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Identification and characterization of Arabidopsis indole-3-butyric acid response mutants defective in novel peroxisomal enzymes |
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Neutrophils establish rapid and robust WAVE complex polarity in an actin-dependent fashion |
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Diffusion, capture and recycling of SCAR/WAVE and Arp2/3 complexes observed in cells by single-molecule imaging |
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Chemotaxis in neutrophil-like HL-60 cells |
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Manipulation of neutrophil-like HL-60 cells for the study of directed cell migration |
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Improved prediction of lysine acetylation by support vector machines |
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A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation |
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TLR4-induced NF-κB and MAPK signaling regulate the IL-6 mRNA stabilizing protein Arid5a |
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Quantifying sequence and structural features of protein–RNA interactions |
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Structural basis for the assembly of the Ragulator-Rag GTPase complex |
NATURE COMMUNICATIONS, 2017, 8, 1625-1625 |
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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 |
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Transcriptional regulatory network shapes the genome structure of Saccharomyces cerevisiae |
NUCLEUS, 2013, 4, 216-228 |
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MAFFT-DASH: integrated protein sequence and structural alignment |
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Clonal evolution and antigen recognition of anti-nuclear antibodies in acute systemic lupus erythematosus |
SCIENTIFIC REPORTS, 2017, 7, 16428-16428 |
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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 |
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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 |
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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 |
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Using chimaeric expression sequence tag as the reference to identify three-dimensional chromosome contacts |
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Structural modeling of lymphocyte receptors and their antigens |
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Functional clustering of B cell receptors using sequence and structural features |
MOLECULAR SYSTEMS DESIGN & ENGINEERING, 2019, 4, 769-778 |
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Structural Determinants of the APOBEC3G N-terminal domain for HIV-1 RNA association |
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, 2019, 9, 129-129 |
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Modeling Biocatalysts |
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The IκB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR–IL-1R by controlling degradation of regnase-1 |
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Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions |
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Drag force, jet quenching, and an AdS/QCD model |
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Systems biology approaches to toll‐like receptor signaling |
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Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system |
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Intrinsic disorder mediates cooperative signal transduction in STIM1 |
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Heterotic E 6 GUTs and partition functions |
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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 |
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A rare subset of skin-tropic regulatory T cells expressing Il10/Gzmb inhibits the cutaneous immune response |
SCIENTIFIC REPORTS, 2016, 6, 35002-35002 |
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Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins |
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Drag force, jet quenching, and AdS/QCD |
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Stochastic binary modeling of cells in continuous time as an alternative to biochemical reaction equations |
PHYSICAL REVIEW E, 2011, 84, 62903-62903 |
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Functional annotation of intrinsically disordered domains by their amino acid content using IDD navigator |
BIOCOMPUTING, 2012, 2012, 164-175 |
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Reformulation of boundary string field theory in terms of boundary state |
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B Nosirov, J Billaud, A Vandenbon, D Diez, E Wijaya, KJ Ishii, ... |
Mapping circulating serum miRNAs to their immune-related target mRNAs |
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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 |
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On the general action of boundary (super) string field theory |
JOURNAL OF HIGH ENERGY PHYSICS, 2008, 2008, 20-20 |
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Probabilistic Nearest Neighbor Estimation of Diffusion Constants from Single Molecular Measurement without Explicit Tracking |
ARXIV PREPRINT ARXIV:1601., 2016, 756 |
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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 |
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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 |
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On open-closed extension of boundary string field theory |
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Theoretical modeling reveals that regulatory T cells increase T-cell interaction with antigen-presenting cells for stable immune tolerance |
INTERNATIONAL IMMUNOLOGY, 2019 |
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Estimation of diffusion constants from single molecular measurement without explicit tracking |
BMC SYSTEMS BIOLOGY, 2018, 12, 15-15 |
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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 |
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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 |
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The influence of ciprofloxacin on hamster ovarian cancer cell line CHO AA8 |
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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 |
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Serum levels of macrophage migration inhibitory factor are associated with rheumatoid arthritis course |
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A cut-point value of uncarboxylated to carboxylated index is associated with glycemic status markers in type 2 diabetes |
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Clinical and immunological aspects of anti-peptidylarginine deiminase type 4 (anti-PAD4) autoantibodies in rheumatoid arthritis |
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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 |
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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 |
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APOA1 and APOB polymorphisms and apolipoprotein concentrations as biomarkers of risk in acute coronary syndrome: Relationship with lipid-lowering therapy effectiveness. |
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Association of A-604G ghrelin gene polymorphism and serum ghrelin levels with the risk of obesity in a mexican population |
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Efectos de la grelina y la obestatina en la salud y la enfermedad |
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Relationship of uncarboxylated osteocalcin concentrations and ucOC/cOC index with the glycemic status in type 2 diabetes mellitus |
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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 … |
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Nuevas terapias antirretrovirales en la infección por VIH |
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Rectal Plasmablastic Lymphoma in HIV/AIDS: Two Cases |
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MAFFT multiple sequence alignment software version 7: improvements in performance and usability |
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Recent developments in the MAFFT multiple sequence alignment program |
BRIEFINGS IN BIOINFORMATICS, 2008, 9, 286-298 |
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Multiple alignment of DNA sequences with MAFFT |
BIOINFORMATICS FOR DNA SEQUENCE ANALYSIS, 2009, 39-64 |
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MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization |
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Parallelization of the MAFFT multiple sequence alignment program |
BIOINFORMATICS, 2010, 26, 1899-1900 |
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Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework |
BMC BIOINFORMATICS, 2008, 9, 212-212 |
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GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters |
NUCLEIC ACIDS RESEARCH 43 (W1), W7-W, 2015, 14 |
