|MAFFT multiple sequence alignment software version 7: improvements in performance and usability|
K Katoh, DM Standley
Molecular biology and evolution 30 (4), 772-780, 2013
|The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection|
T Satoh, O Takeuchi, A Vandenbon, K Yasuda, Y Tanaka, Y Kumagai, ...
Nature immunology 11 (10), 936-944, 2010
|Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay|
K Matsushita, O Takeuchi, DM Standley, Y Kumagai, T Kawagoe, ...
Nature 458 (7242), 1185-1190, 2009
|MAFFT: iterative refinement and additional methods|
K Katoh, DM Standley
Multiple sequence alignment methods, 131-146, 2014
|A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3|
M Yamamoto, DM Standley, S Takashima, H Saiga, M Okuyama, ...
Journal of Experimental Medicine 206 (12), 2747-2760, 2009
|A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans|
A Kitamura, Y Maekawa, H Uehara, K Izumi, I Kawachi, M Nishizawa, ...
The Journal of clinical investigation 121 (10), 4150-4160, 2011
|A simple method to control over-alignment in the MAFFT multiple sequence alignment program|
K Katoh, DM Standley
Bioinformatics 32 (13), 1933-1942, 2016
|Malt1-Induced Cleavage of Regnase-1 in CD4+ Helper T Cells Regulates Immune Activation|
T Uehata, H Iwasaki, A Vandenbon, K Matsushita, E Hernandez-Cuellar, ...
Cell 153 (5), 1036-1049, 2013
|The IκB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR–IL-1R by controlling degradation of regnase-1|
H Iwasaki, O Takeuchi, S Teraguchi, K Matsushita, T Uehata, K Kuniyoshi, ...
Nature immunology 12 (12), 1167-1175, 2011
|Regnase-1 and roquin regulate a common element in inflammatory mRNAs by spatiotemporally distinct mechanisms|
T Mino, Y Murakawa, A Fukao, A Vandenbon, HH Wessels, D Ori, ...
Cell 161 (5), 1058-1073, 2015
|Community-wide assessment of protein-interface modeling suggests improvements to design methodology|
SJ Fleishman, TA Whitehead, EM Strauch, JE Corn, S Qin, HX Zhou, ...
Journal of molecular biology 414 (2), 289-302, 2011
|Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format|
AR Kinjo, H Suzuki, R Yamashita, Y Ikegawa, T Kudou, R Igarashi, ...
Nucleic Acids Research 40 (D1), D453-D460, 2012
|Outcome of a workshop on applications of protein models in biomedical research|
T Schwede, A Sali, B Honig, M Levitt, HM Berman, D Jones, SE Brenner, ...
Structure 17 (2), 151-159, 2009
|EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results|
S Liang, D Zheng, DM Standley, B Yao, M Zacharias, C Zhang
BMC bioinformatics 11 (1), 1-6, 2010
|Blockade of TLR3 protects mice from lethal radiation-induced gastrointestinal syndrome|
N Takemura, T Kawasaki, J Kunisawa, S Sato, A Lamichhane, ...
Nature communications 5 (1), 1-15, 2014
|Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation|
H Morikawa, N Ohkura, A Vandenbon, M Itoh, S Nagao-Sato, H Kawaji, ...
Proceedings of the National Academy of Sciences 111 (14), 5289-5294, 2014
|Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions|
R Moretti, SJ Fleishman, R Agius, M Torchala, PA Bates, PL Kastritis, ...
Proteins: Structure, Function, and Bioinformatics 81 (11), 1980-1987, 2013
|MAFFT-DASH: integrated protein sequence and structural alignment|
J Rozewicki, S Li, KM Amada, DM Standley, K Katoh
Nucleic acids research 47 (W1), W5-W10, 2019
|Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set|
VA Eyrich, DM Standley, RA Friesner
Journal of Molecular Biology 288 (4), 725-742, 1999
|Protein tertiary structure prediction using a branch and bound algorithm|
VA Eyrich, DM Standley, AK Felts, RA Friesner
Proteins: Structure, Function, and Bioinformatics 35 (1), 41-57, 1999