2007

• P.E. Bourne and A. Godzik 2007 Structural Genomics in Bioinformatics ? From Genomes to Therapies T. Lengauer (Ed.) Wiley-VCH. p419-438.
• L. Xie and P.E. Bourne 2007 A Robust and Efficient Algorithm for the Shape Description of Protein Structures and Its Application in Predicting Ligand Binding Sites BMC Bioinformatics, Accepted
• J. Gu and P.E.Bourne 2007 Allosteric Fluctuation Transitions as Applied to Cyclin Dependent Kinase 2 BMC Bioinformatics 8(1):45.
• Podtelezhnikov, A., Ghahramani, Z. and Wild, D.L. Learning about Protein Hydrogen Bonding by Minimizing Contrastive Divergence. Proteins: Structure, Function and Bioinformatics , 66:588-599 (2007)

2006

• C.L. Dupont, S.Yang, B. Palenik and P.E.Bourne 2006 Modern Proteomes Contain Imprints of Ancient Shifts in Ocean Chemistry PNAS, 103(47) 17822-17827.
• Kouranov, L. Xie, J. de la Cruz, L. Chen, J. Westbrook, P.E. Bourne and H.M. Berman 2006 The RCSB PDB Information Portal for Structural Genomics Nucleic Acids Research , 34 D302-5
• Chang PL, Rinne AW, Dewey TG 2006 Structure alignment based on coding of local geometric measures BMC Bioinformatics 7:346.
• Chu , W., Ghahramani, Z., Krause, R. and Wild, D.L. Identifying Protein Complexes in High Throughput Protein Interaction Screens Using an Infinite Latent Feature Model. Pacific Symposium on Biocomputing 2006, Ed. R.B. Altman, A.K. Dunker, L. Hunter T. Murray and T.E. Klein. World Scientific Publishing , Singapore , 231-242 (2006).
• Chu , W., Ghahramani, Z. and Wild, D.L. Bayesian Segmental Models with Multiple Sequence Alignment Profiles for Protein Secondary Structure and Contact Map Prediction . IEEE/ACM Transactions on Computational Biology & Bioinformatics 3(2): 98-113 (2006) (Featured Cover Article).
• Veretnik S, Shindyalov I . Computational Methods for Domain Partitioning of Protein Structures. In: “Computational Methods for Protein Structure Prediction and Modeling” (Xu Y, Xu D, Liang J, eds), Springer-Verlag, 2006 (in press).
• Y. Ye, Z. Li and A. Godzik “Modeling and analyzing three dimensional structures of human disease proteins” (2006) Pacific Symposium in Biocomputing
• Li Z, Ye Y, Godzik A. “Flexible Structural Neighborhood--a database of protein structural similarities and alignments.” Nucleic Acids Res . (2006) 34(Database issue):D277-80.
• A. Gramada and P.E. Bourne Multipolar Representation of Protein Structure BMC Bioinformatics 2006 May 4;7:242 .
• Friedberg I., Harder T. and Godzik A. JAFA: a protein function annotation meta-server. Nucleic Acids Res. 2006 Jul 1;34:W379-81
• Friedberg I. Automated Function Prediction: the Genomic Challenge Briefings in Bioinformatics (2006) 7(3):225-242
• Friedberg I., Jambon M. and Godzik A. New Avenues in Protein Function Prediction Protein Science (2006) Jun;15(6):1527-9
• Friedberg I., Harder T., Kolodny R., Sitbon E., Li Z. and Godzik A. Using an alignment of fragment strings for comparing protein structures Bioinformatics (2007) Accepted
• L. Xie and P.E. Bourne 2006 A Robust and Efficient Algorithm for the Shape Description of Protein Structures and Its Application in Predicting Ligand Binding Sites BMC Bioinformatics, Submitted.
• E.D Scheeff and P.E. Bourne 2006 Application of Protein Structure Alignments to Iterated Hidden Markov Model Protocols for Structure Prediction. BMC Bioinformatics, 7:410
• P.E. Bourne and A. Godzik 2006 Structural Genomics in Bioinformatics ->From Genomes to Drugs T. Lengauer (Ed.) Wiley-VCH. Submitted

