Bourne
Laboratory - Publications
Last Update October
2009
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2009
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C. L. Dupont, A
Butcher, R. Valas, P.E. Bourne, and G. Caetano-Anollés 2009 The Impact
of Trace Metal Chemistry on the Evolution of Life. In Preparation.
·
R.L Chang, L. Xie, L. Xie, P.E. Bourne B.O. Palsson 2009 Structural
Analysis and Metabolic Modeling Predicts Drug Off-targets Causing Response
Phenotypes. In Preparation.
·
L. Xie, T. Evangelidis, L. Xie and P.E. Bourne 2009 Repositioning HIV
Protease Inhibitors to Target the Human Kinome: A Chemical Systems Biology
Approach. In Preparation.
·
H. Zhang, P. Wang, N.
Papangelopoulos, Y. Xu, A. Sette, P.E. Bourne, O. Lund, J. Ponomarenko, M.
Nielsen and B. Peters 2009 Limitations of ab initio Predictions of Peptide Binding
to MHC class II Molecules PLoS ONE
Submitted.
·
A. Prlić, M.A. Martinez,
B.T. Yukich, B. Beran, P.W. Rose, P.E. Bourne, J.L. Fink 2009 Integration of
Open Access Literature into the RCSB Protein Data Bank Using BioLit. BMC Bioinformatics Submitted.
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J.L. Fink, P. Fernicola, R. Chandran, L Dirks, S. Parastatidis, A. Wade,
T. Hey, G. Quinn & P.E. Bourne 2009 Word Add-in for Ontology Recognition:
Semantic Enrichment of Scientific Literature. BMC Bioinformatics Submitted.
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J Hodlin, C.D. Bishop, F.A. Sharp and R.E. Valas 2009 A Creative
Celebration of Evolution Nature 461:733 [PDF]
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A. Bateman & P.E. Bourne 2009 Ten Simple Rules for Chairing a
Scientific Session PLoS Comp. Biol. 5(9):e1000517 [PDF]
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R.E. Valas & P.E. Bourne 2009 Structural Analysis of Polarizing
Indels: An Emerging Consensus on the Root of the Tree of Life. Biology Direct. 4(1) 30 [PDF]
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J.D. Durant, R.E. Amaro, L. Xie, M.D. Urbaniak, M.A.J. Ferguson, A.
Haapalainen, Z-J. Chen, A.M. Di Guilmi, F. Wunder, A. Tersteegen. P.E. Bourne
& J.A. McCammon 2009 A Multidimensional Strategy to Detect Secondary
Pharmacological Targets in the Absence of Global Structure and Sequence
Homology PLoS Comp Biol. Submitted.
·
H. Asher & P.E. Bourne 2009 Drivers of Change - Emergent Information
and Biotechnologies in Pharmacy
Informatics P.H. Anderson, S.M. McGuinness & P.E. Bourne (Eds.) Taylor
& Francis Chapter 2, pp 7-19.
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P.E. Bourne 2009 Computer and Informatics Basics in Pharmacy Informatics P.H. Anderson, S.M. McGuinness & P.E.
Bourne (Eds.) Taylor & Francis, Chapter 3, pp23-35.
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P.E. Bourne & S.M. McGuinness 2009 Controlled Vocabularies in Pharmacy Informatics P.H. Anderson, S.M.
McGuinness & P.E. Bourne (Eds.) Taylor & Francis, Chapter 4, pp37-52.
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P.E. Bourne 2009 Pharmaceutical Sciences in a Virtual World in Pharmacy Informatics P.H. Anderson, S.M.
McGuinness & P.E. Bourne (Eds.) Taylor & Francis Chapter 17, pp251-259.
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P.O. Anderson, S.M. McGuinness & P.E. Bourne 2009 What is Pharmacy
Informatics in in Pharmacy Informatics
P.H. Anderson, S.M. McGuinness & P.E. Bourne (Eds.) Taylor & Francis,
Chapter 1, pp3-5.
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R.E. Valas, S. Yang and P.E. Bourne 2009 Nothing in Protein Structure
Classification Makes Sense Except in the Light of Evolution Current Opinions in Structural Biology
19:1-6 [PDF]
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P.E. Bourne, K.
Briedis, C. Dupont, R. Valas, S. Yang 2008 Evolution of Molecular Repertoires: Genome Evolution in 
Evolutionary
Genomics and Systems Biology
G. Caetano-Anolles (Ed.) Wiley-Blackwell Inc. Accepted.
·
Q. Vicens and P.E.
Bourne 2009 Ten Simple Rules for Combining Teaching and Research PLoS Comp. Biol. 5(4):
e1000358 [PDF]
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J.L. Fink, H.
Weissig and P.E. Bourne 2009 Other Structure Based Databases in Structural Bioinformatics 2nd Edition J.
Gu and P.E. Bourne (Eds.) John Wiley and Sons NJ 321-338. [PDF]
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M.A.
Marti-Renom, E. Capriotti, I.N. Shindyalov and P.E. Bourne 2009 Structure
Comparison and Alignment in Structural
Bioinformatics 2nd Edition J. Gu and P.E. Bourne (Eds.) John Wiley and Sons
NJ 397-417. [PDF]
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S. Yang, R.
Valas and P.E. Bourne 2009 Evolution Studies Through Protein Structure in Structural Bioinformatics 2nd Edition J.
Gu and P.E. Bourne (Eds.) John Wiley and Sons NJ 559-571. [PDF]
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J. Gu and P.E.
