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Jacobsen S, Comery T, Kreft A, Mayer S, Zaleska M, Riddell D, Bard J, Gonzales C, Frick G, Raje S, Forlow S, Balliet C, Burczynski M, Wan H, Harrison B, Reinhart P, Pangalos M, Martone R. O3-06-07: GSI-953 is a potent APP-selective gamma-secretase inhibitor for the treatment of Alzheimer's disease. Alzheimers Dement 2009. [DOI: 10.1016/j.jalz.2009.05.472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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77
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Hirst WD, Kubek K, Bard J, Turner J, Fan K, Malamas M, Reinhart PH, Robichaud AJ. P3‐293: Investigation of the critical amino acids in the BACE1 binding site that interact with small molecule inhibitors using a novel radioligand and X‐ray crystallography. Alzheimers Dement 2009. [DOI: 10.1016/j.jalz.2009.04.964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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78
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Smedley D, Swertz MA, Wolstencroft K, Proctor G, Zouberakis M, Bard J, Hancock JM, Schofield P. Solutions for data integration in functional genomics: a critical assessment and case study. Brief Bioinform 2009; 9:532-44. [PMID: 19112082 DOI: 10.1093/bib/bbn040] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The torrent of data emerging from the application of new technologies to functional genomics and systems biology can no longer be contained within the traditional modes of data sharing and publication with the consequence that data is being deposited in, distributed across and disseminated through an increasing number of databases. The resulting fragmentation poses serious problems for the model organism community which increasingly rely on data mining and computational approaches that require gathering of data from a range of sources. In the light of these problems, the European Commission has funded a coordination action, CASIMIR (coordination and sustainability of international mouse informatics resources), with a remit to assess the technical and social aspects of database interoperability that currently prevent the full realization of the potential of data integration in mouse functional genomics. In this article, we assess the current problems with interoperability, with particular reference to mouse functional genomics, and critically review the technologies that can be deployed to overcome them. We describe a typical use-case where an investigator wishes to gather data on variation, genomic context and metabolic pathway involvement for genes discovered in a genome-wide screen. We go on to develop an automated approach involving an in silico experimental workflow tool, Taverna, using web services, BioMart and MOLGENIS technologies for data retrieval. Finally, we focus on the current impediments to adopting such an approach in a wider context, and strategies to overcome them.
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Wan H, Bard J, Martone R, Rage S, Forlow S, Kreft A, Jacobsen S, Silver P, Paul J, Frick G. P3‐101: GSI‐953, a potent and selective gamma‐secretase inhibitor, modulates Abeta peptides in mice and humans: Translating the PK/PD biomarker relationships in different biological compartments between rodent and human. Alzheimers Dement 2008. [DOI: 10.1016/j.jalz.2008.05.1666] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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80
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Malamas M, Erdei J, Gunawan I, Robichaud A, Turner J, Hu Y, Wagner E, Aschmies S, Comery T, Fan K, Chopra R, Magolda R, Pangalos M, Reinhart P, Riddell D, Jacobsen S, Abou-Gharbia M, Bard J. P2‐481: Small molecule BACE‐1 inhibitors are potent, selective and orally active. Alzheimers Dement 2008. [DOI: 10.1016/j.jalz.2008.05.1559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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81
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82
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Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2008; 25:1251-5. [PMID: 17989687 DOI: 10.1038/nbt1346] [Citation(s) in RCA: 1139] [Impact Index Per Article: 71.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or 'ontologies'. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium is pursuing a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality. We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved.
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83
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Cole DC, Stock JR, Chopra R, Cowling R, Ellingboe JW, Fan KY, Harrison BL, Hu Y, Jacobsen S, Jennings LD, Jin G, Lohse PA, Malamas MS, Manas ES, Moore WJ, O’Donnell MM, Olland AM, Robichaud AJ, Svenson K, Wu J, Wagner E, Bard J. Acylguanidine inhibitors of β-secretase: Optimization of the pyrrole ring substituents extending into the S1 and S3 substrate binding pockets. Bioorg Med Chem Lett 2008; 18:1063-6. [DOI: 10.1016/j.bmcl.2007.12.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Revised: 12/05/2007] [Accepted: 12/06/2007] [Indexed: 10/22/2022]
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84
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85
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Jennings LD, Cole DC, Stock JR, Sukhdeo MN, Ellingboe JW, Cowling R, Jin G, Manas ES, Fan KY, Malamas MS, Harrison BL, Jacobsen S, Chopra R, Lohse PA, Moore WJ, O’Donnell MM, Hu Y, Robichaud AJ, Turner MJ, Wagner E, Bard J. Acylguanidine inhibitors of β-secretase: Optimization of the pyrrole ring substituents extending into the substrate binding pocket. Bioorg Med Chem Lett 2008; 18:767-71. [DOI: 10.1016/j.bmcl.2007.11.043] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 11/08/2007] [Accepted: 11/12/2007] [Indexed: 12/21/2022]
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86
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Aitken S, Chen Y, Bard J. OBO Explorer: an editor for Open Biomedical Ontologies in OWL. Bioinformatics 2007; 24:443-4. [PMID: 18056066 DOI: 10.1093/bioinformatics/btm593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION To clarify the semantics, and take advantage of tools and algorithms developed for the Semantic Web, a mapping from the Open Biomedical Ontologies (OBO) format to the Web Ontology Language (OWL) has been established. We present an ontology editor that allows end users to work directly with this OWL representation of OBO format ontologies. AVAILABILITY http://www.aiai.ed.ac.uk/project/cobra-ct.
