Theoretical molecular biology: prospectives and perspectives.
暂无分享,去创建一个
[1] A Klug,et al. Sequence-dependent variation in the conformation of DNA. , 1981, Journal of molecular biology.
[2] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.
[3] Peter H. Sellers,et al. The Theory and Computation of Evolutionary Distances: Pattern Recognition , 1980, J. Algorithms.
[4] Manolo Gouy,et al. Codon catalog usage is a genome strategy modulated for gene expressivity , 1981, Nucleic Acids Res..
[5] S. Elgin,et al. Analysis of chromatin structure and DNA sequence organization: use of the 1,10-phenanthroline-cuprous complex. , 1982, Nucleic acids research.
[6] A. Gibbs,et al. The Diagram, a Method for Comparing Sequences , 1970 .
[7] R. Tjian,et al. The promoter-specific transcription factor Sp1 binds to upstream sequences in the SV40 early promoter , 1983, Cell.
[8] R. Martin,et al. Use of an 125I-labelled DNA ligand to probe DNA structure , 1983, Nature.
[9] J. Fickett. Recognition of protein coding regions in DNA sequences. , 1982, Nucleic acids research.
[10] R Nussinov. Promoter helical structure variation at the Escherichia coli polymerase interaction sites. , 1984, The Journal of biological chemistry.
[11] R. Nussinov,et al. Hydrophobic interactions in the major groove can influence DNA local structure. , 1986, Journal of biomolecular structure & dynamics.
[12] James W. Fickett,et al. Fast optimal alignment , 1984, Nucleic Acids Res..
[13] R. Nussinov,et al. TGTG, G clustering and other signals near non-mammalian vertebrate mRNA 3' termini: some implications. , 1986, Journal of biomolecular structure & dynamics.
[14] A. Mclachlan,et al. Analysis of gene duplication repeats in the myosin rod. , 1983, Journal of molecular biology.
[15] G. M. Landau,et al. An efficient string matching algorithm with K substitutions for nucleotide and amino acid sequences. , 1987, Journal of theoretical biology.
[16] P. Sellers. On the Theory and Computation of Evolutionary Distances , 1974 .
[17] R. Dickerson,et al. Kinematic model for B-DNA. , 1981, Proceedings of the National Academy of Sciences of the United States of America.
[18] K. S. Chen,et al. A theoretical investigation on the sequence selective binding of adriamycin to double-stranded polynucleotides. , 1986, Nucleic acids research.
[19] W. Fiers,et al. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. , 1982, Gene.
[20] H. Drew. Structural specificities of five commonly used DNA nucleases. , 1984, Journal of molecular biology.
[21] G. Gargiulo,et al. Analogous cleavage of DNA by micrococcal nuclease and a 1-10-phenanthroline-cuprous complex. , 1982, Nucleic acids research.
[22] D. Sankoff,et al. Evolution of 5S RNA and the non-randomness of base replacement. , 1973, Nature: New biology.
[23] H R Drew,et al. Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. , 1981, Journal of molecular biology.
[24] H. Drew,et al. DNA structural variations in the E. coli tyrT promoter , 1984, Cell.
[25] M. I. Kanehisa,et al. Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries , 1982, Nucleic Acids Res..
[26] G. Fink,et al. Repeated DNA sequences upstream from HIS1 also occur at several other co-regulated genes in Saccharomyces cerevisiae. , 1983, The Journal of biological chemistry.
[27] S. Harvey,et al. A molecular mechanical model to predict the helix twist angles of B-DNA. , 1984, Nucleic acids research.
[28] Ignacio Tinoco,et al. A dynamic programming algorithm for finding alternative RNA secondary structures , 1986, Nucleic Acids Res..
[29] Stephen C. Harvey,et al. Computer graphics program to reveal the dependence of the gross three- dimensional structure of the B-DNA double helix on primary structure , 1986, Nucleic Acids Res..
