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James A. Birchler

Education

Ph.D. in Genetics/Biochemistry, Indiana University, 1977

Current position

Curators’ Professor, Division of Biological Sciences , University of Missouri-Columbia, 2009-present

Publications (since 2010)

  1. Li, J., Hou, J., Sun, L., Wilkins, J. M., Lu, Y., Niederhuth, C. E., Merideth, B. R., Mawhinney, T. P., Mossine, V. V., Greenlief, C. M., Walker, J. C., Folk, W. R., Hannink, M., Lubahn, D. B., Birchler, J. A. and Cheng, J. (2015). From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data. PLoS One 10(4): e0125000.
  2. Liu, Y., Su, H., Pang, J., Gao, Z., Wang, X. J., Birchler, J. A. and Han, F. (2015). Sequential de novo centromere formation and inactivation on a chromosomal fragment in maize. Proc Natl Acad Sci U S A 112(11): E1263-1271.
  3. Veitia, R. A. and Birchler, J. A. (2015). Models of buffering of dosage imbalances in protein complexes. Biol Direct 10: 42.
  4. Lough, A. N., Faries, K. M., Koo, D. H., Hussain, A., Roark, L. M., Langewisch, T. L., Backes, T., Kremling, K. A., Jiang, J., Birchler, J. A. and Newton, K. J. (2015). Cytogenetic and Sequence Analyses of Mitochondrial DNA Insertions in Nuclear Chromosomes of Maize. G3 (Bethesda). in press.
  5. Birchler, J. A. and Washburn, J. D. (2015). Polyploidy in maize: Impact on the phenotype by homozygous and hybrid genotypes.
  6. Liu, Y., Su, H., Zhang, J., Liu, Y., Han, F. and Birchler, J. A. (2015). Dynamic functional states of maize centromeres. Front Plant Sci. submitted.
  7. Graham, N. D., Swyers, N. C., Gaeta, R. T., Zhao, C., Cody, J. P. and Birchler, J. A. (2015). Telomere-mediated chromosomal truncation via Agrobacterium tumefaciens or particle bombardment to produce engineered minichromosomes in plants. bio-protocol, Protocols for 21st Century Plant Science, edited by David W. Ehrhardt and Wolf B. Frommer, submitted.
  8. Birchler, J. A. (2015). Mendel, Mechanism, Models, Marketing and More. Cell. in press.
  9. Cody, J. P., Swyers, N. C., McCaw, M. E., Graham, N. D., Zhao, C. and Birchler, J. A. (2015). Minichromosomes: Vectors for Crop Improvement. Agronomy. in press.
  10. Cody, J. P., Swyers, N. C., McCaw, M. E., Graham, N. D., Zhao, C. and Birchler, J. A. (2015). Minichromosomes: Vectors for Crop Improvement. Agronomy 5(3): 309-321.
  11. Birchler, J. A. (2015). Heterosis: The genetic basis of hybrid vigour. Nature Plants 1(3).
  12. Yu, W., Yau, Y. Y. and Birchler, J. A. (2015). Plant artificial chromosome technology and its potential application in genetic engineering. Plant Biotechnol J. In press.
  13. Birchler, J. A. (2015). Promises and pitfalls of synthetic chromosomes in plants. Trends Biotechnol 33(3): 189-194.
  14. Graham, N. D.*, Cody, J. P.*, Swyers, N. C.8, McCaw, M. E.*, Zhao, C. and Birchler, J. A. (2015). Engineered Minichromosomes in Plants: Structure, Function, and Applications. Int Rev Cell Mol Biol 318: 63-119.
  15. Veitia, R. A., Veyrunes, F., Bottani, S. and Birchler, J. A. (2015). X chromosome inactivation and active X upregulation in therian mammals: facts, questions, and hypotheses. J Mol Cell Biol 7(1): 2-11.
  16. Birchler, J. A. (2015). Engineered minichromosomes in plants. Chromosome Res 23(1): 77-85.
  17. Feng, C., Liu, Y., Su, H., Wang, H., Birchler, J. and Han, F. (2015). Recent advances in plant centromere biology. Sci China Life Sci 58(3): 240-245.
  18. Birchler, J. A. (2015). Engineered Minichromosome Technology in Plants. Recent Advancements in Gene Expression and Enabling Technologies in Crop Plants: 383.
  19. Birchler, J. A. and Veitia, R. A. (2014). The Gene Balance Hypothesis: dosage effects in plants. Methods Mol Biol 1112: 25-32.
