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Philip E. Bourne Vis

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*2009
57EELei Xie, Li Xie, Philip E. Bourne: A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. Bioinformatics 25(12): (2009)
2008
56EEK. Bretonnel Cohen, Hong Yu, Philip E. Bourne, Lynette Hirschman: Session Introduction. Pacific Symposium on Biocomputing 2008: 551-555
55EEJ. Gregory Caporaso, Nita Deshpande, J. Lynn Fink, Philip E. Bourne, K. Bretonnel Cohen, Lawrence Hunter: Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks. Pacific Symposium on Biocomputing 2008: 640-651
54EEJulia V. Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E. Bourne, Alessandro Sette, Björn Peters: ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics 9: (2008)
53EEStefan Günther, Michael Kuhn, Mathias Dunkel, Monica Campillos, Christian Senger, Evangelia Petsalaki, Jessica Ahmed, Eduardo Garcia Urdiales, Andreas Gewiess, Lars Juhl Jensen, Reinhard Schneider, Roman Skoblo, Robert B. Russell, Philip E. Bourne, Peer Bork, Robert Preissner: SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Research 36(Database-Issue): 919-922 (2008)
52EEJ. Lynn Fink, Sergey Kushch, Parker R. Williams, Philip E. Bourne: BioLit: integrating biological literature with databases. Nucleic Acids Research 36(Web-Server-Issue): 385-389 (2008)
51EERaphael A. Bauer, Philip E. Bourne, Arno Formella, Cornelius Frömmel, Christoph Gille, Andrean Goede, Aysam Guerler, Andreas Hoppe, Ernst-Walter Knapp, Thorsten Pöschel, Burghardt Wittig, Valentin Ziegler, Robert Preissner: Superimposé: a 3D structural superposition server. Nucleic Acids Research 36(Web-Server-Issue): 47-54 (2008)
50EEQing Zhang, Peng Wang, Yohan Kim, Pernille Haste-Andersen, John E. Beaver, Philip E. Bourne, Huynh-Hoa Bui, Søren Buus, Sune Frankild, Jason Greenbaum, Ole Lund, Claus Lundegaard, Morten Nielsen, Julia V. Ponomarenko, Alessandro Sette, Zhanyang Zhu, Björn Peters: Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Research 36(Web-Server-Issue): 513-518 (2008)
2007
49EELei Xie, Philip E. Bourne: A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. BMC Bioinformatics 8(S-4): (2007)
48EEJo-Lan Chung, Wei Wang, Philip E. Bourne: High-throughput identification of interacting protein-protein binding sites. BMC Bioinformatics 8: (2007)
47EEJenny Gu, Philip E. Bourne: Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2. BMC Bioinformatics 8: (2007)
46EEJo-Lan Chung, John E. Beaver, Eric D. Scheeff, Philip E. Bourne: Con-Struct Map: a comparative contact map analysis tool. Bioinformatics 23(18): 2491-2492 (2007)
2006
45EEPhilip E. Bourne, Søren Brunak: ISMB 2006. ISMB (Supplement of Bioinformatics) 2006: 1-2
44EEAlessandro Sette, Huynh-Hoa Bui, John Sidney, Philip E. Bourne, Søren Buus, Ward Fleri, R. Kubo, Ole Lund, D. Nemazee, Julia V. Ponomarenko, M. Sathiamurthy, S. Stewart, S. Way, S. S. Wilson, Björn Peters: The Immune Epitope Database and Analysis Resource. PRIB 2006: 126-132
43EEApostol Gramada, Philip E. Bourne: Multipolar representation of protein structure. BMC Bioinformatics 7: 242 (2006)
