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 24512
2008 K Katoh, H Toh Recent developments in the MAFFT multiple sequence alignment program BRIEFINGS IN BIOINFORMATICS, 2008, 9, 286-298 3483
2017 K Katoh, J Rozewicki, KD Yamada MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization BRIEFINGS IN BIOINFORMATICS, 2017, 20, 1160-1166 3385
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 3385
2009 K Katoh, G Asimenos, H Toh Multiple alignment of DNA sequences with MAFFT BIOINFORMATICS FOR DNA SEQUENCE ANALYSIS, 2009, 39-64 1274
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 1052
2010 K Katoh, H Toh Parallelization of the MAFFT multiple sequence alignment program BIOINFORMATICS, 2010, 26, 1899-1900 750
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 664
2008 K Katoh, H Toh Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework BMC BIOINFORMATICS, 2008, 9, 1-13 612
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, 14 579
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 575
2018 T Nakamura, KD Yamada, K Tomii, K Katoh Parallelization of MAFFT for large-scale multiple sequence alignments BIOINFORMATICS, 2018, 1, 3-3 462
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, 28 443
2014 K Katoh, DM Standley MAFFT: iterative refinement and additional methods MULTIPLE SEQUENCE ALIGNMENT METHODS, 2014, 131-146 366
2016 K Katoh, DM Standley A simple method to control over-alignment in the MAFFT multiple sequence alignment program BIOINFORMATICS, 2016, 32, 1933-1942 341
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, 489-498 325
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 287
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, 1-11 285
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 276
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 273
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 269
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, 10 257
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 252
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 227
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 203
2012 K Katoh, MC Frith Adding unaligned sequences into an existing alignment using MAFFT and LAST BIOINFORMATICS, 2012, 28, 3144-3146 196
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 162
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, 1-8 158
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, 237-251 151
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, 289-302 146
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, 1-6 144
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, 460 137
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, 151-159 137
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, 1-15 127
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 118
2021 Y Liu, WT Soh, J Kishikawa, M Hirose, EE Nakayama, S Li, M Sasai, ... An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies CELL 184 (13), 3452-3466., 2021, 18 116
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 116
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 116
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, 588-602 109
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 108
2007 K Katoh, H Toh PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences BIOINFORMATICS, 2007, 23, 372-374 107
2009 S Li, H Li, M Li, Y Shyr, L Xie, Y Li Improved prediction of lysine acetylation by support vector machines PROTEIN AND PEPTIDE LETTERS, 2009, 16, 977-983 105
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 100
2009 CB Do, K Katoh Protein multiple sequence alignment FUNCTIONAL PROTEOMICS, 2009, 379-413 99
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 97
2012 M Fritsche, S Li, DW Heermann, PA Wiggins A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation NUCLEIC ACIDS RESEARCH, 2012, 40, 972-980 86
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 82
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 82
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 81
2007 E Nakano, S Teraguchi, WY Wen Drag force, jet quenching, and an AdS/QCD model PHYSICAL REVIEW D, 2007, 75, 85016-85016 81
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 77
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 73
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 73
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 72
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 72
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 71
2009 K Katoh, G Asimenos, H Toh, D Posada Bioinformatics for DNA sequence analysis METHODS MOL. BIOL, 2009, 537, 39-64 64
2010 A Millius, OD Weiner Manipulation of neutrophil-like HL-60 cells for the study of directed cell migration LIVE CELL IMAGING, 2010, 147-158 63
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 63
2009 A Millius, SN Dandekar, AR Houk, OD Weiner Neutrophils establish rapid and robust WAVE complex polarity in an actin-dependent fashion CURRENT BIOLOGY, 2009, 19, 253-259 61
