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Full Publication List of Wataru Iwasaki

Reprint PDFs are available upon request. Asterisks indicate equal contributions.
Selected publications / Full publication list with Japanese abstracts

PubMed

112.
Kei Hiruma, Seishiro Aoki, Junya Takino, Takeshi Higa, Yuniar Devi Utami, Akito Shiina, Masanori Okamoto, Masami Nakamura, Nanami Kawamura, Yoshihiro Ohmori, Ryohei Sugita, Keitaro Tanoi, Toyozo Sato, Hideaki Oikawa, Atsushi Minami, Wataru Iwasaki, and Yusuke Saijo.
A fungal sesquiterpene biosynthesis gene cluster critical for mutualist-pathogen transition in Colletotrichum tofieldiae.
Nature Communications, 14, 5288. (2023)

111.
Joel H. Nitta, Shawn W. Laffan, Brent D. Mishler, and Wataru Iwasaki.
canaper: Categorical analysis of neo- and paleo-endemism in R.
Ecography, 2023, e06638. (2023)

110.
Yibang Wang, Hui Zhang, Weiwei Xian, and Wataru Iwasaki.
Chromosome genome assembly and annotation of the spiny red gurnard (Chelidonichthys spinosus).
Scientific Data, 10, 443. (2023)

109.
Chunlai Tam and Wataru Iwasaki.
AlphaCutter: Efficient removal of non-globular regions from predicted protein structures.
Proteomics, 23, 2300176. (2023)

108.
Tomoyuki Mikami, Takafumi Ikeda, Yusuke Muramiya, Tatsuya Hirasawa, and Wataru Iwasaki.
Three-dimensional anatomy of the Tully monster casts doubt on its presumed vertebrate affinities.
Palaeontology, 66, e12646. (2023)

106.
Tao Zhu, Yukuto Sato, Tetsuya Sado, Masaki Miya, and Wataru Iwasaki.
MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in ten years.
Molecular Biology and Evolution, 43, msad035. (2023)

105.
Naoki Konno and Wataru Iwasaki.
Machine learning enables prediction of metabolic system evolution in bacteria.
Science Advances, 9, eadc9130. (2023)

104.
Kazumori Mise and Wataru Iwasaki.
Unexpected absence of ribosomal protein genes from metagenome-assembled genomes.
ISME Communications, 2, 118. (2022)

103.
Nanako Kanno, Shingo Kato, Moriya Ohkuma, Motomu Matsui, Wataru Iwasaki, and Shinsuke Shigeto.
Nondestructive microbial discrimination using single-cell Raman spectra and random forest machine learning algorithm.
STAR Protocols, 3, 101812. (2022)

102.
Takao K Suzuki, Motomu Matsui, Sira Sriswasdi, and Wataru Iwasaki.
Lifestyle evolution analysis by binary-state speciation and extinction (BiSSE) model.
Methods in Molecular Biology, 2569, 327-342. (2022)

101.
Joel H. Nitta, Eric Schuettpelz, Santiago Ramírez-Barahona, and Wataru Iwasaki.
An open and continuously updated fern tree of life.
Frontiers in Plant Science, 13, 909768. (2022)

100.
Arnon Plianchaisuk, Kazuya Kusama, Kiyoko Kato, Sira Sriswasdi, Kazuhiro Tamura, and Wataru Iwasaki.
Origination of LTR retroelement-derived NYNRIN coincides with therian placental emergence.
Molecular Biology and Evolution, 39, msac176. (2022)

98.
Tsukasa Fukunaga and Wataru Iwasaki.
Mirage 2.0: fast and memory-efficient reconstruction of gene-content evolution considering heterogeneous evolutionary patterns among gene families.
Bioinformatics, 38, 4039–4041. (2022)

97.
Taiki Adachi, Yasuhiko Naito, Patrick W. Robinson, Daniel P. Costa, Luis A. Hückstädt, Rachel R. Holser, Wataru Iwasaki, and Akinori Takahashi.
Whiskers as hydrodynamic prey sensors in foraging seals.
Proc Natl Acad Sci U S A, 119, e2119502119. (2022)

