Open combinatorial problems in computational molecular biology

In the last few years theoretical computer scientists have found new challenges in computational molecular biology. We discuss recent advances and present some open combinatorial problems in different areas of computational molecular biology such as genome rearrangements, DNA physical mapping, DNA sequencing and sequence comparison.<<ETX>>

[1]  R. M. Baer,et al.  Natural sorting over permutation spaces , 1968 .

[2]  J. Hammersley.  A few seedlings of research , 1972 .

[3]  V. Chvátal,et al.  Longest common subsequences of two random sequences , 1975, Advances in Applied Probability.

[4]  B. Logan,et al.  A Variational Problem for Random Young Tableaux , 1977 .

[5]  Christos H. Papadimitriou,et al.  Bounds for sorting by prefix reversal , 1979, Discret. Math..

[6]  Joseph G. Deken.  Some limit results for longest common subsequences , 1979, Discret. Math..

[7]  David Maier,et al.  On Finding Minimal Length Superstrings , 1980, J. Comput. Syst. Sci..

[8]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[9]  Oded Goldreich,et al.  The Minimum-Length Generator Sequence Problem is NP-Hard , 1981, J. Algorithms.

[10]  W. Ewens,et al.  The chromosome inversion problem , 1982 .

[11]  W. R. Pearson.  Automatic construction of restriction site maps , 1982, Nucleic Acids Res..

[12]  P. Seymour,et al.  The Structure of Homometric Sets , 1982 .

[13]  David Sankoff,et al.  Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison , 1983 .

[14]  T. Smith,et al.  Mapping the order of DNA restriction fragments. , 1983, Gene.

[15]  H. Carson,et al.  Chromosomal sequences and interisland colonizations in hawaiian Drosophila. , 1983, Genetics.

[16]  T. Smith,et al.  Optimal sequence alignments. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[17]  J. Nadeau,et al.  Lengths of chromosomal segments conserved since divergence of man and mouse. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[18]  N. Franklin.  Conservation of genome form but not sequence in the transcription antitermination determinants of bacteriophages λ, φ21 and P22☆ , 1985 .

[19]  Mark Jerrum,et al.  The Complexity of Finding Minimum-Length Generator Sequences , 1985, Theor. Comput. Sci..

[20]  A. Vershik,et al.  Asymptotic of the largest and the typical dimensions of irreducible representations of a symmetric group , 1985 .

[21]  Jerrold R. Griggs,et al.  Interval graphs and maps of DNA. , 1986, Bulletin of mathematical biology.

[22]  J. Steele.  An Efron-Stein inequality for nonsymmetric statistics , 1986 .

[23]  M. Waterman,et al.  Phase transitions in sequence matches and nucleic acid structure. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Martin Aigner,et al.  Sorting by insertion of leading elements , 1987, J. Comb. Theory, Ser. A.

[25]  P. Pevzner,et al.  [Effective method for physical mapping the DNA molecule]. , 1987, Molekuliarnaia biologiia.

[26]  M. Waterman,et al.  Mapping DNA by stochastic relaxation , 1987 .

[27]  W. Bains,et al.  A novel method for nucleic acid sequence determination. , 1988, Journal of theoretical biology.

[28]  Lyons Mf.  The William Allan memorial award address: X-chromosome inactivation and the location and expression of X-linked genes. , 1988 .

[29]  Esko Ukkonen,et al.  A Greedy Approximation Algorithm for Constructing Shortest Common Superstrings , 1988, Theor. Comput. Sci..

[30]  M Krawczak.  Algorithms for the restriction-site mapping of DNA molecules. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[31]  C. N. Yee,et al.  Restriction site mapping is in separation theory , 1988, Comput. Appl. Biosci..

[32]  E. Myers,et al.  Sequence comparison with concave weighting functions. , 1988, Bulletin of mathematical biology.

[33]  Raffaele Giancarlo,et al.  Speeding up Dynamic Programming with Applications to Molecular Biology , 1989, Theor. Comput. Sci..

[34]  J. Whiting,et al.  In situ hybridization analysis of chromosomal homologies in Drosophila melanogaster and Drosophila virilis. , 1989, Genetics.

[35]  Jonathan S. Turner,et al.  Approximation Algorithms for the Shortest Common Superstring Problem , 1989, Inf. Comput..

[36]  K. Khrapko,et al.  An oligonucleotide hybridization approach to DNA sequencing , 1989, FEBS letters.

[37]  M. Waterman.  Mathematical Methods for DNA Sequences , 1989 .

[38]  R. Drmanac,et al.  Sequencing of megabase plus DNA by hybridization: theory of the method. , 1989, Genomics.

[39]  P. Pevzner.  1-Tuple DNA sequencing: computer analysis. , 1989, Journal of biomolecular structure & dynamics.

[40]  Lloyd Allison,et al.  Restriction site mapping for three or more enzymes , 1990, Comput. Appl. Biosci..

[41]  Steven Skiena,et al.  Reconstructing sets from interpoint distances (extended abstract) , 1990, SCG '90.

[42]  R. Doolittle.  Molecular evolution: computer analysis of protein and nucleic acid sequences. , 1990, Methods in enzymology.

[43]  Andrey A. Mironov,et al.  Mapping DNA by stochastic relaxation: a new approach to fragment sizes , 1990, Comput. Appl. Biosci..

[44]  D. Sankoff,et al.  Genomic divergence through gene rearrangement. , 1990, Methods in enzymology.

