1. Russell AP, Holleman DS: The thermal denaturation of DNA: average length and composition of denatured areas. Nucleic Acids Res 1974, 1:959–978.

2. Galtier N, Lobry JR: Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J Mol Evol 1997, 44:632-636.

3. Hurst LD, Merchant AR: High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes. Proc R Soc Lond B Biol Sci 2001, 268:493-497.

4. Forsdyke DR, Bell SJ: Purine loading, stem-loops and Chargaff’s second parity rule: a discussion of the application of elementary principles to early chemical observations. Appl Bioinformatics 2004, 3:3-8.

5. Muto A, Osawa S: The guanine and cytosine content of genomic DNA and bacterial evolution. Proc Natl Acad Sci USA 1987, 84:166-169.

6. Singer GAC, Hickey DA: Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol Biol Evol 2000, 17:1581-1588.

7. Sueoka N: Wide intra-genomic G+C heterogeneity in human and chicken is mainly due to strand-symmetric directional mutation pressures: dGTP-oxidation and symmetric cytosine- deamination hypotheses. Gene 2002, 300:141-154. 

8. Singer GAC, Hickey DA: Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content. Gene 2003, 317:39-47.

9. Wang HC, Singer GAC, Hickey DA: Mutational bias affects protein evolution in flowering plants. Mol Biol Evol 2004, 21:90-96.

10. Chen SL, Lee W, Hottes AK, Shapiro L, McAdams HH: Codon usage between genomes is constrained by genome-wide mutational processes. Proc Natl Acad Sci USA 2004, 101:3480-3485.
11. Forterre P: A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genet 2002, 18:236-237.

12. Nakashima H, Fukuchi S, Nishikawa K: Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. J Biochem (Tokyo) 2003, 133:507-513.

13. Wang HC, Hickey DA: Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes. Nucleic Acids Res 2002, 30:2501-2507.

14. Paz A, Mester D, Baca I, Nevo E, Korol A: Adaptive role of increased frequency of polypurine tracts in mRNA sequences of thermophilic prokaryotes. Proc Natl Acad Sci USA 2004, 101:2951-2956.

15. Klein RJ, Misulovin Z, Eddy SR: Noncoding RNA genes identified in AT-rich hyperthermophiles. Proc Natl Acad Sci USA 2002, 99:7542-7547.

16. Gutell RR, Cannone JJ, Shang Z, Du Y, Serra MJ: A story: unpaired adenosine bases in ribosomal RNAs. J Mol Biol 2000, 304:335-354.

17. Lao PJ, Forsdyke DR: Thermophilic bacteria strictly obey Szybalski’s transcription direction rule and politely purine-load RNAs with both adenine and guanine. Genome Res 2000, 10:228-236.

18.Lambros RJ, Mortimer JR, Forsdyke DR: Optimum growth temperature and the base composition of open reading frames in prokaryotes. Extremophiles 2003, 7:443-450. 

19.Ikemura T: Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol 1981, 146:1-21. 

20.Sharp PM, Stenico M, Peden JF, Lloyd AT: Codon usage: mutational bias, translational selection, or both? Biochem Soc Trans 1993, 21:835-841. 

21.Lobry JR, Chessel D: Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria. J Appl Genet 2003, 44:235-261. 

22.Rispe C, Delmotte F, van Ham RC, Moya A: Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids. Genome Res 2004, 14:44-53. 

23.Kanaya S, Kinouchi M, Abe T, Kudo Y, Yamada Y, Nishi T, Mori H, Ikemura T: Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome. Gene 2001, 276:89-99. 

24.Lynn DJ, Singer GAC, Hickey DA: Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res 2002, 30:4272-4277. 

25.Jaenicke R, Böhm G: The stability of proteins in extreme environments. Curr Opin Struct Biol 1998, 8:738-748. 

26.Petsko GA: Structural basis of thermostability in hyperthermophilic proteins, or "there's more than one way to skin a cat". Methods Enzymol 2001, 334:469-478. 

27.Kreil DP, Ouzounis CA: Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Res 2001, 29:1608-1615. 

28.Tekaia F, Yeramian E, Dujon B: Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis. Gene 2002, 297:51-60. 

29.Farias ST, Bonato MC: Preferred amino acids and thermostability. Genet Mol Res 2003, 2:383-393. 

30.Friedman R, Drake JW, Hughes AL: Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of thermophiles. Genetics 2004, 167:1507-1512. 

31.Kawashima T, Amano N, Koike H, Makino S, Higuchi S, Kawashima-Ohya Y, Watanabe K, Yamazaki M, Kanehori K, Kawamoto T, et al.: Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium. Proc Natl Acad Sci USA 2000, 97:14257-14262. 