2009 A Millius, OD Weiner Chemotaxis in neutrophil-like HL-60 cells CHEMOTAXIS, 2009, 167-177 61
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, 899-910 61
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 59
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 57
2012 A Millius, N Watanabe, OD Weiner Diffusion, capture and recycling of SCAR/WAVE and Arp2/3 complexes observed in cells by single-molecule imaging JOURNAL OF CELL SCIENCE, 2012, 125, 1165-1176 56
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 56
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 54
2011 S Liang, D Zheng, C Zhang, DM Standley Fast and accurate prediction of protein side-chain conformations BIOINFORMATICS, 2011, 27, 2913-2914 51
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, 1-19 51
2016 A Vandenbon, VH Dinh, N Mikami, Y Kitagawa, S Teraguchi, N Ohkura, ... Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES 113 (17), E2393-, 2016, 2402 51
2007 DM Standley, H Toh, H Nakamura ASH structure alignment package: sensitivity and selectivity in domain classification BMC BIOINFORMATICS, 2007, 8, 1-8 50
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 50
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 49
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 49
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 47
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 47
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 46
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 46
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 45
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 41
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 39
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 39
2014 R Stojnic, D Diez PWMEnrich: PWM enrichment analysis R PACKAGE VERSION 4 (0), 10., 2014, 18129 39
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 38
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 37
2011 M Fernandez, Y Kumagai, DM Standley, A Sarai, K Mizuguchi, S Ahmad Prediction of dinucleotide-specific RNA-binding sites in proteins BMC BIOINFORMATICS, 2011, 12, 1-10 37
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 36
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 36
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 35
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 35
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 34
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 34
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 32
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, 1-13 32
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 31
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 30
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 30
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 29
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 29
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 29
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, 2018, 251, 609-631 29
2017 A Millius, HR Ueda Systems biology-derived discoveries of intrinsic clocks FRONTIERS IN NEUROLOGY, 2017, 8, 25-25 28
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 28
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 27
2021 N Singh, NV Frey, B Engels, DM Barrett, O Shestova, P Ravikumar, ... Antigen-independent activation enhances the efficacy of 4-1BB-costimulated CD22 CAR T cells NATURE MEDICINE, 2021, 27, 842-850 27
2011 M Ito, S Kuwakino, N Maekawa, S Moriyama, K Takahashi, K Takei, ... E 6 grand unified theory with three generations from heterotic string theory PHYSICAL REVIEW D, 2011, 83, 91703-91703 26
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 25
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 25
2007 D Diez, R Alvarez, A Dopazo Codelink: an R package for analysis of GE healthcare gene expression bioarrays BIOINFORMATICS, 2007, 23, 1168-1168 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 25
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 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
2020 H Nakamura, 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 24
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 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 23
2016 R Ikebuchi, S Teraguchi, A Vandenbon, T Honda, FHW Shand, ... A rare subset of skin-tropic regulatory T cells expressing Il10/Gzmb inhibits the cutaneous immune response SCIENTIFIC REPORTS, 2016, 6, 1-12 23
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 22
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, 1-10 22
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 21
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 21
2021 Z Reyes-Castillo, E Valdés-Miramontes, M Llamas-Covarrubias, ... Troublesome friends within us: The role of gut microbiota on rheumatoid arthritis etiopathogenesis and its clinical and therapeutic relevance CLINICAL AND EXPERIMENTAL MEDICINE, 2021, 21, 1-13 21