Bourne 2009 CASP and Other Community-wide Assessments to Advance the Field of
Structure Prediction in Structural
Bioinformatics 2nd Edition J. Gu and P.E. Bourne (Eds.) John Wiley and Sons
NJ 665-678. [PDF]
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S.L Kinnings, N. Buchmeier, N. Liu, P.J.
Tonge L. Xie and P.E. Bourne 2009 Discovery
of Novel Drug Leads to Treat Multi-drug and Extensively Drug Resistant
Tuberculosis by Repositioning Safe Pharmaceuticals: A Chemical Genomics
Approach with Subsequent Biological Validation. PLoS Comp. Biol. 5(7) e1000423. [PDF]
·
L. Xie, L. Xie and P.E. Bourne 2009 A Unified Statistical Model to
Support Local Sequence Order Independent Similarity Searching for Ligand-binding
Sites and Its Application in Genome-based Drug Discovery 2009 Bioinformatics
25(12) 305-312 [PDF].
·
S. Yang and
P.E.Bourne 2009 The Evolutionary History of Protein Domains Viewed by Species
Phylogeny, PLoS ONE, submitted.
·
L. Xie, J. Li,
L. Xie, and P.E.Bourne 2009 Drug Discovery Using Chemical Systems Biology:
Identification of the Protein-Ligand Binding Network To Explain the Side
Effects of CETP Inhibitors, PLoS Comp.
Biol.. 5(5) e1000387 [PDF]
MiniReview in Genome Biol [PDF]
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S. Veretnik, C. Wills, P. Youkharibache, R.
Valas & P.E. Bourne 2009 Sm/Lsm genes provide a glimpse into the early
evolution of the spliceosome, PLoS Comp.
Biol.5(3) e10000315 [PDF]
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E. Browne, R. Dickin, P.E. Bourne 2009 A
Review of 2008 for PLoS Computational Biology PLoS Comp. Biol. 5(1) e1000275 [PDF]
2008
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P.E. Bourne and J.L.
Fink 2008 I am Not a Scientist I am a Number PLoS Comp. Biol. (Perspective),4(12):e1000247 [PDF]
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J.V. Ponomarenko, H-H. Bui, W. Li, N.
Fusseder, P.E. Bourne, A. Sette and B. Peters 2008 ElliPro: A New
Structure-based Tool for the Prediction of Antibody Epitopes, BMC Bioinformatics 9:514 [PDF].
·
A. Gramada and
P.E.Bourne 2008 Resolving a Distribution of Charge into Intrinsic Multipole
Moments: A Rankwise Distributed Multipole Analysis. Physical Review E,78, 066601 [PDF]..
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P.D. Karp, G. Sherlock, J.A. Gerlt, I. Sim,
I. Paulsen, P.C. Babbitt, K. Laderoute, L. Hunter, P. Sternberg, J. Wooley,
P.E.Bourne 2008 Changes to NIH Grant System May Backfire Science 322(5905) 1187-1188. [PDF]
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M. Corpas, N. Gehlenborg, S. Chandra Janga and P. E.
Bourne 2008 Ten Simple Rules for
Organizing a Scientific Meeting PLoS
Comp. Biol. 4(5) e10000024. [PDF]
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S.Veretnik, J.L.Fink, and P.E. Bourne 2008
Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. (Perspective). 4(7):
e1000136 [PDF].
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P.E.Bourne and L.M.Chalupa 2008 A New
Approach to Scientific Dissemination Materials
Today 11(6) 48 [PDF].
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R.
Bauer, P.E. Bourne, A. Formella, C. Frömmel, G. Cornelius G. Christoph, G.
Andrean, A. Aysam, A. Hoppe, E-W Knapp,
T. Pöschel, B. Wittig, V. Ziegler, R. Preissner 2008 Superimposé: A 3D
structural superposition server NAR 36(S2)
W47-54 [PDF].
·
J.L.Fink, S. Kushch, P. Williams & P.E.Bourne 2008 BioLit:
Integrating Biological Literature with Databases NAR 36(S2) W385-389 [PDF].
·
Q. Zhang, P. Wang, Y. Kim, P.
Haste-Andersen, J. Beaver, P.E. Bourne, H-H. Bui, S. Buus, S. Frankild, J.
Greenbaum, O. Lund, C. Lundegaard, M. Nielsen, J. Ponomarenko, A. Sette, Z.
Zhu, B. Peters 2008 Immune Epitope Database Analysis Resource (IEDB-AR) NAR. 36(S2) W513-W518 [PDF].
·
P.E.Bourne, J.L.Fink, M.Gerstein 2008 Open Access: Taking Full Advantage
of the Content PLoS Comp. Biol.
(Editorial) 4(3) e1000037 [PDF].
·
L. Xie and P.E. Bourne 2008 Detecting Evolutionary Linkages Across Fold
and Functional Space with Sequence Order Independent Profile-profile
Alignments. PNAS, 105(14) 5441-5446 [PDF].
·
R.
Valas and P.E. Bourne 2008 Rethinking Proteasome Evolution: Two Novel Bacterial
Proteasomes. J. Mol. Evol. 66(5)
494-504 [PDF]
[Video].
·
K.
Briedis, A. Starr and P.E. Bourne 2008 Analysis of the Human Kinome Using
Methods Including Fold Recognition Reveals Two Novel Kinases PLoS
ONE, 3(2): e1597 [PDF].