  20. Zhang, J., Zhang, B., Su, H., Birchler, J. A. and Han, F. (2014). Molecular mechanisms of homologous chromosome pairing and segregation in plants. J Genet Genomics 41(3): 117-123.
  21. Birchler, J. A. (2014). Does ectopic cell death cause somatic mutations in the neighboring cells by activating transposons? Mob Genet Elements 4(1): e28040.
  22. Zhang, B., Dong, Q., Su, H., Birchler, J. A. and Han, F. (2014). Histone phosphorylation: its role during cell cycle and centromere identity in plants. Cytogenet Genome Res 143(1-3): 144-149.
  23. Birchler, J. A. (2014). Interploidy hybridization barrier of endosperm as a dosage interaction. Front Plant Sci 5: 281.
  24. Washburn, J. D. and Birchler, J. A. (2014). Polyploids as a "model system" for the study of heterosis. Plant Reprod 27(1): 1-5.
  25. Birchler, J. A. (2014). Facts and artifacts in studies of gene expression in aneuploids and sex chromosomes. Chromosoma 123(5): 459-469.
  26. Birchler, J. A. (2014). Engineered minichromosomes in plants. Curr Opin Plant Biol 19: 76-80.
  27. Conant, G. C., Birchler, J. A. and Pires, J. C. (2014). Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. Curr Opin Plant Biol 19: 91-98.
  28. Birchler, J. A. (2014). Artificial Chromosome Platforms in Maize. IN: Genetics, Genomics, and Breeding of Maize. Wusirika, R., Bohn, M., Lai, J. and Kole, C. (Eds) .CRC Press, Taylor and Francis Group, Boca Raton.
  29. Kass, L. B. and Birchler, J. A. (2014). Setting up a prepared mind: Summary and analysis of “Cytological observations of deficiencies involving known genes, translocations and an inversion in Zea mays”. IN: Perspectives on Nobel Laureate Barbara McClintock’s publications (1926-1984): A Companion Volume. The Internet-First University Press. URI: http://hdl.handle.net/1813/34897
  30. Birchler, J. A. (2013). Genetic rules of heterosis in plants. Polyploid and Hybrid Genomics: 313-321.
  31. Douglas, R. N. and Birchler, J. A. (2013). microRNAs in Eukaryotes. Encyclopedia of Biological Chemistry, pp: 98-102.
  32. Birchler, J. A. (2013). Heterosis in Plants. Encyclopedia of Agriculture and Food Systems.
  33. Douglas, R. N. and Birchler, J. A. (2013). Plant centromere epigenetics. Plant Centromere Biology: 147-158.
  34. Gaeta, R. T. and Birchler, J. A. (2013). Engineered Plant Chromosomes. IN: Plant Centromere Biology. Jiang, J. and Birchler, J. A. (Eds). Wiley-Blackwell, Hoboken, pp: 183-192.
  35. Gao, Z., Han, F., Danilova, T. V., Lamb, J. C., Albert, P. S. and Birchler, J. A. (2013). Labeling meiotic chromosomes in maize with fluorescence in situ hybridization. Methods Mol Biol 990: 35-43.
  36. Birchler, J. A. (2013). Aneuploidy in plants and flies: the origin of studies of genomic imbalance. Semin Cell Dev Biol 24(4): 315-319.
  37. Birchler, J. A. and Han, F. (2013). Meiotic behavior of small chromosomes in maize. Front Plant Sci 4: 505.
  38. Birchler, J. A. and Han, F. (2013). Centromere epigenetics in plants. J Genet Genomics 40(5): 201-204.
  39. Masonbrink, R. E., Fu, S., Han, F. and Birchler, J. A. (2013). Heritable loss of replication control of a minichromosome derived from the B chromosome of maize. Genetics 193(1): 77-84.
  40. Yao, H., Dogra Gray, A., Auger, D. L. and Birchler, J. A. (2013). Genomic dosage effects on heterosis in triploid maize. Proc Natl Acad Sci U S A 110(7): 2665-2669.
  41. Sun, L., Fernandez, H. R., Donohue, R. C., Li, J., Cheng, J. and Birchler, J. A. (2013). Male-specific lethal complex in Drosophila counteracts histone acetylation and does not mediate dosage compensation. Proc Natl Acad Sci U S A 110(9): E808-817.
  42. Kanizay, L. B., Albert, P. S., Birchler, J. A. and Dawe, R. K. (2013). Intragenomic conflict between the two major knob repeats of maize. Genetics 194(1): 81-89.
