Kihara Bioinformatics Laboratory Presentations

Upcoming Presentations

• 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,

• "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.

• Daisuke Kihara, Depatmental Seminar at Biological Sciences, Purdue Univesity, Title TBA, Oct. 15, 2008

Past Presentations

1. 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.

2. 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.

3. 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.

4. 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"

5. 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

6. Poster presentations at Biophysical Society 52nd Annual Meeting February 2-6, 2008, Long Beach, CA
7. (3250-Pos/B553)Predicting the error of template-based protein structure modeling by suboptimal alignment stability, by Hao Chen & D. Kihara
8. (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

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

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

11. 7th KIAS-Soongsil Conference, October 4-6, 2007, Soongsil Univ., Seoul, Korea, "Protein function prediction for proteomics era (invited talk) "

12. 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

13. 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

14. 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)

15. 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)

16. 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.

17. 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"

18. 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

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

20. 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

21. 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

22. 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

23. 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

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

25. 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

26. 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

27. 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)

28. 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)

29. 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)

30. 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)

31. 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

32. 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

33. 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

34. 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

35. 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)

36. 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

37. 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),

38. 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)

39. 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)

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

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

42. 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

43. 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)

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

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

46. 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

47. 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

48. 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

49. 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

50. 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

51. 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

52. 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

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

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

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

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

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

58. 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

59. 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