Publications

[41]			Daisuke Kihara, Hao Chen & Yifeng Yang, Quality assessment of computational protein models, Current Protein and Peptide Science, In revision.(2008).
[40]			David La & Daisuke Kihara, Predicting binding interfaces of protein-protein interactions, (a book chapter in) Biological Data Mining in Protein Interaction Networks, X-L Li, S.K.Ng, (eds), IGI-Global, Hershey, Philadelphia, USA, Accepted. (2008).
[39]			Hu JC, Aramayo R, Bolser D, Conway T, Elsik CG, Gribskov M, Kelder T, Daisuke Kihara, Knight TF Jr, Pico AR, Siegele DA, Wanner BL, Welch RD, The emerging world of wikis, Science, 320: 1289-1290 (2008).
[38]			Troy Hawkins, Meghana Chitale, Stan Luban & Daisuke Kihara, PFP: Automated prediction of gene ontology functional annotations with confidence scores, Proteins: Structure, Function, and Bioinformatics, In press. (2008).
[37]			Lee Sael, David La, Bin Li, Raif Rustamov & Daisuke Kihara, Rapid comparison of properties on protein surface, Proteins: Structure, Function, and Bioinformatics, In press.(2008).
[36]			Meghana Chitale, Troy Hawkins & Daisuke Kihara, Automated prediction of protein function from sequence, In Prediction of Protein Structure, Functions and Interactions, Janusz Bujnicki (ed.), John Wiley & Sons, Ltd. In Press. (2008).
[35]			Yifeng D. Yang, Changsoon Park & Daisuke Kihara, Threading without optimizing weighting factors for scoring function, Proteins: Structure, Function, and Bioinformatics, In press.(2008).
[34]			Lee Sael, Bin Li, David La, Yi Fang, Karthik Ramani, Raif Rustamov & Daisuke Kihara, Fast protein tertiary structure retrieval based on global surface shape similarity, Proteins: Structure, Function, and Bioinformatics, 72: 1259-1273. (2008).
[33]			Luo Si, Danni Yu, Daisuke Kihara, & Yi Fang, Combining gene sequence similarity and textual information for gene function annotation in the literature., Information Retrieval, In press.(2008).
[32]			Troy Hawkins, Meghana Chitale & Daisuke Kihara, New paradigm in protein function prediction for large scale omics analysis., Molecular BioSystems, 4: 223-231 (2008).
[31]			Hao Chen & Daisuke Kihara, Estimating quality of template-based protein models by alignment stability., Proteins: Struct. Funct. Bioinformatics, 71: 1255-1274 (2008).
[30]			Bin Li, Srinivasan Turuvekere, Manish Agrawal, David La, Karthik Ramani & Daisuke Kihara, Characterization of local geometry of protein surfaces with the visibility criterion, Proteins: Struct. Funct. Bioinformatics, 71: 670-683 (2008).
[29]			Mingwu Zhang, Daisuke Kihara & Sunil Prabhakar, Tracing lineage in multi-version scientific databases., IEEE 7th International Symposium on Bioinformatics & Bioengineering (BIBE), 440-447 (2007).
[28]			Yu-Shen Liu, Min Liu, Daisuke Kihara & Karthik Ramani, Salient critical points for meshes. , Proceedings of the 2007 ACM Solid and Physical Modeling, 277-282 (2007).
[27]			Stan Luban & Daisuke Kihara, Comparative genomics of small RNAs in bacterial genomes, Omics, 11: 58-73 (2007).
[26]			Troy Hawkins & Daisuke Kihara, Function prediction of uncharacterized proteins, J. Bioinformatics and Computational Biology, 5:1-30 (2007).
[25]			Daisuke Kihara, Troy Hawkins, Stan Luban Bin Li, Karthik Ramani, & Manish Agrawal, Protein function prediction in Proteomics Era" , Proceedings of the International Symposium on Frontiers of Computational Science, Y Kaneda et al. eds., pp. 143-148, Springer-Verlag, Berlin, Heidelberg. (2007).
[24]			Jianjun Hu, Yifeng David Yang & Daisuke Kihara, EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences, BMC Bioinformatics, 7:342. (2006).
[23]			Yen Hock Tan, He Huang & Daisuke Kihara, Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences, Proteins: Structure Funct, Bioinformatics, 64: 587-600. (2006).
[22]			Troy Hawkins, Stan Luban & Daisuke Kihara, Enhanced automated function prediction using distantly related sequences and contextual association by PFP." , Protein Sci, 15:1550-1556 (2006).
[21]			Daisuke Kihara, Yifeng D. Yang & Troy Hawkins, "Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools." , Cancer Informatics, 2:25-35. (2006).
[20]			Jianjun Hu, Bin Li & Daisuke Kihara, "Limitations and potentials of current motif discovery algorithms." , Nucleic Acid Res. 33: 4899-4913. (2005).
[19]			Daisuke Kihara., "On the effect of long-range interactions on the secondary structure formation of proteins." , Protein Science. 14: 1955-1963. (2005).
