Standley Daron ＳｔａｎｄｌｅｙＤａｒｏｎ

… Alternative Names

STANDLEY Daron スタンドレーダーロン

DARON Standley ダーロンスタンドレイ

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Researcher Number	00448028
Other IDs
Affiliation (Current)	2025: 大阪大学, 微生物病研究所, 教授 2025: 大阪大学, 免疫学フロンティア研究センター, 教授
Affiliation (based on the past Project Information) *help	2023 – 2025: 大阪大学, 微生物病研究所, 教授 2018 – 2020: 大阪大学, 微生物病研究所, 教授 2009 – 2011: Osaka University, 免疫学フロンティア研究センター, 特任准教授 2010: 大阪大学, 免疫学フロティア研究センター, 特任准教授
Review Section/Research Field	Principal Investigator Medium-sized Section 49:Pathology, infection/immunology, and related fields / Basic Section 62010:Life, health and medical informatics-related / Basic Section 43060:System genome science-related / Biophysics / Complex systems
Keywords	Principal Investigator machine learning / adaptive immune receptor / diagnosis / repertoire / immunology / Machine learning / Biomolecular structure / T cell receptor epitope / immunity / T cell; … More / docking / COVID-19 / single cell sequencing / machine-learning / adaptive immunity / structural modeling / machine learning; / epitope / T cell / Adaptive immunity / CAR T cell / SARS-CoV-2 / Single cell sequencing / Machine Learning / Disease / Protein Function / Protein Structure / Immunology / STAT3 / 二重特異性キナーゼ / RNase / 免疫反応 / タンパク質構造モデリング / アルゴリズム / アライメント / ウェブサーバ / タンパク質の機能予測 / タンパク質の構造予測 / ホモロジー / 位置特異的スコアリングマトリクス / ウェブサーバー / タンパク質の機能予想 / タンパク質の構造予想 / 構造モデリング / スレッディング / 多重配列アライメント / alignment / threading / protein function / Protein structure / 酵素反応速度論 / 双極子フィールド / 溶媒和 / タンパク工学 / タンパク質-ヌクレオチド相互作用 / 分子ドッキング / 分子動力学 / 加水分解 / サクシニルCoAシンテターゼ / GTP / 双極子モーメント / 基質特異性 / ATP Less

免疫レパトア解析に基づく機械学習を用いたHTLV-1関連疾患の発症予測法の確立Principal Investigator
- Principal Investigator
  
  Standley Daron
- Project Period (FY)
  2025 – 2027
- Research Category
  
  Grant-in-Aid for Challenging Research (Exploratory)
- Review Section
  
  Medium-sized Section 49:Pathology, infection/immunology, and related fields
- Research Institution
  The University of Osaka
Machine Learning of Disease Biomarkers from B and T cell Receptor RepertoiresPrincipal Investigator
- Principal Investigator
  
  Standley Daron
- Project Period (FY)
  2023 – 2025
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  Osaka University
Identification of epitopes targeted by TCR-MHC pairsPrincipal Investigator
- Principal Investigator
  
  Standley Daron
- Project Period (FY)
  2018 – 2020
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 43060:System genome science-related
- Research Institution
  Osaka University
水の媒介するATPゲートキーパーのシュミレーションPrincipal Investigator
- Principal Investigator
  
  STANDLEY Daron
- Project Period (FY)
  2009 – 2010
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Complex systems
- Research Institution
  Osaka University
Functional annotation of innate immunity proteinsPrincipal Investigator
- Principal Investigator
  
  STANDLEY Daron
- Project Period (FY)
  2009 – 2011
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Biophysics
- Research Institution
  Osaka University

All 2021 2020 2019 2018 2012 2011 2010 2009

All Journal Article Presentation Book

[Book] In Vitro Differentiation of T-Cells2019
- Author(s)
  DARON M. STANDLEY 加藤　和貴 LI　SONGLING VAN　EERDEN　FLORIS　JAN ROZEWICKI　JOHN　JAMES WILAMOWSKI JAN DAVILA ANA XU ZICHANG
- Publisher
  Humana Press
- Data Source
  KAKENHI-PROJECT-18H02430
[Journal Article] Antigen-independent activation enhances the efficacy of 4-1BB-costimulated CD22 CAR T cells2021
- Author(s)
  Nathan Singh + 26+ Daron M Standley +6 + Marco Ruella
- Journal Title
  
  Nat Med. in press
  
  Volume: 1 Pages: 1-1
- Data Source
  KAKENHI-PROJECT-18H02430
[Journal Article] An infectivity-enhancing site on the SARS-CoV-2 spike protein is targeted by COVID-19 patient antibodies2021
- Author(s)
  Liu Yafei +21 +Standley Daron M.、Shioda Tatsuo、Arase Hisashi
- Journal Title
  