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J.G.
Caporaso, N. Deshpande, J.L. Fink, P.E. Bourne, K.B. Cohen and L. Hunter 2008 Intrinsic
Evaluation of Text Mining Systems May Not Predict Performance on Realistic
Tasks. Pacific Symposium on Biocomputing,
640-651 [PDF].
·
S. Günther, M.
Kuhn, M. Dunkel, M. Campillos, C. Senger, E. Petsalaki, J. Ahmed, E. Garcia
Urdiales, A. Gewiess, L. Juhl Jensen, R. Schneider, R. Skoblo, R.B. Russell,
P.E. Bourne, P. Bork and R. Preissner 2007 SuperTarget and Matador: Resources
for exploring drug-target relationships NAR,
36:D919-922 [PDF].
2007
·
J.
Gu and P.E.Bourne 2007 Ten Simple Rules for Graduate Students. PLoS Comp. Biol. 3(11) e229. [PDF]
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L.
Xie, J. Wang and P.E.Bourne 2007 In Silico Elucidation of the Molecular
Mechanism Defining the Adverse Effect of Selective Esterogen Receptor
Modulators. PLoS Comp. Biol., 3(11)
e217 [PDF].
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T.C.
Erren, P. Cullen, M. Erren and P.E.Bourne 2007 Ten Simple Rules for Doing Your
Best Research, According to Hamming PLoS
Comp. Biol., 3(10): e213 [PDF]
·
P.E. Bourne and S.E. Brenner 2007 Developing Computational Biology
3(9):e157 [PDF]
·
J.
Ponomarenko and P.E.Bourne 2007 Antibody-Protein Interactions: Benchmark
Datasets and Prediction Tools Evaluation BMC
Structural Biology 7(1):64 [HTML] [Video].
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J-L Chung, J. Beaver, E.D.
Scheeff and P.E. Bourne 2007 Con-Struct Map: a Comparative Contact Map Analysis
Tool Bioinformatics 23:2491-2492 [PDF].
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J.L.
Fink and P.E.Bourne 2007 Reinventing Scholarly Communication for the Electronic
Age. CT Watch, 3(3) 26-31 [HTML]
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H.M.
Berman, K. Hendrick, H. Nakamura, J. Markley, P.E. Bourne, J. Westbrook (2007) Realism about PDB Nature
Biotechnology, 25(8) 845-6. [PDF]
·
L.
Hunter, R.B.Altman and P.E. Bourne 2007 The International Society for
Computational Biology 10th Anniversary PLoS Comp. Biol. 3(6) e135 [PDF]
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J-L Chung, W Wang and P.E.Bourne 2007 High-throughput identification of
Interacting Protein-Protein Binding Sites. BMC
Bioinformatics, 8(1): 223 [PDF].
·
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, 8(Suppl
4):S9 [PDF].
·
P.E. Bourne 2007 Ten Simple Rules for Making Good Oral Presentations, PLoS Comp. Biol., 3(4)e77 [PDF]
[Video].
·
J.E
Beaver, P.E Bourne and J.V Ponomarenko 2007 EpitopeViewer: a Java Application for
the Visualization and Analysis of Immune Epitopes in the IEDB database. Immunome Research, 3(1):3 [PDF].
·
Q. Vicens and P.E.Bourne 2007 Ten Simple Rules for Collaboration PLoS Comp. Biol., 3(3) e44 [PDF].
·
P.E. Bourne and A. Godzik 2007 Structural Genomics in Bioinformatics – From Genomes to Therapies
T. Lengauer (Ed.) Wiley-VCH. p419-438. [PDF]
·
J.
Gu and P.E.Bourne 2007 Allosteric Fluctuation Transitions as Applied to Cyclin
Dependent Kinase 2 BMC Bioinformatics 8(1):45.
[PDF]
2006
·
P
Guda, P.E. Bourne and C. Guda 2006 Conserved Motifs in Voltahge-sensing and
Pore-forming Modules of Voltage-gated Ion Channel Proteins Biochem. Biophys. Res. Com. 352(2) 292-8 [PDF].
·
P.E.
Bourne and I. Friedberg 2006 Ten Simple Rules for Getting a Post Doc. PLoS Comp. Biol., (Editorial), 2(11)
e121. [PDF]
·
A.Sette,
H.H.Bui, J.Sidney, P.E.Bourne, S. Buus, W. Fleri, R.Kubo, O.Lund, D.Nemazee,
J.V.Ponomarenko, M.Sathiamurthy, S. Stweart, S.Way, S.S.Wilson and B. Peters
2006 The Immune Epitope Database and Analysis Resource Pattern Recognition in
Bioinformatics, Springer, Jagath C. Rajapakse, Limsoon Wong, Raj Acharya
(Eds) [PDF]
·
C.L.
Dupont, S.Yang, B. Palenik and P.E.Bourne 2006 Putative Imprints in Modern
Proteomes of Ancient Shifts in Trace Metal Geochemistry PNAS, 103(47) 17822-17827 [PDF] [Video].
·
P.E.Bourne
and J. McEntyre 2006 Biocurators: Contributors to the World of Science PLoS Comp. Biol., (Editorial) 2(10) e142
[PDF].
·
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 [html].
·
H.M. Berman, S.K. Burley, W. Chiu, A. Sali, A.
