Publications

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. Modeling and solving planning problems in tabled logic programming: Experience from the Cave Diving domain. Science of Computer Programming, 2017.

. Preface. ACM International Conference Proceeding Series, 2017.

. LZ77 Computation Based on the Run-Length Encoded BWT. Algorithmica, 2017.

. Reduction of heterozygosity (ROH) as a method to detect mosaic structural variation. Plant Biotechnology Journal, 2017.

. From LZ77 to the run-length encoded burrows-wheeler transform, and back. Leibniz International Proceedings in Informatics, LIPIcs, 2017.

. On sets and graphs: Perspectives on logic and combinatorics. On Sets and Graphs: Perspectives on Logic and Combinatorics, 2017.

. Set-syllogistics meet combinatorics. Mathematical Structures in Computer Science, 2017.

. Towards a logic programming tool for cancer analysis. CEUR Workshop Proceedings, 2017.

. Optimization of a compiler from PDDL to Picat (Short Paper). CEUR Workshop Proceedings, 2017.

. Deciding weak weighted bisimulation. CEUR Workshop Proceedings, 2017.

. An active learning approach to the falsification of black box cyber-physical systems. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2017.

. Computing LZ77 in Run-Compressed Space. Data Compression Conference Proceedings, 2016.

. Structural operational semantics for non-deterministic processes with quantitative aspects. Theoretical Computer Science, 2016.

. Is Hyper-extensionality Preservable under Deletions of Graph Elements?. Electronic Notes in Theoretical Computer Science, 2016.

. Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2. BMC Bioinformatics, 2016.

. Exploring the use of BDDs in conformant planning. Proceedings - International Conference on Tools with Artificial Intelligence, ICTAI, 2016.

. Reasoning in high schools: Do it with ASP! ?. CEUR Workshop Proceedings, 2016.

. On the bisimulation hierarchy of state-to-function transition systems. CEUR Workshop Proceedings, 2016.

. Multiple-origin-multiple-destination path finding with minimal arc usage: Complexity and models. CEUR Workshop Proceedings, 2016.

. Logic-based multi-objective design of chemical reaction networks. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2016.

. Logic programming applied to genome evolution in cancer?. CEUR Workshop Proceedings, 2016.

. Labelled variables in logic programming: Foundations. CEUR Workshop Proceedings, 2016.

. Compiling and executing PDDL in picat. CEUR Workshop Proceedings, 2016.

. A GPU implementation of the ASP computation. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2016.

. Behavioural equivalences for coalgebras with unobservable moves. Journal of Logical and Algebraic Methods in Programming, 2015.

. On modeling planning problems in tabled logic programming. Proceedings of the 17th International Symposium on Principles and Practice of Declarative Programming, PPDP 2015, 2015.

. On the impact of discreteness and abstractions on modelling noise in gene regulatory networks. Computational Biology and Chemistry, 2015.

. Fast randomized approximate string matching with succinct hash data structures. BMC Bioinformatics, 2015.

. Rank and simulation: The well-founded case. Journal of Logic and Computation, 2015.

. Planning as tabled logic programming. Theory and Practice of Logic Programming, 2015.

. Parallel execution of the ASP computation - An investigation on GPUs. CEUR Workshop Proceedings, 2015.

. Open transactions on shared memory. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2015.

. Mapping Sets and Hypersets into Numbers. Fundamenta Informaticae, 2015.

. Logic programming and bisimulation. CEUR Workshop Proceedings, 2015.

. Large neighborhood search with quality guarantees for distributed constraint optimization problems. Proceedings of the International Joint Conference on Autonomous Agents and Multiagent Systems, AAMAS, 2015.

. Hierarchical assembly of pools. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2015.

. Fast online Lempel-Ziv factorization in compressed space. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2015.

. Constrained community-based gene regulatory network inference. ACM Transactions on Modeling and Computer Simulation, 2015.

. CUD@SAT: SAT solving on GPUs. Journal of Experimental and Theoretical Artificial Intelligence, 2015.

. CNV and structural variation in plants prospects of NGS approaches. Advances in the Understanding of Biological Sciences Using Next Generation Sequencing (NGS) Approaches, 2015.

. Average linear time and compressed space construction of the burrows-wheeler transform. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2015.