  43. Gaeta, R. T., Masonbrink, R. E., Zhao, C., Sanyal, A., Krishnaswamy, L. and Birchler, J. A. (2013). In vivo modification of a maize engineered minichromosome. Chromosoma 122(3): 221-232.
  44. Maron, L. G., Guimaraes, C. T., Kirst, M., Albert, P. S., Birchler, J. A., Bradbury, P. J., Buckler, E. S., Coluccio, A. E., Danilova, T. V., Kudrna, D., Magalhaes, J. V., Pineros, M. A., Schatz, M. C., Wing, R. A. and Kochian, L. V. (2013). Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proc Natl Acad Sci U S A 110(13): 5241-5246.
  45. Fu, S., Lv, Z., Gao, Z., Wu, H., Pang, J., Zhang, B., Dong, Q., Guo, X., Wang, X. J., Birchler, J. A. and Han, F. (2013). De novo centromere formation on a chromosome fragment in maize. Proc Natl Acad Sci U S A 110(15): 6033-6036.
  46. Sun, L., Johnson, A. F., Donohue, R. C., Li, J., Cheng, J. and Birchler, J. A. (2013). Dosage compensation and inverse effects in triple X metafemales of Drosophila. Proc Natl Acad Sci U S A 110(18): 7383-7388.
  47. Veitia, R. A., Bottani, S. and Birchler, J. A. (2013). Gene dosage effects: nonlinearities, genetic interactions, and dosage compensation. Trends Genet 29(7): 385-393.
  48. Xie, W., Donohue, R. C. and Birchler, J. A. (2013). Quantitatively increased somatic transposition of transposable elements in Drosophila strains compromised for RNAi. PLoS One 8(8): e72163.
  49. Sun, L., Johnson, A. F., Li, J., Lambdin, A. S., Cheng, J. and Birchler, J. A. (2013). Differential effect of aneuploidy on the X chromosome and genes with sex-biased expression in Drosophila. Proc Natl Acad Sci U S A 110(41): 16514-16519.
  50. Birchler, J. A. (2012). Heterosis-What art thou? Maydica 57(2): 92-95.
  51. Birchler, J. A. (2012). Genetic consequences of polyploidy in plants. Polyploidy and Genome Evolution, Springer: 21-32.
  52. Fu, S., Gao, Z., Birchler, J. and Han, F. (2012). Dicentric chromosome formation and epigenetics of centromere formation in plants. J Genet Genomics 39(3): 125-130.
  53. Birchler, J. A. (2012). Messing with Mendel. Dev Cell 23(4): 678-679.
  54. Birchler, J. A. (2012). Insights from paleogenomic and population studies into the consequences of dosage sensitive gene expression in plants. Curr Opin Plant Biol 15(5): 544-548.
  55. Birchler, J. A. and Presting, G. G. (2012). Retrotransposon insertion targeting: a mechanism for homogenization of centromere sequences on nonhomologous chromosomes. Genes Dev 26(7): 638-640.
  56. Birchler, J. A. (2012). Claims and counterclaims of X-chromosome compensation. Nat Struct Mol Biol 19(1): 3-5.
  57. Gaeta, R. T., Masonbrink, R. E., Krishnaswamy, L., Zhao, C. and Birchler, J. A. (2012). Synthetic chromosome platforms in plants. Annu Rev Plant Biol 63: 307-330.
  58. Masonbrink, R. E., Gaeta, R. T. and Birchler, J. A. (2012). Multiple maize minichromosomes in meiosis. Chromosome Res 20(4): 395-402.
  59. Masonbrink, R. E. and Birchler, J. A. (2012). Accumulation of multiple copies of maize minichromosomes. Cytogenet Genome Res 137(1): 50-59.
  60. Xie, W. and Birchler, J. A. (2012). Identification of Inverse Regulator-a (Inr-a) as Synonymous with Pre-mRNA Cleavage Complex II Protein (Pcf11) in Drosophila. G3 (Bethesda) 2(6): 701-706.
  61. Chuanhe Yu, Fangpu Han, Jianbo Zhang, James A. Birchler and Thomas Peterson, 2012. A transgenic system for generation of transposon Ac/Ds-induced chromosome rearrangements in rice. Theor Appl Genet 125: 1449-1462.
  62. Birchler, J. A. and Veitia, R. A. (2012). Gene balance hypothesis: connecting issues of dosage sensitivity across biological disciplines. Proc Natl Acad Sci U S A 109(37): 14746-14753.
