Lucian Ilie

98 papers A 3B 10C 6Misc 2Journal 62Unranked 8
YearRankTypeTitle / Venue / Authors
2025 J jnl
Component puzzle protein-protein interaction prediction.
Briefings Bioinform.
Seyedmohsen Hosseini, Geoffrey Brian Golding, Lucian Ilie
2024 J jnl
Scoring alignments by embedding vector similarity.
Briefings Bioinform.
Sepehr Ashrafzadeh, Geoffrey Brian Golding, Silvana Ilie, Lucian Ilie
2024 J jnl
Seq-InSite: sequence supersedes structure for protein interaction site prediction.
Bioinform.
Seyedmohsen Hosseini, Geoffrey Brian Golding, Lucian Ilie
2021 J jnl
ALeS: adaptive-length spaced-seed design.
Bioinform.
Arnab Mallik, Lucian Ilie
2021 J jnl
DELPHI: accurate deep ensemble model for protein interaction sites prediction.
Bioinform.
Yiwei Li, Geoffrey Brian Golding, Lucian Ilie
2020 — ch.
Predicting Protein-Protein Interactions Using SPRINT.
Protein-Protein Interaction Networks
Yiwei Li, Lucian Ilie
2018 J jnl
SAGE2: parallel human genome assembly.
Bioinform.
Michael Molnar, Ehsan Haghshenas, Lucian Ilie
2017 J jnl
HISEA: HIerarchical SEed Aligner for PacBio data.
BMC Bioinform.
Nilesh Khiste, Lucian Ilie
2017 J jnl
SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome.
BMC Bioinform.
Yiwei Li, Lucian Ilie
2016 — ch.
Regular Expression Matching.
Encyclopedia of Algorithms
Lucian Ilie
2015 J jnl
Correcting Illumina data.
Briefings Bioinform.
Michael Molnar, Lucian Ilie
2015 J jnl
E-MEM: efficient computation of maximal exact matches for very large genomes.
Bioinform.
Nilesh Khiste, Lucian Ilie
2014 J jnl
SAGE: String-overlap Assembly of GEnomes.
BMC Bioinform.
Lucian Ilie, Bahlul Haider, Michael Molnar, Roberto Solis-Oba
2013 J jnl
BOND: Basic OligoNucleotide Design.
BMC Bioinform.
Lucian Ilie, Hamid Mohamadi, Geoffrey Brian Golding, William F. Smyth
2013 J jnl
Computing the Longest Previous Factor.
Eur. J. Comb.
Maxime Crochemore, Lucian Ilie, Costas S. Iliopoulos, Marcin Kubica, Wojciech Rytter, Tomasz Walen
2013 J jnl
RACER: Rapid and accurate correction of errors in reads.
Bioinform.
Lucian Ilie, Michael Molnar
2012 J jnl
A comparison of index-based lempel-Ziv LZ77 factorization algorithms.
ACM Comput. Surv.
Anisa Al-Hafeedh, Maxime Crochemore, Lucian Ilie, Evguenia Kopylova, William F. Smyth, German Tischler, Munina Yusufu
2011 J jnl
HiTEC: accurate error correction in high-throughput sequencing data.
Bioinform.
Lucian Ilie, Farideh Fazayeli, Silvana Ilie
2011 J jnl
Minimum Unique Substrings and Maximum Repeats.
Fundam. Informaticae
Lucian Ilie, William F. Smyth
2011 J jnl
SHRiMP2: Sensitive yet Practical Short Read Mapping.
Bioinform.
Matei David, Misko Dzamba, Dan Lister, Lucian Ilie, Michael Brudno
2011 J jnl
SpEED: fast computation of sensitive spaced seeds.
Bioinform.
Lucian Ilie, Silvana Ilie, Anahita Mansouri Bigvand
2011 J jnl
The "runs" conjecture.
Theor. Comput. Sci.
Maxime Crochemore, Lucian Ilie, Liviu Tinta
2010 J jnl
The longest common extension problem revisited and applications to approximate string searching.
J. Discrete Algorithms
Lucian Ilie, Gonzalo Navarro, Liviu Tinta
2009 J jnl
Fast computation of neighbor seeds.
Bioinform.
Lucian Ilie, Silvana Ilie
2009 C conf
LPF Computation Revisited.
IWOCA
Maxime Crochemore, Lucian Ilie, Costas S. Iliopoulos, Marcin Kubica, Wojciech Rytter, Tomasz Walen
2009 C conf
Practical Algorithms for the Longest Common Extension Problem.
SPIRE
Lucian Ilie, Liviu Tinta
2009 J jnl
Repetitions in strings: Algorithms and combinatorics.
Theor. Comput. Sci.
Maxime Crochemore, Lucian Ilie, Wojciech Rytter
2008 B conf
A Simple Algorithm for Computing the Lempel Ziv Factorization.
DCC
Maxime Crochemore, Lucian Ilie, William F. Smyth
2008 J jnl
Computing Longest Previous Factor in linear time and applications.