  Cell in press
  
  Volume: 1 Pages: 1-1
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H02430
[Journal Article] Noncanonical STAT1 phosphorylation expands its transcriptional activity into promoting LPS-induced IL-6 and IL-12p40 production2020
- Author(s)
  Metwally Hozaifa、Tanaka Toshio、Li Songling、Parajuli Gyanu、Kang Sujin、Hanieh Hamza、Hashimoto Shigeru、Chalise Jaya P.、Gemechu Yohannes、Standley Daron M.、Kishimoto Tadamitsu
- Journal Title
  
  Science Signaling
  
  Volume: 13 Issue: 624 Pages: 624-624
- DOI
  10.1126/scisignal.aay0574
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H02430, KAKENHI-PROJECT-17K07151, KAKENHI-PROJECT-19K23864
[Journal Article] Analysis of Protein Intermolecular Interactions with MAFFT-DASH2020
- Author(s)
  Rozewicki John、Li Songling、Katoh Kazutaka、Standley Daron M.
- Journal Title
  
  Multiple Sequence Alignment (Methods in Molecular Biology)
  
  Volume: 2232 Pages: 163-177
- DOI
  10.1007/978-1-0716-1036-7_11
- ISBN
  9781071610350, 9781071610367
- Data Source
  KAKENHI-PROJECT-20K06767, KAKENHI-PROJECT-18H02430, KAKENHI-PROJECT-16K07464
[Journal Article] Dysregulated Expression of the Nuclear Exosome Targeting Complex Component Rbm7 in Nonhematopoietic Cells Licenses the Development of Fibrosis2020
- Author(s)
  Fukushima Kiyoharu、Satoh Takashi、Sugihara Fuminori、Sato Yuki、Okamoto Toru、Mitsui Yuichi、Yoshio Sachiyo、Li Songling、Nojima Satoshi、Motooka Daisuke、Nakamura Shota、Kida Hiroshi、Standley Daron M.、Morii Eiichi、Kanto Tatsuya、Yanagita Motoko、Matsuura Yoshiharu、Nagasawa Takashi、Kumanogoh Atsushi、Akira Shizuo
- Journal Title
  
  Immunity
  
  Volume: 52 Issue: 3 Pages: 542-556
- DOI
  10.1016/j.immuni.2020.02.007
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K16557, KAKENHI-INTERNATIONAL-16K21723, KAKENHI-ORGANIZER-16H06429, KAKENHI-PUBLICLY-18H05032, KAKENHI-PROJECT-18H03998, KAKENHI-PROJECT-18H02430, KAKENHI-PROJECT-16K09537, KAKENHI-PROJECT-17K19557, KAKENHI-PROJECT-17K16081, KAKENHI-PROJECT-15H05704, KAKENHI-PROJECT-20H03495, KAKENHI-PROJECT-20H03697, KAKENHI-PROJECT-19K22620
[Journal Article] Methods for sequence and structural analysis of B and T cell receptor repertoires2020
- Author(s)
  Teraguchi Shunsuke、Saputri Dianita S.、Llamas-Covarrubias Mara Anais、Davila Ana、Diez Diego、Nazlica Sedat Aybars、Rozewicki John、Ismanto Hendra S.、Wilamowski Jan、Xie Jiaqi、Xu Zichang、Loza-Lopez Martin de Jesus、van Eerden Floris J.、Li Songling、Standley Daron M.
- Journal Title
  
  Computational and Structural Biotechnology Journal
  
  Volume: 18 Pages: 2000-2011
- DOI
  10.1016/j.csbj.2020.07.008
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-20K06610, KAKENHI-PROJECT-20K16286, KAKENHI-PROJECT-18H02430
[Journal Article] MAFFT-DASH: integrated protein sequence and structural alignment2019
- Author(s)
  Rozewicki John、Li Songling、Amada Karlou Mar、Standley Daron M、Katoh Kazutaka
- Journal Title
  
  Nucleic Acids Research
  
  Volume: 47
- DOI
  10.1093/nar/gkz342
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K07464, KAKENHI-PROJECT-18H02430
[Journal Article] Repertoire Builder: High-throughput structural modeling of B and T cell receptors Mol.2019
- Author(s)
  D. Schritt, S. Li, J. Rozewicki, K. Katoh, K. Yamashita, W. Volkmuth, G. Cavet and D. Standley,
- Journal Title
  
  Syst. Des. Eng
  
  Volume: in press
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H02430
[Journal Article] Structural Determinants of the APOBEC3G N-Terminal Domain for HIV-1 RNA Association2019
- Author(s)
  Fukuda Hirofumi、Li Songling、Sardo Luca、Smith Jessica L.、Yamashita Kazuo、Sarca Anamaria D.、Shirakawa Kotaro、Standley Daron M.、Takaori-Kondo Akifumi、Izumi Taisuke
- Journal Title
  
