Bioinformatics pp 129-174 | Cite as

The Nature of Living Things

Part of the Computational Biology book series (COBO, volume 21)


This chapter attempts to cover all of biology above the molecular level. Particular attention is devoted to genes and genome, given their importance within bioinformatics. Hence, the mechanisms of DNA replication and the structure of chromosomes are covered in some detail. Gene expression (transcription and translation) is accorded similar attention. Ontogeny (development) includes coverage of epigenesis and r-and K-selection. Hence, intracellular molecular machinery, the cell cycle and higher-level processes such as evolution are all covered.


Cellular Automaton Double Helix Mass Extinction Fitness Landscape Promoter Site 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Ahnert SE, Fink TMA, Zinovyev A (2008) How much non-coding DNA do eukaryotes require? J Theor Biol 252:587–592Google Scholar
  2. Arber W (1998) Molecular mechanisms of biological evolution. In: Chou C-H, Shao K-T (eds) Frontiers in biology, pp 19–24. Taipei: Academia SinicaGoogle Scholar
  3. Ashby WR (1956) An introduction to cybernetics. Chapman & Hall, LondonGoogle Scholar
  4. Audit B, Audit N, Vaillant C et al (2002) Long-range correlations between DNA bending sites: relation to the structure and dynamics of nucleosomes. J Mol Biol 316:903–918CrossRefGoogle Scholar
  5. Bak P, Sneppen K (1993) Punctuated equilibrium and criticality in a simple model of evolution. Phys Rev Lett 71:4083–4086Google Scholar
  6. Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev. 16:6–21CrossRefGoogle Scholar
  7. Blake WJ, Kaern M, Cantor C, Collins JJ (2003) Noise in eukaryotic gene expression. Nature 422:633–637CrossRefGoogle Scholar
  8. Buss LW, Blackstone NW (1991) An experimental exploration of Waddington’s epigenetic landscape. Phil Trans R Soc Lond B 332:49–58Google Scholar
  9. Chan DC (2006) Mitochondrial fusion and fission in mammals. Annu Rev Cell Dev Biol 22:79–99Google Scholar
  10. Chelly J, Concordet JP, Kaplan JC, Kahn A (1989) Illegitimate transcription: transcription of any gene in any cell type. Proc Natl Acad Sci USA 86:2617–2621CrossRefGoogle Scholar
  11. Crick FHC, Barnett L, Watts-Tobin RJ (1961) General nature of the genetic code for proteins. Nat Lond 192:1227–1232Google Scholar
  12. Ding S-W, Voinnet O (2014) Antiviral RNA silencing in mammals: no newsis not good news. Cell Rep 9:795–797CrossRefGoogle Scholar
  13. Doerfler W, Toth M, Kochanek S, Achten S, Freisem-Rabien U, Behn-Krappa A, Orend G (1990) Eukaryotic DNA methylation: facts and problems. FEBS Lett 268:329–333CrossRefGoogle Scholar
  14. Eigen M (1976) Wie entsteht Information? Ber Bunsenges 76:1059–1081Google Scholar
  15. Ellis RJ (2001) Macromolecular crowding: obvious but underappreciated. Trends Biochem Sci 26:597–604CrossRefGoogle Scholar
  16. Érdi P, Barna Gy (1984) Self-organizing mechanism for the formation of ordered neural mappings. Biol Cybern 51:93–101Google Scholar
  17. Fernández A (1989) Pause sites and regulatory role of secondary structure in RNA replication. Biophys Chem 34:29–33CrossRefGoogle Scholar
  18. Gilbert SF (1991) Epigenetic landscaping: Waddington’s use of cell fate bifurcation diagrams. Biol Philos 6:135–154CrossRefGoogle Scholar
  19. Goldberg AD, Allis CD, Bernstein E (2007) Epigenetics: a landscape takes shape. Cell 128:635–638CrossRefGoogle Scholar
  20. Gould SJ (1977) Ontogeny and phylogeny. Cambridge, Mass.: Belknap PressGoogle Scholar
  21. Guo W, Chung W-Y, Qian M, Pellegrini M, Zhang MQ (2014) Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. Nucleic Acids Res 42:3009–3016CrossRefGoogle Scholar
  22. Hillman H (1991) The case for new paradigms in cell biology and in neurobiology. Edwin Mellen Press, LewistonGoogle Scholar
  23. Hittinger CT, Carroll SB (2007) Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449:677–681CrossRefGoogle Scholar
  24. Hooke R (1665) Micrographia. The Royal Society, LondonGoogle Scholar
  25. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080CrossRefGoogle Scholar
  26. Jongeling TB (1996) Self-organization and competition in evolution: a conceptual problem in the use of fitness landscapes. J Theor Biol 178:369–373Google Scholar
  27. Karlin S, Brendel V (1993) Patchiness and correlations in DNA sequences. Science 259:677–679CrossRefGoogle Scholar
  28. Kauffman SA (1984) Emergent properties in random complex automata. PhysicaD 10:145–156MathSciNetGoogle Scholar
  29. Kellenberger E (1972) Assembly in biological systems. CIBA Found Symp (New Ser) 7:189–206Google Scholar