. A declarative concurrent system for protein structure prediction on GPU. Journal of Experimental and Theoretical Artificial Intelligence, 2015.

. A Theoretical Perspective of Coinductive Logic Programming. Fundamenta Informaticae, 2015.

. Exploring the use of GPUs in constraint solving. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2014.

. Set graphs VI: Logic programming and bisimulation ?. CEUR Workshop Proceedings, 2014.

. Multi-agent systems design and prototyping with bigraphical reactive systems. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2014.

. Hyper-extensionality and one-node elimination on membership graphs. CEUR Workshop Proceedings, 2014.

. Hashing and indexing: Succinct data structures and smoothed analysis. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2014.

. GSOS for non-deterministic processes with quantitative aspects. Electronic Proceedings in Theoretical Computer Science, EPTCS, 2014.

. Finding a forest in a tree: The matching problem for wide reactive systems. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2014.

. Chimera: A Bioconductor package for secondary analysis of fusion products. Bioinformatics, 2014.

. A parallel algorithm for the best k-mismatches alignment problem. Proceedings - 2014 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, PDP 2014, 2014.

. A model of countable nondeterminism in guarded type theory. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2014.

. A GPU implementation of large neighborhood search for solving constraint optimization problems. Frontiers in Artificial Intelligence and Applications, 2014.

. A constraint solver for flexible protein models. Journal of Artificial Intelligence Research, 2013.

. Encodings of sets and hypersets. CEUR Workshop Proceedings, 2013.

. CUD@ASP: Experimenting with GPUs in ASP solving. CEUR Workshop Proceedings, 2013.

. (Hybrid) automata and (stochastic) programs: The hybrid automata lattice of a stochastic program. Journal of Logic and Computation, 2013.

. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nature Genetics, 2013.

. GAM-NGS: Genomic assemblies merger for next generation sequencing. BMC Bioinformatics, 2013.

. Autonomous agents coordination: Action languages meet CLP(f d) and Linda. Theory and Practice of Logic Programming, 2013.

. A catalog of molecular diversity of prunus germplasm gathered from aligning ngs reads to the peach reference sequence: Bioinformatic approaches and challenges. Acta Horticulturae, 2013.

. Protein structure prediction on GPU: A declarative approach in a multi-Agent framework. Proceedings of the International Conference on Parallel Processing, 2013.

. Markov chain algorithms for generating sets uniformly at random. Ars Mathematica Contemporanea, 2013.

. A multi-paradigm tool for large neighborhood search. Studies in Computational Intelligence, 2013.

. Rank-based simulation on acyclic graphs. CEUR Workshop Proceedings, 2012.

. Introduction to the technical communications of the 28th international conference on logic programming special issue. Leibniz International Proceedings in Informatics, LIPIcs, 2012.

. Infinity, in short. Journal of Logic and Computation, 2012.

. Exploiting unexploited computing resources for computational logics. CEUR Workshop Proceedings, 2012.

. ERNE-BS5: Aligning BS-treated sequences by multiple hits on a 5-letters alphabet. 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012, 2012.

. A multi-objective optimisation approach to the design of experiment in de novo assembly projects. Proceedings - International Workshop on Database and Expert Systems Applications, DEXA, 2012.

. Implementing the stochastics brane calculus in a generic stochastic abstract machine. Electronic Proceedings in Theoretical Computer Science, EPTCS, 2012.

. A filtering technique for fragment assembly- based proteins loop modeling with constraints. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2012.

. GapFiller: A de novo assembly approach to fill the gap within paired reads. BMC Bioinformatics, 2012.

. Synthesis of distributed mobile programs using monadic types in Coq. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2012.

. Structural operational semantics for continuous state probabilistic processes. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2012.

. Introduction to the 28th international conference on logic programming special issue. Theory and Practice of Logic Programming, 2012.

. Measurable stochastics for Brane Calculus. Theoretical Computer Science, 2012.

. rNA: A fast and accurate short reads numerical aligner. Bioinformatics, 2012.

. mrNA: The MPI randomized numerical aligner. Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011, 2011.

. PrettyCLP: A light java implementation for teaching CLP. CEUR Workshop Proceedings, 2011.

