@book{waterman:89,
	title = "Mathematical Methods for {DNA} Sequences",
	author = "M. Waterman, ed.",
	publisher = "CRC Press",
	address = "Boca Raton, FL",
	year = 1989,
	note = "contains a representative survey of methods and
		references"
	}


@book{bell:90,
	title = "Computers and {DNA}",
	author = "G. Bell and T. Marr, eds.",
	publisher = "Addison Wesley",
	address = "Reading, MA",
	year = 1990,
	note = "also contains representative work in this field",
	}

@article{bmb-special:84,
	journal = "Bull. Math. Biol.",
 	volume = 46,
	number = 4,
	year = 1984,
	note = "is a special issue devoted to mathematical and
		computational problems in the analysis of molecular
		sequences"
	}

@article{nar-special,
	journal = "Nucl. Acids Res.",
	note = "has produced three special volumes on The Application
		of Computers to Research on Nucleic Acids"
	}

@article{little:82,
	author = "J.W. Little and D.W. Mount",
	year = 1982,
	title = "The {SOS} Regulatory System of {Escherichia coli}",
	journal = "Cell",
 	volume = 29,
	pages = "11-22"
	}

@article{brendel:86,
	author = "V. Brendel and G. Hamm and E. Trifonov",
	year = 1986,
	title = "Terminators of Transcription with RNA Polymerase
		  from Escherichia coli: What They Look Like and How
		  to Find Them",
	journal = "J. Biomolec. Str. Dyn.",
 	volume = 3,
        pages = "705-723"
        }

@article{nussinov:85,
	author = "R. Nussinov", 
	year = 1985,  
	title = "Large Helical Conformational Deviations from Ideal
		{B-DNA} and Prokaryotic Regulatory Sites",  
	journal = "J. Theor. Biol.",
	volume = 115,
	pages = "179-189"
	}

@article{nussinov:84:jbc,
	author = "R. Nussinov", 
	year = 1984,  
	title = "Promoter Helical Structural Variation at the 
		{Escherichia coli} Polymerase Interactions Sites",
	journal = "J. Biol. Chem.",
 	volume = 259,
	pages = "6798-6805"
	}

@article{nussinov:84:jme,
	author = "R. Nussinov", 
	year = 1984,
	title = "Structural Features are as Important as Sequence
		  Homologies in {\em Drosophila} Heat Shock Upstream
		  Regions", 
	journal = "J. Molec. Evol.",
	volume = 20,
	pages = "106-110"
	}

@article{nussinov:85:jme,
	author = "R. Nussinov", 
	year = 1985,
	title = "Structural Wrinkles and the Genomic Regulatory Sites
		  of Eukaryotes",  
	journal = "J. Molec. Evol.",
 	volume = 22,
	pages = "150-159"
	}

@article{nussinov:84:bba,
	author = "R. Nussinov and B. Shapiro and L. Lipkin and
		J. Maizel",  
	year = 1984,
	title = "Enhancer Elements Share Local Homologous Twist-angle
		  Variations with a Helical Periodicity", 
	journal = "Biochim. Biophys. Acta",
 	volume = 783,
	pages = "246-257"
	}

@article{tung:87,
	author = "C. S. Tung and S. Harvey", 
	year = 1987,
	title = "A common structural feature in promoter sequences of
		  {\em E. coli}",   
	journal = "Nuc. Acids Res.",
	volume = 15,
	pages = "4973-4985"
	}

@article{Teckdahl:90,
	author = "T. Eckdahl and J.N. Anderson", 
	year = 1990,
	title = "Conserved {DNA} Structures in Origins of Replication", 
	journal = "Nucl. Acids Res.",
 	volume = 18,
	pages = "1609-1612"
	}

@article{williams:88,
	author = "J.S. Williams and T.T. Eckdahl and J.N. Anderson", 
	year = 1988,
	title = "Bent {DNA} Functions as a Replication Enhancer in {\em
		  Saccharomyces cerevisiae}", 
	journal = "Mol. Cell. Biol.",
 	volume = 8,
	pages = "2763-2769"
	}

@article{snyder:86,
	author = "M. Snyder and A.R. Buchman and R.W. Davis", 
	year = 1986,
	title = "Bent {DNA} at a yeast autonomously replicating
		  sequence",  
	journal = "Nature",
 	volume = 324,
	pages = "87-89"
	}

