Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops

Authors: Gao, Rui-Fang ^{a, b, 1}, Wang, Jie-Yu ^{c, d, 1}, Liu, Ke-Wei ^{e, f, g, 1}, Yoshida, Kouki ^{h, 1}, Hsiao, Yu-Yun ^{i, 1}, Shi, Yi-Xiang ^j, Tsai, Kun-Chan ^k, Chen, You-Yi ^l, Mitsuda, Nobutaka ^m, Liang, Chieh-Kai ^l, Wang, Zhi-Wen ⁿ, Wang, Ying ^{a, b}, Zhang, Di-Yang ^c, Huang, Laiqiang ^{e, f}, Zhao, Xiang ⁿ, Zhong, Wen-Ying ⁿ, Cheng, Ying-Hui ^o, Jiang, Zi-De ^p, Li, Ming-He ^c, Sun, Wei-Hong ^c, Yu, Xia ^c, Hu, Wenqi ^c, Zhou, Zhuang ^{c, q}, Zhou, Xiao-Fan ^p, Yeh, Chuan-Ming ^{m, r, s, ∗∗}, Katoh, Kazutaka ^{t, ∗∗∗}, Tsai, Wen-Chieh ^{i, l, u, ∗∗∗∗}, Liu, Zhong-Jian ^{c, f, q, v, ∗}, Martin, Francis ^{w, ∗∗∗∗∗}, Zhang, Gui-Ming ^{a, b, ∗∗∗∗∗∗}

Source: In Heliyon February 2021 7(2)

Lamassemble: Multiple Alignment and Consensus Sequence of Long Reads

Authors: Frith, Martin C., Mitsuhashi, Satomi, Katoh, Kazutaka

Source: Methods in molecular biology. 2231:135-146

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN625406478&indx=1&recIds=ETOCRN625406478

Analysis of Protein Intermolecular Interactions with MAFFT-DASH

Authors: Rozewicki, John, Li, Songling, Katoh, Kazutaka, Standley, Daron M.

Source: Methods in molecular biology. 2231:163-178

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN625406492&indx=1&recIds=ETOCRN625406492

Structural Modeling of Lymphocyte Receptors and Their Antigens

Authors: Li, Songling, Wilamowski, Jan, Teraguchi, Shunsuke, van Eerden, Floris J., Rozewicki, John, Davila, Ana, Xu, Zichang, Katoh, Kazutaka, Standley, Daron M.

Source: Methods in molecular biology. 2048:207-230

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN621345691&indx=1&recIds=ETOCRN621345691

Repertoire Builder: high-throughput structural modeling of B and T cell receptorsElectronic supplementary information (ESI) available. See DOI: 10.1039/c9me00020h

Authors: SchrittCurrent address: Department of Biosciences and Nutrition, Karolinska Institutet.Equal contribution., Dimitri, Li, Songling, Rozewicki, John, Katoh, Kazutaka, YamashitaCurrent address: KOTAI Biotechnologies Inc, 3-1 Yamadaoka, Suita, Osaka 565-0871., Kazuo, Volkmuth, Wayne, Cavet, Guy, Standley, Daron M.

Source: Molecular Systems Design and Engineering. 4(4):761-768

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100086176270.0x000001&indx=1&recIds=ETOCvdc_100086176270.0x000001

Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease

Authors: Sone, Jun, Mitsuhashi, Satomi, Fujita, Atsushi, Mizuguchi, Takeshi, Hamanaka, Kohei, Mori, Keiko, Koike, Haruki, Hashiguchi, Akihiro, Takashima, Hiroshi, Sugiyama, Hiroshi, Kohno, Yutaka, Takiyama, Yoshihisa, Maeda, Kengo, Doi, Hiroshi, Koyano, Shigeru, Takeuchi, Hideyuki, Kawamoto, Michi, Kohara, Nobuo, Ando, Tetsuo, Ieda, Toshiaki, Kita, Yasushi, Kokubun, Norito, Tsuboi, Yoshio, Katoh, Kazutaka, Kino, Yoshihiro, Katsuno, Masahisa, Iwasaki, Yasushi, Yoshida, Mari, Tanaka, Fumiaki, Suzuki, Ikuo, Frith, Martin, Matsumoto, Naomichi, Sobue, Gen

Source: Nature genetics. 51(8):1215-1221

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100185662457.0x000001&indx=1&recIds=ETOCvdc_100185662457.0x000001

Benchmarking the discrimination power of commonly used markers and amplicons in marine fish (e)DNA (meta)barcoding.

Authors: Fontes, João T., Katoh, Kazutaka, Pires, Rui, Soares, Pedro, Costa, Filipe O.

Source: Metabarcoding & Metagenomics; 2024, Issue 8, p1-26, 26p

Molecular Evolution of Arthropod Color Vision Deduced from Multiple Opsin Genes of Jumping Spiders.

