Botany Department
Genetics Department
Crop Sciences
Biochemistry

Publications:

1.   Thompson, W. F. and R. Cleland, 1971.  Auxin and RNA synthesis in pea stem tissue as studied by DNA/RNA hybridization.  Plant Physiol. 48: 663-670.

2.   Cleland, R., W. F. Thompson, P. M. Haughton and D. L.  Rayle, 1971.  Macromolecule synthesis and wall extensibility in relation to the mechanism of auxin-induced cell elongation.  In:  Plant Growth Substances 1970, VII International Congress on Plant Growth Substances, Canberra, Australia.

3.   Thompson, W. F. and R. Cleland, l972.  Effect of light and gibberellin on RNA synthesis in pea stem tissue as studied by DNA/RNA hybridization.  Plant Physiol. 50:289-292.

4.   Gardner, G., W. F. Thompson, and W. R. Briggs, 1974.  Differential reactivity of the red and far-red absorbing forms of phytochrome to 14C N-ethyl maleimide.  Planta (Berl.) 117:367-372.

5.   Stein, D. B. and W. F. Thompson, 1975.  DNA hybridization and evolutionary relationships in three Osmunda species.  Science 189:888-890.

6.   Rogler, C. E. and W. F. Thompson, 1976.  Plasmid modification associated with loss and acquisition of virulence in Agrobacterium tumefaciens.  Carnegie Institution of Washington Year Book 75:367-373.[1]

7.   Thompson, W. F., 1976.  Aggregate formation from short fragments of plant DNA.  Plant Physiol.  56:616-622.

8.   Murray, M. G., H. S. Belford, and W. F Thompson, 1977.  Contaminants affecting plant DNA reassociation.  Carnegie Institution of Washington Year Book 76:255-259.

9.   Murray, M. G., H. S. Belford, and W. F. Thompson, l977. In vitro labeling of single stranded DNA. Carnegie Institution of Washington Year Book 76: 262-267.

10.  Murray, M. G. and W. F. Thompson, 1977.  Single-strand DNA fragment length determination by alkaline agarose electrophoresis:  Applications for DNA renaturation studies.  Carnegie Institution of Washington Year Book 76:  259-262.

11.  Rogler, C. E., S. N. Cohen and W. F. Thompson, 1977.  Restriction endonuclease analysis of Agrobacterium plasmids.  Carnegie Institution of Washington Year Book 76:267-273.

12.  Stein, D. B. and W. F. Thompson, 1977.  Interspecific hybridization of fern DNA.  Carnegie Institution of Washington Year Book 76:252-255.

13.  Stein, D. B. and W. F. Thompson, 1977.  Isolation of DNA from tannin-containing plants.  Plant Science Letters 11:323-328.

14.  Cuellar, R. E., G. A. Ford, W. R. Briggs and W. F. Thompson, 1978.  Application of higher derivative techniques to analysis of high resolution thermal denaturation profiles of reassociated repetitive DNA.  Proc. Natl.  Acad. Sci., USA, 75:6026-6030.

15.  Murray, M. G., R. E. Cuellar and W. F. Thompson, 1978.  DNA sequence organization in the pea genome.  Biochemistry 17:5781-5790.

16.  Thompson, W. F., 1978.  Perspectives on the evolution of plant DNA.  Carnegie Institution of Washington Year Book 77:310-316.

17.  Cuellar, R. E., E. U. Selker and W. F. Thompson, 1979.  Cloning of plant DNA.  Comparison of five host strains of Escherichia coli.  Carnegie Institution of Washington Year Book 78:215-217.

18.  Murray, M. G., J. D. Palmer, R. E. Cuellar and W. F. Thompson, 1979.  DNA sequence organization in the mung bean genome.  Biochemistry 18:5259-5266.

19.  Palmer, J. D., M. G. Murray and W. F. Thompson, 1979.  Studies on chloroplast DNA of mung bean and pea.  Carnegie Intitution of Washington Year Book 78:226-231.

20.  Stein, D. B., W. F. Thompson and H. S. Belford, 1979.  Studies on DNA sequence in the Osmundaceae.  J. Mol. Evol. 12:215-232.

21.  Murray, M. G. and W. F. Thompson, 1980.  Rapid isolation of high molcular weight plant DNA.  Nucleic Acids Research 8:4321-4325.

22.  Palmer, J. D. and W. F. Thompson, 1980.  Studies on higher plant chloroplast and mitochondrial DNA.  Carnegie Institution of Washington Year Book 79:120-123.

