Lucian Ilie

Publication Activity (10 Years)

Years Active: 1994-2024
Publications (10 Years): 8

Top Topics

Approximate Matches

Phylogenetic Analysis

Protein Interaction

Gene Expression Time Series

Top Venues

Briefings Bioinform.

Publications

Seyedmohsen Hosseini, Geoffrey Brian Golding, Lucian Ilie
Seq-InSite: sequence supersedes structure for protein interaction site prediction. Bioinform. 40 (1) (2024)
Yiwei Li, Geoffrey Brian Golding, Lucian Ilie
DELPHI: accurate deep ensemble model for protein interaction sites prediction. Bioinform. 37 (7) (2021)
Arnab Mallik, Lucian Ilie
ALeS: adaptive-length spaced-seed design. Bioinform. 37 (9) (2021)
Michael Molnar, Ehsan Haghshenas, Lucian Ilie
SAGE2: parallel human genome assembly. Bioinform. 34 (4) (2018)
Nilesh Khiste, Lucian Ilie
HISEA: HIerarchical SEed Aligner for PacBio data. BMC Bioinform. 18 (1) (2017)
Yiwei Li, Lucian Ilie
SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome. BMC Bioinform. 18 (1) (2017)
Nilesh Khiste, Lucian Ilie
E-MEM: efficient computation of maximal exact matches for very large genomes. Bioinform. 31 (4) (2015)
Michael Molnar, Lucian Ilie
Correcting Illumina data. Briefings Bioinform. 16 (4) (2015)
Lucian Ilie, Bahlul Haider, Michael Molnar, Roberto Solis-Oba
SAGE: String-overlap Assembly of GEnomes. BMC Bioinform. 15 (2014)
Lucian Ilie, Hamid Mohamadi, Geoffrey Brian Golding, William F. Smyth
BOND: Basic OligoNucleotide Design. BMC Bioinform. 14 (2013)
Maxime Crochemore, Lucian Ilie, Costas S. Iliopoulos, Marcin Kubica, Wojciech Rytter, Tomasz Walen
Computing the Longest Previous Factor. Eur. J. Comb. 34 (1) (2013)
Lucian Ilie, Michael Molnar
RACER: Rapid and accurate correction of errors in reads. Bioinform. 29 (19) (2013)
Anisa Al-Hafeedh, Maxime Crochemore, Lucian Ilie, Evguenia Kopylova, William F. Smyth, German Tischler, Munina Yusufu
A comparison of index-based lempel-Ziv LZ77 factorization algorithms. ACM Comput. Surv. 45 (1) (2012)
Matei David, Misko Dzamba, Dan Lister, Lucian Ilie, Michael Brudno
SHRiMP2: Sensitive yet Practical Short Read Mapping. Bioinform. 27 (7) (2011)
Maxime Crochemore, Lucian Ilie, Liviu Tinta
The "runs" conjecture. Theor. Comput. Sci. 412 (27) (2011)
Lucian Ilie, Silvana Ilie, Anahita Mansouri Bigvand
SpEED: fast computation of sensitive spaced seeds. Bioinform. 27 (17) (2011)
Lucian Ilie, William F. Smyth
Minimum Unique Substrings and Maximum Repeats. Fundam. Informaticae 110 (1-4) (2011)
Lucian Ilie, Farideh Fazayeli, Silvana Ilie
HiTEC: accurate error correction in high-throughput sequencing data. Bioinform. 27 (3) (2011)
Lucian Ilie, Gonzalo Navarro, Liviu Tinta
The longest common extension problem revisited and applications to approximate string searching. J. Discrete Algorithms 8 (4) (2010)
Maxime Crochemore, Lucian Ilie, Costas S. Iliopoulos, Marcin Kubica, Wojciech Rytter, Tomasz Walen
LPF Computation Revisited. IWOCA (2009)
Lucian Ilie, Silvana Ilie
Fast computation of neighbor seeds. Bioinform. 25 (6) (2009)
Maxime Crochemore, Lucian Ilie, Wojciech Rytter
Repetitions in strings: Algorithms and combinatorics. Theor. Comput. Sci. 410 (50) (2009)
Lucian Ilie, Liviu Tinta
Practical Algorithms for the Longest Common Extension Problem. SPIRE (2009)
Maxime Crochemore, Lucian Ilie
Computing Longest Previous Factor in linear time and applications. Inf. Process. Lett. 106 (2) (2008)
Maxime Crochemore, Lucian Ilie, Liviu Tinta
