Featured Publications

Featured Publications

Year Authors Title Publication Cites
2013 K Katoh, DM Standley MAFFT multiple sequence alignment software version 7: improvements in performance and usability MOLECULAR BIOLOGY AND EVOLUTION, 2013, 30, 772-780 15216
2010 T Satoh, O Takeuchi, A Vandenbon, K Yasuda, Y Tanaka, Y Kumagai, ... The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection NATURE IMMUNOLOGY, 2010, 11, 936-944 862
2009 K Matsushita, O Takeuchi, DM Standley, Y Kumagai, T Kawagoe, ... Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay NATURE, 2009, 458, 1185-1190 458
2014 K Katoh, DM Standley MAFFT: iterative refinement and additional methods MULTIPLE SEQUENCE ALIGNMENT METHODS, 2014, 131-146 265
2009 M Yamamoto, DM Standley, S Takashima, H Saiga, M Okuyama, ... A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3 JOURNAL OF EXPERIMENTAL MEDICINE, 2009, 206, 2747-2760 227
2011 A Kitamura, Y Maekawa, H Uehara, K Izumi, I Kawachi, M Nishizawa, ... A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans THE JOURNAL OF CLINICAL INVESTIGATION, 2011, 121, 4150-4160 222
2016 K Katoh, DM Standley A simple method to control over-alignment in the MAFFT multiple sequence alignment program BIOINFORMATICS, 2016, 32, 1933-1942 213
2013 T Uehata, H Iwasaki, A Vandenbon, K Matsushita, E Hernandez-Cuellar, ... Malt1-Induced Cleavage of Regnase-1 in CD4+ Helper T Cells Regulates Immune Activation CELL, 2013, 153, 1036-1049 212
2011 H Iwasaki, O Takeuchi, S Teraguchi, K Matsushita, T Uehata, K Kuniyoshi, ... The IκB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR–IL-1R by controlling degradation of regnase-1 NATURE IMMUNOLOGY, 2011, 12, 1167-1175 195
2015 T Mino, Y Murakawa, A Fukao, A Vandenbon, HH Wessels, D Ori, ... Regnase-1 and roquin regulate a common element in inflammatory mRNAs by spatiotemporally distinct mechanisms CELL, 2015, 161, 1058-1073 188
2011 SJ Fleishman, TA Whitehead, EM Strauch, JE Corn, S Qin, HX Zhou, ... Community-wide assessment of protein-interface modeling suggests improvements to design methodology JOURNAL OF MOLECULAR BIOLOGY, 2011, 414, 289-302 133
2012 AR Kinjo, H Suzuki, R Yamashita, Y Ikegawa, T Kudou, R Igarashi, ... Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format NUCLEIC ACIDS RESEARCH 40 (D1), D453-D, 2012, 460 123
2009 T Schwede, A Sali, B Honig, M Levitt, HM Berman, D Jones, SE Brenner, ... Outcome of a workshop on applications of protein models in biomedical research STRUCTURE, 2009, 17, 151-159 122
2010 S Liang, D Zheng, DM Standley, B Yao, M Zacharias, C Zhang EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results BMC BIOINFORMATICS, 2010, 11, 1-6 117
2014 N Takemura, T Kawasaki, J Kunisawa, S Sato, A Lamichhane, ... Blockade of TLR3 protects mice from lethal radiation-induced gastrointestinal syndrome NATURE COMMUNICATIONS, 2014, 5, 1-15 98
2014 H Morikawa, N Ohkura, A Vandenbon, M Itoh, S Nagao-Sato, H Kawaji, ... Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, 2014, 111, 5289-5294 95
2013 R Moretti, SJ Fleishman, R Agius, M Torchala, PA Bates, PL Kastritis, ... Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2013, 81, 1980-1987 92
2014 S Tartey, K Matsushita, A Vandenbon, D Ori, T Imamura, T Mino, ... Akirin2 is critical for inducing inflammatory genes by bridging IκB‐ζ and the SWI/SNF complex THE EMBO JOURNAL, 2014, 33, 2332-2348 59
2012 K Maruyama, M Fukasaka, A Vandenbon, T Saitoh, T Kawasaki, T Kondo, ... The transcription factor Jdp2 controls bone homeostasis and antibacterial immunity by regulating osteoclast and neutrophil differentiation IMMUNITY, 2012, 37, 1024-1036 58
2019 J Rozewicki, S Li, KM Amada, DM Standley, K Katoh MAFFT-DASH: integrated protein sequence and structural alignment NUCLEIC ACIDS RESEARCH 47 (W1), W5-W, 2019, 10 52
2017 KK Nyati, K Masuda, MMU Zaman, PK Dubey, D Millrine, JP Chalise, ... TLR4-induced NF-κB and MAPK signaling regulate the IL-6 mRNA stabilizing protein Arid5a NUCLEIC ACIDS RESEARCH, 2017, 45, 2687-2703 50
2013 Y Enokizono, H Kumeta, K Funami, M Horiuchi, J Sarmiento, K Yamashita, ... Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, 2013, 110, 19908-19913 49
2010 T Katayama, K Arakawa, M Nakao, K Ono, KF Aoki-Kinoshita, ... The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows JOURNAL OF BIOMEDICAL SEMANTICS, 2010, 1, 8-8 49
2007 DM Standley, H Toh, H Nakamura ASH structure alignment package: sensitivity and selectivity in domain classification BMC BIOINFORMATICS, 2007, 8, 116-116 47
