Presentations

Upcoming Presentations

Past Presentations

  1. "Why Protein Folds and Superfamilies have Skewed Distributions?" Zing Conference on Protein Folding, July 16-19, 2014, Punta Cana, Dominican Republic
  2. Plant Biology 2014, Portland, Oregon, Jul 12-16 , 2014.
    • "Small-angle x-ray scattering reveals the structure of the catalytic domain of a plant cellulose synthase and its assembly into dimers." P.S. Rushton, N. Carpita A.T. Olek, C.V. Stauffacher, C. Rayon, L. Makowski, H.R. Kim, P. Ciesielski, J. Badger, L.N. Paul, D. Kihara, M. Crowley, & M. E. Himmel
    • "Towards Plant-specific protein gene function prediction", Akshay Kumar, Ishita Khan, D. Kihara
  3. "Genome-scale Identification and Characterization of Moonlighting Proteins" (selected oral presentation), Automatic Function Prediction Meeting (AFP-SIG alongside of ISMB 2014), Boston, July 11-12 , 2014
  4. 3D-SIG (alongside of ISMB), Boston, July 11-12 , 2014
    • "Predicting protein complex assembly pathway using multiple-protein docking algorithm" (selected oral presentation), Yoichiro Togawa, Juan Esquivel-Rodriguez, Amit Roy, & D. Kihara
    • "Fast large scale comparison and structrue fitting for low-resolution electron microscopy maps (poster), Juan Esquivel-Rodriguez & D. Kihara
  5. PhD thesis defense, Juan Esquivel-Rodriguez, Computer Science, Purdue University, June 18 , 2014
  6. "Navigating 3D Electron Microscopy Density Maps and Protein Shapes with EM-SURFER and 3D-SURFER 2.0 ", Juan Esquivel-Rodriguez, Yi Xiong, Juan Esquivel-Rodriguez, Xusi Han, Shuomeng Guang, and Daisuke Kihara, GLBIO 2014 , May 16-18 , 2014
  7. "Exploring protein interfaces: Steered molecular dynamics and free energy calculations to rank protein-protein docking poses". L.J. Kingsley, J. Esquivel-Rodriguez, D. Kihara, M. Lill, Great Lakes Drug Metabolism & Disposition Group 2014 Meeting, Sheraton Indianapolis City Centre Hotel, Indianapolis, IN, May 15-16 , 2014
    • Logic patterns for finding functionally related genes in Escherichia coli, Ishita Khan, Tiange Dong, Linzi Chen, Weichuan Luo
    • Interactive visualization of Gene Ontology hierarchy, Qing Wei
  8. Undergraduate Research Poster Symposium, Purdue University, April 8, 2014
  9. Yoichiro Togawa, MS thesis defense, Dept. of Biological Sciences, 1:30pm, Lilly 117, April 11, 2014
  10. Lecture series in Bioinformatics and Computational Biology, Iowa State University, April 10, 2014
  11. "Faster Comparison of Electron Microscopy Density Maps of Proteins", Charles Christoffer, Juan Esquivel-Rodriguez, and Daisuke Kihara, Discovery Park Undergraduate Student Poster Session, Hall of Discovery and Learning Research, April 3, 4:30-6:30pm, 2014
  12. The Office of Interdisciplinary Graduate Programs, Spring Reception Poster Presentation , Purdue University, April 2, 2014
    • Assessing Protein Side‐Chain Conformation Prediction Methods in Different Residue Environments, Lenna Peterson
    • Genome‐scale Identification and Characterization of Moonlighting Proteins, Ishita Khan
    • Enhanced Electron Microscopy Fitting Using Markov Random Fields, Juan Esquivel-Rodriguez
  13. Computational modeling of macromolecular structures, Juan Esquivel-Rodriguez, Interdisciplinary graduate program, LWSN3102, Purdue, March 5, 2014
  14. 2nd Zing Protein and RNA Structure Prediction Conference, Cancun, Mexico, Dec. 1-5, 2013
  15. Beckman Institute, Univ. Illinois at Urbana-Chanpain, Oct 28, 2013
  16. Daisuke Kihara, Department seminar, Dept. of Bilogical Sciences, Purdue University, Oct 2, 2013
  17. "Prediction of macromolecular structures of protein interactions", Cold Spring Harbor Asia Conferences on Frontiers in Bioinformatics and Computational Biology , Sep 23-27, 2013
  18. University College London, UK Sep 13, 2013
  19. 2nd ACSL International Summer School, Imperial College London, Sep 8-14, 2013
  20. "Unified biomolecular 3D surface matching for proteins, ligands, and interactions", Eli Lilly, seminar at Lilly Grand Rounds, Eli Lilly, Indianapolis, Aug 14, 2013
  21. "3D-SURFER 2.0:Web platform for real-time comparison, visualization and characterization of protein surfaces" Yi Xiong, J. Esquivel-Rodriguez, L. Sael & D. Kihara, Annual Symposium of the Protein Society , Boston, MA, July 20-23, 2013
  22. Biochemical characterization of an Arabidopsis pectin methylesterase AtPME3 and a pectin methylesterase inhibitor. (poster) 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
  23. "Machine learning approach for protein structure modeling" Telluride Workshop on "Modeling biomolecular structures, interactions and functions", telluride, CO, July 1-5, 2013
  24. "On protein docking prediction", Seoul National University, Chemistry department, Seoul, Korea, 3pm, June 27, 2013
  25. "Information flow in biological systems", The 4th International Conference on Statistical Methods in Biomedical Science and Bioinformatics, Chung-Ang University, Seoul, Korea, June 25, 2013
  26. "Predicting gene function in biological contexts", Seoul National University, Computer Science and Engineering, Seoul, Korea 11am, June 24, 2013
  27. "Preditions of structures of protein interactions". D. Kihara, Toyota Technological Institute at Chicago, Chicago, IL, May 20, 2013
  28. 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.
  29. 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.
  30. Predictions of Protein Function, Structures, Dynamics, and Interactions. Bioinformatics and Machine Learning Roundtable, Qatar Computing Res. Institute, Doha, Qatar, March 19-20, 2013.
  31. EM-LZerD: EM Map Fitting for Multimeric Protein Complexes Using Rotation Invariant Surface Representation. J Esquivel-Rodriguez & D. Kihara Structural Analysis of Supramolecular Assemblies by Hybrid Methods, Keystone Symposia, Lake Tahoe, March 3-7, 2013.
  32. 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.
  33. Macromolecular Structure Modeling and Electron Microscopy Fitting Using 3D Zernike Descriptors. Highlights Track, ISCB-Asia/SCCG 2012, Shenzhen, China, Dec. 17-19, 2012.
  34. 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
  35. 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.
  36. 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
  37. 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.
  38. 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
  39. 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
