Antigen-independent activation enhances the efficacy of 4-1BB-costimulated CD22 CAR T cells

Nathan Singh, Noelle V. Frey, Boris Engels, David M. Barrett, Olga Shestova, Pranali Ravikumar, Katherine D. Cummins, Yong Gu Lee, Raymone Pajarillo, Inkook Chun, Amy Shyu, Steven L. Highfill, Andrew Price, Linlin Zhao, Liaomin Peng, Brian Granda, Melissa Ramones, Xueqing Maggie Lu, David A. Christian, Jessica Perazzelli, Simon F. Lacey, Nathan H. Roy, Janis K. Burkhardt, Florent Colomb, Mohammad Damra, Mohamed Abdel-Mohsen, Ting Liu, Dongfang Liu, Daron M. Standley, Regina M. Young, Jennifer L. Brogdon, Stephan A. Grupp, Carl H. June, Shannon L. Maude, Saar Gill, Marco Ruella

Nature Medicine　Vol. 27　No. 5　p. 842-850　2021/05　Research paper (scientific journal)

Analysis of Protein Intermolecular Interactions with MAFFT-DASH

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

Methods in molecular biology (Clifton, N.J.)　Vol. 2231　p. 163-177　2021　Research paper (scientific journal)

Flexible, Functional, and Familiar: Characteristics of SARS-CoV-2 Spike Protein Evolution

Dianita S. Saputri, Songling Li, Floris J. van Eerden, John Rozewicki, Zichang Xu, Hendra S. Ismanto, Ana Davila, Shunsuke Teraguchi, Kazutaka Katoh, Daron M. Standley

Frontiers in Microbiology　Vol. 11　2020/09/17　Research paper (scientific journal)

Various miRNAs compensate the role of miR-122 on HCV replication

Chikako Ono, Takasuke Fukuhara, Songling Li, Jian Wang, Asuka Sato, Takuma Izumi, Yuzy Fauzyah, Takuya Yamamoto, Yuhei Morioka, Nikolay V. Dokholyan, Daron M. Standley, Yoshiharu Matsuura

PLoS Pathogens　Vol. 16　No. 6 June　2020/06　Research paper (scientific journal)

Control of enantioselectivity in the enzymatic reduction of halogenated acetophenone analogs by substituent positions and sizes

Afifa Ayu Koesoema, Daron M. Standley, Shusuke Ohshima, Mayumi Tamura, Tomoko Matsuda

Tetrahedron Letters　Vol. 61　No. 18　2020/04　Research paper (scientific journal)

Impact and relevance of alcohol dehydrogenase enantioselectivities on biotechnological applications

Afifa Ayu Koesoema, Daron M. Standley, Toshiya Senda, Tomoko Matsuda

Applied Microbiology and Biotechnology　Vol. 104　No. 7　p. 2897-2909　2020/04

Access to both enantiomers of substituted 2-tetralol analogs by a highly enantioselective reductase

Afifa Ayu Koesoema, Daron M. Standley, Kotchakorn T.sriwong, Mayumi Tamura, Tomoko Matsuda

Tetrahedron Letters　Vol. 61　No. 13　2020/03/26　Research paper (scientific journal)

Noncanonical STAT1 phosphorylation expands its transcriptional activity into promoting LPS-induced IL-6 and IL-12p40 production

Hozaifa Metwally, Toshio Tanaka, Songling Li, Gyanu Parajuli, Sujin Kang, Hamza Hanieh, Shigeru Hashimoto, Jaya P. Chalise, Yohannes Gemechu, Daron M. Standley, Tadamitsu Kishimoto

Science Signaling　Vol. 13　No. 624　2020/03/24　Research paper (scientific journal)

Dysregulated Expression of the Nuclear Exosome Targeting Complex Component Rbm7 in Nonhematopoietic Cells Licenses the Development of Fibrosis

Kiyoharu Fukushima, Takashi Satoh, Fuminori Sugihara, Yuki Sato, Toru Okamoto, Yuichi Mitsui, Sachiyo Yoshio, Songling Li, Satoshi Nojima, Daisuke Motooka, Shota Nakamura, Hiroshi Kida, Daron M. Standley, Eiichi Morii, Tatsuya Kanto, Motoko Yanagita, Yoshiharu Matsuura, Takashi Nagasawa, Atsushi Kumanogoh, Shizuo Akira

Immunity　Vol. 52　No. 3　p. 542-556.e13　2020/03/17　Research paper (scientific journal)

Methods for sequence and structural analysis of B and T cell receptor repertoires

Shunsuke Teraguchi, Dianita S. Saputri, Mara Anais Llamas-Covarrubias, Ana Davila, Diego Diez, Sedat Aybars Nazlica, John Rozewicki, Hendra S. Ismanto, Jan Wilamowski, Jiaqi Xie, Zichang Xu, Martin de Jesus Loza-Lopez, Floris J. van Eerden, Songling Li, Daron M. Standley

Computational and Structural Biotechnology Journal　Vol. 18　p. 2000-2011　2020

Initial phospholipid-dependent Irgb6 targeting to Toxoplasma gondii vacuoles mediates host defense

Youngae Lee, Hiroshi Yamada, Ariel Pradipta, Ji Su Ma, Masaaki Okamoto, Hikaru Nagaoka, Eizo Takashima, Daron M. Standley, Miwa Sasai, Kohji Takei, Masahiro Yamamoto

Life Science Alliance　Vol. 3　No. 1　2020　Research paper (scientific journal)

Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain

Afifa Ayu Koesoema, Yosuke Sugiyama, Zichang Xu, Daron M. Standley, Miki Senda, Toshiya Senda, Tomoko Matsuda

Applied Microbiology and Biotechnology　Vol. 103　No. 23-24　p. 9543-9553　2019/12/01　Research paper (scientific journal)

Reversible control of enantioselectivity by the length of ketone substituent in biocatalytic reduction

Afifa Ayu Koesoema, Yosuke Sugiyama, Kotchakorn T. Sriwong, Zichang Xu, Samantha Verina, Daron M. Standley, Miki Senda, Toshiya Senda, Tomoko Matsuda

Applied Microbiology and Biotechnology　Vol. 103　No. 23-24　p. 9529-9541　2019/12/01　Research paper (scientific journal)

Correction to: Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain (Applied Microbiology and Biotechnology, (2019), 103, 23-24, (9543-9553), 10.1007/s00253-019-10093-w)

Afifa Ayu Koesoema, Yosuke Sugiyama, Zichang Xu, Daron M. Standley, Miki Senda, Toshiya Senda, Tomoko Matsuda

Applied Microbiology and Biotechnology　Vol. 103　No. 23-24　p. 9555-9555　2019/12/01　Research paper (scientific journal)

Translation-dependent unwinding of stem-loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs

Takashi Mino, Noriki Iwai, Masayuki Endo, Kentaro Inoue, Kotaro Akaki, Fabian Hia, Takuya Uehata, Tomoko Emura, Kumi Hidaka, Yutaka Suzuki, Daron M. Standley, Mariko Okada-Hatakeyama, Shigeo Ohno, Hiroshi Sugiyama, Akio Yamashita, Osamu Takeuchi

Nucleic acids research　Vol. 47　No. 16　p. 8838-8859　2019/09/19　Research paper (scientific journal)

N4BP1 restricts HIV-1 and its inactivation by MALT1 promotes viral reactivation

Daichi Yamasoba, Kei Sato, Takuya Ichinose, Tomoko Imamura, Lennart Koepke, Simone Joas, Elisabeth Reith, Dominik Hotter, Naoko Misawa, Kotaro Akaki, Takuya Uehata, Takashi Mino, Sho Miyamoto, Takeshi Noda, Akio Yamashita, Daron M. Standley, Frank Kirchhoff, Daniel Sauter, Yoshio Koyanagi, Osamu Takeuchi

Nature Microbiology　Vol. 4　No. 9　p. 1532-1544　2019/09/01　Research paper (scientific journal)

Functional clustering of B cell receptors using sequence and structural features

Zichang Xu, Songling Li, John Rozewicki, Kazuo Yamashita, Shunsuke Teraguchi, Takeshi Inoue, Ryo Shinnakasu, Sarah Leach, Tomohiro Kurosaki, Daron M. Standley