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MAFFT: iterative refinement and additional methods |
MULTIPLE SEQUENCE ALIGNMENT METHODS, 2014, 131-146 |
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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 |
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K Katoh, DM Standley |
A simple method to control over-alignment in the MAFFT multiple sequence alignment program |
BIOINFORMATICS, 2016, 32, 1933-1942 |
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Adding unaligned sequences into an existing alignment using MAFFT and LAST |
BIOINFORMATICS, 2012, 28, 3144-3146 |
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Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees |
BIOINFORMATICS, 2016, 32, 3246-3251 |
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Protein multiple sequence alignment |
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Parallelization of MAFFT for large-scale multiple sequence alignments |
BIOINFORMATICS, 2018, 1, 3-3 |
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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 |
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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 |
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Comparative analyses of lysophosphatidic acid receptor-mediated signaling |
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Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease |
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Functional lysophosphatidic acid receptors expressed in Oryzias latipes |
GENE, 2014, 551, 189-200 |
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1P267 application of novel amino acid substitution matrix, MIQS, to the mafft multiple sequence aligner (22c. Bioinformatics: Comparative genomics, poster, the 52nd annual … |
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A method for complete characterization of complex germline rearrangements from long DNA reads |
MEDRXIV, 2019, 19006379 |
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K Takahashi, K Katoh, N Iwabe |
Phylogenetic position of ctenophores and early evolution of metazoans |
GENES & GENETIC SYSTEMS, 2015, 90, 394-394 |
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K Takahashi, K Katoh, N Iwabe |
Molecular phylogenetic analyses of deuterostomes: evolutionary position of cephalochordates |
GENES & GENETIC SYSTEMS, 2014, 89, 312-312 |
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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 |
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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 |
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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 |
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Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex |
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B Liu, C Åberg, FJ van Eerden, SJ Marrink, B Poolman, AJ Boersma |
Design and properties of genetically encoded probes for sensing macromolecular crowding |
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Molecular dynamics of photosystem II embedded in the thylakoid membrane |
THE JOURNAL OF PHYSICAL CHEMISTRY B, 2016, 121, 3237-3249 |
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Prediction of thylakoid lipid binding sites on photosystem II |
BIOPHYSICAL JOURNAL, 2017, 113, 2669-2681 |
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Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology |
THE JOURNAL OF MEMBRANE BIOLOGY 251 (5-6), 2018, 609-631 |
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Photosynthesis in Silico: Simulations of Photosystem II and Thylakoid Membrane |
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Simulation of Photosystem Ii Dynamics in the Thylakoid Membrane |
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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 |
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Systems biology approaches and pathway tools for investigating cardiovascular disease |
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A novel affinity-based method for the isolation of highly purified extracellular vesicles |
SCIENTIFIC REPORTS, 2016, 6, 33935-33935 |
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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 … |
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Neuronal exosomes facilitate synaptic pruning by up-regulating complement factors in microglia |
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Distinct transcriptional regulatory modules underlie STAT3’s cell type-independent and cell type-specific functions |
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Network analysis in the investigation of chronic respiratory diseases. From basics to application |
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Evolutionary expansion of the Ras switch regulatory module in eukaryotes |
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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 |
24 |
| 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 |
23 |
| 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 |
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 |
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 |
D Diez |
rTRMui: a shiny user interface for the identification of transcriptional regulatory modules |
, 2019 |
0 |
| 2019 |
A Vandenbon, D Diez |
singleCellHaystack: A clustering-independent method for finding differentially expressed genes in single-cell transcriptome data |
BIORXIV, 2019, 557967 |
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 |
| 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 |
793 |
| 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 |
412 |
| 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 |
201 |
| 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 |
200 |
| 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 |
181 |
| 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 |
156 |
| 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 |
125 |
| 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 |
114 |
| 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 |
114 |
| 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 |
102 |
| 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 |
81 |
| 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 |
77 |
| 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 |
53 |
| 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 |
51 |
| 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 |
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 |
| 2007 |
DM Standley, H Toh, H Nakamura |
ASH structure alignment package: sensitivity and selectivity in domain classification |
BMC BIOINFORMATICS, 2007, 8, 116-116 |
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 |
40 |
| 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 |
40 |
| 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 |
38 |
| 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 |
35 |
| 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 |
34 |
| 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 |
33 |
| 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 |
33 |
| 2011 |
S Liang, D Zheng, C Zhang, DM Standley |
Fast and accurate prediction of protein side-chain conformations |
BIOINFORMATICS, 2011, 27, 2913-2914 |
33 |
| 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 |
31 |
| 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 |
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 |
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 |
| 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 |
24 |
| 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 |
23 |
| 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 |
| 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 |
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 |
20 |
| 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 |
| 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 |
16 |
| 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 |
16 |
| 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 |
15 |
| 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 |
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 |
14 |
| 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 |
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 |
| 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 |
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 |
10 |
| 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 |
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 |
8 |
| 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 |
| 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 |
| 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 |
5 |
| 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 |
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 |
| 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, 1 |
2 |
| 2014 |
J Hirano, Y Iesato, Y Toriyama, A Imai, T Murata |
BVS Integralidade em Saúde |
OPHTHALMIC RES, 2014, 52, 65-73 |
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 |
| 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, 1-11 |
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 |
| 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, 1-13 |
0 |
| 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 |
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, 2019, 1 |
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 |