[45]  S. P. Fodor,et al.  Light-directed, spatially addressable parallel chemical synthesis. , 1991, Science.

[46]  Tao Jiang,et al.  Linear approximation of shortest superstrings , 1991, STOC '91.

[47]  P. Pevzner,et al.  Improved chips for sequencing by hybridization. , 1991, Journal of biomolecular structure & dynamics.

[48]  Mark Allen Weiss,et al.  Data structures and algorithm analysis , 1991 .

[49]  P. Pevzner,et al.  [Optimal chips for megabase DNA sequencing]. , 1991, Molekuliarnaia biologiia.

[50]  M. Waterman,et al.  Multiple solutions of DNA restriction mapping problems , 1991 .

[51]  Roland H. C. Yap,et al.  Restriction Site Mapping in CLP(R) , 1991, ICLP.

[52]  E. Lander,et al.  Parametric sequence comparisons. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[53]  Linda A. Raubeson,et al.  Chloroplast DNA Evidence on the Ancient Evolutionary Split in Vascular Land Plants , 1992, Science.

[54]  Pavel A. Pevzner.  DNA Physical Mapping, Flows in Networks and Minimum Cycles Mean in Graphs , 1992, Mathematical Methods Of Analysis Of Biopolymer Sequences.

[55]  Ivan Hal Sudborough,et al.  On Sorting by Prefix Reversals and the Diameter of Pancake Networks , 1992, Heinz Nixdorf Symposium.

[56]  D. Sankoff,et al.  Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[57]  R. J. Hoffmann,et al.  A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. , 1992, Genetics.

[58]  Dan Gusfield,et al.  Parametric optimization of sequence alignment , 1992, SODA '92.

[59]  Jordan Lampe,et al.  Theoretical and Empirical Comparisons of Approximate String Matching Algorithms , 1992, CPM.

[60]  F. Frances Yao,et al.  Approximating shortest superstrings , 1997, Proceedings of 1993 IEEE 34th Annual Foundations of Computer Science.

[61]  Vineet Bafna,et al.  Genome rearrangements and sorting by reversals , 1993, Proceedings of 1993 IEEE 34th Annual Foundations of Computer Science.

[62]  T. Jukes.  A Robust Model for Finding Optimal Evolutionary Trees , 1993 .

[63]  E. Lander,et al.  A genetic linkage map of the mouse: current applications and future prospects. , 1993, Science.

[64]  Richard M. Karp,et al.  Mapping the genome: some combinatorial problems arising in molecular biology , 1993, STOC.

[65]  Tao Jiang,et al.  Approximating Shortest Superstrings with Constraints (Extended Abstract) , 1993, WADS.

[66]  E. Koonin,et al.  Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. , 1993, Critical reviews in biochemistry and molecular biology.

[67]  David Sankoff,et al.  Exact and Approximation Algorithms for the Inversion Distance Between Two Chromosomes , 1993, CPM.

[68]  J. Palmer,et al.  Chloroplast genome rearrangements and the evolution of giant lobelias from herbaceous ancestors , 1993 .

[69]  L. Newberg,et al.  A Lower Bound on the Number of Solutions to the Probed Partial Digest Problem , 1993 .

[70]  M S Waterman,et al.  Sequence alignment and penalty choice. Review of concepts, case studies and implications. , 1994, Journal of molecular biology.

[71]  Tao Jiang,et al.  Approximating Shortest Superstrings with Constraints , 1994, Theor. Comput. Sci..

[72]  P. Pevzner,et al.  Gray code masks for sequencing by hybridization. , 1994, Genomics.

[73]  Daniela R. Martin,et al.  Equivalence Classes for the Double-Digest Problem with Coincident Cut Sites , 1994, J. Comput. Biol..

[74]  Wojciech Rytter,et al.  Parallel and Sequential Approximations of Shortest Superstrings , 1994, SWAT.

[75]  Zheng Zhang.  An Exponential Example for a Partial Digest Mapping Algorithm , 1994, J. Comput. Biol..

[76]  Kenneth S. Alexander,et al.  Shortest Common Superstrings for Strings of Random Letters , 1994, CPM.

[77]  M. Waterman,et al.  A Phase Transition for the Score in Matching Random Sequences Allowing Deletions , 1994 .

[78]  Pavel A. Pevzner,et al.  Towards DNA Sequencing Chips , 1994, MFCS.

[79]  David Sankoff,et al.  Efficient Bounds for Oriented Chromosome Inversion Distance , 1994, CPM.

[80]  Clifford Stein,et al.  Long tours and short superstrings , 1994, Proceedings 35th Annual Symposium on Foundations of Computer Science.

[81]  P. Pevzner,et al.  Sorting by Reversals: Genome Rearrangements in Plant Organelles and Evolutionary History of X Chromosome , 1995 .

[82]  Mike Paterson,et al.  Upper Bounds for the Expected Length of a Longest Common Subsequence of Two Binary Sequences , 1995, Random Struct. Algorithms.

[83]  Michael S. Waterman,et al.  Introduction to computational biology , 1995 .

[84]  Chris Armen.  Approximation algorithms for the shortest superstring problem , 1996 .

[85]  Susan R. Wilson.  INTRODUCTION TO COMPUTATIONAL BIOLOGY: MAPS, SEQUENCES AND GENOMES. , 1996 .

[86]  Wojciech Rytter,et al.  Sequential and Parallel Approximation of Shortest Superstrings , 1997, J. Algorithms.