2014 MF Lensink, IH Moal, PA Bates, PL Kastritis, ASJ Melquiond, E Karaca, ... Blind prediction of interfacial water positions in CAPRI PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2014, 82, 620-632 44
2008 DM Standley, AR Kinjo, K Kinoshita, H Nakamura Protein structure databases with new web services for structural biology and biomedical research BRIEFINGS IN BIOINFORMATICS, 2008, 9, 276-285 44
2016 K Masuda, B Ripley, KK Nyati, PK Dubey, MMU Zaman, H Hanieh, M Higa, ... Arid5a regulates naive CD4+ T cell fate through selective stabilization of Stat3 mRNA JOURNAL OF EXPERIMENTAL MEDICINE, 2016, 213, 605-619 43
2015 M Onishi, K Ozasa, K Kobiyama, K Ohata, M Kitano, K Taniguchi, ... Hydroxypropyl-β-cyclodextrin spikes local inflammation that induces Th2 cell and T follicular helper cell responses to the coadministered antigen THE JOURNAL OF IMMUNOLOGY, 2015, 194, 2673-2682 42
2014 H Shirai, K Ikeda, K Yamashita, Y Tsuchiya, J Sarmiento, S Liang, ... High‐resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2014, 82, 1624-1635 42
2014 K Yamashita, K Ikeda, K Amada, S Liang, Y Tsuchiya, H Nakamura, ... Kotai Antibody Builder: automated high-resolution structural modeling of antibodies BIOINFORMATICS, 2014, 30, 3279-3280 39
2013 T Kawasaki, N Takemura, DM Standley, S Akira, T Kawai The second messenger phosphatidylinositol-5-phosphate facilitates antiviral innate immune signaling CELL HOST & MICROBE, 2013, 14, 148-158 38
2011 S Liang, D Zheng, C Zhang, DM Standley Fast and accurate prediction of protein side-chain conformations BIOINFORMATICS, 2011, 27, 2913-2914 38
2010 K Zhuo, R Cui, WM Ye, M Luo, H Wang, X Hu, J Liao Morphological and molecular characterization of Aphelenchoides fujianensis n. sp.(Nematoda: Aphelenchoididae) from Pinus massoniana in China ZOOTAXA, 2010, 2509, 39-52 36
2011 M Fernandez, Y Kumagai, DM Standley, A Sarai, K Mizuguchi, S Ahmad Prediction of dinucleotide-specific RNA-binding sites in proteins BMC BIOINFORMATICS 12 (S13), S, 2011, 5 35
2017 M Sasai, N Sakaguchi, JS Ma, S Nakamura, T Kawabata, H Bando, Y Lee, ... Essential role for GABARAP autophagy proteins in interferon-inducible GTPase-mediated host defense NATURE IMMUNOLOGY, 2017, 18, 899-899 34
2014 S Li, K Yamashita, KM Amada, DM Standley Quantifying sequence and structural features of protein–RNA interactions NUCLEIC ACIDS RESEARCH, 2014, 42, 10086-10098 34
2017 R Yonehara, S Nada, T Nakai, M Nakai, A Kitamura, A Ogawa, ... Structural basis for the assembly of the Ragulator-Rag GTPase complex NATURE COMMUNICATIONS, 2017, 8, 1-11 30
2011 S Liang, Y Zhou, N Grishin, DM Standley Protein side chain modeling with orientation‐dependent atomic force fields derived by series expansions JOURNAL OF COMPUTATIONAL CHEMISTRY, 2011, 32, 1680-1686 30
2007 E Kanamori, Y Murakami, Y Tsuchiya, DM Standley, H Nakamura, ... Docking of protein molecular surfaces with evolutionary trace analysis PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2007, 69, 832-838 29
2012 A Vandenbon, S Teraguchi, S Akira, K Takeda, DM Standley Systems biology approaches to toll‐like receptor signaling WILEY INTERDISCIPLINARY REVIEWS: SYSTEMS BIOLOGY AND MEDICINE, 2012, 4, 497-507 28
2016 M Yokogawa, T Tsushima, NN Noda, H Kumeta, Y Enokizono, ... Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions SCIENTIFIC REPORTS, 2016, 6, 1-10 24
2014 Y Furukawa, S Teraguchi, T Ikegami, O Dagliyan, L Jin, D Hall, ... Intrinsic disorder mediates cooperative signal transduction in STIM1 JOURNAL OF MOLECULAR BIOLOGY, 2014, 426, 2082-2097 24
2011 J Ikebe, DM Standley, H Nakamura, J Higo Ab initio simulation of a 57‐residue protein in explicit solvent reproduces the native conformation in the lowest free‐energy cluster PROTEIN SCIENCE, 2011, 20, 187-196 24
2008 K Hamblin, DM Standley, MB Rogers, A Stechmann, AJ Roger, R Maytum, ... Localization and nucleotide specificity of Blastocystis succinyl‐CoA synthetase MOLECULAR MICROBIOLOGY, 2008, 68, 1395-1405 24
2015 J Ohshima, M Sasai, J Liu, K Yamashita, JS Ma, Y Lee, H Bando, ... RabGDIα is a negative regulator of interferon-γ–inducible GTPase-dependent cell-autonomous immunity to Toxoplasma gondii PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES 112 (33), E4581-, 2015, 4590 21
2011 YH Lee, T Ikegami, DM Standley, K Sakurai, T Hase, Y Goto Binding Energetics of Ferredoxin‐NADP+ Reductase with Ferredoxin and Its Relation to Function CHEMBIOCHEM, 2011, 12, 2062-2070 21
