60% Biology, 40% Computer Sciences
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Our research area is bioinformatics; bioinformatics is beginning to have a large impact on the field of biology now that more and more structure, sequence, gene expression data, and pathway data have become available in the past decade. These large data enable us to employ comprehensive analysis of protein sequences/structures, genomes, and pathways. Our enthusiasm for scientific research comes from a desire to have a global view of protein folding; the relationship between protein function, sequence, and structure; and evolution of protein families, pathways, and organisms. Now complete genome sequences of more than 210 organisms are available in public databases. Using these genome data, we can directly investigate evolution of organisms/protein families, gene transfer, or mechanism of coding principle of pathways in a genome. Linking protein tertiary structure information which comes from both experimental data and prediction will add another important aspect in our understanding. Therefore, in practical terms our main research interest is to develop computational methods to predict and analyze protein structure/function, pathway structure and their applications in genome-scale, or pathway/network scale.
Ph.D., Kyoto University (Japan)
BS., The University of Tokyo (Japan)
Faculty Presentations, 2012-2013, August:
-  Unified biomolecular 3D surface matching for proteins, ligands, and interactions, Eli Lilly, Lilly Grand Rounds, Eli Lilly, Indianapolis, Aug 14, 2013
-  Machine learning approach for protein structure modeling, Telluride Workshop on Modeling Biomolecular Structures, Interactions, and Functions, Telluride, CO, July 1-5, 2013.
-  Structure prediction of protein interactions, Seoul National University, Dept. of Chemistry, Seoul, Korea, June 27, 2013
-  Information flow in biological systems, Chung-Ang University, 4th International Conference of Biostatistics and Bioinformatics, Seoul, Korea, June 25, 2013
-  Predicting gene function in biological contexts, Seoul National University, Computer Science and Engineering, Seoul, Korea, June 24, 2013.
-  Information flow in biological systems, Tokyo Institute of Technology, June 21, 2013
-  Predictions of structures of protein interactions. Univ. Chicago Computation Institute, Chicago, IL, May 20, 2013
-  Macromolecular structure modeling and EM fitting. D. Kihara & J. Esquivel-Rodriguez, 5th CAPRI (Critical Assessment of Predicted Interactions), Utrecht, the Netherlands, April 17-19, 2013.
-  Predictions of Protein Function, Structures, Dynamics, and Interactions. Bioinformatics and Machine Learning Roundtable, Qatar Computing Res. Institute, Doha, Qatar, March 19-20, 2013.
-  Macromolecular Structure Modeling and Electron Microscopy Fitting Using 3D Zernike Descriptors. Highlights Track, ISCB-Asia/SCCG 2012, Shenzhen, China, Dec. 17-19, 2012.
-  Binding ligand prediction by comparing local surface patches of potential pocket regions. Zing conference, Mathematical and Computational Medicine, Xcaret, Cancun, Mexico, Dec. 1-15, 2012.
-  Predictions of structures of protein interactions. International Summer School of Life & Health Science, Education Academy of Computational Life Sciences, Tokyo Institute of Technology, Shonan, Kanagawa, Sept. 3-5, 2012
-  Suboptimal alignments & 3D Zernike descriptors for structure prediction and docking. Workshop on Coarse-grained modeling of structure and dynamics of biomacromolecules, Telluride, CO, July 23-27, 2012.
-  A "catalytic dimer" hypothesis for the synthesis of cellulose and other (1,4)-beta-glycans Nicholas C. Carpita, Anna T. Olek, Catherine J. Rayon, Lee Makowski, Shi-you Ding , Peter Ciesielski, Lake Paul, Subhangi Ghosh, Daisuke Kihara, Michael Crowley, Michael Himmel, Jeffrey Bolin, The 23rd International Conference on Arabidopsis Research (ICAR), Vienna, Austria, July 3-7, 2012
-  Predictions of structures of protein interactions. Telluride Meeting on Protein folding and Dynamics: From experiment to theory, Telluride, Colorado, June 17-21, 2012
-  Predicting binding ligand and protein docking using surface shape". D. Kihara, Graduate School of Information Science, Tohoku University, Sendai, Japan. May 30, 2012
-  Predictions of structures of protein interactions. Bioinformatics Seminar series at Institute of Chemical Research, Kyoto University , Uji, Kyoto, Japan. May 28, 2012
-  Structural features that predict real-value fluctuations of globular proteins, M. Jamroz, A. Kolinski & D. Kihara, at Special Session, " Proteins in motion: Computational studies in protein flexibility and dynamics" co-organized by D. Kihara & L. Kurgan, Great Lakes Bioinformatics Conference (GLBIO) 2012, May 15-17, 2012, Ann Arbor, MI.
-  Computational characterization of moonlighting proteins using Gene Ontology annotations (selected talk), by I. Khan, M. Chitale, & D. Kihara, Great Lakes Bioinformatics Conference (GLBIO) 2012, May 15-17, 2012, Ann Arbor, MI.
-  Macromolecular structure modeling and electron microscopy fitting using 3D Zernike descriptors (selected talk), J. Esquivel-Rodriguez, & D. Kihara, Great Lakes Bioinformatics Conference (GLBIO) 2012, May 15-17, 2012, Ann Arbor, MI.
-  Sequence- and structure-based protein function prediction. The Research Institute at Nationwide Children’s hospital, The Ohio State University, March, 22, 2012.