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Fobare WF, Solvibile WR, Robichaud AJ, Malamas MS, Manas E, Turner J, Hu Y, Wagner E, Chopra R, Cowling R, Jin G, Bard J. Thiophene substituted acylguanidines as BACE1 inhibitors. Bioorg Med Chem Lett 2007; 17:5353-6. [PMID: 17761418 DOI: 10.1016/j.bmcl.2007.08.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Revised: 08/03/2007] [Accepted: 08/06/2007] [Indexed: 10/23/2022]
Abstract
A series of thiophene-substituted acylguanidines were designed from a pyrrole substituted acylguanidine HTS lead. This template allowed a greater flexibility, through differential Suzuki couplings, to explore the binding site of BACE1 and to enhance the inhibitory potencies. This exploration provided a 25-fold enhancement in potency to yield compound 10a, which was 150 nM in a BACE1 FRET assay.
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88
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Bard J. Systems developmental biology: the use of ontologies in annotating models and in identifying gene function within and across species. Mamm Genome 2007; 18:402-11. [PMID: 17566825 PMCID: PMC1998887 DOI: 10.1007/s00335-007-9027-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Revised: 03/06/2007] [Accepted: 03/12/2007] [Indexed: 11/24/2022]
Abstract
Systems developmental biology is an approach to the study of embryogenesis that attempts to analyze complex developmental processes through integrating the roles of their molecular, cellular, and tissue participants within a computational framework. This article discusses ways of annotating these participants using standard terms and IDs now available in public ontologies (these are areas of hierarchical knowledge formalized to be computationally accessible) for tissues, cells, and processes. Such annotations bring two types of benefit. The first comes from using standard terms: This allows linkage to other resources that use them (e.g., GXD, the gene-expression [G-E] database for mouse development). The second comes from the annotation procedure itself: This can lead to the identification of common processes that are used in very different and apparently unrelated events, even in other organisms. One implication of this is the potential for identifying the genes underpinning common developmental processes in different tissues through Boolean analysis of their G-E profiles. While it is easiest to do this for single organisms, the approach is extendable to analyzing similar processes in different organisms. Although the full computational infrastructure for such an analysis has yet to be put in place, two examples are briefly considered as illustration. First, the early development of the mouse urogenital system shows how a line of development can be graphically formalized using ontologies. Second, Boolean analysis of the G-E profiles of the mesenchyme-to-epithelium transitions that take place during mouse development suggest Lhx1, Foxc1, and Meox1 as candidate transcription factors for mediating this process.
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Mattarolo G, Bard J, Schmid J. Experimental Testing and Modelling Approach of a TPV Prototype. ACTA ACUST UNITED AC 2007. [DOI: 10.1063/1.2711744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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90
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Cole DC, Manas ES, Stock JR, Condon JS, Jennings LD, Aulabaugh A, Chopra R, Cowling R, Ellingboe JW, Fan KY, Harrison BL, Hu Y, Jacobsen S, Jin G, Lin L, Lovering FE, Malamas MS, Stahl ML, Strand J, Sukhdeo MN, Svenson K, Turner MJ, Wagner E, Wu J, Zhou P, Bard J. Acylguanidines as Small-Molecule β-Secretase Inhibitors. J Med Chem 2006; 49:6158-61. [PMID: 17034121 DOI: 10.1021/jm0607451] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACE1 is an aspartyl protease responsible for cleaving amyloid precursor protein to liberate Abeta, which aggregates leading to plaque deposits implicated in Alzheimer's disease. We have identified small-molecule acylguanidine inhibitors of BACE1. Crystallographic studies show that these compounds form unique hydrogen-bonding interactions with the catalytic site aspartic acids and stabilize the protein in a flap-open conformation. Structure-based optimization led to the identification of potent analogs, such as 10d (BACE1 IC(50) = 110 nM).
