Publications

Journal

Stein, A. (2010) Possible Origin of Gravity and the Holographic Principle arXiv:1010.2487v1[physics.gen.ph]"

Stein, A., Takasuka, T.E., Collings, C.K. 2010. Are nucleosome positions /in vivo/ primarily determined by histone-DNA sequence preferences. Nucleic Acids Res. 38: 709-719.

Stein, A. 2010. Nucleosome positioning, gene regulation and disease. Epigenomics. 2: 351-355.

Takasuka, TE, Stein, A. 2010. Direct measurements of the nucleosone-forming preferences of periodic DNA motifs challenge established models. Nucleic Acids Res. 38: 5672-5680.

Takasuka, T. E., Cioffi, A., Stein, A. 2008. Sequence information encoded in DNA that may influence long-range chromatin structure correlates with human chromosome functions. PLoS ONE. 3: e2643.

Cioffi, A., Fleury, T. J., Stein, A. 2006. Aspects of large-scale chromatin structures in mouse liver nuclei can be predicted from the DNA sequence. Nucleic Acids Res. 34: 1974-1981.

Fleury, T. J., Cioffi, A., Stein, A. 2006. Detecting nucleosome ladders on unique DNA sequences in mouse liver nuclei. Methods Mol Biol. 338: 209-224.

Dalal, Y., Fleury, T. J., Cioffi, A., Stein, A. 2005. Long-range oscillation in a periodic DNA sequence motif may influence nucleosome array formation. Nucleic Acids Res. 33: 934-945.

Fan, Y., Nikitina, T., Zhao, J., Fleury, T. J., Bhattacharyya, R., Bouhassira, E. E., Stein, A., Woodcock, C. L., Skoultchi, A. I. 2005. Histone H1 depletion in mammals alters global chromatin structure but causes specific changes in gene regulation. Cell. 123: 1199-1212.

Bina, M., Wyss, P., Ren, W., Szpankowski, W., Thomas, E., Randhawa, R., Reddy, S., John, P. M., Pares-Matos, E. I., Stein, A., Xu, H., Lazarus, S. A. 2004. Exploring the characteristics of sequence elements in proximal promoters of human genes. Genomics. 84: 929-940.

Cioffi, A., Dalal, Y., Stein, A. 2004. DNA sequence alterations affect nucleosome array formation of the chicken ovalbumin gene. Biochemistry. 43: 6709-6722.

Stein, A., Dalal, Y., Fleury, T. J. 2002. Circle ligation of in vitro assembled chromatin indicates a highly flexible structure. Nucleic Acids Res. 30: 5103-5109.

Stein, A., Bina, M. 1999. A signal encoded in vertebrate DNA that influences nucleosome positioning and alignment. Nucleic Acids Res. 27: 848-853.

Stein, A., Hill, S. A., Cheng, Z., Bina, M. 1998. Simple miniaturized gel system for DNA sequence analysis. Nucleic Acids Res. 26: 452-455.

Liu, K., Stein, A. 1997. DNA sequence encodes information for nucleosome array formation. J Mol Biol. 270: 559-573.

Shin, B. S., Stein, A., Zalkin, H. 1997. Interaction of Bacillus subtilis purine repressor with DNA. J Bacteriol. 179: 7394-7402.

Stein, A. 1996. Signals in eukaryotic DNA promote and influence formation of nucleosome arrays. Prog Nucleic Acid Res Mol Biol. 54: 333-381.

Liu, K., Sandgren, E. P., Palmiter, R. D., Stein, A. 1995. Rat growth hormone gene introns stimulate nucleosome alignment in vitro and in transgenic mice. Proc Natl Acad Sci U S A. 92: 7724-7728.

Jeong, S., Stein, A. 1994. Micrococcal nuclease digestion of nuclei reveals extended nucleosome ladders having anomalous DNA lengths for chromatin assembled on non-replicating plasmids in transfected cells. Nucleic Acids Res. 22: 370-375.

Jeong, S. W., Stein, A. 1994. DNA sequence affects nucleosome ordering on replicating plasmids in transfected COS-1 cells and in vitro. J Biol Chem. 269: 2197-2205.

