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Items: 49

1.

SonicParanoid: fast, accurate, and easy orthology inference.

Cosentino S, Iwasaki W.

Bioinformatics. 2018 Jul 19. doi: 10.1093/bioinformatics/bty631. [Epub ahead of print]

PMID:
30032301
2.

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.

3.

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.

4.

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.

5.

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
6.

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.

7.

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.

8.

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.

9.

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.

PMID:
29027707
10.

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.

11.

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
12.

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.

13.

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.

14.

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.

15.

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
16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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
22.

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.

23.

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.

24.

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.

25.

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.

26.

Tepidicaulis marinus gen. nov., sp. nov., a marine bacterium that reduces nitrate to nitrous oxide under strictly microaerobic conditions.

Takeuchi M, Yamagishi T, Kamagata Y, Oshima K, Hattori M, Katayama T, Hanada S, Tamaki H, Marumo K, Maeda H, Nedachi M, Iwasaki W, Suwa Y, Sakata S.

Int J Syst Evol Microbiol. 2015 Jun;65(Pt 6):1749-54. doi: 10.1099/ijs.0.000167. Epub 2015 Mar 4.

PMID:
25740933
27.

GroupTracker: Video tracking system for multiple animals under severe occlusion.

Fukunaga T, Kubota S, Oda S, Iwasaki W.

Comput Biol Chem. 2015 Aug;57:39-45. doi: 10.1016/j.compbiolchem.2015.02.006. Epub 2015 Feb 18.

PMID:
25736254
28.

Discovery of osmotic sensitive transcription factors in fish intestine via a transcriptomic approach.

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

BMC Genomics. 2014 Dec 18;15:1134. doi: 10.1186/1471-2164-15-1134.

29.

Parallel selection on gene copy number variations through evolution of three-spined stickleback genomes.

Hirase S, Ozaki H, Iwasaki W.

BMC Genomics. 2014 Aug 29;15:735. doi: 10.1186/1471-2164-15-735.

30.

Methylocaldum marinum sp. nov., a thermotolerant, methane-oxidizing bacterium isolated from marine sediments, and emended description of the genus Methylocaldum.

Takeuchi M, Kamagata Y, Oshima K, Hanada S, Tamaki H, Marumo K, Maeda H, Nedachi M, Hattori M, Iwasaki W, Sakata S.

Int J Syst Evol Microbiol. 2014 Sep;64(Pt 9):3240-6. doi: 10.1099/ijs.0.063503-0. Epub 2014 Jun 30.

PMID:
24981325
31.

Complete Genome Sequence of Winogradskyella sp. Strain PG-2, a Proteorhodopsin-Containing Marine Flavobacterium.

Kumagai Y, Yoshizawa S, Oshima K, Hattori M, Iwasaki W, Kogure K.

Genome Announc. 2014 May 29;2(3). pii: e00490-14. doi: 10.1128/genomeA.00490-14.

32.

Functional characterization of flavobacteria rhodopsins reveals a unique class of light-driven chloride pump in bacteria.

Yoshizawa S, Kumagai Y, Kim H, Ogura Y, Hayashi T, Iwasaki W, DeLong EF, Kogure K.

Proc Natl Acad Sci U S A. 2014 May 6;111(18):6732-7. doi: 10.1073/pnas.1403051111. Epub 2014 Mar 31.

33.

Crossing borders for science.

Schultheiss SJ, Yang JS, Iwasaki W, Lin SH, Jean A, Michaut M.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003519. doi: 10.1371/journal.pcbi.1003519. eCollection 2014 Mar.

34.

CLOCK-controlled polyphonic regulation of circadian rhythms through canonical and noncanonical E-boxes.

Yoshitane H, Ozaki H, Terajima H, Du NH, Suzuki Y, Fujimori T, Kosaka N, Shimba S, Sugano S, Takagi T, Iwasaki W, Fukada Y.

Mol Cell Biol. 2014 May;34(10):1776-87. doi: 10.1128/MCB.01465-13. Epub 2014 Mar 3.

