Philip E. Bourne

	2009
59		Lei 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
58		K. Bretonnel Cohen, Hong Yu, Philip E. Bourne, Lynette Hirschman: Session Introduction. Pacific Symposium on Biocomputing 2008: 551-555
57		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
56		Julia 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)
55		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)
54		J. 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)
53		Raphael 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)
52		Qing 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
51		Lei 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)
50		Jo-Lan Chung, Wei Wang, Philip E. Bourne: High-throughput identification of interacting protein-protein binding sites. BMC Bioinformatics 8: (2007)
49		Jenny Gu, Philip E. Bourne: Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2. BMC Bioinformatics 8: (2007)
48		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
47		Philip E. Bourne, Søren Brunak: ISMB 2006. ISMB (Supplement of Bioinformatics) 2006: 1-2
46		Alessandro Sette, Huynh-Hoa Bui, John Sidney, Philip E. Bourne, Søren Buus, Ward Fleri, R. Kubo, Ole Lund, D. Nemazee, Julia V. Ponomarenko, Muthu Sathiamurthy, Scott Stewart, Scott Way, Stephen S. Wilson, Björn Peters: The Immune Epitope Database and Analysis Resource. PRIB 2006: 126-132
45		Apostol Gramada, Philip E. Bourne: Multipolar representation of protein structure. BMC Bioinformatics 7: 242 (2006)
44		Randi Vita, Kerrie Vaughan, Laura Zarebski, Nima Salimi, Ward Fleri, Howard Grey, Muthu Sathiamurthy, John Mokili, Huynh-Hoa Bui, Philip E. Bourne, Julia V. Ponomarenko, Romulo de Castro Jr., Russell K. Chan, John Sidney, Stephen S. Wilson, Scott Stewart, Scott Way, Björn Peters, Alessandro Sette: Curation of complex, context-dependent immunological data. BMC Bioinformatics 7: 341 (2006)
43		Eric D. Scheeff, Philip E. Bourne: Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction. BMC Bioinformatics 7: 410 (2006)
42		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		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		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		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		Philip E. Bourne: The Future of Bioinformatics. APBC 2004: 3
36		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		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		Sean D. Mooney, Philip E. Bourne, Patricia C. Babbitt: Session Introduction. Pacific Symposium on Biocomputing 2004: 372-374
33		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		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		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		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		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		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		Philip E. Bourne: High Performance Computational Biology - Past Progress and Future Promise. CSB 2003: 13
23		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		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		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		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	[55]
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	Raphael A. Bauer	[53]
9	John E. Beaver	[48] [52]
10	Francine Berman (Fran Berman)	[27]
11	Helen M. Berman	[9] [15] [18] [26] [30] [39] [42]
12	T. N. Bhat	[9] [15] [18]
13	John Biggs	[6]
14	Adam Birnbaum	[27] [35]
15	Wolfgang Bluhm	[18] [26] [39]
16	Peer Bork	[55]
17	Søren Brunak	[47]
18	Huynh-Hoa Bui	[44] [46] [52] [56]
19	Søren Buus	[46] [52]
20	Oleksandr V. Buzko	[40]
21	Robert W. Byrnes	[27] [36]
22	Monica Campillos	[55]
23	J. Gregory Caporaso	[57]
