@article{Brun/08a,
AUTHOR = {Brun, Yuriy},
TITLE = {Nondeterministic polynomial time factoring in the tile assembly model},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {1},
PAGES = {3-23},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {self-assembly, factoring, tile assembly model, crystal growth, molecular computation, natural computation, distributed computing, parallel computing, nondeterministic computation},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4PJM9SW-1/1/b0e958f1b77bfe8c79052f020f59e424},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Langille-Petre/08,
AUTHOR = {Langille, Miika and Petre, Ion},
TITLE = {Sequential vs. parallel complexity in simple gene assembly},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {1},
PAGES = {24-30},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {ciliates, simple gene assembly, strings, parallelism},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4PJCYJD-3/1/52b2b35dbf8dbf308c17bafcce9b8a04},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Brun/08b,
AUTHOR = {Brun, Yuriy},
TITLE = {Solving $NP$-complete problems in the tile assembly model},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {1},
PAGES = {31-46},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {self-assembly, np-complete, tile assembly model, crystal-growth, molecular computation, natural computation, distributed computing, parallel computing, nondeterministic computation, subsetsum},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4PJM9SW-2/1/a3e1fc4e09de53465b3af53f57353625},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Gao-Ding/08,
AUTHOR = {Gao, Shile and Ding, Kequan},
TITLE = {A graphical criterion of planarity for RNA secondary structures with pseudoknots in Rivas-Eddy class},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {1},
PAGES = {47-56},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {pseudoknots, rna secondary structures, planar graph, generator, graph composition},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4PRRBSY-1/1/859fdcf0ebcf3e45ac5f2d9223bdd01b},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Zaharakis-Kameas/08,
AUTHOR = {Zaharakis, Ioannis D. and Kameas, Achilles D.},
TITLE = {Modeling spiking neural networks},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {1},
PAGES = {57-76},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {formal models, neural networks, specification, systems design methodology},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4R53WHX-1/1/bcaedc57cad8acebfe4102b979d4c4bc},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Barbuti-Maggiolo-Schettini-Milazzo-Tini/08,
AUTHOR = {Barbuti, Roberto and Maggiolo-Schettini, Andrea and Milazzo, Paolo and Tini, Simone},
TITLE = {Compositional semantics and behavioral equivalences for P systems},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {1},
PAGES = {77-100},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {p systems, structural operational semantics, behavioral equivalence, congruence},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4RRFNGR-C/1/4c5e3f60e0410b25f5ef5d8e00b22e33},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Morita/08,
AUTHOR = {Morita, Kenichi},
TITLE = {Reversible computing and cellular automata --- A survey},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {1},
PAGES = {101-131},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {reversible logic element, reversible turing machine, reversible cellular automata, computation-universality},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4RRNXST-2/1/69926b53707dfc64a1fe9566e565c49d},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Barrett-Hunt-Marathe-Ravi-Rosenkrantz-Stearns-Thakur/08,
AUTHOR = {Barrett, Chris and Hunt III, Harry B. and Marathe, Madhav V. and Ravi, S.S. and Rosenkrantz, Daniel J. and Stearns, Richard E. and Thakur, Mayur},
TITLE = {Erratum to ``Predecessor existence problems for finite discrete dynamical systems''},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {1},
PAGES = {132-133},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4R3C0D8-1/1/00c7921dec43a8ba090ddfedb7f2d343},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
NOTE = {Originally in Theor.~Comput.~Sci., Vol. 386, 2007, No. 1-2, 3-37},
}
@article{Pizzi-Ukkonen/08,
AUTHOR = {Pizzi, Cinzia and Ukkonen, Esko},
TITLE = {Fast profile matching algorithms --- A survey},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {2-3},
PAGES = {137-157},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {profile matching, position-specific scoring matrix, pssm, algorithms, computational complexity},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4STYP2P-2/1/e9c5d0c325a3c13664e0fe271de8c91e},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Comin-Parida/08,
AUTHOR = {Comin, Matteo and Parida, Laxmi},
TITLE = {Detection of subtle variations as consensus motifs},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {2-3},
PAGES = {158-170},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {pattern discovery, subtle motifs, consensus motifs, transcription factors, binding sites},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4STYP2P-3/1/8195952a8bdb8afe7673aba8967ee886},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Lemaitre-Sagot/08,