23.  Thompson, W. F. and M. G. Murray, 1980.  Sequence organization in pea and mung bean DNA and a model for genome evolution. In: The Plant Genome, D. R.  Davies and D. A. Hopwood (eds.), John Innes Charity, Norwich, England, pp.  31-45.

24.  Thompson, W. F., M. G. Murray and R. E. Cuellar, 1980.  Contrasting patterns of DNA sequence organization in plants.  In:  Genome Organization and Expression in Plants, C. J. Leaver, ed., Plenum, NY, pp. 1-15.

25.  Thompson, W. F., M. G. Murray, H. S. Belford and R. E. Cuellar, 1980.  Patterns of DNA sequence repetition and interspersion in higher plants.  In: Genetic Improvement of Crops, I. Rubenstein, R. L. Phillips, C. E. Green and B. G.  Gegenbach, (eds.), University of Minnesota Press, pp. 47-75.

26.  Belford, H. S. and W. F. Thompson, 1981.  Single copy DNA homologies in Atriplex.  I. Cross reactivity estimates and the rate of deletions in genome evolution. Heredity 46:91-108.

27.  Belford, H. S. and W. F. Thompson, 1981.  Single copy DNA homologies in Atriplex. II. Hybrid thermal stabilities and molecular phylogeny.  Heredity, 46:109-122.

28.  Belford, H. S., W. F. Thompson and D. B. Stein, 1981.  DNA hybridization techniques for the study of plant evolution.  In:  Phytochemistry and Angiosperm Phylogeny, D. A. Young and D. S.  Seigler (eds.), Praeger Scientific, NY, pp. 1-18.

29.  Murray, M. G., D. L. Peters and W. F. Thompson, 1981.  Ancient repeated sequences in the pea and mung bean genomes and implications for genome evolution.  J. Mol. Evol. 17:31-42.

30.  Palmer, J. D. and W. F. Thompson, 1981.  Rearrangements in the chloroplast genomes of mung bean and pea. Proc.  Natl. Acad. Sci. U. S. A., 78:5533-5537.

31.  Palmer, J. D. and W. F. Thompson, 1981.  Clone banks of mung bean, pea, and spinach chloroplast DNA.  Gene, 15:21-26.

32.  Preisler, R, S. and W. F. Thompson, 1981.  Evolutionary sequence divergence within repeated DNA families of higher plant genomes.  I.  Analysis of reassociation kinetics.  J. Mol. Evol.  17:78-84.

33.  Preisler, R. S. and W. F. Thompson, 1981.  Evolutionary sequence divergence within repeated DNA families of higher plant genomes.  II. Analysis of thermal denaturation.  J. Mol. Evol., 17: 85-93.

34.  Thompson, W. F. and M. G. Murray, 1981.  The nuclear genome: Structure and Function.  In: The Biochemistry of Plants, Vol. 6, A. Marcus, (ed.), Academic Press, NY, 1-81.

35.  Cuellar, R. E. and W. F. Thompson, 1981.  Complex organization of repetitive DNA families as analyzed with cloned DNA fragments.  Carnegie Institution of Washington Year Book 80:81-82.

36.  Jorgensen, R. A., R. E. Cuellar, and W. F. Thompson, 1982.  Modes and tempos in the evolution of nuclear-encoded ribosomal RNA genes in legumes.  Carnegie Institution of Washington Year Book 81: 98-101.

37.  Murray, M. G. and W. F. Thompson, 1982.  Repeat sequence interspersion in coding DNA of peas does not reflect that in total pea DNA.  Plant Mol. Biol. 1:  143-153.

38.  Palmer, J. D. and W. F. Thompson, 1982.  Chloroplast DNA rearrangements are more frequent when a large inverted repeat is lost.  Cell 29:537-550.

39.  Palmer, J. D., H. Edwards, R. A. Jorgensen and W. F. Thompson, 1982.  Novel evolutionary variation in transcription and location of two chloroplast genes.  Nucleic Acids Res. 10:6819-6832.

40.  Flavell, R. B., M. O'Dell, and W. F. Thompson, 1983.  Cytosine methylation of ribosomal RNA genes and nucleolus organizer activity in wheat.  Proc. Kew Chromosome Conf. II, 11-17.

41.  Spiker, S., M. G. Murray, and W. F. Thompson, 1983.  DNase I sensitivity of transcriptionally active genes in intact nuclei and isolated chromatin of plants. Proc. Natl. Acad. Sci. U.S.A. 80:815-819.

