Model organisms - A historical perspective

Journal of Proteomics

Volumn 73, Issue 11, 2010, Pages 2054-2063

  Müller, Bruno ^a   Grossniklaus, Ueli ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Animal models; Genetics; Historical perspective; Microorganismal models; Model organisms; Plant models; Tree of life

Indexed keywords

AMPHIBIA; ARABIDOPSIS; BACTERIOPHAGE; BACTERIUM; CAENORHABDITIS ELEGANS; CELL DEATH; CELL MATURATION; CHICKEN; DROSOPHILA; ESCHERICHIA COLI; GENE SEQUENCE; GENOME ANALYSIS; MAIZE; MOLECULAR GENETICS; MOUSE; NEUROSPORA; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; REVIEW; RICE; SACCHAROMYCES CEREVISIAE; TRANSCRIPTOMICS; XENOPUS; YEAST; ZEBRA FISH;

ANIMALS; EUKARYOTA; GENOME-WIDE ASSOCIATION STUDY; HISTORY, 20TH CENTURY; HISTORY, 21ST CENTURY; MODELS, ANIMAL; MODELS, BIOLOGICAL; PROTEOMICS;

ANIMALIA; ARABIDOPSIS; CAENORHABDITIS ELEGANS; DANIO RERIO; ZEA MAYS;

EID: 77957227475     PISSN: 18743919     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jprot.2010.08.002     Document Type: Review

References (170)

1. Olby R.C. Origins of Mendelism 1966, Schocken Books, New York.
2. Orel V. Mendel and new scientific ideas at the Vienna University. Folia Mendeliana 1972, 7:27-36.
3. Stern C., Sherwood E.R. The origin of genetics: a Mendel source book 1966, W.H. Freeman and Company, San Francisco.
4. Bechtold N., Ellis J., Pelletier G. In planta Agrobacterium- mediated gene transfer by infiltration of adult Arabidopsis thaliana plants. C R Acad Sci Paris, Life Sci 1993, 316. 1194 1199.
5. Clough S.J., Bent A.F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 1998, 16:735-743.
6. Meyerowitz E., Pruitt R. Arabidopsis thaliana and plant molecular genetics. Science 1985, 229:1214-1218.
7. Crow J., Little C.C. Cancer and inbred mice. Genetics 2002, 161:1357-1361.
8. De Vries H. Das Spaltungsgesetz der Bastarde. Berichte der Deutschen Botanischen Gesellschaft 1900, 18:83-90.
9. Correns C. G Mendels' Regel über das Verhalten der Nachkommenschaft der Rassenbastarde. Berichte der Deutschen Botanischen Gesellschaft 1900, 18:158-168.
10. Wilson E.B. The cell in development and heredity 1896, The Mcmillan Co., New York.
11. Avery O.T., MacLeod C.M., McCarty M. Thomas Hunt Morgan, 1866-1945. Biograph memoirs Nat Acad Sci 1959, 33:283-325.
12. Morgan T.H., Sturtevant A.H., Muller H.J., Bridges C.B. The mechanism of Mendelian heredity 1915, Henry Holt and Co, New York.
13. Lewis E.B. Some aspects of position pseudoallelism. Am Nat 1955, 89:73-89.
14. Lewis E.B. A gene complex controlling segmentation in Drosophila. Nature 1978, 276:565-570.
15. Gehring W., Kloter U., Suga H. Evolution of the Hox gene complex from an evolutionary ground state. Curr Top Dev Biol 2009, 88:35-61.
16. Lemons D., McGinnis W. Genomic evolution of Hox gene clusters. Science 2006, 313:1918-1922.
17. McGinnis W., Krumlauf R. Homeobox genes and axial patterning. Cell 1992, 68:283-302.
18. Nüsslein-Volhard C., Wieschaus E. Mutations affecting segment number and polarity in Drosophila. Nature 1980, 287:795-801.
19. Cohen B. Nobel committee rewards pioneers of development studies in fruitflies. Nature 1995, 377:465.
20. St Johnston D., Nüsslein-Volhard C. The origin of pattern and polarity in the Drosophila embryo. Cell 1992, 68:201-219.
21. Nüsslein-Volhard C. Of flies and fishes. Science 1994, 266:572-574.
22. Lander E., Linton L., Birren B., Nusbaum C., Zody M., Baldwin J., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
23. Venter J.C., Adams M., Myers E.W., Li P.W., Mural R., Sutton G., et al. The sequence of the human genome. Science 2001, 291:1304-1351.
