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Publication List in Brief

Reprint PDFs are available upon request. Asterisks indicate equal contributions.
A longer list that contains book chapters, essays, conference presentations, and Japanese introductions is available here.

PubMed

48.
Tsukasa Fukunaga and Wataru Iwasaki.
Inactivity periods and postural change speed can explain atypical postural change patterns of Caenorhabditis elegans mutants.
BMC Bioinformatics, 18, 46. (2017)

47.
Koji Yano, Seishiro Aoki, Meng Liu, Yosuke Umehara, Norio Suganuma, Wataru Iwasaki, Shusei Sato, Takashi Soyano, Hiroshi Kouchi and Masayoshi Kawaguchi.
Function and evolution of a Lotus japonicus AP2/ERF family transcription factor that is required for development of infection threads.
DNA Research, published online. (2016)

46.
Yoshio Takei, Marty Kwok-Shing Wong, Supriya Pipil, Haruka Ozaki, Yutaka Suzuki, Wataru Iwasaki, and Makoto Kusakabe.
Molecular mechanisms underlying active desalination and low water permeability in the esophagus of eels acclimated to seawater.
American Journal of Physiology - Regulatory, Integrative and Comparative Physiology, 312, R231-R244. (2017)

45.
Hideki Terajima, Hikari Yoshitane, Haruka Ozaki, Yutaka Suzuki, Shigeki Shimba, Shinya Kuroda, Wataru Iwasaki, and Yoshitaka Fukada.
ADARB1 catalyzes circadian A-to-I editing and regulates RNA rhythm.
Nature Genetics, 49, 146-151. (2017)

43.
Sira Sriswasdi, Masako Takashima, Ri-ichiroh Manabe, Moriya Ohkuma, Takashi Sugita, and Wataru Iwasaki.
Global deceleration of gene evolution following recent genome hybridizations in fungi.
Genome Research, 26, 1081-1090. (2016)

42.
Shotaro Hirase, Yusuke Yokoyama, Cin-Ty Leed, and Wataru Iwasaki.
The Pliocene-Pleistocene transition had dual effects on north American migratory bird speciation.
Palaeogeography, Palaeoclimatology, Palaeoecology, 462, 85-91. (2016)

41.
Shotaro Hirase, Minoru Ikeda, Shun Hayasaka, Wataru Iwasaki, and Akihiro Kijima.
Stability of genetic diversity in an intertidal goby population after exposure to tsunami disturbance.
Marine Ecology, 37, 1161-1167. (2016)

40.
Marty Kwok-Shing Wong, Supriya Pipil, Haruka Ozaki, Yutaka Suzuki, Wataru Iwasaki, and Yoshio Takei.
Flexible selection of diversified Na+/K+-ATPase α-subunit isoforms for osmoregulation in teleosts.
Zoological Letters, 2, 15. (2016)

39. (Review)
Satoshi Hiraoka, Ching-chia Yang, and Wataru Iwasaki.
Metagenomics and bioinformatics in microbial ecology: Current status and beyond.
Microbes and Environments, 31, 204-212. (2016)

38.
Toshiaki Hosaka, Susumu Yoshizawa, Yu Nakajima, Noboru Ohsawa, Masakatsu Hato, Edward F. DeLong, Kazuhiro Kogure, Shigeyuki Yokoyama, Tomomi Kimura-Someya, Wataru Iwasaki (Co-Corresponding Author), and Mikako Shirouzu.
Structural mechanism for light-driven transport by a new type of chloride ion pump, Nonlabens marinus rhodopsin-3.
Journal of Biological Chemistry, 291, 17488-17495. (2016)

  • DOI: 10.1074/jbc.M116.728220 / PubMed: 27365396
  • Selected as Papers of the Week of Journal of Biological Chemistry (representing the top-2% overall importance).

