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Review Article

Looking back to the future: From the development of the gene concept to toxicogenomics

Pages 263-277 | Received 06 Feb 2009, Accepted 27 Feb 2009, Published online: 01 May 2009

References

  • Adams MD, Dubnick M, Kerlavage AR, Moreno R, Kelley JM, Utterback TR, Nagle JW, Fields C, Venter JC. 1992. Sequence identification of 2,375 human brain genes. Nature 355:632–634.
  • Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF, Kerlavage AR, McCombie WR, Venter JC. 1991. Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651–1656.
  • Alwine JC, Kemp DJ, Stark GR. 1977. Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc Natl Acad Sci USA 74:5350–5354.
  • Avery OT, MacLeod CM, McCarty M. 1944. Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Inductions of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. J Exp Med 79:137–158.
  • Beadle GW. 1958. Nobel Lecture, p. 588. Available online at: http://nobelprize.org/nobel_prizes/medicine/laureates/1958/beadle-lecture.pdf Accessed 11 January 2009.
  • Beadle GW, Tatum E. 1941. Genetic control of biochemical reactions in Neurospora. Proc Natl Acad Sci USA 27:499–506.
  • Benzer S. 1955. Fine structure of a genetic region in bacteriophage. Proc Natl Acad Sci USA 41:344–354.
  • Bera TK, Lee B. 2009. Mining of genomic sequence databases to identify new targets for prostate and breast cancer therapy. In: Choudhuri S, Carlson DB ( Eds.), Genomics: Fundamentals and applications, Informa Healthcare, New York, pp. 191–205.
  • Berget SM, Moore C, Sharp PA. 1977. Spliced segments at the 5’ terminus of adenovirus 2 late mRNA. Proc Natl Acad Sci USA 74:3171–3175.
  • Bridges CB. 1935. Salivary chromosome maps: with a key to the banding of the chromosomes of Drosophila melanogaster. J Hered 26:60–64.
  • Bridges CB. 1936. The ‘bar’ gene, a duplication. Science 83:210–211.
  • Carlson EA. 1966. The gene: A critical history, Saunders, Philadelphia, PA.
  • Carlson EA. 1991. Defining the gene: an evolving concept. Am J Hum Genet 49:475–487.
  • Choudhuri S. 2003. The path from nuclein to human genome: a brief history of DNA with a note on human genome sequencing and its impact on future research in biology. Bull Sci Technol Soc 23:360–367.
  • Choudhuri S. 2004. Microarrays in biology and medicine. J Biochem Mol Toxicol 18:171–179.
  • Choudhuri S. 2005. Gene regulation and molecular toxicology. Toxicol Mech Methods 15:1–23.
  • Choudhuri S. 2009. Fundamentals of structure-function analysis of eukaryotic protein coding genes. In: Choudhuri S, Carlson DB ( Eds.), Genomics: Fundamentals and applications, Informa Healthcare, New York, pp. 1–48.
  • Choudhuri S, Ogura K, Klaassen CD. 2000. Cloning of the full-length coding sequence of rat liver-specific organic anion transporter-1 (rlst-1) and a splice variant and partial characterization of the rat lst-1 gene. Biochem Biophy Res Commun 274:79–86.
  • Chow LT, Gelinas RE, Broker TR, Roberts RJ. 1977. An amazing sequence arrangement at the 5’ ends of adenovirus 2 messenger RNA. Cell 12:1–8.
  • Cook-Deegan R. 1994. The gene wars: Science, politics, and the human genome, Norton, New York.
  • Crawford IP, Yanofsky C. 1958. On the separation of the tryptophan synthetase of Escherichia coli into two protein components. Proc Natl Acad Sci USA 44:1161–1170.
  • Davies K. 2001. Cracking the human genome: Inside the race to unlock human DNA, Free Press, New York.
  • Demerec M. 1933. What is a gene? J Hered 24:368–378.
  • Dulbecco R. 1986. A turning point in cancer research: sequencing the human genome. Science 231:1055–1056.
  • Dunn LC. 1965. A short history of genetics: The development of the main lines of thought, 1864–1939 ( Reprint Edition, 1991), Iowa State University Press, Ames, IA.
  • Durnam DM, Palmiter RD. 1983. A practical approach for quantitating specific mRNAs by solution hybridization. Anal Biochem 131:385–393.
  • Fostel J. 2009. Toxicogenomic data and databases. In: Choudhuri S, Carlson DB ( Eds.), Genomics: Fundamentals and applications, Informa Healthcare, New York, pp. 289–303.
