, Iwasaki W.

Front Microbiol. 2017 Aug 11;8:1506. doi: 10.3389/fmicb.2017.01506. eCollection 2017.

31.

Environmental DNA enables detection of terrestrial mammals from forest pond water.

Ushio M, Fukuda H, Inoue T, Makoto K, Kishida O, Sato K, Murata K, Nikaido M, Sado T, Sato Y, Takeshita M, Iwasaki W, Yamanaka H, Kondoh M, Miya M.

Mol Ecol Resour. 2017 Nov;17(6):e63-e75. doi: 10.1111/1755-0998.12690. Epub 2017 Jun 11.

PMID:
28603873
32.

Small Bowel Obstruction Caused by the Ingestion of a Wooden Toothpick: The CT findings and a Literature Review.

Izumi J, Satoh K, Iwasaki W, Miura T, Fujimori S.

Intern Med. 2017;56(6):657-660. doi: 10.2169/internalmedicine.56.7463. Epub 2017 Mar 17.

33.

[A Case of Heterochronic Ovarian Metastasis from Sigmoid Colon Cancer after Sigmoidectomy Treated with CapeOX That Included Bevacizumab].

Ono R, Ise N, Yoshioka H, Iwasaki W, Sato K, Niwa M.

Gan To Kagaku Ryoho. 2017 Jan;44(1):83-85. Japanese.

PMID:
28174387
34.

Inactivity periods and postural change speed can explain atypical postural change patterns of Caenorhabditis elegans mutants.

Fukunaga T, Iwasaki W.

BMC Bioinformatics. 2017 Jan 19;18(1):46. doi: 10.1186/s12859-016-1408-8.

35.

Function and evolution of a Lotus japonicus AP2/ERF family transcription factor that is required for development of infection threads.

Yano K, Aoki S, Liu M, Umehara Y, Suganuma N, Iwasaki W, Sato S, Soyano T, Kouchi H, Kawaguchi M.

DNA Res. 2017 Apr 1;24(2):193-203. doi: 10.1093/dnares/dsw052.

36.

Molecular mechanisms underlying active desalination and low water permeability in the esophagus of eels acclimated to seawater.

Takei Y, Wong MK, Pipil S, Ozaki H, Suzuki Y, Iwasaki W, Kusakabe M.

Am J Physiol Regul Integr Comp Physiol. 2017 Feb 1;312(2):R231-R244. doi: 10.1152/ajpregu.00465.2016. Epub 2016 Dec 21.

37.

ADARB1 catalyzes circadian A-to-I editing and regulates RNA rhythm.

Terajima H, Yoshitane H, Ozaki H, Suzuki Y, Shimba S, Kuroda S, Iwasaki W, Fukada Y.

Nat Genet. 2017 Jan;49(1):146-151. doi: 10.1038/ng.3731. Epub 2016 Nov 28.

PMID:
27893733
38.

Rad51 and RecA juxtapose dsDNA ends ready for DNA ligase-catalyzed end-joining under recombinase-suppressive conditions.

Konomura N, Arai N, Shinohara T, Kobayashi J, Iwasaki W, Ikawa S, Kusano K, Shibata T.

Nucleic Acids Res. 2017 Jan 9;45(1):337-352. doi: 10.1093/nar/gkw998. Epub 2016 Oct 27.

39.

Flexible selection of diversified Na(+)/K(+)-ATPase α-subunit isoforms for osmoregulation in teleosts.

Wong MK, Pipil S, Ozaki H, Suzuki Y, Iwasaki W, Takei Y.

Zoological Lett. 2016 Aug 3;2:15. doi: 10.1186/s40851-016-0050-7. eCollection 2016.

40.

Global deceleration of gene evolution following recent genome hybridizations in fungi.

Sriswasdi S, Takashima M, Manabe R, Ohkuma M, Sugita T, Iwasaki W.

Genome Res. 2016 Aug;26(8):1081-90. doi: 10.1101/gr.205948.116. Epub 2016 Jul 20.

41.

Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.

Hiraoka S, Yang CC, Iwasaki W.

Microbes Environ. 2016 Sep 29;31(3):204-12. doi: 10.1264/jsme2.ME16024. Epub 2016 Jul 5. Review.

42.

Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3.

Hosaka T, Yoshizawa S, Nakajima Y, Ohsawa N, Hato M, DeLong EF, Kogure K, Yokoyama S, Kimura-Someya T, Iwasaki W, Shirouzu M.

J Biol Chem. 2016 Aug 19;291(34):17488-17495. doi: 10.1074/jbc.M116.728220. Epub 2016 Jun 30.

43.

Parallel Mitogenome Sequencing Alleviates Random Rooting Effect in Phylogeography.

Hirase S, Takeshima H, Nishida M, Iwasaki W.

Genome Biol Evol. 2016 Apr 28;8(4):1267-78. doi: 10.1093/gbe/evw063.

44.

MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.

Ozaki H, Iwasaki W.

Comput Biol Chem. 2016 Aug;63:62-72. doi: 10.1016/j.compbiolchem.2016.01.014. Epub 2016 Feb 13.

PMID:
26971251
45.

Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami.

Hiraoka S, Machiyama A, Ijichi M, Inoue K, Oshima K, Hattori M, Yoshizawa S, Kogure K, Iwasaki W.

BMC Genomics. 2016 Jan 14;17:53. doi: 10.1186/s12864-016-2380-4.

46.

MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species.

Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M, Iwasaki W.

R Soc Open Sci. 2015 Jul 22;2(7):150088. doi: 10.1098/rsos.150088. eCollection 2015 Jul.

47.

Detection of Site-Specific Blood Flow Variation in Humans during Running by a Wearable Laser Doppler Flowmeter.

Iwasaki W, Nogami H, Takeuchi S, Furue M, Higurashi E, Sawada R.

Sensors (Basel). 2015 Oct 5;15(10):25507-19. doi: 10.3390/s151025507.

48.

Selection of Orthologous Genes for Construction of a Highly Resolved Phylogenetic Tree and Clarification of the Phylogeny of Trichosporonales Species.

Takashima M, Manabe R, Iwasaki W, Ohyama A, Ohkuma M, Sugita T.

PLoS One. 2015 Aug 4;10(8):e0131217. doi: 10.1371/journal.pone.0131217. eCollection 2015. Erratum in: PLoS One. 2015;10(9):e0138637.

49.

Somatic Primary piRNA Biogenesis Driven by cis-Acting RNA Elements and trans-Acting Yb.

Ishizu H, Iwasaki YW, Hirakata S, Ozaki H, Iwasaki W, Siomi H, Siomi MC.

Cell Rep. 2015 Jul 21;12(3):429-40. doi: 10.1016/j.celrep.2015.06.035. Epub 2015 Jul 9.

50.

Influence of Contact Force on Electrochemical Responses of Redox Species Flowing in Nitrocellulose Membrane at Micropyramid Array Electrode.

Iwasaki W, Sathuluri RR, Niwa O, Miyazaki M.

Anal Sci. 2015;31(7):729-32. doi: 10.2116/analsci.31.729.

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