96.
Asano Ishikawa, Shun Yamanouchi, Wataru Iwasaki, and Jun Kitano.
Convergent copy number increase of genes associated with freshwater colonization in fishes.
Philosophical Transactions of the Royal Society B: Biological Sciences, 377, 20200509. (2022)

95.
Yannis Nevers, Tamsin E. M. Jones, Dushyanth Jyothi, Bethan Yates, Meritxell Ferret, Laura Portell-Silva, Laia Codo, Salvatore Cosentino, Marina Marcet-Houben, Anna Vlasova, Laetitia Poidevin, Arnaud Kress, Mark Hickman, Emma Persson, Ivana Piližota, Cristina Guijarro-Clarke, the OpenEBench team, the Quest for Orthologs Consortium, Wataru Iwasaki, Odile Lecompte, Erik Sonnhammer, David S. Roos, Toni Gabaldón, David Thybert, Paul D. Thomas, Yanhui Hu, David M Emms, Elspeth Bruford, Salvador Capella-Gutierrez, Maria J Martin, Christophe Dessimoz, and Adrian Altenhoff.
The Quest for Orthologs orthology benchmark service in 2022.
Nucleic Acids Research, 50, W623–W632. (2022)

94.
Joel H. Nitta, Brent D. Mishler, Wataru Iwasaki, and Atsushi Ebihara.
Spatial phylogenetics of Japanese ferns: Patterns, processes, and implications for conservation.
American Journal of Botany, 109, 727-745. (2022)

92.
Tsukasa Fukunaga and Wataru Iwasaki.
Inverse Potts model improves accuracy of phylogenetic profiling.
Bioinformatics, 38, 1794-1800. (2022)

91.
Naoki Konno, Yusuke Kijima, Keito Watano, Soh Ishiguro, Keiichiro Ono, Mamoru Tanaka, Hideto Mori, Nanami Masuyama, Dexter Pratt, Trey Ideker, Wataru Iwasaki, and Nozomu Yachie.
Deep distributed computing to reconstruct extremely large lineage trees.
Nature Biotechnology, 40, 566-575. (2022)

90.
Tsukasa Fukunaga and Wataru Iwasaki.
Mirage: Estimation of ancestral gene-copy numbers by considering different evolutionary patterns among gene families.
Bioinformatics Advances, 1, vbab014. (2021)

89.
Masako Nishikawa, Hiroshi Kanno, Yuqi Zhou, Ting-Hui Xiao, Takuma Suzuki, Yuma Ibayashi, Jeffrey Harmon, Shigekazu Takizawa, Kotaro Hiramatsu, Nao Nitta, Risako Kameyama, Walker Peterson, Jun Takiguchi, Mohammad Shifat-E-Rabbi, Yan Zhuang, Xuwang Yin, Abu Hasnat Mohammad Rubaiyat, Yunjie Deng, Hongqian Zhang, Shigeki Miyata, Gustavo K. Rohde, Wataru Iwasaki, Yutaka Yatomi, and Keisuke Goda.
Massive image-based single-cell profiling reveals high levels of circulating platelet aggregates in patients with COVID-19.
Nature Communications, 12, 7135. (2021)

88.
Gokalp Yildirir, Jana Sperschneider, Mathu Malar C., Eric C. H. Chen, Wataru Iwasaki, Calvin Cornell, and Nicolas Corradi.
Long reads and Hi-C sequencing illuminate the two compartment genome of the model arbuscular mycorrhizal symbiont Rhizophagus irregularis.
New Phytologist, 233, 1097-1107. (2022)

87.
Nanako Kanno, Shingo Kato, Moriya Ohkuma, Motomu Matsui, Wataru Iwasaki, and Shinsuke Shigeto.
Machine learning-assisted single-cell Raman fingerprinting for in situ and nondestructive classification of prokaryotes.
iScience, 24, 102975. (2021)