24. Dodge B.O. Nuclear phenomena associated with heterothallism and homothallism in the ascomycete Neurospora. J Agric Res 1927, 35:289-305.
25. Lindegren C.C. The genetics of Neurospora. II. Segregation of the sex factors in asci of N. crassa, N. sitophila, and N. tetrasperma. Bull Torrey Botan Club 1932, 59:119-138.
26. Davis R., Perkins D. Timeline: Neurospora: a model of model microbes. Nat Rev Genet 2002, 3:397-403.
27. Beadle G.W., Tatum E.L. Genetic control of biochemical reactions in Neurospora crassa. Proc Natl Acad Sci USA 1941, 27:499-506.
28. Selker E.U. Genome defense and DNA methylation in Neurospora. Cold Spring Harb Symp Quant Biol 2004, 69:119-124.
29. Galagan J., Calvo S., Borkovich K., Selker E., Read N., Jaffe D., et al. The genome sequence of the filamentous fungus Neurospora crassa. Nature 2003, 422:859-868.
30. Dunlap J., Borkovich K., Henn M., Turner G., Sachs M., Glass N., et al. Enabling a community to dissect an organism: overview of the Neurospora functional genomics project. Adv Genet 2007, 57:49-96.
31. Avery O.T., MacLeod C.M., McCarty M. Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desosyribonucleic acid fraction isolated from Pneumococcus type III. J Exp Med 1944, 79:137-158.
32. Ryan F.J., Lederberg J. Reverse-mutation and adaptation in leucineless Neurospora. Proc Natl Acad USA 1946, 32:163-173.
33. Lederberg J. Genetic recombination in Escherichia coli: disputation at Cold Spring Harbor, 1946-1996. Genetics 1996, 144:439-443.
34. Lederberg J., Tatum E.L. Gene recombination in Escherichia coli. Nature 1946, 158:558.
35. Tatum E.L. Induced biochemical mutations in bacteria. Cold Spring Harb Symp Quant Biol 1946, 11:278-284.
36. Watson J.D., Crick F.H.C. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 1953, 171:737-738.
37. Bessman M., Lehman I., Simms E., Kornberg A. Enzymatic synthesis of deoxyribonucleic acid. II. General properties of the reaction. J Biol Chem 1958, 233:171-177.
38. Lehman I.R., Bessman M.J., Simms E.S., Kornberg A. Enzymatic synthesis of deoxyribonucleic acid. I. Preparation of substrates and partial purification of an enzyme from Escherichia coli. J Biol Chem 1958, 233:163-170.
39. Jacob F., Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 1961, 3:318-356.
40. Vladimirov N., Sourjik V. Chemotaxis: how bacteria use memory. Biol Chem 2009, 390:1097-1104.
41. Croxen M., Finlay B. Molecular mechanisms of Escherichia coli pathogenicity. Nat Rev Microbiol 2010, 8:26-38.
42. Pennazio S. The origin of phage virology. Riv Biol 2006, 99:103-129.
43. Ellis E., Delbrück M. The growth of bacteriophage. J Gen Physiol 1938, 22:365-384.
44. Morange M., Cobb M. A history of molecular biology 1998, Harvard University Press, Cambridge, MA.
45. Luria S.E., Delbrück M. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 1943, 28:491-511.
46. Barnett J. A history of research on yeasts 10: foundations of yeast genetics. Yeast 2007, 24:799-845.
47. Winge Ø. On haplophase and diplophase in some Saccharomycetes. Comptes Rendus des Travaux du Laboratoire Carlsberg, Se ́rie Physiologique 1935, 21:77-112.
48. Anderson E. Crossing over in a case of attached X chromosomes in Drosophila melanogaster. Genetics 1925, 10:403-417.
49. Sturtevant A.H. The linear arrangement of six sex-linked factors in Drosophila, as shown by their mode of association. J Exp Zool 1913, 14:43-59.
50. Morgan T.H. The explanation of a new sex ratio in Drosophila. Science 1912, 36:718-719.
51. Griffith F. The significance of pneumococcal types. J Hyg 1928, 27:113-159.
52. Hartwell L.H., McLaughlin C.S. Temperature-sensitive mutants of yeast exhibiting a rapid inhibition of protein synthesis. J Bacteriol 1968, 96:1664-1671.