  63. Birchler, J. A., Gao, Z. and Han, F. (2011). Plant Centromeres. Plant Cytogenetics: Genome Structure and Chromosome Function 4: 133.
  64. Birchler, J. A. and Danilova, T. V. (2011). Fluorescence In Situ Hybridization and In Situ PCR. Plant Cytogenetics: Genome Structure and Chromosome Function 4: 295.
  65. Yin, W., Birchler, J. A. and Han, F. (2011). Maize centromeres: where sequence meets epigenetics. Frontiers in Biology 6(2): 102-108.
  66. Birchler, J. A. (2011). RNA interference: what is it? IN: RNA Interference: Application to Drug Discovery and Challenges to Pharmaceutical Development. Johnson, P. H. (Ed). Wiley-Blackwell, Hoboken, pp: 3-11.
  67. Birchler, J. A., Sun, L., Donohue, R., Sanyal, A. and Xie, W. (2011). Implications of the gene balance hypothesis for dosage compensation. Frontiers in Biology 6(2): 118-124.
  68. Birchler, J., Sun, L., Fernandez, H., Donohue, R., Xie, W. and Sanyal, A. (2011). Re-evaluation of the function of the male specific lethal complex in Drosophila. J Genet Genomics 38(8): 327-332.
  69. Birchler, J. A. and Veitia, R. A. (2011). Protein-Protein and Protein-DNA Dosage Balance and Differential Paralog Transcription Factor Retention in Polyploids. Front Plant Sci 2: 64.
  70. Birchler, J. A. and Xie, W. (2011). Reflections on the inhibition of RNAi by cell death signaling. Fly (Austin) 5(4): 337-339.
  71. Birchler, J. A., Gao, Z., Sharma, A., Presting, G. G. and Han, F. (2011). Epigenetic aspects of centromere function in plants. Curr Opin Plant Biol 14(2): 217-222.
  72. Gaeta, R. T., Danilova, T. V., Zhao, C., Masonbrink, R. E., McCaw, M. E. and Birchler, J. A. (2011). Recovery of a telomere-truncated chromosome via a compensating translocation in maize. Genome 54(3): 184-195.
  73. Yao, H., Kato, A., Mooney, B. and Birchler, J. A. (2011). Phenotypic and gene expression analyses of a ploidy series of maize inbred Oh43. Plant Mol Biol 75(3): 237-251.
  74. Koo, D. H., Han, F., Birchler, J. A. and Jiang, J. (2011). Distinct DNA methylation patterns associated with active and inactive centromeres of the maize B chromosome. Genome Res 21(6): 908-914.
  75. Xie, W., Liang, C. and Birchler, J. A. (2011). Inhibition of RNA interference and modulation of transposable element expression by cell death in Drosophila. Genetics 188(4): 823-834.
  76. Findley, S. D., Pappas, A. L., Cui, Y., Birchler, J. A., Palmer, R. G. and Stacey, G. (2011). Fluorescence in situ hybridization-based karyotyping of soybean translocation lines. G3 (Bethesda) 1(2): 117-129.
  77. Gao, Z., Fu, S., Dong, Q., Han, F. and Birchler, J. A. (2011). Inactivation of a centromere during the formation of a translocation in maize. Chromosome Res 19(6): 755-761.
  78. Birchler, J. A., Yao, H., Chudalayandi, S., Vaiman, D. and Veitia, R. A. (2010). Heterosis. Plant Cell 22(7): 2105-2112.
  79. Birchler, J. A. (2010). Reflections on studies of gene expression in aneuploids. Biochem J 426(2): 119-123.
  80. Birchler, J. A. and Veitia, R. A. (2010). The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution. New Phytol 186(1): 54-62.
  81. Veitia, R. A. and Birchler, J. A. (2010). Dominance and gene dosage balance in health and disease: why levels matter! J Pathol 220(2): 174-185.
  82. Birchler, J. A., Krishnaswamy, L., Gaeta, R. T., Masonbrink, R. E. and Zhao, C. (2010). Engineered minichromosomes in plants. Crit rev plant sci 29(3): 135-147.
  83. Kato, A., Lamb, J., Albert, P., Danilova, T., Han, F., Gao, Z., Findley, S. and Birchler, J. (2010). Chromosome painting for plant biotechnology. Methods in molecular biology (Clifton, NJ) 701: 67-96.
  84. Riddle, N. C., Jiang, H., An, L., Doerge, R. W. and Birchler, J. A. (2010). Gene expression analysis at the intersection of ploidy and hybridity in maize. Theor Appl Genet 120(2): 341-353.