  40. Invited talk by D. Kihara at Telluride Meeting on Coarse-grained modeling of structure and dynamics of biomacromolecules, Telluride, Colorado, July 23-27, 2012
  41. 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
  42. Invited talk by D. Kihara at Telluride Meeting on Protein folding and Dynamics: From experiment to theory, Telluride, Colorado, June 17-21, 2012
  43. "Predicting binding ligand and protein docking using surface shape". D. Kihara, Graduate School of Information Science, Tohoku University, Sendai, Japan. May 30, 2012
  44. "Preditions of structures of protein interactions". D. Kihara, Bioinformatics Seminar series at Institute of Chemical Research, Kyoto University , Uji, Kyoto, Japan. May 28, 2012
  45. "Systems Level Gene Function Prediction for Assessing Outcome of SNPs", D. Kihara, Chung-Ang University, Seoul, Korea, May 25, 2012
  46. Great Lakes Bioinformatics Conference (GLBIO) 2012, May 15-17, 2012, Ann Arbor, MI
    • "Macromolecular structure modeling and electron microscopy fitting using 3D Zernike descriptors" by J. Esquivel-Rodriguez & D. Kihara
    • "Computational characterization of moonlighting proteins using Gene Ontology annotations" by I. Khan, M. Chitale, & D. Kihara
    • Special Session, " Proteins in motion: Computational studies in protein flexibility and dynamics" session co-chaired by D. Kihara & L. Kurgan, "Structural features that predict real-value fluctuations of globular proteins" by M. Jamroz, A. Kolinski & D. Kihara
  47. Chao Yuan, MS Thesis defense "Investigation of optimal residue contact definitions for template-based protein structure prediction", April 10, 3-5pm, 2012, Lilly 1-224, Purdue University
  48. "Logic Patterns of Homologous Genes Across Species" by Lillian Liu, Huairuo Ren, Yu Leng, Meghana Chitale, Daisuke Kihara, poster presentation at 2012 Undergraduate Research and Poster Symposium, Purdue Memorial Union, North & South Ball Room, Apirl 10 2012, 2-7pm
  49. "Domain-based protein function prediction in terms of GO vocabulary" by Su Lin Ooi, Meghana Chitale, Ishita Khan, & D. Kihara, Poster presentation at Discovery Park Undergraguate Research Interns (DURI) poster presentation, DLR 131, Purdue University, April 5, 4:30-6:30pm, 2012.
  50. Invited seminar, D. Kihara, The Research Institute at Nationwide Children's Hospital, Department of Pediatrics, The Ohio State University College of Medicine, March 22, 2012
  51. "Computational methods for multiple protein docking for asymmetric complexes" (poster: B85, 1315-Pos, 2/27/2012), Juan Esquivel-Rodriguez, Daisuke Kihara, Biophysical Society 56th Annual Meeting, San Diego, Carifornia, Feb. 25-29, 2012 .
  52. 2 poster presentations at Sigma Xi Graduate Student Research Award Competition , Steward Center, Rooms 214/218, Purdue University, Feb. 15 (Wed), 2012 , 12:30-4pm, 6-9pm.
    • "Macromolecular structure modeling and electron microscopy fitting using 3D Zernike descriptors" Juan Esquivel-Rodriguez & D. Kihara
    • "In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment", Ishita Khan, Meghana Chitale, & D. Kihara
  53. Oral presentation, "Functional coherence assessment for protein groups and its application to pathway assignment", D. Kihara, Zing conference, IECA (Internatinal E. coli Alliance) 2011 , Xcaret, Cancun, Mexico, Dec. 5-9, 2011
  54. Invited speaker, "Unified Molecular Representation for Protein Shape Comparison and Interaction", D. Kihara, Zing conference on Protein and RNA Structure Prediction", Xcaret, Cancun, Mexico, Dec. 3-7, 2011
  55. Ph.D. thesis defense, David La, "Computational models of mutations for predicting and classifying protein-protein interaction sites", Dept. of Bilogical Sciences, Purdue University, Dec. 1, 2011. Presentation available at Ustream video
  56. Ph.D. thesis defense, Bin Li, "Geometrical Analysis Of Interaction Sites Of Proteins", Dept. of Computer Science, Purdue University, Nov. 29, 2011.
  57. "Next generation structural bioinformatics and gene function prediction", D. Kihara, Biological Scieces Researh Retreat, Swan Lake resort, Plymonth IN, November 5, 2011
  58. "Next generation protein 3D structure analysis: Rapid global/local surface comparison, docking, and low-resolution data", D. Kihara, Dept. of Biological Sciences Faculty Research Presentations, Lilly 1-117, Purdue University, 12-1pm, October 27, 2011
  59. "Protein 3D global/local shape search for function prediction and drug design" by D. Kihara at CS591 (graduate seminar), LWSN B155, Purdue University, October 5, 2011
  60. Invited Seminar, "Protein surface representation for ligand binding site screening" D. Kihara, Eli Lilly, Indianapolis,October 3, 2011
  61. Invited Seminar, "Next Generation Protein 3D Structure Analysis: Rapid Global/Local Surface Comparison, Docking and Low-Resolution Data" D. Kihara, University of Alberta, Edmonton, Canada, September 16, 2011
  62. Invited Seminar,"Binding Ligand Prediction by Comparing Local Surface Patches of Potential Pocket Regions" D. Kihara, Computational Biology Res. Center, Tokyo, Japan, September 2, 2011
  63. Purdue University Nano-Bio Student Symposium, MRGN 129, Purdue University, Sept. 1, 2011
    • "Protein Docking Prediction Using Predicted Protein-Protein Interface" Bin Li
    • "Multi-LZerD: Multiple Protein Docking for Asymmetric Complexes"Juan Esquivel-Rodriguez
  64. Invited Seminar, "Next generation protein 3D structure analysis: Rapid global/local surface comparison, docking, and low-resolution data", D. Kihara, Fukushima Medical University, September 1, 2011
  65. Invited Seminar,"Binding Ligand Prediction by Comparing Local Surface Patches of Potential Pocket Regions" D. Kihara, RIKEN, Yokahama, Japan, August 30, 2011
  66. ICR Bioinformatics Center, 10 Year Anniversary and New Reconstructing Symposium "Unified molecular representation for protein shape comparison and interaction" D.Kihara, Kyoto University, Uji, Kyoto, Japan, August 29 2011
  67. Invited Seminar, "Next generation protein 3D structure analysis: Rapid global/local surface comparison, docking and low-resolution data", D. Kihara, Dept. of Computer Science and Engineering, Seoul National University, Seoul, Korea, Building 301, Room 315, August 22, 2011
  68. ISMB, Viena, Austria, July 15-19, 2011
    • AFP-SIG: "Function Prediction for Systems Level: Functional Coherence of Protein Groups and Identification of Missing Genes" M. Chitale, D. Kihara(oral presentation)