  Frontiers in Cellular and Infection Microbiology
  
  Volume: 9 Pages: 1-13
- DOI
  10.3389/fcimb.2019.00129
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H02430
[Journal Article] Initial phospholipid-dependent Irgb6 targeting to Toxoplasma gondii vacuoles mediates host defense.2019
- Author(s)
  Lee, Y., Yamada, H., Pradipta, A., Ma, J.S., Okamoto, M., Nagaoka, H., Takashima, E., Standley, D.M., Sasai, M., Takei, K., Yamamoto, M.
- Journal Title
  
  Life Science Alliance
  
  Volume: 3 Issue: 1 Pages: 000-000
- DOI
  10.26508/lsa.201900549
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K07084, KAKENHI-PROJECT-18KK0226, KAKENHI-PROJECT-19H00970, KAKENHI-PROJECT-18H02430, KAKENHI-PROJECT-18H02642, KAKENHI-PROJECT-19H03225, KAKENHI-PROJECT-17K08808, KAKENHI-PROJECT-18K05970, KAKENHI-PROJECT-18K15135, KAKENHI-PUBLICLY-19H04809
[Journal Article] Reversible control of enantioselectivity by the length of ketone substituent in biocatalytic reduction.2019
- Author(s)
  Koesoema AA, Sugiyama Y, Sriwong KT, Xu Z, Verina S, Standley DM, Senda M, Senda T, Matsuda T.
- Journal Title
  
  Applied Microbiology and Biotechnology
  
  Volume: 103 Pages: 9529-9541
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H02430
[Journal Article] MAFFT-DASH: integrated protein sequence and structural alignment.2019
- Author(s)
  Rozewicki, J., Li, S., K., A., Standley, D. M. & Kazutaka, K.
- Journal Title
  
  Nucleic Acids Res.
  
  Volume: in press
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H02430
[Journal Article] N4BP1 restricts HIV-1 and its inactivation by MALT1 promotes viral reactivation.2019
- Author(s)
  Yamasoba D, Sato K, Ichinose T, Imamura T, Koepke L, Joas S, Reith E, Hotter D, Misawa N, Akaki K, Uehata T, Mino T, Miyamoto S, Noda T, Yamashita A, Standley DM, Kirchhoff F, Sauter D, Koyanagi Y, Takeuchi O.
- Journal Title
  
  Nat Microbiol
  
  Volume: 4 Issue: 9 Pages: 1532-1544
- DOI
  10.1038/s41564-019-0460-3
- NAID
  120006731123
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K22529, KAKENHI-PROJECT-19K22601, KAKENHI-PROJECT-18KK0447, KAKENHI-INTERNATIONAL-16K21723, KAKENHI-ORGANIZER-16H06429, KAKENHI-PROJECT-18H05278, KAKENHI-PROJECT-17H04082, KAKENHI-PROJECT-18H02430, KAKENHI-PROJECT-18H02662, KAKENHI-PROJECT-19H03488, KAKENHI-PROJECT-17J10132, KAKENHI-PROJECT-18K15185
[Journal Article] Translation-dependent unwinding of stem?loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs2019
- Author(s)
  Mino Takashi、Iwai Noriki、Endo Masayuki、Inoue Kentaro、Akaki Kotaro、Hia Fabian、Uehata Takuya、Emura Tomoko、Hidaka Kumi、Suzuki Yutaka、Standley Daron M、Okada-Hatakeyama Mariko、Ohno Shigeo、Sugiyama Hiroshi、Yamashita Akio、Takeuchi Osamu
- Journal Title
  
  Nucleic Acids Research
  
  Volume: 47 Pages: 8838-8859
- DOI
  10.1093/nar/gkz628
- NAID
  120006708220
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19K22601, KAKENHI-PROJECT-18KK0139, KAKENHI-PROJECT-18H05278, KAKENHI-PROJECT-18H02430, KAKENHI-PROJECT-19H03488, KAKENHI-PROJECT-16H06279, KAKENHI-PROJECT-16H06356, KAKENHI-PROJECT-18K15185
[Journal Article] Repertoire Builder: high-throughput structural modeling of B and T cell receptors2019
- Author(s)
  Schritt Dimitri、Li Songling、Rozewicki John、Katoh Kazutaka、Yamashita Kazuo、Volkmuth Wayne、Cavet Guy、Standley Daron M.
- Journal Title
  