Adzhubei, P.E. Bourne, S.H. Bryant, R.L. Dunbrack, Jr., K. Fidelis, J. Frank,
A. Godzik, K. Henrick, A. Joachimiak, B. Heymann, D. Jones, J.L.
Markley, John Moult, G.T. Montelione, C. Orengo, M.G. Rossmann, B.
Rost,21 H. Saibil, T. Schwede, D.M. Standley, J.D. Westbrook 2006 Acrhiving
Structural Models of Biological Macromolecules. Structure, 14:1211-1217. [PDF]
·
P.E.Bourne
and A. Korngreen 2006 Ten Simple Rules for Reviewers. PLoS Comp. Biol., (Editorial), 2(9) e110 [HTML]
·
P.E.Bourne
2006 One Year of PLoS Computational Biology PLoS
Comp. Biol., (Editorial) 2(8):e111. [PDF]
·
P.E.
Bourne and S. Brunak 2006 ISMB 2006 (Editorial) Bioinformatics 22(14):e1-2 [PDF]
·
R.
Vita, K. Vaughan, L. Zarebski, N. Salimi, W. Fleri, H. Grey, M. Sathiamurthy,
J. Mokili, H-H. Bui, P.E Bourne, J. Ponomarenko, R. DE Castro Jr, R.K Chan, J.
Sidney, S.S Wilson, S. Stewart, S. Way, B. Peters and A. Sette 2006 Curation of
Complex, Content-dependant Immunological Data BMC Bioinformatics, 7(1), 341 [HTML]
·
J.
Gu, M. Gribskov and P.E. Bourne 2006 Wiggle – Predicting Functionally Flexible
Regions from Primary Sequence PLoS Comp.
Biol., 2(7) e90. [PDF][Video]
·
T.
Holland, S. Veretnik, I.N. Shindyalov, P.E. Bourne 2006 A Benchmark for Domain Assignment from Protein 3-dimensional Structure and it’s Applications J. Mol. Biol., 361(3), 562-590. [HTML].
·
A.
Gramada and P.E. Bourne 2006 Multipolar Representation of Protein Structure BMC Bioinformatics, 7:242 [HTML][Video].
·
J-L
Chung, W. Wang and P.E. Bourne 2006 Exploiting Sequence and Structure Homology
to Identify Protein-Protein Binding Sites Proteins: Structure, Function and
Bioinformatics 62(3) 630-640.
[PDF].
·
P.E.Bourne
and L.M.Chalupa 2006 Ten Simple Rules for Getting a Grant PLoS Comp. Biol., (Editorial) 2(2) e12 [pdf] [Video].
·
A.
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. [HTML]
2005.
·
E.
Scheeff and P.E. Bourne 2005 Structural Evolution of the Protein Kinase-Like
Superfamily PLoS Comp. Biol. 1(5): e49.
·
P.E.
Bourne, W.F. Bluhm, N. Deshpande, Q. Zhang, K. Burkhardt, H.M. Berman, J.L.
Flippen-Anderson 2005 The Protein Data Bank. The Encyclopedia of Medicinal
Chemistry Accepted.
·
P.E.
Bourne 2005 Ten Simple Rules for Getting Published PLoS Comp. Biol. 1(5) e57. [open
access][Video]
·
M.
Sathiamurthy, B. Peters, H. Bui, J. Sidney, J.Mokili, S.S. Wilson, W. Fleri,
D.L. McGuinness, P.E. Bourne and A. Sette 2005 An Ontology for Immune Epitopes:
Application to the Design of a Broad Scope Database of Immune Reactivities Immunome Research 1:2 [Open Access]
·
P.E.
Bourne 2005 In the Future will a Biological Database Really be Different from a
Biological Journal? PLoS Comp. Biol. 1(3) e34 [PDF]
·
P.M.D.
Fitzgerald, J. Westbrook, P.E. Bourne, B. McMahon, K.D. Watenpaugh, and H.M.
Berman 2003 The Macromolecular Crystallographic Information File (mmCIF) The
International Tables for X-ray Crystallography Volume G. In Press. [PDF]
·
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. [PDF]
·
B.
Peters, J. Sidney, P.E. Bourne, H-H Bui, S. Buus, G. Doh, W. Fleri, M.
Kronenberg, R. Kubo, O. Lund, D. Nemazee, J.V. Ponomarenko, M. Sathiamurthy, S.
Schoenberger, S. Stewart, P. Surko, S. Way, S. Wilson, A. Sette 2005 The Design
and Implementation of the Immune Epitope Data Base and Analysis Resource Immunogenetics.
57(5): 326-36
·
P.E.
Bourne, S.E. Brenner, M.B. Eisen (2005) PLoS Computational Biology: A New Community Journal. PLoS
Comp Biol 1(1): e4 [HTML]
·
B.
Peters, J. Sidney, P.E. Bourne, H-H Bui, S. Buus, G. Doh, W. Fleri, M.
Kronenberg, R. Kubo, O. Lund, D. Nemazee, J.V. Ponomarenko, M. Sathiamurthy, S.
Schoenberger, S. Stewart, P. Surko, S. Way, S. Wilson, A. Sette 2005 The Immune
Epitope Database and Analysis Resource: From Vision to Blueprint. PLoS
Biology, 3(3) e91. [PDF]
·
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.
·
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: 68-61.
·
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. [PDF] [Open Access]
·
J.V.
Ponomarenko, P.E. Bourne and I.N. Shindyalov 2005 Assigning New GO Annotations
to Protein Data Bank Sequences by Structural Homology Proteins: Structure,
Function and Bioinformatics 58: 855-865. [PDF]
·
Q.