. Exploring protein fragment assembly using CLP. IJCAI International Joint Conference on Artificial Intelligence, 2011.

. BAAC: A prolog system for action description and agents coordination. Leibniz International Proceedings in Informatics, LIPIcs, 2011.

. A tabled prolog program for solving sokoban. CEUR Workshop Proceedings, 2011.

. Unobservable intrusion detection based on call traces in paravirtualized systems. SECRYPT 2011 - Proceedings of the International Conference on Security and Cryptography, 2011.

. Counting extensional acyclic digraphs. Information Processing Letters, 2011.

. Well-quasi-ordering hereditarily finite sets. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2011.

. Perspectives on logic-based approaches for reasoning about actions and change. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2011.

. Morphos configuration engine: The core of a commercial configuration system in CLP(FD). Fundamenta Informaticae, 2010.

. Enhanced reference guided assembly. Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010, 2010.

. Autonomous agents coordination: Action description languages meet CLP(FD) and Linda. CEUR Workshop Proceedings, 2010.

. An investigation of multi-agent planning in CLP. Fundamenta Informaticae, 2010.

. The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture amongst varieties of different geographic origin. Theoretical and Applied Genetics, 2010.

. A randomized Numerical Aligner (rNA). Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2010.

. The bernays-schönfinkel-ramsey class for set theory: Semidecidability. Journal of Symbolic Logic, 2010.

. Hybrid dynamics of stochastic programs. Theoretical Computer Science, 2010.

. Physical mapping in highly heterozygous genomes: A physical contig map of the Pinot Noir grapevine cultivar. BMC Genomics, 2010.

. Correction: High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera. BMC Genomics, 2010.

. Constraint-Based Methods for Bioinformatics. Trends in Constraint Programming, 2010.

. Computing approximate solutions of the protein structure determination problem using global constraints on discrete crystal lattices. International Journal of Data Mining and Bioinformatics, 2010.

. CLP-based protein fragment assembly. Theory and Practice of Logic Programming, 2010.

. Stochastic programs and hybrid automata for (biological) modeling. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2009.

. GASP: Answer set programming with lazy grounding. Fundamenta Informaticae, 2009.

. GAM: Genomic assemblies merger: A graph based method to integrate different assemblies. 2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009, 2009.

. Discrete semantics for hybrid automata: Avoiding misleading assumptions in systems biology. Discrete Event Dynamic Systems: Theory and Applications, 2009.

. Dynamical systems and stochastic programming: To ordinary differential equations and back. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2009.

. High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera. BMC Genomics, 2009.

. DBtk: A toolkit for directed bigraphs. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2009.

. Representing multi-agent planning in CLP. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2009.

. Present and future challenges for ASP systems (Extended abstract). Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2009.

. Logic programming techniques in protein structure determination: Methodologies and results. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2009.

. Answer set programming with constraints using lazy grounding. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2009.

. Applying model-checking to solve queries on semistructured data. Computer Languages, Systems and Structures, 2009.

. An empirical study of constraint logic programming and answer set programming solutions of combinatorial problems. Journal of Experimental and Theoretical Artificial Intelligence, 2009.

. Automated fingerprint background removal: FPB. BMC Bioinformatics, 2009.

. Hybrid dynamics of stochastic π-calculus. Mathematics in Computer Science, 2009.

. The Importance of Being (A Little Bit) Discrete. Electronic Notes in Theoretical Computer Science, 2009.

. A hybrid solver for large neighborhood search: Mixing gecode and EasyLocal++. CEUR Workshop Proceedings, 2009.

. Inclusion dynamics hybrid automata. Information and Computation, 2008.

. Hybrid approximation of stochastic process algebras for systems biology. IFAC Proceedings Volumes (IFAC-PapersOnline), 2008.

. Compiling and executing declarative modeling languages to gecode. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2008.

. Undecidability of Model Checking in Brane Logic. Electronic Notes in Theoretical Computer Science, 2008.

. A complete axiomatic system for a process-based spatial logic. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2008.

. A Categorical Model of the Fusion Calculus. Electronic Notes in Theoretical Computer Science, 2008.

. Discreteness, hybrid automata, and biology. Proceedings - 9th International Workshop on Discrete Event Systems, WODES’ 08, 2008.

