Methodology capture: Discriminating between the "best" and the rest of community practice

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Eales, James M ^a   Pinney, John W ^a   Stevens, Robert D ^a   Robertson, David L ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS SOFTWARE; EVOLUTIONARY BIOLOGY; EXPERIMENTAL PROTOCOLS; LOCAL COMMUNITY; MOLECULAR PHYLOGENETICS; SCIENTIFIC ARTICLES; SCIENTIFIC DISCIPLINE; STRUCTURED COMMUNITIES;

BIOINFORMATICS; BIOLOGY;

RESEARCH;

ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; DATA EXTRACTION; EXPERIMENTAL DESIGN; INTERMETHOD COMPARISON; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; CLASSIFICATION; INFORMATION RETRIEVAL; NATURAL LANGUAGE PROCESSING; PUBLICATION; QUALITY CONTROL; RESEARCH;

ARTIFICIAL INTELLIGENCE; INFORMATION STORAGE AND RETRIEVAL; NATURAL LANGUAGE PROCESSING; PATTERN RECOGNITION, AUTOMATED; PERIODICALS AS TOPIC; QUALITY CONTROL; RESEARCH;

EID: 52649177788     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-359     Document Type: Article

References (47)

1. Giles J The trouble with replication Nature 2006, 442(7101):344-347 16871184
2. Editorial Let's replicate Nature 2006, 442(7101):330
3. Felsenstein J Phylogeny Programs http://evolution.genetics.washington.edu/phylip/software.html
4. Sackett DL Rosenberg WMC Gray JAM Haynes RB Richardson WS Evidence based medicine: What it is and what it isn't. It's about integrating individual clinical expertise and the best external evidence BMJ 1996, 312(7023):71-72 2349778 8555924
5. Excellence NIC National Institute of Clinical Excellence webpage: "Our guidance" http://www.nice.org.uk/guidance/index.jsp
6. MRC Medical Research Council webpage: "Good Research Practice" http://www.mrc.ac.uk/PolicyGuidance/EthicsAndGovernance/ GoodResearchPractice/index.htm
7. Egger M Smith GD Phillips AN Meta-analysis: Principles and procedures BMJ 1997, 315(7121):1533-1537 2127925 9432252
8. Szulanski G Exploring Internal Stickiness: Impediments to the Transfer of Best Practice Within the Firm Strategic Management Journal 1996, 17:27-43
9. Confederation of British Industry webpage: "Best practice benchmarking" http://www.cbi.org.uk/ndbs/content.nsf/ 802737AED3E3420580256706005390AE/9AF00ADE5AF840E080256B97004CFCBE
10. Goldman N Phylogenetic information and experimental design in molecular systematics Proc Biol Sci 1998, 265(1407):1779-1786 9787470 1689363
11. Tanabe L Wilbur WJ Tagging gene and protein names in biomedical text Bioinformatics 2002, 18(8):1124-1132 12176836
12. Chaussabel D Sher A Mining microarray expression data by literature profiling Genome Biology 2002, 3 10 134484 12372143
13. Creighton C Hanash S Mining gene expression databases for association rules Bioinformatics Oxford Univ Press 2003, 19(1):79-86 12499296
14. Bassett DE Eisen MB Boguski MS Gene expression informatics - it's all in your mine Nat Genet 1999, 21(1 Suppl):51-55 9915502
15. Marcotte EM Xenarios I Eisenberg D Mining literature for protein-protein interactions Bioinformatics 2001, 17(4):359-363 11301305
16. Jang H Lim J Lim JH Park SJ Lee KC Park SH Finding the evidence for protein-protein interactions from PubMed abstracts Bioinformatics 2006, 22(14):e220 16873475
17. Shah P Perez-Iratxeta C Bork P Andrade M Information extraction from full text scientific articles: Where are the keywords? BMC Bioinformatics 2003, 4(1):20 166134 12775220
18. Natarajan J Mulay N DeSesa C Hack CJ Dubitzky W Bremer EG A Grid Infrastructure for Text Mining of Full Text Articles and Creation of a Knowledge Base of Gene Relations Lecture Notes in Computer Science 2005, 3745:101
19. Natarajan J Berrar D Dubitzky W Hack C Zhang Y DeSesa C Van Brocklyn J Bremer E Text mining of full-text journal articles combined with gene expression analysis reveals a relationship between sphingosine-1-phosphate and invasiveness of a glioblastoma cell line BMC Bioinformatics 2006, 7(1):373 1557675 16901352
20. Rzhetsky A Iossifov I Koike T Krauthammer M Kra P Morris M Yu H Duboue PA Weng W Wilbur WJ Hatzivassiloglou V Friedman C GeneWays: A system for extracting, analyzing, visualizing, and integrating molecular pathway data Journal of Biomedical Informatics 2004, 37:43-53 15016385