86.
Yuka W Iwasaki, Sira Sriswasdi, Yasuha Kinugasa, Jun Adachi, Yasunori Horikoshi, Aoi Shibuya, Wataru Iwasaki, Satoshi Tashiro, Takeshi Tomonaga, and Haruhiko Siomi.
Piwi–piRNA complexes induce stepwise changes in nuclear architecture at target loci.
EMBO Journal, 40, e108345. (2021)

85. (Review)
Benjamin Linard, Ingo Ebersberger, Shawn E. McGlynn, Natasha Glover, Tomohiro Mochizuki, Mateus Patricio, Odile Lecompte, Yannis Nevers, QFO Consortium, Paul D. Thomas, Toni Gabaldón, Erik Sonnhammer, Christophe Dessimoz, and Ikuo Uchiyama.
Ten years of collaborative progress in the Quest for Orthologs.
Molecular Biology and Evolution, 38, 3033-3045. (2021)

84.
Tomoyuki Mikami and Wataru Iwasaki.
The flipping t‐ratio test: phylogenetically informed assessment of the Pareto theory for phenotypic evolution.
Methods in Ecology and Evolution, 12, 696-706. (2021)

83.
Shotaro Hirase, Ayumi Tezuka, Atsushi J. Nagano, Mana Sato, Sho Hosoya, Kiyoshi Kikuchi, and Wataru Iwasaki.
Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population.
Evolution, 75, 176-194. (2021)

81.
Kazumori Mise and Wataru Iwasaki.
Environmental atlas of prokaryotes enables powerful and intuitive habitat-based analysis of community structures.
iScience, 23, 101624. (2020)

80.
Kaori Motoki, Tomo-o Watsuji, Yoshihiro Takaki, Ken Takai, and Wataru Iwasaki.
Metatranscriptomics by in situ RNA stabilization directly and comprehensively revealed episymbiotic microbial communities of deep-sea squat lobsters.
mSystems, 5, e00551-20. (2020)

79.
Hui Jia, Yibang Wang, Susumu Yoshizawa, Wataru Iwasaki, Yuquan Li, Weiwei Xian, and Hui Zhang. Seasonal variation and assessment of fish resources in the Yangtze Estuary based on environmental DNA.
Water, 12, 2874. (2020)

78.
Yu Maeda, Kazumori Mise, Wataru Iwasaki, Akira Watanabe, Susumu Asakawa, Rasit Asiloglu, and Jun Murase.
Invention of artificial rice field soil: A tool to study the effect of soil components on the activity and community of microorganisms involved in anaerobic organic matter decomposition.
Microbes and Environments, 35, ME20093. (2020)

77. (Commentary)
Toshifumi Minamoto, Masaki Miya, Tetsuya Sado, Satoquo Seino, Hideyuki Doi, Michio Kondoh, Keigo Nakamura, Teruhiko Takahara, Satoshi Yamamoto, Hiroki Yamanaka, Hitoshi Araki, Wataru Iwasaki, Akihide Kasai, Reiji Masuda, and Kimiko Uchii.
An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols.
Environmental DNA, 3, 8–13. (2021)

76.
Adrian M Altenhoff, Javier Garrayo-Ventas, Salvatore Cosentino, David Emms, Natasha M Glover, Ana Hernández-Plaza, Yannis Nevers, Vicky Sundesha, Damian Szklarczyk, José M Fernández, Laia Codó, Quest for Orthologs Consortium; Josep Ll Gelpi, Jaime Huerta-Cepas, Wataru Iwasaki, Steven Kelly, Odile Lecompte, Matthieu Muffato, Maria J Martin, Salvador Capella-Gutierrez, Paul D Thomas, Erik Sonnhammer, and Christophe Dessimoz.
The Quest for Orthologs benchmark service and consensus calls in 2020.
Nucleic Acids Research, 48, W538-W545. (2020)

75.
Tsukasa Fukunaga and Wataru Iwasaki.
Logicome Profiler: Exhaustive detection of statistically significant logic relationships from comparative omics data.
PLOS ONE, 15, e0232106. (2020)