    • AFP-SIG: "Binding Ligand Prediction for Proteins Using Partial Matching of Local Surface Patches" L. Sael, D. Kihara (poster)
    • 3D-SIG: "Multi-LZerD: Multiple protein docking for asymmetric complexes" J. Esquivel-Rodriguez, YD. Yang, D. Kihara(poster)
    • 3D-SIG: "Rapid comparison and multimeric protein complex fitting for low-resolution electron microscopy data" D. Kihara, L. Sael, J. Esquivel-Rodriguez (poster)
    • 3D-SIG: "Binding Ligand Prediction for Proteins Using Partial Matching of Local Surface Patches" L. Sael, D. Kihara (poster)
    • main conference: "Functional coherence assessment for protein groups and its application to pathway assignment" M. Chitale, S. Palakodety, D. Kihara
    • main-conference: "Multi-LZerD: Multiple protein docking for asymmetric complexes" J. Esquivel-Rodriguez, YD. Yang, D. Kihara(poster)
    • main conference: "Binding Ligand Prediction for Proteins Using Partial Matching of Local Surface Patches" L. Sael, D. Kihara (poster)
  69. "Protein-protein docking prediction: from pairwise docking, docking interface prediction, and multiple protein docking" by Kihara at workshop on "Modeling Biomolecular Structures, Interactions, and Functions" (organized by Jianpeng Ma, Jeff Skolnick), Telluride, Colorado, June 13-17, 2011.
  70. 4 lectures at International PhD Studies program, Faculty of Chemistry, Warsaw University , Poland, May 23-27, 2011
    • May 23 (Mon) "Template-based structure prediction and quality assessment using suboptimal alignments"
    • May 25 (Wed) "Sequence-based function prediction: from prediction of single genes to functional coherence for protein groups"
    • May 26 (Thr) "Protein-protein docking prediction: from pairwise docking, docking using docking interface information, and multiple protein docking"
    • May 27 (Fri) "Binding ligand prediction by Comparing Local Surface Patches of Potential Pocket Regions"
  71. "Surface Representation for Molecular Global and Local Shape Comparison and Docking", International Institute of Molecular and Cell Biology, Warsaw, Poland, 12:00-13:00, May 25, 2011
  72. 2 poster presentations at International Conference on Structural Genomics , May 10-14, 2011, Toronto, Canada
    • "Binding Ligand Prediction by Comparing Local Surface Patches of Potential Pocket Regions", L. Sael & D. Kihara (received nternational Structural Genomics Organization Poster Prize)
    • "Rapid comparison and multimeric protein complex fitting for low-resolution electron microscopy data", J. Esquivel-Rodriguez, L. Sael & D. Kihara
  73. 6 oral presentations at Great Lakes Bioinformatics Conference 2011, May 2-4, 2011, Ohio University, Athens, Ohio
    • "Protein-protein Interaction Sites Prediction using Phylogenetic Substitution Models", D. La, D.Kihara
    • "Protein Docking Prediction Using Predicted Protein-Protein Interface" Bin Li, D. Kihara
    • "Multi-LZerD: Multiple Protein Docking for Asymmetric Complexes" Juan Esquivel-Rodriguez, D. Kihara
    • "Rapid Comparison and Multimeric Protein Complex Fitting for Low-Resolution Electron Microscopy Data", Juan Esquivel-Rodriguez, Lee Sael, D. Kihara
    • "Patch-Surfer: Alignment Free Surface Patch-Based Ligand Binding Pocket Comparison", Lee Sael, D. Kihara
    • "Functional Coherence Assessment for Protein Groups and its Application to Pathway Assignment", Meghana Chitale, D. Kihara
  74. 3 poster presentations at 2011 Undergraduate Research and Poster Symposium , 2:00-7:00pm, April 12 (Tue) 2011, North Ball Room, Purdue Memorial Union, Purdue University
    • Fast identification of interacting proteins by considering shape and sequence features(Roshna Agarwal, Lee Sael, D. Kihara)
    • SiteHunter: Interactive web applicatdion for determining protein ligand binding site location (Yinlong Jin, R. Ren, K. Modi, S. Jain, D. La, D. Kihara)
    • Mining association between gene ontology terms by using protein-protein interaction networks(Satwica Yersini, Meghana Chitale, D. Kihara)
  75. "General framework for multiple protein docking" Juan Esquivel-Rodriguez, D. Kihara, 2011 Interdisciplinary Graduate Program Spring Reception, PMU, Purdue University, April 20, 2011
  76. 3 poster presentations at Discovery Park Student Poster Session, April 6 (Wed) 2011, Hall for Discovery and Learning Research (DLR), 4:30-6:30pm
    • Information theoretical approaches for protein sequences and structure, (Yingfei Ma, D. Kihara)
    • SiteHunter: Interactive web applicatdion for determining protein ligand binding site location (Yinlong Jin, R. Ren, K. Modi, S. Jain, D. La, D. Kihara)
    • Docking low-resolucion cryo-EM density maps aided by structural homology searching (Wansuk Lim, L. Sael, D. Kihara)
  77. 2 posters at 55st Annual meeting of Biophysical Society, Baltimore MD, March 5-9, 2011 :
    • "Novel methods for rapid comparison and multimeric protein complex fitting for low-resolution electron microscopy data", L. Sael, J. Esquivel-Rodriguez, D. Kihara, (March 7, Program #: 1750-Pos, Board #: B660)
    • "Local protein surface patch method for protein-ligand binding prediction", L. Sael, D. Kihara (March 8, Program #: 2131-Pos, Board #: B117)
  78. "Predicting protein function by surface comparison" by Sael Lee, at Bioinformatics seminar, Statistics on Feb 15, 4:30pm, HORT 117, Purdue.
  79. "Prediction of protein-protein interaction sites, pair-wise, and multiple protein docking", December 20, 2010 , Academy of Mathematics and Systems Science, Chinese Academy of Science, Beijing, China
  80. 1 oral presentation and 4 posters at The 21st International Conference on Genome Informatics, Hangzhou, China, December 16-18, 2010 :
    • (oral) "Improved Protein Surface Comparison and Application to Low-Resolution Protein Structure Data" L. Sael, D. Kihara
    • (poster)"Multiple Protein Docking for Asymmetric Hetero Oligomeric Complexes" J. Esquivel-Rodriquez, Y. Yang, D. Kihara
    • (poster) "Functional coherence for protein groups by considering associations between gene ontology terms" Meghana Chitale, Shriphani Palakodety, D. Kihara
    • (poster) "Protein Docking Prediction Using Predicted Protein-Protein Interface", Bin Li, D. Kihara
    • (poster) "Performance of SUPRB Threading Method in CASP9", Chao Yuan, Mateusz Kurcinski, D. Kihara
  81. "Binding ligand prediction using local surface Zernike descriptors". December 15, 2010, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, China