Zhang, S. Veretnik and P.E.Bourne 2005 Structural Bioinformatics in
Bioinformatics Technologies, pp. 15-40, Ed. Y-P.P. Chen, Springer-Verlag,
Berlin.
- 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. [PDF] [Supplimental
Material] [Editor’s choice Science]
- N. Deshpande, K.J. Addess, W.F. Bluhm, J.C. Merino-Ott,
W.Townsend-Merino, Q. Zhang, C. Knezevich, L. Chen, Z. Feng, R. Kramer
Green, J.L. Flippen-Anderson, J. Westbrook, H.M. Berman and
P.E. Bourne 2005 The RCSB Protein Data
Bank: A Redesigned Query System and Relational Database Based on the mmCIF
Schema Nucleic Acids Research. 33: D233-D237. [PDF]
- 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. [PDF]
- P.E.Bourne
2004. Protein Resources in Encyclopedia of Biological Chemistry,
Eds W.J. Lennarz & M.D. Lane, Elsevier, Oxford, Vol. 3 pp 478-483.
- Li, W. W.,
Byrnes, R. W., Hayes, J., Birnbaum, A., Reyes, V. M., Shahab,A., Mosley,
C., Pekurovsky, D., Quinn, G. B., Shindyalov, I. N., Casanova, H., Ang,
L., Berman, F., Arzberger, P. W., Miller, M. A. & Bourne, P. E. 2004.
The Encyclopedia of Life Project: Grid Software and Deployment. New
Generation Computing, 22: 127-136.
- Y. Jia, G.T.
Dewey, I.N. Shindyalov and P.E. Bourne 2004 A New Scoring
Function and Associated Statistical Significance for Structure Alignment
by CE. J. Comp. Biol. 11(5) 787-799. [PDF]
- W.G Krebs and
P.E. Bourne 2004 Statistical and Visual Morph Movie Analysis of
Crystallographic Mutant Selection Bias in Protein Mutation Resource Data. J.
Bioinformatics and Computational Biology, 2(1) 61-75. [PDF]
- C. Guda, S.
Lu, E.D. Scheeff, P.E. Bourne and I.N. Shindyalov 2004 CE-MC: A
multiple protein structure alignment server. Nucleic Acids Research,
32 W100-W103. [PDF]
- 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 [PDF].
- D. Pekurovsky, I.N. Shindyalov, P.E.
Bourne 2004 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 [PDF].
- P.E. Bourne, J. Westbrook and
H.M. Berman 2004. The Protein Data Bank and Lessons Learned in Data
Management. Briefings in Bioinformatics. 5(1), 23-30. [PDF]
- W.G. Krebs and P.E. Bourne 2004
Statistically Rigorous Automated Protein Annotation Bioinformatics 10(7) 1066-1073 [PDF]
- H.M. Berman, P.E. Bourne and J.
Westbrook 2004 The Protein Data Bank: A Case Study in the Management of
Community Data. Current Proteomics 1, 49-57. [PDF]
- P.E.
Bourne, K.J. Addess, W.F. Bluhm, L. Chen, N. Deshpande, Z. Feng3,
R. Kramer Green, J. C. Merino-Ott, W. Townsend-Merino, H. Weissig, J.
Westbrook, H. M. Berman 2004. The Distribution and
Query Systems of the RCSB Protein Data Bank Nucleic Acids Research,
32, D223-225 [PDF]
- 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. 2004 Pacific Symposium on Biocomputing 404-416.
[html]
2003
- P.E. Bourne 2003 The Status of
Structural Genomics Targets 2(5) 181-1182 (Editorial). [PDF]
- W.G Krebs and P.E. Bourne 2003
Statistical and Visual Morph Movie Analysis of Crystallographic Mutant
Selection Bias in Protein Mutation Resource Data. Proceedings of the
2003 IEEE Computer Society Bioinformatics Conference Proceedings 180-189
[PDF]..
- W.W. Li1, G.B.
Quinn, N. N. Alexandrov, P.E. Bourne and I.N. Shindyalov 2003
Proteins of Arabidopsis thaliana (PAT) database: A resource for
comparative proteomics Genome Biology 4(8), R51 [PDF]
- K.S. Doctor, J. Reed, A. Godzik
and P.E.Bourne 2003 The Apoptosis Database Cell Death and Differentiation
10(6), 621-633. [PDF]
- P. Yang, P.A. Craig, D.
Goodsell and P.E. Bourne 2003 BioEditor - Simplifying Macromolecular
Structure Annotation Bioinformatics 19(7) 897-898. [PDF]
- P.E.Bourne 2003 Free access to
publicly funded databases is vital Nature 421, 786 [PDF]
- H.M. Berman, P.E. Bourne, J.D.
Westbrook and C. Zardecki 2003 The Protein Data Bank pp 389-406 from Structure
(ed.) Chasman Marcel Decker Inc. NY.
- 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.
2002
- J.V. Ponaramenko, I.N. Shindyalov and P.E.
Bourne 2002 Building
an Automated Classification of DNA-binding Protein Domains Bioinformatics
18:S192-201.[pdf]
- P Craig, P Yang and PE Bourne 2002
BioEditor A Tool for Structure Annotation FASEB J 16 (5):
A741-A742.
- P.E. Bourne 2002 Science's Policy on
Data Deposition. Science 296, 1609 (Letter)
- I.N. Shindyalov and P.E. Bourne 2002
New Insights into Protein Fold Space and Sequence-Structure Relationships.