  Molecular Systems Design & Engineering
  
  Volume: 4 Issue: 4 Pages: 761-768
- DOI
  10.1039/c9me00020h
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16K07464, KAKENHI-PROJECT-18H02430
[Journal Article] Structural modeling of lymphocyte receptors and their antigens.2019
- Author(s)
  Li S, Wilamowski J, Teraguchi S, Van Eerden F, Rozewiki J, Davila A, Xu Z, Katoh K, Standley DM,
- Journal Title
  
  Meth Mol Biol
  
  Volume: in press
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H02430
[Journal Article] Allergic conversion of protective mucosal immunity against nasal bacteria in patients with chronic rhinosinusitis with nasal polyposis.2019
- Author(s)
  Takeda K, Sakakibara S, Yamashita K, Motooka D, Nakamura S, El Hussien MA, Katayama J, Maeda Y, Nakata M, Hamada S, Standley DM, Hayama M, Shikina T, Inohara H, Kikutani H.
- Journal Title
  
  J Allergy Clin Immunol
  
  Volume: 143 Issue: 3 Pages: 1163-1175
- DOI
  10.1016/j.jaci.2018.07.006
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17K11610, KAKENHI-PROJECT-17K11958, KAKENHI-PROJECT-18K19643, KAKENHI-PROJECT-15KK0306, KAKENHI-PROJECT-16H05847, KAKENHI-PROJECT-17H04369, KAKENHI-PROJECT-18H02430, KAKENHI-PROJECT-16K08837, KAKENHI-PROJECT-17K19751, KAKENHI-PROJECT-19H03825
[Journal Article] Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain.2019
- Author(s)
  Koesoema AA, Sugiyama Y, Xu Z, Standley DM, Senda M, Senda T, Matsuda T
- Journal Title
  
  Applied microbiology and biotechnology
  
  Volume: 103 Pages: 9543-9553
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H02430
[Journal Article] Functional clustering of B cell receptors using sequence and structural features2019
- Author(s)
  Xu Zichang、Li Songling、Rozewicki John、Yamashita Kazuo、Teraguchi Shunsuke、Inoue Takeshi、Shinnakasu Ryo、Leach Sarah、Kurosaki Tomohiro、Standley Daron M.
- Journal Title
  
  Molecular Systems Design & Engineering
  
  Volume: 4 Issue: 4 Pages: 769-778
- DOI
  10.1039/c9me00021f
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H02430, KAKENHI-PROJECT-17K08856
[Journal Article] Arid5a stabilizes OX40 mRNA in murine CD4+ T cells by recognizing a stem-loop structure in its 3′UTR2018
- Author(s)
  Hanieh Hamza、Masuda Kazuya、Metwally Hozaifa、Chalise Jaya P.、Mohamed Maged、Nyati Kishan K.、Standley Daron M.、Li Songling、Higa Mitsuru、Zaman Mohammad M.、Kishimoto Tadamitsu
- Journal Title
  
  European Journal of Immunology
  
  Volume: 48 Issue: 4 Pages: 593-604
- DOI
  10.1002/eji.201747109
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H02430
[Journal Article] Modeling the alternative oxidase from the human pathogen Blastocystis using automated hybrid structural template assembly2012
- Author(s)
  Standley DM, van der Giezen M
- Journal Title
  
  Research and Reports in Biochemistry
  
  Volume: 2 Pages: 1-8
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Protein loop modeling with optimized backbone potential functions2012
- Author(s)
  Liang S, Zhang C, Sarmiento J, Standley DM
- Journal Title
  
  J Chem Theory Comput
  
  Volume: (in press)
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster2011
- Author(s)
  Ikebe J, Standley DM
- Journal Title
  
  Protein Science
  
  Volume: 20 Pages: 187-196
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-21118513
[Journal Article] Community-wide assessment of protein-interface modeling suggests improvements to design methodology2011
- Author(s)
  Fleishman SJ, Standley DM, et al
- Journal Title
  
  J Mol Biol
  
  Volume: 414(2) Pages: 289-302
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Protein Side Chain Modeling with Orientation Dependent Atomic Force Fields Derived by Series Expansions2011
- Author(s)
  Liang S, Standley DM
- Journal Title
  
  J COMPUT CHEM
  
  Volume: (印刷中)
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-21118513
[Journal Article] Prediction of dinucleotide-specific RNA-binding sites in proteins2011
- Author(s)
  Fernandez M, Kumagai Y, Standley DM, Sarai A, Mizuguchi K, Ahmad S
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 12 Suppl 13:S5
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Binding Energetics of Ferredoxin-NADP(+) Reductase with Ferredoxin and Its Relation to Function2011
- Author(s)
  Lee YH, Ikegami T, Standley DM, Sakurai K, Hase T, Goto Y
- Journal Title
  