[30] T. Miyata,et al. Extraordinarily high evolutionary rate of pseudogenes: evidence for the presence of selective pressure against changes between synonymous codons. , 1981, Proceedings of the National Academy of Sciences of the United States of America.
[31] J. Bishop,et al. The protein products of the myc and myb oncogenes and adenovirus E1a are structurally related , 1983, Nature.
[32] R Nussinov,et al. Some guidelines for identification of recognition sequences: regulatory sequences frequently contain (T)GTG/CAC(A), TGA/TCA and (T)CTC/GAG(A). , 1986, Biochimica et biophysica acta.
[33] M. Waterman,et al. Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli. , 1985, Journal of molecular biology.
[34] Rosalind C. Lee,et al. The mouse c-abl locus: Molecular cloning and characterization , 1984, Cell.
[35] R. Dickerson,et al. Base sequence and helix structure variation in B and A DNA. , 1983, Journal of molecular biology.
[36] T. Ikemura. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. , 1981, Journal of molecular biology.
[37] Robert Tjian,et al. Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins , 1985, Nature.
[38] M. Vigneron,et al. Requirement of stereospecific alignments for initiation from the simian virus 40 early promoter , 1986, Nature.
[39] J. Richardson,et al. Simultaneous comparison of three protein sequences. , 1985, Proceedings of the National Academy of Sciences of the United States of America.
[40] A. Mclachlan. Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c 551 . , 1971, Journal of molecular biology.
[41] Donald E. Knuth,et al. Fast Pattern Matching in Strings , 1977, SIAM J. Comput..
[42] A. Mclachlan,et al. Confidence limits for homology in protein or gene sequences. The c-myc oncogene and adenovirus E1a protein. , 1985, Journal of molecular biology.
[43] Michael Zuker,et al. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..
[44] H. Buc,et al. Cyclic AMP receptor protein: role in transcription activation. , 1984, Science.
[45] S. B. Needleman,et al. A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.
[46] The predicted presence of large helical structural variation in yeast HIS4 upstream region is correlated with general amino acid control on the CYC1 gene. , 1985, Journal of biomolecular structure & dynamics.
[47] S. McKnight,et al. The distal transcription signals of the herpesvirus tk gene share a common hexanucleotide control sequence , 1984, Cell.
[48] J. C. Shepherd. Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification. , 1981, Proceedings of the National Academy of Sciences of the United States of America.
[49] R Nussinov,et al. Eukaryotic dinucleotide preference rules and their implications for degenerate codon usage. , 1981, Journal of molecular biology.
[50] T. Maniatis,et al. The primary structure of rabbit β-globin mRNA as determined from cloned DNA , 1977, Cell.
[51] D J Lipman,et al. Contextual constraints on synonymous codon choice. , 1983, Journal of molecular biology.
[52] M. Waterman,et al. Pattern recognition in several sequences: consensus and alignment. , 1984, Bulletin of mathematical biology.
[53] J. Josse,et al. Enzymatic synthesis of deoxyribonucleic acid. VIII. Frequencies of nearest neighbor base sequences in deoxyribonucleic acid. , 1961, The Journal of biological chemistry.
[54] R Staden,et al. An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. , 1982, Nucleic acids research.
[55] M. Gouy,et al. Codon usage in bacteria: correlation with gene expressivity. , 1982, Nucleic acids research.
[56] D. Lipman,et al. Rapid similarity searches of nucleic acid and protein data banks. , 1983, Proceedings of the National Academy of Sciences of the United States of America.
[57] L. Bossi,et al. The influence of codon context on genetic code translation , 1980, Nature.
[58] F. Sanger,et al. Gene F of bacteriophage phiX174. Correlation of nucleotide sequences from the DNA and amino acid sequences from the gene product. , 1976, Journal of molecular biology.
[59] Michael J. Fischer,et al. The String-to-String Correction Problem , 1974, JACM.
[60] L. J. Korn,et al. Computer analysis of nucleic acid regulatory sequences. , 1977, Proceedings of the National Academy of Sciences of the United States of America.