Structure Prediction:Bioinformtic Approach, Chapter 17, pp 417-428,
Ed. I. Tsigelny. Int'l University Line, La Jolla, CA.
- Chittibabu Guda, Eric D. Scheeff,
Philip E. Bourne, and Ilya N. Shindyalov 2002, Comparative Analysis of
Protein Structure: New Concepts and Approaches for Multiple Structure
Alignment. Structure Prediction:Bioinformtic Approach. Chapter 19,
pp 449-459. Ed. I. Tsigelny, Int'l University Line, La Jolla, CA.
- Eric D. Scheeff, Philip E. Bourne, and
Ilya N. Shindyalov 2002 Comparative Analysis of Protein Structure:
Automated vs. Manual Alignment of the Protein Kinase Family. Protein
Structure Prediction:Bioinformtic Approach, Chapter 20, pp 463-475.
Ed. I. Tsigelny, Int'l University Line, La Jolla, CA.
- H.M. Berman, T. Battistuz, T.N.Bhat,
W.F. Bluhm, P.E. Bourne, K. Burkhardt, Z. Feng, G.L. Gilliland, L. Iype,
S. Jain, P. Fagan, J. Marvin, V. Ravichandran, B. Schneider, N. Thanki, D.
Padilla, H. Weissig, J.D. Westbrook, C. Zardecki 2002 The Protein Data
Bank Acta Cryst. D58, 899-907. [pdf]
- I.N. Shindyalov and P.E. Bourne 2002 Structure
Structure Comparison and Alignment Structural Bioinformatics
Chapter 16 Ed. H. Weissig and P.E. Bourne Wiley and Associates, NY.
- H. Wessig and P.E. Bourne 2002 Other Structure
Based Databases Structural Bioinformatics Chapter 11 Ed. H. Weissig
and P.E. Bourne Wiley and Associates, NY.
- B.V.B Reddy and P.E. Bourne 2002 A User's
Perspective on the Structure Classification of Proteins (SCOP) Structural
Bioinformatics Chapter 12 Ed. H. Weissig and P.E. Bourne Wiley and
Associates, NY.
- H.M. Berman, D. Goodsell and P.E. Bourne 2002
Proteins Sturctures: From Famine to Feast American Scientist 90:
350-359. [synopsis]
[Full PDF]
- DS. Greer, JD.
Westbrook and PE. Bourne 2002 An Ontology Driven Architecture for
Derived Representations of Macromolecular Structure Bioinformatics 18: 1280-128 [pdf].
- BVB Reddy, W. Li, and P.E.Bourne 2002
Conserved Key Amino Acid Positions Used to Morph Protein Folds Biopolymers
64(3):139-145. [pdf]
- H.Weissig and P.E. Bourne 2002
Macromolecular Structure Databases Acta Cryst. D 58(6) 908-915. [pdf]
- A. Kuller, W. Fleri, W.F. Bluhm, J.L.
Smith, J. Westbrook and P.E.Bourne 2001. BioSync: A Biologist's Guide to
Synchrotron Resources TIBS 27(4):213-215 [pdf].
- J. Westbrook, Z.Feng, S. Jain,
T.N.Bhat, N. Thanki, V.Ravichandran, G.L.Gilliland, W.Bluhm, H. Weissig,
D.S.Greer, P.E.Bourne, and H.M.Berman 2002 The Protein Data Bank: Unifying
the Archive. Nucleic Acids Research, 30:245-248. [pdf]
- W. Li, BVB Reddy, J. Tate, IN
Shindyalov and P.E.Bourne 2002 CKAAPs DB: A Conserved Key Amino Acid
Positions Database. Nucleic Acids Research 30: 409-411. [pdf]
2001
- D.Greer, J. Westbrook, and P.E.Bourne
2001 OpenMMS: An Ontology Driven Architecture for Macromolecular Structure
Objects in Bio- and Chem-informatics (OIBC)
- A. Kuller, W. Fleri, W.F. Bluhm, J.L.
Smith, J. Westbrook and P.E.Bourne 2001. BioSync: A Biologist's Guide to
Synchrotron Resources Nature Structure Biology 8(8) 663.
- I.N.Shindyalov and P.E.Bourne
2001 Proceedings of the International
Conference on Mathematics and Engineering Techniques in Medicine and Biological
Sciences (METMBS’01). The Sequence-Structure Space and Data Redundancy in the
Protein Data Bank. 139-145.
- D.S. Greer, J. Westbrook, P.E. Bourne
2001 Proceedings NETTAB - Network Tools and Applications in Biology
CORBA and XML: Towards a Bioinformatics Integrated Network Environment. An
Ontology Driven Architecture for Macromolecular Structure.
- J.G. Tate, J. Moreland, and P.E.
Bourne 2001 J. Mol. Graphics 19, 280-287. Design and Implementation
of of a Collaborative Molecular Graphics Environment.[PDF file]
- B.V.B Reddy, W. Li, I.N. Shindyalov,
and P.E. Bourne 2001 Proteins: Structure, Function and
Genetics 42(2) 148-163. Conserved key amino acid
positions (CKAAPs) derived from the analysis of common substructures in
proteins. [PDF file]
- H.M. Berman, J. Westbrook, Z.
Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov,
and P.E. Bourne 2001 International Tables for Crystallography Volume F:
Crystallography of Biological Macromolecules Rossmann, M.G. and Arnold, E.
