Lucian Ilie

Bioinform., January, 2024

2021

ALeS: adaptive-length spaced-seed design.

[BibT_eX]

[DOI]

Arnab Mallik

Bioinform., 2021

DELPHI: accurate deep ensemble model for protein interaction sites prediction.

[BibT_eX]

[DOI]

Yiwei Li

Geoffrey Brian Golding

Bioinform., 2021

2020

Predicting Protein-Protein Interactions Using SPRINT.

[BibT_eX]

[DOI]

Yiwei Li

Proceedings of the Protein-Protein Interaction Networks, Methods and Protocols., 2020

2018

SAGE2: parallel human genome assembly.

[BibT_eX]

[DOI]

Michael Molnar

Ehsan Haghshenas

Bioinform., 2018

2017

SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome.

[BibT_eX]

[DOI]

Yiwei Li

BMC Bioinform., 2017

HISEA: HIerarchical SEed Aligner for PacBio data.

[BibT_eX]

[DOI]

Nilesh Khiste

BMC Bioinform., 2017

2016

Regular Expression Matching.

[BibT_eX]

[DOI]

Encyclopedia of Algorithms, 2016

2015

E-MEM: efficient computation of maximal exact matches for very large genomes.

[BibT_eX]

[DOI]

Nilesh Khiste

Bioinform., 2015

Correcting Illumina data.

[BibT_eX]

[DOI]

Michael Molnar

Briefings Bioinform., 2015

2014

SAGE: String-overlap Assembly of GEnomes.

[BibT_eX]

[DOI]

BMC Bioinform., 2014

2013

Computing the Longest Previous Factor.

[BibT_eX]

[DOI]

Eur. J. Comb., 2013

BOND: Basic OligoNucleotide Design.

[BibT_eX]

[DOI]

Hamid Mohamadi

Geoffrey Brian Golding

William F. Smyth

BMC Bioinform., 2013

RACER: Rapid and accurate correction of errors in reads.

[BibT_eX]

[DOI]

Michael Molnar

Bioinform., 2013

2012

A comparison of index-based lempel-Ziv LZ77 factorization algorithms.

[BibT_eX]

[DOI]

ACM Comput. Surv., 2012

2011

The "runs" conjecture.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2011

Minimum Unique Substrings and Maximum Repeats.

[BibT_eX]

[DOI]

William F. Smyth

Fundam. Informaticae, 2011

SpEED: fast computation of sensitive spaced seeds.

[BibT_eX]

[DOI]

Anahita Mansouri Bigvand

Bioinform., 2011

HiTEC: accurate error correction in high-throughput sequencing data.

[BibT_eX]

[DOI]

Farideh Fazayeli

Bioinform., 2011

SHRiMP2: Sensitive yet Practical Short Read Mapping.

[BibT_eX]

[DOI]

Bioinform., 2011

2010

The longest common extension problem revisited and applications to approximate string searching.

[BibT_eX]

[DOI]

Gonzalo Navarro

J. Discrete Algorithms, 2010

2009

Repetitions in strings: Algorithms and combinatorics.

[BibT_eX]

[DOI]

Wojciech Rytter

Theor. Comput. Sci., 2009

Fast computation of neighbor seeds.

[BibT_eX]

[DOI]

Bioinform., 2009

Practical Algorithms for the Longest Common Extension Problem.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2009

LPF Computation Revisited.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Algorithms, 20th International Workshop, 2009

2008

Regular Expression Matching.

[BibT_eX]

[DOI]

Proceedings of the Encyclopedia of Algorithms - 2008 Edition, 2008

Maximal repetitions in strings.

[BibT_eX]

[DOI]

J. Comput. Syst. Sci., 2008

Computing Longest Previous Factor in linear time and applications.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2008

Understanding Maximal Repetitions in Strings.

[BibT_eX]

[DOI]

Proceedings of the STACS 2008, 2008

A Simple Algorithm for Computing the Lempel Ziv Factorization.