  85. Masonbrink, R. E. and Birchler, J. A. (2010). Sporophytic nondisjunction of the maize B chromosome at high copy numbers. J Genet Genomics 37(1): 79-84.
  86. Albert, P. S., Gao, Z., Danilova, T. V. and Birchler, J. A. (2010). Diversity of chromosomal karyotypes in maize and its relatives. Cytogenet Genome Res 129(1-3): 6-16.
  87. Roark, L. M., Hui, A. Y., Donnelly, L., Birchler, J. A. and Newton, K. J. (2010). Recent and frequent insertions of chloroplast DNA into maize nuclear chromosomes. Cytogenet Genome Res 129(1-3): 17-23.
  88. Yu, C., Danilova, T., Zhang, J., Birchler, J. and Peterson, T. (2010). Constructing defined chromosome segmental duplications in maize. Cytogenet genome res 129(1-3): 72-81.
  89. Findley, S. D., Cannon, S., Varala, K., Du, J., Ma, J., Hudson, M. E., Birchler, J. A. and Stacey, G. (2010). A fluorescence in situ hybridization system for karyotyping soybean. Genetics 185(3): 727-744.
  90. Ubiquitous RNA-dependent RNA polymerase and gene silencing. Genome Biol 10(11): 243.
  91. Birchler, J. A. and Han, F. (2009). Maize centromeres: structure, function, epigenetics. Annu Rev Genet 43: 287-303.
  92. Birchler, J. A. (2009). Dosage compensation for the birds. Heredity (Edinb) 102(5): 423-424.
  93. Birchler, J. A., Gao, Z. and Han, F. (2009). A tale of two centromeres--diversity of structure but conservation of function in plants and animals. Funct Integr Genomics 9(1): 7-13.
  94. Birchler, J. A. (2009). Ploidy variation in plants. Encyclopedia of Life Sciences.
  95. Birchler, J. A., Gao, Z. and Han, F. (2009). Pairing in plants: Import is important. Proc Natl Acad Sci U S A 106(47): 19751-19752.
  96. Birchler, J. A. (2009). Compensation Contemplation. IN: Sex chromosomes: Genetics, Abnormalities, and Disorders. Columbus, F. (Ed). Nova Science Publishers, Hauppauge, NY.
  97. Birchler, J. A. (2009). Artificial Chromosomes in Plants. IN: Encyclopedia of Biotechnology in Agriculture and Food. Heldman, D. R., Bridges, A., Hoover, D. and Wheeler, M. B. (Eds). Taylor and Francis, New York.
  98. Birchler, J. A. and Bass, H. W. (2009). Cytogenetics and chromosome structural diversity. IN: The Maize Handbook. Sarah, H. and Jeffrey B. (Eds). Pp:163-177.
  99. Birchler, J. A. (2009). Role of small RNAs in establishing chromosomal architecture in Drosophila. IN: Epigenomics. Anne, F. S., Rob M. and John G. (Eds).Springer Publishers, New York, pp: 177-186.
  100. Sun, X. and Birchler, J. A. (2009). Interaction study of the male specific lethal (MSL) complex and trans-acting dosage effects in metafemales of Drosophila melanogaster. Cytogenet Genome Res 124(3-4): 298-311.
  101. Sun, X. and Birchler, J. A. (2009). Studies on the short range spreading of the male specific lethal (MSL) complex on the X chromosome in Drosophila. Cytogenet Genome Res 124(2): 158-169.
  102. Zhang, J., Yu, C., Pulletikurti, V., Lamb, J., Danilova, T., Weber, D. F., Birchler, J. A. and Peterson, T. (2009). Alternative Ac/Ds transposition induces major chromosomal rearrangements in maize. Gene Dev 23: 755-765.
  103. Han, F., Gao, Z. and Birchler, J. A. (2009). Reactivation of an inactive centromere reveals epigenetic and structural components for centromere specification in maize. Plant Cell 21(7): 1929-1939.
  104. Kavi, H. H. and Birchler, J. A. (2009). Drosophila KDM2 is a H3K4me3 demethylase regulating nucleolar organization. BMC Res Notes 2: 217.
  105. Kavi, H. H. and Birchler, J. A. (2009). Interaction of RNA polymerase II and the small RNA machinery affects heterochromatic silencing in Drosophila. Epigenetics Chromatin 2(1): 15.