74.
Yuji Tokumoto, Kayo Hashimoto, Takashi Soyano, Seishiro Aoki, Wataru Iwasaki, Mai Fukuhara, Tomomi Nakagawa, Kazuhiko Saeki, Jun Yokoyama, Hironori Fujita, and Masayoshi Kawaguchi.
Assessment of Polygala paniculata (Polygalaceae) characteristics for evolutionary studies of legume–rhizobia symbiosis.
Journal of Plant Research, 133, 109-122. (2020)

73.
David M. Needham*, Susumu Yoshizawa*, Toshiaki Hosaka*, Camille Poirier, Chang Jae Choi, Elisabeth Hehenberger, Nicholas A. T. Irwin, Susanne Wilken, Cheuk-Man Yung, Charles Bachy, Rika Kurihara, Yu Nakajima, Keiichi Kojima, Tomomi Kimura-Someya, Guy Leonard, Rex R. Malmstrom, Daniel R. Mende, Daniel K. Olson, Yuki Sudo, Sebastian Sudek, Thomas A. Richards, Edward F. DeLong, Patrick J. Keeling, Alyson E. Santoro, Mikako Shirouzu, Wataru Iwasaki (Co-Corresponding Author), and Alexandra Z. Worden.
A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators.
Proc Natl Acad Sci U S A, 116, 20574-20583. (2019)

72.
Shotaro Hirase, Ayumi Tezuka, Atsushi J. Nagano, Kiyoshi Kikuchi, and Wataru Iwasaki.
Genetic isolation by distance in the yellowfin goby populations revealed by RAD sequencing.
Ichthyological Research, 67, 98–104 (2020)

71.
Hui Zhang, Susumu Yoshizawa, Wataru Iwasaki, and Weiwei Xian.
Seasonal fish assemblage structure using environmental DNA in the Yangtze Estuary and its adjacent waters.
Frontiers in Marine Science, 6, 515. (2019)

70.
Motomu Matsui and Wataru Iwasaki.
Graph splitting: A graph-based approach for superfamily-scale phylogenetic tree reconstruction.
Systematic Biology, 69, 265-279. (2020)

69.
Hikari Yoshitane, Yoshimasa Asano, Aya Sagami, Seinosuke Sakai, Yutaka Suzuki, Hitoshi Okamura, Wataru Iwasaki, Haruka Ozaki, and Yoshitaka Fukada.
Functional D-box sequences reset the circadian clock and drive mRNA rhythms.
Communications Biology, 2, 300. (2019)

68.
Sira Sriswasdi, Masako Takashima, Ri-ichiroh Manabe, Moriya Ohkuma, and Wataru Iwasaki.
Genome and transcriptome evolve separately in recently hybridized Trichosporon fungi.
Communications Biology, 2, 263. (2019)

67.
Sohta A Ishikawa, Anna Zhukova, Wataru Iwasaki, and Olivier Gascuel.
A fast likelihood method to reconstruct and visualize ancestral scenarios.
Molecular Biology and Evolution, 36, 2069-2085. (2019)

66.
Masako Takashima, Ri-ichiroh Manabe, Yuki Nishimura, Rikiya Endoh, Moriya Ohkuma, Sira Sriswasdi, Takashi Sugita, and Wataru Iwasaki.
Recognition and delineation of yeast genera based on genomic data: Lessons from Trichosporonales.
Fungal Genetics and Biology, 130, 31-42. (2019)

65.
Mio Takeuchi, Haruka Ozaki, Satoshi Hiraoka, Yoichi Kamagata, Susumu Sakata, Hideyoshi Yoshioka, and Wataru Iwasaki.
Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8.
PLOS ONE, 14, e0213535. (2019)

64.
Satoshi Hiraoka, Yusuke Okazaki, Mizue Anda, Atsushi Toyoda, Shin-ichi Nakano, and Wataru Iwasaki.
Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community.
Nature Communications, 10, 159. (2019)

63.
Salvatore Cosentino and Wataru Iwasaki.
SonicParanoid: fast, accurate and easy orthology inference.
Bioinformatics, 35, 149–151. (2019)