Conferences (Poster Presentations), 2012-2013. August:
-  3D-SURFER 2.0: web platform for real-time comparison, visualization and characterization of protein surfaces" Y. Xiong, J. Esquivel-Rodriguez, L. Sael & D. Kihara, Annual Symposium of the Protein Society , Boston, MA, July 20-23, 2013
-  Biochemical characterization of an Arabidopsis pectin methylesterase AtPME3 and a pectin methylesterase inhibitor. F. Senechal, M. L’Enfant, JM Domon, E. Rosiau, P. Marcello, O. Surcouf, J. Esquivel-Rodriguez, A. Mareck, F. Guerineau, H-R. Kim, E. Bonnin, E. Jamet, J. Mravec, D. Kihara, M-C. Ralet, P. Lerouge, J. Pelloux, C. Rayon, The XI Cell Wall Meeting, Nantes, July 7-12, 2013
-  Characterization of cytosolic protein complexes in plants using multi-step chromatographic separation and quantitative mass spectrometry. U. Aryal1, Y. Xiong, E. Mallery, M. Hall, J. Xie, D. Kihara, D. Szymanski. American Soc. for Mass Spectrometry, June 9-13, 2013, Minneapolis, MN.
-  Protein docking prediction guided by predicted protein-protein interface. D. Kihara, B. Li, J. Esquivel-Rodriguez, & D. La, 5th CAPRI (Critical Assessment of Predicted Interactions), Utrecht, the Netherlands, April 17-19, 2013.
-  Development of computational method for visualizing disordered regions during protein docking. Arthi Anand & D. Kihara, Undergraduate Research Poster Symposium, Purdue University, March 26, 2013.
-  EM-LZerD: EM Map Fitting for Multimeric Protein Complexes Using Rotation Invariant Surface Representation. J E.-Rodriguez & D. Kihara Structural Analysis of Supramolecular Assemblies by Hybrid Methods, Keystone Symposia, Lake Tahoe, Mar 3-7, 2013.
-  Computational function prediction for moonlighting proteins. I Khan, M. Chitale, C. Rayon, D. Kihara. Sigma Xi Graduate Student/Post Doc Poster Competition, Purdue Univ, Feb.13, 2013.
-  Macromolecular structure modeling and electron microscopy fitting using 3D Zernike descriptors. D. Kihara, J. Esquivel-Rodriguez. Biophysical Society 57th Annual Meeting, February 2-6, 2013, Philadelphia, PA.
-  Next generation molecular surface representation for rapid global/local protein shape comparison, docking, and low-resolution data. D. Kihara, National Centers for Biomedical Computing (NCBC) Showcase, Nov. 8-9, Natcher Conference Center, Bethesda, MD
-  Local Similarity Search of Physicochemical Properties in Protein-Ligand Binding Sites. Lee Sael & Daisuke Kihara Translational Bioinformatics Conference (TBC) 2012, Jeju Island, Korea, Oct 13-16, 2012
-  Novel quantitative proteomic methods to discover and localize protein complexes. U.K. Aryal, Y. Xiong, E. Mallery, M.C. Hall, J. Xie, D. Kihara, P.N. Baker, D. B. Szymanski. 2012 Plant Genome Awardee Meeting, National Science Foundation, Arlington, VA, Sep. 6-7, 2012.
-  Biochemical characterization of an Arabidopsis pectin methylesterase AtPME3 and a pectin methylesterase inhibitor. F. Senechal, J-M Domon, M. L’Enfant, D. Tall-Ndoye, J. Esquievel-Rodriguez, F. Guerineau, HR Kim, E. Jamet, E. Bonnin, D. Kihara, M-C Ralet, J. Pelloux, C. Rayon Gordon Conference on Plant Cell Wall, Colby College, Waterville, ME, August 5-10, 2012
-  Computational function prediction for moonlighting proteins. Ishita Khan, Meghana Chitale, Catherine Rayon, Daisuke Kihara Automatic Function Prediction-Special Interest Group (AFP-SIG), ISMB Satellite meeting, Long Beach, CA, July 13-14, 2012
- [141-2] 3DSIG 2012, Structural Bioinformatics and Computational Biophysics, ISMB Satellite meeting, Long Beach, CA, July 13-14, 2012
- Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors, Juan Esquivel-Rodriguez, Daisuke Kihara
- Prediction of real-value fluctuation of globular proteins, Michal Jamroz, Andrzej Kolinski, Daisuke Kihara
-  A ‘catalytic dimer’ hypothesis for the synthesis of cellulose and other (1,4)-beta-glycans. Nicholas C. Carpita (oral presentation), Anna T. Olek, Catherine J. Rayon, Lee Makowski, Shi-you Ding , Peter Ciesielski, Lake Paul, Subhangi Ghosh, Daisuke Kihara, Michael Crowley, Michael Himmel, Jeffrey Bolin. The 23rd International Conference on Arabidopsis Research (ICAR), Vienna, Austria, July 3-7, 2012
-  Logic Patterns of Homologous Genes Across Species. Lillian Liu, Huairuo Ren, Yu Leng, Meghana Chitale, Daisuke Kihara, 2012 Undergraduate Research and Poster Symposium, Purdue University, Apirl 10 2012
-  Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors. Juan Esquivel-Rodriguez, Daisuke Kihara. 6th International Conference on Structural Analysis of Supramolecular Assemblies by Hybrid Methods. Lake Tahoe, CA, March 14-18, 2012
-  Computational methods for multiple protein docking for asymmetric complexes. J. Esquivel-Rodriguez, Daisuke Kihara. Biophysical Society 56th Annual Meeting, San Diego, California, Feb. 25-29, 2012
Professional Faculty Research
(Bioinformatics, computational biology) protein tertiary structure prediction/comparison, protein-protein docking, protein-ligand docking, protein function prediction, protein sequence analysis, metabolic/regulatory pathway analysis.