  106. Wolfgruber, T. K., Sharma, A., Schneider, K. L., Albert, P. S., Koo, D. H., Shi, J., Gao, Z., Han, F., Lee, H., Xu, R., Allison, J., Birchler, J. A., Jiang, J., Dawe, R. K. and Presting, G. G. (2009). Maize centromere structure and evolution: sequence analysis of centromeres 2 and 5 reveals dynamic Loci shaped primarily by retrotransposons. PLoS Genet 5(11): e1000743.
  107. Veitia, R. A., Bottani, S. and Birchler, J. A. (2008). Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects. Trends Genet 24(8): 390-397.
  108. Birchler, J. A., Yu, W. and Han, F. (2008). Plant engineered minichromosomes and artificial chromosome platforms. Cytogenet Genome Res 120(3-4): 228-232.
  109. Lamb, J. C., Yu, W., Han, F. and Birchler, J. A. (2008). Plant centromeres. Genome Dyn 4: 95-107.
  110. Birchler, J. A. and Kavi, H. H. (2008). Molecular biology. Slicing and dicing for small RNAs. Science 320(5879): 1023-1024.
  111. Kavi, H. H., Fernandez, H. R., Xie, W. and Birchler, J. A. (2008). RNA-mediated gene regulation in Drosophila. In: RNA and regulation of gene expression. Morris, K. (Ed). Horizon Scientific Press, Norwich, UK.
  112. Lough, A. N., Roark, L. M., Kato, A., Ream, T. S., Lamb, J. C., Birchler, J. A. and Newton, K. J. (2008). Mitochondrial DNA transfer to the nucleus generates extensive insertion site variation in maize. Genetics 178(1): 47-55.
  113. Riddle, N. C. and Birchler, J. A. (2008). Comparative analysis of inbred and hybrid maize at the diploid and tetraploid levels. Theor Appl Genet 116(4): 563-576.
  114. Birchler, J. A., Albert, P. S. and Gao, Z. (2008). Stability of repeated sequence clusters in hybrids of maize as revealed by FISH. Trop Plant Biol 1: 34-39.
  115. Danilova, T. V. and Birchler, J. A. (2008). Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: resolution, sensitivity, and banding paint development. Chromosoma 117(4): 345-356.
  116. Vega, J. M., Yu, W., Han, F., Kato, A., Peters, E. M., Zhang, Z. J. and Birchler, J. A. (2008). Agrobacterium-mediated transformation of maize (Zea mays) with Cre-lox site specific recombination cassettes in BIBAC vectors. Plant Mol Biol 66(6): 587-598.
  117. Jin, W., Lamb, J. C., Zhang, W., Kolano, B., Birchler, J. A. and Jiang, J. (2008). Histone modifications associated with both A and B chromosomes of maize. Chromosome Res 16(8): 1203-1214.
  118. Yu, W., Han, F. and Birchler, J. A. (2007). Engineered minichromosomes in plants. Curr Opin Biotechnol 18(5): 425-431.
  119. Birchler, J. A. and Veitia, R. A. (2007). The gene balance hypothesis: from classical genetics to modern genomics. Plant Cell 19(2): 395-402.
  120. Lamb, J. C., Yu, W., Han, F. and Birchler, J. A. (2007). Plant chromosomes from end to end: telomeres, heterochromatin and centromeres. Curr Opin Plant Biol 10(2): 116-122.
  121. Birchler, J. A., Yao, H. and Chudalayandi, S. (2007). Biological consequences of dosage dependent gene regulatory systems. Biochim Biophys Acta 1769(5-6): 422-428.
  122. Kavi, H. H., Fernandez, H., Xie, W. and Birchler, J. A. (2007). Genetics and biochemistry of RNAi in Drosophila. IN: Current Topics in Microbiology and Immunology. Patrick, P. and Peter V. (Eds).Springer Publishers, New York.
  123. Birchler, J. A. (2007). B chromosomes in plants. McGraw-Hill Encyclopedia of Science and Technology.
  124. Yu, W., Han, F. and Birchler, J. A. (2007). Minichromosomes: The next generation technology for plant genetic engineering. Biotechnology News Report. August issue.
  125. Lamb, J. C., Meyer, J. M., Corcoran, B., Kato, A., Han, F. and Birchler, J. A. (2007). Distinct chromosomal distributions of highly repetitive sequences in maize. Chromosome Res 15(1): 33-49.
  126. Yu, W., Lamb, J. C., Han, F. and Birchler, J. A. (2007). Cytological visualization of DNA transposons and their transposition pattern in somatic cells of maize. Genetics 175(1): 31-39.
