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Ow SY, Salim M, Noirel J, Evans C, Rehman I, Wright PC. iTRAQ Underestimation in Simple and Complex Mixtures: “The Good, the Bad and the Ugly”. J Proteome Res 2009; 8:5347-55. [DOI: 10.1021/pr900634c] [Citation(s) in RCA: 416] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Saw Yen Ow
- ChELSI Institute, Chemical and Process Engineering, University of Sheffield, Mappin Street, S1 3JD Sheffield, United Kingdom, and Mellanby Centre for Bone Research, University of Sheffield, Medical School, Sheffield, S10 2RX, United Kingdom
| | - Malinda Salim
- ChELSI Institute, Chemical and Process Engineering, University of Sheffield, Mappin Street, S1 3JD Sheffield, United Kingdom, and Mellanby Centre for Bone Research, University of Sheffield, Medical School, Sheffield, S10 2RX, United Kingdom
| | - Josselin Noirel
- ChELSI Institute, Chemical and Process Engineering, University of Sheffield, Mappin Street, S1 3JD Sheffield, United Kingdom, and Mellanby Centre for Bone Research, University of Sheffield, Medical School, Sheffield, S10 2RX, United Kingdom
| | - Caroline Evans
- ChELSI Institute, Chemical and Process Engineering, University of Sheffield, Mappin Street, S1 3JD Sheffield, United Kingdom, and Mellanby Centre for Bone Research, University of Sheffield, Medical School, Sheffield, S10 2RX, United Kingdom
| | - Ishtiaq Rehman
- ChELSI Institute, Chemical and Process Engineering, University of Sheffield, Mappin Street, S1 3JD Sheffield, United Kingdom, and Mellanby Centre for Bone Research, University of Sheffield, Medical School, Sheffield, S10 2RX, United Kingdom
| | - Phillip C. Wright
- ChELSI Institute, Chemical and Process Engineering, University of Sheffield, Mappin Street, S1 3JD Sheffield, United Kingdom, and Mellanby Centre for Bone Research, University of Sheffield, Medical School, Sheffield, S10 2RX, United Kingdom
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Elhai J, Taton A, Massar JP, Myers JK, Travers M, Casey J, Slupesky M, Shrager J. BioBIKE: a Web-based, programmable, integrated biological knowledge base. Nucleic Acids Res 2009; 37:W28-32. [PMID: 19433511 PMCID: PMC2703918 DOI: 10.1093/nar/gkp354] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BioBIKE (biobike.csbc.vcu.edu) is a web-based environment enabling biologists with little programming expertise to combine tools, data, and knowledge in novel and possibly complex ways, as demanded by the biological problem at hand. BioBIKE is composed of three integrated components: a biological knowledge base, a graphical programming interface and an extensible set of tools. Each of the five current BioBIKE instances provides all available information (genomic, metabolic, experimental) appropriate to a given research community. The BioBIKE programming language and graphical programming interface employ familiar operations to help users combine functions and information to conduct biologically meaningful analyses. Many commonly used tools, such as Blast and PHYLIP, are built-in, allowing users to access them within the same interface and to pass results from one to another. Users may also invent their own tools, packaging complex expressions under a single name, which is immediately made accessible through the graphical interface. BioBIKE represents a partial solution to the difficult question of how to enable those with no background in computer programming to work directly and creatively with mass biological information. BioBIKE is distributed under the MIT Open Source license. A description of the underlying language and other technical matters is available at www.Biobike.org.
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Affiliation(s)
- Jeff Elhai
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond VA, USA
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Ow SY, Wright PC. Current trends in high throughput proteomics in cyanobacteria. FEBS Lett 2009; 583:1744-52. [DOI: 10.1016/j.febslet.2009.03.062] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 03/17/2009] [Accepted: 03/27/2009] [Indexed: 02/07/2023]
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Cardona T, Battchikova N, Zhang P, Stensjö K, Aro EM, Lindblad P, Magnuson A. Electron transfer protein complexes in the thylakoid membranes of heterocysts from the cyanobacterium Nostoc punctiforme. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:252-63. [DOI: 10.1016/j.bbabio.2009.01.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Revised: 12/15/2008] [Accepted: 01/13/2009] [Indexed: 10/21/2022]
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Noirel J, Ow SY, Sanguinetti G, Wright PC. Systems biology meets synthetic biology: a case study of the metabolic effects of synthetic rewiring. MOLECULAR BIOSYSTEMS 2009; 5:1214-23. [DOI: 10.1039/b904729h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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