  82. "Sequence-based function prediction: from prediction of single genes to functional coherence for protein groups". December 15, 2010, Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai, China
  83. "Protein-protein docking prediction: from pairwise docking, docking using docking interface information, and multiple docking". December 14, 2010, Shanghai Jiaotong University, Shanghai, China
  84. "Sequence-based function prediction: from prediction of single genes to functional coherence for protein groups". December 13, 2010, Fudan University, Shanghai, China
  85. "Detecting surface shape complementarity for quick identification of interacting proteins", Roshna Agarwal, Paul Justin Tack, Sael Lee, D. Kihara, Grace Hopper Celebration of Women in Computing, Atlanta, Georgia, Sep 28 - Oct 2, 2010
  86. "A novel method for protein-protein interaction site prediction with phylogenetic substitution models", David La, D. Kihara, The 24th Annual Symposium of the Protein Society, August 1-5, 2010, San Diego, CA, USA.
  87. Ph.D. thesis defense, Sael Lee, "High throughput screening of global and local protein surfaces.", Dept. of Computer Science, Purdue University, July 16, 2010.
  88. "Multiple protein docking prediction based on genetic algorithms and physics based scoring", Juan Esquivel-Rodriguez, D. Kihara, 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), July 11-13, 2010, Boston, MA.
  89. 3 presentations at 3DSIG 2010 at ISMB 2010, Boston, July 9-10, 2010:
    • (oral) "Real-Time Ligand Binding Pocket Database Search Using Local Surface Zernike Descriptors" R. Chikhi, L. Sael, D. Kihara
    • (oral or poster)"Multiple Protein Docking Prediction Method Which Can Handle Asymmetric Hetero Oligomeric Complexes" J. Esquivel-Rodriquez, Y. Yang, D. Kihara
    • (poster) "Fitting Multimeric Complexes into Cryo-EM Maps Using Protein Docking Procedure and 3D Zernike Descriptors" D. Kihara, J. Esquivel-Rodriguez, L. Sael
  90. Invited talk "Protein surface representation for structure-based function prediction and docking" by D. Kihara at Telluride workshop on "Coarse-grained modeling of structure and dynamics of biomacromolecules", July 5-9, 2010, Telluride, CO, USA
  91. Invited talk, "Molecular surface representation for protein shape comparison and docking", D. Kihara, Korea Institute for Advanced Study (KIAS), June 30, 2010, Seoul, Korea.
  92. Invited talk "Structure of gene functional space in genomes" by D. Kihara at The First International Conference for Industrial Statistics and Bioinformatics, The Research Center for Data Science, Chung-Ang University, Seoul, Korea, June 29, 2010
  93. "Scoring Functions for Predicting Protein Structure and Protein-protein Interatcion", Yifeng Yang, Ph.D. thesis defense. Monday, April 19, 2010, 2:00 p.m, LILY 1-117, Purdue University.
  94. 2010 Undergraduate Reserach Poster Symposium, April 7 (Wed), Purdue Memorial Union, 2-6:30pm, Purdue University
    • "Why is there a limited number of protein fold in nature?", Abram Magner, Yifeng D. Yang, D. Kihara
    • "Classification of local surface shape of ligand binding pockets", Gabriele Martinez, Sael Lee, D. Kihara
    • "Structure-basis for protein-DNA interaction", William Hoffmann, D. Kihara
    • "Detecting surface shape complementarity for quick identification of interacting proteins", Paul Justin Tack, Roshna Agarwal, Sael Lee, D. Kihara
    • "Conservation of sequence and atoimc interactions in ligand binding sites of proteins", Sang Wook Lee, Sael Lee, D. Kihara
  95. "Comparative study of protein structure prediction methods" Priyanka Surana, D. Kihara, Sigma, 18th Undergradaute Research Day, Apr 3 (Sat), 10am, Lilly Hall,Dept. of Biological Sciences, Purdue University
  96. "Exploring applications of suboptimal alignments in threading protein structure prediction" Hao Chen, Ph.D. Thesis defense. Apr. 6, 2pm, Lilly 1-117, Purdue University.
  97. Purdue University Interdisciplinary Graduate Program Reception Monday, April 5th 2010, Purdue Memorial Union, South Ballroom
    • "Unified Protein Docking Procedure with a Shape Complementarity Screening Using 3D Zernike Descriptors and Ranking by Physics-Based Scoring", Juan Esquivel-Rodriguez, et al.
    • "Quantification of protein group coherence and pathway assignment in yeast using functional association", M. Chitale et al.
  98. "Comparative study of protein structure prediction methods" Priyanka Surana, D. Kihara, Sigma, 18th Undergradaute Research Day, Apr 3 (Sat), 10am, Lilly Hall,Dept. of Biological Sciences, Purdue University
  99. "Comparative study of protein structure prediction methods", Oral presentation of honors students, Priyanka Surana, D. Kihara, March 30, Lilly 1-117, Dept. of Biological Sci., Purdue University
  100. Sigma Xi Graduate student research presentation, Feb 17 (Wed), 12:30-9pm, Stewart Center, Rm 214/218, Purdue University
    • "A statistical method dor comparing flexible protein tertiary structures", Farrukh Arslan, Yifeng Yang, D. Kihara.
    • Application of 3D Zernike descriptors to shape-based ligand similarity searching", Padmasini Chakravarthy, V. Venkatraman, D. Kihara
    • Quantification of protein group coherence and pathway assignment in yeast using functional association", Meghana Chitale, Shriphani Palakodety, D. Kihara
  101. "A unified protein docking procedure with a shape complementarity screening using 3D Zernike descriptors", D. Kihara, V. Venkatraman, YD Yang, L. Sael, Biophysical Society meeting, San Francisco, CA, Feb 20-24, 2010
  102. "Protein surface representation for fast structure search, docking and function prediction", Tokyo Institute of Technology, Dept. of Computer Science, Tokyo, Japan, Dec 28, 2009
  103. "Protein surface representation for fast structure search, docking and function prediction", Nara Institute of Science and Technology (NAIST), Graduate School of Biological Sciences, Nara, Japan, January 7, 2009
  104. "A unified protein docking procedure with a shape complementarity screening using 3D Zernike descriptors and ranking by physics-based scoring" CAPRI Critical Assessment of Predicted Interactions 4th Evaluation Meeting, Barcelona, Spain, Dec 9-11, 2009
  105. "Protein Structure Bioinformatics for Predicting Structure, Docking, and Function" Univ. Cincinnati, Nov. 5, 2009
