2024
Phylogenetic network-assisted rooting of unrooted gene trees.
J. Comb. Optim., July, 2024
2022
Rooting Gene Trees via Phylogenetic Networks.
Proceedings of the Computing and Combinatorics - 28th International Conference, 2022
2021
The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost.
IEEE ACM Trans. Comput. Biol. Bioinform., 2021
2020
Minimizing genomic duplication episodes.
Comput. Biol. Chem., 2020
2019
Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects.
Bioinform., 2019
2017
FastBill: An Improved Tool for Prediction of Cis-Regulatory Modules.
J. Comput. Biol., 2017
2016
Enhanceosome transcription factors preferentially dimerize with high mobility group proteins.
BMC Syst. Biol., 2016
Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data.
Bioinform., 2016
2014
eCAMBer: efficient support for large-scale comparative analysis of multiple bacterial strains.
BMC Bioinform., 2014
2013
Unrooted Tree Reconciliation: A Unified Approach.
IEEE ACM Trans. Comput. Biol. Bioinform., 2013
Bioinformatics and Computational Biology in Poland.
PLoS Comput. Biol., 2013
A Probabilistic Model of Neutral and Selective Dynamics of Protein Network Evolution.
J. Comput. Biol., 2013
2012
Inferring Evolutionary Scenarios in the Duplication, Loss and Horizontal Gene Transfer Model.
Proceedings of the Logic and Program Semantics, 2012
2011
Bi-Billboard: Symmetrization and Careful Choice of Informant Species Results in Higher Accuracy of Regulatory Element Prediction.
J. Comput. Biol., 2011
Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data.
BMC Bioinform., 2011
CAMBerVis: visualization software to support comparative analysis of multiple bacterial strains.
Bioinform., 2011
2010
Introducing Knowledge into Differential Expression Analysis.
J. Comput. Biol., 2010
MODEVO: exploring modularity and evolution of protein interaction networks.
Bioinform., 2010
CAMBer: An approach to support comparative analysis of multiple bacterial strains.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010
2009
Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs.
BMC Bioinform., 2009
Phylogeny-guided interaction mapping in seven eukaryotes.
BMC Bioinform., 2009
2007
Evolution of Gene Families Based on Gene Duplication, Loss, Accumulated Change, and Innovation.
J. Comput. Biol., 2007
A new approach to the assessment of the quality of predictions of transcription factor binding sites.
J. Biomed. Informatics, 2007
URec: a system for unrooted reconciliation.
Bioinform., 2007
Inferring phylogeny from whole genomes.
Bioinform., 2007
Identification of functional modules from conserved ancestral protein-protein interactions.
Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007
Reconstruction of Mammalian Cell Cycle Regulatory Network from Microarray Data Using Stochastic Logical Networks.
Proceedings of the Computational Methods in Systems Biology, International Conference, 2007
2006
DLS-trees: A model of evolutionary scenarios.
Theor. Comput. Sci., 2006
Alignment with Context Dependent Scoring Function.
J. Comput. Biol., 2006
Using local gene expression similarities to discover regulatory binding site modules.
BMC Bioinform., 2006
Applying dynamic Bayesian networks to perturbed gene expression data.
BMC Bioinform., 2006
On Genome Evolution with Accumulated Change and Innovation.
Proceedings of the Comparative Genomics, 2006
On Genome Evolution with Innovation.
Proceedings of the Mathematical Foundations of Computer Science 2006, 2006
Regulatory Network Reconstruction Using Stochastic Logical Networks.
Proceedings of the Computational Methods in Systems Biology, International Conference, 2006
2005
Introducing Dependencies into Alignment Analysis and Its Use for Local Structure Prediction in Proteins.
Proceedings of the Parallel Processing and Applied Mathematics, 2005
2004
On the Structure of Reconciliations.
Proceedings of the Comparative Genomics, 2004
A Case Study of Genome Evolution: From Continuous to Discrete Time Model.
Proceedings of the Mathematical Foundations of Computer Science 2004, 2004
2003
Substructural logic and partial correctness.
