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In the last years, it was observed an increasing interest of computer scientists in the structure of biological molecules and the way how they can be manipulated in vitro in order to define theoretical models of computation based on genetic engineering tools. Along the same lines, a parallel interest is growing regarding the process of evolution of living organisms. Much of the current data for genomes are expressed in the form of maps which are now becoming available and permit the study of the evolution of organisms at the scale of genome for the first time. On the other hand, there is an active trend nowadays throughout the field of computational biology toward abstracted, hierarchical views of biological sequences, which is very much in the spirit of computational linguistics. In the last decades, results and methods in the field of formal language theory that might be applied to the description of biological sequences were pointed out.
List of contents
1 The Games of His Life.- I Grammars and Grammar Systems.- 2 Deterministic Stream X-Machines Based on Grammar Systems.- 3 Some Ghosts that Arise in a Spliced Linguistic String: Evidence from Catalan.- 4 On Size Complexity of Context-Free Returning Parallel Communicating Grammar Systems.- 5 Subregularly Controlled Derivations: Restrictions by Syntactic Parameters.- 6 Neo-Modularity and Colonies.- 7 Sewing Contexts and Mildly Context-Sensitive Languages.- 8 Towards Grammars of Decision Algorithms.- II Automata.- 9 Computational Complementarity for Probabilistic Automata.- 10 Acceptance of ?-Languages by Communicating Deterministic Turing Machines.- 11 Counter Machines and the Safety and Disjointness Problems for Database Queries with Linear Constraints.- 12 Automata Arrays and Context-Free Languages.- 13 On Special Forms of Restarting Automata.- 14 The Time Dimension of Computation Models.- III Languages and Combinatorics.- 15 An Infinite Sequence of Full AFL-Structures, Each of Which Possesses an Infinite Hierarchy.- 16 Trellis Languages.- 17 Pictures, Layers, Double Stranded Molecules: On Multi-Dimensional Sentences.- 18 Transduction in Polypodes.- 19 Some Algebraic Properties of Contexts and Their Applications to Contextual Languages.- 20 On Fatou Properties of Rational Languages.- 21 Multiple Keyword Patterns in Context-Free Languages.- 22 Reading Words in Graphs Generated by Hyperedge Replacement.- 23 Regularly Controlled Formal Power Series.- 24 Forbidden Subsequences and Permutations Sortable on Two Parallel Stacks.- 25 Approximate Identification and Finite Elasticity.- 26 Insertion of Languages and Differential Semirings.- IV Models of Molecular Computing.- 27 Molecular Structures.- 28 A Characterization of Non-Iterated Splicing with Regular Rules.- 29 Universaland Simple Operations for Gene Assembly in Ciliates.- 30 Semi-Simple Splicing Systems.- 31 Writing By Methylation Proposed For Aqueous Computing.- 32 Context-Free Recombinations.- 33 Simplified Simple H Systems.- 34 On Some Forms of Splicing.- 35 Time-Varying Distributed H-Systems of Degree 2 Generate All Recursively Enumerable Languages.- 36 On Membrane Computing Based on Splicing.- 37 Is Evolutionary Computation Using DNA Strands Feasible?.- 38 Splicing Systems Using Merge and Separate Operations.
Summary
In the last years, it was observed an increasing interest of computer scientists in the structure of biological molecules and the way how they can be manipulated in vitro in order to define theoretical models of computation based on genetic engineering tools. Along the same lines, a parallel interest is growing regarding the process of evolution of living organisms. Much of the current data for genomes are expressed in the form of maps which are now becoming available and permit the study of the evolution of organisms at the scale of genome for the first time. On the other hand, there is an active trend nowadays throughout the field of computational biology toward abstracted, hierarchical views of biological sequences, which is very much in the spirit of computational linguistics. In the last decades, results and methods in the field of formal language theory that might be applied to the description of biological sequences were pointed out.