2016 Y Kamikawa, Y Hori, K Yamashita, L Jin, S Hirayama, DM Standley, ... Design of a protein tag and fluorogenic probe with modular structure for live-cell imaging of intracellular proteins CHEMICAL SCIENCE, 2016, 7, 308-314 19
2018 H Hanieh, K Masuda, H Metwally, JP Chalise, M Mohamed, KK Nyati, ... Arid5a stabilizes OX40 mRNA in murine CD4+ T cells by recognizing a stem‐loop structure in its 3′UTR EUROPEAN JOURNAL OF IMMUNOLOGY, 2018, 48, 593-604 17
2016 T Kouwaki, T Okamoto, A Ito, Y Sugiyama, K Yamashita, T Suzuki, ... Hepatocyte factor JMJD5 regulates hepatitis B virus replication through interaction with HBx JOURNAL OF VIROLOGY, 2016, 90, 3530-3542 17
2013 S Liang, D Zheng, DM Standley, H Guo, C Zhang A novel function prediction approach using protein overlap networks BMC SYSTEMS BIOLOGY, 2013, 7, 61-61 17
2013 AJ Hobro, DM Standley, S Ahmad, NI Smith Deconstructing RNA: optical measurement of composition and structure PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2013, 15, 13199-13208 17
2011 M Lis, T Kim, JJ Sarmiento, D Kuroda, HV Dinh, AR Kinjo, K Amada, ... Bridging the gap between single-template and fragment based protein structure modeling using Spanner IMMUNOME RESEARCH, 2011, 7, 1-1 17
2019 K Takeda, S Sakakibara, K Yamashita, D Motooka, S Nakamura, ... Allergic conversion of protective mucosal immunity against nasal bacteria in patients with chronic rhinosinusitis with nasal polyposis JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY 143 (3), 1163-1175., 2019, 15 16
2017 M Hayashi, T Aoshi, Y Haseda, K Kobiyama, E Wijaya, N Nakatsu, ... Advax, a delta inulin microparticle, potentiates in-built adjuvant property of co-administered vaccines EBIOMEDICINE, 2017, 15, 127-136 15
2017 S Sakakibara, T Arimori, K Yamashita, H Jinzai, D Motooka, S Nakamura, ... Clonal evolution and antigen recognition of anti-nuclear antibodies in acute systemic lupus erythematosus SCIENTIFIC REPORTS, 2017, 7, 1-14 14
2014 T Hirano, Y Iesato, Y Toriyama, A Imai, T Murata Detection of fovea-threatening diabetic macular edema by optical coherence tomography to maintain good vision by prophylactic treatment OPHTHALMIC RESEARCH, 2014, 52, 65-73 14
2009 R Apostolov, Y Yonezawa, DM Standley, G Kikugawa, Y Takano, ... Membrane attachment facilitates ligand access to the active site in monoamine oxidase A BIOCHEMISTRY, 2009, 48, 5864-5873 13
2010 DM Standley, R Yamashita, AR Kinjo, H Toh, H Nakamura SeSAW: balancing sequence and structural information in protein functional mapping BIOINFORMATICS, 2010, 26, 1258-1259 12
2007 J Liao, K Zhuo, S Yu, X Li, D Li Bursaphelenchus uncispicularis n. sp.(Nematoda: Parasitaphelenchidae) from Pinus yunnanensis in China NEMATOLOGY, 2007, 9, 237-242 12
2012 A Vandenbon, Y Kumagai, S Akira, DM Standley A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription BMC GENOMICS 13 (S7), S, 2012, 11 11
2012 S Liang, C Zhang, J Sarmiento, DM Standley Protein loop modeling with optimized backbone potential functions JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2012, 8, 1820-1827 11
2019 D Schritt, S Li, J Rozewicki, K Katoh, K Yamashita, W Volkmuth, G Cavet, ... Repertoire builder: high-throughput structural modeling of B and T cell receptors MOLECULAR SYSTEMS DESIGN & ENGINEERING, 2019, 4, 761-768 10
2019 D Yamasoba, K Sato, T Ichinose, T Imamura, L Koepke, S Joas, E Reith, ... N4BP1 restricts HIV-1 and its inactivation by MALT1 promotes viral reactivation NATURE MICROBIOLOGY, 2019, 4, 1532-1544 9
2011 S Teraguchi, Y Kumagai, A Vandenbon, S Akira, DM Standley Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations PHYSICAL REVIEW E, 2011, 84, 62903-62903 9
2010 S Teraguchi, A Patil, DM Standley Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins BMC BIOINFORMATICS 11 (S7), S, 2010, 7 9
2008 DM Standley, H Toh, H Nakamura Functional annotation by sequence‐weighted structure alignments: Statistical analysis and case studies from the Protein 3000 structural genomics project in Japan PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2008, 72, 1333-1351 9
2012 A Patil, S Teraguchi, H Dinh, K Nakai, DM Standley Functional annotation of intrinsically disordered domains by their amino acid content using IDD navigator BIOCOMPUTING, 2012, 2012, 164-175 7
2011 S Liang, C Zhang, DM Standley Protein loop selection using orientation‐dependent force fields derived by parameter optimization PROTEINS: STRUCTURE, FUNCTION, AND BIOINFORMATICS, 2011, 79, 2260-2267 7