Inf. Process. Lett.
Maxime Crochemore, Lucian Ilie
2008 J jnl
Maximal repetitions in strings.
J. Comput. Syst. Sci.
Maxime Crochemore, Lucian Ilie
2008 — ch.
Regular Expression Matching.
Encyclopedia of Algorithms
Lucian Ilie
2008 B conf
Towards a Solution to the "Runs" Conjecture.
CPM
Maxime Crochemore, Lucian Ilie, Liviu Tinta
2008 A conf
Understanding Maximal Repetitions in Strings.
STACS
Maxime Crochemore, Lucian Ilie
2008 J jnl
Understanding maximal repetitions in strings
CoRR
Maxime Crochemore, Lucian Ilie
2007 J jnl
A note on the number of squares in a word.
Theor. Comput. Sci.
Lucian Ilie
2007 B conf
Analysis of Maximal Repetitions in Strings.
MFCS
Maxime Crochemore, Lucian Ilie
2007 C conf
Fast Computation of Good Multiple Spaced Seeds.
WABI
Lucian Ilie, Silvana Ilie
2007 — conf
Long spaced seeds for finding similarities between biological sequences.
BIOCOMP
Lucian Ilie, Silvana Ilie
2007 J jnl
Multiple spaced seeds for homology search.
Bioinform.
Lucian Ilie, Silvana Ilie
2007 J jnl
The Lempel--Ziv Complexity of Fixed Points of Morphisms.
SIAM J. Discret. Math.
Sorin Constantinescu, Lucian Ilie
2007 J jnl
The Structure of Factor Oracles.
Int. J. Found. Comput. Sci.
Maxime Crochemore, Lucian Ilie, Emine Seid-Hilmi
2006 — ch.
Combinatorial Complexity Measures for Strings.
Recent Advances in Formal Languages and Applications
Lucian Ilie
2006 C conf
Factor Oracles.
CIAA
Maxime Crochemore, Lucian Ilie, Emine Seid-Hilmi
2006 J jnl
Fine and Wilf's Theorem for Abelian Periods.
Bull. EATCS
Sorin Constantinescu, Lucian Ilie
2006 B conf
Gene Assembly Algorithms for Ciliates.
DNA
Lucian Ilie, Roberto Solis-Oba
2006 J jnl
Periodic and Sturmian languages.
Inf. Process. Lett.
Lucian Ilie, Solomon Marcus, Ion Petre
2006 B conf
The Lempel-Ziv Complexity of Fixed Points of Morphisms.
MFCS
Sorin Constantinescu, Lucian Ilie
2006 J jnl
The Shortest Common Superstring Problem and Viral Genome Compression.
Fundam. Informaticae
Lucian Ilie, Cristian Popescu
2006 B conf
Viral Genome Compression.
DNA
Lucian Ilie, Liviu Tinta, Cristian Popescu, Kathleen A. Hill
2005 J jnl
A generalization of repetition threshold.
Theor. Comput. Sci.
Lucian Ilie, Pascal Ochem, Jeffrey O. Shallit
2005 J jnl
A simple proof that a word of length
J. Comb. Theory A
Lucian Ilie
2005 J jnl
Fast Data Compression with Antidictionaries.
Fundam. Informaticae
Michael Davidson, Lucian Ilie
2005 J jnl
Generalised fine and Wilf's theorem for arbitrary number of periods.
Theor. Comput. Sci.
Sorin Constantinescu, Lucian Ilie
2005 B conf
Reducing the Size of NFAs by Using Equivalences and Preorders.
CPM
Lucian Ilie, Roberto Solis-Oba, Sheng Yu
2004 — ed.
6th International Workshop on Descriptional Complexity of Formal Systems - DCFS 2004, London, Ontario, Canada, July 26 - 28, 2004. Pre-proceedings
DCFS
Lucian Ilie, Detlef Wotschke
2004 B conf
A Generalization of Repetition Threshold.
MFCS
Lucian Ilie, Pascal Ochem, Jeffrey O. Shallit
2004 — conf
On NFA Reductions.
Theory Is Forever
Lucian Ilie, Gonzalo Navarro, Sheng Yu
2004 J jnl
Word Complexity And Repetitions In Words.
Int. J. Found. Comput. Sci.
Lucian Ilie, Sheng Yu, Kaizhong Zhang
2003 J jnl
A Generalization of Repetition Threshold
CoRR
Lucian Ilie, Jeffrey O. Shallit
2003 — conf
Crossing-Over on Languages: A Formal Representation of Chromosomes Recombination.
Grammars and Automata for String Processing
Lucian Ilie, Victor Mitrana
2003 A conf
Fast Algorithms for Extended Regular Expression Matching and Searching.
STACS
Lucian Ilie, Baozhen Shan, Sheng Yu
2003 J jnl
Follow automata.
Inf. Comput.
Lucian Ilie, Sheng Yu
2003 Misc conf
Introduction to Process Traces.