  106. "Protein Representation for Efficient Comparison of Surface Properties" (poster) by Sael Lee, 4th Annual KIST/PU Global Research Laboratory Symposium, Sep. 22 (Tue), 8:30-9:30am, Room 214, Steward Center, Purdue University
  107. PULSe program retreat poster presentation, August 22 (Sat), Beck Agriclutural Center, West Lafayette, IN
    • Local surface shape-based protein function prediction using Zernike descriptors, by D. Kihara, Sael Lee & Rayan Chikhi
    • Protein structure prediction without optimizing weighting factors for scoring function, by Yifeng D. Yang, Changsoon Park, & D. Kihara
  108. D. Kihara, "Global and local protein surface comparison and its applications", at TSRC workshop on "Method development for protein structure prediction and design", Telluride Science Res. Center, Telluride, Colorado, June 15-19, 2009.
  109. Poster presentations at American Society for Microbiology May 17-21, 2009, Philadelphia, PA
    • www.EcoliHub.org: An information resource for experimentation and modeling of E. coli K-12, by BL Wanner, WG Aref, T. Conway, KA Datsenko, SC Ess, MR Gribskov, JC Hu, D Kihara, H Mori, D Siegele, DR Whitaker
    • N terminal Gly224-Gly411 domain in Listeria adhesion protein (LAP) interacts with receptor Hsp60, by B. Jagadessan, D La, D Kihara, AK. Bhunia
  110. D. Kihara, Seminars at Statistics Dept, Chung-Ang University, Seoul, Korea, May 14-15, 2009
    • May 14: lectures on "Algorithms for biological sequence analysis"
    • May 15: research presentation on "Protein surface comparison for function prediction and docking"
  111. D. Kihara, "Novel bioinformatics approaches for studying protein sequence, structure, and function in omics era", Division of Bio-Medical Informatics, Center for Genome Science, National Institute of Health, Seoul, Korea, May 13, 2009
  112. The 21st Undergraduate Research Conference at Butler University, Butler University, Indianapolis, IN, April 17, 2009
    • Gregg Thomas, "Computational protein function prediction"
    • Matt Herron, "Protein Tertiary Structure Universe Viewed from the Perspective of Surface Shape"
    • Priyanka Surana, "Comparative study of tertiary structure prediction methods"
  113. Priyanka Surana, oral presentation on "Computational characterization of proteins having specific cellular localization patterns", Honor thesis oral presentation, Dept. Biological Sciences, Purdue, March 31, 2009.
  114. SIAM@Purdue Student Conference 09, Stewart Center, Purdue, March 30, 2009
    • (oral presentation), Meghana Chitale, 5:30-6pm, Room 313; "ESG: Extended similarity method for automated protein function prediction"
    • (oral presentation), Sael Lee, 6-6:30pm, Room 214C; "Protein representation for efficient comparison of surface properties"
    • (poster) Bin Li, "Predicting organism of a genome based on word frequences for metagenomics research"
    • (poster) David La, "Predicting Protein-Protein Interaction Sites by Computational Modeling of Mutational Patterns"
  115. Ph.D. thesis defense, Troy Hawkins, Dept. of Biological Sciences, Purdue University, October 6, 2008
  116. Poster presentations at Biophysical Society 53nd Annual Meeting February 28-March4, 2008, Boston MA
    • (3358-Pos/B405, March 4)Local surface shape-based protein function prediction using Zernike descriptors, by D. Kihara, Sael Lee & Rayan Chikhi
    • (3371-Pos/B418, March 4)Protein structure prediction without optimizing weighting factors for scoring function, by Yifeng D. Yang, Changsoon Park, & D. Kihara
  117. Seminar at the Biochemistry seminar series "Annotating protein structures by surface shape comparison" by D. Kihara, Feb 27th, 11:30-12:15, WTHR 201
  118. Sigma-Xi graduate students poster presentation, Feb. 18 (Wed) afternooon, Steward Center, Rooms 214/218, Purdue Univ.
    • ESG: Extended similarity group method for automated protein function prediction, by M. Chitale et al.
    • Protein representation for efficient comparison of surface properties, by Sael Lee et al.
    • Improvement of template-based protein structure prediction by suboptimal alignments, by Hao Chen et al.
    • Threading without optimizing weighting factors for scoring function, by Yifeng D Yang et al.
  119. Guest lecture on our research projects in protein bioinformatics at CS 197 Honors Seminar, Feb 16, 9:30-10:20, LWSN B134.
  120. Workshop organizer and oral presentation at e-Bioinformatics Workshop at IEEE e-Science '08, Dec. 12, IUPUI University Conference Center & Hotel, Room 232 "Annotating Protein Structures by Surface Shape Comparison" by D. Kihara
  121. Daisuke Kihara, Depatmental Seminar at Biological Sciences, Purdue Univesity, "Informatics approaches for studying protein sequence, structure, and function in omics era, Oct. 15, 2008
  122. Matt Herron, Brian Denton, David La, D. Kihara, "The protein structure universe viewed from the perspective of surface shape", The 19th Annual Argonne Symposium for Undergraduates in Science, Engineering and Mathematics, Argonne National Laboratory, November 7, 2008
  123. "Protein representation for efficient comparison of surface properties" Sael Lee, Bin Li, David La, Raif Rustamov, Daisuke Kihara, (poster presentation), 2008 Grace Hopper Celebration of Women in Computing, Keystone, Colorado, Oct 1, 2008.
  124. Presentations for Graduate student orientations 2008:
    • Biology: Poster presentation by Troy Hawkins, main lobby in Lilly Hall, August 19, 3:30-5:00PM.
    • CS: Two poster presentations by Sael Lee and Meghana Chitale, at Research Showcase, 11am-12:30pm, September 8 (Mon), 2008, Buchanan room, Ross Ade Stadium, 5th floor, Purdue.
    • PULSe: Two poster presentations by Hao Chen and Yifeng Yang, at PULSe retreat, John S. Wright Forestry Center at Martell Forest, West Lafaytte, August 23, 2008,
  125. ISMB 2008, Toronto, Canada, July 19-23, 2008. Two posters:
    • Automated protein function prediction using Extended Similarity Group (ESG) of sequences. M. Chitale, T. Hawkins, C. Park, D. Kihara.
    • EcoliHub: An information resource for experimentalists and modelers. DR Whitaker, WG Aref, KA Datsenko, S Ess, MR Gribskov, D Kihara, S Kim, H Mori, A Roumani, BL Wanner.
  126. Oral presentation at AFP/Biosapiens 2008(Automated Function Prediction special Interesting Group at ISMB2008), July 18-19, Toronto, Canada, "ESG: Extended Similarity Group Method for Improved Automated protein Function Prediction" by Meghana Chitale, Troy Hawkins, Changsoon Park & D. Kihara.