@article{plaskon:87,
	author = "R. Plaskon and R. Wartell", 
	year = 1987,
	title = "Sequence Distributions Associated with {DNA} Curvature
		  are found Upstream of Strong {\em E. coli} Promoters", 
	journal = "Nuc. Acids Res.",
 	volume = 15,
	pages = "785-796"
	}

@article{shrader:89,
	author = "T.E. Shrader and D.M. Crothers", 
	year = 1989,
	title = "Artificial nucleosome positioning sequences", 
	journal = "Proc. Nat'l. Acad. Sci. USA",
	volume = 86,
	pages = "7418-7422"
	}

@article{costanzo:90,
	author = "G. Costanzo and E. DiMauro and G. Salina and
		R. Negri",
	year = 1990, 
	title = "Attraction, Phasing and Neighbour Effects of Histone
		Octomers on Curved {DNA}", 
	journal = "J.  Mol. Biol.",
 	volume = 216,
	pages = "363-374"
	}

@article{trifonov:82,
	author = "E.N. Trifonov", 
	year = 1982,
	title = "Sequence-dependent Variations of {B-DNA} Structure and
		Protein-{DNA} Recognition",  
	journal = "Cold Spring Harbor Symp. Quant. Biol.",
 	volume = 47,
	pages = "271-278"
	}

@article{kabsch:82,
	author = "W. Kabsch, C. Sander and E.N. Trifonov", 
	year = 1982,
	title = "The ten helical twist angles of {B-DNA}", 
	journal = "Nucl. Acids Res.",
 	volume = 10,
	pages = "1097-1102"
	}

@article{hagerman:90,
	author = "P.J. Hagerman", 
	year = 1990,
	title = "Sequence-Directed Curvature of {DNA}",
	journal = "Ann.  Rev. Biochem.",
 	volume = 59,
	pages = "755-781"
	}

@article{bolshoy:91,
	author = "A. Bolshoy, P. McNamara, R.E. Harrington and
		E.N. Trifonov",
	year = 1991,
	title = "Curved {DNA} without {A-A}: Experimental
		estimation of all 16 {DNA} wedge angles",
	journal = "Proc. Nat'l. Acad. Sci. USA",
 	volume = 88,
	pages = "2312-2316"
	}

@article{gorin:95,
	author = "A.A Gorin, V.B. Zhurkin and W.K. Olson", 
	year = 1995,
	title = "{B-DNA} Twisting Correlates with Base-pair
		Morphology",  
	journal = "J. Mol. Biol.",
	volume = 247,
	pages = "34-48"
	}

@article{berman:92,
	author = "H.M. Berman and W.K. Olson and D.L. Beveridge and
		J. Westbrook and A. Gelbin and T. Demeny and
		S.-H. Hsieh and A.R. Srinivasan and B. Schneider",
	year = 1992,
	title = "The Nucleic Acid Database", 
	journal = "Biophys. J.",
	volume = 63,
	pages = "751-759"
	}

@article{kowalski:89,
	author = "D. Kowalski and M. Eddy", 
	year = 1989,
	title = "The {DNA} Unwinding Element: A Novel {\em
		cis}-acting Component that Facilitates Opening of the  
		{Escherichia coli} Replication Origin", 
	journal = "EMBO Jour.",
 	volume = 8,
	pages = "4335-4344"
	}

@article{umek:88,
	author = "R. Umek and D. Kowalski", 
	year = 1988,
	title = "The Ease of {DNA} Unwinding as a Determinant of
		Initiation at Yeast Replication Origins",  
	journal = "Cell",
 	volume = 52,
	pages = "559-567"
	}

@article{benham:93,
	author = "C.J. Benham", 
	year = 1993,
	title = "Sites of Predicted Stress-Induced {DNA} Duplex
		Destabilization Occur Preferentially at Regulatory
		Loci",   
	journal = "Proc. Nat'l.  Acad. Sci. USA",
 	volume = 90,
	pages = "2999-3003"
	}

@article{benham:96,
	author = "C.J. Benham", 
	year = 1996,
	title = "Duplex Destabilization in Superhelical {DNA} is
		Predicted to Occur at Specific Transcriptional
		Regulatory Regions", 
	journal = "J.  Mol. Biol.",
 	volume = 255,
	pages = "425-434"
	}