[18]			Daisuke Kihara., "Biomolecular Structure Databases." , Genome Function Research Handbook, Chapter 2. pp. 73-81. Yodosha Publishers, Tokyo, Japan. (2004).
[17]			Jeffrey Skolnick, Daisuke Kihara and Yang Zhang., " Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm." , Proteins: Structure, Funct. Bioinformatics 56:502-518. (2004)
[16]			Daisuke Kihara and Jeffrey Skolnick., " Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q." , Proteins: Structure, Funct. Bioinformatics 55: 464-473 (2004)
[15]			Daisuke Kihara and Jeffrey Skolnick., " The PDB is a covering set of small protein structures." , J. Mol. Biol. 334: 793-802 (2003)
[14]			Jeffrey Skolnick, Yang Zhang, Adrian Arakaki, Andrzej Kolinski, Michael Boniecki, Andras Szilagyi and Daisuke Kihara., " TOUCHSTONE: a unified approach to protein structure prediction." , Proteins: Structure, Funct. Genet. 53: Suppl.6: 469-479 (2003)
[13]			Wei Li, Yang Zhang, Daisuke Kihara, Yuanpeng J. Huang, Deyou Zheng, Gaetano T. Montelione, Andrzej Kolinski, and Jeffrey Skolnick, " TOUCHSTONEX: Protein Structure Prediction Using Sparse NMR Data." , Proteins: Structure, Funct. Genet. 53: 290-306 (2003)
[12]			Yang, Zhang, Daisuke Kihara and Jeffrey Skolnick, " Local Energy Landscape Flattening: Parallel Hyperbolic Monte Carlo Sampling of Protein Folding." , Proteins: Structure, Funct. Genet. 48: 192-201 (2002)
[11]			Daisuke Kihara, Yang Zhang, Hui Lu, Andrzej Kolinski and Jeffrey Skolnick, " Ab initio Protein Structure Prediction on a Genomic Scale: Application to the Mycoplasma genitalium Genome." , Proc. Natl. Acad. Sci. USA, 99: 5993-5998 (2002)
[10]			Jeffrey Skolnick, Andrzej Kolinski, Daisuke Kihara, Marcos Betancourt, Piotr Rotkiewicz and Michael Boniecki, " Ab initio Protein Structure Prediction via a Combination of Threading, Lattice Folding, Clustering, and Structure Refinement." , Proteins: Structure, Funct. Genet. 45 (Suppl 5): 149-156 (2001)
[9]			Daisuke Kihara, " Genome Databases on the Internet." , Tanpakushitsu Kakusan Koso (Protein, Nucleic Acid and Enzyme) 46 (16 Suppl): 2639-2645 (2001)
[8]			Daisuke Kihara and Minoru Kanehisa, " Prediction of Membrane Proteins in Post-Genomic Era." , Recent Res. Developments in Protein Engng. 1: 179-196 (2001)
[7]			Daisuke Kihara, Hui Lu, Andrzej Kolinski and Jeffrey Skolnick, " TOUCHSTONE: An ab initio Protein Structure Prediction Method that Uses Threading-based Tertiary Restraints." , Proc. Natl. Acad. Sci. USA 98: 10125-10130 (2001)
[6]			Andrzej Kolinski, Marcos Betancourt, Daisuke Kihara, Piotr Rotkiewicz and Jeffrey Skolnick, " Generalized Comparative Modeling (GENCOMP): A Combination of Sequence Comparison, Threading, and Lattice Modeling for Protein Structure Prediction and Refinement." , Proteins: Structure, Funct. Genet. 44: 133-149 (2001)
[5]			Jeffrey Skolnick and Daisuke Kihara, " Defrosting the Frozen Approximation: PROSPECTOR - A New Approach to Threading." , Proteins: Structure, Funct. Genet. 42: 319-331 (2001)
[4]			Daisuke Kihara and Minoru Kanehisa, " Tandem Cluster of Membrane Proteins in Complete Genome Sequences." , Genome Res. 10: 731-743 (2000)
[3]			Daisuke Kihara and Minoru Kanehisa., " The Genome Projects and Bioinformatics." , Iwanami Kouza (Iwanami Lecture Series): Gendai Igaku no Kiso (The Basis of Modern Medical Science), vol.1, Chap.11, pp: 215-235, Iwanami Shoten Publishers, Tokyo Japan (1998)
[2]			Daisuke Kihara, Toshio Shimizu and Minoru Kanehisa, " Prediction of Membrane Proteins Based on Classification of Transmembrane Segments." , Protein Engng., 11: 961-970 (1998)
[1]			Daisuke Kihara, Minoru Kanehisa and Toshihisa Takagi., " Internet Resources for Genome Research." , Tanpakushitsu Kakusan Koso (Protein, Nucleic Acid and Enzyme), 42(17 Suppl): 3090-3099 (1997)

Created originally by Katie Krajnak
Updated: September 3rd, 2007