2005

• E. Scheeff and P.E. Bourne “Structural evolution of the protein kinase-like superfamily.” PLoS Comput Biol. 2005 Oct;1(5):e49. Epub 2005 Oct 21.
• PC Babbitt, PE Bourne, SD Mooney 2005 Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure. Pacific Symposium on Biocomputing 319-321
• J-L Chung, W. Wang and P.E. Bourne 2005 Exploiting Sequence and Structure Homology to Find Protein-Protein Binding Sites Proteins: Structure, Function and Bioinformatics. 62(3) 630-640.
• J.L. Moreland, A.Gramada, O.V. Buzko, Q. Zhang and P.E. Bourne 2005 The Molecular Biology Toolkit (mbt): A Modular Platform for Developing Molecular Visualization Applications. BMC Bioinformatics , 6:21.
• L. Xie and P.E. Bourne 2005 Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets and Homology Models. PLoS Comp Biol 1(3) e31.
• S. Yang, R.F. Doolittle and P.E. Bourne 2005 Phylogeny Determined through Protein Domain Content Proc. Nat. Acad. Sci. ( USA ) 102(2) 373-378. (Science, Editors Choice.)
• Y. Jia and T. G. Dewey “A Random Polymer Model of the Statistical Significance of Structure Alignment” J. Comp. Biol. (2005) 12 , 298-313.
• P. Chang, A. Rinne and T. G. Dewey, “Protein Structure Alignment Based on Coding of Topological Measures” submitted Bioinformatics (2005). (*)
• Podtelezhnikov, A. and Wild, D.L. Exhaustive Metropolis Monte Carlo sampling and analysis of polyalanine conformations adopted under the influence of hydrogen bonds. Proteins: Structure, Function and Bioinformatics , 61:94-104 (2005).
• Saqi, M.A.S. and Wild, D.L. Expectations from structural genomics revisited: an analysis of structural genomics targets. American Journal of Pharmacogenomics , 5(5):339-342 (2005).
• Chu W., Ghahramani, Z., Falciani, F. and Wild, D.L. Biomarker Discovery in Microarray Gene Expression Data with Gaussian Processes. Bioinformatics , 21: 3385-3393 (2005).
• Y.Ye and A.Godzik “Multiple flexible structure alignment using partial order graphs” Bioinformatics, 2005, 21 :2362-9
• I. Friedberg and A. Godzik “Fragnostic: walking through protein structure space” Nucleic Acids Res (2005), 33 (Web Server issue):W249-51.
• I. Friedberg and A. Godzik “Connecting the Protein Structure Universe using Recurring Fragments” (2005) Structure , 13 :1213-24.
• Birnbaum, A., Hayes, J., Li, W. W., Miller, M. A., Arzberger, P.W., Bourne, P. E. & Casanova, H. (2005). Grid Workflow Software for High-Throughput Proteome Annotation Pipeline. Lecture Notes In Computer Science. 3370:68-71
• Shahab, A., Chuon, D., Suzumura, T., Li, W. W., Byrnes, R. W.,Tanaka, K., Ang, L., Matsuoka, S., Bourne, P. E., Miller, M. A. & Arzberger, P. W. (2005). Grid Portal Interface for Interactive Use and Monitoring of High-Throughput Proteome Annotation. Lecture Notes In Computer Science. 3370:53-67