42.  Stern, D. B., J. D. Palmer, W. F. Thompson, and D. M. Lonsdale, 1983.  Mitochondrial DNA sequence evolution and homology to chloroplast DNA in angiosperms. UCLA Symposia on Molecular and Cellular Biology 12, 467-477.

43.  Thompson, W. F., M. Everett, N. O. Polans, R. A. Jorgensen and J. D. Palmer, 1983.  Phytochrome control of RNA levels in developing pea and mung bean leaves.  Planta 158:487-500.

44.  Watson. J. C., J. D. Palmer, and W. F. Thompson, 1983. Chloroplast genes for components of the translational apparatus.  Carnegie Inst. Wash. Year Book 82, 24-26.

45.  Kaufman, L. S., W. F. Thompson and W. R. Briggs, 1984.Different red light requirements for phytochrome-induced accumulation of Cab RNA and RbcS RNA.  Science 226, 1447-1449.

46.  Palmer, J. D., B. Osorio, J. C. Watson, H. Edwards, J. Dodd, and W. F. Thompson. 1984. Evolutionary aspects of chloroplast genome expression and organization.  In: "Biosynthesis of the Photosynthetic Apparatus: Molecular Biology, Development and Regulation", UCLA Symposia on Molecular and Cellular Biology, New Series, vol. 14, eds. R. Hallick, L. A. Staehelin, and J. P.  Thornber.  Alan R. Liss, Inc., N. Y., pp. 273-283.

47.  Briggs, W. R., D. F. Mandoli, J. R. Shinkle, L. S. Kaufman, J. C. Watson and W.  F. Thompson. 1985. Phytochrome regulation of plant development at whole plant, physiological, and molecular levels. In G. Colombetti and P.-S. Song, eds., Sensory Perception and Transduction in Aneural Organisms, Plenum Press, N. Y., pp. 265-280.

48.  Flavell, R. B., M. O'Dell, D. B. Smith and W. F. Thompson. 1985.  Chromosome architecture: the distribution of recombination sites, the structure of ribosomal DNA loci, and the multiplicity of sequences containing inverted repeats.  In: "Molecular Form and Function of the Plant Genome", ed. L. van Vloten-Doting, G. S. P. Groot, and T. C. Hall, Plenum Press, N. Y.

49.  Kaufman, L. S., W. R. Briggs and W. F. Thompson. 1985. Phytochrome control of specific mRNA levels in developing pea buds: The presence of both very low fluence and low fluence responses.  Plant Physiology 78, 388-393.

50.  Kaufman, L. S., J. C. Watson, W. R. Briggs, and W. F. Thompson.  1985.  Photoregulation of nuclear-encoded transcripts: blue light regulation of specific transcript abundance.  In: "The Molecular Biology of the Photosynthetic Aparatus", K. Steinback et al., eds.  Cold Spring Harbor Press, pp. 367-376.

51.  Palmer, J. D., R. A. Jorgensen, and W. F. Thompson. 1985. Chloroplast DNA variation and evolution in Pisum: patterns of change and phylogenetic analysis. Genetics 109, 195-213.

52.  Polans, N. O., N. F. Weeden and W. F. Thompson. 1985. The inheritance, organization and mapping of RbcS and Cab multigene families in pea.  Proc.  Natl. Acad. Sci. USA 82, 5083-5087.

53.  Watson, J. C. and W. F. Thompson. 1985. Purification and restriction endonuclease analysis of plant nuclear DNA.  Methods in Enzymology 118, 57-75.

54.  Thompson, W. F., L. S. Kaufman, and J. C. Watson. 1985. Induction of plant gene expression by light. Bioessays 3, 153-159.

55.  Flavell, R. B., M. O'Dell, W. F. Thompson, M. Vincentz, R. Sardana, and R. F. Barker.  1986. The differential expression of ribosomal RNA genes.  Phil. Trans. Royal Soc. Lond. B314, 385-397.

56.  Kaufman, L. S., L. R. Roberts, W. R. Briggs, and W. F. Thompson. 1986.  Phytochrome control of specific mRNA levels in developing pea buds:  Kinetics of accumulation, reciprocity, and escape kinetics of the low fluence response.  Plant Physiology 81, 1033-1038.

57.  Polans, N. O., N. F. Weeden, and W. F. Thompson. 1986. Distribution, inheritance, and linkage relationships of ribosomal DNA spacer length variants in pea.  Theor. Appl. Genetics 72, 289-295.

58.  Stein, D. B., J. D. Palmer, and W. F. Thompson. 1986. Structural evolution and flip-flop recombination of chloroplast DNA in the fern genus Osmunda.  Current Genetics 10, 835-841.