  ChemBioChem
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Degree of Pyramidality Governs the Height and Peak position of the Free-Energy-Barrier for the cis-trans Isomerization of N-Methylacetamide2011
- Author(s)
  Yonezawa Y, Standley DM
- Journal Title
  
  Chem Phys Lett
  
  Volume: (印刷中)
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-21118513
[Journal Article] Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions2011
- Author(s)
  Liang S, Zhou Y, Grishin N, Standley DM
- Journal Title
  
  J COMPUT CHEM
  
  Volume: 32 Pages: 1680-1686
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Bridging the gap between single-template and fragment based protein structure modeling using Spanner2011
- Author(s)
  Lis M, Kim T, Sarmiento J, Kuroda D, Dinh H, Kinjo AR, Devadas S, Nakamura H, Standley DM
- Journal Title
  
  Immunome Research
  
  Volume: 7
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Protein Data Bank Japan (PDBj) : maintaining a structural data archive and resource description framework format2011
- Author(s)
  Kinjo AR, Suzuki H, Yamashita R, Ikegawa Y, Kudou T, Igarashi R, Kengaku Y, Cho H, Standley DM, Nakagawa A, Nakamura H
- Journal Title
  
  Nucleic Acids Res
  
  Volume: 40(Database issue)
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Protein Data Bank Japan(PDBj): maintaining a structural data archive and resource description framework format2011
- Author(s)
  Kinjo AR, Suzuki H, Yamashita R, Ikegawa Y, Kudou T, Igarashi R, Kengaku Y, Cho H, Standley DM, Nakagawa A, Nakamura H
- Journal Title
  
  Nucleic Acids Res
  
  Volume: 40 Pages: 453-460
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Protein loop selection using orientation-dependent force fields derived by parameter optimization2011
- Author(s)
  Liang S, Zhang C, Standley DM
- Journal Title
  
  Proteins
  
  Volume: 79 Pages: 2260-2267
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] FUNCTIONAL ANNOTATION OF INTRINSICALLY DISORDERED DOMAINS BY THEIR AMINO ACID CONTENT USING IDD NAVIGATOR2011
- Author(s)
  Patil A, Teraguchi S, Dinh H, Nakai K, Standley DM
- Journal Title
  
  Pac Symp Biocomput
  
  Volume: 17 Pages: 164-175
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Binding energetics of ferredoxin-NADP+ reductase with ferredoxin and its relation to function2011
- Author(s)
  Lee YH, Ikegami T, Standley DM, Sakurai K, Hase T, Goto Y
- Journal Title
  
  Chembiochem
  
  Volume: 12(13) Issue: 13 Pages: 2062-70
- DOI
  10.1002/cbic.201100189
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations2011
- Author(s)
  Teraguchi S, Kumagai Y, Vandenbon A, Akira S, Standley DM
- Journal Title
  
  Phys Rev E Stat Nonlin Soft Matter Phys
  
  Volume: 84(6-1):062903
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using Idd Navigator2011
- Author(s)
  Patil A, Teraguchi S, Dinh H, Nakai K, Standley DM
- Journal Title
  
  Pac Symp Biocomput
  
  Volume: 17 Pages: 164-175
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Fast and accurate prediction of protein side-chain conformations2011
- Author(s)
  Liang S, Zheng D, Zhang C, Standley DM
- Journal Title
  
  Bioinformatics
  
  Volume: 27 Pages: 2913-2914
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Functional characterization of protein domains common to animal viruses and mouse2011
- Author(s)
  Kinjo AR, Kumagai Y, Dinh H, Takeuchi O, Standley DM
- Journal Title
  
  BMC Genomics
  
  Volume: 12 Suppl 3:S21
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans2011
- Author(s)
  Kitamura A, Maekawa Y, Uehara H, Izumi K, Kawachi I, Nishizawa M, Toyoshima Y, Takahashi H, Standley DM, Tanaka K, Hamazaki J, Murata S, Obara K, Toyoshima I, Yasutomo K.
- Journal Title
  
  J Clin Invest
  
  Volume: 121 Issue: 10 Pages: 4150-4160
- DOI
  10.1172/jci58414
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20679005, KAKENHI-PROJECT-21000012, KAKENHI-PROJECT-21570169, KAKENHI-PROJECT-21590536, KAKENHI-PROJECT-23591236, KAKENHI-PROJECT-23657083, KAKENHI-PROJECT-23791179
[Journal Article] Bridging the gap between single-template and fragment based protein structure modeling using Spanner2011
- Author(s)
  Lis M, Kim T, Sarmiento JJ, Kuroda D, Dinh HV, Kinjo AR, Amada K, Devadas S, Nakamura H, Standley DM
- Journal Title
  
  Immunome Res
  
  Volume: 7(1) Pages: 1-8
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions2011
- Author(s)
  Liang S, Zhou Y, Grishin N, Standley DM
- Journal Title
  
  J Comput Chem
  
  Volume: 32(8) Issue: 8 Pages: 1680-6
- DOI
  10.1002/jcc.21747
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] The IκB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR-IL-1R by controlling degradation of regnase-1.2011
- Author(s)
  Iwasaki H, Takeuchi O, Teraguchi S, Matsushita K, Uehata T, Kuniyoshi K, Satoh T, Saitoh T, Matsushita M, Standley DM, Akira S.
- Journal Title
  
  Nat Immunol.
  