  127. Preston Spratt, Honors research presentation, "Structure modeling of E. coli proteome", March 27, 20008, Lilly 3-418, 5:30pm, Dept. of Biological Sci, Purdue University.

  128. 2008 Undergraduate Research and Poster Symposium, 2-7pm, March 31, 2008, Purdue Memorial Union Ballrooms.
    • Priyanka Surana, Yifeng Yang, D. Kihara "Computatinal modeling of ABC transporters"
    • Rupal Trivedi, Yifeng Yang, D. Kihara, "Disorder region prediction of E. coli proteins"

  129. Invited talk "Quality assessment of template-based protein structure prediction", Dept. of Bioengineering, University of Illinois at Chicago, College of Medicine West, Room 221, 1853 W Polk St., Chicago, IL, February 26, 2008

  130. Poster presentations at Biophysical Society 52nd Annual Meeting February 2-6, 2008, Long Beach, CA
  131. (3250-Pos/B553)Predicting the error of template-based protein structure modeling by suboptimal alignment stability, by Hao Chen & D. Kihara
  132. (3282-Pos/B585)A fast methodology for high throughput comparison of tertiary structure and physicochemical properties, by D. Kihara, Sael Lee, Bin Li, David La, Raif Rustamov

  133. Invited talk "Template-based protein structure prediction and beyond" at Korea Institute of Science and Technology Information (KISTI), December 26, 2007, Daejeon, Korea

  134. Invited talk "Computational protein structure and function prediction" at Chung-Ang University, December 27, 2007, Seoul, Korea

  135. 7th KIAS-Soongsil Conference, October 4-6, 2007, Soongsil Univ., Seoul, Korea, "Protein function prediction for proteomics era (invited talk) "

  136. Structural Biology Seminar Series, Dept. of Biolgical Sciences, Purdue University, September 19, 2007, 1:30-2:20pm, Lilly Hall, 1-117, Dept. of Biological Sciences, Purdue University, " Predicting protein function from sequence: theory and applications ", by Troy Hawkins

  137. Structural Biology Seminar Series, Dept. of Biolgical Sciences, Purdue University, September 26, 2007, 1:30-2:20pm, Lilly Hall, 1-117, Dept. of Biological Sciences, Purdue University, "Error estimation for template-based protein structure prediction ", by Hao Chen

  138. Biomedical Engineering Society Annual Meeting, September 26-29, 2007, Los Angeles, CA, "A fast method for high throughput comparison of tertiary structure and physicochemical properties (talk) " in the Bioinformatics and Systems Biology track (Session co-chair: Kihara)

  139. The 21st Symposium of the Protein Society, July 21-25, 2007 Boston, MA

    • (poster #268)"Protein surface representation for fast comparison of tertiary structure and physicochemical properties" by S. Lee, B. Li, D. La, R. Rustamov & D. Kihara (July 23)
    • (poster #464)"High-throughput function assignment for proteomics datasets with PFP" by T. Hawkins, M. Chitale & D. Kihara (July 24)

  140. ISMB 2007, July 21-25, 2007 Vienna, Austria

    • (talk)"Enriching functional knowledge in proteomics data using high-throughput PFP prediction", by T. Hawkins, M. Chitale & D. Kihara, AFP/Biosapiens Special Interest Group, July 20, 2007
    • (poster)"Functional enrichment of proteomics datasets with PFP", T. Hawkins, M. Chitale, S. Luban & D. Kihara.

  141. Indy '07: Indy Regional Bioinformatics Conference, May 31-June 2, 2007,

    • (selected talk) H. Chen & D. Kihara, "Estimating quality of template-based protein models by alignment stability"
    • (poster) T. Hawkins, M. Chitale, S. Luban, & D. Kihara, "Function prediction for proteomics datasets using PFP"
    • (poster) M. Chitale, T. Hawkins & D. Kihara, "Development of methods for missing enzyme/gene prediction with PFP"
    • (poster) S. Lee, D. La, B. Li, R. Rustamov, D. Kihara, "A fast methodology for high throughput comparison of tertiary structure and physicochemical properties"
    • (poster) B. Li, S. Turuvekere, M. Agrawal, K. Ramani & D. Kihara, "Local geometry characterization of protein surfaces with the visibility criteria"
    • (poster) P. Spratt, S. Krawczyk, Y.D. Yang & D. Kihara, "EcoliPredict: structure modeling of E. coli proteome"
    • (poster)Y.D. Yang & D. Kihara, "Threading without training weighting factors for scoring functions"
    • (poster)L. Si, D. Yu, D. Kihara & Y. Fang, "Using sequence similarity scores for automatic gene function annotation in the biomedical literature"

  142. Program Committee member and Session Chair at Interface 2007: the 39th Symposium on the interface of statistics, computing science, and applications, May 23-26, 2007, Doubletree Hotel, Philadelphia, "Computational techniques for structural genomics (session title)", "Surface shape-based protein structure classification and search (talk) ", Daisuke Kihara

  143. " Protein function and structure prediction for proteomics analyses " Invisted talk at Indiana University, Informatics Department, May 3, 2007, Bloomington, IN

  144. The Computer Research Insistute Poster Presentation, April 5, 2007, 4-6pm, Atrium of MSEE building, Purdue Univeresity, "Structure modeling of E. coli proteome: Quality Evaluation ", Preston Spratt, Steve Krawczyk, Yifeng Yang & Daisuke Kihara

  145. 2007 Undergraduate Research and Poster Symposium, April 4, 2007, College of Science, Agriculture, Engineering, and Technology, Purdue University,

