The Systems Immunology Lab is actively pursuing two major immunology research themes: analysis of immune repertoire sequence data and post-transcriptional regulation of immune responses. In addition, we are developing several core bioinformatics methods, including the MAFFT multiple alignment platform (Katoh, K. & Standley, D. M. Mol Biol Evol (2013)) and the OSCAR protein modeling force field (Liang, S. et al. Bioinformatics 27, 2913-2914 (2011)).
For analysis of immune repertoires, we have taken a structure-based approach. First, we developed a method for high-throughput B cell receptor modeling from sequence data (Yamashita, K. et al. Bioinformatics (2014)). We are currently utilizing sequence and structural features to predict the phenotype of B and T cell receptors in order to develop novel biomarkers and therapeutics.
With regard to post-transcriptional regulation, we are interested in molecular mechanism by which RNA-binding proteins (RBPs) regulate gene expression in immune cells. In order to study RBP-RNA interactions computationally, we have developed a tool for predicting RNA binding sites on proteins (Li, S. et al. Nucleic Acids Res (2014)) and for carrying out flexible protein-RNA docking (Nyati, K. K. et al. Nucleic Acids Res (2017)). These tools have recently been used to investigate the immune-regulatory roles of the RBPs Regnase-1 (Mino, T. et al. Cell (2015)) and Arid5a (Masuda, K. et al. J Exp Med (2016)).
Daron M. Standley Professor
bioinformatics, systems biology
|1998||Ph.D. Chemistry, Columbia University, New York|
|1993||BS Physics, Harvey Mudd College, Claremont, CA|
Research and career history
|2015.4-||Professor, IFReC, Osaka University|
|2014.10||Professor, Institute for Virus Research, Kyoto University|
|2008.10||Associate Professor, IFReC, Osaka University|
|2003.4||Senior Researcher, Protein Data Bank Japan, Institute for Protein Research, Osaka University (-2008.9)|
|1998.9||Scientific Software Developer Schrodinger, Inc. (-2003.3)|
|2014||K. Katoh: Young Scientist Initiative Award from the Society of Evolutionary Studies, Japan, 2014.|
|2009||D. Standley: 2009 Prize for Outstanding Achievement in Education and Research at Osaka University|
- Daron M. Standley Professor
- Kazutaka Katoh Associate Professor
- Soyoung Park Associate Professor
- Songling Li Associate Professor
T Nakamura, KD Yamada, K Tomii, K Katoh Parallelization of MAFFT for large-scale multiple sequence alignments (2018).
S Teraguchi, Y Kumagai Estimation of diffusion constants from single molecular measurement without explicit tracking (2018).
K Katoh, J Rozewicki, KD Yamada MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization (2017).
M Sasai, N Sakaguchi, JS Ma, S Nakamura, T Kawabata, H Bando, Y Lee. et al. Essential role for GABARAP autophagy proteins in interferon-inducible GTPase-mediated host defense (2017).
Nyati, K. K. et al. TLR4-induced NF-kappaB and MAPK signaling regulate the IL-6 mRNA stabilizing protein Arid5a. Nucleic Acids Res (2017).
Yokogawa, M. et al. Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions. Sci Rep 6, 22324 (2016)
Katoh, K. & Standley, D. M. A simple method to control over-alignment in the MAFFT multiple sequence alignment program. Bioinformatics (2016)
Masuda, K. et al. Arid5a regulates naive CD4+ T cell fate through selective stabilization of Stat3 mRNA. J Exp Med (2016).
Kamikawa, Y. et al. Design of a protein tag and fluorogenic probe with modular structure for live-cell imaging of intracellular proteins. Chemical Science 7, 308-314 (2016)
Yamashita, K. et al. Kotai Antibody Builder: automated high-resolution structural modeling of antibodies. Bioinformatics 30, 3279-3280 (2014).
Li, S., Yamashita, K., Amada, K. M. & Standley, D. M. Quantifying sequence and structural features of protein-RNA interactions. Nucleic Acids Res 42, 10086-10098 (2014).
Uehata, T. et al. Malt1-induced cleavage of regnase-1 in CD4(+) helper T cells regulates immune activation. Cell 153, 1036-1049 (2013).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30, 772-780 (2013).
Mino, T. et al. Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms. Cell 161, 1058-1073 (2015).
Liang, S., Zheng, D., Zhang, C. & Standley, D. M. Fast and accurate prediction of protein side-chain conformations. Bioinformatics 27, 2913-2914 (2011).
Kitamura, A. et al. A mutation in the immunoproteasome subunit PSMB8 causes autoinflammation and lipodystrophy in humans. J Clin Invest 121, 4150-4160 (2011)
Iwasaki, H. et al. The IkappaB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR-IL-1R by controlling degradation of regnase-1. Nat Immunol 12, 1167-1175 (2011).
Satoh, T. et al. The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection. Nat Immunol 11, 936-944 (2010)
Yamamoto, M. et al. A single polymorphic amino acid on Toxoplasma gondii kinase ROP16 determines the direct and strain-specific activation of Stat3. J Exp Med 206, 2747-2760 (2009).
Standley, D. M., Yamashita, R., Kinjo, A. R., Toh, H. & Nakamura, H. SeSAW: balancing sequence and structural information in protein functional mapping. Bioinformatics 26, 1258-1259 (2010)
Matsushita, K. et al. Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay. Nature 458, 1185-1190 (2009).