42EEAndrei Kouranov, Lei Xie, Joanna de la Cruz, Li Chen, John D. Westbrook, Philip E. Bourne, Helen M. Berman: The RCSB PDB information portal for structural genomics. Nucleic Acids Research 34(Database-Issue): 302-305 (2006)
2005
41EEPatricia C. Babbitt, Philip E. Bourne, Sean D. Mooney: Introduction to Informatics Approaches in Structural Genomics: Modeling and Representation of Function from Macromolecular STructure. Pacific Symposium on Biocomputing 2005
40EEJohn L. Moreland, Apostol Gramada, Oleksandr V. Buzko, Qing Zhang, Philip E. Bourne: The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications. BMC Bioinformatics 6: 21 (2005)
39EENita Deshpande, Kenneth J. Addess, Wolfgang Bluhm, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Qing Zhang, Charlie Knezevich, Lie Xie, Li Chen, Zukang Feng, Rachel Kramer Green, Judith L. Flippen-Anderson, John D. Westbrook, Helen M. Berman, Philip E. Bourne: The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Research 33(Database-Issue): 233-237 (2005)
2004
38 Philip E. Bourne, Dan Gusfield: Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004, San Diego, California, USA, March 27-31, 2004 ACM 2004
37EEPhilip E. Bourne: The Future of Bioinformatics. APBC 2004: 3
36EEAtif Shahab, Danny Chuon, Toyotaro Suzumura, Wilfred W. Li, Robert W. Byrnes, Kouji Tanaka, Larry Ang, Satoshi Matsuoka, Philip E. Bourne, Mark A. Miller, Peter W. Arzberger: Grid Portal Interface for Interactive Use and Monitoring of High-Throughput Proteome Annotation. LSGRID 2004: 53-67
35EEAdam Birnbaum, James Hayes, Wilfred W. Li, Mark A. Miller, Peter W. Arzberger, Philip E. Bourne, Henri Casanova: Grid Workflow Software for a High-Throughput Proteome Annotation Pipeline. LSGRID 2004: 68-81
34EESean D. Mooney, Philip E. Bourne, Patricia C. Babbitt: Session Introduction. Pacific Symposium on Biocomputing 2004: 372-374
33EEPhilip E. Bourne, C. K. J. Allerston, Werner G. Krebs, Wilfred W. Li, Ilya N. Shindyalov, Adam Godzik, Iddo Friedberg, Tong Liu, David L. Wild, Seungwoo Hwang, Zoubin Ghahramani, Li Chen, John D. Westbrook: The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures. Pacific Symposium on Biocomputing 2004: 375-386
32EEDmitry Pekurovsky, Ilya N. Shindyalov, Philip E. Bourne: A case study of high-throughput biological data processing on parallel platforms. Bioinformatics 20(12): 1940-1947 (2004)
31EEWerner G. Krebs, Philip E. Bourne: Statistically rigorous automated protein annotation. Bioinformatics 20(7): 1066-1073 (2004)
30 Philip E. Bourne, John D. Westbrook, Helen M. Berman: The Protein Data Bank and lessons in data management. Briefings in Bioinformatics 5(1): 23-30 (2004)
29EEWerner G. Krebs, Philip E. Bourne: Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. J. Bioinformatics and Computational Biology 2(1): 61-76 (2004)
28EEYuting Jia, T. Gregory Dewey, Ilya N. Shindyalov, Philip E. Bourne: A New Scoring Function and Associated Statistical Significance for Structure Alignment by CE. Journal of Computational Biology 11(5): 787-799 (2004)