ACM Trans. Comput. Log., 2003
Type Inference for Nested Self Types.
Proceedings of the Types for Proofs and Programs, International Workshop, 2003
2002
The Subtyping Problem for Second-Order Types Is Undecidable.
Inf. Comput., 2002
Products and Polymorphic Subtypes.
Fundam. Informaticae, 2002
Contextual alignment of biological sequences.
Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002
2001
On the completeness of propositional Hoare logic.
Inf. Sci., 2001
A Sequent Calculus for Subtyping Polymorphic Types.
Inf. Comput., 2001
Intuitionistic Linear Logic and Partial Correctness.
Proceedings of the 16th Annual IEEE Symposium on Logic in Computer Science, 2001
1999
Alpha-Conversion and Typability.
Inf. Comput., 1999
Discrimination by Parallel Observers: The Algorithm.
Inf. Comput., 1999
Type Reconstruction for Functional Programs with Subtyping over a Lattice of Atomic Types.
Proceedings of the Mathematical Foundations of Computer Science 1999, 1999
1997
Discrimination by Parallel Observers.
Proceedings of the Proceedings, 12th Annual IEEE Symposium on Logic in Computer Science, Warsaw, Poland, June 29, 1997
Subtyping over a Lattice (Abstract).
Proceedings of the Computational Logic and Proof Theory, 5th Kurt Gödel Colloquium, 1997
1996
Satisfiability of Inequalities in a Poset.
Fundam. Informaticae, 1996
Untyped Lambda-Calculus with Input-Output.
Proceedings of the Trees in Algebra and Programming, 1996
1995
Equational Axiomatization of Bicoercibility for Polymorphic Types.
Proceedings of the Foundations of Software Technology and Theoretical Computer Science, 1995
1994
An Analysis of ML Typability.
J. ACM, 1994
1993
The Undecidability of the Semi-unification Problem
Inf. Comput., January, 1993
Type Reconstruction in the Presence of Polymorphic Recursion.
ACM Trans. Program. Lang. Syst., 1993
A New Characterization of Lambda Definability.
Proceedings of the Typed Lambda Calculi and Applications, 1993
Type Reconstruction with Recursive Types and Atomic Subtyping.
Proceedings of the TAPSOFT'93: Theory and Practice of Software Development, 1993
1992
Type Reconstruction in Finite Rank Fragments of the Second-Order lambda-Calculus
Inf. Comput., June, 1992
On the Expressive Power of Finitely and Universally Polymorphic Recursive Procedures.
Theor. Comput. Sci., 1992
Proceedings of the Seventh Annual Symposium on Logic in Computer Science (LICS '92), 1992
Solving Equational Constraints in Polymorphic Types.
Proceedings of the Logical Foundations of Computer Science, 1992
1990
Fixed Points in Free Process Algebras, Part II.
Theor. Comput. Sci., 1990
The Undecidability of the Semi-Unification Problem (Preliminary Report)
Proceedings of the 22nd Annual ACM Symposium on Theory of Computing, 1990
Type Inference Problems: A Survey.
Proceedings of the Mathematical Foundations of Computer Science 1990, 1990
Type Reconstruction in Finite-Rank Fragments of the Polymorphic lambda-Calculus (Extended Summary)
Proceedings of the Fifth Annual Symposium on Logic in Computer Science (LICS '90), 1990
ML Typability is DEXTIME-Complete.
Proceedings of the CAAP '90, 1990
Proceedings of the Handbook of Theoretical Computer Science, 1990
1989
A Simplified Proof of DDL < DL
Inf. Comput., April, 1989
Fixed Points in Free Process Algebras, Part I.
Theor. Comput. Sci., 1989
Computational Consequences and Partial Solutions of a Generalized Unification Problem (Partial Report)
Proceedings of the Fourth Annual Symposium on Logic in Computer Science (LICS '89), 1989
1988
Some Relationships Between Logics of Programs and Complexity Theory.
Theor. Comput. Sci., 1988
A Proper Extension of ML with an Effective Type-Assignment.