  Volume: 12 Issue: 12 Pages: 1167-1175
- DOI
  10.1038/ni.2137
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20002008, KAKENHI-PROJECT-21570169, KAKENHI-PROJECT-22689016, KAKENHI-PROJECT-22890224
[Journal Article] A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans2011
- Author(s)
  Kitamura A, Maekawa Y, Uehara H, Izumi K, Kawachi I, Nishizawa M, Toyoshima Y, Takahashi H, Standley DM, Tanaka K, et al
- Journal Title
  
  J Clin Invest
  
  Volume: 121 Pages: 4150-4160
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Ab initio simulation of a 57-residue protein in explicit solvent reproduces the native conformation in the lowest free-energy cluster2010
- Author(s)
  Ikebe J, Standley DM, Nakamura H, Higo J
- Journal Title
  
  Protein Science
  
  Volume: 20 Pages: 187-196
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] The DBCLS BioHackathon : standardization and interoperability for bioinformatics web services and workflows2010
- Author(s)
  Katayama T, Arakawa K, Nakao M, Ono K, K. F A-K, Yamamoto Y, Aerts J, Aranda B, Barboza LH, Bonnal R, (+ 36 authors), Standley DM, (+ 10 authors)
- Journal Title
  
  Journal of Biomedical Semantics
  
  Volume: 1
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] The DBCLS BioHackathon : standardization and interoperability for bioinformatics web services and workflows2010
- Author(s)
  Katayama T, Standley D
- Journal Title
  
  Journal of Biomedical Semantics
  
  Volume: 21 Pages: 8-27
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] SeSAW : balancing sequence and structural information in protein functional mapping2010
- Author(s)
  Standley DM, Yamashita R, Kinjo AR, Toh H, Nakamura H
- Journal Title
  
  Bioinformatics (印刷中)
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-21118513
[Journal Article] SeSAW balancing sequence and structural information in protein functional mapping2010
- Author(s)
  Standley DM, Yamashita R, Kinjo AR, Toh H, Nakamura H
- Journal Title
  
  Bioinformatics
  
  Volume: 26 Pages: 1258-1259
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] SeSAW : balancing sequence and structural information in protein functional mapping2010
- Author(s)
  Standley DM, Yamashita R, Kinjo AR, Toh H, Nakamura H
- Journal Title
  
  Bioinformatics (印刷中)
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] SeSAW : balancing sequence and structural information in protein functional mapping2010
- Author(s)
  Standley DM
- Journal Title
  
  Bioinformatics
  
  Volume: 26 Pages: 1258-1259
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins2010
- Author(s)
  Teraguchi S, Patil A, Standley DM
- Journal Title
  
  BMC Bioinformatics
  
  Volume: S7 Pages: 11-11
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins2010
- Author(s)
  Teraguchi S, Standley D
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 11 Pages: 2-12
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Outcome of a workshop on applications of protein models in biomedical research2009
- Author(s)
  Schwede T, et al. (23 authors), Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA
- Journal Title
  
  Structure 17
  
  Pages: 151-159
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Zc3hl2a is an RNase essential for controlling immune responses by regulating mRNA decay2009
- Author(s)
  Matsushita K, Takeuchi O, Standley DM, Kumagai Y, Kawagoe T, Miyake T, Satoh T, Kato H, Tsujimura T, Nakamura H, Akira S
- Journal Title
  
  Nature 458
  
  Pages: 1185-1190
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-21118513
[Journal Article] Outcome of a workshop on applications of protein models in biomedical research2009
- Author(s)
  Schwede T, et al. (23 authors), Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA
- Journal Title
  
  Structure 17
  
  Pages: 151-159
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-21118513
[Journal Article] A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat32009
- Author(s)
  Yamamoto M, Standley DM, Takashima S, Saiga H, Okuyama M, Kayama H, Kubo E, Ito H, Takaura M, Matsuda T, Soldati-Favre D, Takeda K
- Journal Title
  
  J Exp Med 206
  
  Pages: 2747-2760
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-21118513
[Journal Article] Outcome of a workshop on applications of protein models in biomedical research2009
- Author(s)
  Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV(+ 16 authors), Standley DM, (+ 5 authors)
- Journal Title
  