59.  Stern, D. B., A. G. Bang, and W. F. Thompson. 1986. The watermelon mitochondrial URF-1 gene: evidence for a complex structure.  Current Genetics 10, 857-869.

60.  Dobres, M. S., R. C. Elliot, J. C. Watson, and W. F. Thompson. 1987. A phytochrome-regulated transcript encodes ferredoxin in Pisum sativum.  Plant Mol. Biol. 8, 53-59.

61.  Jorgensen, R. A., R. E. Cuellar, and W. F. Thompson. 1987. Structure and variation in ribosomal RNA genes of pea: Characterization of a cloned rDNA repeat and chromosomal rDNA variants.  Plant Mol. Biol. 8, 3-12.

62.  Kaufman, L. S., J. C. Watson, and W. F. Thompson. 1987. Light-regulated changes in DNase I hypersensitive sites in the rRNA genes of Pisum sativum.  Proc.Nat. Acad.Sci. USA 84, 1550-1554.

63.  Palmer, J. D., B. Osorio, K. J. Aldrich, and W. F. Thompson. 1987.  Chloroplast DNA evolution among legumes: Loss of a large inverted repeat occurred prior to other sequence rearrangements. Current Genetics 11, 275-286.

64.  Spiller, S., L. S. Kaufman, W. F. Thompson, and W. R. Briggs. 1987. Specific mRNA and rRNA levels in greening pea leaves during recovery from iron stress. Plant Physiology 84, 409-414.

65.  Watson, J. C., L. S. Kaufman, and W. F. Thompson. 1987. Developmental regulation of cytosine methylation in the nuclear ribosomal RNA genes of Pisum sativum.  J. Mol. Biol. 193, 15-26.

66.  Flavell, R. B.,  M. O'Dell, and W. F. Thompson 1988 Cytosine methylation in ribosomal DNA and nucleolus organiser expression in wheat.   J. Mol. Biol. 204, (500-534).

67.  Horwitz, B. A., W. F. Thompson, and W. R. Briggs. 1988. Phytochrome regulation of greening in Pisum: chlorophyll accumulation and abundance of mRNA for the light-harvesting chlorophyll a/b binding proteins.  Plant Physiology 86, 299-305.

68.  Murphy, T. M. and W. F. Thompson. 1988. Molecular Plant Development, Prentice Hall, Englewood Cliffs, NJ

69.  Palmer, J. D., B. O. Osorio, and W. F. Thompson. 1988. Inversions in legume chloroplast DNAs. Current Genetics 14, 65-74.

70.  Sagar, A. D., Horwitz, B. A., Elliott, R. C., Thompson, W. F., and Briggs, W. R. 1988. Light effects on several chloroplast components in Norflurazon-treated pea seedlings.  Plant Physiology 88, 340-347.

71.  Sagar, A. D., W. R. Briggs, and W. F. Thompson. 1988. Nuclear - cytoplasmic partitioning of phytochrome - regulated transcripts in Pisum sativum.  Plant Physiology 88, 1397-1402.

72.  Thompson. W. F., R. B. Flavell, J. C. Watson, and L. S. Kaufman. 1988. Chromatin structure and expression of plant ribosomal RNA genes. pp 385-396 in: G. Kahl, ed., Architecture of Eukaryotic Genes, VCH Verlagsgesellschaft, Weinheim.

73.  Thompson, W. F. and R. B. Flavell 1988 DNase I sensitivity of ribosomal RNA genes in chromatin and nucleolar dominance in wheat. J. Mol. Biol. 204, 535-548.

74.  Thompson, W. F. 1988. Photoregulation: Diverse gene responses in greening seedlings.  Plant, Cell, and Environment 11, 319-328.

75.  Thompson. W. F., L. S. Kaufman, B. A. Horwitz, A. D. Sagar, J. C. Watson, and W. R. Briggs 1988. Patterns of phytochrome-induced gene expression in etiolated pea buds.  pp 269-284 in: G. L. Steffans and T. S. Rumsey, eds., Biomechanisms Regulating Growth and Development (Beltsville Symposium XII).

76.  Watson, J. C. and W. F. Thompson. 1988. Purification and restriction endonuclease analysis of plant nuclear DNA.  In: Methods for Plant Molecular Biology, A. Weissbach and H. Weissbach, eds., Academic Press, Orlando FL.

77.  Woodbury, N. W., L. L. Roberts, J. D. Palmer, and W. F. Thompson. 1988. A transcription map of the pea chloroplast genome. Current Genetics 14, 75-89.