53. Hartwell L., Culotti J., Reid B. Genetic control of the cell-division cycle in yeast. I. Detection of mutants. Proc Natl Acad Sci USA 1970, 66:352-359.
54. Hartwell L., Weinert T. Checkpoints: controls that ensure the order of cell cycle events. Science 1989, 246:629-634.
55. Nurse P., Thuriaux P., Nasmyth K. Genetic control of the cell division cycle in the fission yeast Schizosaccharomyces pombe. Mol Gen Genet 1976, 146:167-178.
56. Nurse P. Nobel Lecture. Cyclin-dependent kinases and cell cycle control. Biosci Rep 2002, 22:487-499.
57. Piel M., Tran P. Cell shape and cell division in fission yeast. Curr Biol 2009, 19:R823-R827.
58. Wang Y. Chromosome instability in yeast and its implications to the study of human cancer. Front Biosci 2008, 13:2091-2102.
59. Kaeberlein M. Lessons on longevity from budding yeast. Nature 2010, 464:513-519.
60. Brenner S. In the beginning was the worm. Genetics 2009, 182:413-415.
61. Brenner S. The genetics of Caenorhabditis elegans. Genetics 1974, 77:71-94.
62. The C. Elegans sequencing consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 1998, 282:2012-2018.
63. De Bono M., Maricq A. Neuronal substrates of complex behaviors in C. elegans. Annu Rev Neurosci 2005, 28:451-501.
64. Horvitz H. Worms, life, and death (Nobel lecture). Chembiochem 2003, 4:697-711.
65. Tatar M., Bartke A., Antebi A. The endocrine regulation of aging by insulin-like signals. Science 2003, 299:1346-1351.
66. Kenyon C.J. The genetics of ageing. Nature 2010, 464:504-512.
67. Colon-Ramos D.A. Synapse formation in developing neural circuits. Curr Top Dev Biol 2009, 87:53-79.
68. Fire A., Xu S., Montgomery M., Kostas S., Driver S., Mello C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391:806-811.
69. Napoli C., Lemieux C., Jorgensen R. Introduction of a chimeric chalcone synthase gene into Petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 1990, 2:279-289.
70. Van der Krol A.R., Mur L., De Lange P., Mol J., Stuitje A.R. Inhibition of flower pigmentation by antisense CHS genes: promoter and minimal sequence requirements for the antisense effect. Plant Mol Biol 1990, 14:457-466.
71. Smith C., Watson C., Bird C., Ray J., Schuch W., Grierson D. Expression of a truncated tomato polygalacturonase gene inhibits expression of the endogenous gene in transgenic plants. Mol Gen Genet 1990, 224:477-481.
72. Fraser A., Kamath R., Zipperlen P., Martinez-Campos M., Sohrmann M., Ahringer J. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 2000, 408:325-330.
73. Kamath R., Fraser A., Dong Y., Poulin G., Durbin R., Gotta M., et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 2003, 421:231-237.
74. Agaisse H., Burrack L., Philips J., Rubin E., Perrimon N., Higgins D. Genome-wide RNAi screen for host factors required for intracellular bacterial infection. Science 2005, 309:1248-1251.
75. Boutros M., Kiger A., Armknecht S., Kerr K., Hild M., Koch B., et al. Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 2004, 303:832-835.
76. Kittler R., Putz G., Pelletier L., Poser I., Heninger A., Drechsel D., et al. An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Nature 2004, 432:1036-1040.
77. Grunwald D., Eisen J. Headwaters of the zebrafish - emergence of a new model vertebrate. Nat Rev Genet 2002, 3:717-724.
78. Ingham P. Zebrafish genetics and its implications for understanding vertebrate development. Hum Mol Genet 1997, 6:1755-1760.
79. Amores A., Force A., Yan Y., Joly L., Amemiya C., Fritz A., et al. Zebrafish Hox clusters and vertebrate genome evolution. Science 1998, 282:1711-1714.
80. Taylor J., Braasch I., Frickey T., Meyer A., Van De Peer Y. Genome duplication, a trait shared by 22,000 species of ray-finned fish. Genome Res 2003, 13:382-390.
81. Waskiewicz A., Rikhof H., Moens C. Eliminating zebrafish pbx proteins reveals a hindbrain ground state. Dev Cell 2002, 3:723-733.
82. Draper B., Stock D., Kimmel C. Zebrafish fgf24 functions with fgf8 to promote posterior mesodermal development. Development 2003, 130:4639-4654.