27EEWilfred W. Li, Robert W. Byrnes, Jim Hayes, Adam Birnbaum, Vicente M. Reyes, Atif Shahab, Coleman Mosley, Dmitry Pekurovsky, Greg B. Quinn, Ilya N. Shindyalov, Henri Casanova, Larry Ang, Fran Berman, Peter W. Arzberger, Mark A. Miller, Philip E. Bourne: The Encyclopedia of Life Project: Grid Software and Deployment. New Generation Comput. 22(2): (2004)
26 Philip E. Bourne, Kenneth J. Addess, Wolfgang Bluhm, Li Chen, Nita Deshpande, Zukang Feng, Ward Fleri, Rachel Kramer Green, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Helge Weissig, John D. Westbrook, Helen M. Berman: The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Research 32(Database-Issue): 223-225 (2004)
25 Chittibabu Guda, Sifang Lu, Eric D. Scheeff, Philip E. Bourne, Ilya N. Shindyalov: CE-MC: a multiple protein structure alignment server. Nucleic Acids Research 32(Web-Server-Issue): 100-103 (2004)
2003
24EEPhilip E. Bourne: High Performance Computational Biology - Past Progress and Future Promise. CSB 2003: 13
23EEWerner G. Krebs, Philip E. Bourne: Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. CSB 2003: 180-189
22 Dmitry Pekurovsky, Ilya N. Shindyalov, Philip E. Bourne: Parallel Processing on Large Redudant Biological Data Sets: Protein Structures Classification with CEPAR. PARCO 2003: 661-668
21 Peng Yang, Paul A. Craig, David Goodsell, Philip E. Bourne: BioEditor - Simplifying Macromolecular Structure Annotation. Bioinformatics 19(7): 897-898 (2003)
2002
20 Julia V. Ponomarenko, Philip E. Bourne, Ilya N. Shindyalov: Building an automated classification of DNA-binding protein domains. ECCB 2002: 192-201
19 Douglas S. Greer, John D. Westbrook, Philip E. Bourne: An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics 18(9): 1280-1281 (2002)
18 John D. Westbrook, Zukang Feng, Shri Jain, T. N. Bhat, Narmada Thanki, Veerasamy Ravichandran, Gary Gilliland, Wolfgang Bluhm, Helge Weissig, Douglas S. Greer, Philip E. Bourne, Helen M. Berman: The Protein Data Bank: unifying the archive. Nucleic Acids Research 30(1): 245-248 (2002)
17 Wilfred W. Li, Boojala V. B. Reddy, John G. Tate, Ilya N. Shindyalov, Philip E. Bourne: CKAAPs DB: a Conserved Key Amino Acid Positions DataBase. Nucleic Acids Research 30(1): 409-411 (2002)
2001
16EEChittibabu Guda, Eric D. Scheeff, Philip E. Bourne, Ilya N. Shindyalov: A New Algorithm for the Alignment of Multiple Protein Structures Using Monte Carlo Optimization. Pacific Symposium on Biocomputing 2001: 275-286
15 T. N. Bhat, Philip E. Bourne, Zukang Feng, Gary Gilliland, Shri Jain, Veerasamy Ravichandran, Bohdan Schneider, Kata Schneider, Narmada Thanki, Helge Weissig, John D. Westbrook, Helen M. Berman: The PDB data uniformity project. Nucleic Acids Research 29(1): 214-218 (2001)
14 Ilya N. Shindyalov, Philip E. Bourne: A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm. Nucleic Acids Research 29(1): 228-229 (2001)
13 Wilfred W. Li, Boojala V. B. Reddy, Ilya N. Shindyalov, Philip E. Bourne: CKAAPs DB: a conserved key amino acid positions database. Nucleic Acids Research 29(1): 329-331 (2001)
2000