62.
Yukuto Sato, Masaki Miya, Tsukasa Fukunaga, Tetsuya Sado, and Wataru Iwasaki.
MitoFish and MiFish pipeline: a mitochondrial genome database of fish with an analysis pipeline for environmental DNA metabarcoding.
Molecular Biology and Evolution, 35, 1553–1555. (2018)

61.
Masayuki Ushio, Koichi Murata, Tetsuya Sado, Isao Nishiumi, Masamichi Takeshita, Wataru Iwasaki, and Masaki Miya.
Demonstration of the potential of environmental DNA as a tool for the detection of avian species.
Scientific Reports, 8, 4493. (2018)

60.
Daniel K. Olson, Susumu Yoshizawa, Dominique Boeuf, Wataru Iwasaki, and Edward F. DeLong.
Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre.
The ISME Journal, 12, 1047–1060. (2018)

59.
Tazro Ohta, Takeshi Kawashima, Natsuko O. Shinozaki, Akito Dobashi, Satoshi Hiraoka, Tatsuhiko Hoshino, Keiichi Kanno, Takafumi Kataoka, Shuichi Kawashima, Motomu Matsui, Wataru Nemoto, Suguru Nishijima, Natsuki Suganuma, Haruo Suzuki, Y-h. Taguchi, Yoichi Takenaka, Yosuke Tanigawa, Momoka Tsuneyoshi, Kazutoshi Yoshitake, Yukuto Sato, Riu Yamashita, Kazuharu Arakawa, and Wataru Iwasaki.
Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago.
Journal of Plant Research, 131, 709–717. (2018)

58.
Yohei Kumagai, Susumu Yoshizawa, Yu Nakajima, Mai Watanabe, Tsukasa Fukunaga, Yoshitoshi Ogura, Tetsuya Hayashi, Kenshiro Oshima, Masahira Hattori, Masahiko Ikeuchi, Kazuhiro Kogure, Edward F. DeLong, and Wataru Iwasaki.
Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine Flavobacteriia.
The ISME Journal, 12, 1329-1343. (2018)

57.
Md. Nurul Haider, Masahiko Nishimura, Minoru Ijichi, Ching-chia Yang, Wataru Iwasaki, and Kazuhiro Kogure.
Habitability analyses of aquatic bacteria.
Journal of Oceanography, 74, 197–207. (2018)

56.
Masako Takashima*, Sira Sriswasdi*, Ri-ichiroh Manabe, Moriya Ohkuma, Takashi Sugita, and Wataru Iwasaki.
A Trichosporonales genome tree based on 27 haploid and three evolutionarily.
Yeast, 35, 99-111. (2018)

55.
Marty Kwok Shing Wong, Takehiro Tsukada, Nobuhiro Ogawa, Supriya Pipil, Haruka Ozaki, Yutaka Suzuki, Wataru Iwasaki, and Yoshio Takei.
A sodium binding system alleviates acute salt stress during seawater acclimation in eels.
Zoological Letters, 3, 22. (2017)

54.
Sira Sriswasdi, Ching-chia Yang, and Wataru Iwasaki.
Generalist species drive microbial dispersion and evolution.
Nature Communications, 8, 1162. (2017)

53.
Satoshi Hiraoka, Masaya Miyahara, Kazushi Fujii, Asako Machiyama, and Wataru Iwasaki.
Seasonal analysis of microbial communities in precipitation in the Greater Tokyo Area, Japan.
Frontiers in Microbiology, 8, 1506. (2017)

52.
Masayuki Ushio, Hisato Fukuda, Toshiki Inoue, Kobayashi Makoto, Osamu Kishida, Keiichi Sato, Koichi Murata, Masato Nikaido, Tetsuya Sado, Yukuto Sato, Masamichi Takeshita, Wataru Iwasaki, Hiroki Yamanaka, Michio Kondoh, and Masaki Miya.
Environmental DNA enables detection of terrestrial mammals from forest pond water.
Molecular Ecology Resources, 17, e63-e75. (2017)

51.
Shotaro Hirase, Sherrie Chambers, Kathryn Hassell, Melissa Carew, Vincent Pettigrove, Kiyoshi Soyano, Masaki Nagae, and Wataru Iwasaki.
Phylogeography of the yellowfin goby Acanthogobius flavimanus in native and non-native distributions.
Marine Biology, 164, 106. (2017)

49.
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)

48.
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, 24, 193-203. (2017)

47.
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)

46.
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
  • News 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.).
  • Selected as a highly-cited paper in Environment/Ecology (top 1% by citations for field and year in the Web of Science) by Clarivate.