Molecular Systems Design and Engineering　Vol. 4　No. 4　p. 769-778　2019/08　Research paper (scientific journal)

Repertoire Builder: High-throughput structural modeling of B and T cell receptors

Dimitri Schritt, Songling Li, John Rozewicki, Kazutaka Katoh, Kazuo Yamashita, Wayne Volkmuth, Guy Cavet, Daron M. Standley

Molecular Systems Design and Engineering　Vol. 4　No. 4　p. 761-768　2019/08　Research paper (scientific journal)

MAFFT-DASH: Integrated protein sequence and structural alignment

John Rozewicki, Songling Li, Karlou Mar Amada, Daron M. Standley, Kazutaka Katoh

Nucleic Acids Research　Vol. 47　No. W1　p. W5-W10　2019/07/01　Research paper (scientific journal)

Allergic conversion of protective mucosal immunity against nasal bacteria in patients with chronic rhinosinusitis with nasal polyposis

Kazuya Takeda, Shuhei Sakakibara, Kazuo Yamashita, Daisuke Motooka, Shota Nakamura, Marwa Ali El Hussien, Jun Katayama, Yohei Maeda, Masanobu Nakata, Shigeyuki Hamada, Daron M. Standley, Masaki Hayama, Takashi Shikina, Hidenori Inohara, Hitoshi Kikutani

Journal of Allergy and Clinical Immunology　Vol. 143　No. 3　p. 1163-1175.e15　2019/03　Research paper (scientific journal)

Structural determinants of the APOBEC3G N-terminal domain for HIV-1 RNA association

Hirofumi Fukuda, Songling Li, Luca Sardo, Jessica L. Smith, Kazuo Yamashita, Anamaria D. Sarca, Kotaro Shirakawa, Daron M. Standley, Akifumi Takaori-Kondo, Taisuke Izumi

Frontiers in Cellular and Infection Microbiology　Vol. 9　No. MAY　p. 129-129　2019　Research paper (scientific journal)

Structural Modeling of Lymphocyte Receptors and Their Antigens

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

Methods in Molecular Biology　Vol. 2048　p. 207-229　2019　Part of collection (book)

Arid5a stabilizes OX40 mRNA in murine CD4⁺ T cells by recognizing a stem-loop structure in its 3′UTR

Hamza Hanieh, Kazuya Masuda, Hozaifa Metwally, Jaya P. Chalise, Maged Mohamed, Kishan K. Nyati, Daron M. Standley, Songling Li, Mitsuru Higa, Mohammad M. Zaman, Tadamitsu Kishimoto

European Journal of Immunology　Vol. 48　No. 4　p. 593-604　2018/04　Research paper (scientific journal)

Characterization of SPP inhibitors suppressing propagation of HCV and protozoa

Junki Hirano, Toru Okamoto, Yukari Sugiyama, Tatsuya Suzuki, Shinji Kusakabe, Makoto Tokunaga, Takasuke Fukuhara, Miwa Sasai, Takahiro Tougan, Yasue Matsunaga, Kazuo Yamashita, Yusuke Sakai, Masahiro Yamamoto, Toshihiro Horii, Daron M. Standley, Kohji Moriishi, Kyoji Moriya, Kazuhiko Koike, Yoshiharu Matsuura

Proceedings of the National Academy of Sciences of the United States of America　Vol. 114　No. 50　p. E10782-E10791　2017/12/12　Research paper (scientific journal)

Clonal evolution and antigen recognition of anti-nuclear antibodies in acute systemic lupus erythematosus

Shuhei Sakakibara, Takao Arimori, Kazuo Yamashita, Hideyuki Jinzai, Daisuke Motooka, Shota Nakamura, Songling Li, Kazuya Takeda, Jun Katayama, Marwa Ali El Hussien, Masashi Narazaki, Toshio Tanaka, Daron M. Standley, Junichi Takagi, Hitoshi Kikutani

Scientific Reports　Vol. 7　No. 1　p. 16428-16428　2017/12/01　Research paper (scientific journal)

Structural basis for the assembly of the Ragulator-Rag GTPase complex

Ryo Yonehara, Shigeyuki Nada, Tomokazu Nakai, Masahiro Nakai, Ayaka Kitamura, Akira Ogawa, Hirokazu Nakatsumi, Keiichi I. Nakayama, Songling Li, Daron M. Standley, Eiki Yamashita, Atsushi Nakagawa, Masato Okada

Nature Communications　Vol. 8　No. 1　p. 1625-1625　2017/12/01　Research paper (scientific journal)

Modeling Biocatalysts

Dimitri Schritt, Kazutaka Katoh, Songling Li, Daron M. Standley

Future Directions in Biocatalysis: Second Edition　p. 385-398　2017/08/15　Part of collection (book)

Essential role for GABARAP autophagy proteins in interferon-inducible GTPase-mediated host defense

Miwa Sasai, Naoya Sakaguchi, Ji Su Ma, Shuhei Nakamura, Tsuyoshi Kawabata, Hironori Bando, Youngae Lee, Tatsuya Saitoh, Shizuo Akira, Akiko Iwasaki, Daron M. Standley, Tamotsu Yoshimori, Masahiro Yamamoto

Nature Immunology　Vol. 18　No. 8　p. 899-910　2017/07/19　Research paper (scientific journal)

TLR4-induced NF-κB and MAPK signaling regulate the IL-6 mRNA stabilizing protein Arid5a

Kishan K. Nyati, Kazuya Masuda, Mohammad Mahabub-Uz Zaman, Praveen K. Dubey, David Millrine, Jaya P. Chalise, Mitsuru Higa, Songling Li, Daron M. Standley, Kazunobu Saito, Hamza Hanieh, Tadamitsu Kishimoto

Nucleic Acids Research　Vol. 45　No. 5　p. 2687-2703　2017/03/17　Research paper (scientific journal)

Advax, a Delta Inulin Microparticle, Potentiates In-built Adjuvant Property of Co-administered Vaccines

Masayuki Hayashi, Taiki Aoshi, Yasunari Haseda, Kouji Kobiyama, Edward Wijaya, Noriyuki Nakatsu, Yoshinobu Igarashi, Daron M. Standley, Hiroshi Yamada, Yoshikazu Honda-Okubo, Hiromitsu Hara, Takashi Saito, Toshiyuki Takai, Cevayir Coban, Nikolai Petrovsky, Ken J. Ishii

EBioMedicine　Vol. 15　p. 127-136　2017/02/01　Research paper (scientific journal)

Mapping circulating serum miRNAs to their immune-related target mRNAs

Bakhtiyor Nosirov, Joël Billaud, Alexis Vandenbon, Diego Diez, Edward Wijaya, Ken J. Ishii, Shunsuke Teraguchi, Daron M. Standley

Advances and Applications in Bioinformatics and Chemistry　Vol. 10　No. 1　p. 1-9　2017　Research paper (scientific journal)

Identification of nasal resident bacteria as causative allergens in eosinophilic chronic rhinosinusitis

K. Takeda, S. Sakakibara, D. Motooka, S. Nakamura, K. Yamashita, D. M. Standley, M. Hayama, T. Shikina, H. Inohara, H. Kikutani

EUROPEAN JOURNAL OF IMMUNOLOGY　Vol. 46　p. 1114-1114　2016/08

A simple method to control over-alignment in the MAFFT multiple sequence alignment program

Kazutaka Katoh, Daron M. Standley

Bioinformatics　Vol. 32　No. 13　p. 1933-1942　2016/07/01　Research paper (scientific journal)

Arid5a regulates naive CD4⁺ T cell fate through selective stabilization of Stat3 mRNA

Kazuya Masuda, Barry Ripley, Kishan Kumar Nyati, Praveen Kumar Dubey, Mohammad Mahabub Uz Zaman, Hamza Hanieh, Mitsuru Higa, Kazuo Yamashita, Daron M. Standley, Tsukasa Mashima, Masato Katahira, Toru Okamoto, Yoshiharu Matsuura, Osamu Takeuchi, Tadamitsu Kishimoto