21. Rzhetsky A Iossifov I Loh JM White KP Microparadigms: Chains of collective reasoning in publications about molecular interactions Proc Natl Acad Sci USA 2006, 103(13):4940-4945 1402650 16543380
22. Aerts S Haeussler M van Vooren S Griffith O Hulpiau P Jones S Montgomery S Bergman C The Open Regulatory Annotation C Text-mining assisted regulatory annotation Genome Biology 2008, 9(2):R31 2374703 18271954
23. Stevens RD myGrid: Personalised bioinformatics on the information grid Bioinformatics 2003, 19(Suppl 1):i302-4 12855473
24. Ludäscher B Altintas I Berkley C Higgins D Jaeger-Frank E Jones M Lee E Tao J Zhao Y Scientific Workflow Management and the Kepler System Concurrency and Computation: Practice & Experience 2005, 18(10):1039-1065
25. Stevens RD Tipney HJ Wroe CJ Oinn TM Senger M Lord PW Goble CA Brass A Tassabehji M Exploring Williams Beuren Syndrome Using my Grid Bioinformatics Oxford University Press Oxford, UK 2004, 20(suppl 1):i303-310 15262813
26. Fisher P Hedeler C Wolstencroft K Hulme H Noyes H Kemp S Stevens RD Brass A A systematic strategy for large-scale analysis of genotype-phenotype correlations: Identification of candidate genes involved in African trypanosomiasis Nucl Acids Res 2007, 35(16):5625-5633 2018629 17709344
27. PubMed Home http://www.ncbi.nlm.nih.gov/pubmed/
28. Newman ME Mixing patterns in networks Phys Rev E Stat Nonlin Soft Matter Phys 200,3 67(2 Pt 2):026126 12636767
29. Newman MEJ The structure of scientific collaboration networks PNAS 2001, 98(2):404-409 14598 11149952
30. Newman ME Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality Phys Rev E Stat Nonlin Soft Matter Phys 2001, 64(1 Pt 2):016132 11461356
31. Leitner T Escanilla D Franzen C Uhlen M Albert J Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis Proc Natl Acad Sci USA National Acad Sciences 1996, 38248 8855273
32. Huelsenbeck JP Performance of Phylogenetic Methods in Simulation Systematic Biology 1995, 44(1):17-48
33. Eisen JA Fraser CM Phylogenomics: Intersection of Evolution and Genomics Science American Association for the Advancement of Science 2003, 300(626):1706-1707 12805538
34. Delsuc F Brinkmann H Philippe H Phylogenomics and the reconstruction of the tree of life Nature Reviews Genetics 2005, 6(5):361-375 15861208
35. Ciccarelli FD Doerks T von Mering C Creevey CJ Snel B Bork P Toward Automatic Reconstruction of a Highly Resolved Tree of Life Science American Association for the Advancement of Science 2006, 311(5765):1283-1287 16513982
36. Letunic I Bork P Interactive Tree Of Life (iTOL): An online tool for phylogenetic tree display and annotation Bioinformatics 2007, 23(1):127 17050570
37. Maddison DR Schulz KS Maddison WP The tree of life web project Zootaxa 2007, 1668:19-40
38. Gentleman R Carey V Bates D Bolstad B Dettling M Dudoit S Ellis B Gautier L Ge Y Gentry J Hornik K Hothorn T Huber W Iacus S Irizarry R Leisch F Li C Maechler M Rossini A Sawitzki G Smith C Smyth G Tierney L Yang J Zhang J Bioconductor: Open software development for computational biology and bioinformatics Genome Biology 2004, 5(10):R80 545600 15461798
39. Gentleman R Reproducible research: A bioinformatics case study Stat Appl Genet Mol Biol 2005, 4 Article 2 16646837
40. Quosa Homepage http://www.quosa.com/
41. Xpdf Homepage http://www.foolabs.com/xpdf/
42. Feldman R Sanger J The Text Mining Handbook: Advanced approaches in analyzing unstructured data New York, Cambridge University Press 2006
43. Newman MEJ Scientific collaboration networks. I. Network construction and fundamental results Phys Rev E Stat Nonlin Soft Matter Phys 2001, 64(1 Pt 2):016131 11461355
44. Vlasblom J Wu S Pu S Superina M Liu G Orsi C Wodak SJ GenePro: A cytoscape plug-in for advanced visualization and analysis of interaction networks Bioinformatics 2006, 22(17):2178-2179 16921162
45. Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N Schwikowski B Ideker T Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks Genome Research 2003, 13(11):2498-2504 403769 14597658
46. Newman MEJ Assortative Mixing in Networks Physical Review Letters 2002, 89(20):208701 12443515
47. NCBI ESummary Entrez Utility http://www.ncbi.nlm.nih.gov/entrez/query/ static/esummary_help.html