32.Kumar S, Nussinov R: How do thermophilic proteins deal with heat? Cell Mol Life Sci 2001, 58:1216-1233. 

33.Suhre K, Claverie JM: Genomic correlates of hyperthermostability, an update. J Biol Chem 2003, 278:17198-17202. 

34.Thompson MJ, Eisenberg D: Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability. J Mol Biol 1999, 290:595-604. 

35.Zhang J: Protein-length distributions for the three domains of life. Trends Genet 2000, 16:107-109. 

36.Das R, Gerstein M: The stability of thermophilic proteins: a study based on comprehensive genome comparison. Funct Integr Genomics 2000, 1:76-88. 

37.Chakravarty S, Varadarajan R: Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study. Biochemistry 2002, 41:8152-8161. 

38.Alsop E, Silver M, Livesay DR: Optimized electrostatic surfaces parallel increased thermostability : a structural bioinformatic analysis. Protein Eng 2003, 16:871-874. 

39.Pack SP, Yoo YJ: Protein thermostability: structure-based difference of amino acid between thermophilic and mesophilic proteins. J Biotechnol 2004, 111:269-277.

40.Kumar S, Nussinov R: Fluctuations in ion pairs and their stabilities in proteins. Proteins 2001, 43:433-454. 

41.Shockley KR, Ward DE, Chhabra SR, Conners SB, Montero CI, Kelly RM: Heat shock response by the hyperthermophilic archaeon Pyrococcus furiosus. Appl Environ Microbiol 2003, 69:2365-2371. 

42.Makarova KS, Wolf YI, Koonin EV: Potential genomic determinants of hyperthermophily. Trends Genet 2003, 19:172-176. 

43.Foster PG, Jermiin LS, Hickey DA: Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J Mol Evol 1997, 44:282-288. 

44.Knight RD, Freeland SJ, Landweber LF: A simple model based on mutation and selection explains trends in codon and aminoacid usage and GC composition within and across genomes. Genome Biol 2001, 2:research0010.1-0010.13. 

45.Lobry JR: Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 1996, 13:660-665. 

46.Lafay B, Lloyd AT, McLean MJ, Devine KM, Sharp PM, Wolfe KH: Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Res 1999, 27:1642-1649. 

47.Foster PG, Hickey DA: Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J Mol Evol 1999, 48:284-290. 

48.Phillips MJ, Delsuc F, Penny D: Genome-scale phylogeny and the detection of systematic biases. Mol Biol Evol 2004, 21:1455-1458. 

49.Musto H, Naya H, Zavala A, Romero H, Alvarez-Valin F, Bernardi G: Correlations between genomic GC levels and optimal growth temperatures in prokaryotes. FEBS Lett 2004, 573:73-77. 

50.Roberts D: Eukaryotic cells under extreme conditions. In Enigmatic Microorganisms and Life in Extreme Environments. Edited by Seckbach J. Dordrecht: Kluwer; 1999:163-173. 


51.Tansey MR, Brock TD: The upper temperature limit for eukaryotic organisms. Proc Natl Acad Sci USA 1972, 69:2426-2428. 

52.Forterre P: Thermoreduction, a hypothesis for the origin of prokaryotes. C R Acad Sci III 1995, 318:415-422. 

53.Sprott GD: Structures of archaebacterial membrane lipids. J Bioenerg Biomembr 1992, 24:555-566.

54.Portner HO: Climate variations and the physiological basis of temperature dependent biogeography: systemic to molecular hierarchy of thermal tolerance in animals. Comp Biochem Physiol A Mol Integr Physiol 2002, 132:739-761. 

55.Bernardi G: Isochores and the evolutionary genomics of vertebrates. Gene 2000, 241:3-17. 

56.Montoya-Burgos JI, Boursot P, Galtier N: Recombination explains isochores in mammalian genomes. Trends Genet 2003, 19:128-130. 

57.Meunier J, Duret L: Recombination drives the evolution of GC-content in the human genome. Mol Biol Evol 2004, 21:984-990. 

58.Vieille C, Zeikus GJ: Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev 2001, 65:1-43. 

59.Haki GD, Rakshit SK: Developments in industrially important thermostable enzymes: a review. Bioresour Technol 2003, 89:17-34. 

60.Henne A, Bruggemann H, Raasch C, Wiezer A, Hartsch T, Liesegang H, Johann A, Lienard T, Gohl O, Martinez-Arias R, et al.: The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol 2004, 22:547-553. 

61.Huang SL, Wu LC, Liang HK, Pan KT, Horng JT, Ko MT: PGTdb: a database providing growth temperatures of prokaryotes. Bioinformatics 2004, 20:276-278. 

62.Korbel JO, Snel B, Huynen MA, Bork P: SHOT: a web server for the construction of genome phylogenies. Trends Genet 2002, 18:158-162.