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

107. (Book chapter, review in Japanese)
西村祐貴，綿野桂人，岩崎渉.
機械学習によるマイクロバイオームと機能未知遺伝子の解析 〜メタゲノム・対偶遺伝学・近傍遺伝子解析
清水秀幸編『実験医学別冊 Pythonで実践　生命科学データの機械学習』，387-422. (2023)

99. (Review in Japanese)
山内駿，岩崎渉．
de novo遺伝子誕生学〜「遺伝子とは何か？」を改めて問う鍵として
実験医学，40，1835-1841．(2022)

93. (Review in Japanese)
岩崎渉．
機能未知遺伝子の機能を推測するバイオインフォマティクス：AlphaFoldから遺伝子誕生学へ
日本微生物生態学会誌，37，3-13．(2022)

82. (Book chapter, review in Japanese)
岩崎渉.
環境DNA解析とバイオインフォマティクス：いま必要なこと、今後に向けて考えるべきこと
一般社団法人環境DNA学会企画、土居秀幸・近藤倫生編『環境DNA―生態系の真の姿を読み解く―』，225-229. (2021)

50. (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)

45. (Book chapter, review in Japanese)
岩崎渉.
環境DNA解析
服部正平編『NGSアプリケーション 今すぐ始める！ メタゲノム解析 実験プロトコール』，170-174. (2016)

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)
岩崎渉，尾崎遼．
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)

岩崎 渉 /
Wataru IWASAKI, Ph.D.

トップ
プロフィール・学会活動等
研究発表
　論文
　学会講演・口頭発表
　ポスター発表・共著発表
　学生の表彰・学会発表賞
出演・書籍・アウトリーチ
プレスリリース・エッセイ
講義・教科書
ソフトウェア・データベース

EN / JP

twitter / facebook
googlescholar / orcid
web of science
researchmap / linkedin

Lab Webpage

Iwasaki Lab
岩崎研ウェブページ

岩崎研ゲストセミナー

Resources Developed

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MitoFish & MitoAnnotator

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MiFish Pipeline

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SonicParanoid

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Evodictor

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ProkAtlas

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Graph Splitting

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Logicome Profiler

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Mirage

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Inverse Potts Model

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AlphaCutter

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Orthology Benchmark

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Flipping t-ratio Test

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Fern Tree of Life

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canaper

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MetaMetaDB

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GroupTracker

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MOCCS for ChIP-Seq Data

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ImageManipulationDetector

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TogoDoc Client

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TogoDocMobile@AppStore

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車輪樹法／Wheel Tree

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Arabimarklet 3.1

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NaviCluster

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NaviClusterCS

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Quest for Orthologs

Links

東京大学
大学院新領域創成科学研究科
　先端生命科学専攻
　メディカル情報生命専攻
大学院理学系研究科
　生物科学専攻
理学部 生物情報科学科
大気海洋研究所
　地球表層圏変動研究センター
　生物遺伝子変動分野
定量生命科学研究所
微生物科学イノベーション連携研究機構

日本学術会議
若手アカデミー

株式会社tayo

International Society for Computational Biology
日本バイオインフォマティクス学会
日本微生物生態学会
日本ゲノム微生物学会
日本進化学会
環境DNA学会
日本分子生物学会

京都大学化学研究所
Global Young Academy
ライフサイエンス統合データベースセンター
バイオサイエンスデータベースセンター
科学技術・学術政策研究所

アジア若手会議AYRCOB
生命情報科学若手の会
NGS現場の会
Acafe
Kashiwa.R