78.  Dobres, M. S. and W. F. Thompson. 1989. A developmentally regulated bud specific mRNA sequence in pea has sequence similarity to seed lectins.  Plant Physiology 89, 833-837.

79.  Elliott, R. C., T. J. Pedersen, B. Fristensky, M. J. White, L. F. Dickey, and W. F. Thompson. 1989  Characterization of a single copy gene encoding ferredoxin I from pea.  The Plant Cell, 1, 681-690.

80.  Elliott, R. C.,  L. F. Dickey, M. J. White, and W. F. Thompson. 1989  Cis-acting elements for light regulation of pea ferredoxin I gene expression are located within transcribed sequences.  The Plant Cell, 1, 691-698.

81.  Jordan, B. R., J. G. Hopley, and W. F. Thompson. 1989. Chloroplast gene expression in lettuce grown under different irradiances.  Planta 178, 69-75.

82.  Woodbury, N. W., M. S. Dobres and W. F. Thompson. 1989  The identification and localization of 33 pea chloroplast transcription initiation sites.  Current Genetics 16, 433-445.

83.  Thompson, W. F., R. C. Elliott, Dickey L. F., B. R. Fristensky, and M. J. White.  1990.  Light regulated expression of the Fed-1 gene in pea involves cis-acting elements within the transcription unit. In British Society for Plant Growth Regulation, Monograph 20, Mechanisms of Plant Perception and Response to Environmental Stimuli. Edited by T. Thomas and A. Smith. 3-17.

84.  Alexander, L., D. Falconet, B. W. Fristensky, M. J. White, J. C. Watson, B. A. Roe and W. F. Thompson. 1991. Nucleotide sequence of a new Type I gene encoding a chlorophyll a/b binding protein of LHC II in Pisum. Plant Mol. Biol. 17, 523-526.

85.  Coleman, A. W., W. F. Thompson, and L. J. Goff. 1991. Identification of the mitochondrial genome in the chrysophyte alga Ochromonas danica. J. Protozool. 38, 129-135. 

86.  Falconet, D., M. J. White, B. R. Fristensky, M. S. Dobres and W. F. Thompson. 1991. Nucleotide sequence of Cab-215, a Type II gene encoding a photosystem II chlorophyll a/b binding protein in Pisum. Plant Mol. Biol. 17, 135-139.

87.  Hall, G., G. C. Allen, D. S. Loer, W. F. Thompson and S. Spiker. (1991). Nuclear scaffold and scaffold attachment regions (SARs) in higher plants. Proc. Natl. Acad. Sci. USA 88, 9320-9324.

88. Pedersen, T. J., L. J. Arwood, S. Spiker, M. J. Guiltinan, and W. F. Thompson. 1991. High mobility group non-histone chromosomal proteins bind to AT-rich tracts flanking plant genes. Plant Mol. Biol. 16, 95-104.

89.  Polans, N. O., K. M. Folta, R. C. Elliott, and W. F. Thompson. 1991. The inheritance and intrachromosomal mapping of ferredoxin I in pea. J. Heredity 82, 259-261.

90.  Thompson, W. F., R. C. Elliott, L. F. Dickey, M. Gallo, and T. J. Pedersen. 1991. Unusual features of the light respose system regulating ferredoxin gene expression. In Phytochrome Properties and Biological Action. Edited by B. Thomas and C. B. Johnson. Berlin: Springer-Verlag, pp. 201-216.

91.  Thompson, W. F. and M. J. White. 1991. Physiological and molecular studies of light regulated nuclear genes in higher plants. Annu. Rev. Plant Physiol. Mol. Biol. 42: 423-466.

92.  White, M. J., B. W. Fristensky and W. F. Thompson. (1991). Concatemer chain reaction: A Taq DNA polymerase-mediated mechanism for generating long tandemly repetitive DNA sequences. Anal. Biochem. 199, 184-190.

93.  Dickey, L. F., M. Gallo-Meagher, and W. F. Thompson. 1992. Ferredoxin gene expression and its regulation by light.  In: Control of Gene Expression (DPS Verma, ed.), CRC Press, pp 211-222

94.  Dickey, L. F., M. Gallo-Meagher, and W. F. Thompson.  (1992) Light regulatory sequences are located within the 5' portion of the Fed-1 message sequence. EMBO J. 11, 2311-2317.

95.  Fitzmaurice, W. P., L. V. Nguyen, W. F. Thompson, E. A. Wernsman and M. A. Conkling. (1992). Development and characterization of a generalized gene tagging system for higher plants using an engineered maize transposon Ac. Plant Mol. Biol. 20, 177-198.