[BibT_eX]

[DOI]

William F. Smyth

Proceedings of the 2008 Data Compression Conference (DCC 2008), 2008

Towards a Solution to the "Runs" Conjecture.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching, 19th Annual Symposium, 2008

2007

A note on the number of squares in a word.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2007

The Lempel--Ziv Complexity of Fixed Points of Morphisms.

[BibT_eX]

[DOI]

Sorin Constantinescu

SIAM J. Discret. Math., 2007

The Structure of Factor Oracles.

[BibT_eX]

[DOI]

Emine Seid-Hilmi

Int. J. Found. Comput. Sci., 2007

Multiple spaced seeds for homology search.

[BibT_eX]

[DOI]

Bioinform., 2007

Fast Computation of Good Multiple Spaced Seeds.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Analysis of Maximal Repetitions in Strings.

[BibT_eX]

[DOI]

Proceedings of the Mathematical Foundations of Computer Science 2007, 2007

Long spaced seeds for finding similarities between biological sequences.

[BibT_eX]

Proceedings of the International Conference on Bioinformatics & Computational Biology, 2007

2006

Combinatorial Complexity Measures for Strings.

[BibT_eX]

[DOI]

Proceedings of the Recent Advances in Formal Languages and Applications, 2006

Periodic and Sturmian languages.

[BibT_eX]

[DOI]

Solomon Marcus

Ion Petre

Inf. Process. Lett., 2006

The Shortest Common Superstring Problem and Viral Genome Compression.

[BibT_eX]

[DOI]

Cristian Popescu

Fundam. Informaticae, 2006

Fine and Wilf's Theorem for Abelian Periods.

[BibT_eX]

Sorin Constantinescu

Bull. EATCS, 2006

Factor Oracles.

[BibT_eX]

[DOI]

Emine Seid-Hilmi

Proceedings of the Implementation and Application of Automata, 2006

Viral Genome Compression.

[BibT_eX]

[DOI]

Proceedings of the DNA Computing, 12th International Meeting on DNA Computing, 2006

Gene Assembly Algorithms for Ciliates.

[BibT_eX]

[DOI]

Roberto Solis-Oba

Proceedings of the DNA Computing, 12th International Meeting on DNA Computing, 2006

2005

A generalization of repetition threshold.

[BibT_eX]

[DOI]

Pascal Ochem

Jeffrey O. Shallit

Theor. Comput. Sci., 2005

Generalised fine and Wilf's theorem for arbitrary number of periods.

[BibT_eX]

[DOI]

Sorin Constantinescu

Theor. Comput. Sci., 2005

A simple proof that a word of length <i>n</i> has at most 2<i>n</i> distinct squares.

[BibT_eX]

[DOI]

J. Comb. Theory, Ser. A, 2005

Fast Data Compression with Antidictionaries.

[BibT_eX]

[DOI]

Michael Davidson

Fundam. Informaticae, 2005

Reducing the Size of NFAs by Using Equivalences and Preorders.

[BibT_eX]

[DOI]

Roberto Solis-Oba

Proceedings of the Combinatorial Pattern Matching, 16th Annual Symposium, 2005

2004

Word Complexity And Repetitions In Words.

[BibT_eX]

[DOI]

Kaizhong Zhang

Int. J. Found. Comput. Sci., 2004

On NFA Reductions.

[BibT_eX]

[DOI]

Gonzalo Navarro

Proceedings of the Theory Is Forever, 2004

2003

Reducing NFAs by invariant equivalences.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2003

Follow automata.

[BibT_eX]

[DOI]

Inf. Comput., 2003

A Generalization of Repetition Threshold

[BibT_eX]

[DOI]

Jeffrey O. Shallit

CoRR, 2003

Fast Algorithms for Extended Regular Expression Matching and Searching.

[BibT_eX]

[DOI]

Baozhen Shan

Proceedings of the STACS 2003, 20th Annual Symposium on Theoretical Aspects of Computer Science, Berlin, Germany, February 27, 2003

Introduction to Process Traces.

[BibT_eX]

Qing Zhao

Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, 2003

Crossing-Over on Languages: A Formal Representation of Chromosomes Recombination.