2004

• P.E. Bourne, C.K.J. Allerston, W. Krebs, W. Li, I.N Shindyalov, A. Godzik, I. Friedberg, T. Liu, D. Wild, S. Hwang, Z. Ghahramani L. Chen, and J. Westbrook (2004). The Status of Structural Genomics through the analysis of current targets and structures. Pacific Symposium on Biocomputing ed. R.B. Altman, A.K. Dunker, L. Hunter and T.E. Klein. World Scientific Publishing, Singapore, 404-416.
• A. Dubey, S. Hwang, C. Rangel, C.E. Rasmussen, Z. Ghahramani and D.L. Wild (2004). Clustering protein sequence and structure space with infinite Gaussian mixture models. Pacific Symposium in Biocomputing ed. R.B. Altman, A.K. Dunker, L. Hunter and T.E. Klein. World Scientific Publishing, Singapore, 399-410.
• Wilfred.W. Li, R.W. Byrnes, J. Hayes, V.M. Reyes, A. Birnbaum, A. Shahab, C. Mosley, D. Pekurovsky, G.B. Quinn, I.N. Shindyalov, H. Casanova, L. Ang, F. Berman, M. Miller, P.E. Bourne. (2004). The Encyclopedia of Life Project: Grid Software and Deployment. New Generation Computing.  22: 127-136 .
• Wild, D.L. and Saqi, M.A.S. (2004) Structural Proteomics: Inferring function from protein structure. Current Proteomics, 59-65.
• Y. Ye and A. Godzik (2004).Database Searching by Flexible Structure Alignment. Protein Science. 2004 Jul;13(7):1841-50.
• Y.Ye and A.Godzik (2004). FATCAT: a web server for flexible structure comparison and structure analog searching. Nucleic Acids Research. 2004 Jul 1;32(Web Server issue):W582-5.
• Y. Jia, T. G. Dewey, I. Shindyalov and P. Bourne “A New Scoring Function and Associated Statistical Significance for Structure Alignment by CE” , J. Comp. Biol. (2004) 11 , 787-799.
• I. Friedberg, L. Jaroszewski, Y. Ye, A. Godzik The interplay of fold recognition and experimental structure determination in structural genomics. Curr Opin Struct Biol. 2004 14:307-12.
• S. Verentik, P.E. Bourne, N.N. Alexandrov, I.N. Shindyalov. (2004) Towards consistent assignment of structural domains in proteins. Journal of Molecular Biology. 339(3), 647-678
• Alonso A., Sasin J., Bottini N., Friedberg I., Friedberg I., Osterman A., Godzik A., Hunter T., Dixon J., and Mustelin T. Protein Tyrosine Phosphatases in the Human Genome Cell (2004) Jun 11;117(6):699-711
• Chu W., Ghahramani Z. and Wild D.L. A Graphical Model for Protein Secondary Structure Prediction. Proceedings of the 21st International Conference on Machine learning, Banff, Canada, 2004.
• Chu W., Ghahramani Z. and Wild D. Predicting Protein Secondary Structure using Sigmoid Belief Networks to Parameterize Segmental Semi-Markov Models. Proceedings of the 12th European Symposium on Artificial Neural Networks (2004). D-side publications, Evere, Belgium.

2003

• Y. Ye and A. Godzik “Flexible structure alignment by chaining aligned fragment pairs allowing twists.” Bioinformatics (2003) 19, 246-255.
• K. Baldridge and P.E. Bourne (2003), The New Biology and the Grid. Chapter 40 pp 907-922 from Grid Computing - Making the Global Infrastructure a Reality (eds) F.Berman, G. Fox and T.Hey Wiley, New York.
• P.E. Bourne (2003) The Status of Structural Genomics Targets 2(5) 181-1182 (Editorial).
• Wilfred W. Li, Greg B. Quinn, Nickolai N. Alexandrov, Philip E. Bourne, and Ilya N. Shindyalov (2003) Proteins of Arabidopsis thaliana (PAT) database: A resource for comparative proteomics. Genome Biology 4(8). R51.
• D. Pekurovsky, I.N. Shindyalov, P.E. Bourne (2003) High Throughput Biological Data Processing on Massively Parallel Computers. A Case Study of Pairwise Structure Comparison and Alignment Using the Combinatorial Extension (CE) Algorithm. Bioinformatics. 20(12) 1940-1947.
• Y. Ye, W. Li, L. Jaroszewski, and A. Godzik (2003). A Segment Alignment Approach to Protein Comparison. Bioinformatics, 19:742-749.
• Y. Ye and A. Godzik (2003). Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics. Suppl 2:II246-II255.

2002

• J.V. Ponaramenko, P.E. Bourne and I.N. Shindyalov (2002) Building an Automated Classification of DNA-binding Protein Domains Bioinformatics 18:S192-201.