Towards a Solution to the "Runs" Conjecture. CPM (2008)
Maxime Crochemore, Lucian Ilie
Understanding Maximal Repetitions in Strings. STACS (2008)
Maxime Crochemore, Lucian Ilie
Maximal repetitions in strings. J. Comput. Syst. Sci. 74 (5) (2008)
Maxime Crochemore, Lucian Ilie
Understanding maximal repetitions in strings CoRR (2008)
Maxime Crochemore, Lucian Ilie, William F. Smyth
A Simple Algorithm for Computing the Lempel Ziv Factorization. DCC (2008)
Lucian Ilie
A note on the number of squares in a word. Theor. Comput. Sci. 380 (3) (2007)
Maxime Crochemore, Lucian Ilie
Analysis of Maximal Repetitions in Strings. MFCS (2007)
Lucian Ilie, Silvana Ilie
Fast Computation of Good Multiple Spaced Seeds. WABI (2007)
Maxime Crochemore, Lucian Ilie, Emine Seid-Hilmi
The Structure of Factor Oracles. Int. J. Found. Comput. Sci. 18 (4) (2007)
Lucian Ilie, Silvana Ilie
Multiple spaced seeds for homology search. Bioinform. 23 (22) (2007)
Lucian Ilie, Silvana Ilie
Long spaced seeds for finding similarities between biological sequences. BIOCOMP (2007)
Sorin Constantinescu, Lucian Ilie
The Lempel--Ziv Complexity of Fixed Points of Morphisms. SIAM J. Discret. Math. 21 (2) (2007)
Maxime Crochemore, Lucian Ilie, Emine Seid-Hilmi
Factor Oracles. CIAA (2006)
Lucian Ilie, Cristian Popescu
The Shortest Common Superstring Problem and Viral Genome Compression. Fundam. Informaticae 73 (1-2) (2006)
Lucian Ilie, Liviu Tinta, Cristian Popescu, Kathleen A. Hill
Viral Genome Compression. DNA (2006)
Lucian Ilie, Roberto Solis-Oba
Gene Assembly Algorithms for Ciliates. DNA (2006)
Sorin Constantinescu, Lucian Ilie
The Lempel-Ziv Complexity of Fixed Points of Morphisms. MFCS (2006)
Sorin Constantinescu, Lucian Ilie
Fine and Wilf's Theorem for Abelian Periods. Bull. EATCS 89 (2006)
Lucian Ilie, Solomon Marcus, Ion Petre
Periodic and Sturmian languages. Inf. Process. Lett. 98 (6) (2006)
Lucian Ilie, Roberto Solis-Oba, Sheng Yu
Reducing the Size of NFAs by Using Equivalences and Preorders. CPM (2005)
Lucian Ilie
distinct squares. J. Comb. Theory, Ser. A 112 (1) (2005)
Sorin Constantinescu, Lucian Ilie
Generalised fine and Wilf's theorem for arbitrary number of periods. Theor. Comput. Sci. 339 (1) (2005)
Michael Davidson, Lucian Ilie
Fast Data Compression with Antidictionaries. Fundam. Informaticae 64 (1-4) (2005)
Lucian Ilie, Pascal Ochem, Jeffrey O. Shallit
A generalization of repetition threshold. Theor. Comput. Sci. 345 (2-3) (2005)
Lucian Ilie, Sheng Yu, Kaizhong Zhang
Word Complexity And Repetitions In Words. Int. J. Found. Comput. Sci. 15 (1) (2004)
Lucian Ilie, Pascal Ochem, Jeffrey O. Shallit
A Generalization of Repetition Threshold. MFCS (2004)
Lucian Ilie, Gonzalo Navarro, Sheng Yu
On NFA Reductions. Theory Is Forever (2004)
Lucian Ilie, Sheng Yu
Reducing NFAs by invariant equivalences. Theor. Comput. Sci. 306 (1-3) (2003)
Lucian Ilie, Victor Mitrana
Crossing-Over on Languages: A Formal Representation of Chromosomes Recombination. Grammars and Automata for String Processing (2003)
Lucian Ilie, Sheng Yu, Qing Zhao
Introduction to Process Traces. PDPTA (2003)
Lucian Ilie, Jeffrey O. Shallit
A Generalization of Repetition Threshold CoRR (2003)
Lucian Ilie, Sheng Yu
Follow automata. Inf. Comput. 186 (1) (2003)
Lucian Ilie, Baozhen Shan, Sheng Yu
Fast Algorithms for Extended Regular Expression Matching and Searching. STACS (2003)
Lucian Ilie, Sheng Yu, Kaizhong Zhang