AUTHOR = {Lemaitre, Claire and Sagot, Marie-France},
TITLE = {A small trip in the untranquil world of genomes --- A survey on the detection and analysis of genome rearrangement breakpoints},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {2-3},
PAGES = {171-192},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {genome dynamics, rearrangement, breakpoint region, whole genome alignment, conserved segment, synteny block},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4STYP2P-4/1/08ef134aa1ae13fc29c63190bfa1c381},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Alekseyev-Pevzner/08,
AUTHOR = {Alekseyev, Max A. and Pevzner, Pavel A.},
TITLE = {Multi-break rearrangements and chromosomal evolution},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {2-3},
PAGES = {193-202},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {multi-break, reversal, translocation, transposition, genome rearrangement, breakpoint graph, genomic distance},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4STYP2P-5/1/d202bf9ff93334c426cb925d325e325b},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Jacquet-Seroussi-Szpankowski/08,
AUTHOR = {Jacquet, Philippe and Seroussi, Gadiel and Szpankowski, Wojciech},
TITLE = {On the entropy of a hidden Markov process},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {2-3},
PAGES = {203-219},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {hidden markov process, shannon entropy, r{\'o}nyi entropy, product of random matrices, top lyapunov exponent, spectral representation of matrices},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4STYP2P-6/1/2afdd2fd6be4b816943cb075ba7463b8},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Schurmann-Stoye/08,
AUTHOR = {Sch{\"u}rmann, Klaus-Bernd and Stoye, Jens},
TITLE = {Counting suffix arrays and strings},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {2-3},
PAGES = {220-234},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {strings, suffix arrays, permutations},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4STYP2P-7/1/16cde73152e21178ea1a1d6b7cba4a78},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Nederhof-Satta/08,
AUTHOR = {Nederhof, Mark-Jan and Satta, Giorgio},
TITLE = {Computation of distances for regular and context-free probabilistic languages},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {2-3},
PAGES = {235-254},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {probabilistic context-free languages, probabilistic finite automata, probabilistic language distances, language entropy, kullback-leibler divergence},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4STYP2P-8/1/d9e188c64186d0905fc3ce5e76be6e0a},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Iliopoulos-Sohel_Rahman/08,
AUTHOR = {Iliopoulos, Costas S. and Sohel Rahman, M.},
TITLE = {Algorithms for computing variants of the longest common subsequence problem},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {2-3},
PAGES = {255-267},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {algorithm, longest common subsequence, strings},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4STYP2P-9/1/8e1f8ce232f6184e0d12f14ce92077e9},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Kim-Amir-Landau-Park/08,
AUTHOR = {Kim, Jin Wook and Amir, Amihood and Landau, Gad M. and Park, Kunsoo},
TITLE = {Computing similarity of run-length encoded strings with affine gap penalty},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {2-3},
PAGES = {268-282},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {run-length encoding, affine gap penalty, similarity},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4STYP2P-B/1/20305f3200825bd6b81f121eee3ba05b},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Crochemore-Hermelin-Landau-Rawitz-Vialette/08,
AUTHOR = {Crochemore, Maxime and Hermelin, Danny and Landau, Gad M. and Rawitz, Dror and Vialette, St{\'e}phane},
TITLE = {Approximating the 2-interval pattern problem},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {2-3},
PAGES = {283-297},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {2-interval, rna secondary structure prediction, combinatorial approximation algorithms},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4STYP2P-C/1/95543afe23b156c28503da933c01db3f},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}
@article{Amir-Chencinski-Iliopoulos-Kopelowitz-Zhang/08,
AUTHOR = {Amir, Amihood and Chencinski, Eran and Iliopoulos, Costas and Kopelowitz, Tsvi and Zhang, Hui},
TITLE = {Property matching and weighted matching},
JOURNAL = {Theor.~Comput.~Sci.},
VOLUME = {395},
NUMBER = {2-3},
PAGES = {298-310},
YEAR = {2008},
EDITOR = {Ausiello, G. and Sannella, D.},
KEYWORDS = {pattern matching, weighted indexing, position-weight-matrices, weighted swap matching},
URL = {http://www.sciencedirect.com/science/article/B6V1G-4STYP2P-D/1/ffafbcf04c53c6ff9b7409919510efbb},
PUBLISHER = {Elsevier B.V.},
ADDRESS = {Amsterdam-Boston-Jena-London-New York-Oxford-Paris-Philadelphia-San Diego-St. Louis},
}