  • Gall JG, Pardue ML. 1969. Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc Natl Acad Sci USA 63:378–383.
  • Garrod AE. 1909. Inborn Errors of Metabolism (2nd Edition, 1923), Oxford University Press, London. Available online at: http://www.esp.org/books/garrod/inborn-errors/facsimile/ Accessed 11 January 2009.
  • Ghosh D, Tapsell LC. 2009. Nutrigenomics: a genomic approach to human nutrition. In: Choudhuri S, Carlson DB ( Eds.), Genomics: Fundamentals and applications, Informa Healthcare, New York, pp. 337–344.
  • Gilbert W. 1978. Why genes in pieces? Nature 271:501.
  • Gilbert W, Muller-Hill B. 1966. Isolation of the lac repressor. Proc Natl Acad Sci USA 56:1891–1898.
  • Gillespie D, Spiegelman SA. 1965. Quantitative assay for DNA-RNA hybrids with DNA immobilized on a membrane. J Mol Biol 12:829–842.
  • Green E. 2002. Sequencing the human genome. In: Yudell M, DeSalle R ( Eds.), The genomic revolution, Joseph Henry Press, Washington, DC, pp. 35–47.
  • Green MM, Green KC. 1949. Crossing over between alleles at the lozenge locus in Drosophila melanogaster. Proc Natl Acad Sci USA 35:586–591.
  • Hall BD, Spiegelman S. 1961. Sequence complementarity of T2-DNA and T2-specific RNA. Proc Natl Acad Sci USA 47:137–163.
  • Haymes KM, Hester SD, Benson WH, McClintock JT. 2009. Potential use of microarray technology at the U.S. environmental protection agency. In: Choudhuri S, Carlson DB ( Eds.), Genomics: Fundamentals and applications, Informa Healthcare, New York, pp. 379–396.
  • Huang S-M, Kim M-J, Goodsaid F, Frueh F, Lesko LJ. 2009. Application of pharmacogenetics and pharmacogenomics in drug development and regulatory review. In: Choudhuri S, Carlson DB ( Eds.), Genomics: Fundamentals and applications, Informa Healthcare, New York, pp. 357–378.
  • International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860–921.
  • Itano HA, Robinson EA. 1960. Genetic control of the α- and β-chains of hemoglobin. Proc Natl Acad Sci USA 46:1492–1501.
  • Kafatos FC, Jones CW, Efstratiadis A. 1979. Determination of nucleic acid sequence homologies and relative concentrations by a dot hybridization procedure. Nucl Acids Res 7:1541–1552.
  • Kevles DJ. 1992. Out of eugenics: the historical politics of the human genome. In: Code of codes, Harvard University Press, Cambridge, MA, pp. 3–36.
  • Kevles DJ, Hood L. ( Eds.) 1992. Code of codes. Cambridge, MA: Harvard University Press.
  • Kitcher P. 1982. Genes. Br J Philos Sci 33:337–359.
  • Ma Y, Li D, Chai L, Luciani AM, Ford D, Morgan J, Maizel AL. 2001. Cloning and characterization of two promoters for the human HSAL2 gene and their transcriptional repression by the Wilm’s tumor suppressor gene product. J Biol Chem 276:48223–48230.
  • Mahata SK, Rodriguez JL, Mahata M, O’Connor DT. 2009. From plus-minus sequencing to next generation sequencing with a focus on pyrosequencing. In: Choudhuri S, Carlson DB ( Eds.), Genomics: Fundamentals and applications, Informa Healthcare, New York, pp. 141–157.
  • Mayr E. 1982. The growth of biological thought: Diversity, evolution, and inheritance, Belknap, Cambridge, MA.
  • Moody G. 2004. Digital code of life: How bioinformatics is revolutionizing science, medicine, and business, John Wiley, Hoboken, NJ.
  • Morgan. 1934. Nobel Lecture by Thomas Hunt Morgan, p. 315. Available online at: http://nobelprize.org/nobel_prizes/medicine/laureates/1933/morgan-lecture.pdf Accessed 11 January 2009.
  • Müller HJ, Prokofyeva AA. 1935. The individual gene in relation to the chromomere and the chromosome. Proc Natl Acad Sci USA 21:16–26.
  • Müller HJ, Prokofyeva-Belgovskaya AA, Kossikov KV. 1936. Unequal crossing over in the bar mutant as a result of duplication of a minute chromosome section. CR (Dokl) Acad Sci URSS 1:83–88 ( Cited in Sturtevant AH. 1965. A history of genetics (Reprint Edition in 2001). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY).
  • Olby R. 1974. The path to double helix (Reprint Edition, 1994), Dover, New York.
  • Oliver CP. 1940. A reversion to wild-type associated with crossing-over in Drosophila melanogaster. Proc Natl Acad Sci USA 26:452–454.