96.  Frances, S., M. J. White, M. D. Edgerton, A. M. Jones, R. C. Elliott and W. F. Thompson. (1992) Initial characterization of a pea mutant with light-independent photomorphogenesis.  Plant Cell 4, 1519-1530.

97.  Gallo-Meagher, M., D. A. Sowinski and W. F. Thompson (1992)  The pea ferredoxin I gene exhibits different light responses in etiolated seedlings of pea and tobacco.  Plant Cell 4, 383-388.

98.  Gallo-Meagher, M., D. A. Sowinski, R. C. Elliott and W. F. Thompson (1992)  Both internal and external elements control expression of the pea Fed-1 gene in etiolated seedlings.  Plant Cell 4, 389-395.

99.  White, M. J., B. W. Fristensky, D. Falconet, L. C. Childs, J. C. Watson, L. Alexander, B. A. Roe and W. F. Thompson. (1992). Expression of the chlorophyll a/b protein multigene family in pea (Pisum sativum L.): Evidence for distinct developmental responses. Planta 188, 190-198.

100.  Allen, G. C., G. E. Hall, L. C. Childs, A. K. Weissinger, S. L. Spiker, and W. F. Thompson. (1993) Scaffold attachment regions increase reporter gene expresssion in stably transformed plant cells.  Plant Cell 5, 603-613.

101.  Falconet, D., C. Godon, M. J. White and W. F. Thompson (1993). Sequence of Lhcb3*1, a gene encoding a photosystem II chlorophyll a/b-binding protein in Pisum. Biochim. Biophys. Acta 1173, 333-336.

102.  Dickey, L. F. T.-T. Nguyen, G. C. Allen, and W. F. Thompson (1994) Light modulation of ferredoxin mRNA abundance requires an open reading frame.  Plant Cell 6, 1171-1176.

103.  Quail, P. H., W. R. Briggs, J. Chory, R. P. Hangarter, N. P. Harberd, R. E. Kendrick, M. Koorneef, B. Parks, R. A. Sharrock, E. Schäfer, W. F. Thompson and G. C. Whitelam (1994). Spotlight on phytochrome nomenclature. Plant Cell 6, 468-471.

104. Bovy, A., C. van den Berg, G. de Vrieze, W. F. Thompson, P. Weisbeek and S. Smeekens. (1995). Light-regulated expression of the Arabidopsis thaliana ferredoxin gene requires sequences upstream and downstream of the transcription initiation site. Plant Molecular Biol. 27, 27-39.

105.  Thompson, W. F., G. C. Allen, G. Hall, S. Michalowski, W. Newman, S. Spiker and A. Weissinger. (1995). A nuclear scaffold attachment region from tobacco greatly increases transgene expression in plant cells. In  R. Phillips and K. Oono (ed.), Proceedings of the US-Japan Symposium on Modification of Gene Expression and Non-Mendelian Inheritance, pp 281-295. 

106.  White, M. J., L. S. Kaufman, B. A. Horwitz, W. R. Briggs, and W. F. Thompson. (1995) Individual members of the Cab gene family differ widely in fluence response.  Plant Physiology 107, 161-165.

107.  Allen, G. C., G. Hall, S. Michalowski, W. Newman, A. K. Weissinger, S. Spiker and W. F. Thompson. (1996). High level transgene expression in plant cells:  Effects of a strong SAR from tobacco.  Plant Cell 8, 899-913. 

108.  Petracek, M. E., L. F. Dickey, T. Nguyen, G. C. Allen, D. A. Sowinski, E. R. Hansen and W. F. Thompson (1996). Post-transcriptional regulation by light. In: W. R. Briggs, R. L. Heath and E. M. Tobin, eds., Regulation of Plant Growth and Development by Light, American Society of Plant Physiologists, Rockville, MD

109.  Spiker, S. and W. F. Thompson (1996) Matrix attachment regions and transgene expression in plants. Plant Physiology 110, 15-21.

110.  Thompson, W. F., G. C. Allen, G. H. Jr. and S. Spiker. (1996). Matrix attachment regions and transgene expression. In P. Gustafson and R. B. Flavell (ed.), Genomes of Plants and Animals (Proceedings of the 21st Stadler Genetics Symposium). New York, Plenum Press, pp 243-269. 

111.  Frances, S. and W. F. Thompson (1997).  The dark adaptation response of the de-etiolated pea mutant, lip1, is modulated by external signals and endogenous programs.  Plant Physiol., 115: 23-28. 