37.
Shotaro Hirase, Hirohiko Takeshima, Mutsumi Nishida, and Wataru Iwasaki.
Parallel mitogenome sequencing alleviates random rooting effect in phylogeography.
Genome Biology and Evolution, 8, 1267-1278. (2016)

36.
Haruka Ozaki and Wataru Iwasaki.
MOCCS: clarifying DNA-binding motif ambiguity using ChIP-Seq data.
Computational Biology and Chemistry, 63, 62-72. (2016)

35.
Satoshi Hiraoka, Asako Machiyama, Minoru Ijichi, Kentaro Inoue, Kenshiro Oshima, Masahira Hattori, Susumu Yoshizawa, Kazuhiro Kogure, and Wataru Iwasaki.
Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake Tsunami.
BMC Genomics, 17, 53. (2016)


32.
Masako Takashima, Ri-ichiroh Manabe, Wataru Iwasaki, Akira Ohyama, Moriya Ohkuma, and Takashi Sugita.
Selection of orthologous genes for construction of a highly resolved phylogenetic tree and clarification of the phylogeny of Trichosporonales species.
PLOS ONE, 10, e0131217. (2015)

31.
Masaki Miya, Yukuto Sato, Tsukasa Fukunaga, Tetsuya Sado, Jan Yde Poulsen, Keiichi Sato, Toshifumi Minamoto, Satoshi Yamamoto, Hiroki Yamanaka, Hitoshi Araki, Michio Kondoh, and Wataru Iwasaki.
MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species.
Royal Society Open Science, 2, 150088. (2015)

  • DOI: 10.1098/rsos.150088 / PubMed: 26587265
  • Featured in NHK news (July 22, 2015) and several newspapers (Nikkei Shimbun, Nikkei Sangyo Shimbun, Asahi Shimbun, Yomiuri Shimbun, Okinawa Times, Ryukyu Shimpo, Chiba Nippo, etc.).

30.
Hirotsugu Ishizu, Yuka W. Iwasaki, Shigeki Hirakata, Haruka Ozaki, Wataru Iwasaki, Haruhiko Siomi, and Mikiko C. Siomi.
Somatic primary piRNA biogenesis driven by cis-acting RNA elements and trans-acting Yb.
Cell Reports, 12, 429-440. (2015)

29.
Mio Takeuchi, Takao Yamagishi, Yoichi Kamagata, Kenshiro Oshima, Masahira Hattori, Taiki Katayama, Satoshi Hanada, Hideyuki Tamaki, Katsumi Marumo, Hiroto Maeda, Munetomo Nedachi, Wataru Iwasaki, Yuichi Suwa, and Susumu Sakata.
Tepidicaulis marinus gen. nov., sp. nov., a novel marine bacterium reducing nitrate to nitrous oxide strictly under microaerobic conditions.
International Journal of Systematic and Evolutionary Microbiology, 65, 1749-1754. (2015)

27.
Tsukasa Fukunaga, Shoko Kubota, Shoji Oda, and Wataru Iwasaki.
GroupTracker: Video tracking system for multiple animals under severe occlusion.
Computational Biology and Chemistry, 57, 39-45. (2015)

25.
Marty Kwok-Shing Wong, Haruka Ozaki, Yutaka Suzuki, Wataru Iwasaki, and Yoshio Takei.
Discovery of osmotic sensitive transcription factors in fish intestine via a transcriptomic approach.
BMC Genomics, 15, 1134. (2014)

24.
Shotaro Hirase*, Haruka Ozaki*, and Wataru Iwasaki.
Parallel selection on gene copy number variations through evolution of three-spined stickleback genomes.
BMC Genomics, 15, 735. (2014)

23.
Mio Takeuchi, Yoichi Kamagata, Kenshiro Oshima, Satoshi Hanada, Hideyuki Tamaki, Katsumi Marumo, Hiroto Maeda, Munetomo Nedachi, Masahira Hattori, Wataru Iwasaki, and Susumu Sakata.
Methylocaldum marinum sp. nov., a novel thermotolerant methane oxidizing bacterium isolated from marine sediments.
International Journal of Systematic and Evolutionary Microbiology, 64, 3240-3246 (2014)

22.
Yohei Kumagai, Susumu Yoshizawa, Kenshiro Oshima, Masahira Hattori, Wataru Iwasaki, and Kazuhiro Kogure.
Complete genome sequence of Winogradskyella sp. strain PG-2, a proteorhodopsin-containing marine flavobacterium.
Genome Announcements, 2, e00490-14. (2014)

21. (Commentary)
Sebastian J. Schultheiss, Joshua SungWoo Yang, Wataru Iwasaki, Shu-Hsi Lin, Angela Jean, and Magali Michaut
Crossing borders for science.
PLOS Computational Biology, 10, e1003519. (2014)