83. Kikuta H., Laplante M., Navratilova P., Komisarczuk A., Engstrom P., Fredman D., et al. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res 2007, 17:545-555.
84. Iovine M.K. Conserved mechanisms regulate outgrowth in zebrafish fins. Nat Chem Biol 2007, 3:613-618.
85. Poss K., Wilson L., Keating M. Heart regeneration in zebrafish. Science 2002, 298:2188-2190.
86. Maienschein J. The origins of Entwicklungsmechanik. Dev Biol (N Y 1985) 1991, 7:43-61.
87. Wolpert L. Much more from the chicken's egg than breakfast - a wonderful model system. Mech Dev 2004, 121:1015-1017.
88. Spemann H., Mangold I. Über Induktion von Embryonanlagen durch Implantation artfremder Organisatoren. Roux' Arch f Entw mech 1924, 100:599-638.
89. Towers M., Tickle C. Generation of pattern and form in the developing limb. Int J Dev Biol 2009, 53:805-812.
90. Roux W. Beiträge zur Entwickelungsmechanik des Embryo. Über die künstliche Hervorbringung halber Embryonen durch Zerstörung einer der beiden ersten Furchungskugeln, sowie über die Nachentwickelung (Postgeneration) der fehlenden Körperhälfte. Virchows Arch Pathol Anat Physiol Klin Med 1888, 114:113-153.
91. Driesch H. Entwicklungsmechanische Studien I. Der Werth der beiden ersten Furchunqszellen in der Echinodermentwicklung. Experimentelle Erzeugung von Theil-und Doppelbildung. Zeitschrift für wissenschaftliche Zoologie 1891, 53:160-178.
92. Waterston R., Lindblad-Toh K., Birney E., Rogers J., Abril J., Agarwal P., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562.
93. Solter D. From teratocarcinomas to embryonic stem cells and beyond: a history of embryonic stem cell research. Nat Rev Genet 2006, 7:319-327.
94. Hogan B. A shared vision. Dev Cell 2007, 13:769-771.
95. Nolan P., Peters J., Strivens M., Rogers D., Hagan J., Spurr N., et al. A systematic, genome-wide, phenotype-driven mutagenesis programme for gene function studies in the mouse. Nat Genet 2000, 25:440-443.
96. Gondo Y., Fukumura R., Murata T., Makino S. Next-generation gene targeting in the mouse for functional genomics. BMB Rep 2009, 42:315-323.
97. Nowotschin S., Eakin G., Hadjantonakis A. Live-imaging fluorescent proteins in mouse embryos: multi-dimensional, multi-spectral perspectives. Trends Biotechnol 2009, 27:266-276.
98. Paigen K. One hundred years of mouse genetics: an intellectual history. I. The classical period (1902-1980). Genetics 2003, 163:1-7.
99. Cuénot L. Notes et revues. Arch Zool Exp Gen 1902, xxvii.
100. Castle W.E., Little C.C. On a modified Mendelian ratio among yellow mice. Science 1910, 32:868-870.
101. Haldane J.B.S., Sprunt A.D., Haldane M.N. Reduplication in mice. J Genet 1915, 5:133-135.
102. Paigen K. One hundred years of mouse genetics: an intellectual history. II. The molecular revolution (1981-2002). Genetics 2003, 163:1227-1235.
103. Pruitt R., Bowman J., Grossniklaus U. Plant genetics: a decade of integration. Nat Genet 2003, 33(Suppl):294-304.
104. East E.M., Hayes H.K. Inheritance in maize. Conn Agric Exp Stn Bull 1911, 167:1-142.
105. Emerson R.A. The unexpected occurence of aleurone colors in F2 of a cross between non-colored varieties in maize. Am Nat 1912, 46:612-615.
106. Emerson R.A., Beadle G.W., Fraser A.C. A summary of linkage studies in maize. Nebr Agric Exp Stn Res Bull 1935, 2:1-120.
107. East E.M. A Mendelian interpretation of variation that is apparently continuous. Am Nat 1910, 44:65-82.
108. Shull G.H. A pureline method of corn breeding. Amer Breeders' Assoc Rep 1909, 5:51-59.
109. McClintock B. A cytological demonstration of the location of an interchange between two non-homologous chromosomes of Zea mays. Proc Natl Acad Sci USA 1930, 16:791-796.