35.

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kalaš M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T.

J Biomed Semantics. 2014 Feb 5;5(1):5. doi: 10.1186/2041-1480-5-5.

36.

MetaMetaDB: a database and analytic system for investigating microbial habitability.

Yang CC, Iwasaki W.

PLoS One. 2014 Jan 27;9(1):e87126. doi: 10.1371/journal.pone.0087126. eCollection 2014.

37.

CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data.

Fukunaga T, Ozaki H, Terai G, Asai K, Iwasaki W, Kiryu H.

Genome Biol. 2014 Jan 21;15(1):R16. doi: 10.1186/gb-2014-15-1-r16.

38.

The spirit of competition: to win or not to win.

Szczepinska T, Iwasaki W, Abeel T.

PLoS Comput Biol. 2013;9(12):e1003413. doi: 10.1371/journal.pcbi.1003413. Epub 2013 Dec 26.

39.

From β- to α-proteobacteria: the origin and evolution of rhizobial nodulation genes nodIJ.

Aoki S, Ito M, Iwasaki W.

Mol Biol Evol. 2013 Nov;30(11):2494-508. doi: 10.1093/molbev/mst153. Epub 2013 Sep 11.

PMID:
24030554
40.

Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families.

Miya M, Friedman M, Satoh TP, Takeshima H, Sado T, Iwasaki W, Yamanoue Y, Nakatani M, Mabuchi K, Inoue JG, Poulsen JY, Fukunaga T, Sato Y, Nishida M.

PLoS One. 2013 Sep 4;8(9):e73535. doi: 10.1371/journal.pone.0073535. eCollection 2013.

41.

MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline.

Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M, Nishida M.

Mol Biol Evol. 2013 Nov;30(11):2531-40. doi: 10.1093/molbev/mst141. Epub 2013 Aug 16.

42.

Integration of interactive, multi-scale network navigation approach with Cytoscape for functional genomics in the big data era.

Praneenararat T, Takagi T, Iwasaki W.

BMC Genomics. 2012;13 Suppl 7:S24. doi: 10.1186/1471-2164-13-S7-S24. Epub 2012 Dec 13.

43.

Generalized centroid estimators in bioinformatics.

Hamada M, Kiryu H, Iwasaki W, Asai K.

PLoS One. 2011 Feb 18;6(2):e16450. doi: 10.1371/journal.pone.0016450.

44.

Interactive, multiscale navigation of large and complicated biological networks.

Praneenararat T, Takagi T, Iwasaki W.

Bioinformatics. 2011 Apr 15;27(8):1121-7. doi: 10.1093/bioinformatics/btr083. Epub 2011 Feb 23.

45.

TogoDoc server/client system: smart recommendation and efficient management of life science literature.

Iwasaki W, Yamamoto Y, Takagi T.

PLoS One. 2010 Dec 13;5(12):e15305. doi: 10.1371/journal.pone.0015305.

46.

An intuitive, informative, and most balanced representation of phylogenetic topologies.

Iwasaki W, Takagi T.

Syst Biol. 2010 Oct;59(5):584-93. doi: 10.1093/sysbio/syq044. Epub 2010 Sep 3.

47.

Rapid pathway evolution facilitated by horizontal gene transfers across prokaryotic lineages.

Iwasaki W, Takagi T.

PLoS Genet. 2009 Mar;5(3):e1000402. doi: 10.1371/journal.pgen.1000402. Epub 2009 Mar 6.

48.

Reconstruction of highly heterogeneous gene-content evolution across the three domains of life.

Iwasaki W, Takagi T.

Bioinformatics. 2007 Jul 1;23(13):i230-9.

PMID:
17646301
49.

Structural basis of the water-assisted asparagine recognition by asparaginyl-tRNA synthetase.

Iwasaki W, Sekine S, Kuroishi C, Kuramitsu S, Shirouzu M, Yokoyama S.

J Mol Biol. 2006 Jul 7;360(2):329-42. Epub 2006 May 15.

PMID:
16753178

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