2010 RJ Milewski, Y Kumagai, K Fujita, DM Standley, NI Smith Automated processing of label-free Raman microscope images of macrophage cells with standardized regression for high-throughput analysis IMMUNOME RESEARCH, 2010, 6, 1-10 7
2019 AA Koesoema, Y Sugiyama, Z Xu, DM Standley, M Senda, T Senda, ... Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 103 (23-24), 2019, 9543-9553 6
2019 T Mino, N Iwai, M Endo, K Inoue, K Akaki, F Hia, T Uehata, T Emura, ... Translation-dependent unwinding of stem–loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs NUCLEIC ACIDS RESEARCH, 2019, 47, 8838-8859 6
2017 J Hirano, T Okamoto, Y Sugiyama, T Suzuki, S Kusakabe, M Tokunaga, ... Characterization of SPP inhibitors suppressing propagation of HCV and protozoa PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES 114 (50), E10782-, 2017, 10791 5
2017 B Nosirov, J Billaud, A Vandenbon, D Diez, E Wijaya, KJ Ishii, ... Mapping circulating serum miRNAs to their immune-related target mRNAs ADVANCES AND APPLICATIONS IN BIOINFORMATICS AND CHEMISTRY: AABC, 2017, 10, 1-1 5
2012 DM Standley, M van der Giezen Modeling the alternative oxidase from the human pathogen Blastocystis using automated hybrid structural template assembly RES. REP. BIOCHEM, 2012, 2, 1-8 5
2019 AA Koesoema, Y Sugiyama, KT Sriwong, Z Xu, S Verina, DM Standley, ... Reversible control of enantioselectivity by the length of ketone substituent in biocatalytic reduction APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 103 (23-24), 2019, 9529-9541 4
2015 D Hall, S Li, K Yamashita, R Azuma, JA Carver, DM Standley RNA–LIM: A novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure ANALYTICAL BIOCHEMISTRY, 2015, 472, 52-61 4
2020 AA Koesoema, DM Standley, T Senda, T Matsuda Impact and relevance of alcohol dehydrogenase enantioselectivities on biotechnological applications APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 2020, 1-13 3
2019 Z Xu, S Li, J Rozewicki, K Yamashita, S Teraguchi, T Inoue, R Shinnakasu, ... Functional clustering of B cell receptors using sequence and structural features MOLECULAR SYSTEMS DESIGN & ENGINEERING, 2019, 4, 769-778 3
2014 D Hall, S Li, K Yamashita, R Azuma, JA Carver, DM Standley A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein BIOPHYSICAL CHEMISTRY, 2014, 190, 50-55 3
2013 A Vandenbon, Y Kumagai, S Teraguchi, KM Amada, S Akira, DM Standley A Parzen window-based approach for the detection of locally enriched transcription factor binding sites BMC BIOINFORMATICS, 2013, 14, 26-26 3
2011 Y Yonezawa, DM Standley, H Nakamura Degree of pyramidality governs the height and peak position of the free-energy-barrier for the cis–trans isomerization of N-Methylacetamide CHEMICAL PHYSICS LETTERS 503 (1-3), 2011, 139-144 3
2020 H Metwally, T Tanaka, S Li, G Parajuli, S Kang, H Hanieh, S Hashimoto, ... Noncanonical STAT1 phosphorylation expands its transcriptional activity into promoting LPS-induced IL-6 and IL-12p40 production SCIENCE SIGNALING, 2020, 13 2
2020 K Fukushima, T Satoh, F Sugihara, Y Sato, T Okamoto, Y Mitsui, S Yoshio, ... Dysregulated Expression of the Nuclear Exosome Targeting Complex Component Rbm7 in Nonhematopoietic Cells Licenses the Development of Fibrosis IMMUNITY 52 (3), 542-556., 2020, 13 2
2020 AA Koesoema, DM Standley, S Ohshima, M Tamura, T Matsuda Control of enantioselectivity in the enzymatic reduction of halogenated acetophenone analogs by substituent positions and sizes TETRAHEDRON LETTERS, 2020, 151820 2
2020 AA Koesoema, DM Standley, M Tamura, T Matsuda Access to both enantiomers of substituted 2-tetralol analogs by a highly enantioselective reductase TETRAHEDRON LETTERS, 2020, 151682 2
2020 Y Lee, H Yamada, A Pradipta, JS Ma, M Okamoto, H Nagaoka, ... Initial phospholipid-dependent Irgb6 targeting to Toxoplasma gondii vacuoles mediates host defense LIFE SCIENCE ALLIANCE, 2020, 3 2
2019 H Fukuda, S Li, L Sardo, JL Smith, K Yamashita, AD Sarca, K Shirakawa, ... Structural Determinants of the APOBEC3G N-terminal domain for HIV-1 RNA association FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, 2019, 9, 129-129 2
2019 S Li, J Wilamowski, S Teraguchi, FJ van Eerden, J Rozewicki, A Davila, ... Structural modeling of lymphocyte receptors and their antigens IN VITRO DIFFERENTIATION OF T-CELLS, 2019, 207-229 2
