Bourne Laboratory - Publications

Last Update October 2009


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2009

·         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.

·         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.

·         J Hodlin, C.D. Bishop, F.A. Sharp and R.E. Valas 2009 A Creative Celebration of Evolution Nature 461:733 [PDF]

·         A. Bateman & P.E. Bourne 2009 Ten Simple Rules for Chairing a Scientific Session PLoS Comp. Biol. 5(9):e1000517 [PDF]

·         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]

·         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.

·         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.

·         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.

·         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.

·         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.

·         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]

·         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]

·         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]

·         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]

·         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]

·         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]

·         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]

·         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]

·         E. Browne, R. Dickin, P.E. Bourne 2009 A Review of 2008 for PLoS Computational Biology PLoS Comp. Biol. 5(1) e1000275 [PDF]

2008

·         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]

·         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]..

·         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]

·         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]

·         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].

·         P.E.Bourne and L.M.Chalupa 2008 A New Approach to Scientific Dissemination Materials Today 11(6) 48 [PDF].

·        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].

·        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]

·        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].

·        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].

·        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].

·        J.L. Fink and P.E.Bourne 2007 Reinventing Scholarly Communication for the Electronic Age. CT Watch, 3(3) 26-31 [HTML]

·        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]

·        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. [open access] [Video]

·         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  [PDF]

·         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 Biology3(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. [PDF]

·         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.  [PDF]

·         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.

2004

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CORBA and XML: Towards a Bioinformatics Integrated Network Environment. An Ontology Driven Architecture for Macromolecular Structure.

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