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 20
2020 AA Koesoema, DM Standley, T Senda, T Matsuda Impact and relevance of alcohol dehydrogenase enantioselectivities on biotechnological applications APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 2020, 104, 2897-2909 19
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 19
2021 Y Liu, N Arase, J Kishikawa, M Hirose, S Li, A Tada, S Matsuoka, ... The SARS-CoV-2 Delta variant is poised to acquire complete resistance to wild-type spike vaccines BIORXIV, 2021 18
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 13 (624), EAAY, 2020, 574 18
2021 A Srivathsan, L Lee, K Katoh, E Hartop, SN Kutty, J Wong, D Yeo, R Meier ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone BMC BIOLOGY, 2021, 19, 1-21 18
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 17
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 16
2020 M Lei, D Liang, Y Yang, S Mitsuhashi, K Katoh, N Miyake, MC Frith, L Wu, ... Long-read DNA sequencing fully characterized chromothripsis in a patient with Langer–Giedion syndrome and Cornelia de Lange syndrome-4 JOURNAL OF HUMAN GENETICS, 2020, 65, 667-674 16
2018 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, 2018, 17, 94-102 16
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 15
2021 A Srivathsan, L Lee, K Katoh, E Hartop, SN Kutty, J Wong, D Yeo, R Meier MinION barcodes: biodiversity discovery and identification by everyone, for everyone BIORXIV, 2021 15
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 14
2016 Y Kumagai, A Vandenbon, S Teraguchi, S Akira, Y Suzuki Genome-wide map of RNA degradation kinetics patterns in dendritic cells after LPS stimulation facilitates identification of primary sequence and secondary structure motifs in mRNAs BMC GENOMICS, 2016, 17, 127-140 14
2012 A Vandenbon, Y Kumagai, S Akira, DM Standley A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription BMC GENOMICS, 2012, 13, 1-15 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 13
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
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 12
2011 M Ito, S Kuwakino, N Maekawa, S Moriyama, K Takahashi, K Takei, ... Heterotic E 6 GUTs and partition functions JOURNAL OF HIGH ENERGY PHYSICS, 2011, 2011, 1-42 12
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, 61, 151820-151820 11
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, 2019, 103, 9543-9553 11
2020 S Mitsuhashi, S Ohori, K Katoh, MC Frith, N Matsumoto A pipeline for complete characterization of complex germline rearrangements from long DNA reads GENOME MEDICINE, 2020, 12, 1-17 11
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, 18, 2000-2011 10
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 10
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 10
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 10
2013 S Li, DW Heermann Transcriptional regulatory network shapes the genome structure of Saccharomyces cerevisiae NUCLEUS, 2013, 4, 216-228 10
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, 2019, 103, 9529-9541 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, 2010, 11, 1-11 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
2019 A Millius, KL Ode, HR Ueda A period without PER: understanding 24-hour rhythms without classic transcription and translation feedback loops F1000RESEARCH, 2019, 8 8
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 8
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 8
2021 MC Frith, S Mitsuhashi, K Katoh lamassemble: multiple alignment and consensus sequence of long reads MULTIPLE SEQUENCE ALIGNMENT, 2021, 135-145 8
2020 JI Aguayo-Ruiz, TA García-Cobián, S Pascoe-González, ... Effect of supplementation with vitamins D3 and K2 on undercarboxylated osteocalcin and insulin serum levels in patients with type 2 diabetes mellitus: A randomized, double … DIABETOLOGY & METABOLIC SYNDROME, 2020, 12, 1-10 8
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 8
2008 E Nakano, S Teraguchi, W Wen Drag Force, Jet Quenching, and AdS/QCD , 2008 8
2020 Y Liu, WT Soh, A Tada, A Arakawa, S Matsuoka, EE Nakayama, S Li, ... An infectivity-enhancing site on the SARS-CoV-2 spike protein is targeted by COVID-19 patient antibodies BIORXIV, 2020 7
2019 S Li, J Wilamowski, S Teraguchi, FJ Eerden, J Rozewicki, A Davila, Z Xu, ... Structural modeling of lymphocyte receptors and their antigens IN VITRO DIFFERENTIATION OF T-CELLS, 2019, 207-229 7
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
2020 EA Rivera-León, MA Llamas-Covarrubias, S Sánchez-Enríquez, ... Leu72Met polymorphism of GHRL gene decreases susceptibility to type 2 diabetes mellitus in a Mexican population BMC ENDOCRINE DISORDERS, 2020, 20, 1-5 7
2017 IM Llamas-Covarrubias, MA Llamas-Covarrubias, E Martinez-López, ... Association of A-604G ghrelin gene polymorphism and serum ghrelin levels with the risk of obesity in a mexican population MOLECULAR BIOLOGY REPORTS, 2017, 44, 289-293 7