112.  Mankin S. L., G. C. Allen, and W. F. Thompson (1997). Introduction of a plant intron into the luciferase gene of Photinus pyralis. Plant Molecular Biology Reporter 15: 186-196. 

113.  Petracek, M. E., L. F. Dickey, S. Huber, and W. F. Thompson (1997).  Light-regulated changes in abundance and polyribosome association of ferredoxin mRNA are dependent on photosynthesis.  Plant Cell 9:  2291-2300. 

114. Tanzer, M. M., W. F. Thompson, M. D. Law, E. A. Wernsman and S. Uknes (1997).  Characterization of post-transcriptionally suppressed transgene expression that confers resistance to tobacco etch virus infection in tobacco. Plant Cell 9: 1411-1423. 

115.  Thompson, W. F., A. F. Bevan, B. Wells, and P. Shaw (1997).  Sites of rDNA transcription are widely disppersed through the nucleolus in Pisum sativum and can comprise single genes.  Plant J. 12: 571-581. 

116.  Dickey, L. F., M. E. Petracek, E. R. Hansen, and W. F. Thompson (1998).  Light regulation of Fed-1 mRNA requires an element in the 5’ untranslated region and correlates with differential polyribosome association.  Plant Cell 10: 475-484. 

117.  Kjemtrup, S., K. S. Sampson, C. Peele, L. V. Nguyen, M. A. Conkling, W. F. Thompson, and D. Robertson (1998).  Gene silencing from plant DNA carried by a geminivirus.  Plant J. 14, 91-100. 

118.  Mackerness, S. A.-H., L.S. Liu, B. Thomas, W. F. Thompson, B. R. Jordan and M. J. White  (1998). Individual members of the light-harvesting complex II chlorophyll a/b binding protein gene family in pea (Pisum sativum) show differential responses to ultraviolet-B radiation.  Physiol. Plant.103: 377-384. 

119.  Petracek, M. E.,  L. F. Dickey, E. R. Hansen, D. A. Sowinski, T. Nguyen, G. C. Allen and W. F. Thompson (1998). The dependence of Fed-1 light regulation on translation. In: J. Bailey-Serres and D. Gallie, ed., A Look Beyond Transcription: Mechanisms Determining mRNA Stability and Translation in Plants, American Society of Plant Physiologists, Rockville, MD, pp. 96-101.

120.  Petracek, M. E., L. F. Dickey, T. T. Nguyen, C. Gatz, D. A. Sowinski, G. C. Allen, and W. F. Thompson. (1998) Ferredoxin mRNA is destabilized by changes in photosynthetic electron transport.  Proc. Natl. Acad. Sci. USA 95, 9009-9013.

121.  Fitzmaurice, W. P., L. V. Nguyen, E. A. Wernsman, W. F. Thompson, and M. A. Conkling (1999) Transposon tagging of the Sulfur gene of tobacco using engineered maize Ac/Ds elements.  Genetics 153, 1919-1928. 

122.  Michalowski, S.M., G. C. Allen, G. E. Hall, W. F. Thompson and S. Spiker (1999) Characterization of randomly-obtained matrix attachment regions (MARs) from higher plants.  Biochemistry 38, 12795-12804.

123. Ulker, B., G. C. Allen, S. L. Spiker, W. F. Thompson, and A. K. Weissinger (1999)  A tobacco matrix attachment region reduces the loss of transgene expression in the progeny of transgenic tobacco plants. Plant J. 18: 253-263. 

124.  Vain, P., B. Worland, A. Kohli, J. W. Snape, P. Christou, G. C. Allen and W. F. Thompson (1999)  Matrix attachment regions increase transgene expression levels and stability in transgenic rice plants and their progeny. Plant J. 18: 233-242. 

125.  Allen, G. C., S Spiker, and W. F. Thompson (2000)  Use of matrix attachment regions (MARs) to minimize transgene silencing.  Plant Molecular Biology 43, 361-376.  (Invited review in special issue)

126.  Ling, J., Wells, D. R., Tanguay, R. L., Dickey, L. F., Thompson, W. F. and Gallie, D. R. (2000). Heat shock protein HSP101 binds to the Fed-1 internal light regulatory element and mediates its high translational activity. Plant Cell 12, 1213-1228. 

127.  Love, J., A. Scott and W. F. Thompson (2000) Stringent control of transgene expression in Arabidopsis thaliana using the Top10 promoter system.  Plant J. 21: 579-588. 