Journal of Experimental Medicine　Vol. 213　No. 4　p. 605-619　2016/04　Research paper (scientific journal)

Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions

Mariko Yokogawa, Takashi Tsushima, Nobuo N. Noda, Hiroyuki Kumeta, Yoshiaki Enokizono, Kazuo Yamashita, Daron M. Standley, Osamu Takeuchi, Shizuo Akira, Fuyuhiko Inagaki

Scientific Reports　Vol. 6　2016/03/01　Research paper (scientific journal)

Hepatocyte factor JMJD5 regulates hepatitis B virus replication through interaction with HBx

Takahisa Kouwaki, Toru Okamoto, Ayano Ito, Yukari Sugiyama, Kazuo Yamashita, Tatsuya Suzuki, Shinji Kusakabe, Junki Hirano, Takasuke Fukuhara, Atsuya Yamashita, Kazunobu Saito, Daisuke Okuzaki, Koichi Watashi, Masaya Sugiyama, Sachiyo Yoshio, Daron M. Standley, Tatsuya Kanto, Masashi Mizokami, Kohji Moriishi, Yoshiharu Matsuura

Journal of Virology　Vol. 90　No. 7　p. 3530-3542　2016　Research paper (scientific journal)

Design of a protein tag and fluorogenic probe with modular structure for live-cell imaging of intracellular proteins

Yuko Kamikawa, Yuichiro Hori, Kazuo Yamashita, Lin Jin, Shinya Hirayama, Daron M. Standley, Kazuya Kikuchi

Chemical Science　Vol. 7　No. 1　p. 308-314　2016/01/01　Research paper (scientific journal)

RabGDIα is a negative regulator of interferon-γ-inducible GTPase-dependent cell-autonomous immunity to Toxoplasma gondii

Jun Ohshima, Miwa Sasai, Jianfa Liu, Kazuo Yamashita, Ji Su Ma, Youngae Lee, Hironori Bando, Jonathan C. Howard, Shigeyuki Ebisu, Mikako Hayashi, Kiyoshi Takeda, Daron M. Standley, Eva Maria Frickel, Masahiro Yamamoto

Proceedings of the National Academy of Sciences of the United States of America　Vol. 112　No. 33　p. E4581-E4590　2015/08/18　Research paper (scientific journal)

Regnase-1 and roquin regulate a common element in inflammatory mRNAs by spatiotemporally distinct mechanisms

Takashi Mino, Yasuhiro Murakawa, Akira Fukao, Alexis Vandenbon, Hans Hermann Wessels, Daisuke Ori, Takuya Uehata, Sarang Tartey, Shizuo Akira, Yutaka Suzuki, Carola G. Vinuesa, Uwe Ohler, Daron M. Standley, Markus Landthaler, Toshinobu Fujiwara, Osamu Takeuchi

Cell　Vol. 161　No. 5　p. 1058-1073　2015/05/30　Research paper (scientific journal)

Hydroxypropyl-β-cyclodextrin spikes local inflammation that induces Th2 cell and T follicular helper cell responses to the coadministered antigen

Motoyasu Onishi, Koji Ozasa, Kouji Kobiyama, Keiichi Ohata, Mitsutaka Kitano, Keiichi Taniguchi, Tomoyuki Homma, Masanori Kobayashi, Akihiko Sato, Yuko Katakai, Yasuhiro Yasutomi, Edward Wijaya, Yoshinobu Igarashi, Noriyuki Nakatsu, Wataru Ise, Takeshi Inoue, Hiroshi Yamada, Alexis Vandenbon, Daron M. Standley, Tomohiro Kurosaki, Cevayir Coban, Taiki Aoshi, Etsushi Kuroda, Ken J. Ishii

Journal of Immunology　Vol. 194　No. 6　p. 2673-2682　2015/03/15　Research paper (scientific journal)

RNA-LIM: A novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure

Damien Hall, Songling Li, Kazuo Yamashita, Ryuzo Azuma, John A. Carver, Daron M. Standley

Analytical Biochemistry　Vol. 472　p. 52-61　2015/03/01　Research paper (scientific journal)

Akirin2 is critical for inducing inflammatory genes by bridging IκB-ζ and the SWI/SNF complex

Sarang Tartey, Kazufumi Matsushita, Alexis Vandenbon, Daisuke Ori, Tomoko Imamura, Takashi Mino, Daron M. Standley, Jules A. Hoffmann, Jean Marc Reichhart, Shizuo Akira, Osamu Takeuchi

EMBO Journal　Vol. 33　No. 20　p. 2332-2348　2014/10/16　Research paper (scientific journal)

Quantifying sequence and structural features of protein-RNA interactions

Songling Li, Kazuo Yamashita, Karlou Mar Amada, Daron M. Standley

Nucleic Acids Research　Vol. 42　No. 15　p. 10086-10098　2014/09/02　Research paper (scientific journal)

High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations

Hiroki Shirai, Kazuyoshi Ikeda, Kazuo Yamashita, Yuko Tsuchiya, Jamica Sarmiento, Shide Liang, Tatsuaki Morokata, Kenji Mizuguchi, Junichi Higo, Daron M. Standley, Haruki Nakamura

Proteins: Structure, Function and Bioinformatics　Vol. 82　No. 8　p. 1624-1635　2014/08　Research paper (scientific journal)

A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein

Damien Hall, Songling Li, Kazuo Yamashita, Ryuzo Azuma, John A. Carver, Daron M. Standley

Biophysical Chemistry　Vol. 190-191　p. 50-55　2014/06

Intrinsic disorder mediates cooperative signal transduction in STIM1

Yukio Furukawa, Shunsuke Teraguchi, Takahisa Ikegami, Onur Dagliyan, Lin Jin, Damien Hall, Nikolay V. Dokholyan, Keiichi Namba, Shizuo Akira, Tomohiro Kurosaki, Yoshihiro Baba, Daron M. Standley

Journal of Molecular Biology　Vol. 426　No. 10　p. 2082-2097　2014/05/15　Research paper (scientific journal)

Blind prediction of interfacial water positions in CAPRI

Marc F. Lensink, Iain H. Moal, Paul A. Bates, Panagiotis L. Kastritis, Adrien S.J. Melquiond, Ezgi Karaca, Christophe Schmitz, Marc van Dijk, Alexandre M.J.J. Bonvin, Miriam Eisenstein, Brian Jiménez-García, Solène Grosdidier, Albert Solernou, Laura Pérez-Cano, Chiara Pallara, Juan Fernández-Recio, Jianqing Xu, Pravin Muthu, Krishna Praneeth Kilambi, Jeffrey J. Gray, Sergei Grudinin, Georgy Derevyanko, Julie C. Mitchell, John Wieting, Eiji Kanamori, Yuko Tsuchiya, Yoichi Murakami, Joy Sarmiento, Daron M. Standley, Matsuyuki Shirota, Kengo Kinoshita, Haruki Nakamura, Matthieu Chavent, David W. Ritchie, Hahnbeom Park, Junsu Ko, Hasup Lee, Chaok Seok, Yang Shen, Dima Kozakov, Sandor Vajda, Petras J. Kundrotas, Ilya A. Vakser, Brian G. Pierce, Howook Hwang, Thom Vreven, Zhiping Weng, Idit Buch, Efrat Farkash, Haim J. Wolfson, Martin Zacharias, Sanbo Qin, Huan Xiang Zhou, Shen You Huang, Xiaoqin Zou, Justyna A. Wojdyla, Colin Kleanthous, Shoshana J. Wodak

Proteins: Structure, Function and Bioinformatics　Vol. 82　No. 4　p. 620-632　2014/04　Research paper (scientific journal)

Blockade of TLR3 protects mice from lethal radiation-induced gastrointestinal syndrome

Naoki Takemura, Takumi Kawasaki, Jun Kunisawa, Shintaro Sato, Aayam Lamichhane, Kouji Kobiyama, Taiki Aoshi, Junichi Ito, Kenji Mizuguchi, Thangaraj Karuppuchamy, Kouta Matsunaga, Shoichiro Miyatake, Nobuko Mori, Tohru Tsujimura, Takashi Satoh, Yutaro Kumagai, Taro Kawai, Daron M. Standley, Ken J. Ishii, Hiroshi Kiyono, Shizuo Akira, Satoshi Uematsu