  Structure
  
  Volume: 17 Pages: 151-159
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Membrane attachment facilitates ligand access to the active site in monoamine oxidase A2009
- Author(s)
  Apostolov R, Yonezawa Y, Standley DM, Kikugawa G, Takano Y, Nakamura H
- Journal Title
  
  Biochemistry 48
  
  Pages: 5864-5873
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay2009
- Author(s)
  Matsushita K, Takeuchi O, Standley DM, Kumagai Y, Kawagoe T, Miyake T, Satoh T, Kato H, Tsujimura T, Nakamura H, Akira S
- Journal Title
  
  Nature
  
  Volume: 458 Pages: 1185-1190
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat32009
- Author(s)
  Yamamoto M, Standley DM, Takashima S, Saiga H, Okuyama M, Kayama H, Kubo E, Ito H, Takaura M, Matsuda T, et al
- Journal Title
  
  J Exp Med
  
  Volume: 206 Pages: 2747-2760
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay2009
- Author(s)
  Matsushita K, Takeuchi O, Standley DM, Kumagai Y, Kawagoe T, Miyake T, Satoh T, Kato H, Tsujimura T, Nakamura H, Akira S
- Journal Title
  
  Nature 458
  
  Pages: 1185-1190
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat32009
- Author(s)
  Yamamoto M, Standley DM, Takashima S, Saiga H, Okuyama M, Kayama H, Kubo E, Ito H, Takaura M, Matsuda T, Soldati-Favre D, Takeda K
- Journal Title
  
  J Exp Med 206
  
  Pages: 2747-2760
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21570169
[Journal Article] Membrane attachment facilitates ligand access to the active site in monoamine oxidase A2009
- Author(s)
  Apostolov R, Yonezawa Y, Standley DM, Kikugawa GS Takano Y, Nakamura H
- Journal Title
  
  Biochemistry 48
  
  Pages: 5864-5873
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-21118513
[Journal Article] Membrane attachment facilitates ligand access to the active site in monoamine oxidase A2009
- Author(s)
  Apostolov R, Yonezawa Y, Standley DM, Kikugawa G, Takano Y, Nakamura H
- Journal Title
  
  Biochemistry
  
  Volume: 48 Pages: 5864-5873
- Data Source
  KAKENHI-PROJECT-21570169
[Presentation] "Toward high-throughput antibody-antigen modeling"2020
- Author(s)
  Daron Standley
- Organizer
  Kobe Univ. (The Basis for Computational Life Science 7)
- Invited
- Data Source
  KAKENHI-PROJECT-18H02430
[Presentation] Modeling the structure and function of lymphocyte receptors from their sequences2019
- Author(s)
  Daron Standley
- Organizer
  Immunogenomics 2019
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H02430
[Presentation] High-throughput modeling of lymphocyte receptors and their antigens2018
- Author(s)
  Daron Standley
- Organizer
  Hot Spring Harbor International Symposium
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H02430
[Presentation] Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator2012
- Author(s)
  Standley DM
- Organizer
  Pacific Symposium on Biocomputing
- Place of Presentation
  Hawaii, USA
- Year and Date
  2012-01-06
- Data Source
  KAKENHI-PROJECT-21570169
[Presentation] Function prediction of structured and unstructured proteins2011
- Author(s)
  Standley DM
- Organizer
  China 5th China Medical Biotech Forum(CMBF-2011)
- Place of Presentation
  Beiing
- Year and Date
  2011-11-08
- Data Source
  KAKENHI-PROJECT-21570169
[Presentation] A structural view of Innate immunity2011
- Author(s)
  Standley DM
- Organizer
  Dana-Farber Cancer Institute
- Place of Presentation
  Cancer Vaccine Center, USA
- Data Source
  KAKENHI-PROJECT-21570169
[Presentation] Prediction of dinucleotide-specific RNA-binding sites in proteins2011
- Author(s)
  Standley DM
- Organizer
  Malaysia
- Place of Presentation
  Kuala Lumpur
- Year and Date
  2011-11-14
- Data Source
  KAKENHI-PROJECT-21570169
[Presentation] Restrained docking of protein molecular surfaces2010
- Author(s)
  Daron M.Standley
- Organizer
  Department of Chemistry Colloquium
- Place of Presentation
  Columbia Univ.(U.S.A.)
- Year and Date
  2010-11-08
- Data Source
  KAKENHI-PUBLICLY-21118513
[Presentation] Restrained docking of protein molecular surfaces2010
- Author(s)
  Daron M.Standley
- Organizer
  Department of Chemistry Colloquium
- Place of Presentation
  Columbia Univ.
- Year and Date
  2010-11-08
- Data Source
  KAKENHI-PROJECT-21570169
[Presentation] Restrained docking of protein molecular surfaces2010
- Author(s)
  Standley DM
- Organizer
  Department of Chemistry
- Place of Presentation
  New York, USA : Columbia Univ
- Data Source
  KAKENHI-PROJECT-21570169
[Presentation] Functional Annotation using SeSAW2009
- Author(s)
  Standley DM
- Organizer
  MEI Center lecture series
- Place of Presentation
  Osaka, Japan
- Data Source
  KAKENHI-PROJECT-21570169
[Presentation] Functional Annotation using SeSAW2009
- Author(s)
  Daron M.Standley
- Organizer
  MEI Center lecture series
- Place of Presentation
  大阪大学中の島センター
- Year and Date
  2009-11-07
- Data Source
  KAKENHI-PROJECT-21570169
[Presentation] An introduction to protein-protein docking II2009
- Author(s)
  Daron M.Standley
- Organizer
  Ochanomizu Univ.Predictive Biology lecture series
- Place of Presentation
  お茶の水大学
- Year and Date
  2009-11-11
- Data Source
  KAKENHI-PUBLICLY-21118513
[Presentation] An introduction to protein-protein docking II2009
- Author(s)
  Standley DM
- Organizer
  Predictive Biology lecture series
- Place of Presentation
  Tokyo, Japan : Ochanomizu Univ
- Data Source
  KAKENHI-PROJECT-21570169
[Presentation] Functional Annotation using SeSAW2009
- Author(s)
  Daron M.Standley
- Organizer
  MEI Center lecture series
- Place of Presentation
  大阪大学中の島センター
- Year and Date
  2009-11-07
- Data Source
  KAKENHI-PUBLICLY-21118513
[Presentation] An introduction to protein-protein docking II2009
- Author(s)
  Daron M.Standley
- Organizer
  Ochanomizu Univ. Predictive Biology lecture series
- Place of Presentation
  お茶の水大学
- Year and Date
  2009-11-11
- Data Source
  KAKENHI-PROJECT-21570169

