Presentations

Upcoming Presentations

  • 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
  • "Systems Level Gene Function Prediction for Assessing Outcome of SNPs", D. Kihara, Chung-Ang University, Seoul, Korea, May 25, 2012
  • "Preditions of structures of protein interactions". D. Kihara, Bioinformatics Seminar series at Institute of Chemical Research, Kyoto University , Uji, Kyoto, Japan. May 28, 2012
  • "Predicting binding ligand and protein docking using surface shape". D. Kihara, Graduate School of Information Science, Tohoku University, Sendai, Japan. May 30, 2012
  • Invited talk by D. Kihara at Telluride Meeting on Protein folding and Dynamics: From experiment to theory, Telluride, Colorado, June 17-21, 2012
  • 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
  • Invited talk by D. Kihara at Telluride Meeting on Coarse-grained modeling of structure and dynamics of biomacromolecules, Telluride, Colorado, July 23-27, 2012

Past Presentations

  1. 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
  2. "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
  3. "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.
  4. 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
  5. "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 .
  6. 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
  7. 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
  8. 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
  9. 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
  10. Ph.D. thesis defense, Bin Li, "Geometrical Analysis Of Interaction Sites Of Proteins", Dept. of Computer Science, Purdue University, Nov. 29, 2011.
  11. "Next generation structural bioinformatics and gene function prediction", D. Kihara, Biological Scieces Researh Retreat, Swan Lake resort, Plymonth IN, November 5, 2011
  12. "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
  13. "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
  14. Invited Seminar, "Protein surface representation for ligand binding site screening" D. Kihara, Eli Lilly, Indianapolis,October 3, 2011
  15. 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
  16. 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
  17. 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
  18. 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
  19. Invited Seminar,"Binding Ligand Prediction by Comparing Local Surface Patches of Potential Pocket Regions" D. Kihara, RIKEN, Yokahama, Japan, August 30, 2011
  20. 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
  21. 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
  22. 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)
  23. "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.
  24. 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"
  25. "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
  26. 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
  27. 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
  28. 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)
  29. "General framework for multiple protein docking" Juan Esquivel-Rodriguez, D. Kihara, 2011 Interdisciplinary Graduate Program Spring Reception, PMU, Purdue University, April 20, 2011
  30. 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)
  31. 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)
  32. "Predicting protein function by surface comparison" by Sael Lee, at Bioinformatics seminar, Statistics on Feb 15, 4:30pm, HORT 117, Purdue.
  33. "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
  34. 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
  35. "Binding ligand prediction using local surface Zernike descriptors". December 15, 2010, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai, China
  36. "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
  37. "Protein-protein docking prediction: from pairwise docking, docking using docking interface information, and multiple docking". December 14, 2010, Shanghai Jiaotong University, Shanghai, China
  38. "Sequence-based function prediction: from prediction of single genes to functional coherence for protein groups". December 13, 2010, Fudan University, Shanghai, China
  39. "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
  40. "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.
  41. Ph.D. thesis defense, Sael Lee, "High throughput screening of global and local protein surfaces.", Dept. of Computer Science, Purdue University, July 16, 2010.
  42. "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.
  43. 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
  44. 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
  45. Invited talk, "Molecular surface representation for protein shape comparison and docking", D. Kihara, Korea Institute for Advanced Study (KIAS), June 30, 2010, Seoul, Korea.
  46. 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
  47. "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.
  48. 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
  49. "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
  50. "Exploring applications of suboptimal alignments in threading protein structure prediction" Hao Chen, Ph.D. Thesis defense. Apr. 6, 2pm, Lilly 1-117, Purdue University.
  51. 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.
  52. "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
  53. "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
  54. 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
  55. "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
  56. "Protein surface representation for fast structure search, docking and function prediction", Tokyo Institute of Technology, Dept. of Computer Science, Tokyo, Japan, Dec 28, 2009
  57. "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
  58. "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
  59. "Protein Structure Bioinformatics for Predicting Structure, Docking, and Function" Univ. Cincinnati, Nov. 5, 2009
  60. "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
  61. 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
  62. 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.
  63. 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
  64. 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"
  65. 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
  66. 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"
  67. 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.
  68. 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"
  69. Ph.D. thesis defense, Troy Hawkins, Dept. of Biological Sciences, Purdue University, October 6, 2008
  70. 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
  71. Seminar at the Biochemistry seminar series "Annotating protein structures by surface shape comparison" by D. Kihara, Feb 27th, 11:30-12:15, WTHR 201
  72. 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.
  73. Guest lecture on our research projects in protein bioinformatics at CS 197 Honors Seminar, Feb 16, 9:30-10:20, LWSN B134.
  74. 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
  75. Daisuke Kihara, Depatmental Seminar at Biological Sciences, Purdue Univesity, "Informatics approaches for studying protein sequence, structure, and function in omics era, Oct. 15, 2008
  76. 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
  77. "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.
  78. 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,
  79. 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.

  80. 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.

  81. 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.

  82. 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"

  83. 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

  84. Poster presentations at Biophysical Society 52nd Annual Meeting February 2-6, 2008, Long Beach, CA
  85. (3250-Pos/B553)Predicting the error of template-based protein structure modeling by suboptimal alignment stability, by Hao Chen & D. Kihara
  86. (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

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

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

  89. 7th KIAS-Soongsil Conference, October 4-6, 2007, Soongsil Univ., Seoul, Korea, "Protein function prediction for proteomics era (invited talk) "

  90. 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

  91. 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

  92. 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)

  93. 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)

  94. 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.

  95. 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"

  96. 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

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

  98. 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

  99. 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

  100. 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

  101. 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

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

  103. 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

  104. 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

  105. 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)

  106. 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)

  107. 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)

  108. 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)

  109. 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

  110. 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

  111. 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

  112. 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

  113. 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)

  114. 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

  115. 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),

  116. 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)

  117. 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)

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

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

  120. 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

  121. 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)

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

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

  124. 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

  125. 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

  126. 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

  127. 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

  128. 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

  129. 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

  130. 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

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

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

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

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

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

  136. 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

  137. 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

Recent News

Follow us on Twitter!Follow kiharalab on Twitter News Archives are available here.

  • 1 postdoc position is available. Please see here
  • Xuejiao Kang (CS) joined our lab. Welcome, Xuejiao!
  • Lillian Liu got Best Abstract Award at Undergrad Research Poster Symposium, Purdue University! Congratulations, Lillian!
  • Chao Yuan defended his MS thesis. Congratulations, Chao!
  • Dr. Choi Youn Im, postdoc researcher, joined our lab. Welcome Choi!
  • "Multi-LZerD: Multiple protein docking for asymmetric complexes" by Juan Esquivel-Rodriguez & D. Kihara accepted on Proteins.
  • "Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors" by Juan Esquivel-Rodriguez & D. Kihara accepted on J. Phys. Chemistry.
  • Ross VerHeul (the PULSe program)started rotation. Welcome!
  • "Formyl-coenzyme A (CoA):oxalate CoA-transferase from the acidophile Acetobacter aceti has a distinctive electrostatic surface and inherent acid stability" by Mullins,Starks, Francois, Sael, Kihara, & Kappock accepted on Protein Science.
  • Juan Esquivel-Rodriguez got the 1st Place Award at the Sigma Xi grad poster competition at Purdue! Congratulations! His poster was on "Macromolecular structure modeling and electron microscopy fitting using 3D Zernike descriptors".

Openings

Kihara Bioinformatics Laboratory is always looking for new people to join the lab. Our current list of openings is available here.