110. McClintock B. Mutable loci in maize: the mechanism of transposition of the Ds Locus. Carnegie Institution of Washington Year Book 1949, 48:142-154.
111. Kermicle J. Dependence of the R-mottled aleurone phenotype in maize on mode of sexual transmission. Genetics 1970, 66:69-85.
112. Candela H., Hake S. The art and design of genetic screens: maize. Nat Rev Genet 2008, 9:192-203.
113. Mcmullen M., Kresovich S., Sanchez Villeda H., Bradbury P., Li H., Sun Q., et al. Genetic properties of the maize nested association mapping population. Science 2009, 325:737-740.
114. Goff S.A., Ricke D., Lan T.-H., Presting G., Wang R., Dunn M., et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 2002, 296:92-100.
115. Fitzgerald M.A., McCouch S.R., Hall R.D. Not just a grain of rice: the quest for quality. Trends Plant Sci 2009, 14:133-139.
116. Yang X., Hwa C. Genetic modification of plant architecture and variety improvement in rice. Heredity 2008, 101:396-404.
117. Meyerowitz E. Prehistory and history of Arabidopsis research. Plant Physiol 2001, 125:15-19.
118. Stahl Y., Simon R. Plant primary meristems: shared functions and regulatory mechanisms. Curr Opin Plant Biol 2010, 13:53-58.
119. Nawy T., Lukowitz W., Bayer M. Talk global, act local-patterning the Arabidopsis embryo. Curr Opin Plant Biol 2008, 11:28-33.
120. Sundaresan V., Alandete-Saez M. Pattern formation in miniature: the female gametophyte of flowering plants. Development 2010, 137:179-189.
121. Petricka J., Benfey P. Root layers: complex regulation of developmental patterning. Curr Opin Genet Dev 2008, 18:354-361.
122. Chinchilla D., Boller T., Robatzek S. Flagellin signalling in plant immunity. Adv Exp Med Biol 2007, 598:358-371.
123. Ryan C., Huffaker A., Yamaguchi Y. New insights into innate immunity in Arabidopsis. Cell Microbiol 2007, 9:1902-1908.
124. Mas P., Yanovsky M. Time for circadian rhythms: plants get synchronized. Curr Opin Plant Biol 2009, 12:574-579.
125. Alonso-Blanco C., Aarts M., Bentsink L., Keurentjes J., Reymond M., Vreugdenhil D., et al. What has natural variation taught us about plant development, physiology, and adaptation?. Plant Cell 2009, 21:1877-1896.
126. Chen M., Chory J., Fankhauser C. Light signal transduction in higher plants. Annu Rev Genet 2004, 38:87-117.
127. Morita M.T., Tasaka M. Gravity sensing and signaling. Curr Opin Plant Biol 2004, 7:712-718.
128. Santner A., Estelle M. Recent advances and emerging trends in plant hormone signalling. Nature 2009, 459:1071-1078.
129. Yu J., Hu S., Wang J., Wong G., Li S., Liu B., et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002, 296:79-92.
130. Schnable P., Ware D., Fulton R., Stein J., Wei F., Pasternak S., et al. The B73 maize genome: complexity, diversity, and dynamics. Science 2009, 326:1112-1115.
131. Tuskan G., Difazio S., Jansson S., Bohlmann J., Grigoriev I., Hellsten U., et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006, 313:1596-1604.
132. Lang D., Zimmer A., Rensing S., Reski R. Exploring plant biodiversity: the Physcomitrella genome and beyond. Trends Plant Sci 2008, 13:542-549.
133. Rensing S., Lang D., Zimmer A., Terry A., Salamov A., Shapiro H., et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 2008, 319:64-69.
134. Banks J. Selaginella and 400 million years of separation. Annu Rev Plant Biol 2009, 60:223-238.
135. Bowman J., Floyd S., Sakakibara K. Green genes-comparative genomics of the green branch of life. Cell 2007, 129:229-234.
136. Flavell R. Role of model plant species. Methods Mol Biol 2009, 513:1-18.
137. Koch R. Die Aetiologie der Tuberculose. Berliner Klinische Wochenschrift 1882, 19:221-230.
138. Fleming A. On the antibacterial action of cultures of a Penicillium, with special reference to their use in the isolation of B. injluenzae. Br J Exp Pathol 1929, 10:226-236.