12 Philip E. Bourne, Michael Gribskov, Russ B. Altman, Nancy Jensen, Debra A. Hope, Thomas Lengauer, Julie C. Mitchell, Eric D. Scheeff, Chris Smith, Shawn Strande, Helge Weissig: Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, August 19-23, 2000, La Jolla / San Diego, CA, USA AAAI 2000
11 John D. Westbrook, Philip E. Bourne: STAR/mmCIF: An ontology for macromolecular structure. Bioinformatics 16(2): 159-168 (2000)
10 Philip E. Bourne, Michael Gribskov: ISMB-2000: Bioinformatics enters a new millennium. Bioinformatics 16(9): 749 (2000)
9 Helen M. Berman, John D. Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne: The Protein Data Bank. Nucleic Acids Research 28(1): 235-242 (2000)
1999
8EEGreg B. Quinn, H.-P. Wang, D. Martinez, Philip E. Bourne: Developing Protein Documentaries and Other Multimedia Presentations for Molecular Biology. Pacific Symposium on Biocomputing 1999: 380-391
7 Helge Weissig, Philip E. Bourne: An analysis of the Protein Data Bank in search of temporal and global trends. Bioinformatics 15(10): 807-831 (1999)
1997
6 John Biggs, Calton Pu, Philip E. Bourne: Code Generation through Annotation of Macromolecular Structure Data. ISMB 1997: 52-55
5 Ilya N. Shindyalov, Philip E. Bourne: Protein data representation and query using optimized data decomposition. Computer Applications in the Biosciences 13(5): 487-496 (1997)
1995
4EEIlya N. Shindyalov, Weider Chang, J. A. Cooper, Philip E. Bourne: Design and use of a software framework to obtain information derived from macromolecular structure data. HICSS (5) 1995: 207-216
1994
3 Weider Chang, Ilya N. Shindyalov, Calton Pu, Philip E. Bourne: Design and Application of a C++ Macromolecular Class Library. ISMB 1994: 70-77
2 P. Zhang, E. A. Schon, S. G. Fischer, E. Cayanis, J. Weiss, S. Kistler, Philip E. Bourne: An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA. Computer Applications in the Biosciences 10(3): 309-317 (1994)
1 Weider Chang, Ilya N. Shindyalov, Calton Pu, Philip E. Bourne: Design and application of PDBlib, a C++ macromolecular class library. Computer Applications in the Biosciences 10(6): 575-586 (1994)

Coauthor Index

1Kenneth J. Addess [26] [39]
2Jessica Ahmed [53]
3C. K. J. Allerston [33]
4Russ B. Altman [12]
5Larry Ang [27] [36]
6Peter W. Arzberger [27] [35] [36]
7Patricia C. Babbitt [34] [41]
8Raphael A. Bauer [51]
9John E. Beaver [46] [50]
10Francine Berman (Fran Berman) [27]
11Helen M. Berman [9] [15] [18] [26] [30] [39] [42]
12T. N. Bhat [9] [15] [18]
13John Biggs [6]
14Adam Birnbaum [27] [35]
15Wolfgang Bluhm [18] [26] [39]
16Peer Bork [53]
17Søren Brunak [45]
18Huynh-Hoa Bui [44] [50] [54]
19Søren Buus [44] [50]
20Oleksandr V. Buzko [40]
21Robert W. Byrnes [27] [36]
22Monica Campillos [53]
23J. Gregory Caporaso [55]
24Henri Casanova [27] [35]
25E. Cayanis [2]
26Weider Chang [1] [3] [4]
27Li Chen [26] [33] [39] [42]
28Jo-Lan Chung [46] [48]
29Danny Chuon [36]
30K. Bretonnel Cohen [55] [56]
31J. A. Cooper [4]
32Paul A. Craig [21]
33Joanna de la Cruz [42]
34Nita Deshpande [26] [39] [55]
35T. Gregory Dewey [28]
36Mathias Dunkel [53]
