Philip E. Bourne

2008
49	EE	K. Bretonnel Cohen, Hong Yu, Philip E. Bourne, Lynette Hirschman: Session Introduction. Pacific Symposium on Biocomputing 2008: 551-555
48	EE	J. 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
47	EE	Stefan 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)
2007
46	EE	Jo-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
45	EE	Philip E. Bourne, Søren Brunak: ISMB 2006. ISMB (Supplement of Bioinformatics) 2006: 1-2
44	EE	Alessandro Sette, Huynh-Hoa Bui, John Sidney, Philip E. Bourne, Soren Buus, Ward Fleri, R. Kubo, O. 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
43	EE	Apostol Gramada, Philip E. Bourne: Multipolar representation of protein structure. BMC Bioinformatics 7: 242 (2006)
42	EE	Andrei 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
41	EE	Patricia 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
40	EE	John 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)
39	EE	Nita 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
37	EE	Philip E. Bourne: The Future of Bioinformatics. APBC 2004: 3
36	EE	Atif 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
35	EE	Adam 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
34	EE	Sean D. Mooney, Philip E. Bourne, Patricia C. Babbitt: Session Introduction. Pacific Symposium on Biocomputing 2004: 372-374
33	EE	Philip 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
32	EE	Dmitry 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)
31	EE	Werner 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)
29	EE	Werner 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)
28	EE	Yuting 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)
27	EE	Wilfred 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
24	EE	Philip E. Bourne: High Performance Computational Biology - Past Progress and Future Promise. CSB 2003: 13
23	EE	Werner 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
16	EE	Chittibabu 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
8	EE	Greg 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
4	EE	Ilya 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

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

Colors in the list of coauthors