[BibT_eX]

Victor Mitrana

Proceedings of the Grammars and Automata for String Processing: From Mathematics and Computer Science to Biology, 2003

2002

Algorithms for Computing Small NFAs.

[BibT_eX]

[DOI]

Proceedings of the Mathematical Foundations of Computer Science 2002, 2002

Repetition Complexity of Words.

[BibT_eX]

Kaizhong Zhang

Proceedings of the Fourth International Workshop on Descriptional Complexity of Formal Systems - DCFS 2002, London, Canada, August 21, 2002

Constructing NFA s by Optimal Use of Positions in Regular Expressions.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching, 13th Annual Symposium, 2002

2001

On Generalized Slenderness of Context-Free Languages.

[BibT_eX]

Proceedings of the Words, Semigroups, and Transductions, 2001

Forbidden subsequences and permutations sortable on two parallel stacks.

[BibT_eX]

Proceedings of the Where Mathematics, 2001

2000

On lengths of words in context-free languages.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2000

Periods and Binary Words.

[BibT_eX]

[DOI]

Vesa Halava

J. Comb. Theory, Ser. A, 2000

A characterization of poly-slender context-free languages.

[BibT_eX]

[DOI]

Grzegorz Rozenberg

RAIRO Theor. Informatics Appl., 2000

Two-variable word equations.

[BibT_eX]

[DOI]

Wojciech Plandowski

RAIRO Theor. Informatics Appl., 2000

On strongly context-free languages.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2000

On the Expressiveness of Subset-Sum Representations.

[BibT_eX]

[DOI]

Acta Informatica, 2000

Uniformly Scattered Factors.

[BibT_eX]

[DOI]

Ion Petre

Grzegorz Rozenberg

Proceedings of the Finite Versus Infinite, 2000

1999

Subwords and Power-Free Words are not Expressible by Word Equations.

[BibT_eX]

[DOI]

Fundam. Informaticae, 1999

1998

On Well Quasi Orders of Free Monoids.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 1998

On Quasi Orders of Words and the Confluence Property.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 1998

2-Testability and Relabelings Produce Everything.

[BibT_eX]

[DOI]

J. Comput. Syst. Sci., 1998

Generalized Factors of Words.

[BibT_eX]

[DOI]

Fundam. Informaticae, 1998

1997

On Computational Complexity of Contextual Languages.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 1997

Languages Obtained from Infinite Words.

[BibT_eX]

[DOI]

RAIRO Theor. Informatics Appl., 1997

On a Geometric Problem of Zigzags.

[BibT_eX]

[DOI]

Vesa Halava

Inf. Process. Lett., 1997

On the Computational Complexity of Marcus Contextual Languages.

[BibT_eX]

[DOI]

Fundam. Informaticae, 1997

Some Recent Results on Contextual Languages.

[BibT_eX]

Bull. EATCS, 1997

Remarks on Well Quasi Orders of Words.

[BibT_eX]

Proceedings of the 3rd International Conference Developments in Language Theory, 1997

The Decidability of the Generalized Confluence Problem for Context-Free Languages.

[BibT_eX]

[DOI]

Proceedings of the New Trends in Formal Languages, 1997

1996

Binary self-adding sequences and languages.

[BibT_eX]

[DOI]

Victor Mitrana

Int. J. Comput. Math., 1996

Collapsing Hierarchies in PCGSs with Communication by Commands.

[BibT_eX]

[DOI]

Comput. Artif. Intell., 1996

On Regular Characterizations of Languages by Grammar Systems.

[BibT_eX]

[DOI]

Acta Cybern., 1996

Crossing-over on Languages. A Formal Representation of the Chromosome Recombination.

[BibT_eX]

Victor Mitrana

Proceedings of the German Conference on Bioinformatics, 1996

1995

on Subwords of Infinite Words.

[BibT_eX]

[DOI]

Discret. Appl. Math., 1995

On Disjunctivity, Ultimate Periodicity and Ultimate Identity.

[BibT_eX]

Proceedings of the Developments in Language Theory II, 1995

1994

On a Conjecture about Slender Context-Free Languages.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 1994

On Contextual Grammars with Parallel Derivation.

[BibT_eX]

[DOI]