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 9079
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, 936-936 741
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, 1185-1185 384
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 189
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 187
2014 K Katoh, DM Standley MAFFT: iterative refinement and additional methods MULTIPLE SEQUENCE ALIGNMENT METHODS, 2014, 131-146 174
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 159
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, 1167-1167 153
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 127
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, 289-302 122
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, 151-159 106
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 (DATABASE ISSUE), D, 2012, 453 105
2016 K Katoh, DM Standley A simple method to control over-alignment in the MAFFT multiple sequence alignment program BIOINFORMATICS, 2016, 32, 1933-1942 101
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, 381-381 91
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 84
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, 3492-3492 70
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 69
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 51
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 43
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 42
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 42
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 39
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 39
2007 DM Standley, H Toh, H Nakamura ASH structure alignment package: sensitivity and selectivity in domain classification BMC BIOINFORMATICS, 2007, 8, 116-116 36
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 35
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 (13), S, 2011, 5 30
2011 S Liang, D Zheng, C Zhang, DM Standley Fast and accurate prediction of protein side-chain conformations BIOINFORMATICS, 2011, 27, 2913-2914 30
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 30
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 28
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 28
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 27
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 26
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 25
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 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 23
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 22
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 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 19
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 19
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 18
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, 22324-22324 18
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 18
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 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 16
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 15
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 13
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 12
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 12
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
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 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 11
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, 1625-1625 10
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 10
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 (7), S, 2012, 11 10
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 9
2010 S Teraguchi, A Patil, DM Standley Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins BMC BIOINFORMATICS 11 (7), S, 2010, 7 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 8
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 8
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 6
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 6
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, 11-11 6
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 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 4
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 4
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, 16428-16428 4
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 4
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
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 2
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 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 (10), 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 12 (3), S, 2011, 21 2
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 1
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
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
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, 489-498 128
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 96
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 95
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 86
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 73
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 70
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 60
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 56
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 55
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 55
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 40
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 39
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 24
2007 D Diez, R Alvarez, A Dopazo Codelink: an R package for analysis of GE healthcare gene expression bioarrays BIOINFORMATICS, 2007, 23, 1168-1168 24
2013 R Stojnic, D Diez PWMEnrich: PWM enrichment analysis R PACKAGE VERSION 4 (0), 10., 2013, 18129 23
2013 D Diez, AP Hutchins, D Miranda-Saavedra Systematic identification of transcriptional regulatory modules from protein–protein interaction networks NUCLEIC ACIDS RESEARCH 42 (1), E6-, 2013, 6 21
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 21
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 21
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 20
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 12
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 5
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 1
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 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
2019 A Vandenbon, D Diez singleCellHaystack: Finding surprising genes in 2-dimensional representations of single cell transcriptome data BIORXIV, 2019, 557967 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 307
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 100
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 64
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, 15214-15214 18
2016 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, 2016, 121, 3237-3249 18
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 15
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 7
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 1
2016 FJ van Eerden Photosynthesis in Silico: Simulations of Photosystem II and 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
2017 K Katoh, J Rozewicki, KD Yamada MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization BRIEFINGS IN BIOINFORMATICS, 2017 308
2008 K Katoh, H Toh Recent developments in the MAFFT multiple sequence alignment program BRIEFINGS IN BIOINFORMATICS, 2008, 9, 286-298 2778
2009 K Katoh, G Asimenos, H Toh Multiple alignment of DNA sequences with MAFFT BIOINFORMATICS FOR DNA SEQUENCE ANALYSIS, 2009, 39-64 913
2010 K Katoh, H Toh Parallelization of the MAFFT multiple sequence alignment program BIOINFORMATICS, 2010, 26, 1899-1900 498
2008 K Katoh, H Toh Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework BMC BIOINFORMATICS, 2008, 9, 212-212 455
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, 14 202
2012 K Katoh, MC Frith Adding unaligned sequences into an existing alignment using MAFFT and LAST BIOINFORMATICS, 2012, 28, 3144-3146 108
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, 28 104
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 81
2009 CB Do, K Katoh Protein multiple sequence alignment FUNCTIONAL PROTEOMICS, 2009, 379-413 66
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 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 35
2018 T Nakamura, KD Yamada, K Tomii, K Katoh Parallelization of MAFFT for large-scale multiple sequence alignments BIOINFORMATICS, 2018, 1, 3-3 19
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 18
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
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
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 41
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 29
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 15
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
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 4
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 3
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 1
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 1
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
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
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
2014 LA González-Hernández, MA Llamas-Covarrubias, ... Nuevas terapias antirretrovirales en la infección por VIH REVISTA MEDICA MD, 2014, 5, 143-149 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
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 16
2007 E Nakano, S Teraguchi, WY Wen Drag force, jet quenching, and an AdS/QCD model PHYSICAL REVIEW D, 2007, 75, 85016-85016 70
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 23
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 14
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, 100-100 11
2008 E Nakano, S Teraguchi, W Wen Drag force, jet quenching, and AdS/QCD , 2008 9
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, 1032-1032 8
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, 35002-35002 8
2007 S Teraguchi Reformulation of boundary string field theory in terms of boundary state JOURNAL OF HIGH ENERGY PHYSICS, 2007, 2007, 17-17 5
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
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 2
2012 A Ishida, S Teraguchi On open-closed extension of boundary string field theory JOURNAL OF HIGH ENERGY PHYSICS, 2012, 2012, 59-59 1
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, 15576-15576 0
2018 S Teraguchi, Y Kumagai Estimation of diffusion constants from single molecular measurement without explicit tracking BMC SYSTEMS BIOLOGY, 2018, 12, 15-15 0
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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 82
2011 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, 2011, 40, 972-980 62
2013 S Li, DW Heermann Transcriptional regulatory network shapes the genome structure of Saccharomyces cerevisiae NUCLEUS, 2013, 4, 216-228 8
2012 S Li, DW Heermann Using chimaeric expression sequence tag as the reference to identify three-dimensional chromosome contacts DNA RESEARCH, 2012, 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, 237-251 107
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 46
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 J CELL SCI, 2012, 125, 1165-1176 41
2009 A Millius, OD Weiner Chemotaxis in neutrophil-like HL-60 cells CHEMOTAXIS, 2009, 167-177 36
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 33
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