Editors Dordrecht: Kluwer Academic Publishers, The Netherlands pp.
675-681. The Protein Data Bank 1999-.
- W.W.Li, B.V.B. Reddy, I.N. Shindyalov
and P.E. Bourne 2001 Nucleic Acid Research, 29(1) 329-331. CKAAPs DB:
A Conserved Key Amino Acid Position Database. [PDF file]
- I.N. Shindyalov and P.E.Bourne 2001 Nucleic
Acid Research, 29(1) 228-229. CE: A Resource to Compute and Review 3-D
Protein Structure Alignments. [PDF file]
- P.M.D Fitzgerald, J. Westbrook, P.E.
Bourne, B. McMahon, K. Watenpaugh, H.M. Berman 2001 The International
Tables for X-ray Crystallography, In Press, The Macromolecular
Crystallographic Information File.
- H.M. Berman, T.N. Bhat, P.E. Bourne,
G. Gilliland, H.Weissig, and J. Westbrook 2001 Nucleic Acid Research,
29(1) 214-218, The PDB Uniformity Project [PDF
file].
- C. Guda, E.D. Scheeff, P.E. Bourne and
I.N. Shindyalov 2001 Pacific Symposium on Biocomputing 6: 275-286.
A New Algorithm for Alignment of Multiple Protein Structures Using Monte
Carlo Optimization. [PDF file]
2000
- P.E. Bourne and Michael Gribskov 2000 Bioinformatics
Editorial 16 749. ISMB2000: Bioinformatics Enters a New Millennium.
- P.E. Bourne 2000 Encyclopedia of
Life Sciences Macmillian Reference Ltd. Primary Protein and Nucleic
Acid Three-dimensional Databases.
- H.M. Berman, T.N. Bhat, P.E. Bourne,
G. Gilliland, H.Weissig, and J. Westbrook 2000 Nature Structure Biology,
7sup. 957-959. The Protein Data Bank and the Challenge of Structural
Genomics [PDF file]
- J.D. Westbrook and P.E. Bourne 2000 Bioinformatics
16(2) 159-168. STAR/mmCIF: An Extensive Ontology for Macromolecular
Structure and Beyond. [PDF File].
- P.E. Bourne 2000 Trends in
Biotechnology 2000 18(6), 228-230. Bioinformatics Meets Data
Mining, Time to Dance? A Report of the Data Mining Conference held at the
EBI from Nov. 10-12, 1999. [PDF file]
- I.N. Shindyalov and P.E. Bourne 2000
Proteins: Structure, Function and Genetics 38(3), 247-260.
An Alternative View of Protein Fold Space. [PDF
file]
- H.M. Berman, J. Westbrook, Z.
Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov,
and P.E. Bourne Nucleic Acid Research 2000 28(1), 235-242.
The Protein Data Bank. [PDF file]
- I. Tsigelny1, I. N. Shindyalov, P. E.
Bourne, T. Südhof and P. Taylor Protein Science 2000 9(1)
180-185 Common EF-hand Motifs in Cholinesterases and Neuroligins Suggest
a Role for CA2+ Binding in Cell Surface Associations. [PDF file]
1999
- M. Gribskov, P.E. Bourne, C.M Smith
PKR - The Protein Kinase Resource Genetics Databases Ed. Martin J.
Bishop Hardcourt Press pp 241-246.
- M.P. Ponomarenko, I.N. Shindyalov,
P.E. Bourne, and N.A. Kolchanov LIKENESS: a real-time system for
searching and aligning protein spatial structures. Biofizika. 1999. V. 44.
N. 5. pp. 821-831 (Russ).
- P.E.Bourne Bioinformatics 15(9)
715-716. Editorial
- J.G. Tate, J. Moreland and P.E. Bourne
J. App. Cryst. 32, 1026-1027. MSG (Molecular Scene
Generator): A Web-based Application for the Visualization of
Macromolecular Structures. [PDF file]
- G. Quinn, A. Taylor, H-P Wang and P.E.
Bourne 1999 TIBS 24 321-324. Development of
Internet-based Multimedia Applications. [PDF
file]
- H. Weissig, and P.E. Bourne 1999 Bioinformatics
15(10) 807-831. An Analysis of the Protein Data Bank in Search of
Temporal and Global Trends. [PDF]
- G. Quinn, H-P. Wang, D. Martinez,
P.E.Bourne 1999 Pacific Symposium on Biocomputing Developing
Protein Documentaries and other Multimedia Presentations for Molecular
Biology. Ed. R Altman, K. Dunker, L.Hunter, T. Klein, and K.
Lauderdale pp. 380-391. [PDF
File] Update on client-side speech synthesis [PDF File].
1998
- M.P. Ponomarenko, N.A.
Kolchanov, I.N. Shindyalov and P.E. Bourne Proc. First Int. Conf. on
Bioinformatics of Gene Regulation Novosibirsk Russia 37-374. Likeness:
A System Searching for and Aligning Similar Protein Conformations.
- R. Holstein, J. McMullen, and
P.E. Bourne Digital Press MA 1998 ISBN: 1555581552 In Press Unix
for Openvms Users.
- D. Hart and P.E.Bourne Prentice
Hall NJ 1998, ISBN: 0135200164 In Press A
Cookbook for Serving the Internet - Mac Version.