128.  Petracek, M. E., T. Nuygen, W. F. Thompson and L. F. Dickey (2000) Premature Termination codons destabilize Fed-1 mRNA when Fed-1 is translated.  Plant J.21: 563-569. 

In Press: 

Ascenzi, R., Ingram, J. L., Massel, M., Thompson, W. F., Spiker, S. and Weissinger, A. K. (2000). The Role of cell differentiation state and HMG-I/Y in the expression of transgenes flanked by matrix attachment regions. Transgenic Research (in press). 

Hansen, E. R., M. E. Petracek, L. F. Dickey and W. F. Thompson (2000). The 5' end of the pea Ferredoxin-1 mRNA mediates rapid and reversible light-directed changes in translation in tobacco. Plant Physiol. (in press). 

Petracek, M. E. and W. F. Thompson (2000). Post-transcriptional light regulation of nuclear encoded genes. In: J. Setlow, ed., Genetic Engineering, Principles and Methods, vol. 22, Kluwer Academic Publishers (In Press) (Invited Review) 

Patents and Patent Applications:

Thompson, W. F., Spiker, S. L., Allen, G. C., Hall, G., and Childs, L. C. Method for increasing expression of foreign genes in plant cells.  US Patent 5,773,689.  Issued 6/30/98

Thompson, W. F., G. E. Hall, S. L. Spiker, G. C. Allen.  A plant nuclear scaffold attachment region and method for increasing gene expression in transgenic cells.  US Patent 5,773,695. Issued 6/30/98.

Thompson, W. F., S. L. Mankin, G. C. Allen.  Method for reducing the expression variability of transgenes.  US Patent 6,037,525.  Issued 3/14/00

Thompson, W. F., G. C. Allen, B. Ulker, A. K. Weissinger, S. L. Spiker.  Method for decreasing gene silencing of transgenes in plants.

Helmer, G. L., G. C. Allen, and W. F. Thompson.  Chromatin domain tagging using site-specific recombinases. 

Helmer, G. L., G. C. Allen, and W. F. Thompson.  High Efficiency gene targeting using FLP recombinase and IMS (Intragenomic Mobilization Strategy).

George C. Allen, Georgia L Helmer, Tuyen Nguyen, and William F. Thompson.  Use of Site-Specific Recombination to Achieve Targeted Gene Replacement in Plants.

Georgia L Helmer, Tuyen Nguyen, George C. Allen, and William F. Thompson.  Optimized Agrobacterium tumefaciens Vectors and Protocols for Plant Transformation.

Tuyen Nguyen, George C. Allen,  Georgia L Helmer, , and William F. Thompson.  High Efficiency Germline Transformation System for Maize.

George C. Allen, Georgia L Helmer, Tuyen Nguyen, and William F. Thompson.  Use of Matrix Attachment Regions (MARs) Plus a Site-Specific Recombinase System as a Bipartite System for Gene Targeting.

Georgia Helmer, George C. Allen and William F. Thompson.  High Efficiency Gene Targeting in Plants Using a Site Specific Recombinase.   

Georgia Helmer, George C. Allen and William F. Thompson. High Efficiency Transformation using a Site Specific Recombinase in Plants. 

Manuscripts Submitted and In Preparation: 

Ascenzi, R., B. Ülker, J. J. Todd, D. A. Sowinski, C. R. Schimeneck, G. C. Allen, S. L. Spiker, A. K. Weissinger and W. F. Thompson (2000). The effect of a tobacco nuclear matrix attachment region on trans-silencing. (in preparation). 

Love, J., Allen, G. C., Gatz, C. and Thompson, W. F. (2000). Off-on switching of the Top10 promoter by tetracycline analogues in plant cells. Nucleic Acids Research (submitted)

Mankin, S. L., and W. F. Thompson (2000). Generation of Intron-Containing, ER-Localized, Soluble-Modified Green Fluorescent Protein Genes for use in Plant Transformation.  Plant Journal (submitted).

Mankin, S. L., G. C. Allen, T. Phelan, S. Spiker, A. Weissinger and W. F. Thompson (2000). Reporter Genes Flanked by SCS and SCS' Elements Exhibit Elevated Expression Levels in Tobacco Cells. (in preparation)

Mankin, S. L., G. C. Allen, T. Phelan, S. Spiker and W. F. Thompson Elevation of transgene expression level by flanking matrix attachment regions (MAR) is promoter dependent: A study of the interactions of six promoters with the RB7 3' MAR. (in preparation).

Matrix Attachment Regions

Gene Targeting