2014 A Vandenbon, S Teraguchi, O Takeuchi, Y Suzuki, DM Standley Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation BMC GENOMICS 15 (S10), S, 2014, 4 2
2011 AR Kinjo, Y Kumagai, H Dinh, O Takeuchi, DM Standley Functional characterization of protein domains common to animal viruses and mouse BMC GENOMICS, 2011, 12, 1-10 2
2013 E KANAMORI, Y MURAKAMI, JOY SARMIENTO, S LIANG, ... PREDICTION OF PROTEIN-PROTEIN COMPLEX STRUCTURES BIOMOLECULAR FORMS AND FUNCTIONS: A CELEBRATION OF 50 YEARS OF THE …, 2013 1
2008 DM Standley, AR Kinjo, M Lis, M van der Giezen, H Nakamura Structure-based functional annotation of protein sequences guided by comparative models THE SECOND INTERNATIONAL SYMPOSIUM ON OPTIMIZATION AND SYSTEMS BIOLOGY …, 2008 1
2020 S Teraguchi, DS Saputri, MA Llamas-Covarrubias, A Davila, D Diez, ... Methods for sequence and structural analysis of B and T cell receptor repertoires COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 2020 0
2020 C Ono, T Fukuhara, S Li, J Wang, A Sato, T Izumi, Y Fauzyah, ... Various miRNAs compensate the role of miR-122 on HCV replication PLOS PATHOGENS, 2020, 16, 1008308 0
2020 DS Saputri, S Li, FJ Van Eerden, J Rozewicki, Z Xu, HS Ismanto, A Davila, ... Flexible, functional and familiar: characteristics of SARS-CoV-2 spike protein evolution FRONTIERS IN MICROBIOLOGY, 2020, 11, 2112-2112 0
2020 C Ono, T Fukuhara, S Li, J Wang, A Sato, T Izumi, Y Fauzyah, ... Various miRNAs are involved in efficient HCV replication BIORXIV, 2020 0
2019 AA Koesoema, Y Sugiyama, Z Xu, DM Standley, M Senda, T Senda, ... 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 103 (23-24), 2019, 9555 0
2019 DM Standley, JDO Nieri, S Li, D Schritt, K Yamashita Immunological entity clustering software US PATENT APP. 16/333,875, 2019 0
2017 D Schritt, K Katoh, S Li, DM Standley Modeling Biocatalysts FUTURE DIRECTIONS IN BIOCATALYSIS, 2017, 385-398 0
2016 K Takeda, S Sakakibara, D Motooka, S Nakamura, K Yamashita, ... Identification of Nasal Resident Bacteria as Causative Allergens in Eosinophilic Chronic Rhinosinusitis EUROPEAN JOURNAL OF IMMUNOLOGY, 2016, 46, 1114-1114 0
2016 S Sakakibara, T Arimori, K Yamashita, H Jinzai, D Motooka, S Nakamura, ... Antigen-specific maturation of autoantibodies in systemic lupus erythematosus EUROPEAN JOURNAL OF IMMUNOLOGY, 2016, 46, 313-314 0
2014 DM Standley 2SCP-07 Intrinsic disorder mediates cooperative signal transduction in STIM1 (構造バイオインフォマティクスによる蛋白質機能予測・解析, シンポジウム, 第 52 回日本生物物理学会年会 (2014 年度)) 生物物理 54 (1), S, 2014, 133 0
2013 Y Furukawa, S Teraguchi, T Ikegami, Y Suenari, O Dagliyan, L Jin, D Hall, ... Calcium-dependent Unfolding of the STIM1 EF-SAM Domain Drives Cooperative Calcium Influx: 362 PROTEIN SCIENCE, 2013, 22, 141-142 0
2013 AP Hutchins, D Diez, D Miranda-Saavedra The IL-10/STAT3-mediated anti-inflammatory response: recent developments and future challenges BRIEFINGS IN FUNCTIONAL GENOMICS, 2013, 12, 489-498 213
2016 W Nakai, T Yoshida, D Diez, Y Miyatake, T Nishibu, N Imawaka, K Naruse, ... A novel affinity-based method for the isolation of highly purified extracellular vesicles SCIENTIFIC REPORTS, 2016, 6, 33935-33935 131
2010 B Morte, A Ceballos, D Diez, C Grijota-Martínez, AM Dumitrescu, ... Thyroid hormone-regulated mouse cerebral cortex genes are differentially dependent on the source of the hormone: a study in monocarboxylate transporter-8-and deiodinase-2 … ENDOCRINOLOGY, 2010, 151, 2381-2381 105
2009 CE Wheelock, ÅM Wheelock, S Kawashima, D Diez, M Kanehisa, ... Systems biology approaches and pathway tools for investigating cardiovascular disease MOL. BIOSYST., 2009, 5, 588-602 103
2010 D Diez, ÅM Wheelock, S Goto, JZ Haeggström, G Paulsson-Berne, ... The use of network analyses for elucidating mechanisms in cardiovascular disease MOL. BIOSYST., 2010, 6, 289-304 92
2015 I Bahrini, J Song, D Diez, R Hanayama Neuronal exosomes facilitate synaptic pruning by up-regulating complement factors in microglia SCIENTIFIC REPORTS, 2015, 5, 7989-7989 88
2008 D Diez, C Grijota-Martinez, P Agretti, G De Marco, M Tonacchera, ... Thyroid hormone action in the adult brain: gene expression profiling of the effects of single and multiple doses of triiodo-L-thyronine in the rat striatum ENDOCRINOLOGY, 2008, 149, 3989-3989 75
2010 B Morte, D Díez, E Ausó, MM Belinchón, P Gil-Ibáñez, C Grijota-Martínez, ... Thyroid hormone regulation of gene expression in the developing rat fetal cerebral cortex: prominent role of the Ca2+/calmodulin-dependent protein kinase IV pathway ENDOCRINOLOGY, 2010, 151, 810-810 69