. Hybrid semantics for stochastic π-calculus. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2008.

. PicNIc - Pi-calculus Non-Interference checker. Proceedings - International Conference on Application of Concurrency to System Design, ACSD, 2008.

. Implementing spi calculus using nominal techniques. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2008.

. Hybrid systems and biology: Continuous and discrete modeling for systems biology. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2008.

. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2008.

. Modeling biological systems in stochastic concurrent constraint programming. Constraints, 2008.

. Introduction to the special issue on bioinformatics and constraints. Constraints, 2008.

. A uniform approach to constraint-solving for lists, multisets, compact lists, and sets. ACM Transactions on Computational Logic, 2008.

. An Algebra for Directed Bigraphs. Electronic Notes in Theoretical Computer Science, 2008.

. Systems biology: Models and logics. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2008.

. Symbolic graphs: Linear solutions to connectivity related problems. Algorithmica (New York), 2008.

. Reactive systems over directed bigraphs. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2007.

. Multivalued action languages with constraints in CLP(FD). Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2007.

. Enhancing the computation of approximate solutions of the protein structure determination problem through global constraints for discrete crystal lattices. Proceedings - 2007 IEEE International Conference on Bioinformaticsand Biomedicine Workshops, BIBMW, 2007.

. Constraint-based simulation of biological systems described by Molecular Interaction Maps. Proceedings - 2007 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2007, 2007.

. An experimental comparison of constraint logic programming and answer set programming. Proceedings of the National Conference on Artificial Intelligence, 2007.

. A constraint solver for discrete lattices, its parallelization, and application to protein structure prediction. Software - Practice and Experience, 2007.

. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 2007.

. Stochastic Concurrent Constraint Programming and Differential Equations. Electronic Notes in Theoretical Computer Science, 2007.

. Reasoning about object-based calculi in (Co)inductive type theory and the theory of contexts. Journal of Automated Reasoning, 2007.

. Scoring predictive models using a reduced representation of proteins: Model and energy definition. BMC Structural Biology, 2007.

. Directed Bigraphs. Electronic Notes in Theoretical Computer Science, 2007.

. Agent-based protein structure prediction. Multiagent and Grid Systems, 2007.

. BuST-Bundled Suffix Trees. IFIP International Federation for Information Processing, 2006.

. Reconstruction with interval constraints propagation. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2006.

. Foreword. Journal of Applied Non-Classical Logics, 2006.

. A computerized referee. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2006.

. Set unification. Theory and Practice of Logic Programming, 2006.

. About permutation algebras, (pre)sheaves and named sets. Higher-Order and Symbolic Computation, 2006.

. Decidability results for sets with atoms. ACM Transactions on Computational Logic, 2006.

. Consistency of the theory of contexts. Journal of Functional Programming, 2006.

. Modal logics for brane calculus. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2006.

. Hybrid approaches for rostering: A case study in the integration of constraint programming and local search. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2006.

. Translating specifications from nominal logic to CIC with the theory of contexts. MERLIN’05 - Proceedings of the Third ACM SIGPLAN Workshop in Mechanized Reasoning about Languages with varIable biNding, 2005.

. Heuristics, optimizations, and parallelism for protein structure prediction in CLP(ℱD). PPDP’05 - Proceedings of the Seventh ACM SIGPLAN Conference on Principles and Practice of Declarative Programming, 2005.

. An algorithmic account of ehrenfeucht games on labeled successor structures. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2005.

. A new constraint solver for 3D lattices and its application to the protein folding problem. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2005.

. A comparison of CLP(FD) and ASP solutions to NP-complete problems. Lecture Notes in Computer Science, 2005.

. Algorithmic algebraic model checking I: Challenges from systems biology. Lecture Notes in Computer Science, 2005.

. Structured motifs search. Journal of Computational Biology, 2005.

. A unifying model of variables and names. Lecture Notes in Computer Science, 2005.

. The axiom of elementary sets on the edge of peircean expressibility. Journal of Symbolic Logic, 2005.

. Modeling fresh names in the π-calculus using abstractions. Electronic Notes in Theoretical Computer Science, 2004.

. Protein folding in CLP(FD) with empirical contact energies. Lecture Notes in Artificial Intelligence (Subseries of Lecture Notes in Computer Science), 2004.