    • "Structure modeling of E. coli proteome: Homology models" by Steve Krawczyk, Preston Spratt, Yifeng Yang & D. Kihara,
    • "Structure modeling of E. coli proteome: Quality Evaluation" by Preston Spratt, Steve Krawczyk, Yifeng Yang & D. Kihara,
    • "Benchmark of new amino acid similarity matrices on recognition of distant protein structures" by Yu-Hsuan Rex Cheng, Hao Chen & D. Kihara
  146. Dept. of Biological Science Undergraduate Reserach Presentation, March 31, 2007, Lilly Hall, Purdue Univeresity, "Structure modeling of E. coli proteome: Quality Evaluation ", Preston Spratt, Steve Krawczyk, Yifeng Yang & Daisuke Kihara

  147. Nara Institute of Science and Technology, Nara, Japan, December 28, 2006, "Advanced techniques for protein function prediction and protein tertiary structure search for proteomics analyses", Daisuke Kihara

  148. One-day course on bioinformatics , Graduate program, Kansai Medical University, Osaka, Japan, December 25, 2006, "Bioinformatics: Introduction and advanced topics", Daisuke Kihara

  149. Ajinomoto Life Science Institute, Kawasaki, Japan, December 22, 2006, "Advanced techniques for protein function prediction and protein tertiary structure search for proteomics analyses", Daisuke Kihara

  150. Critical Assessment of Techniques for Protein Structure Prediction (CASP7) November 26-30, 2006, Asilomar Conference Center, CA, Invited talk in Function prediction category, Daisuke Kihara

  151. BMES2006: (Biomedical Engineering Society Annual Meeting 2006) "Systems Biology and Bioinformatics" Track Oct. 12-14, 2006, Hyatt Regency Chicago, Chicago, IL "Computational techniques for genomics, proteomic, structural and pathway data" session, Oct. 12, session co-chair with Dr. Christina Chan, "Enhanced protein function prediction for proteomics analysis", Daisuke Kihara (invited talk)

  152. Center for Comp. Biology & Bioinformatics Seminar Series, October. 6, 2006, Medical Science Building Rm326, 3:30-4:30, Indiana Univ. School of Medicine, Indianapolis, IN, "Predicting protein function from sequence and structure", Daisuke Kihara (invited talk)

  153. The Second Automated Function Prediction Meeting, August 30 - September 1 2006, Cal-(IT)2 buidling, UC San Diego, CA, "PFP: sequence-based annotation of sequences and local sequence motifs with contextual GO term association", Troy Hawkins, Stan Luban & Daisuke Kihara (poster)

  154. Symposium on "Protein motion for function and folding(temporal title)", September. 28-29, 2006, Institute for Protein Research, Osaka University, Japan, "Low-resolution and uncertainty in protein function and structure prediction", Daisuke Kihara (invited talk)

  155. TeraGrid '06, June 12-15, 2006, Indianapolis, IN,

      "EMD: an ensemble DNA regulatory motif discovery algortihm for Grid computing.", Yifeng D. Yang, Jianjun Hu & Daisuke Kihara

  156. The Third Annual Indiana Bioinformatics Conference, May 19-20, 2006,Center for Computational Biology and Bioinformatics, Indiana Univ. School of Medicine,

    • "Bridging geometric protein surface features and phylogenetic information for rapid identification of protein-protein interaction interfaces(invited oral presentation)", David La, Dennis Livesay & Daisuke Kihara
    • "PFP: sequence-based annotation of sequences and local sequence motifs with contextual GO term asssociation(invited oral presentation)", Troy Hawkins, Stan Luban, & Daisuke Kihara
    • "Template-based protein structure prediction with a reliability measure for structural genomics era(poster)", Hao Chen, Yen Hock Tan, & Daisuke Kihara
    • "Ligand binding site prediction with the visibility criteria(poster)", Bin Li, S. Thruvekere, M. Agrawal, K. Ramani & Daisuke Kihara
    • "Multi-resolution protein representation for fact protein structure searching(poster)", Sael Lee, Bin Li, David La, Raiv Rustamov, & Daisuke Kihara
    • "On the effect of long-range interactions on the secondary structure formation of proteins(poster)", Daisuke Kihara
    • "Coiled-coil structures in E. coli interactome (poster)", Stan Luban, Akiyasu Yoshizawa & Daisuke Kihara
    • "Neural network based protein domain prediction (poster)", Yen Hock Tan, Otoniel Venezuela, Evans A. Tapia & Daisuke Kihara
    • "Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences (poster)", Yen Hock Tan, He Huang & Daisuke Kihara
    • "Accounting for natural flexibility in protein structure prediction comparisons(poster)", Jairav Desai & Daisuke Kihara
    • "EcoliPredict: bioinformatics prediction resource for EcoliHub (poster)", Barry Wanner, Daisuke Kihara, Troy Hawkins & Yifeng D. Yang

  157. American Society for Microbiology ASM-FEMS Conference on Protein Traffic in Prokaryotes, , May 6-10, 2006, Crete, Greece,

      "EcoliPredict: Bioinformatics prediction resource for EcoliHub.", Barry Wanner, Daisuke Kihara, Troy Hawkins & Yifeng D. Yang

  158. Undergraduate Research Poster Presentation, April 11, 2006, College of Science, Purdue Univ.,

    • "Use of Neural Network for Protein Domain Prediction", Yen Hock Tan & Daisuke Kihara
    • "Including Natural Protein Fexibility in Predicted Protein Structure Comparisons", Jairav Desai & Daisuke Kihara
  159. 2006 Sigma Xi Graduate Studnet ReserachPoster Presentation, Feb. 14, 2006, Stewart Center Rm 214, Purdue, Poster presentations:

    • "Protein Structure-Sequence Alignment with a Reliability Measure "(H.Chen, D. Kihara),
    • "A New Perspective on an Old Tool: Extending the Coverage of Sequence Similarity-Based Function Prediction with PFP "(T.B.Hawkins, S.Luban, D.Kihara),
    • "Bridging Geometric Protein Surface Features and Phylogenetic Information for Rapid Indentification of Protein-Protein Interaction Interfaces "(D.La, D. Liversay, D. Kihara),
    • "Multi-Resolution Protein Representation" (S.Lee, B.Li, D. La, R. Rustamov, D.Kihara),
    • "Ligand Binding Sites Prediction with the Visibility Criteria "(B.Li, S.Turuvekere, M.Agrawal, K.Ramani, D.Kihara)
    • "EMD: An ensemble algorithm for discoverying regulatory motifs in DNA sequences. "(Y.D.Yang, J.Hu, D. Kihara)

  160. Bioinformatics Seminar Series, , January 24 (Tue), 2006, Mechanical Engineering Building ME161, 4:30-5:30, Purdue University, "Enhanced Automated Function Prediction for Proteomics Analysis", Daisuke Kihara