2013 AP Hutchins, D Diez, Y Takahashi, S Ahmad, R Jauch, ML Tremblay, ... Distinct transcriptional regulatory modules underlie STAT3’s cell type-independent and cell type-specific functions NUCLEIC ACIDS RESEARCH, 2013, 41, 2155-70 68
2011 C Grijota-Martínez, D Díez, G Morreale de Escobar, J Bernal, B Morte Lack of action of exogenously administered T3 on the fetal rat brain despite expression of the monocarboxylate transporter 8 ENDOCRINOLOGY, 2011, 152, 1713-1721 68
2013 AP Hutchins, S Liu, D Diez, D Miranda-Saavedra The repertoires of ubiquitinating and deubiquitinating enzymes in eukaryotic genomes MOLECULAR BIOLOGY AND EVOLUTION, 2013, 30, 1172-1187 56
2014 D Diez, A Agustí, CE Wheelock Network analysis in the investigation of chronic respiratory diseases. From basics to application AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, 2014, 190, 981-988 46
2014 R Stojnic, D Diez PWMEnrich: PWM enrichment analysis R PACKAGE VERSION 4 (0), 10., 2014, 18129 30
2011 D Díez, F Sanchez-Jimenez, JAG Ranea Evolutionary expansion of the Ras switch regulatory module in eukaryotes NUCLEIC ACIDS RESEARCH, 2011, 39, 5526-5537 30
2013 AP Hutchins, D Diez, D Miranda-Saavedra Genomic and computational approaches to dissect the mechanisms of STAT3’s universal and cell type-specific functions JAK-STAT, 2013, 2, 25097 26
2014 D Diez, AP Hutchins, D Miranda-Saavedra Systematic identification of transcriptional regulatory modules from protein–protein interaction networks NUCLEIC ACIDS RESEARCH 42 (1), E6-, 2014, 6 25
2012 D Diez, S Goto, JV Fahy, DJ Erle, PG Woodruff, ÅM Wheelock, ... Network analysis identifies a putative role for the PPAR and type 1 interferon pathways in glucocorticoid actions in asthmatics BMC MEDICAL GENOMICS, 2012, 5, 27-27 23
2007 D Diez, R Alvarez, A Dopazo Codelink: an R package for analysis of GE healthcare gene expression bioarrays BIOINFORMATICS, 2007, 23, 1168-1168 23
2008 CN Hayes, D Diez, N Joannin, W Honda, M Kanehisa, M Wahlgren, ... varDB: a pathogen-specific sequence database of protein families involved in antigenic variation BIOINFORMATICS, 2008, 24, 2564-2565 21
2009 L Folkersen, D Diez, CE Wheelock, JZ Haeggström, S Goto, P Eriksson, ... GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome BIOINFORMATICS, 2009, 25, 1978-1979 13
2010 D Diez, N Hayes, N Joannin, J Normark, M Kanehisa, M Wahlgren, ... varDB: A database of antigenic variant sequences—Current status and future prospects ACTA TROPICA, 2010, 114, 144-151 4
2016 A Bueno, I Morilla, D Diez, AA Moya-Garcia, J Lozano, JAG Ranea Exploring the interactions of the RAS family in the human protein network and their potential implications in RAS-directed therapies ONCOTARGET, 2016, 7, 75810-75810 3
2011 GM Kirwan, D Diez, JZ Haeggström, S Goto, CE Wheelock Systems Biology Approaches for Investigating the Relationship Between Lipids and Cardiovascular Disease CURRENT CARDIOVASCULAR RISK REPORTS, 2011, 1-10 2
2009 CN Hayes, D Diez, N Joannin, M Kanehisa, M Wahlgren, CE Wheelock, ... Tools for investigating mechanisms of antigenic variation: new extensions to varDB GENOME INFORMATICS 2009: GENOME INFORMATICS SERIES VOL., 2009, 23, 46-59 1
2020 A Vandenbon, D Diez A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data NATURE COMMUNICATIONS, 2020, 11, 1-10 0
2015 D Diez rTRMui: a shiny user interface for the identification of transcriptional regulatory modules , 2015 0
2014 D Diez rTRM: an R package for the identification of transcription regulatory modules (TRMs) , 2014 0
2013 D Diez Codelink Legacy: the old Codelink class , 2013 0
2014 HI Ingólfsson, MN Melo, FJ Van Eerden, C Arnarez, CA Lopez, ... Lipid organization of the plasma membrane JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2014, 136, 14554-14559 477
2013 CA López, Z Sovova, FJ van Eerden, AH de Vries, SJ Marrink Martini force field parameters for glycolipids JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2013, 9, 1694-1708 128
2015 FJ van Eerden, DH de Jong, AH de Vries, TA Wassenaar, SJ Marrink Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations BIOCHIMICA ET BIOPHYSICA ACTA (BBA)-BIOMEMBRANES, 2015, 1848, 1319-1330 92
2017 FJ Van Eerden, MN Melo, PWJM Frederix, X Periole, SJ Marrink Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex NATURE COMMUNICATIONS, 2017, 8, 1-8 40