  30. Kellermayer M, Ludány A, Jobst K, Szúcs G, Trombitas K, Hazlewood CF (1986) Cocompartmentation of proteins and K+ within the living cell. Proc Natl Acad Sci USA 83:1011–1015CrossRefGoogle Scholar
  31. Kempner ES, Miller JH (1968) The molecular biology of Euglena gracilis IV. Cellular stratification by centrifuging. Exp Cell Res 51(1968) 141–149; idem, V. Enzyme localization. Exp Cell Res 51(1968) 150–156Google Scholar
  32. Kim PM, Lu LJ, Xia Y, Gerstein MB (2006) Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314:1938–1941CrossRefGoogle Scholar
  33. Kirchner JW (2002) Evolutionary speed limits inferred from the fossil record. Nature 415:65–68CrossRefGoogle Scholar
  34. Kornyshev AA, Leikin S (2001) Sequence recognition in the pairing of DNA duplexes. Phys Rev Lett 86:3666–3669CrossRefGoogle Scholar
  35. Lechler T, Fuchs E (2005) Asymmetric cell divisions promote stratification and differentiation of mammalian skin. Nature 437:208–275CrossRefGoogle Scholar
  36. Luthi PO, Preiss A, Chopard B, Ramsden JJ (1998) A cellular automatonmodel for neurogenesis in Drosophila. Physica D 118:151–160CrossRefMATHGoogle Scholar
  37. Marshall JAR (2011) Group selection and kin selection: formally equivalent approaches. Trends Ecol Evol 26:325–332Google Scholar
  38. Matthew P (1831) On naval timber and arboriculture. Adam Black, EdinburghGoogle Scholar
  39. McAndrew FT (2002) New evolutionary perspectives on altruism: multilevel-selection and costly-signaling theories. Current Directions Psychol Sci 11:79–82CrossRefGoogle Scholar
  40. McClintock B (1950) The origin and behavior of mutable loci in maize. Proc Natl Acad Sci USA 36:344–355CrossRefGoogle Scholar
  41. Newman MEJ (1996) Self-organized criticality, evolution and the fossil extinction record. Proc R Soc Lond B 263:1605–1610CrossRefGoogle Scholar
  42. Peliti L (1996) Fitness landscapes and evolution. In: Riste T, Sherrington D (eds) Physics of Biomaterials, pp 287–308. Kluwer, DordrechtGoogle Scholar
  43. Percus JK, Percus OE, Perelson AS (1993) Predicting the size of the T-cell receptor and antibody combining region from consideration of efficient self-nonself discrimination. Proc Natl Acad Sci USA 90:1691–1695CrossRefGoogle Scholar
  44. Ramsahoye BH, Biniszkiewicz D, Lyko F, Clark V, Bird AP, Jaenisch R (2000) Non-CpH methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci USA 97:5237–5242CrossRefGoogle Scholar
  45. Raser JM, O’Shea EK (2005) Noise in gene expression: origins, consequences, and control. Science 309:2010–2013CrossRefGoogle Scholar
  46. Rényi A (1953) Kémiai reakciók tárgyalása a sztochasztikus folyamatok elmélete segítségével. Magy Tud Akad Mat Kut Int Közl 2:83–101Google Scholar
  47. Richards EJ, Elgin SCR (2002) Epigenetic codes for heterochromatin formation and silencing. Cell 108:489–500CrossRefGoogle Scholar
  48. Sander JD, Joung JK (2014) CRISPR-Cas systems for editing, regulatingand targeting genomes. Nat Biotechnol 32:347–355CrossRefGoogle Scholar
  49. Sarkar G, Sommer SS (1989) Access to a messenger RNA sequence or its protein product is not limited by tissue or species specificity. Science 244:331–334CrossRefGoogle Scholar
  50. Scherrer K, Jost J (2007) The gene and the genon concept. Mol Syst Biol 3(87):1–11Google Scholar
  51. Shapiro JA (1992) Natural genetic engineering in evolution. Genetica 86:99–111CrossRefGoogle Scholar
  52. Solomon AK (1960) Red cell membrane structure and ion transport. J Gen Physiol 43:1–15CrossRefGoogle Scholar
  53. Stanley SM (1975) A theory of evolution above the species level. Proc Natl Acad Sci USA 72:646–650CrossRefGoogle Scholar
  54. Taft RJ, Pheasant M, Mattick JS (2007) The relationship between non-proton-coding DNA and eukaryotic complexity. BioEssays 29:288–299CrossRefGoogle Scholar
  55. Tonegawa S (1983) Somatic generation of antibody diversity. Nature (Lond) 302:575–581Google Scholar
  56. Voinnet O (2001) RNA silencing as a plant immune system against viruses. Trends Genet 17:449–459CrossRefGoogle Scholar
  57. Voss RF (1992) Evolution of long-range fractal correlations and 1/f noise inDNA base sequences. Phys Rev Lett 68:3805–3808CrossRefGoogle Scholar
  58. Wakamoto Y, Ramsden JJ, Yasuda K (2005) Single-cell growth and division dynamics showing epigenetic correlations. Analyst, 311–317Google Scholar
  59. Westermann B (2010) Mitochondrial fusion and fission in cell life and death. Nat Rev Mol Cell Biol 11:872–884Google Scholar
  60. White SH (1994) Global statistics of protein sequences. A Rev Biophys Biomol Struct. 23:407–439CrossRefGoogle Scholar

Copyright information

© Springer-Verlag London 2015

Authors and Affiliations

  1. 1.The University of BuckinghamBuckinghamUK

Personalised recommendations