20.
Susumu Yoshizawa, Yohei Kumagai, Hana Kim, Yoshitoshi Ogura, Tetsuya Hayashi, Wataru Iwasaki, Edward F. DeLong, and Kazuhiro Kogure.
Functional characterization of flavobacteria rhodopsins reveals a unique class of light-driven chloride pump in bacteria.
Proc Natl Acad Sci U S A, 111, 6732-6737. (2014)

19.
Hikari Yoshitane*, Haruka Ozaki*, Hideki Terajima*, Ngoc-Hien Du, Yutaka Suzuki, Taihei Fujimori, Naoki Kosaka, Shigeki Shimba, Sumio Sugano, Toshihisa Takagi, Wataru Iwasaki (Co-Corresponding Author), and Yoshitaka Fukada.
CLOCK-controlled polyphonic regulations of circadian rhythms through canonical and non-canonical E-boxes.
Molecular and Cellular Biology, 34, 1776-1787. (2014)

18. (Review)
Toshiaki Katayama, Mark D Wilkinson, Kiyoko F Aoki-Kinoshita, Shuichi Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin-Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano, Hiromasa Ono, Hidemasa Bono, Simon Kocbek, Jan Aerts, Yukie Akune, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Joachim Baran, Jerven Bolleman, Raoul JP Bonnal, Pier Luigi Buttigieg, Matthew P Campbell, Yi-an Chen, Hirokazu Chiba, Peter JA Cock, Kevin B Cohen, Alexandru Constantin, Geraint Duck, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Naohisa Goto, Robert Hoehndorf, Yoshinobu Igarashi, Hidetoshi Itaya, Maori Ito, Wataru Iwasaki, Matús Kalas, Takeo Katoda, Taehong Kim, Anna Kokubu, Yusuke Komiyama, Masaaki Kotera, Camille Laibe, Hilmar Lapp, Thomas Lütteke, M Scott Marshall, Takaaki Mori, Hiroshi Mori, Mizuki Morita, Katsuhiko Murakami, Mitsuteru Nakao, Hisashi Narimatsu, Hiroyo Nishide, Yosuke Nishimura, Johan Nystrom-Persson, Soichi Ogishima, Yasunobu Okamura, Shujiro Okuda, Kazuki Oshita, Nicki H Packer, Pjotr Prins, Rene Ranzinger, Philippe Rocca-Serra, Susanna Sansone, Hiromichi Sawaki, Sung-Ho Shin, Andrea Splendiani, Francesco Strozzi, Shu Tadaka, Philip Toukach, Ikuo Uchiyama, Masahito Umezaki, Rutger Vos, Patricia L Whetzel, Issaku Yamada, Chisato Yamasaki, Riu Yamashita, William S York, Christian M Zmasek, Shoko Kawamoto, and Toshihisa Takagi.
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
Journal of Biomedical Semantics, 5, 5. (2014)

17.
Ching-chia Yang and Wataru Iwasaki.
MetaMetaDB: A database and analytic system for investigating microbial habitability.
PLOS ONE, 9, e87126. (2014)

16.
Tsukasa Fukunaga, Haruka Ozaki, Goro Terai, Kiyoshi Asai, Wataru Iwasaki, and Hisanori Kiryu
CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data.
Genome Biology, 15, R16. (2014)

15. (Commentary)
Teresa Szczepinska, Wataru Iwasaki, and Thomas Abeel.
The spirit of competition: To win or not to win.
PLOS Computational Biology, 9, e1003413. (2013)

14.
Seishiro Aoki, Motomi Ito, and Wataru Iwasaki.
From beta- to alpha-proteobacteria: the origin and evolution of rhizobial nodulation genes nodIJ.
Molecular Biology and Evolution, 30, 2494-2508. (2013)

13.
Wataru Iwasaki, Tsukasa Fukunaga, Ryota Isagozawa, Koichiro Yamada, Yasunobu Maeda, Takashi P. Satoh, Tetsuya Sado, Kohji Mabuchi, Hirohiko Takeshima, Masaki Miya, and Mutsumi Nishida.
MitoFish and MitoAnnotator: A mitochondrial genome database of fish with an accurate and automatic annotation pipeline.
Molecular Biology and Evolution, 30, 2531-2540. (2013)