2017 B Liu, C Åberg, FJ van Eerden, SJ Marrink, B Poolman, AJ Boersma Design and properties of genetically encoded probes for sensing macromolecular crowding BIOPHYSICAL JOURNAL, 2017, 112, 1929-1939 31
2017 FJ Van Eerden, T Van Den Berg, PWJM Frederix, DH De Jong, X Periole, ... Molecular dynamics of photosystem II embedded in the thylakoid membrane THE JOURNAL OF PHYSICAL CHEMISTRY B, 2017, 121, 3237-3249 25
2017 FJ Van Eerden, MN Melo, PWJM Frederix, SJ Marrink Prediction of thylakoid lipid binding sites on photosystem II BIOPHYSICAL JOURNAL, 2017, 113, 2669-2681 17
2018 R Friedman, S Khalid, C Aponte-Santamaría, E Arutyunova, M Becker, ... Understanding conformational dynamics of complex lipid mixtures relevant to biology THE JOURNAL OF MEMBRANE BIOLOGY 251 (5-6), 2018, 609-631 14
2016 FJ van Eerden Photosynthesis in Silico: Simulations of Photosystem II and the Thylakoid Membrane RIJKSUNIVERSITEIT GRONINGEN, 2016 0
2014 FJ van Eerden, DH de Jong, X Periole, SJ Marrink Simulation of Photosystem Ii Dynamics in the Thylakoid Membrane BIOPHYSICAL JOURNAL 106 (2), 181A, 2014 0
2019 K Katoh, J Rozewicki, KD Yamada MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization BRIEFINGS IN BIOINFORMATICS, 2019, 20, 1160-1166 1262
2008 K Katoh, H Toh Recent developments in the MAFFT multiple sequence alignment program BRIEFINGS IN BIOINFORMATICS, 2008, 9, 286-298 3150
2009 K Katoh, G Asimenos, H Toh Multiple alignment of DNA sequences with MAFFT BIOINFORMATICS FOR DNA SEQUENCE ANALYSIS, 2009, 39-64 1064
2010 K Katoh, H Toh Parallelization of the MAFFT multiple sequence alignment program BIOINFORMATICS, 2010, 26, 1899-1900 605
2008 K Katoh, H Toh Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework BMC BIOINFORMATICS, 2008, 9, 212-212 527
2015 I Sela, H Ashkenazy, K Katoh, T Pupko GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters NUCLEIC ACIDS RESEARCH 43 (W1), W7-W, 2015, 14 359
2013 S Kuraku, CM Zmasek, O Nishimura, K Katoh aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity NUCLEIC ACIDS RESEARCH 41 (W1), W22-W, 2013, 28 224
2018 T Nakamura, KD Yamada, K Tomii, K Katoh Parallelization of MAFFT for large-scale multiple sequence alignments BIOINFORMATICS, 2018, 1, 3-3 176
2016 KD Yamada, K Tomii, K Katoh Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees BIOINFORMATICS, 2016, 32, 3246-3251 145
2012 K Katoh, MC Frith Adding unaligned sequences into an existing alignment using MAFFT and LAST BIOINFORMATICS, 2012, 28, 3144-3146 144
2007 K Katoh, H Toh PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences BIOINFORMATICS, 2007, 23, 372-374 90
2009 CB Do, K Katoh Protein multiple sequence alignment FUNCTIONAL PROTEOMICS, 2009, 379-413 84
2008 M Koyanagi, T Nagata, K Katoh, S Yamashita, F Tokunaga Molecular evolution of arthropod color vision deduced from multiple opsin genes of jumping spiders JOURNAL OF MOLECULAR EVOLUTION, 2008, 66, 130-137 59
2019 J Sone, S Mitsuhashi, A Fujita, T Mizuguchi, K Hamanaka, K Mori, H Koike, ... Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease NATURE GENETICS, 2019, 51, 1215-1221 49
2007 G Sasaki, K Katoh, N Hirose, H Suga, K Kuma, T Miyata, ZH Su Multiple receptor-like kinase cDNAs from liverwort Marchantia polymorpha and two charophycean green algae, Closterium ehrenbergii and Nitella axillaris: extensive gene … GENE 401 (1-2), 2007, 135-144 42
2015 N Fukushima, S Ishii, T Tsujiuchi, N Kagawa, K Katoh Comparative analyses of lysophosphatidic acid receptor-mediated signaling CELLULAR AND MOLECULAR LIFE SCIENCES, 2015, 72, 2377-2394 27
2020 H Nakamura, H Doi, S Mitsuhashi, S Miyatake, K Katoh, MC Frith, T Asano, ... Long-read sequencing identifies the pathogenic nucleotide repeat expansion in RFC1 in a Japanese case of CANVAS JOURNAL OF HUMAN GENETICS, 2020, 65, 475-480 3
2014 Y Morimoto, S Ishii, J Ishibashi, K Katoh, T Tsujiuchi, N Kagawa, ... Functional lysophosphatidic acid receptors expressed in Oryzias latipes GENE, 2014, 551, 189-200 3
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2014 K Yamada, K Katoh, K Tomii 1P267 application of novel amino acid substitution matrix, MIQS, to the mafft multiple sequence aligner (22c. Bioinformatics: Comparative genomics, poster, the 52nd annual … SEIBUTSU BUTSURI 54 (SUPPLEMENT1-2), S, 2014, 185 1
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2019 S Mitsuhashi, S Ohori, K Katoh, MC Frith, N Matsumoto A method for complete characterization of complex germline rearrangements from long DNA reads MEDRXIV, 2019, 19006379 0