Authors: Koyanagi, Mitsumasa, Nagata, Takashi, Katoh, Kazutaka

Source: Journal of Molecular Evolution; February 2008, Vol. 66 Issue 2, p130-137, 8p

A pipeline for complete characterization of complex germline rearrangements from long DNA reads

Authors: Mitsuhashi, Satomi, Ohori, Sachiko, Katoh, Kazutaka, Frith, Martin C., Matsumoto, Naomichi

Source: Genome medicine. 12(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100171974913.0x000001&indx=1&recIds=ETOCvdc_100171974913.0x000001

Parallelization of MAFFT for large-scale multiple sequence alignments

Authors: Nakamura, Tsukasa, Yamada, Kazunori D, Tomii, Kentaro, Katoh, Kazutaka

Source: Bioinformatics. 34(14):2490-2492

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100108453448.0x000001&indx=1&recIds=ETOCvdc_100108453448.0x000001

Amino Acid Specificity of Ancestral Aminoacyl-tRNA Synthetase Prior to the Last Universal Common Ancestor Commonote commonote.

Authors: Furukawa, Ryutaro^1,2, Yokobori, Shin-ichi¹, Sato, Riku¹, Kumagawa, Taimu¹, Nakagawa, Mizuho¹, Katoh, Kazutaka³, Yamagishi, Akihiko¹, Yamagish@toyaku.ac.jp

Source: Journal of Molecular Evolution; Feb2022, Vol. 90 Issue 1, p73-94, 22p

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization.

Authors: Katoh, Kazutaka (AUTHOR) katoh@ifrec.osaka-u.ac.jp, Rozewicki, John (AUTHOR), Yamada, Kazunori D (AUTHOR)

Source: Briefings in Bioinformatics. Jul2019, p1160-1166. 7p.

Subject Terms: *SEQUENCE alignment, *VISUALIZATION, *BIOLOGISTS

Corrigendum to “Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops” [Heliyon 7 (2) (February 2021) e06317]

Authors: Gao, Rui-Fang ^{a, b, 1}, Wang, Jie-Yu ^{c, d, 1}, Liu, Ke-Wei ^{e, f, g, 1}, Yoshida, Kouki ^{h, 1}, Hsiao, Yu-Yun ^{i, 1}, Shi, Yi-Xiang ^j, Tsai, Kun-Chan ^k, Chen, You-Yi ^l, Mitsuda, Nobutaka ^m, Liang, Chieh-Kai ^l, Wang, Zhi-Wen ⁿ, Wang, Ying ^{a, b}, Zhang, Diyang ^c, Huang, Laiqiang ^{e, f}, Zhao, Xiang ⁿ, Zhong, Wen-Ying ⁿ, Cheng, Ying-Hui ^o, Jiang, Zi-De ^p, Li, Ming-He ^c, Sun, Wei-Hong ^c, Yu, Xia ^c, Hu, Wenqi ^c, Zhou, Zhuang ^{c, q}, Zhou, Xiao-Fan ^p, Yeh, Chuan-Ming ^{m, r, s, ∗∗}, Katoh, Kazutaka ^{t, ∗∗∗}, Tsai, Wen-Chieh ^{i, l, u, ∗∗∗∗}, Liu, Zhong-Jian ^{c, f, q, v, ∗}, Martin, Francis ^{w, ∗∗∗∗∗}, Zhang, Gui-Ming ^{a, b, ∗∗∗∗∗∗}

Source: In Heliyon June 2021 7(6)

The evolution of structural genomics.

Authors: Standley, Daron M., Nakanishi, Tokuichiro, Xu, Zichang, Haruna, Soichiro, Li, Songling, Nazlica, Sedat Aybars, Katoh, Kazutaka

Source: Biophysical Reviews; Dec2022, Vol. 14 Issue 6, p1247-1253, 7p

An engineered ACE2 decoy neutralizes the SARS-CoV-2 Omicron variant and confers protection against infection in vivo.

Authors: Ikemura, Nariko, Taminishi, Shunta, Inaba, Tohru, Arimori, Takao, Motooka, Daisuke, Katoh, Kazutaka, Kirita, Yuhei, Higuchi, Yusuke, Li, Songling, Suzuki, Tatsuya, Itoh, Yumi, Ozaki, Yuki, Nakamura, Shota, Matoba, Satoaki, Standley, Daron M., Okamoto, Toru, Takagi, Junichi, Hoshino, Atsushi

Source: Science Translational Medicine; 6/22/2022, Vol. 14 Issue 650, p1-13, 13p

Subject Terms: SARS-CoV-2 Omicron variant, ANGIOTENSIN converting enzyme, SARS-CoV-2 Delta variant, CHIMERIC proteins, CONVALESCENT plasma, MONOCLONAL antibodies, VIRAL antibodies

Geographic Terms: WUHAN (China)

Bacterial induction of B cell senescence promotes age-related changes in the gut microbiota

Authors: Kawamoto, Shimpei, Uemura, Ken, Hori, Nozomi, Takayasu, Lena, Konishi, Yusuke, Katoh, Kazutaka, Matsumoto, Tomonori, Suzuki, Masae, Sakai, Yusuke, Matsudaira, Tatsuyuki, Adachi, Takahiro, Ohtani, Naoko, Standley, Daron M., Suda, Wataru, Fukuda, Shinji, Hara, Eiji

Source: Nature Cell Biology; 20230101, Issue: Preprints p1-12, 12p

Airbag device provided with airbags located on driver's seat side and passenger's seat side

Air bag device having a minimized cone depth

Airbag system

Airbag safety module for vehicle