Nature Communications　Vol. 5　2014/03/18　Research paper (scientific journal)

Kotai Antibody Builder: Automated high-resolution structural modeling of antibodies

Kazuo Yamashita, Kazuyoshi Ikeda, Karlou Amada, Shide Liang, Yuko Tsuchiya, Haruki Nakamura, Hiroki Shirai, Daron M. Standley

Bioinformatics　Vol. 30　No. 22　p. 3279-3280　2014/02/27　Research paper (scientific journal)

2SCP-07 Intrinsic disorder mediates cooperative signal transduction in STIM1(Prediction and analysis of protein functions from structural bioinformatics,Symposium,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Daron M. Standley

Seibutsu Butsuri　Vol. 54　No. 1　2014

MAFFT: Iterative refinement and additional methods

Kazutaka Katoh, Daron M. Standley

Methods in Molecular Biology　Vol. 1079　p. 131-146　2014　Research paper (scientific journal)

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

Hiromasa Morikawa, Naganari Ohkura, Alexis Vandenbon, Masayoshi Itoh, Sayaka Nagao-Sato, Hideya Kawaji, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Daron M. Standley, Hiroshi Date, Shimon Sakaguchi

Proceedings of the National Academy of Sciences of the United States of America　Vol. 111　No. 14　p. 5289-5294　2014　Research paper (scientific journal)

Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation

Alexis Vandenbon, Shunsuke Teraguchi, Osamu Takeuchi, Yutaka Suzuki, Daron M. Standley

BMC Genomics　Vol. 15　2014　Research paper (scientific journal)

Structures and interface mapping of the TIR domaincontaining adaptor molecules involved in interferon signaling

Yoshiaki Enokizono, Hiroyuki Kumeta, Kenji Funami, Masataka Horiuchi, Joy Sarmiento, Kazuo Yamashita, Daron M. Standley, Misako Matsumoto, Tsukasa Seya, Fuyuhiko Inagaki

Proceedings of the National Academy of Sciences of the United States of America　Vol. 110　No. 49　p. 19908-19913　2013/12/03　Research paper (scientific journal)

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

Rocco Moretti, Sarel J. Fleishman, Rudi Agius, Mieczyslaw Torchala, Paul A. Bates, Panagiotis L. Kastritis, João P.G.L.M. Rodrigues, Mikaël Trellet, Alexandre M.J.J. Bonvin, Meng Cui, Marianne Rooman, Dimitri Gillis, Yves Dehouck, Iain Moal, Miguel Romero-Durana, Laura Perez-Cano, Chiara Pallara, Brian Jimenez, Juan Fernandez-Recio, Samuel Flores, Michael Pacella, Krishna Praneeth Kilambi, Jeffrey J. Gray, Petr Popov, Sergei Grudinin, Juan Esquivel-Rodríguez, Daisuke Kihara, Nan Zhao, Dmitry Korkin, Xiaolei Zhu, Omar N.A. Demerdash, Julie C. Mitchell, Eiji Kanamori, Yuko Tsuchiya, Haruki Nakamura, Hasup Lee, Hahnbeom Park, Chaok Seok, Jamica Sarmiento, Shide Liang, Shusuke Teraguchi, Daron M. Standley, Hiromitsu Shimoyama, Genki Terashi, Mayuko Takeda-Shitaka, Mitsuo Iwadate, Hideaki Umeyama, Dmitri Beglov, David R. Hall, Dima Kozakov, Sandor Vajda, Brian G. Pierce, Howook Hwang, Thom Vreven, Zhiping Weng, Yangyu Huang, Haotian Li, Xiufeng Yang, Xiaofeng Ji, Shiyong Liu, Yi Xiao, Martin Zacharias, Sanbo Qin, Huan Xiang Zhou, Sheng You Huang, Xiaoqin Zou, Sameer Velankar, Joël Janin, Shoshana J. Wodak, David Baker

Proteins: Structure, Function and Bioinformatics　Vol. 81　No. 11　p. 1980-1987　2013/11　Research paper (scientific journal)

Deconstructing RNA: Optical measurement of composition and structure

Alison J. Hobro, Daron M. Standley, Shandar Ahmad, Nicholas I. Smith

Physical Chemistry Chemical Physics　Vol. 15　No. 31　p. 13199-13208　2013/08/21　Research paper (scientific journal)

The second messenger phosphatidylinositol-5-phosphate facilitates antiviral innate immune signaling

Takumi Kawasaki, Naoki Takemura, Daron M. Standley, Shizuo Akira, Taro Kawai

Cell Host and Microbe　Vol. 14　No. 2　p. 148-158　2013/08/14　Research paper (scientific journal)

A novel function prediction approach using protein overlap networks

Shide Liang, Dandan Zheng, Daron M. Standley, Huarong Guo, Chi Zhang

BMC Systems Biology　Vol. 7　2013/07/17　Research paper (scientific journal)

XMalt1-induced cleavage of regnase-1 in CD4⁺ helper T cells regulates immune activation

Takuya Uehata, Hidenori Iwasaki, Alexis Vandenbon, Kazufumi Matsushita, Eduardo Hernandez-Cuellar, Kanako Kuniyoshi, Takashi Satoh, Takashi Mino, Yutaka Suzuki, Daron M. Standley, Tohru Tsujimura, Hiromi Rakugi, Yoshitaka Isaka, Osamu Takeuchi, Shizuo Akira

Cell　Vol. 153　No. 5　p. 1036-1049　2013/05/23　Research paper (scientific journal)

MAFFT multiple sequence alignment software version 7: Improvements in performance and usability

Kazutaka Katoh, Daron M. Standley

Molecular Biology and Evolution　Vol. 30　No. 4　p. 772-780　2013/04　Research paper (scientific journal)

A Parzen window-based approach for the detection of locally enriched transcription factor binding sites

Alexis Vandenbon, Yutaro Kumagai, Shunsuke Teraguchi, Karlou Mar Amada, Shizuo Akira, Daron M. Standley

BMC Bioinformatics　Vol. 14　2013/01/21　Research paper (scientific journal)

The Transcription Factor Jdp2 Controls Bone Homeostasis and Antibacterial Immunity by Regulating Osteoclast and Neutrophil Differentiation

Kenta Maruyama, Masahiro Fukasaka, Alexis Vandenbon, Tatsuya Saitoh, Takumi Kawasaki, Takeshi Kondo, Kazunari K. Yokoyama, Hiroyasu Kidoya, Nobuyuki Takakura, Daron Standley, Osamu Takeuchi, Shizuo Akira

Immunity　Vol. 37　No. 6　p. 1024-1036　2012/12/14　Research paper (scientific journal)

Systems biology approaches to toll-like receptor signaling

Alexis Vandenbon, Shunsuke Teraguchi, Shizuo Akira, Kiyoshi Takeda, Daron M. Standley

Wiley Interdisciplinary Reviews: Systems Biology and Medicine　Vol. 4　No. 5　p. 497-507　2012/09　Research paper (scientific journal)

Protein loop modeling with optimized backbone potential functions

Shide Liang, Chi Zhang, Jamica Sarmiento, Daron M. Standley

Journal of Chemical Theory and Computation　Vol. 8　No. 5　p. 1820-1827　2012/05/08　Research paper (scientific journal)

Prediction of protein-protein complex structures

Eiji Kanamori, Yoichi Murakami, Joy Sarmiento, Shide Uang, Daron M. Standley, Matsuyuki Shirota, Kengo Kinoshita, Yuko Tsucillya, Junicill Higo, Haruki Nakamura

Biomolecular Forms and Functions: A Celebration of 50 Years of the Ramachandran Map　p. 160-172　2012/01/01　Part of collection (book)

A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription.