  • Pachl C, Todd JA, Kern DG, Sheridan PJ, Fong SJ, Stempien M, Hoo B, Besemer D, Yeghiazarian T, Irvine B, Kolberg J, Kokka R, Neuward P, Urdea MS. 1995. Rapid and precise quantification of HIV-1 RNA in plasma using a branched DNA signal amplification assay. J Acquir Immune Defic Syndr Hum Retrovirol 8:446–454.
  • Painter TS. 1934. Salivary chromosomes and the attack on the gene. J Hered 25:465–476.
  • Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, Fodor SP. 1994. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci USA 91:5022–5026.
  • Pennisi E. 2003. Reaching their goals early, sequencing labs celebrate. Science 300:409.
  • Portin P. 1993. The concept of the gene: short history and present status. Quart Rev Biol 68:173–223.
  • Rédei GP, Koncz C, Phillips JD. 2006. Changing images of the gene. Adv Genet 56:53–100.
  • Roberts L. 1988. Academy backs genome project. Science 239:725–726.
  • Roberts L, Davenport RJ, Pennisi E, Marshall E. 2001. A history of the human genome project. Science 291:1195–1200.
  • Rose MR. 1998. Darwin’s spectre: Evolutionary biology in the modern world, Princeton University Press, Princeton, NJ.
  • Rubin G, Lewis EB. 2000. A brief history of Drosophila’s contribution to genome research. Science 287:2216–2218.
  • Sarabhai AS, Stretton AO, Brenner S, Bolle A. 1964. Co-linearity of the gene with the polypeptide chain. Nature 201:13–17.
  • Schena M, Shalon D, Davis RW, Brown PO. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470.
  • Schildkraut CL, Marmur J, Fresco JR, Doty P. 1961. Formation and properties of polyribonucleotide-polydeoxy-ribonucleotide helical complexes. J Biol Chem 236:C2–PC4.
  • Schlenk F. 1988. Early nucleic acid chemistry. Trends Biochem Sci 13:67–69.
  • Singer M, Berg P. 1991. Genes and genomes: A changing perspective, University Science Books, Mill Valley, CA.
  • Snyder M, Gerstein M. 2003. Defining genes in the genomic era. Science 300:258–260.
  • Southern EM. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 98:503–517.
  • Sturtevant AH. 1925. The effects of unequal crossing over at the bar locus in Drosophila. Genetics 10:117–147.
  • Sturtevant AH. 1965. A history of genetics (Reprint Edition, 2001), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
  • Sulston J, Ferry G. 2002. The common thread: A story of the science, politics, ethics, and the human genome, The Joseph Henry Press, Washington, DC.
  • Venter JC, Adams MD, Myers E, Li PW, Mural RJ, Sutton GG, et al. 2001. The sequence of the human genome. Science 291:1304–1351.
  • Vickers A. 2009. Toxicogenomics in non-clinical safety studies: models of animal and human tissues to assess target organ injury. In: Choudhuri S, Carlson DB ( Eds.), Genomics: Fundamentals and applications, Informa Healthcare, New York, pp. 175–189.
  • Wang D. 2005. ‘Molecular gene’: interpretation in the right context. Biol Philos 20:453–464.
  • Watson JD. 2003. DNA: The secret of life, Knopf, New York.
  • Wexler N. 1992. Clairvoyance and caution: Repercussions from the human genome project. Code of codes, Harvard University Press, Cambridge, MA, pp. 211–243.
  • Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen Y-J, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM. 2008. The complete genome of an individual by massively parallel DNA sequencing. Nature 452:872–877.
  • Whitehouse HLK. 1973. Towards an understanding of the mechanisms of heredity, St Martin’s Press, New York.
  • Yanofsky C, Carlton BC, Guest JR, Helinski DR, Henning U. 1964. On the colinearity of gene structure and protein structure. Proc Natl Acad Sci USA 51:266–272.
  • Yanofsky C, Crawford IP. 1959. The Effects of deletions, point mutations, reversions and suppressor mutations on the two components of the tryptophan synthetase of Escherichia Coli. Proc Natl Acad Sci USA 45:1016–1026.
  • Yudell M, DeSalle R. 2002. The genomic revolution: Unveiling the unity of life, Joseph Henry Press, Washington, DC.

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