[61] D. Sankoff. Minimal Mutation Trees of Sequences , 1975 .
[62] R Nussinov,et al. Large helical conformational deviations from ideal B-DNA and prokaryotic regulatory sites. , 1985, Journal of theoretical biology.
[63] C R Calladine,et al. Mechanics of sequence-dependent stacking of bases in B-DNA. , 1982, Journal of molecular biology.
[64] E. Trifonov,et al. Sequence-dependent deformational anisotropy of chromatin DNA. , 1980, Nucleic acids research.
[65] R Nussinov,et al. An efficient code searching for sequence homology and DNA duplication. , 1983, Journal of theoretical biology.
[66] S. Harvey,et al. Base sequence, local helix structure, and macroscopic curvature of A-DNA and B-DNA. , 1986, The Journal of biological chemistry.
[67] E. Trifonov,et al. The pitch of chromatin DNA is reflected in its nucleotide sequence. , 1980, Proceedings of the National Academy of Sciences of the United States of America.
[68] Jerrold R. Griggs,et al. Algorithms for Loop Matchings , 1978 .
[69] Ruth Nussinov,et al. An accelerated algorithm for calculating the secondary structure of single stranded RNAs , 1984, Nucleic Acids Res..
[70] R. Nussinov,et al. Fast algorithm for predicting the secondary structure of single-stranded RNA. , 1980, Proceedings of the National Academy of Sciences of the United States of America.
[71] A. Mclachlan,et al. Repeating sequences and gene duplication in proteins. , 1972, Journal of molecular biology.
[72] M. Gouy,et al. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. , 1980, Nucleic acids research.
[73] W. Fitch. An improved method of testing for evolutionary homology. , 1966, Journal of molecular biology.
[74] T. Miyata,et al. Secondary structure of MS2 phage RNA and bias in code word usage. , 1979, Nucleic acids research.
[75] R. Britten,et al. Rates of DNA sequence evolution differ between taxonomic groups. , 1986, Science.
[76] I. Tinoco,et al. Estimation of Secondary Structure in Ribonucleic Acids , 1971, Nature.
[77] R Nussinov,et al. Some rules in the ordering of nucleotides in the DNA. , 1980, Nucleic acids research.
[78] R. Tjian,et al. Essential contact residues within SV40 large T antigen binding sites I and II identified by alkylation-interference , 1984, Cell.
[79] Robert S. Boyer,et al. A fast string searching algorithm , 1977, CACM.
[80] D Sankoff,et al. Matching sequences under deletion-insertion constraints. , 1972, Proceedings of the National Academy of Sciences of the United States of America.
[81] R. Nussinov. Sequence signals which may be required for efficient formation of mRNA 3' termini. , 1986, Nucleic acids research.
[82] D. Baltimore,et al. Double-stranded cleavage by cell extracts near recombinational signal sequences of immunoglobulin genes , 1984, Nature.
[83] Esko Ukkonen,et al. On Approximate String Matching , 1983, FCT.
[84] H. M. Martinez,et al. An RNA folding rule , 1984, Nucleic Acids Res..
[85] Gad M. Landau,et al. An efficient string matching algorithm with k differences for nucleotide and amino acid sequences , 2018, Nucleic Acids Res..
[86] M. Ptashne,et al. Cooperative binding of λ repressors to sites separated by integral turns of the DNA helix , 1986, Cell.
[87] J. P. Dumas,et al. Efficient algorithms for folding and comparing nucleic acid sequences , 1982, Nucleic Acids Res..
[88] J. Maizel,et al. Enhanced graphic matrix analysis of nucleic acid and protein sequences. , 1981, Proceedings of the National Academy of Sciences of the United States of America.
[89] H R Drew,et al. DNA bending and its relation to nucleosome positioning. , 1985, Journal of molecular biology.
[90] R Nussinov,et al. Doublet frequencies in evolutionary distinct groups. , 1984, Nucleic acids research.
[91] T. D. Schneider,et al. Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. , 1982, Nucleic acids research.