Proceedings of the Conference Record of the Fifteenth Annual ACM Symposium on Principles of Programming Languages, 1988
On the Computational Power of Universally Polymorphic Recursion
Proceedings of the Third Annual Symposium on Logic in Computer Science (LICS '88), 1988
1987
The Hierarchy of Finitely Typed Functional Programs (Short Version)
Proceedings of the Symposium on Logic in Computer Science (LICS '87), 1987
1986
Higher-Order Arrays and Stacks in Programming. An Application of Complexity Theory to Logics of Programs.
Proceedings of the Mathematical Foundations of Computer Science 1986, 1986
1985
Fixed Ponts in Process Algebras with Internal Actions ( a preliminary note).
Proceedings of the Mathematical Foundations of Programming Semantics, 1985
1984
Equivalences among Logics of Programs.
J. Comput. Syst. Sci., 1984
Unbounded Program Memory Adds to the Expressive Power of First-Order Programming Logic
Inf. Control., 1984
Remarks on Comparing Expressive Power of Logics of Programs.
Proceedings of the Mathematical Foundations of Computer Science 1984, 1984
1983
PC-Compactness, a Necessary Condition for the Existence of Sound and Complete Logics of Partial Correctness.
Proceedings of the Logics of Programs, 1983
Implicit definability of finite binary trees by sets of equations.
Proceedings of the Logic and Machines: Decision Problems and Complexity, 1983
Some Relationships between Logics of Programs and Complexity Theory (Extended Abstract)
Proceedings of the 24th Annual Symposium on Foundations of Computer Science, 1983
1982
Another Incompleteness Result for Hoare's Logic
Inf. Control., February, 1982
Floyds Principle, Correctness Theories and Program Equivalence.
Theor. Comput. Sci., 1982
On the Power of Nondeterminism in Dynamic Logic.
Proceedings of the Automata, 1982
1981
Logic of effective definitions.
Fundam. Informaticae, 1981
Regular extensions of iterative algebras and metric interpretations.
Fundam. Informaticae, 1981
Algorithmic degrees of algebraic structures.
Fundam. Informaticae, 1981
Logic of effective definitions.
Fundam. Informaticae, 1981
A Note On Equivalences Among Logics of Programs.
Proceedings of the Logics of Programs, Workshop, Yorktown Heights, New York, USA, May 1981, 1981
Hoare's Logic is Incomplete When It Does Not Have To Be.
Proceedings of the Logics of Programs, Workshop, Yorktown Heights, New York, USA, May 1981, 1981
Unbounded Program Memory Adds to the Expressive Power of First-Order Dynamic Logic (Extended Abstract)
Proceedings of the 22nd Annual Symposium on Foundations of Computer Science, 1981
1980
Unique Fixed Points Vs. Least Fixed Points.
Theor. Comput. Sci., 1980
1979
Fixed Points in the Power-Set Algebra of Infinite Trees (Abstract).
Proceedings of the Mathematical Foundations of Computer Science 1979, 1979
A Survey of the Logic of Effective Definitions.
Proceedings of the Logics of Programs, Workshop, ETH Zürich, May-July 1979, 1979
Unique Fixed Points v. Least Fixed Points.
Proceedings of the Automata, 1979
Implicit definability of algebraic structures by means of program properties.
Proceedings of the Fundamentals of Computation Theory, 1979
1978
Some Results on the Decomposition of Finite Automata
Inf. Control., September, 1978
1977
Fixed-Points and Algebras with Infinitely Long Expressions, I.
Proceedings of the Mathematical Foundations of Computer Science 1977, 1977
Fixed-Points and Algebras with Infinitely Long Expressions, II.
Proceedings of the Fundamentals of Computation Theory, 1977
1976
On the Domain of Iteration in Iterative Algebraic Theories.
Proceedings of the Mathematical Foundations of Computer Science 1976, 1976
1974
The Algebraic Approach to the Theory of Computing Systems.
Proceedings of the Mathematical Foundations of Computer Science, 1974