2015 K Takahashi, K Katoh, N Iwabe Phylogenetic position of ctenophores and early evolution of metazoans GENES & GENETIC SYSTEMS, 2015, 90, 394-394 0
2014 K Takahashi, K Katoh, N Iwabe Molecular phylogenetic analyses of deuterostomes: evolutionary position of cephalochordates GENES & GENETIC SYSTEMS, 2014, 89, 312-312 0
2013 MA Llamas-Covarrubias, Y Valle, R Bucala, RE Navarro-Hernández, ... Macrophage migration inhibitory factor (MIF): genetic evidence for participation in early onset and early stage rheumatoid arthritis CYTOKINE, 2013, 61, 759-765 57
2012 MA Llamas-Covarrubias, Y Valle, RE Navarro-Hernández, ... Serum levels of macrophage migration inhibitory factor are associated with rheumatoid arthritis course RHEUMATOLOGY INTERNATIONAL, 2012, 32, 2307-2311 32
2014 JR Villafán-Bernal, MA Llamas-Covarrubias, JF Muñoz-Valle, ... A cut-point value of uncarboxylated to carboxylated index is associated with glycemic status markers in type 2 diabetes JOURNAL OF INVESTIGATIVE MEDICINE, 2014, 62, 33-36 18
2017 Z Reyes-Castillo, JF Muñoz-Valle, MA Llamas-Covarrubias Clinical and immunological aspects of anti-peptidylarginine deiminase type 4 (anti-PAD4) autoantibodies in rheumatoid arthritis AUTOIMMUNITY REVIEWS, 2017 9
2011 JR Padilla-Gutiérrez, CA Palafox-Sánchez, Y Valle, G Orozco-Barocio, ... Plasminogen activator inhibitor-1 polymorphisms (− 844 G> A and HindIII C> G) in systemic lupus erythematosus: association with clinical variables CLINICAL AND EXPERIMENTAL MEDICINE, 2011, 11, 11-17 7
2017 F Casillas-Muñoz, Y Valle, JF Muñoz-Valle, DE Martínez-Fernández, ... APOA1 and APOB polymorphisms and apolipoprotein concentrations as biomarkers of risk in acute coronary syndrome: Relationship with lipid-lowering therapy effectiveness. MEDICINA CLINICA, 2017 6
2011 AJL Brambila-Tapia, JI Gámez-Nava, M Salazar-Páramo, JF Muñoz-Valle, ... Increased CD28 serum levels are not associated with specific clinical activity in systemic lupus erythematosus RHEUMATOLOGY INTERNATIONAL, 2011, 31, 1321-1324 4
2014 LA González-Hernández, MA Llamas-Covarrubias, ... Nuevas terapias antirretrovirales en la infección por VIH REVISTA MEDICA MD, 2014, 5, 143-149 3
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2015 IM Llamas-Covarrubias, L del Sagrario Ruiz-Solorio, ... Efectos de la grelina y la obestatina en la salud y la enfermedad REVISTA MEDICA MD, 2015, 6, 196-208 1
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2013 A Lopez-Iniguez, MA Llamas-Covarrubias, G Navarro-Blackaller, ... Rectal Plasmablastic Lymphoma in HIV/AIDS: Two Cases WORLD JOURNAL OF ONCOLOGY, 2013, 4, 54-54 0
2010 T Kloskowski, J Olkowska, A Nazlica, T Drewa The influence of ciprofloxacin on hamster ovarian cancer cell line CHO AA8 ACTA POL PHARM, 2010, 67, 345-9 21
2007 E Nakano, S Teraguchi, WY Wen Drag force, jet quenching, and an AdS/QCD model PHYSICAL REVIEW D, 2007, 75, 85016-85016 78
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2007 S Teraguchi Reformulation of boundary string field theory in terms of boundary state JOURNAL OF HIGH ENERGY PHYSICS, 2007, 2007, 17-17 5
2018 KZ Latt, K Honda, M Thiri, Y Hitomi, Y Omae, H Sawai, Y Kawai, ... Identification of a two-SNP PLA2R1 Haplotype and HLA-DRB1 Alleles as primary risk associations in idiopathic membranous nephropathy SCIENTIFIC REPORTS, 2018, 8, 1-9 4
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2019 T Yamaguchi, S Teraguchi, C Furusawa, H Machiyama, TM Watanabe, ... Theoretical modeling reveals that regulatory T cells increase T-cell interaction with antigen-presenting cells for stable immune tolerance INTERNATIONAL IMMUNOLOGY, 2019, 31, 743-753 2
2016 S Teraguchi, Y Kumagai Probabilistic Nearest Neighbor Estimation of Diffusion Constants from Single Molecular Measurement without Explicit Tracking ARXIV PREPRINT ARXIV:1601., 2016, 756 1
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2013 S Li, DW Heermann Transcriptional regulatory network shapes the genome structure of Saccharomyces cerevisiae NUCLEUS, 2013, 4, 216-228 9
2013 S Li, DW Heermann Using chimaeric expression sequence tag as the reference to identify three-dimensional chromosome contacts DNA RESEARCH, 2013, 20, 45-53 2
2008 BK Zolman, N Martinez, A Millius, AR Adham, B Bartel Identification and characterization of Arabidopsis indole-3-butyric acid response mutants defective in novel peroxisomal enzymes GENETICS, 2008, 180, 237-251 128
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