  161. The 16th International Conference on Genome Informatics, Dec. 19-21, 2005, Yokohama, Japan, Poster presentations:

    • "Dependence of the Accuracy of Protein Secondary Structure Prediction on Long-Range Interactions "(D. Kihara),
    • "Protein-Protein Docking Algorithm Using Pre-Identified Binding Site Patches" (D.Kihara, S.Lee, K.Ramani, S.Turuvekere, M.Agrawal, B.Li),
    • "Ligand Binding Sites Prediction with the Visibility Criteria "(B.Li, S.Turuvekere, M.Agrawal, K.Ramani, D.Kihara),
    • "A New Perspective on an Old Tool: Extending the Coverage of Sequence Similarity-Based Function Prediction with PFP "(T.B.Hawkins, S.Luban, D.Kihara),

  162. International Symposium "From Genomics to Chemical Genomics: 10th Anniversary of KEGG, Dec. 15-16, 2005, PALULU Plaza, Kyoto, Japan, , "Protein function prediction in the Structural Genomics Era", Daisuke Kihara (invited talk)

  163. International Symposium on Frontiers of Computational Science 2005, Dec. 12-13, 2005, Noyori Conference Hall, Nagoya University, Japan, , "Protein function prediction in the Proteomics Era", Daisuke Kihara (invited talk)

  164. Structural Biology Seminar, November 16, 2005, Department of Biological Sciences, Purdue University, "Protein function prediction methods beyond BLAST search", Daisuke Kihara

  165. Computer Research Institute Seminar, October 19, 2005, Computing Reserach Institute, Purdue University, "Protein function prediction in Structural Genomics Era", Daisuke Kihara

  166. 16th Annual Argonne Symposium for Undergraduates in Science, Engineering and Mathematics, November 4-5, 2005, Argonne National Laboratory

    • "Evaluation and Development of Protein Function Prediction", Stan Luban

    • "Using Neural Network in Protein Domain Prediction", Yen Hock Tan

  167. Mini-Workshop on Computational Studies on Proteins, September 8, 2005, Children's Hospital Research Foundation, Cincinnati, Ohio, "Protein function prediction from sequence and structure", Daisuke Kihara (invited talk)

  168. PULSe Retreat, August 20, 2005, John S. Wright Forestry Center at Martell Forest, "Computational Function Prediction", Troy Hawkins, Stan Luban, Daisuke Kihara

  169. Biology Department New Graduate Students Orientation, August 12, 2005, Lilly Hall of Life Sciences, Purdue University, "Bioinformatics Research in Kihara Lab", Daisuke Kihara

  170. 2005 Summer Undergraduate Research Fellowship (SURF) Poster Presentation, August 2 2005, MSEE Atrium, Purdue University

    • "Protein-Protein Interaction Data Assessment", Ei Ei Phyu

    • "Comparative Study of Small RNA and Small Peptides in Complete Genome Sequences", Stan Luban

    • "BioQ: A 3D Querying Engine for Proteins", Athurva Goa

    • "Comparison of Distantly Related Protein Sequence Alignments with Multiple Amino Acid Similarity Matrices", Yen Hock Tan

  171. Marc/Aim Research Presentation, July 28 2005, Burton Morgan Center for Entrepreneurship, "Protein Structure Prediction with ZDOCK 2.3", Luis Avila, Bin Li, Daisuke Kihara

  172. ISMB, June 25-29 2005, Detroit, Michigan

    • "The use of context-based functional association in automated protein function prediction methods", Troy Hawkins, Daisuke Kihara

    • "PFP: Automatic annotation of protein function by relative GO association in multiple functional contexts", Troy Hawkins, Daisuke Kihara

    ISMB oral presentation program

  173. Midwest Computational Structural Biology Workshop, April 30 – May 1, 2005, Brook Lodge, Michigan State University, Augusta, Michigan

    • "Voxelized Protein Model for Fast Protein Docking and Function Prediction", Srinivasan Turuvekerel, Manish Agrawal, Karthik Ramani, Daisuke Kihara

    • "Protein Structure-Sequence Alignment with a Reliability Measure", Hao Chen, Daisuke Kihara

  174. Guest lecture at BIOL 517 (Molecular Biology: Proteins), April 13 2005, Lilly Hall of Life Sciences, Purdue University, "Computational Protein Structure Prediction Methods", Daisuke Kihara

  175. Undergraduate Research Poster Presentation, College of Science & College of Agriculture, April 11, 2005, PMU Faculty Lounges, Purdue University

    • "Comparing Tertiary Structures of Protein Active Sites", Yuhao Lin

    • "Comparative Study of Small RNA and Small Peptides in Complete Genome Sequences", Stan Luban

    • "Computer Graphics Program in Foreign Language Instruction", Ei Ei Phyu

    • "Comparison of Distantly Related Protein Sequence Alignments with Multiple Amino Acid Similarity Matrices", Yen Hock Tan

    • "Structure-basis of protein-protein interaction", Brian Trisler

    Department of Computer Science Purdue University news article

  176. The thirteenth Annual Undergraduate Research Day, Dept of Biological Sciences, April 2, 2005, Lilly Hall of Life Sciences, Purdue University, "Comparative study of small RNA and small peptides in complete genome sequences", Stan Luban

  177. Biochemistry Division Seminar, April 1 2005, "Toward a better template-based protein structure prediction", Daisuke Kihara

  178. Biology Honors Research (BIOL 497) Presentation, March 31 2005 , Lilly Hall of Life Sciences, Purdue University, Stan Luban

  179. PULSe Graduate Students Recruitment, March 5 2005, Hansen Hall, Purdue University, "Protein Sequence-Structure Alignment with a Reliability Measure", Hao Chen

  180. CS department Graduate Student Recruitment, March 5 2005, Computer Science Building, Purdue University, "Bioinformatics Research in Kihara group", Daisuke Kihara

  181. Biology Graduate Students Recruitment, February 26 2005, "Research in Kihara Bioinformatics Lab!", Troy Hawkins

  182. Sigma Xi Graduate Student Research Poster Presentation, February 17 2005, Steward Center, Purdue University

    • "Protein Sequence-Structure Alignment with a Reliability Measure", Hao Chen

    • "A structured approach to computational protein function prediction", Troy Hawkins

    • "A novel method for constructing phylogenetic trees based on complete genome sequences", Bin Li

  183. 15th Annual Argonne Symposium for Undergraduates in Science, Engineering and Mathematics, November 5-6, 2004, Argonne National Laboratory, "Improvement of Protein Sequence Alignments for Better Protein Structure Prediction", Yen Hock Tan

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