1. KATOH Kazutaka

# of Collaborated Projects: 0 results

# of Collaborated Products: 3 results
2. NAKATA Masanobu

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
3. SAITOH Tatsuya

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
4. SATOH Takashi

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
5. 竹居孝二

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
6. 山田浩司

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
7. 野田岳志

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
8. 山下暁朗

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
9. 安友康二

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
10. 審良静男

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
11. 竹内理

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
12. 野島聡

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
13. 寺口俊介

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Standley Daron Ｓｔａｎｄｌｅｙ Ｄａｒｏｎ

STANDLEY Daron スタンドレー ダーロン

DARON Standley ダーロン スタンドレイ

Research Projects

Research Products

Co-Researchers

免疫レパトア解析に基づく機械学習を用いたHTLV-1関連疾患の発症予測法の確立Principal Investigator

Principal Investigator

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Review Section

Research Institution

Machine Learning of Disease Biomarkers from B and T cell Receptor RepertoiresPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Identification of epitopes targeted by TCR-MHC pairsPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

水の媒介するATPゲートキーパーのシュミレーションPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Functional annotation of innate immunity proteinsPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

[Book] In Vitro Differentiation of T-Cells2019

Author(s)

Publisher

Data Source

[Journal Article] Antigen-independent activation enhances the efficacy of 4-1BB-costimulated CD22 CAR T cells2021

Author(s)

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Data Source

[Journal Article] An infectivity-enhancing site on the SARS-CoV-2 spike protein is targeted by COVID-19 patient antibodies2021

Author(s)

Journal Title

Data Source

[Journal Article] Noncanonical STAT1 phosphorylation expands its transcriptional activity into promoting LPS-induced IL-6 and IL-12p40 production2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Analysis of Protein Intermolecular Interactions with MAFFT-DASH2020

Author(s)

Journal Title

DOI

ISBN

Data Source

[Journal Article] Dysregulated Expression of the Nuclear Exosome Targeting Complex Component Rbm7 in Nonhematopoietic Cells Licenses the Development of Fibrosis2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Methods for sequence and structural analysis of B and T cell receptor repertoires2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] MAFFT-DASH: integrated protein sequence and structural alignment2019

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Repertoire Builder: High-throughput structural modeling of B and T cell receptors Mol.2019

Author(s)

Journal Title

Data Source

[Journal Article] Structural Determinants of the APOBEC3G N-Terminal Domain for HIV-1 RNA Association2019

Author(s)

Standley Daron ＳｔａｎｄｌｅｙＤａｒｏｎ

STANDLEY Daron スタンドレーダーロン

DARON Standley ダーロンスタンドレイ