. Unifying recursive and co-recursive definitions in sheaf categories. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2004.

. Rasiowa-Sikorski style relational elementary set theory. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2004.

. Protein folding simulation in CCP. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2004.

. Improving reachability analysis of hybrid automata for engine control. Proceedings of the IEEE Conference on Decision and Control, 2004.

. Binary extensions of S1S and the composition method. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2004.

. Constraint logic programming approach to protein structure prediction. BMC Bioinformatics, 2004.

. Some characterization results for permutation algebras. Electronic Notes in Theoretical Computer Science, 2004.

. Electrical notice in theoretical computer science: Preface. Electronic Notes in Theoretical Computer Science, 2004.

. Taming the complexity of biochemical models through bisimulation and collapsing: Theory and practice. Theoretical Computer Science, 2004.

. Designing an urban-scale auditory alert system. Computer, 2004.

. Ackermann encoding, bisimulations and OBDDs. Theory and Practice of Logic Programming, 2004.

. Three-variable statements of set-pairing. Theoretical Computer Science, 2004.

. An efficient algorithm for computing bisimulation equivalence. Theoretical Computer Science, 2004.

. Disunification in ACI1 Theories. Constraints, 2004.

. From Bisimulation to Simulation: Coarsest Partition Problems. Journal of Automated Reasoning, 2003.

. Intensional sets in CLP. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2003.

. Integrating Finite Domain Constraints and CLP with Sets. Proceedings of the ACM SIGPLAN Conference on Principles and Practice of Declarative Programming, 2003.

. Biconnectivity on symbolically represented graphs: A linear solution. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2003.

. A unifying approach to recursive and co-recursive definitions. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2003.

. A Framework for Typed HOAS and Semantics. Proceedings of the ACM SIGPLAN Conference on Principles and Practice of Declarative Programming, 2003.

. The Subgraph Bisimulation Problem. IEEE Transactions on Knowledge and Data Engineering, 2003.

. Model building and model checking for biochemical processes. Cell Biochemistry and Biophysics, 2003.

. Theoretical Computer Science: Preface. Theoretical Computer Science, 2003.

. Reasoning on an imperative object-based calculus in higher order abstract syntax. Proceedings of the 2003 ACM SIGPLAN Workshop on Mechanized Reasoning about Languages with Variable Binding, MERLIN 2003, 2003.

. Modeling cellular behavior with hybrid automata: Bisimulation and collapsing. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2003.

. Imperative object-based calculi in co-inductive type theories. Lecture Notes in Artificial Intelligence (Subseries of Lecture Notes in Computer Science), 2003.

. Foundations of a query and simulation system for the modeling of biochemical and biological processes.. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2003.

. Computing strongly connected components in a linear number of symbolic steps. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, 2003.

. A Sense of Life: Computational and Experimental Investigations with Models of Biochemical and Evolutionary Processes. OMICS A Journal of Integrative Biology, 2003.

. Simulation as coarsest partition problem. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2002.

. Ambient Calculus and its logic in the Calculus of inductive constructions. Electronic Notes in Theoretical Computer Science, 2002.

. Using secondary structure information for protein folding in CLP(ℱFD). Electronic Notes in Theoretical Computer Science, 2002.

. Simulation reduction as constraint. Electronic Notes in Theoretical Computer Science, 2002.

. Rank-based symbolic bisimulation: (And model checking). Electronic Notes in Theoretical Computer Science, 2002.

. Extending Kamp's theorem to model time granularity. Journal of Logic and Computation, 2002.

. The theory of contexts for first order and higher order abstract syntax. Electronic Notes in Theoretical Computer Science, 2002.

. Electronic Notes in Theoretical Computer Science: Preface. Electronic Notes in Theoretical Computer Science, 2002.

. Comparing higher-order encodings in logical frameworks and tile logic. Electronic Notes in Theoretical Computer Science, 2002.

. Alternative translation techniques for propositional and first-order modal logics. Journal of Automated Reasoning, 2002.

. Operational and abstract semantics of the query language G-Log. Theoretical Computer Science, 2002.

. Xs-systems: Extended S-systems and algebraic differential automata for modeling cellular behavior. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2002.