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91
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Bard J. Introducing developmentEssential developmental biology. (2005). By Jonathan Slack. Blackwell Publishing Ltd. Paperback. 365 pp. ISBN 1-4051-2216-1.Principles of developmental biology. (2003) Edited by Fred Wilt & Sarah Hake. Hardback. 450 pp. ISBN 0-393-97430-8. Bioessays 2006. [DOI: 10.1002/bies.20451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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92
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Bridges KG, Chopra R, Lin L, Svenson K, Tam A, Jin G, Cowling R, Lovering F, Akopian TN, DiBlasio-Smith E, Annis-Freeman B, Marvell TH, LaVallie ER, Zollner RS, Bard J, Somers WS, Stahl ML, Kriz RW. A novel approach to identifying beta-secretase inhibitors: bis-statine peptide mimetics discovered using structure and spot synthesis. Peptides 2006; 27:1877-85. [PMID: 16574278 DOI: 10.1016/j.peptides.2006.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Accepted: 02/03/2006] [Indexed: 10/24/2022]
Abstract
Beta-secretase 1 (BACE1) is an aspartic protease believed to play a critical role in Alzheimer's disease. Inhibitors of this enzyme have been designed by incorporating the non-cleavable hydroxyethylene and statine isosteres into peptides corresponding to BACE1 substrate sequences. We sought to develop new methods to quickly characterize and optimize inhibitors based on the statine core. Minimal sequence requirements for binding were first established using both crystallography and peptide spot synthesis. These shortened peptide inhibitors were then optimized by using spot synthesis to perform iterative cycles of substitution and deletion. The present study resulted in the identification of novel "bis-statine" inhibitors shown by crystallography to have a unique binding mode. Our results demonstrate the application of peptide spot synthesis as an effective method for enhancing peptidomimetic drug discovery.
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93
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Bard J. Book review. J Anat 2006. [DOI: 10.1111/j.1469-7580.2006.00516.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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94
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El-Aal AA, Schmid J, Bard J. MODELLING AND SIMULATION OF A STAND-ALONE HYDROGEN PHOTOVOLTAIC FUEL CELL HYBRID SYSTEM FOR LONG-TERM OPERATION. INTERNATIONAL JOURNAL OF MODELLING AND SIMULATION 2006; 26. [DOI: 10.2316/journal.205.2006.4.205-4475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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95
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Schofield P, Bard J, Rozell B, Sundberg J. Computational Pathology. GENETICALLY ENGINEERED MICE HANDBOOK 2005. [DOI: 10.1201/9781420039078.ch6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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96
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Bard J. Book Review:An introduction to bioinformatics. Bioessays 2005. [DOI: 10.1002/bies.20297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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97
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Spence P, Bard J, Jones P, Betty M. The identification of G-protein coupled receptors in sequence databases. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.8.3.235] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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98
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Lo MC, Aulabaugh A, Jin G, Cowling R, Bard J, Malamas M, Ellestad G. Evaluation of fluorescence-based thermal shift assays for hit identification in drug discovery. Anal Biochem 2005; 332:153-9. [PMID: 15301960 DOI: 10.1016/j.ab.2004.04.031] [Citation(s) in RCA: 506] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Indexed: 11/22/2022]
Abstract
The fluorescence-based thermal shift assay is a general method for identification of inhibitors of target proteins from compound libraries. Using an environmentally sensitive fluorescent dye to monitor protein thermal unfolding, the ligand-binding affinity can be assessed from the shift of the unfolding temperature (Delta Tm) obtained in the presence of ligands relative to that obtained in the absence of ligands. In this article, we report that the thermal shift assay can be conducted in an inexpensive, commercially available device for temperature control and fluorescence detection. The binding affinities obtained from thermal shift assays are compared with the binding affinities measured by isothermal titration calorimetry and with the IC(50) values from enzymatic assays. The potential pitfalls in the data analysis of thermal shift assays are also discussed.
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99
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Bard J, Rhee SY, Ashburner M. An ontology for cell types. Genome Biol 2005; 6:R21. [PMID: 15693950 PMCID: PMC551541 DOI: 10.1186/gb-2005-6-2-r21] [Citation(s) in RCA: 262] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2004] [Revised: 11/10/2004] [Accepted: 12/09/2004] [Indexed: 11/27/2022] Open
Abstract
An ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds is described. It includes over 680 cell types. These cell types are classified under several generic categories and are organized as a directed acyclic graph. We describe an ontology for cell types that covers the prokaryotic, fungal, animal and plant worlds. It includes over 680 cell types. These cell types are classified under several generic categories and are organized as a directed acyclic graph. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. The ontology is freely available at and can be viewed using standard ontology visualization tools such as OBO-Edit and COBrA.
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Abstract
COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Semantic Web formats RDF, RDFS and OWL.
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