  127. Lamb, J. C., Danilova, T., Bauer, M. J., Meyer, J. M., Holland, J. J., Jensen, M. D. and Birchler, J. A. (2007). Single-gene detection and karyotyping using small-target fluorescence in situ hybridization on maize somatic chromosomes. Genetics 175(3): 1047-1058.
  128. Han, F., Lamb, J. C., Yu, W., Gao, Z. and Birchler, J. A. (2007). Centromere function and nondisjunction are independent components of the maize B chromosome accumulation mechanism. Plant Cell 19(2): 524-533.
  129. Lamb, J. C., Meyer, J. M. and Birchler, J. A. (2007). A hemicentric inversion in the maize line knobless Tama flint created two sites of centromeric elements and moved the kinetochore-forming region. Chromosoma 116(3): 237-247.
  130. Lamb, J. C., Riddle, N. C., Cheng, Y. M., Theuri, J. and Birchler, J. A. (2007). Localization and transcription of a retrotransposon-derived element on the maize B chromosome. Chromosome Res 15(3): 383-398.
  131. Yu, W., Han, F., Gao, Z., Vega, J. M. and Birchler, J. A. (2007). Construction and behavior of engineered minichromosomes in maize. Proc Natl Acad Sci U S A 104(21): 8924-8929.
  132. Han, F., Gao, Z., Yu, W. and Birchler, J. A. (2007). Minichromosome analysis of chromosome pairing, disjunction, and sister chromatid cohesion in maize. Plant Cell 19(12): 3853-3863.
  133. Birchler, J. A., Yao, H. and Chudalayandi, S. (2006). Unraveling the genetic basis of hybrid vigor. Proc Natl Acad Sci U S A 103(35): 12957-12958.
  134. Birchler, J. A., Fernandez, H. R. and Kavi, H. H. (2006). Commonalities in compensation. Bioessays 28(6): 565-568.
  135. An, L., Riddle, N. C., Birchler, J. A. and Doerge, R. W. (2006). Clustering gene expression: Maize ploidy series with repeated measurements. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture, Manhattan, Kansas, pp:52-66.
  136. Kavi, H. H., Fernandez, H. R., Xie, W. and Birchler, J. A. (2006). Polycomb, pairing and PIWI--RNA silencing and nuclear interactions. Trends Biochem Sci 31(9): 485-487.
  137. Yao, H., Chudalayandi, S. and Birchler, J. A. (2006). The epigenetics of plants. IN: Epigenetics: principles, methodology and practice. Xue, J. (Ed).
  138. Lamb, J. C., Kato, A., Yu, W., Han, F., Albert, P. S. and Birchler, J. A. (2006). Cytogenetics and chromosome analytical techniques. IN: Floriculture, Ornamental and Plant Biotechnology: Advanced and Topical Issues. Jaime A. Teixeira da Silva. Global Science Books, London.
  139. Kato, A. and Birchler, J. A. (2006). Induction of tetraploid derivatives of maize inbred lines by nitrous oxide gas treatment. J Hered 97(1): 39-44.
  140. Han, F., Lamb, J. C. and Birchler, J. A. (2006). High frequency of centromere inactivation resulting in stable dicentric chromosomes of maize. Proc Natl Acad Sci U S A 103(9): 3238-3243.
  141. Bauer, M. J. and Birchler, J. A. (2006). Organization of endoreduplicated chromosomes in the endosperm of Zea mays L. Chromosoma 115(5): 383-394.
  142. Kato, A., Albert, P. S., Vega, J. M. and Birchler, J. A. (2006). Sensitive fluorescence in situ hybridization signal detection in maize using directly labeled probes produced by high concentration DNA polymerase nick translation. Biotech Histochem 81(2-3): 71-78.
  143. Lamb, J. C. and Birchler, J. A. (2006). Retroelement genome painting: cytological visualization of retroelement expansions in the genera Zea and Tripsacum. Genetics 173(2): 1007-1021.
  144. Yu, W., Han, F., Kato, A. and Birchler, J. A. (2006). Characterization of a maize isochromosome 8S*8S. Genome 49(6): 700-706.
  145. Riddle, N. C., Kato, A. and Birchler, J. A. (2006). Genetic variation for the response to ploidy change in Zea mays L. Theor Appl Genet 114(1): 101-111.
  146. Pal Bhadra, M., Bhadra, U. and Birchler, J. A. (2006). Misregulation of sex-lethal and disruption of male-specific lethal complex localization in Drosophila species hybrids. Genetics 174(3): 1151-1159.