PDPTA
Lucian Ilie, Sheng Yu, Qing Zhao
2003 J jnl
Reducing NFAs by invariant equivalences.
Theor. Comput. Sci.
Lucian Ilie, Sheng Yu
2002 B conf
Algorithms for Computing Small NFAs.
MFCS
Lucian Ilie, Sheng Yu
2002 B conf
Constructing NFA s by Optimal Use of Positions in Regular Expressions.
CPM
Lucian Ilie, Sheng Yu
2002 Misc conf
Repetition Complexity of Words.
COCOON
Lucian Ilie, Sheng Yu, Kaizhong Zhang
2002 — conf
Repetition Complexity of Words.
DCFS
Lucian Ilie, Sheng Yu, Kaizhong Zhang
2001 — conf
Forbidden subsequences and permutations sortable on two parallel stacks.
Where Mathematics, Computer Science, Linguistics and Biology Meet
Tero Harju, Lucian Ilie
2001 — conf
On Generalized Slenderness of Context-Free Languages.
Words, Semigroups, and Transductions
Lucian Ilie
2000 J jnl
A characterization of poly-slender context-free languages.
RAIRO Theor. Informatics Appl.
Lucian Ilie, Grzegorz Rozenberg, Arto Salomaa
2000 J jnl
On lengths of words in context-free languages.
Theor. Comput. Sci.
Lucian Ilie
2000 J jnl
On strongly context-free languages.
Discret. Appl. Math.
Lucian Ilie, Gheorghe Paun, Grzegorz Rozenberg, Arto Salomaa
2000 J jnl
On the Expressiveness of Subset-Sum Representations.
Acta Informatica
Lucian Ilie, Arto Salomaa
2000 J jnl
Periods and Binary Words.
J. Comb. Theory A
Vesa Halava, Tero Harju, Lucian Ilie
2000 A conf
Two-Variable Word Equations.
STACS
Lucian Ilie, Wojciech Plandowski
2000 J jnl
Two-variable word equations.
RAIRO Theor. Informatics Appl.
Lucian Ilie, Wojciech Plandowski
2000 — ch.
Uniformly Scattered Factors.
Finite Versus Infinite
Lucian Ilie, Ion Petre, Grzegorz Rozenberg
1999 J jnl
Subwords and Power-Free Words are not Expressible by Word Equations.
Fundam. Informaticae
Lucian Ilie
1998 J jnl
2-Testability and Relabelings Produce Everything.
J. Comput. Syst. Sci.
Lucian Ilie, Arto Salomaa
1998 J jnl
Generalized Factors of Words.
Fundam. Informaticae
Lucian Ilie
1998 J jnl
On Quasi Orders of Words and the Confluence Property.
Theor. Comput. Sci.
Tero Harju, Lucian Ilie
1998 J jnl
On Well Quasi Orders of Free Monoids.
Theor. Comput. Sci.
Lucian Ilie, Arto Salomaa
1997 J jnl
Languages Obtained from Infinite Words.
RAIRO Theor. Informatics Appl.
Tero Harju, Lucian Ilie
1997 J jnl
On Computational Complexity of Contextual Languages.
Theor. Comput. Sci.
Lucian Ilie
1997 J jnl
On a Geometric Problem of Zigzags.
Inf. Process. Lett.
Vesa Halava, Tero Harju, Lucian Ilie
1997 J jnl
On the Computational Complexity of Marcus Contextual Languages.
Fundam. Informaticae
Lucian Ilie
1997 C conf
Remarks on Well Quasi Orders of Words.
Developments in Language Theory
Lucian Ilie
1997 J jnl
Some Recent Results on Contextual Languages.
Bull. EATCS
Lucian Ilie
1997 — conf
The Decidability of the Generalized Confluence Problem for Context-Free Languages.
New Trends in Formal Languages
Lucian Ilie
1996 J jnl
Binary self-adding sequences and languages.
Int. J. Comput. Math.
Lucian Ilie, Victor Mitrana
1996 J jnl
Collapsing Hierarchies in PCGSs with Communication by Commands.
Comput. Artif. Intell.
Lucian Ilie
1996 — conf
Crossing-over on Languages. A Formal Representation of the Chromosome Recombination.
German Conference on Bioinformatics
Lucian Ilie, Victor Mitrana
1996 J jnl
On Regular Characterizations of Languages by Grammar Systems.
Acta Cybern.
Lucian Ilie, Arto Salomaa
1995 C conf
On Disjunctivity, Ultimate Periodicity and Ultimate Identity.
Developments in Language Theory
Lucian Ilie
1995 J jnl
on Subwords of Infinite Words.
Discret. Appl. Math.
Lucian Ilie
1994 — ch.
On Contextual Grammars with Parallel Derivation.
Mathematical Aspects of Natural and Formal Languages
Lucian Ilie
1994 J jnl
On a Conjecture about Slender Context-Free Languages.
Theor. Comput. Sci.
Lucian Ilie