24	Henri Casanova	[27] [35]
25	Romulo de Castro Jr.	[44]
26	E. Cayanis	[2]
27	Russell K. Chan	[44]
28	Weider Chang	[1] [3] [4]
29	Li Chen	[26] [33] [39] [42]
30	Jo-Lan Chung	[48] [50]
31	Danny Chuon	[36]
32	K. Bretonnel Cohen	[57] [58]
33	J. A. Cooper	[4]
34	Paul A. Craig	[21]
35	Joanna de la Cruz	[42]
36	Nita Deshpande	[26] [39] [57]
37	T. Gregory Dewey	[28]
38	Mathias Dunkel	[55]
39	Zukang Feng	[9] [15] [18] [26] [39]
40	J. Lynn Fink	[54] [57]
41	S. G. Fischer	[2]
42	Ward Fleri	[26] [44] [46]
43	Judith L. Flippen-Anderson	[39]
44	Arno Formella	[53]
45	Sune Frankild	[52]
46	Iddo Friedberg	[33]
47	Cornelius Frömmel	[53]
48	Nicholas Fusseder	[56]
49	Andreas Gewiess	[55]
50	Zoubin Ghahramani	[33]
51	Christoph Gille	[53]
52	Gary Gilliland	[9] [15] [18]
53	Adam Godzik	[33]
54	Andrean Goede	[53]
55	David Goodsell	[21]
56	Apostol Gramada	[40] [45]
57	Rachel Kramer Green	[26] [39]
58	Jason Greenbaum	[52]
59	Douglas S. Greer	[18] [19]
60	Howard Grey	[44]
61	Michael Gribskov	[10] [12]
62	Jenny Gu	[49]
63	Chittibabu Guda	[16] [25]
64	Aysam Guerler	[53]
65	Stefan Günther	[55]
66	Dan Gusfield	[38]
67	Pernille Haste-Andersen	[52]
68	Jim Hayes (James Hayes)	[27] [35]
69	Lynette Hirschman	[58]
70	Debra A. Hope	[12]
71	Andreas Hoppe	[53]
72	Lawrence Hunter	[57]
73	Seungwoo Hwang	[33]
74	Shri Jain	[15] [18]
75	Lars Juhl Jensen	[55]
76	Nancy Jensen	[12]
77	Yuting Jia	[28]
78	Yohan Kim	[52]
79	S. Kistler	[2]
80	Ernst-Walter Knapp	[53]
81	Charlie Knezevich	[39]
82	Andrei Kouranov	[42]
83	Werner G. Krebs	[23] [29] [31] [33]
84	R. Kubo	[46]
85	Michael Kuhn	[55]
86	Sergey Kushch	[54]
87	Thomas Lengauer	[12]
88	Wei Li	[56]
89	Wilfred W. Li	[13] [17] [27] [33] [35] [36]
90	Tong Liu	[33]
91	Sifang Lu	[25]
92	Ole Lund	[46] [52]
93	Claus Lundegaard	[52]
94	D. Martinez	[8]
95	Satoshi Matsuoka	[36]
96	Jeffrey C. Merino-Ott	[26] [39]
97	Mark A. Miller	[27] [35] [36]
98	Julie C. Mitchell	[12]
99	John Mokili	[44]
100	Sean D. Mooney	[34] [41]
101	John L. Moreland	[40]
102	Coleman Mosley	[27]
103	D. Nemazee	[46]
104	Morten Nielsen	[52]
105	Dmitry Pekurovsky	[22] [27] [32]
106	Björn Peters	[44] [46] [52] [56]
107	Evangelia Petsalaki	[55]
108	Julia V. Ponomarenko	[20] [44] [46] [52] [56]
109	Thorsten Pöschel	[53]
110	Robert Preissner	[53] [55]
111	Calton Pu	[1] [3] [6]
112	Greg B. Quinn	[8] [27]
113	Veerasamy Ravichandran	[15] [18]
114	Boojala V. B. Reddy	[13] [17]
115	Vicente M. Reyes	[27]
116	Robert B. Russell	[55]
117	Nima Salimi	[44]
118	Muthu Sathiamurthy	[44] [46]
119	Eric D. Scheeff	[12] [16] [25] [43] [48]
120	Bohdan Schneider	[15]
121	Kata Schneider	[15]
122	Reinhard Schneider	[55]
123	E. A. Schon	[2]
124	Christian Senger	[55]
125	Alessandro Sette	[44] [46] [52] [56]
126	Atif Shahab	[27] [36]
127	Ilya N. Shindyalov	[1] [3] [4] [5] [9] [13] [14] [16] [17] [20] [22] [25] [27] [28] [32] [33]
128	John Sidney	[44] [46]
129	Roman Skoblo	[55]
130	Chris Smith	[12]
131	Scott Stewart	[44] [46]
132	Shawn Strande	[12]
133	Toyotaro Suzumura	[36]
134	Kouji Tanaka	[36]
135	John G. Tate	[17]
136	Narmada Thanki	[15] [18]
137	Wayne Townsend-Merino	[26] [39]
138	Eduardo Garcia Urdiales	[55]
139	Kerrie Vaughan	[44]
140	Randi Vita	[44]
141	H.-P. Wang	[8]
142	Peng Wang	[52]
143	Wei Wang	[50]
144	Scott Way	[44] [46]
145	J. Weiss	[2]
146	Helge Weissig	[7] [9] [12] [15] [18] [26]
147	John D. Westbrook	[9] [11] [15] [18] [19] [26] [30] [33] [39] [42]
148	David L. Wild	[33]
149	Parker R. Williams	[54]
150	Stephen S. Wilson	[44] [46]
151	Burghardt Wittig	[53]
152	Lei Xie	[42] [51] [59]
153	Li Xie	[59]
154	Lie Xie	[39]
155	Peng Yang	[21]
156	Hong Yu	[58]
157	Laura Zarebski	[44]
158	P. Zhang	[2]
159	Qing Zhang	[39] [40] [52]
160	Zhanyang Zhu	[52]
161	Valentin Ziegler	[53]

Colors in the list of coauthors