@article{benham:90,
	author = "C.J. Benham", 
	year = 1990,
	title = "Theoretical Analysis of Heteropolymeric Transitions
		in Superhelical {DNA} Molecules of Specified Sequence",  
	journal = "J. Chem. Phys.",
 	volume = 92,
	pages = "6294-6305"
	}

@article{benham:92,
	author = "C.J. Benham", 
	year = 1992,
	title = "The Energetics of the Strand Separation Transition
		in Superhelical {DNA}",  
	journal = "J. Mol. Biol.",
 	volume = 225,
	pages = "835-847"
	}

@article{sun:95,
	author = "H. Sun and M. Mezei and R. Fye and C.J. Benham", 
	year = 1995,
	title = "{Monte Carlo} analysis of conformational transitions
		in superhelical {DNA}",  
	journal = "J. Chem. Phys.",
 	volume = 103,
	pages = "8653-8665"
	}

@book{fukunaga:90,
	author = "Fukunaga",
	year = 1990,
	title = "Statistical Pattern Recognition",
	publisher = "Academic Press",
	address = "San Diego, CA"
	}


@article{umek:89,
	author = "R. Umek and M. Linskens and D. Kowalski and
		J. Huberman",  
	year = 1989,
	title = "New Beginnings in Studies of Eucaryotic {DNA}
		Replication Origins",  
	journal = "Biochim.  Biophys. Acta",
	volume = 1007,
	pages = "1-14"
	}

@article{nussinov:lennon:84:jbc,
	author = "R. Nussinov and G.G. Lennon", 
	year = 1984,
	title = "Structural Features are as Important as Sequence
		Homologies in {\em Drosophila} Heat Shock Gene
		Upstream",
	}

@article{tung:86,
	author = "C. S. Tung and S. Harvey", 
	year = 1986,
	title = "Base Sequence, Local Helix Structure, and
		Macroscopic Curvature of {A-DNA} and {B-DNA}",  
	journal = "J. Biol. Chem.",
 	volume = 261,
	pages = "3700-3709"
	}

@article{tachibana:85,
	author = "H. Tachibana and A. Ishihama", 
	year = 1985,
	title = "Correlation between the Rate of Productive
		Transcription Initiation and the Strand-melting 
		Property of {Escherichia coli} Promoters",
	journal = "Nuc. Acids Res.",
	volume = 13,
	pages = "9031-9042"
	}

@article{margalit:88,
	author = "H. Margalit and B. Shapiro and R. Nussinov and
		J. Owens and R. Jernigan", 
	year = 1988,
	title = "Helix Stability in Prokaryotic Promoter Regions",
	journal = "Biochemistry",
 	volume = 27,
	pages = "5179-5188"
	}

@article{kowalski:88,
	author = "D. Kowalski and D. Natale and M. Eddy", 
	year = 1988,
	title = "Stable {DNA} Unwinding, not Breathing Accounts for
		Single-Strand Specific Nuclease Hypersensitivity of
		Specific {A+T}-Rich Regions",  
	journal = "Proc. Nat'l. Acad. Sci. USA",
 	volume = 85,
	pages = "9464-9468"
	}

@article{bhriain:89,
	author = "N. Bhriain and C. Dorman and C. Higgins", 
	year = 1989,
	title = "An Overlap between Osmotic and Anaerobic Stress
		Responses: A Potential Role for {DNA} Supercoiling in
		the Coordinate Regulation of Gene Expression",  
	journal = "Molec. Micro.",
	volume = 3,
	pages = "933-942"
	}

@article{malkhosyan:91,
	author = "S. Malkhosyan and Y. Panchenko and A. Rekesh", 
	year = 1991,
	title = "A Physiological Role for {DNA} Supercoiling in the
		Anaerobic Regulation of Colicin Gene Expression", 
	journal = "Molec. Gen. Genet.",
 	volume = 225,
	pages = "342-345"
	}

@article{schnos:88,
	author = "M. Schnos and K. Zahn and R. Inman and F. Blattner", 
	year = 1988,
	title = "Initiation of Protein-Induced Helix Destabilization
		at the $\lambda$ Origin - A Prepriming Step in {DNA}
		Replication",  
	journal = "Cell",
	volume = 52,
	pages = "385-395"
	}

@article{trifonov:86,
	author = "E. Trifonov", 
	year = 1986,
	title = "Curved {DNA}", 
	journal = "CRC Crit. Rev. Biochem.",
 	volume = 19,
	pages = "89-106"
	}