  147. Yu, W., Lamb, J. C., Han, F. and Birchler, J. A. (2006). Telomere-mediated chromosomal truncation in maize. Proc Natl Acad Sci U S A 103(46): 17331-17336.
  148. Kato, A., Vega, J. M., Han, F., Lamb, J. C. and Birchler, J. A. (2005). Advances in plant chromosome identification and cytogenetic techniques. Curr Opin Plant Biol 8(2): 148-154.
  149. Kavi, H. H., Xie, W., Fernandez, H. R. and Birchler, J. A. (2005). Global analysis of siRNA-mediated transcriptional gene silencing. Bioessays 27(12): 1209-1212.
  150. Matzke, M. A. and Birchler, J. A. (2005). RNAi-mediated pathways in the nucleus. Nat Rev Genet 6(1): 24-35.
  151. Birchler, J. A., Riddle, N. C., Auger, D. L. and Veitia, R. A. (2005). Dosage balance in gene regulation: biological implications. Trends Genet 21(4): 219-226.
  152. Fernandez, H. R., Kavi, H. H., Xie, W. and Birchler, J. A. (2005). Heterochromatin: on the ADAR radar? Curr Biol 15(4): R132-134.
  153. Kato, A., Lamb, J. C., Han, F., Vega, J. M. and Birchler, J. A. (2005). Molecular Analysis of Maize Chromosomes. Maydica 50: 311-320.
  154. Kavi, H. H., Fernandez, H. R., Xie, W. and Birchler, J. A. (2005). RNA silencing in Drosophila. FEBS Lett 579(26): 5940-5949.
  155. Birchler, J. A. and Auger, D. L. (2005). Biological consequences of dosage dependent gene regulatory mechanisms in multicellular eukaryotes. IN: Biology of Dominance. Veitia, R. (Ed).Landes Bioscience, pp:89-100.
  156. Kato, A., Zheng, Y. Z., Auger, D. L., Phelps-Durr, T., Bauer, M. J., Lamb, J. C. and Birchler, J. A. (2005). Minichromosomes derived from the B chromosome of maize. Cytogenet Genome Res 109(1-3): 156-165.
  157. Theuri, J.,Tara, P. D., Mathews, S. and Birchler, J. A. (2005). A comparative study of retrotransposons in the centromeric regions of A and B chromosomes of maize. Cytogenet Genome Res 110: 203-208.
  158. Lamb, J. C., Kato, A. and Birchler, J. A. (2005). Centromere associated sequences are present throughout the maize B chromosome. Chromosoma 113: 337-349.
  159. Auger, D. L., Gray, A. D., Ream, T. S., Kato, A., Coe, E. H., Jr. and Birchler, J. A. (2005). Nonadditive gene expression in diploid and triploid hybrids of maize. Genetics 169(1): 389-397.
  160. Bhadra, M. P., Bhadra, U., Kundu, J. and Birchler, J. A. (2005). Gene expression analysis of the function of the male-specific lethal complex in Drosophila. Genetics 169(4): 2061-2074.
  161. Jin, W., Lamb, J. C., Vega, J. M., Dawe, R. K., Birchler, J. A. and Jiang, J. (2005). Molecular and functional dissection of the maize B chromosome centromere. Plant Cell 17(5): 1412-1423.
  162. Vedova, C. B. D., Lorbiecke, R., Kirsch, H., Schulte, M. B., Scheets, K., Borchert, L. M., Scheffler, B. E., Wienand, U., Cone, K. C. and Birchler, J. A. (2005). The dominant inhibitory chalcone synthase allele C2-Idf (Inhibitor diffuse) from Zea mays (L.) acts via an endogenous RNA silencing mechanism. Genetics 170: 1989-2002.
  163. Ream, T. S., Strobel, J., Roller, B., Auger, D. L., Kato, A., Halbrook, C., Peters, E. M., Theuri, J., Bauer, M. J., Addae, P., Dioh, W., Staub, J. M., Gilbertson, L. A. and Birchler, J. A. (2005). A test for ectopic exchange catalyzed by Cre recombinase in maize. Theor Appl Genet 111(2): 378-385.
  164. Auger, D. L., Peters, E. M. and Birchler, J. A. (2005). A genetic test of bioactive gibberellins as regulators of heterosis in maize. J Hered 96(5): 614-617.

Protocols by James A. Birchler
  1. Telomere-mediated Chromosomal Truncation via Agrobacterium tumefaciens or Particle Bombardment to Produce Engineered Minichromosomes in Plants