. Model-checking based data retrieval. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2002.

. Multiset constraints and P systems. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2001.

. An axiomatic approach to metareasoning on nominal algebras in HOAS. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2001.

. Developing (meta)theory of λ-calculus in the theory of contexts. Electronic Notes in Theoretical Computer Science, 2001.

. Refining and compressing abstract model checking. Electronic Notes in Theoretical Computer Science, 2001.

. Modeling concurrent systems specified in a temporal concurrent constraint language-I. Electronic Notes in Theoretical Computer Science, 2001.

. π-calculus in (Co)inductive-type theory. Theoretical Computer Science, 2001.

. Designing the minimal structure of hidden Markov model by bisimulation. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2001.

. Constructive Negation and constraint logic programming with sets. New Generation Computing, 2001.

. A fast Bisimulation algorithm. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2001.

. Towards tableau-based decision procedures for non-well-founded fragments of Set Theory. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2000.

. Sets and Constraint Logic Programming. ACM Transactions on Programming Languages and Systems, 2000.

. Necessary condition for Constructive Negation in Constraint Logic Programming. Information Processing Letters, 2000.

. Derivability in locally quantified modal logics via translation in set theory. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2000.

. Comparing expressiveness of set constructor symbols. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2000.

. Solvable set/hyperset contexts: II. A goal-driven unification algorithm for the blended case. Applicable Algebra in Engineering, Communications and Computing, 1999.

. Finite families with few symmetric differences. Proceedings of the American Mathematical Society, 1999.

. T-resolution: Refinements and model elimination. Journal of Automated Reasoning, 1999.

. Formalizing a lazy substitution proof system for μ -calculus in the calculus of inductive constructions. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 1999.

. A Uniform Axiomatic View of Lists, Multisets, and Sets, and the Relevant Unification Algorithms. Fundamenta Informaticae, 1998.

. Encoding modal logics in logical frameworks. Studia Logica, 1998.

. Witnessing differences without redundancies. Proceedings of the American Mathematical Society, 1997.

. A set-theoretic approach to automated deduction in graded modal logics. IJCAI International Joint Conference on Artificial Intelligence, 1997.

. Modal deduction in second-order logic and set theory - I. Journal of Logic and Computation, 1997.

. Decidability of ∃*∀-sentences in membership theories. Mathematical Logic Quarterly, 1996.

. A natural deduction approach to dynamic logic. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 1996.

. Complementation in the lattice of equivalence relations. Discrete Mathematics, 1996.

. {log}: a language for programming in logic with finite sets. Journal of Logic Programming, 1996.

. T-Theorem proving I. Journal of Symbolic Computation, 1995.

. Solvable set/hyperset contexts: I. Some decision procedures for the pure, finite case. Communications on Pure and Applied Mathematics, 1995.

. Modal μ-types for processes. Proceedings - Symposium on Logic in Computer Science, 1995.

. Minimal set unification. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 1995.

. A set-theoretic translation method for (Poly)modal logics. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 1995.

. The expressive power of structural operational semantics with explicit assumptions. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 1994.

. A language with finite sets embedded in the CLP-scheme. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 1994.

. Undecidability results for restricted universally quantified formulae of set theory. Communications on Pure and Applied Mathematics, 1993.

. Embedding finite sets in a logic programming language. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 1993.

. Decision procedures for set/hyperset contexts. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 1993.

. A derived algorithm for evaluating ɛ-expressions over abstract sets. Journal of Symbolic Computation, 1993.

. A WAM-based implementation of a logic language with sets. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 1993.

. THE DECISION PROBLEM FOR RESTRICTED UNIVERSAL QUANTIFICATION IN SET THEORY AND THE AXIOM OF FOUNDATION. Mathematical Logic Quarterly, 1992.

. {log}: A logic programming language with finite sets. UNKNOWN, 1991.

. The automation of syllogistic - II. Optimization and complexity issues. Journal of Automated Reasoning, 1990.

. Set-theoretic reductions of hilbert’s tenth problem. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 1990.

. Note on “the logically simplest form of the infinity axiom”. Proceedings of the American Mathematical Society, 1990.

. The logically simplest form of the infinity axiom. Proceedings of the American Mathematical Society, 1988.