# Lucian Ilie

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^{1}, Lucian Ilie## Timeline

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## Bibliography

2018

SAGE2: parallel human genome assembly.

Bioinformatics, 2018

2017

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

BMC Bioinformatics, 2017

HISEA: HIerarchical SEed Aligner for PacBio data.

BMC Bioinformatics, 2017

2016

Regular Expression Matching.

Encyclopedia of Algorithms, 2016

2015

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

Bioinformatics, 2015

Correcting Illumina data.

Briefings in Bioinformatics, 2015

2014

SAGE: String-overlap Assembly of GEnomes.

BMC Bioinformatics, 2014

2013

Computing the Longest Previous Factor.

Eur. J. Comb., 2013

BOND: Basic OligoNucleotide Design.

BMC Bioinformatics, 2013

RACER: Rapid and accurate correction of errors in reads.

Bioinformatics, 2013

2012

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

ACM Comput. Surv., 2012

2011

The "runs" conjecture.

Theor. Comput. Sci., 2011

Minimum Unique Substrings and Maximum Repeats.

Fundam. Inform., 2011

SpEED: fast computation of sensitive spaced seeds.

Bioinformatics, 2011

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

Bioinformatics, 2011

SHRiMP2: Sensitive yet Practical Short Read Mapping.

Bioinformatics, 2011

2010

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

J. Discrete Algorithms, 2010

2009

Repetitions in strings: Algorithms and combinatorics.

Theor. Comput. Sci., 2009

Fast computation of neighbor seeds.

Bioinformatics, 2009

Practical Algorithms for the Longest Common Extension Problem.

Proceedings of the String Processing and Information Retrieval, 2009

LPF Computation Revisited.

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

2008

Regular Expression Matching.

Proceedings of the Encyclopedia of Algorithms, 2008

Maximal repetitions in strings.

J. Comput. Syst. Sci., 2008

Computing Longest Previous Factor in linear time and applications.

Inf. Process. Lett., 2008

Understanding maximal repetitions in strings

CoRR, 2008

Understanding Maximal Repetitions in Strings.

Proceedings of the STACS 2008, 2008

A Simple Algorithm for Computing the Lempel Ziv Factorization.

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

Towards a Solution to the "Runs" Conjecture.

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

2007

A note on the number of squares in a word.

Theor. Comput. Sci., 2007

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

SIAM J. Discrete Math., 2007

The Structure of Factor Oracles.

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

Multiple spaced seeds for homology search.

Bioinformatics, 2007

Fast Computation of Good Multiple Spaced Seeds.

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

Analysis of Maximal Repetitions in Strings.

Proceedings of the Mathematical Foundations of Computer Science 2007, 2007

Long spaced seeds for finding similarities between biological sequences.

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

2006

Combinatorial Complexity Measures for Strings.

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

Periodic and Sturmian languages.

Inf. Process. Lett., 2006

The Shortest Common Superstring Problem and Viral Genome Compression.

Fundam. Inform., 2006

Fine and Wilf's Theorem for Abelian Periods.

Bulletin of the EATCS, 2006

Factor Oracles.

Proceedings of the Implementation and Application of Automata, 2006

The Lempel-Ziv Complexity of Fixed Points of Morphisms.

Proceedings of the Mathematical Foundations of Computer Science 2006, 2006

Viral Genome Compression.

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

Gene Assembly Algorithms for Ciliates.

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

2005

A generalization of repetition threshold.

Theor. Comput. Sci., 2005

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

Theor. Comput. Sci., 2005

J. Comb. Theory, Ser. A, 2005

Fast Data Compression with Antidictionaries.

Fundam. Inform., 2005

Reducing the Size of NFAs by Using Equivalences and Preorders.

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

2004

Word Complexity And Repetitions In Words.

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

A Generalization of Repetition Threshold.

Proceedings of the Mathematical Foundations of Computer Science 2004, 2004

On NFA Reductions.

Proceedings of the Theory Is Forever, 2004

2003

Reducing NFAs by invariant equivalences.

Theor. Comput. Sci., 2003

Follow automata.

Inf. Comput., 2003

A Generalization of Repetition Threshold

CoRR, 2003

Fast Algorithms for Extended Regular Expression Matching and Searching.

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

Introduction to Process Traces.

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

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

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

2002

Algorithms for Computing Small NFAs.

Proceedings of the Mathematical Foundations of Computer Science 2002, 2002

Repetition Complexity of Words.

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.

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

Repetition Complexity of Words.

Proceedings of the Computing and Combinatorics, 8th Annual International Conference, 2002

2001

On Generalized Slenderness of Context-Free Languages.

Proceedings of the Words, Semigroups, and Transductions, 2001

Forbidden subsequences and permutations sortable on two parallel stacks.

Proceedings of the Where Mathematics, 2001

2000

On lengths of words in context-free languages.

Theor. Comput. Sci., 2000

Periods and Binary Words.

J. Comb. Theory, Ser. A, 2000

A characterization of poly-slender context-free languages.

ITA, 2000

Two-variable word equations.

ITA, 2000

On strongly context-free languages.

Discrete Applied Mathematics, 2000

On the Expressiveness of Subset-Sum Representations.

Acta Inf., 2000

Two-Variable Word Equations.

Proceedings of the STACS 2000, 2000

1999

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

Fundam. Inform., 1999

1998

On Well Quasi Orders of Free Monoids.

Theor. Comput. Sci., 1998

On Quasi Orders of Words and the Confluence Property.

Theor. Comput. Sci., 1998

2-Testability and Relabelings Produce Everything.

J. Comput. Syst. Sci., 1998

Generalized Factors of Words.

Fundam. Inform., 1998

1997

On Computational Complexity of Contextual Languages.

Theor. Comput. Sci., 1997

Languages Obtained from Infinite Words.

ITA, 1997

On a Geometric Problem of Zigzags.

Inf. Process. Lett., 1997

On the Computational Complexity of Marcus Contextual Languages.

Fundam. Inform., 1997

Some Recent Results on Contextual Languages.

Bulletin of the EATCS, 1997

Remarks on Well Quasi Orders of Words.

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

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

Proceedings of the New Trends in Formal Languages, 1997

1996

Collapsing Hierarchies in PCGSs with Communication by Commands.

Computers and Artificial Intelligence, 1996

On Regular Characterizations of Languages by Grammar Systems.

Acta Cybern., 1996

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

German Conference on Bioinformatics, 1996

1995

on Subwords of Infinite Words.

Discrete Applied Mathematics, 1995

On Disjunctivity, Ultimate Periodicity and Ultimate Identity.

Proceedings of the Developments in Language Theory II, 1995

1994

On a Conjecture about Slender Context-Free Languages.

Theor. Comput. Sci., 1994