Lauderdale, J. D., Stein, A. 1993. Effects of plasmid length and positioned nucleosomes on chromatin assembly in vitro. Biochemistry. 32: 489-499.

Liu, K., Lauderdale, J. D., Stein, A. 1993. Signals in chicken beta-globin DNA influence chromatin assembly in vitro. Mol Cell Biol. 13: 7596-7603.

Lauderdale, J. D., Stein, A. 1992. Introns of the chicken ovalbumin gene promote nucleosome alignment in vitro. Nucleic Acids Res. 20: 6589-6596.

Jeong, S. W., Lauderdale, J. D., Stein, A. 1991. Chromatin assembly on plasmid DNA in vitro. Apparent spreading of nucleosome alignment from one region of pBR327 by histone H5. J Mol Biol. 222: 1131-1147.

Stein, A. 1989. Reconstitution of chromatin from purified components. Methods Enzymol. 170: 585-603.

Stein, A., Mitchell, M. 1988. Generation of different nucleosome spacing periodicities in vitro. Possible origin of cell type specificity. J Mol Biol. 203: 1029-1043.

Stein, A. 1987. Unique positioning of reconstituted nucleosomes occurs in one region of simian virus 40 DNA. J Biol Chem. 262: 3872-3879.

Blasquez, V., Stein, A., Ambrose, C., Bina, M. 1986. Simian virus 40 protein VP1 is involved in spacing nucleosomes in minichromosomes. J Mol Biol. 191: 97-106.

Stein, A., Holley, K., Zeliff, J., Townsend, T. 1985. Interactions between core histones and chromatin at physiological ionic strength. Biochemistry. 24: 1783-1790.

Stein, A., Bina, M. 1984. A model chromatin assembly system. Factors affecting nucleosome spacing. J Mol Biol. 178: 341-363.

Kunzler, P., Stein, A. 1983. Histone H5 can increase the internucleosome spacing in dinucleosomes to nativelike values. Biochemistry. 22: 1783-1789.

Stein, A., Kunzler, P. 1983. Histone H5 can correctly align randomly arranged nucleosomes in a defined in vitro system. Nature. 302: 548-550.

Stein, A., Townsend, T. 1983. HMG 14/17 binding affinities and DNAase I sensitivities of nucleoprotein particles. Nucleic Acids Res. 11: 6803-6819.

Bina, M., Sturtevant, J. M., Stein, A. 1980. Stability of DNA in nucleosomes. Proc Natl Acad Sci U S A. 77: 4044-4047.

Simpson, R. T., Stein, A. 1980. Random protection of single cut restriction endonuclease sites in SV40 mini-chromosomes assembled in vitro. FEBS Lett. 111: 337-339.

Stein, A. 1980. DNA wrapping in nucleosomes. The linking number problem re-examined. Nucleic Acids Res. 8: 4803-4820.

Stein, A., Page, D. 1980. Core histone associations in solutions of high salt. An osmotic pressure study. J Biol Chem. 255: 3629-3637.

Stein, A. 1979. DNA folding by histones: the kinetics of chromatin core particle reassembly and the interaction of nucleosomes with histones. J Mol Biol. 130: 103-134.

Stein, A., Whitlock, J. P., Jr., Bina, M. 1979. Acidic polypeptides can assemble both histones and chromatin in vitro at physiological ionic strength. Proc Natl Acad Sci U S A. 76: 5000-5004.

Whitlock, J. P., Jr., Stein, A. 1978. Folding of DNA by histones which lack their NH2-terminal regions. J Biol Chem. 253: 3857-3861.

Stein, A., Bina-Stein, M., Simpson, R. T. 1977. Crosslinked histone octamer as a model of the nucleosome core. Proc Natl Acad Sci U S A. 74: 2780-2784.

Bina-Stein, M., Stein, A. 1976. Allosteric interpretation of Mg2+ binding to the denaturable Escherichia coli tRNAGlu2+. Biochemistry. 15: 3912-3917.