37Zukang Feng [9] [15] [18] [26] [39]
38J. Lynn Fink [52] [55]
39S. G. Fischer [2]
40Ward Fleri [26] [44]
41Judith L. Flippen-Anderson [39]
42Arno Formella [51]
43Sune Frankild [50]
44Iddo Friedberg [33]
45Cornelius Frömmel [51]
46Nicholas Fusseder [54]
47Andreas Gewiess [53]
48Zoubin Ghahramani [33]
49Christoph Gille [51]
50Gary Gilliland [9] [15] [18]
51Adam Godzik [33]
52Andrean Goede [51]
53David Goodsell [21]
54Apostol Gramada [40] [43]
55Rachel Kramer Green [26] [39]
56Jason Greenbaum [50]
57Douglas S. Greer [18] [19]
58Michael Gribskov [10] [12]
59Jenny Gu [47]
60Chittibabu Guda [16] [25]
61Aysam Guerler [51]
62Stefan Günther [53]
63Dan Gusfield [38]
64Pernille Haste-Andersen [50]
65Jim Hayes (James Hayes) [27] [35]
66Lynette Hirschman [56]
67Debra A. Hope [12]
68Andreas Hoppe [51]
69Lawrence Hunter [55]
70Seungwoo Hwang [33]
71Shri Jain [15] [18]
72Lars Juhl Jensen [53]
73Nancy Jensen [12]
74Yuting Jia [28]
75Yohan Kim [50]
76S. Kistler [2]
77Ernst-Walter Knapp [51]
78Charlie Knezevich [39]
79Andrei Kouranov [42]
80Werner G. Krebs [23] [29] [31] [33]
81R. Kubo [44]
82Michael Kuhn [53]
83Sergey Kushch [52]
84Thomas Lengauer [12]
85Wei Li [54]
86Wilfred W. Li [13] [17] [27] [33] [35] [36]
87Tong Liu [33]
88Sifang Lu [25]
89Ole Lund [44] [50]
90Claus Lundegaard [50]
91D. Martinez [8]
92Satoshi Matsuoka [36]
93Jeffrey C. Merino-Ott [26] [39]
94Mark A. Miller [27] [35] [36]
95Julie C. Mitchell [12]
96Sean D. Mooney [34] [41]
97John L. Moreland [40]
98Coleman Mosley [27]
99D. Nemazee [44]
100Morten Nielsen [50]
101Dmitry Pekurovsky [22] [27] [32]
102Björn Peters [44] [50] [54]
103Evangelia Petsalaki [53]
104Julia V. Ponomarenko [20] [44] [50] [54]
105Thorsten Pöschel [51]
106Robert Preissner [51] [53]
107Calton Pu [1] [3] [6]
108Greg B. Quinn [8] [27]
109Veerasamy Ravichandran [15] [18]
110Boojala V. B. Reddy [13] [17]
111Vicente M. Reyes [27]
112Robert B. Russell [53]
113M. Sathiamurthy [44]
114Eric D. Scheeff [12] [16] [25] [46]
115Bohdan Schneider [15]
116Kata Schneider [15]
117Reinhard Schneider [53]
118E. A. Schon [2]
119Christian Senger [53]
120Alessandro Sette [44] [50] [54]
121Atif Shahab [27] [36]
122Ilya N. Shindyalov [1] [3] [4] [5] [9] [13] [14] [16] [17] [20] [22] [25] [27] [28] [32] [33]
123John Sidney [44]
124Roman Skoblo [53]
125Chris Smith [12]
126S. Stewart [44]
127Shawn Strande [12]
128Toyotaro Suzumura [36]
129Kouji Tanaka [36]
130John G. Tate [17]
131Narmada Thanki [15] [18]
132Wayne Townsend-Merino [26] [39]
133Eduardo Garcia Urdiales [53]
134H.-P. Wang [8]
135Peng Wang [50]
136Wei Wang [48]
137S. Way [44]
138J. Weiss [2]
139Helge Weissig [7] [9] [12] [15] [18] [26]
140John D. Westbrook [9] [11] [15] [18] [19] [26] [30] [33] [39] [42]
141David L. Wild [33]
142Parker R. Williams [52]
143S. S. Wilson [44]
144Burghardt Wittig [51]
145Lei Xie [42] [49] [57]
146Li Xie [57]
147Lie Xie [39]
148Peng Yang [21]
149Hong Yu [56]
150P. Zhang [2]
151Qing Zhang [39] [40] [50]
152Zhanyang Zhu [50]
153Valentin Ziegler [51]

Colors in the list of coauthors

Copyright © Tue Nov 3 08:52:44 2009 by Michael Ley (ley@uni-trier.de)