On the growth of scientific knowledge: Yeast biology as a case study

PLoS Computational Biology

Volumn 5, Issue 3, 2009, Pages

  He, Xionglei ^a   Zhang, Jianzhi ^b  

^a SUN YAT SEN UNIVERSITY   (China)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BEHAVIORAL RESEARCH;

BAKER'S YEAST; CASE-STUDIES; DIFFERENT DOMAINS; EXPONENTIALS; GENETIC INTERACTION; HUMAN KNOWLEDGE; KNOWLEDGE EXPANSION; PROTEIN INTERACTION; SCIENTIFIC KNOWLEDGE; TEMPORAL NETWORKS;

YEAST;

FUNGAL PROTEIN;

ARTICLE; FUNGUS GROWTH; GENE INTERACTION; MEDICAL EDUCATION; MEDICAL RESEARCH; NONHUMAN; PROTEIN METABOLISM; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; ATTITUDE TO HEALTH; BIBLIOMETRICS; BIOLOGY; GENE EXPRESSION PROFILING; PHYSIOLOGY; PROTEIN ANALYSIS; PROTEIN DATABASE; PUBLICATION; SCIENCE; STATISTICS;

BIBLIOMETRICS; BIOLOGY; DATABASES, PROTEIN; GENE EXPRESSION PROFILING; HEALTH KNOWLEDGE, ATTITUDES, PRACTICE; PERIODICALS AS TOPIC; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE; SCIENCE;

EID: 63549136582     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000320     Document Type: Article

References (32)

1. Popper K (1972) Objective Knowledge, An Evolutionary Approach. Oxford, UK: Oxford University Press.
2. Kuhn T (1962) The Structure of Scientific Revolutions. Chicago: University of Chicago Press.
3. Carnabuci GMA (2005) A Theory of Knowledge Growth: Network Analysis of US Patents, 1975-1999. [PhD dissertation]. Amsterdam University Press.
4. Fujimura JH, Luce HR (1998) Authorizing knowledge in science and anthropology. Am Anthropol 100: 347-360.
5. Romer PM (1990) Endogenous technological change. J Pol Econ 98: S71-S102.
6. Schechner S (1999) To advance and diffuse the knowledge of physics. Am J Phys 68: 595-636.
7. van Diest R, van Dalen J, Bak M, Schruers K, van der Vleuten C, et al. (2004) Growth of knowledge in psychiatry and behavioural sciences in a problem-based learning curriculum. Med Educ 38: 1295-1301.
8. Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, et al. (1996) Life with 6000 genes. Science 274: 546, 563-547.
9. Wong SL, Zhang LV, Roth FP (2005) Discovering functional relationships: biochemistry versus genetics. Trends Genet 21: 424-427.
10. Guimera R, Uzzi B, Spiro J, Amaral LA (2005) Team assembly mechanisms determine collaboration network structure and team performance. Science 308: 697-702.
11. Wuchty S, Jones BF, Uzzi B (2007) The increasing dominance of teams in production of knowledge. Science 316: 1036-1039.
12. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285: 901-906.
13. Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411: 41-42.
14. He X, Zhang J (2006) Why do hubs tend to be essential in protein networks? PLoS Genet 2: e88. doi:10.1371/journal.pgen.0020088.
15. Guimera R, Nunes Amaral LA (2005) Functional cartography of complex metabolic networks. Nature 433: 895-900.
16. Cokol M, Iossifov I, Weinreb C, Rzhetsky A (2005) Emergent behavior of growing knowledge about molecular interactions. Nat Biotechnol 23: 1243-1247.
17. Pfeiffer T, Hoffmann R (2007) Temporal patterns of genes in scientific publications. Proc Natl Acad Sci U S A 104: 12052-12056.
18. Newman MEJ (2003) The structure and function of complex networks. SIAM Rev 45: 167-256.
19. Albert R, Jeong H, Barabasi AL (2000) Error and attack tolerance of complex networks. Nature 406: 378-382.
20. Thoreau V, Berges T, Callebaut I, Guillier-Gencik Z, Gressin L, et al. (1999) Molecular cloning, expression analysis, and chromosomal localization of human syntaxin 8 (STX8). Biochem Biophys Res Commun 257: 577-583.
21. Gissen P, Johnson CA, Morgan NV, Stapelbroek JM, Forshew T, et al. (2004) Mutations in VPS33B, encoding a regulator of SNARE-dependent membrane fusion, cause arthrogryposis-renal dysfunction-cholestasis (ARC) syndrome. Nat Genet 36: 400-404.
22. Sprecher E, Ishida-Yamamoto A, Mizrahi-Koren M, Rapaport D, Goldsher D, et al. (2005) A mutation in SNAP29, coding for a SNARE protein involved in intracellular trafficking, causes a novel neurocutaneous syndrome characterized by cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma. Am J Hum Genet 77: 242-251.
23. Howell GJ, Holloway ZG, Cobbold C, Monaco AP, Ponnambalam S (2006) Cell biology of membrane trafficking in human disease. Int Rev Cytol 252: 1-69.
24. Venturi GM, Bloecher A, Williams-Hart T, Tatchell K (2000) Genetic interactions between GLC7, PPZ1 and PPZ2 in Saccharomyces cerevisiae. Genetics 155: 69-83.
25. Lewis MJ, Pelham HR (2002) A new yeast endosomal SNARE related to mammalian syntaxin 8. Traffic 3: 922-929.
26. Gould KL, Ren L, Feoktistova AS, Jennings JL, Link AJ (2004) Tandem affinity purification and identification of protein complex components. Methods 33: 239-244.
27. Fields S, Song O (1989) A novel genetic system to detect protein-protein interactions. Nature 340: 245-246.
28. Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98: 4569-4574.
29. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643.
30. Hart GT, Ramani AK, Marcotte EM (2006) How complete are current yeast and human protein-interaction networks? Genome Biol 7: 120.
31. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, et al. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34: D535-D539.
32. Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, et al. (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95: 717-728.