Alexis Vandenbon, Yutaro Kumagai, Shizuo Akira, Daron M. Standley

BMC genomics　Vol. 13 Suppl 7　2012　Research paper (scientific journal)

Functional annotation of intrinsically disordered domains by their amino acid content using IDD navigator

Ashwini Patil, Shunsuke Teraguchi, Huy Dinh, Kenta Nakai, Daron M. Standley

Pacific Symposium on Biocomputing　p. 164-175　2012　Research paper (international conference proceedings)

Protein Data Bank Japan (PDBj): Maintaining a structural data archive and resource description framework format

Akira R. Kinjo, Hirofumi Suzuki, Reiko Yamashita, Yasuyo Ikegawa, Takahiro Kudou, Reiko Igarashi, Yumiko Kengaku, Hasumi Cho, Daron M. Standley, Atsushi Nakagawa, Haruki Nakamura

Nucleic Acids Research　Vol. 40　No. D1　p. D453-D460　2012/01　Research paper (scientific journal)

Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations

Shunsuke Teraguchi, Yutaro Kumagai, Alexis Vandenbon, Shizuo Akira, Daron M. Standley

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics　Vol. 84　No. 6　2011/12/15　Research paper (scientific journal)

The IκB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR-IL-1R by controlling degradation of regnase-1

Hidenori Iwasaki, Osamu Takeuchi, Shunsuke Teraguchi, Kazufumi Matsushita, Takuya Uehata, Kanako Kuniyoshi, Takashi Satoh, Tatsuya Saitoh, Mutsuyoshi Matsushita, Daron M. Standley, Shizuo Akira

Nature Immunology　Vol. 12　No. 12　p. 1167-1175　2011/12　Research paper (scientific journal)

Prediction of dinucleotide-specific RNA-binding sites in proteins

Michael Fernandez, Yutaro Kumagai, Daron M. Standley, Akinori Sarai, Kenji Mizuguchi, Shandar Ahmad

BMC Bioinformatics　Vol. 12　No. SUPPL. 13　2011/11/30　Research paper (scientific journal)

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

Sarel J. Fleishman, Timothy A. Whitehead, Eva Maria Strauch, Jacob E. Corn, Sanbo Qin, Huan Xiang Zhou, Julie C. Mitchell, Omar N.A. Demerdash, Mayuko Takeda-Shitaka, Genki Terashi, Iain H. Moal, Xiaofan Li, Paul A. Bates, Martin Zacharias, Hahnbeom Park, Jun Su Ko, Hasup Lee, Chaok Seok, Thomas Bourquard, Julie Bernauer, Anne Poupon, Jérôme Azé, Seren Soner, Şefik Kerem Ovali, Pemra Ozbek, Nir Ben Tal, Türkan Haliloglu, Howook Hwang, Thom Vreven, Brian G. Pierce, Zhiping Weng, Laura Pérez-Cano, Carles Pons, Juan Fernández-Recio, Fan Jiang, Feng Yang, Xinqi Gong, Libin Cao, Xianjin Xu, Bin Liu, Panwen Wang, Chunhua Li, Cunxin Wang, Charles H. Robert, Mainak Guharoy, Shiyong Liu, Yangyu Huang, Lin Li, Dachuan Guo, Ying Chen, Yi Xiao, Nir London, Zohar Itzhaki, Ora Schueler-Furman, Yuval Inbar, Vladimir Potapov, Mati Cohen, Gideon Schreiber, Yuko Tsuchiya, Eiji Kanamori, Daron M. Standley, Haruki Nakamura, Kengo Kinoshita, Camden M. Driggers, Robert G. Hall, Jessica L. Morgan, Victor L. Hsu, Jian Zhan, Yuedong Yang, Yaoqi Zhou, Panagiotis L. Kastritis, Alexandre M.J.J. Bonvin, Weiyi Zhang, Carlos J. Camacho, Krishna P. Kilambi, Aroop Sircar, Jeffrey J. Gray, Masahito Ohue, Nobuyuki Uchikoga, Yuri Matsuzaki, Takashi Ishida, Yutaka Akiyama, Raed Khashan, Stephen Bush, Denis Fouches, Alexander Tropsha, Juan Esquivel-Rodríguez, Daisuke Kihara, P. Benjamin Stranges, Ron Jacak, Brian Kuhlman, Sheng You Huang, Xiaoqin Zou, Shoshana J. Wodak, Joel Janin, David Baker

Journal of Molecular Biology　Vol. 414　No. 2　p. 289-302　2011/11/25　Research paper (scientific journal)

A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans

Akiko Kitamura, Yoichi Maekawa, Hisanori Uehara, Keisuke Izumi, Izumi Kawachi, Masatoyo Nishizawa, Yasuko Toyoshima, Hitoshi Takahashi, Daron M. Standley, Keiji Tanaka, Jun Hamazaki, Shigeo Murata, Koji Obara, Itaru Toyoshima, Koji Yasutomo

Journal of Clinical Investigation　Vol. 121　No. 10　p. 4150-4160　2011/10/03　Research paper (scientific journal)

Fast and accurate prediction of protein side-chain conformations

Shide Liang, Dandan Zheng, Chi Zhang, Daron M. Standley

Bioinformatics　Vol. 27　No. 20　p. 2913-2914　2011/10

Binding energetics of ferredoxin-NADP ⁺ reductase with ferredoxin and its relation to function

Young Ho Lee, Takahisa Ikegami, Daron M. Standley, Kazumasa Sakurai, Toshiharu Hase, Yuji Goto

ChemBioChem　Vol. 12　No. 13　p. 2062-2070　2011/09/05　Research paper (scientific journal)

Protein loop selection using orientation-dependent force fields derived by parameter optimization

Shide Liang, Chi Zhang, Daron M. Standley

Proteins: Structure, Function and Bioinformatics　Vol. 79　No. 7　p. 2260-2267　2011/07　Research paper (scientific journal)

Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions

Shide Liang, Yaoqi Zhou, Nick Grishin, Daron M. Standley

Journal of Computational Chemistry　Vol. 32　No. 8　p. 1680-1686　2011/06　Research paper (scientific journal)

Degree of pyramidality governs the height and peak position of the free-energy-barrier for the cis-trans isomerization of N-Methylacetamide

Yasushige Yonezawa, Daron M. Standley, Haruki Nakamura

Chemical Physics Letters　Vol. 503　No. 1-3　p. 139-144　2011/02/08　Research paper (scientific journal)

Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster

Jinzen Ikebe, Daron M. Standley, Haruki Nakamura, Junichi Higo

Protein Science　Vol. 20　No. 1　p. 187-196　2011/01　Research paper (scientific journal)

Bridging the gap between single-template and fragment based protein structure modeling using Spanner

Mieszko Lis, Taeho Kim, Jamica J. Sarmiento, Daisuke Kuroda, Huy Viet Dinh, Akira R. Kinjo, Karlou Amada, Srinivas Devadas, Haruki Nakamura, Daron M. Standley

Immunome Research　Vol. 7　No. 1　p. 1-8　2011　Research paper (scientific journal)

Functional characterization of protein domains common to animal viruses and mouse

Akira R. Kinjo, Yutaro Kumagai, Huy Dinh, Osamu Takeuchi, Daron M. Standley

10th Int. Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Computational Biology - Proceedings from Asia Pacific Bioinformatics Network (APBioNet)　Vol. 12　No. SUPPL. 3　2011　Research paper (international conference proceedings)

Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins

Shunsuke Teraguchi, Ashwini Patil, Daron M. Standley

BMC Bioinformatics　Vol. 11　No. SUPPL. 7　2010/10/15　Research paper (scientific journal)

The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection

Takashi Satoh, Osamu Takeuchi, Alexis Vandenbon, Koubun Yasuda, Yoshiaki Tanaka, Yutaro Kumagai, Tohru Miyake, Kazufumi Matsushita, Toshihiko Okazaki, Tatsuya Saitoh, Kiri Honma, Toshifumi Matsuyama, Katsuyuki Yui, Tohru Tsujimura, Daron M. Standley, Kenji Nakanishi, Kenta Nakai, Shizuo Akira

Nature Immunology　Vol. 11　No. 10　p. 936-944　2010/10　Research paper (scientific journal)

The DBCLS BioHackathon: Standardization and interoperability for bioinformatics web services and workflows

Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F. Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong Woo Chun, Jan Aerts, Bruno Aranda, Lord H. Barboza, Raoul J.P. Bonnal, Richard Bruskiewich, Jan C. Bryne, José M. Fernández, Akira Funahashi, Paul M.K. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehvaslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwinski, Mark Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi

Journal of Biomedical Semantics　Vol. 1　No. 1　p. 8-8　2010/08/21

EPSVR and EPMeta: Prediction of antigenic epitopes using support vector regression and multiple server results

Shide Liang, Dandan Zheng, Daron M. Standley, Bo Yao, Martin Zacharias, Chi Zhang

BMC Bioinformatics　Vol. 11　2010/07/16　Research paper (scientific journal)

SeSAW: Balancing sequence and structural information in protein functional mapping

Daron M. Standley, Reiko Yamashita, Akira R. Kinjo, Hiroyuki Toh, Haruki Nakamura

Bioinformatics　Vol. 26　No. 9　p. 1258-1259　2010/03/17　Research paper (scientific journal)

Automated processing of label-free Raman microscope images of macrophage cells with standardized regression for high-throughput analysis

Robert J. Milewski, Yutaro Kumagai, Katsumasa Fujita, Daron M. Standley, Nicholas I. Smith

Immunome Research　Vol. 6　No. 1　2010　Research paper (scientific journal)

A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3

Masahiro Yamamoto, Daron M. Standley, Seiji Takashima, Hiroyuki Saiga, Megumi Okuyama, Hisako Kayama, Emi Kubo, Hiroshi Ito, Mutsumi Takaura, Tadashi Matsuda, Dominique Soldati-Favre, Kiyoshi Takeda

Journal of Experimental Medicine　Vol. 206　No. 12　p. 2747-2760　2009/11/23　Research paper (scientific journal)

Membrane attachment facilitates ligand access to the active site in monoamine oxidase A

Rossen Apostolov, Yasushige Yonezawa, Daron M. Standley, Gota Kikugawa, Yu Takano, Haruki Nakamura

Biochemistry　Vol. 48　No. 25　p. 5864-5873　2009/06/30　Research paper (scientific journal)

Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay

Kazufumi Matsushita, Osamu Takeuchi, Daron M. Standley, Yutaro Kumagai, Tatsukata Kawagoe, Tohru Miyake, Takashi Satoh, Hiroki Kato, Tohru Tsujimura, Haruki Nakamura, Shizuo Akira

Nature　Vol. 458　No. 7242　p. 1185-1190　2009/04　Research paper (scientific journal)

Outcome of a Workshop on Applications of Protein Models in Biomedical Research

Torsten Schwede, Andrej Sali, Barry Honig, Michael Levitt, Helen M. Berman, David Jones, Steven E. Brenner, Stephen K. Burley, Rhiju Das, Nikolay V. Dokholyan, Roland L. Dunbrack, Krzysztof Fidelis, Andras Fiser, Adam Godzik, Yuanpeng Janet Huang, Christine Humblet, Matthew P. Jacobson, Andrzej Joachimiak, Stanley R. Krystek, Tanja Kortemme, Andriy Kryshtafovych, Gaetano T. Montelione, John Moult, Diana Murray, Roberto Sanchez, Tobin R. Sosnick, Daron M. Standley, Terry Stouch, Sandor Vajda, Max Vasquez, John D. Westbrook, Ian A. Wilson

Structure　Vol. 17　No. 2　p. 151-159　2009/02/13　Research paper (international conference proceedings)

Functional annotation by sequence-weighted structure alignments: Statistical analysis and case studies from the protein 3000 structural genomics project in Japan

Daron M. Standley, Hiroyuki Toh, Haruki Nakamura

Proteins: Structure, Function and Genetics　Vol. 72　No. 4　p. 1333-1351　2008/09　Research paper (scientific journal)

Protein structure databases with new web services for structural biology and biomedical research

Daron M. Standley, Akira R. Kinjo, Kengo Kinoshita, Haruki Nakamura

Briefings in Bioinformatics　Vol. 9　No. 4　p. 276-285　2008/07　Research paper (scientific journal)

Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase

Karleigh Hamblin, Daron M. Standley, Matthew B. Rogers, Alexandra Stechmann, Andrew J. Roger, Robin Maytum, Mark Van Der Giezen

Molecular Microbiology　Vol. 68　No. 6　p. 1395-1405　2008/06　Research paper (scientific journal)

Structure-based functional annotation of protein sequences guided by comparative models

Daron M. Standley, Akira R. Kinjo, Miesko Lis, Mark van der Giezen, Haruki Nakamura

OPTIMIZATION AND SYSTEMS BIOLOGY, PROCEEDINGS　Vol. 9　p. 395-+　2008　Research paper (international conference proceedings)

Lonidamine, a Novel Modulator for the BvgAS System of Bordetella Species.

Natsuko Ota, Takashi Nishida, Daron M Standley, Aalaa Alrahman Sherif, Satoshi Iwano, Dendi Krisna Nugraha, Toshiya Ueno, Yasuhiko Horiguchi

Microbiology and immunology　Vol. 69　No. 3　p. 133-147　2025/03　Research paper (scientific journal)

Clonal landscape of autoantibody-secreting plasmablasts in COVID-19 patients.

Shuhei Sakakibara, Yu-Chen Liu, Masakazu Ishikawa, Ryuya Edahiro, Yuya Shirai, Soichiro Haruna, Marwa Ali El Hussien, Zichang Xu, Songling Li, Yuta Yamaguchi, Teruaki Murakami, Takayoshi Morita, Yasuhiro Kato, Haruhiko Hirata, Yoshito Takeda, Fuminori Sugihara, Yoko Naito, Daisuke Motooka, Chao-Yuan Tsai, Chikako Ono, Yoshiharu Matsuura, James B Wing, Hisatake Matsumoto, Hiroshi Ogura, Masato Okada, Atsushi Kumanogoh, Yukinari Okada, Daron M Standley, Hitoshi Kikutani, Daisuke Okuzaki

Life science alliance　Vol. 7　No. 12　p. e202402774-e202402774　2024/09　Research paper (scientific journal)

Robust detection of infectious disease, autoimmunity, and cancer from the paratope networks of adaptive immune receptors.

Zichang Xu, Hendra S Ismanto, Dianita S Saputri, Soichiro Haruna, Guanqun Sun, Jan Wilamowski, Shunsuke Teraguchi, Ayan Sengupta, Songling Li, Daron M Standley

Briefings in bioinformatics　Vol. 25　No. 5　2024/07/25　Research paper (scientific journal)

Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz.

Takuya Uehata, Shinnosuke Yamada, Daisuke Ori, Alexis Vandenbon, Amir Giladi, Adam Jelinski, Yasuhiro Murakawa, Hitomi Watanabe, Kazuhiro Takeuchi, Kazunori Toratani, Takashi Mino, Hisanori Kiryu, Daron M Standley, Tohru Tsujimura, Tomokatsu Ikawa, Gen Kondoh, Markus Landthaler, Hiroshi Kawamoto, Hans-Reimer Rodewald, Ido Amit, Ryo Yamamoto, Masaki Miyazaki, Osamu Takeuchi

Blood　Vol. 143　No. 3　p. 243-257　2024/01/18　Research paper (scientific journal)

BCR, not TCR, repertoire diversity is associated with favorable COVID-19 prognosis.

Faith Jessica Paran, Rieko Oyama, Abdullah Khasawneh, Tomohiko Ai, Hendra Saputra Ismanto, Aalaa Alrahman Sherif, Dianita Susilo Saputri, Chikako Ono, Mizue Saita, Satomi Takei, Yuki Horiuchi, Ken Yagi, Yoshiharu Matsuura, Yasushi Okazaki, Kazuhisa Takahashi, Daron M Standley, Yoko Tabe, Toshio Naito

Frontiers in immunology　Vol. 15　p. 1405013-1405013　2024　Research paper (scientific journal)

Structural basis of Irgb6 inactivation by Toxoplasma gondii through the phosphorylation of switch I.

