Latest

• Cascade products and Wheeler automata
• Incremental NFA minimization
• The Rational Construction of a Wheeler DFA
• Towards a Computational Approach to Quantification of Allele Specific Expression at Population Level
• Towards a Computational Approach to Quantification of Allele Specific Expression at Population Level
• A Linear-size Cascade Decomposition for Wheeler Automata
• Co-lexicographically Ordering Automata and Regular Languages - Part I
• Continued Hereditarily Finite Set-Approximations
• Optimal Wheeler Language Recognition
• Ordering regular languages and automata: Complexity
• Hybrid automata in systems biology
• Hybrid automata in systems biology
• Incremental NFA Minimization
• Solving String Problems on Graphs Using the Labeled Direct Product
• Special Issue on Algorithms and Data-Structures for Compressed Computation
• Ordering Regular Languages: A Danger Zone
• Squeezing multisets into real numbers
• Wheeler Languages
• Image Approximation for Feed Forward Neural Nets
• Optimization and multistage systems. The thawing case
• Regular languages meet prefix sorting
• Towards a Logic Programming Tool for Cancer Data Analysis
• Adding the power-set to description logics
• Extending$$mathcal ALC$$ with the Power-Set Construct
• Preface
• Reasoning on Relations, Modalities, and Sets
• An active learning approach to the falsification of black box cyber-physical systems
• From LZ77 to the run-length encoded burrows-wheeler transform, and back
• LZ77 Computation Based on the Run-Length Encoded BWT
• Martin Davis on Computability, Computational Logic, and Mathematical Foundations
• On Sets and Graphs: Perspectives on Logic and Combinatorics
• Reduction of heterozygosity (ROH) as a method to detect mosaic structural variation
• Towards a Logic Programming Tool for Cancer Analysis
• Banishing Ultrafilters from Our Consciousness
• Computing LZ77 in Run-Compressed Space
• Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2
• Is Hyper-extensionality Preservable under Deletions of Graph Elements?
• Logic programming applied to genome evolution in cancer?
• Logic-based multi-objective design of chemical reaction networks
• Preface
• Average Linear Time and Compressed Space Construction of the Burrows-Wheeler Transform
• CNV and structural variation in plants prospects of NGS approaches
• Fast online Lempel-Ziv factorization in compressed space
• Fast randomized approximate string matching with succinct hash data structures
• Hierarchical Assembly of Pools
• Mapping Sets and Hypersets into Numbers
• On the impact of discreteness and abstractions on modelling noise in gene regulatory networks
• Rank and simulation: the well-founded case
• Set-syllogistics meet combinatorics
• A Parallel Algorithm for the Best k-Mismatches Alignment Problem
• Algorithms and Data Structures for Next Generation Sequences
• Chimera: a Bioconductor package for secondary analysis of fusion products
• Hashing and Indexing: Succinct DataStructures and Smoothed Analysis
• Hyper-Extensionality and One-Node Elimination on Membership Graphs
• (Hybrid) automata and (stochastic) programs - The hybrid automata lattice of a stochastic program
• A Catalog of Molecular Diversity of Prunus Germplasm Gathered from Aligning NGS Reads to the Peach Reference Sequence: Bioinformatic Approaches and Challenges
• Encodings of Sets and Hypersets
• GAM-NGS: genomic assemblies merger for next generation sequencing
• Markov chain algorithms for generating sets uniformly at random
• The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution
• Well-quasi-ordering hereditarily finite sets
• A Randomized Numerical Aligner -- rNA
• ERNE-BS5: Aligning BS-treated sequences by multiple hits on a 5-letters alphabet
• Infinity, in short
• Rank-Based Simulation on Acyclic Graphs
• rNA: a Fast and Accurate Short Reads Numerical Aligner
• The Bernays-Schoenfinkel-Ramsey Class in Set Theory: Decidability
• Counting extensional acyclic digraphs
• mrNA: the MPI randomized Numerical Aligner
• WELL-QUASI-ORDERING HEREDITARILY FINITE SETS
• A Randomized Numerical Aligner (rNA)
• High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera (vol 11 pg 109 2010)
• Hybrid dynamics of stochastic programs
• Physical mapping in highly heterozygous genomes: a physical contig map of the Pinot Noir grapevine cultivar
• The Bernays Schoenfinkel Ramsey class for set theory: semidecidability
• The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture among varieties of different geographic origin
• Automated FingerPrint Background removal: FPB
• Discrete Semantics for Hybrid Automata
• Dynamical Systems and Stochastic Programming: To Ordinary Differential Equations and Back
• Ehrenfeucht Games on Labelled Successor Structures: Remoteness and Optimal Strategies
• GAM: Genomic Assemblies Merger: A Graph Based Method to Integrate Different Assemblies
• High throughput approaches reveal splicing of primary microrna transcripts and tissue specific expression of mature micrornas in vitis vinifera
• Hybrid dynamics of stochastic pi-calculus
• Stochastic Programs and Hybrid Automata for (Biological) Modeling
• TEA: a Transposable Elements Annotator
• The Importance of Being (A Little Bit) Discrete
• A complete axiomatic system for a process-based spatial logic
• Discreteness, hybrid automata, and biology
• Hybrid approximation of stochastic process algebras for systems biology
• Hybrid semantics for stochastic pi-calculus
• Hybrid systems and biology. continuous and discrete modeling for systems biology
• Inclusion dynamics hybrid automata
• Modeling Biological Systems in Stochastic Concurrent Constraint Programming
