On Contextual Grammars with Parallel Derivation. - Lucian Ilie (Mathematical Aspects of Natural and Formal Languages, 1994)

On a Conjecture about Slender Context-Free Languages. - Lucian Ilie (Theor. Comput. Sci., 1994)

On Disjunctivity, Ultimate Periodicity and Ultimate Identity. - Lucian Ilie (Developments in Language Theory, 1995)

on Subwords of Infinite Words. - Lucian Ilie (Discret. Appl. Math., 1995)

Crossing-over on Languages. A Formal Representation of the Chromosome Recombination. - Lucian Ilie; Victor Mitrana (German Conference on Bioinformatics, 1996)

On Regular Characterizations of Languages by Grammar Systems. - Lucian Ilie; Arto Salomaa (Acta Cybern., 1996)

Collapsing Hierarchies in PCGSs with Communication by Commands. - Lucian Ilie (Comput. Artif. Intell., 1996)

Binary self-adding sequences and languages. - Lucian Ilie; Victor Mitrana (Int. J. Comput. Math., 1996)

The Decidability of the Generalized Confluence Problem for Context-Free Languages. - Lucian Ilie (New Trends in Formal Languages, 1997)

Remarks on Well Quasi Orders of Words. - Lucian Ilie (Developments in Language Theory, 1997)

Some Recent Results on Contextual Languages. - Lucian Ilie (Bull. EATCS, 1997)

On the Computational Complexity of Marcus Contextual Languages. - Lucian Ilie (Fundam. Informaticae, 1997)

On a Geometric Problem of Zigzags. - Vesa Halava; Tero Harju; Lucian Ilie (Inf. Process. Lett., 1997)

Languages Obtained from Infinite Words. - Tero Harju; Lucian Ilie (RAIRO Theor. Informatics Appl., 1997)

On Computational Complexity of Contextual Languages. - Lucian Ilie (Theor. Comput. Sci., 1997)

Generalized Factors of Words. - Lucian Ilie (Fundam. Informaticae, 1998)

2-Testability and Relabelings Produce Everything. - Lucian Ilie; Arto Salomaa (J. Comput. Syst. Sci., 1998)

On Quasi Orders of Words and the Confluence Property. - Tero Harju; Lucian Ilie (Theor. Comput. Sci., 1998)

On Well Quasi Orders of Free Monoids. - Lucian Ilie; Arto Salomaa (Theor. Comput. Sci., 1998)

Subwords and Power-Free Words are not Expressible by Word Equations. - Lucian Ilie (Fundam. Informaticae, 1999)

Uniformly Scattered Factors. - Lucian Ilie; Ion Petre; Grzegorz Rozenberg (Finite Versus Infinite, 2000)

On the Expressiveness of Subset-Sum Representations. - Lucian Ilie; Arto Salomaa (Acta Informatica, 2000)

On strongly context-free languages. - Lucian Ilie; Gheorghe Paun; Grzegorz Rozenberg; Arto Salomaa (Discret. Appl. Math., 2000)

Two-variable word equations. - Lucian Ilie; Wojciech Plandowski (RAIRO Theor. Informatics Appl., 2000)

A characterization of poly-slender context-free languages. - Lucian Ilie; Grzegorz Rozenberg; Arto Salomaa (RAIRO Theor. Informatics Appl., 2000)

Periods and Binary Words. - Vesa Halava; Tero Harju; Lucian Ilie (J. Comb. Theory A, 2000)

On lengths of words in context-free languages. - Lucian Ilie (Theor. Comput. Sci., 2000)

Forbidden subsequences and permutations sortable on two parallel stacks. - Tero Harju; Lucian Ilie (Where Mathematics, Computer Science, Linguistics and Biology Meet, 2001)

On Generalized Slenderness of Context-Free Languages. - Lucian Ilie (Words, Semigroups, and Transductions, 2001)

Repetition Complexity of Words. - Lucian Ilie; Sheng Yu 001; Kaizhong Zhang (COCOON, 2002)

Constructing NFA s by Optimal Use of Positions in Regular Expressions. - Lucian Ilie; Sheng Yu 001 (CPM, 2002)

Algorithms for Computing Small NFAs. - Lucian Ilie; Sheng Yu 001 (MFCS, 2002)

Crossing-Over on Languages: A Formal Representation of Chromosomes Recombination. - Lucian Ilie; Victor Mitrana (Grammars and Automata for String Processing, 2003)