12.
Masaki Miya, Matt Friedman, Takashi P. Satoh, Hirohiko Takeshima, Tetsuya Sado, Wataru Iwasaki, Yusuke Yamanoue, Masanori Nakatani, Kohji Mabuchi, Jun G. Inoue, Jan Yde Poulsen, Tsukasa Fukunaga, Yukuto Sato, and Mutsumi Nishida.
Evolutionary origin of the Scombridae (tunas and mackerels): Members of a paleogene adaptive radiation with 14 other pelagic fish families.
PLOS ONE, 8, e73535. (2013)

10.
Thanet Praneenararat*, Toshihisa Takagi, and Wataru Iwasaki*.
Integration of interactive, multi-scale network navigation approach with Cytoscape for functional genomics in the big data era.
BMC Genomics, 13(Suppl 7), S24. (2012)

7.
Thanet Praneenararat*, Toshihisa Takagi, and Wataru Iwasaki*.
Interactive, multi-scale navigation of large and complicated biological networks.
Bioinformatics, 27, 1121-1127. (2011)

6.
Michiaki Hamada, Hisanori Kiryu, Wataru Iwasaki, and Kiyoshi Asai.
Generalized centroid estimators in bioinformatics.
PLOS ONE, 6, e16450. (2011)

5.
Wataru Iwasaki*, Yasunori Yamamoto*, and Toshihisa Takagi.
TogoDoc Server/Client System: Smart recommendation and efficient management of life science literature.
PLOS ONE, 5, e15305. (2010)

4.
Wataru Iwasaki and Toshihisa Takagi.
An intuitive, informative, and most balanced representation of phylogenetic topologies.
Systematic Biology, 59, 584-593. (2010)

3.
Wataru Iwasaki and Toshihisa Takagi.
Rapid pathway evolution facilitated by horizontal gene transfers across prokaryotic lineages.
PLOS Genetics, 5, e1000402. (2009)

2.
Wataru Iwasaki and Toshihisa Takagi.
Reconstruction of highly heterogeneous gene-content evolution across the three domains of life.
Bioinformatics, 23, i230-i239. (2007)

  • DOI: 10.1093/bioinformatics/btm165 / PubMed: 17646301
  • Accepted for a conference paper presentation at 15th Annual International Conference on Intelligent Systems for Molecular Biology / 6th European Conference on Computational Biology (ISMB/ECCB2007). Acceptance rate = 15.8%.

1.
Wataru Iwasaki, Shun-ichi Sekine, Chizu Kuroishi, Seiki Kuramitsu, Mikako Shirouzu, and Shigeyuki Yokoyama.
Structural basis of the water-assisted asparagine recognition by asparaginyl-tRNA synthetase.
Journal of Molecular Biology, 360, 329-342. (2006)


 Publications in Japanese

49. (Review in Japanese)
岩崎渉
バイオインフォマティクスの全体像
実験医学35,713-719.(2017)

44. (Review in Japanese)
岩崎渉
遺伝子発現ネットワークとバイオインフォマティクス
医学のあゆみ259,865-869.(2016)

34. (Review in Japanese)
岩崎渉,佐藤行人,源利文,山中裕樹,荒木仁志,宮正樹.
環境DNA解析のインパクト
実験医学34,103-107.(2016)

33. (Review in Japanese)
岩崎由香,岩崎渉
ncRNAのバイオインフォマティクス解析
実験医学33,3379-3384.(2015)

28. (Review in Japanese)
福永津嵩,岩崎渉
Computational Ethology:バイオインフォマティクスと動物行動学の融合
領域融合レビュー4,e003.(2015)

26. (Review in Japanese)
尾崎遼,岩崎渉
NGSデータ解析
実験医学32,3197-3202.(2014)

11. (Review in Japanese)
尾崎遼,岩崎渉
ENCODEプロジェクトで明らかになったこと
細胞工学32,101-106.(2013)

9. (Review in Japanese)
佐藤行人,八谷剛史,岩崎渉
水圏生物学における次世代シーケンサー活用の現状と応用可能性への展望
水産育種, 41,17-32.(2012)

  • (English abstract available)
  • Yukuto Sato, Tsuyoshi Hachiya, and Wataru Iwasaki.
  • Next-generation sequencing in aquatic biology: Current status and future directions.
  • Fish Genetics and Breeding Science, 41, 17-32. (2012)

8. (Review in Japanese)
岩崎渉,山本泰智,高木利久.
文献管理・文献推薦
実験医学29,2556-2562.(2011)