139. Tenover F. Mechanisms of antimicrobial resistance in bacteria. Am J Med 2006, 119:S3-S10. discussion S62-70.
140. Williams B. Unique physiology of host-parasite interactions in microsporidia infections. Cell Microbiol 2009, 11:1551-1560.
141. Takeuchi O., Akira S. Pattern recognition receptors and inflammation. Cell 2010, 140:805-820.
142. Becker D., Selbach M., Rollenhagen C., Ballmaier M., Meyer T., Mann M., et al. Robust Salmonella metabolism limits possibilities for new antimicrobials. Nature 2006, 440:303-307.
143. Young D., Stark J., Kirschner D. Systems biology of persistent infection: tuberculosis as a case study. Nat Rev Microbiol 2008, 6:520-528.
144. Bumann D. Pathogen proteomes during infection: A basis for infection research and novel control strategies. Journal of Proteomics 2010, 73:2267-2276. (this issue).
145. Achtman M. Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. Annu Rev Microbiol 2008, 62:53-70.
146. Arnaud M., Costanzo M., Shah P., Skrzypek M., Sherlock G. Gene ontology and the annotation of pathogen genomes: the case of Candida albicans. Trends Microbiol 2009, 17:295-303.
147. Wright G. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol 2007, 5:175-186.
148. D'Costa V.M., McGrann K., Hughes D., Wright G. Sampling the antibiotic resistome. Science 2006, 311:374-377.
149. Goffeau A., Barrell B., Bussey H., Davis R., Dujon B., Feldmann H., et al. Life with 6000 genes. Science 1996, 274(546):563-567.
150. Winzeler E., Shoemaker D., Astromoff A., Liang H., Anderson K., Andre B., et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 1999, 285:901-906.
151. Ross-Macdonald P., Coelho P., Roemer T., Agarwal S., Kumar A., Jansen R., et al. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 1999, 402:413-418.
152. Uetz P., Giot L., Cagney G., Mansfield T., Judson R., Knight J., et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403:623-627.
153. Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 2001, 98:4569-4574.
154. Steinmetz L., Scharfe C., Deutschbauer A., Mokranjac D., Herman Z.S., Jones T., et al. Systematic screen for human disease genes in yeast. Nat Genet 2002, 31:400-404.
155. Giaever G., Chu A., Ni L., Connelly C., Riles L., Veronneau S., et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 2002, 418:387-391.
156. Ren B., Robert F., Wyrick J., Aparicio O., Jennings E., Simon I., et al. Genome-wide location and function of DNA binding proteins. Science 2000, 290:2306-2309.
157. Nagalakshmi U., Wang Z., Waern K., Shou C., Raha D., Gerstein M., et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320:1344-1349.
158. McGary K.L., Lee I., Marcotte E. Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biol 2007, 8:R258.
159. Lee I., Date S., Adai A., Marcotte E. A probabilistic functional network of yeast genes. Science 2004, 306:1555-1558.
160. Wang P., Marcotte E. It's the machine that matters: predicting gene function and phenotype from protein networks. Journal of Proteomics 2010, 73:2277-2289. (this issue).
161. Blein T., Pulido A., Vialette-Guiraud A., Nikovics K., Morin H., Hay A., et al. A conserved molecular framework for compound leaf development. Science 2008, 322:1835-1839.
162. O'Brien K.P., Remm M., Sonnhammer E. Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res 2005, 33:D476-D480.
163. Kersey P., Bower L., Morris L., Horne A., Petryszak R., Kanz C., et al. Integr8 and genome reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res 2005, 33:D297-D302.
164. De Godoy L.M., Olsen J.V., Cox J., Nielsen M.L., Hubner N.C., Fröhlich F., et al. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 2008, 455:1251-1254.
165. Schrimpf S., Weiss M., Reiter L., Ahrens C., Jovanovic M., Malmstrom J., et al. Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol 2009, 7:e48.
166. Loevenich S., Brunner E., King N., Deutsch E., Stein S., Aebersold R., et al. The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. BMC Bioinform 2009, 10:59.
167. Deutsch E., Lam H., Aebersold R. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep 2008, 9:429-434.
168. Baerenfaller K., Grossmann J., Grobei M., Hull R., Hirsch-Hoffmann M., Yalovsky S., et al. Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 2008, 320:938-941.
169. Ciccarelli F., Doerks T., von Mering C., Creevey C., Snel B., Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science 2006, 311:1283-1287.
170. Letunic I., Bork P. Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 2007, 23:127-128.