Introduction to Process Traces. - Lucian Ilie; Sheng Yu 001; Qing Zhao (PDPTA, 2003)

Fast Algorithms for Extended Regular Expression Matching and Searching. - Lucian Ilie; Baozhen Shan; Sheng Yu 001 (STACS, 2003)

A Generalization of Repetition Threshold - Lucian Ilie; Jeffrey O. Shallit (CoRR, 2003)

Follow automata. - Lucian Ilie; Sheng Yu 001 (Inf. Comput., 2003)

Reducing NFAs by invariant equivalences. - Lucian Ilie; Sheng Yu 001 (Theor. Comput. Sci., 2003)

On NFA Reductions. - Lucian Ilie; Gonzalo Navarro 001; Sheng Yu 001 (Theory Is Forever, 2004)

Word Complexity And Repetitions In Words. - Lucian Ilie; Sheng Yu 001; Kaizhong Zhang (Int. J. Found. Comput. Sci., 2004)

Reducing the Size of NFAs by Using Equivalences and Preorders. - Lucian Ilie; Roberto Solis-Oba; Sheng Yu 001 (CPM, 2005)

Fast Data Compression with Antidictionaries. - Michael Davidson; Lucian Ilie (Fundam. Informaticae, 2005)

A simple proof that a word of length n has at most 2n distinct squares. - Lucian Ilie (J. Comb. Theory A, 2005)

Generalised fine and Wilf's theorem for arbitrary number of periods. - Sorin Constantinescu; Lucian Ilie (Theor. Comput. Sci., 2005)

A generalization of repetition threshold. - Lucian Ilie; Pascal Ochem; Jeffrey O. Shallit (Theor. Comput. Sci., 2005)

Gene Assembly Algorithms for Ciliates. - Lucian Ilie; Roberto Solis-Oba (DNA, 2006)

Viral Genome Compression. - Lucian Ilie; Liviu Tinta; Cristian Popescu; Kathleen A. Hill (DNA, 2006)

Factor Oracles. - Maxime Crochemore; Lucian Ilie; Emine Seid-Hilmi (CIAA, 2006)

Fine and Wilf's Theorem for Abelian Periods. - Sorin Constantinescu; Lucian Ilie (Bull. EATCS, 2006)

The Shortest Common Superstring Problem and Viral Genome Compression. - Lucian Ilie; Cristian Popescu (Fundam. Informaticae, 2006)

Periodic and Sturmian languages. - Lucian Ilie; Solomon Marcus; Ion Petre (Inf. Process. Lett., 2006)

Combinatorial Complexity Measures for Strings. - Lucian Ilie (Recent Advances in Formal Languages and Applications, 2006)

Long spaced seeds for finding similarities between biological sequences. - Lucian Ilie; Silvana Ilie (BIOCOMP, 2007)

Analysis of Maximal Repetitions in Strings. - Maxime Crochemore; Lucian Ilie (MFCS, 2007)

Fast Computation of Good Multiple Spaced Seeds. - Lucian Ilie; Silvana Ilie (WABI, 2007)

Multiple spaced seeds for homology search. - Lucian Ilie; Silvana Ilie (Bioinform., 2007)

The Structure of Factor Oracles. - Maxime Crochemore; Lucian Ilie; Emine Seid-Hilmi (Int. J. Found. Comput. Sci., 2007)

The Lempel–Ziv Complexity of Fixed Points of Morphisms. - Sorin Constantinescu; Lucian Ilie (SIAM J. Discret. Math., 2007)

A note on the number of squares in a word. - Lucian Ilie (Theor. Comput. Sci., 2007)

Towards a Solution to the "Runs" Conjecture. - Maxime Crochemore; Lucian Ilie; Liviu Tinta (CPM, 2008)

A Simple Algorithm for Computing the Lempel Ziv Factorization. - Maxime Crochemore; Lucian Ilie; William F. Smyth (DCC, 2008)

Understanding Maximal Repetitions in Strings. - Maxime Crochemore; Lucian Ilie (STACS, 2008)

Computing Longest Previous Factor in linear time and applications. - Maxime Crochemore; Lucian Ilie (Inf. Process. Lett., 2008)

Maximal repetitions in strings. - Maxime Crochemore; Lucian Ilie (J. Comput. Syst. Sci., 2008)