Repetition Complexity of Words. DCFS (2002)
Lucian Ilie, Sheng Yu
Algorithms for Computing Small NFAs. MFCS (2002)
Lucian Ilie, Sheng Yu, Kaizhong Zhang
Repetition Complexity of Words. COCOON (2002)
Lucian Ilie, Sheng Yu
Constructing NFA s by Optimal Use of Positions in Regular Expressions. CPM (2002)
Lucian Ilie
On Generalized Slenderness of Context-Free Languages. Words, Semigroups, and Transductions (2001)
Tero Harju, Lucian Ilie
Forbidden subsequences and permutations sortable on two parallel stacks. Where Mathematics, Computer Science, Linguistics and Biology Meet (2001)
Vesa Halava, Tero Harju, Lucian Ilie
Periods and Binary Words. J. Comb. Theory, Ser. A 89 (2) (2000)
Lucian Ilie, Grzegorz Rozenberg, Arto Salomaa
A characterization of poly-slender context-free languages. RAIRO Theor. Informatics Appl. 34 (1) (2000)
Lucian Ilie, Arto Salomaa
On the Expressiveness of Subset-Sum Representations. Acta Informatica 36 (8) (2000)
Lucian Ilie
On lengths of words in context-free languages. Theor. Comput. Sci. 242 (1-2) (2000)
Lucian Ilie, Wojciech Plandowski
Two-variable word equations. RAIRO Theor. Informatics Appl. 34 (6) (2000)
Lucian Ilie, Gheorghe Paun, Grzegorz Rozenberg, Arto Salomaa
On strongly context-free languages. Discret. Appl. Math. 103 (1-3) (2000)
Lucian Ilie, Wojciech Plandowski
Two-Variable Word Equations. STACS (2000)
Lucian Ilie
Subwords and Power-Free Words are not Expressible by Word Equations. Fundam. Informaticae 38 (1-2) (1999)
Tero Harju, Lucian Ilie
On Quasi Orders of Words and the Confluence Property. Theor. Comput. Sci. 200 (1-2) (1998)
Lucian Ilie, Arto Salomaa
On Well Quasi Orders of Free Monoids. Theor. Comput. Sci. 204 (1-2) (1998)
Lucian Ilie, Arto Salomaa
2-Testability and Relabelings Produce Everything. J. Comput. Syst. Sci. 56 (3) (1998)
Lucian Ilie
Generalized Factors of Words. Fundam. Informaticae 33 (3) (1998)
Vesa Halava, Tero Harju, Lucian Ilie
On a Geometric Problem of Zigzags. Inf. Process. Lett. 62 (1) (1997)
Tero Harju, Lucian Ilie
Languages Obtained from Infinite Words. RAIRO Theor. Informatics Appl. 31 (5) (1997)
Lucian Ilie
On Computational Complexity of Contextual Languages. Theor. Comput. Sci. 183 (1) (1997)
Lucian Ilie
Some Recent Results on Contextual Languages. Bull. EATCS 62 (1997)
Lucian Ilie
On the Computational Complexity of Marcus Contextual Languages. Fundam. Informaticae 30 (2) (1997)
Lucian Ilie
The Decidability of the Generalized Confluence Problem for Context-Free Languages. New Trends in Formal Languages (1997)
Lucian Ilie
Remarks on Well Quasi Orders of Words. Developments in Language Theory (1997)
Lucian Ilie, Victor Mitrana
Binary self-adding sequences and languages. Int. J. Comput. Math. 62 (3-4) (1996)
Lucian Ilie, Victor Mitrana
Crossing-over on Languages. A Formal Representation of the Chromosome Recombination. German Conference on Bioinformatics (1996)
Lucian Ilie, Arto Salomaa
On Regular Characterizations of Languages by Grammar Systems. Acta Cybern. 12 (4) (1996)
Lucian Ilie
Collapsing Hierarchies in PCGSs with Communication by Commands. Comput. Artif. Intell. 15 (2-3) (1996)
Lucian Ilie
On Disjunctivity, Ultimate Periodicity and Ultimate Identity. Developments in Language Theory (1995)
Lucian Ilie
on Subwords of Infinite Words. Discret. Appl. Math. 63 (3) (1995)
Lucian Ilie
On a Conjecture about Slender Context-Free Languages. Theor. Comput. Sci. 132 (2) (1994)