Hiromichi Okuma, Yumiko Saijo-Hamano, Hiroshi Yamada, Aalaa Alrahman Sherif, Emi Hashizaki, Naoki Sakai, Takaaki Kato, Tsuyoshi Imasaki, Satoshi Kikkawa, Eriko Nitta, Miwa Sasai, Tadashi Abe, Fuminori Sugihara, Yoshimasa Maniwa, Hidetaka Kosako, Kohji Takei, Daron M Standley, Masahiro Yamamoto, Ryo Nitta

Genes to cells : devoted to molecular & cellular mechanisms　Vol. 29　No. 1　p. 17-38　2024/01/01　Research paper (scientific journal)

Deciphering the antigen specificities of antibodies by clustering their complementarity determining region sequences.

Dianita S Saputri, Hendra S Ismanto, Dendi K Nugraha, Zichang Xu, Yasuhiko Horiguchi, Shuhei Sakakibara, Daron M Standley

mSystems　Vol. 8　No. 6　2023/12/21　Research paper (scientific journal)

Enhancement of SARS-CoV-2 Infection via Crosslinking of Adjacent Spike Proteins by N-Terminal Domain-Targeting Antibodies.

Tina Lusiany, Tohru Terada, Jun-Ichi Kishikawa, Mika Hirose, David Virya Chen, Fuminori Sugihara, Hendra Saputra Ismanto, Floris J van Eerden, Songling Li, Takayuki Kato, Hisashi Arase, Matsuura Yoshiharu, Masato Okada, Daron M Standley

Viruses　Vol. 15　No. 12　p. 2421-2421　2023/12/13　Research paper (scientific journal)

Circadian ribosome profiling reveals a role for the Period2 upstream open reading frame in sleep.

Arthur Millius, Rikuhiro G Yamada, Hiroshi Fujishima, Kazuhiko Maeda, Daron M Standley, Kenta Sumiyama, Dimitri Perrin, Hiroki R Ueda

Proceedings of the National Academy of Sciences of the United States of America　Vol. 120　No. 40　2023/10/03　Research paper (scientific journal)

Expression of the readthrough transcript CiDRE in alveolar macrophages boosts SARS-CoV-2 susceptibility and promotes COVID-19 severity.

Yuichi Mitsui, Tatsuya Suzuki, Kanako Kuniyoshi, Jun Inamo, Kensuke Yamaguchi, Mariko Komuro, Junya Watanabe, Mio Edamoto, Songling Li, Tsukasa Kouno, Seiya Oba, Tadashi Hosoya, Kentaro Masuhiro, Yujiro Naito, Shohei Koyama, Nobuo Sakaguchi, Daron M Standley, Jay W Shin, Shizuo Akira, Shinsuke Yasuda, Yasunari Miyazaki, Yuta Kochi, Atsushi Kumanogoh, Toru Okamoto, Takashi Satoh

Immunity　Vol. 56　No. 8　p. 1939-1954　2023/08/08　Research paper (scientific journal)

The ClusPro AbEMap web server for the prediction of antibody epitopes.

Israel T Desta, Sergei Kotelnikov, George Jones, Usman Ghani, Mikhail Abyzov, Yaroslav Kholodov, Daron M Standley, Dmitri Beglov, Sandor Vajda, Dima Kozakov

Nature protocols　Vol. 18　No. 6　p. 1814-1840　2023/06/01　Research paper (scientific journal)

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

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

Nature cell biology　Vol. 25　No. 6　p. 865-876　2023/06/01　Research paper (scientific journal)

Intercellular crosstalk in adult dental pulp is mediated by heparin-binding growth factors Pleiotrophin and Midkine.

Natnicha Jiravejchakul, Gabriela L Abe, Martin Loza, Soyoung Park, Ponpan Matangkasombut, Jun-Ichi Sasaki, Satoshi Imazato, Diego Diez, Daron M Standley

BMC genomics　Vol. 24　No. 1　p. 184-184　2023/04/06　Research paper (scientific journal)

Celastrol suppresses humoral immune responses and autoimmunity by targeting the COMMD3/8 complex

Taiichiro Shirai, Akiko Nakai, Emiko Ando, Jun Fujimoto, Sarah Leach, Takao Arimori, Daisuke Higo, Floris J. van Eerden, Janyerkye Tulyeu, Yu-Chen Liu, Daisuke Okuzaki, Masanori A. Murayama, Haruhiko Miyata, Kazuto Nunomura, Bangzhong Lin, Akiyoshi Tani, Atsushi Kumanogoh, Masahito Ikawa, James B. Wing, Daron M. Standley, Junichi Takagi, Kazuhiro Suzuki

Science Immunology　Vol. 8　No. 81　2023/03/31　Research paper (scientific journal)

External stimulation induces the secretion of autophagosome-like vesicles by B cells

Yu-Diao Kuan, Chao-Yuan Tsai, Shuhei Sakakibara, Daron M Standley, Hitoshi Kikutaniuan

Autophagy Reports　Vol. 2　No. 1　2023/02/21　Research paper (scientific journal)

When the TCR's engaged, the CD3 epsilons will play: A dynamic T cell receptor (TCR) triggering mechanism

Floris J. van Eerden, Aalaa Alrahman Sherif, Mara Anais Llamas-Covarrubias, Daron M. Standley

Biophysical journal　Vol. 122　No. 3S1　2023/02/10　Research paper (scientific journal)

Construction of a T cell receptor signaling range for spontaneous development of autoimmune disease.

Atsushi Tanaka, Shinji Maeda, Takashi Nomura, Mara Anais Llamas-Covarrubias, Satoshi Tanaka, Lin Jin, Ee Lyn Lim, Hiromasa Morikawa, Yohko Kitagawa, Shuji Akizuki, Yoshinaga Ito, Chihiro Fujimori, Keiji Hirota, Tosei Murase, Motomu Hashimoto, Junichi Higo, Rose Zamoyska, Ryuzo Ueda, Daron M Standley, Noriko Sakaguchi, Shimon Sakaguchi

The Journal of experimental medicine　Vol. 220　No. 2　2023/02/06　Research paper (scientific journal)

The evolution of structural genomics.

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

Biophysical reviews　Vol. 14　No. 6　p. 1247-1253　2022/12/01　Research paper (scientific journal)

Structural Modeling of Adaptive Immune Responses to Infection.

Tina Lusiany, Zichang Xu, Dianita S Saputri, Hendra S Ismanto, Sedat Aybars Nazlica, Daron M Standley

Methods in molecular biology (Clifton, N.J.)　Vol. 2552　p. 283-294　2022/11/09　Research paper (scientific journal)

Landscape of infection enhancing antibodies in COVID-19 and healthy donors

Hendra S. Ismanto, Zichang Xu, Dianita S. Saputri, Jan Wilamowski, Songling Li, Dendi K. Nugraha, Yasuhiko Horiguchi, Masato Okada, Hisashi Arase, Daron M Standley

Computational and Structural Biotechnology Journal　Vol. 20　p. 6033-6040　2022/11/04　Research paper (scientific journal)

CiDRE⁺ M2c macrophages hijacked by SARS-CoV-2 cause COVID-19 severity

Yuichi Mitsui, Tatsuya Suzuki, Kanako Kuniyoshi, Jun Inamo, Kensuke Yamaguchi, Mariko Komuro, Junya Watanabe, Mio Edamoto, Songling Li, Tsukasa Kouno, Seiya Oba, Tadashi Hosoya, Shohei Koyama, Nobuo Sakaguchi, Daron M. Standley, Jay W. Shin, Shizuo Akira, Shinsuke Yasuda, Yasunari Miyazaki, Yuta Kochi, Atsushi Kumanogoh, Toru Okamoto, Takashi Satoh

2022/10/03

Advances in antibody discovery from human BCR repertoires.

Zichang Xu, Hendra S Ismanto, Hao Zhou, Dianita S Saputri, Fuminori Sugihara, Daron M Standley

Frontiers in bioinformatics　Vol. 2　p. 1044975-1044975　2022/10/01　Research paper (scientific journal)

Engineering ACE2 decoy receptors to combat viral escapability.