Regular Expression Matching. - Lucian Ilie (Encyclopedia of Algorithms, 2008)

LPF Computation Revisited. - Maxime Crochemore; Lucian Ilie; Costas S. Iliopoulos; Marcin Kubica 001; Wojciech Rytter; Tomasz Walen (IWOCA, 2009)

Practical Algorithms for the Longest Common Extension Problem. - Lucian Ilie; Liviu Tinta (SPIRE, 2009)

Fast computation of neighbor seeds. - Lucian Ilie; Silvana Ilie (Bioinform., 2009)

Repetitions in strings: Algorithms and combinatorics. - Maxime Crochemore; Lucian Ilie; Wojciech Rytter (Theor. Comput. Sci., 2009)

The longest common extension problem revisited and applications to approximate string searching. - Lucian Ilie; Gonzalo Navarro 001; Liviu Tinta (J. Discrete Algorithms, 2010)

SHRiMP2: Sensitive yet Practical Short Read Mapping. - Matei David; Misko Dzamba; Dan Lister; Lucian Ilie; Michael Brudno (Bioinform., 2011)

HiTEC: accurate error correction in high-throughput sequencing data. - Lucian Ilie; Farideh Fazayeli; Silvana Ilie (Bioinform., 2011)

SpEED: fast computation of sensitive spaced seeds. - Lucian Ilie; Silvana Ilie; Anahita Mansouri Bigvand (Bioinform., 2011)

Minimum Unique Substrings and Maximum Repeats. - Lucian Ilie; William F. Smyth (Fundam. Informaticae, 2011)

The "runs" conjecture. - Maxime Crochemore; Lucian Ilie; Liviu Tinta (Theor. Comput. Sci., 2011)

A comparison of index-based lempel-Ziv LZ77 factorization algorithms. - Anisa Al-Hafeedh; Maxime Crochemore; Lucian Ilie; Evguenia Kopylova; William F. Smyth; German Tischler; Munina Yusufu (ACM Comput. Surv., 2012)

RACER: Rapid and accurate correction of errors in reads. - Lucian Ilie; Michael Molnar (Bioinform., 2013)

BOND: Basic OligoNucleotide Design. - Lucian Ilie; Hamid Mohamadi; Geoffrey Brian Golding; William F. Smyth (BMC Bioinform., 2013)

Computing the Longest Previous Factor. - Maxime Crochemore; Lucian Ilie; Costas S. Iliopoulos; Marcin Kubica 001; Wojciech Rytter; Tomasz Walen (Eur. J. Comb., 2013)

SAGE: String-overlap Assembly of GEnomes. - Lucian Ilie; Bahlul Haider; Michael Molnar; Roberto Solis-Oba (BMC Bioinform., 2014)

Correcting Illumina data. - Michael Molnar; Lucian Ilie (Briefings Bioinform., 2015)

E-MEM: efficient computation of maximal exact matches for very large genomes. - Nilesh Khiste; Lucian Ilie (Bioinform., 2015)

Regular Expression Matching. - Lucian Ilie (Encyclopedia of Algorithms, 2016)

HISEA: HIerarchical SEed Aligner for PacBio data. - Nilesh Khiste; Lucian Ilie (BMC Bioinform., 2017)

SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome. - Yiwei Li; Lucian Ilie (BMC Bioinform., 2017)

SAGE2: parallel human genome assembly. - Michael Molnar; Ehsan Haghshenas; Lucian Ilie (Bioinform., 2018)

Predicting Protein-Protein Interactions Using SPRINT. - Yiwei Li; Lucian Ilie (Protein-Protein Interaction Networks, 2020)

DELPHI: accurate deep ensemble model for protein interaction sites prediction. - Yiwei Li; Geoffrey Brian Golding; Lucian Ilie (Bioinform., 2021)

ALeS: adaptive-length spaced-seed design. - Arnab Mallik; Lucian Ilie (Bioinform., 2021)

Scoring alignments by embedding vector similarity. - Sepehr Ashrafzadeh; Geoffrey Brian Golding; Silvana Ilie; Lucian Ilie (Briefings Bioinform., 2024)

Seq-InSite: sequence supersedes structure for protein interaction site prediction. - Seyedmohsen Hosseini; Geoffrey Brian Golding; Lucian Ilie (Bioinform., 2024)