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
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 6
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 6
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 6
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 6
2021 J Hirano, S Yoshio, Y Sakai, L Songling, T Suzuki, Y Itoh, H Zhang, ... Hepatitis C virus modulates signal peptide peptidase to alter host protein processing PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES, 2021, 118, 2026184118 5
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 5
2012 DM Standley, M van der Giezen Modeling the alternative oxidase from the human pathogen Blastocystis using automated hybrid structural template assembly RESEARCH AND REPORTS IN BIOCHEMISTRY, 2012, 2, 1-8 5
2021 PK Chang, TD Chang, K Katoh Deciphering the origin of Aspergillus flavus NRRL21882, the active biocontrol agent of Afla‐Guard® LETTERS IN APPLIED MICROBIOLOGY, 2021, 72, 509-516 5
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 5
2019 LA Hernández-Palma, S García-Arellano, R Bucala, ... Functional MIF promoter haplotypes modulate Th17-related cytokine expression in peripheral blood mononuclear cells from control subjects and rheumatoid arthritis patients CYTOKINE, 2019, 115, 89-96 5
2019 Y Ruiz‐Noa, J Hernández‐Bello, MA Llamas‐Covarrubias, ... PTPN22 1858C>T polymorphism is associated with increased CD154 expression and higher CD4+ T cells percentage in rheumatoid arthritis patients JOURNAL OF CLINICAL LABORATORY ANALYSIS, 2019, 33, 22710 5
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 5
2007 S Teraguchi Reformulation of boundary string field theory in terms of boundary state JOURNAL OF HIGH ENERGY PHYSICS, 2007, 2007, 17-17 5
2019 S Shi, A Millius, HR Ueda Genes and Ion Channels in the Circadian and Homeostatic Regulation of Sleep HANDBOOK OF BEHAVIORAL NEUROSCIENCE, 2019, 30, 181-193 4
2021 N Ikemura, S Taminishi, T Inaba, T Arimori, D Motooka, K Katoh, Y Kirita, ... Engineered ACE2 counteracts vaccine-evading SARS-CoV-2 Omicron variant BIORXIV, 2021 4
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
2021 RF Gao, JY Wang, KW Liu, K Yoshida, YY Hsiao, YX Shi, KC Tsai, ... Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops HELIYON, 2021, 7, 6317 4
2021 K Katoh Multiple sequence alignment , 2021 4
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
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, 61, 151682-151682 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, 1-13 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
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 3
2014 LA González-Hernández, MA Llamas-Covarrubias, ... Nuevas terapias antirretrovirales en la infección por VIH REVISTA MEDICA MD, 2014, 5, 143-149 3
2020 O Gervais, K Ueno, Y Kawai, Y Hitomi, K Misawa, S Teraguchi, YY Wang, ... Genomic heritabilities and correlations of 17 traits related to obesity and associated conditions in the Japanese population G3: GENES, GENOMES, GENETICS, 2020, 10, 2221-2228 3
2008 A Ishida, S Teraguchi On the general action of boundary (super) string field theory JOURNAL OF HIGH ENERGY PHYSICS, 2008, 2008, 20-20 3
2018 A Millius, H Ueda Rhythms: the dark side meets the light SCIENCE, 2018, 359, 1210-1211 2
2021 K Katoh, DM Standley Emerging SARS-CoV-2 variants follow a historical pattern recorded in outgroups infecting non-human hosts COMMUNICATIONS BIOLOGY, 2021, 4, 1-6 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, 2014, 15, 1-14 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
2020 M Enciso-Ramírez, Z Reyes-Castillo, MA Llamas-Covarrubias, L Guerrero, ... CD36 gene polymorphism-31118 G> A (rs1761667) is associated with overweight and obesity but not with fat preferences in Mexican children INTERNATIONAL JOURNAL FOR VITAMIN AND NUTRITION RESEARCH, 2020 2
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
2022 S Beppu, M Kinoshita, J Wilamowski, T Suenaga, Y Yasumizu, K Ogawa, ... High cell surface expression and peptide binding affinity of HLA-DQA1* 05: 03, a susceptible allele of neuromyelitis optica spectrum disorders (NMOSD) SCIENTIFIC REPORTS, 2022, 12, 1-12 1
2022 A Davila, Z Xu, S Li, J Rozewicki, J Wilamowski, S Kotelnikov, D Kozakov, ... AbAdapt: an adaptive approach to predicting antibody–antigen complex structures from sequence BIOINFORMATICS ADVANCES 2 (1), VBAC, 2022, 15 1
2013 E Kanamori, Y Murakami, J Sarmiento, S LIANG, DM Standley, M Shirota, ... 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
2021 D Diez, B Morte, J Bernal Single-Cell Transcriptome Profiling of Thyroid Hormone Effectors in the Human Fetal Neocortex: Expression of SLCO1C1, DIO2, and THRB in Specific Cell Types THYROID, 2021, 31, 1577-1588 1
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
2022 R Furukawa, S Yokobori, R Sato, T Kumagawa, M Nakagawa, K Katoh, ... Amino Acid Specificity of Ancestral Aminoacyl-tRNA Synthetase Prior to the Last Universal Common Ancestor Commonote commonote JOURNAL OF MOLECULAR EVOLUTION, 2022, 90, 73-94 1