• Symbolic Graphs: Linear Solutions to Connectivity Related Problems
• Systems Biology: Models and Logics
• The importance of being (a little bit) discrete
• Module Identification Using Biological Constraints
• Motif discovery fixing mismatch positions
• On Devising Algorithms for Ehrenfeucht-Fraïssé Games
• Stochastic concurrent constraint programming and differential equations
• The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
• BuST: Bundled Suffix Trees
• Connecting process algebras and differential equations for Systems Biology
• Extensions of S1S and the composition method
• Finding regulatory elements fixing error layouts
• Modeling Biological Systems in Stochastic Concurrent Constraint Programming
• Stem-loop structure search for helitron discovery
• Views on Time in Systems Biology
• Algorithmic Algebraic Model Checking I: Challenges from Systems Biology⋆
• An algorithmic account of winning strategies in Ehrenfeucht games on labelled successor structures
• Structured motifs search
• The axiom of elementary sets on the edge of Peircean expressibility
• Ackermann Encodings, Bisimulations, and OBDDs
• An Efficient Algorithm for Computing Bisimulation Equivalence
• Structured Motifs Search
• Taming the complexity of biochemical models through bisimulation and collapsing: theory and practice
• Three-variable statements of set-pairing
• A sense of life: computational and experimental investigations with models of biochemical and evolutionary processes
• Computing strongly connected components in a linear number of symbolic steps
• Foundations of a query and simulation system for the modeling of biochemical and biological processes
• From Bisimulation to Simulation: Coarsest Partition Problems
• Model building and model checking for biochemical processes
• Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing
• Alternative Translation Techniques for Propositional and First-Order Modal Logics
• Automated Search for LTR Retrotransposons
• Extending Kamp's Theorem to Model Time Granularity
• Rank-Based Symbolic Bisimulation (and Model Checking)
• Simulation as Coarsest Partition Problem
• Simulation Reduction as Constraint
• The problem of finding transcription factor binding sites and its impact in defining co-regulated gene-networks
• Xs-systems: extended s-systems and algebraic differential automata for modeling cellular behavior
• A Fast Bisimulation Algorithm
• A logical approach to time granularity
• Ackermann Encoding, Bisimulations, and OBDD's
• Modelling concurrent systems specified in a temporal concurrent constraint language -I
• Set Theory for Computing. From Decision Procedures to Declarative Programming with Sets
• Comparing Expressiveness of Set Constructor Symbols
• Modeling Timed Concurrent systems in a Temporal Concurrent Constraint language
• Supporting automated deduction in first-order modal logics
• The taming (timing) of the states
• Towards tableau-based decision procedures for non-well-founded fragments of set theory
• Editorial
• Finite families with few symmetric differences
• Modal Logic and Set Theory: a Set-Theoretic Interpretation of Modal Logic Liber Amicorum for the Fiftieth Birthday of J. F. A. K. van Benthem
• Solvable set/hyperset contexts: II. A goal driven unification algorithm for the blended case
• T-resolution: refinements and model elimination
• Theories of omega-layered metric temporal structures
• A uniform axiomatic view of list, multisets, and sets, and the relevant unification algorithm
• Modal deduction in second-order logic and set theory. II
• A Set-Theoretic Approach to Automated Deduction in Graded Modal Logics
• Book review: Temporal logic. From ancient ideas to artificial intelligence
• Modal deduction in second-order logic and set theory. I
• On T Logic Programming
• Temporal Logic. From Ancient Ideas to Artificial Intelligence,by Peter Ohrstrom and Per F.V. Hasle (book review)
• Witnessing differences without redundancies
• Complementation in the lattice of equivalence relations
• Decidability of E*A-sentences in Membership Theories
• Decidability results for metric and layered temporal logics
• Integrating lists, multisets, and sets in a logic programming framework.
• Set-theoretic decidability results for modal theorem proving
• A set-theoretic translation method for (poly)modal logics
• A set-theoretic translation method for polymodal logics
• T-theorem proving. I
• A derived algorithm for evaluating epsilon-expressions over abstract sets
• Undecidability Results for Restricted Universally Quantified Formulae of Set Theory
• Decision Procedures for Elementary Sublanguages of Set Theory XIII. Model Graphs, Reflection and Decidability.
• Expressing Infinity without Foundation
• A contribution to the Automated Treatment of Membership Theories
• Note on: The Logically Simplest Form of the Infinity Axiom
• The Automation of Syllogistic II. Optimization and Complexity Issues
• Truth Table for a Combinatorial Kernel of Set Theories
• Decidability results for classes of purely universal formulae and quantifiers elimination in Set Theory
• Decision Procedures for Elementary Sublanguages of Set Theory. IX. Unsolvability of the decision problem for a restricted subclass of delta-0 formulas of set theory.
• Secision Procedures for Elementary Sublanguages of Set Theory XI. Unsolvability of the Decision Problem for a Restricted Subclass of the Delta_0-Formulas in Set Theory
• The Logically Simplest Form of the Infinity Axiom
• Completeness and Decidability of the Deducibility Problem for Some Classes of Formulas of Set Theory