- I.N. Shindyalov and P.E. Bourne
Protein Engineering 1998, 11(9) 739-747. Protein Structure Alignment
by Incremental Combinatorial Extension of the Optimum Path. [PDF File]
- P.E.Bourne and I.N. Shindyalov
1998 Proceedings of ACHE-98. Ed. D.P. Doctor, D.M. Quinn, R.L.
Rotundo, and P. Taylor. A Database of Pairwise Aligned 3-D Structures for
the Aceytlcholinesterases, Lipases and Other Homologous Proteins p
455-460. Plenum Press NY.
- H. Weissig, I.N. Shindyalov,
and P.E. Bourne Acta Cryst 1998 D54 1085-1094.
Macromolecular Structure Databases: Past Progress and Future Challenges. [PDF file]
- P.E. Bourne, M. Gribskov, G.
Johnson, J. Moreland, and H. Weissig Pacific Symposium on Biocomputing
1998 Ed. R Altman, K. Dunker, L.Hunter, and T. Klein pp.118-129. A
Prototype Molecular Interactive Collaborative Environment (MICE). [compressed PostScript
0.12MB] [uncompressed
PostScript 0.4MB]
- W. Chang and P.E. Bourne J.
App. Cryst. 1998 31, 505 - 509. CIF Applications: A New Approach for
Representing and Manipulating STAR Files.
- H.J. Bernstein, F.C. Bernstein,
and P.E. Bourne J. App. Cryst. 1998, .31, 282 - 295. CIF
Applications. pdb2cif:
Translating PDB Entires into mmCIF Format.
1997
- P.E.Bourne Prentice Hall NJ 1997, ISBN
0-13-519992-1 A Cookbook
for Serving the Internet - UNIX Version.
- P.E.Bourne, H.M.Berman, B. McMahon, K.
Watenpaugh, J. Westbrook and P.M.D. Fitzgerald. Methods in Enzymology.
1997 277, 571-590. The Macromolecular CIF Dictionary [PDF] (mmCIF).
- J. Biggs, C. Pu, and P.E. Bourne Fifth
International Conference on Intelligent Systems for Molecular Biololgy
Ed. T. Gaasterland et al. 1997, 52-55. AAAI Press. Code Generation Through
Annotation of Macromolecular Structure Data Postscript [.25MB]
- I.N.Shindyalov and P.E. Bourne CABIOS
1997, 13, 487-496. Protein Data Representation and Query Using
Optimized Data Decomposition. [PDF file .07MB]
- P.E. Bourne, C. Smith, I.N. Shindyalov,
and H. Weissig ACA Transactions ed. G. Gilliland and H.Berman 1997 32
21-31 What Does Database Federation Mean to Crystallography?
[compressed Postscript
0.5MB][PDF]
- C. Smith, M. Gribskov, I.N.
Shindyalov, S.S Taylor, L. Ten Eyck, S. Veretnik, P.E.Bourne TIBS
1997, 22(11) 444-446. The Protein Kinase Resource (PKR).
- M.P. Ponomorenko, I.N. Shindyalov and
P.E. Bourne Proteins 1997, Accepted. 3-D Homology of Proteins by
Comformational Likeness.
1996
- J.Biggs, C.Pu, A Groeninger and
P.E.Bourne J. App. Cryst. 1996, 29(4), 484-490. PDBtool: An Interactive
Browser and Geometry Checker for Protein Structures.
- P.E.Bourne and I.N. Shindyalov Acta
Cryst. Sup. 1996, C78 C-78. A Local Macromolecular Structure
Database for Crystallography Laboratories.
- J.M. Stewart and P.E.Bourne Proceedings
of the International Summer School on Crystallographic Computing
Ed. P.E.Bourne & K.Watenpaugh, 1996, International Union of
Crystallography Computing Schools.
- M.P. Ponomarenko, I.N.Shindyalov &
P.E.Bourne Proceedings
of the International Summer School on Crystallographic Computing
Ed. P.E.Bourne & K.Watenpaugh, 1996, Fast Substructure Searching Using
the Conformational Likeness Method.
1995
- I.N.Shindyalov, J.Cooper,
W.Chang and P.E.Bourne Proceedings of the 28th Annual Hawaii
International Conference on System Sciences (1995), 207-217 IEEE
Computer Society Press. Design and Use of a Software Framework to Obtain
Information Derived from Macromolecular Structure Data.
- I.N.Shindyalov and P.E.Bourne J.
App. Cryst. 1995, 28(6) 847-852. WPDB A PC-based Tool for
Analyzing Protein Structure.
1994
- W.Chang, I.N.Shindyalov, C.Pu, and
P.E.Bourne, CABIOS (1994) 10(6), 575-586. Design and
Application of PDBlib, a C++ Macromolecular Class Library.
- P.Zhang, E.A.Schon, S.G.Fischer, E.
Cayanis, J. Weiss, S. Kistler and P.E.Bourne, CABIOS (1994) 10(3),
309-317. An Algorithm Based on Graph Theory for the Assembly of Contigs in
the Physical Mapping of DNA.
- W.Chang, I.N.Shindyalov, C.Pu, and
P.E.Bourne, Proceedings of the Second International Conference on
Intelligent Systems in Molecular Biology (1994) 70-77. Design and
Application of a C++ Macromolecular Class Library.
- I.N.Shindyalov, W.Chang, C. Pu, and
P.E.Bourne Protein Engineering (1994) 7(11), 1311-1322. MMQL
An Object Oriented Macromolecular Query Language: Prototype Data Model and
Implementation.