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 1
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
2010 JRV Bernal, JFM Valle, MAL Covarrubias, S Sanchez Relationship of uncarboxylated osteocalcin concentrations and ucOC/cOC index with the glycemic status in type 2 diabetes mellitus BONE 46, S, 2010, 56 1
2018 S Teraguchi, Y Kumagai Estimation of diffusion constants from single molecular measurement without explicit tracking BMC SYSTEMS BIOLOGY, 2018, 12, 25-39 1
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
2012 A Ishida, S Teraguchi On open-closed extension of boundary string field theory JOURNAL OF HIGH ENERGY PHYSICS, 2012, 2012, 1-26 1
2022 N Ikemura, S Taminishi, T Inaba, T Arimori, D Motooka, K Katoh, Y Kirita, ... An engineered ACE2 decoy neutralizes the SARS-CoV-2 Omicron variant and confers protection against infection in vivo SCIENCE TRANSLATIONAL MEDICINE, EABN, 2022, 7737 0
2022 YK Chong, S Tartey, Y Yoshikawa, K Imami, S Li, M Yoshinaga, ... Cyclin J–CDK complexes limit innate immune responses by reducing proinflammatory changes in macrophage metabolism SCIENCE SIGNALING 15 (729), EABM, 2022, 5011 0
2022 M Loza, S Teraguchi, DM Standley, D Diez Unbiased integration of single cell transcriptome replicates NAR GENOMICS AND BIOINFORMATICS 4 (1), LQAC, 2022, 22 0
2022 D Standley An adaptive approach to predicting antibody-antigen complex structures from sequence BIOPHYSICAL JOURNAL 121 (3), 39A, 2022 0
2022 Z Xu, A Davila, J Wiamowski, S Teraguchi, DM Standley Improved antibody-specific epitope prediction using AlphaFold and AbAdapt BIORXIV, 2022 0
2022 Y Saijo-Hamano, AA Sherif, A Pradipta, M Sasai, N Sakai, Y Sakihama, ... Structural basis of membrane recognition of Toxoplasma gondii vacuole by Irgb6 LIFE SCIENCE ALLIANCE, 2022, 5 0
2021 H Arase, Y Liu, N Arase, J Kishikawa, M Hirose, S Li, A Tada, S Matsuoka, ... Acquisition of resistance to wild-type spike-immune sera by emerging SARS-CoV-2 variants , 2021 0
2021 K Katoh, DM Standley A simple method for predicting emerging SARS-CoV-2 variants using outgroups infecting non-human hosts , 2021 0
2021 J Rozewicki, S Li, K Katoh, DM Standley Analysis of Protein Intermolecular Interactions with MAFFT-DASH MULTIPLE SEQUENCE ALIGNMENT, 2021, 163-177 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 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
2016 SK Suzuki, J Hirano, T Fukuhara, A Yamashita, K Saito, D Okuzaki, ... Hepatocyte factor JMJD5 regulates HBV replication through interaction with HBx , 2016 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
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
2016 FJ van Eerden Photosynthesis in silico: Simulations of Photosystem II and the Thylakoid Membrane , 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
2021 RF Gao, JY Wang, KW Liu, K Yoshida, YY Hsiao, YX Shi, KC Tsai, ... Corrigendum to “Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops”[Heliyon 7 (2)(February 2021) e06317] HELIYON, 2021, 7 0
2020 K Katoh, N Iwabe, T Miyata Possible changes in fidelity of DNA polymerase δ in ancestral mammals BIORXIV, 2020 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
2019 LA González-Hernández, RA Soria-Rodriguez, EA Rivera-Leon, ... Niveles séricos de Ghrelina y Obestatina en pacientes infectados con VIH: efecto de 36 semanas de tratamiento antirretroviral ENDOCRINOLOGíA, DIABETES Y NUTRICIóN, 2019, 66, 4-10 0
2019 EA Rivera-Leon, IM Llamas-Covarrubias, RA Soria-Rodriguez, ... Serum ghrelin and obestatin levels in HIV-infected patients: Effect of 36 weeks of antiretroviral treatment ENDOCRINOLOGIA, DIABETES Y NUTRICION, 2019, 66, 4-10 0
2017 F Casillas-Muñoz, Y Valle, JF Muñoz-Valle, DE Martínez-Fernández, ... Polimorfismos de los genes APOA1 y APOB y concentraciones de sus apolipoproteínas como biomarcadores de riesgo en el síndrome coronario agudo: relación con la efectividad del … MEDICINA CLíNICA, 2017 0
2015 J Andrade‐Villanueva, L González‐Hernández, M Llamas‐Covarrubias, ... P009 [LINE SEPARATOR] Evaluation of HIV‐infection control, risk behaviours and comorbidities among inmates in Mexico JOURNAL OF THE INTERNATIONAL AIDS SOCIETY, 2015, 18 0
2015 L González‐Hernández, M Llamas‐Covarrubias, R Soria‐Rodríguez, ... P018 [LINE SEPARATOR] An overview of a cohort of elderly patients in Mexico JOURNAL OF THE INTERNATIONAL AIDS SOCIETY, 2015, 18 0
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
2021 ML Lopez, S Teraguchi, D Diez Unbiased integration of single cell transcriptomes using a linear hybrid method BIORXIV, 2021 0
2017 M Tomura, R Ikebuchi, S Teraguchi, A Vandenbon, SHW Francis, ... A rare subset of skin-tropic regulatory T cells expressing Il10/Gzmb inhibits the cutaneous immune response THE JOURNAL OF IMMUNOLOGY 198 (1 SUPPLEMENT), 206.14-206., 2017, 14 0
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