Takao Arimori, Nariko Ikemura, Toru Okamoto, Junichi Takagi, Daron M Standley, Atsushi Hoshino

Trends in pharmacological sciences　Vol. 43　No. 10　p. 838-851　2022/10/01　Research paper (scientific journal)

Improved Antibody-Specific Epitope Prediction Using AlphaFold and AbAdapt.

Zichang Xu, Ana Davila, Jan Wilamowski, Shunsuke Teraguchi, Daron M Standley

Chembiochem : a European journal of chemical biology　Vol. 23　No. 18　2022/09/16　Research paper (scientific journal)

The protein-stabilizing effects of TMAO in aqueous and non-aqueous conditions.

Hassan Monhemi, Hai Nam Hoang, Daron M Standley, Tomoko Matsuda, Mohammad Reza Housaindokht

Physical chemistry chemical physics : PCCP　Vol. 24　No. 35　p. 21178-21187　2022/09/14　Research paper (scientific journal)

Mapping of antibody epitopes based on docking and homology modeling.

Israel T Desta, Sergei Kotelnikov, George Jones, Usman Ghani, Mikhail Abyzov, Yaroslav Kholodov, Daron M Standley, Maria Sabitova, Dmitri Beglov, Sandor Vajda, Dima Kozakov

Proteins　Vol. 91　No. 2　p. 171-182　2022/09/11　Research paper (scientific journal)

InterClone: Store, Search and Cluster Adaptive Immune Receptor Repertoires

Jan Wilamowski, Zichang Xu, Hendra S Ismanto, Songling Li, Shunsuke Teraguchi, Mara Anais Llamas- Covarrubias, Xiuyuan Lu, Sho Yamasaki, Daron M Standley

2022/08/01

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

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

Science translational medicine　Vol. 14　No. 650　2022/06/22　Research paper (scientific journal)

Cyclin J-CDK complexes limit innate immune responses by reducing proinflammatory changes in macrophage metabolism.

Yee Kien Chong, Sarang Tartey, Yuki Yoshikawa, Koshi Imami, Songling Li, Masanori Yoshinaga, Ai Hirabayashi, Guohao Liu, Alexis Vandenbon, Fabian Hia, Takuya Uehata, Takashi Mino, Yutaka Suzuki, Takeshi Noda, Dominique Ferrandon, Daron M Standley, Yasushi Ishihama, Osamu Takeuchi

Science signaling　Vol. 15　No. 729　2022/04/12　Research paper (scientific journal)

AbAdapt: An adaptive approach to predicting antibody-antigen complex structures from sequence

Ana Davila, Zichang Xu, Songling Li, John Rozewicki, Jan Wilamowski, Sergei Kotelnikov, Dima Kozakov, Shunsuke Teraguchi, Daron M Standley, Michael Gromiha

Bioinformatics Advances　Vol. 2　No. 1　2022/03/07　Research paper (scientific journal)

Unbiased integration of single cell transcriptome replicates.

Martin Loza, Shunsuke Teraguchi, Daron M Standley, Diego Diez

NAR genomics and bioinformatics　Vol. 4　No. 1　2022/03/01　Research paper (scientific journal)

The SARS-CoV-2 Delta variant is poised to acquire complete resistance to wild-type spike vaccines

Yafei Liu, Noriko Arase, Jun-ichi Kishikawa, Mika Hirose, Songling Li, Asa Tada, Sumiko Matsuoka, Akemi Arakawa, Kanako Akamatsu, Chikako Ono, Hui Jin, Kazuki Kishida, Wataru Nakai, Masako Kohyama, Atsushi Nakagawa, Yoshiaki Yamagishi, Hironori Nakagami, Atsushi Kumanogoh, Yoshiharu Matsuura, Daron M. Standley, Takayuki Kato, Masato Okada, Manabu Fujimoto, Hisashi Arase

2021/08/23

Development of a scoring method for predicting protein complex structures

Yuko Tsuchiya, Eiji Kanamori, Daron M. Standley, Haruki Nakamura, Kengo Kinoshita

ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES　Vol. 64　p. C227-C227　2008

Docking of protein molecular surfaces with evolutionary trace analysis

Eiji Kanamori, Yoichi Murakami, Yuko Tsuchiya, Daron M. Standley, Haruki Nakamura, Kengo Kinoshita

Proteins: Structure, Function and Genetics　Vol. 69　No. 4　p. 832-838　2007/12　Research paper (international conference proceedings)

ASH structure alignment package: Sensitivity and selectivity in domain classification

Daron M. Standley, Hiroyuki Toh, Haruki Nakamura

BMC Bioinformatics　Vol. 8　2007/04　Research paper (scientific journal)

Higher order structure contributes to specific differences in redox potential and electron transfer efficiency of root and leaf ferredoxins

Ping Gou, Guy T. Hanke, Yoko Kimata-Ariga, Daron M. Standley, Atsushi Kubo, Isao Taniguchi, Haruki Nakamura, Toshiharu Hase

Biochemistry　Vol. 45　No. 48　p. 14389-14396　2006/12/05　Research paper (scientific journal)

Flexible docking of an amyloid-forming peptide from β<inf>2</inf>-microglobulin

Daron M. Standley, Yasushige Yonezawa, Yuji Goto, Haruki Nakamura

FEBS Letters　Vol. 580　No. 26　p. 6199-6205　2006/11/13　Research paper (scientific journal)

Outcome of a Workshop on Archiving Structural Models of Biological Macromolecules

Helen M. Berman, Stephen K. Burley, Wah Chiu, Andrej Sali, Alexei Adzhubei, Philip E. Bourne, Stephen H. Bryant, Roland L. Dunbrack, Krzysztof Fidelis, Joachim Frank, Adam Godzik, Kim Henrick, Andrzej Joachimiak, Bernard Heymann, David Jones, John L. Markley, John Moult, Gaetano T. Montelione, Christine Orengo, Michael G. Rossmann, Burkhard Rost, Helen Saibil, Torsten Schwede, Daron M. Standley, John D. Westbrook

Structure　Vol. 14　No. 8　p. 1211-1217　2006/08　Research paper (international conference proceedings)

GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures

Daron M. Standley, Hiroyuki Toh, Haruki Nakamura

BMC Bioinformatics　Vol. 6　2005/09/08　Research paper (scientific journal)

Detecting local structural similarity in proteins by maximizing number of equivalent residues

Daron M. Standley, Hiroyuki Toh, Haruki Nakamura

Proteins: Structure, Function and Genetics　Vol. 57　No. 2　p. 381-391　2004/11/01　Research paper (scientific journal)

AB initio protein structure prediction using a size-dependent tertiary folding potential

Volker A. Eyrich, Richard A. Friesner, Daron M. Standley

Advances in Chemical Physics　Vol. 120　p. 223-263　2002　Research paper (scientific journal)

Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment

Daron M. Standley, Volker A. Eyrich, Yuling An, David L. Pincus, John R. Gunn, Richard A. Friesner

Proteins: Structure, Function and Genetics　Vol. 45　No. SUPPL. 5　p. 133-139　2001　Research paper (scientific journal)

Prediction of protein tertiauy structure to low resolution: Performance for a large and structurally diverse test set

Volker A. Eyrich, Daron M. Standley, Richard A. Friesner

Journal of Molecular Biology　Vol. 288　No. 4　p. 725-742　1999/05/14　Research paper (scientific journal)

Protein tertiary structure prediction using a branch and bound algorithm

Volker A. Eyrich, Daron M. Standley, Anthony K. Felts, Richard A. Friesner

Proteins: Structure, Function and Genetics　Vol. 35　No. 1　p. 41-57　1999/04　Research paper (scientific journal)

A branch and bound algorithm for protein structure refinement from sparse NMR data sets

Daron M. Standley, Volker A. Eyrich, Anthony K. Felts, Richard A. Friesner, Ann E. McDermott

Journal of Molecular Biology　Vol. 285　No. 4　p. 1691-1710　1999/01/29　Research paper (scientific journal)

Tertiary structure prediction of mixed α/β proteins via energy minimization

Daron M. Standley, John R. Gunn, Richard A. Friesner, Ann E. McDermott

Proteins: Structure, Function and Genetics　Vol. 33　No. 2　p. 240-252　1998/11/01　Research paper (scientific journal)