Lucian Ilie

发表

Preface Program Committee Automaton Models Inspired by Peptide Computing

James M. McQuillan, O. Ibarra, Franziska Biegler, 2007 .

Fast Algorithms for Extended Regular Expression Matching and Searching

Lucian Ilie, Sheng Yu, Baozhen Shan, 2003, STACS.

Reducing NFAs by invariant equivalences

Lucian Ilie, Sheng Yu, Sheng Yu, 2003 .

Sequence analysis Fast computation of neighbor seeds

S. Ilie, Lucian Ilie, 2009 .

Sorting Permutations on Two Parallel Stacks

Lucian Ilie, 2007 .

PITHIA: Protein Interaction Site Prediction Using Multiple Sequence Alignments and Attention

Lucian Ilie, Seyedmohsen Hosseini, 2022, International journal of molecular sciences.

SHRiMP2: Sensitive yet Practical Short Read Mapping

Lucian Ilie, Matei David, Michael Brudno, 2011, Bioinform..

Minimum Unique Substrings and Maximum Repeats

Lucian Ilie, William F. Smyth, W. F. Smyth, 2011, Fundam. Informaticae.

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

Lucian Ilie, Gonzalo Navarro, Liviu Tinta, 2010, J. Discrete Algorithms.

Practical Algorithms for the Longest Common Extension Problem

Lucian Ilie, Liviu Tinta, Lucian Ilie, 2009, SPIRE.

The Lempel--Ziv Complexity of Fixed Points of Morphisms

Lucian Ilie, Sorin Constantinescu, Lucian Ilie, 2006, SIAM J. Discret. Math..

Fast Data Compression with Antidictionaries

Lucian Ilie, Michael Davidson, Lucian Ilie, 2004, Fundam. Informaticae.

Word Complexity And Repetitions In Words

Kaizhong Zhang, Lucian Ilie, Sheng Yu, 2004, Int. J. Found. Comput. Sci..

Repetition Complexity of Words

Kaizhong Zhang, Lucian Ilie, Sheng Yu, 2002, DCFS.

DELPHI: accurate deep ensemble model for protein interaction sites prediction

Lucian Ilie, Yiwei Li, G. B. Golding, 2020, bioRxiv.

BOND: Basic OligoNucleotide Design

Hamid Mohamadi, Lucian Ilie, William F. Smyth, 2013, BMC Bioinformatics.

Seeds for effective oligonucleotide design

Lucian Ilie, Silvana Ilie, Shima Khoshraftar, 2011, BMC Genomics.

Correcting Illumina data

Lucian Ilie, Michael Molnar, Lucian Ilie, 2015, Briefings Bioinform..

RACER: Rapid and accurate correction of errors in reads

Lucian Ilie, Michael Molnar, Lucian Ilie, 2013, Bioinform..

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

Lucian Ilie, Yiwei Li, Lucian Ilie, 2017, BMC Bioinformatics.

Multiple spaced seeds for homology search

Lucian Ilie, Silvana Ilie, S. Ilie, 2007, Bioinform..

A generalization of repetition threshold

Lucian Ilie, Pascal Ochem, Jeffrey Shallit, 2003, Theor. Comput. Sci..

Fine and Wilf's Theorem for Abelian Periods

Lucian Ilie, Sorin Constantinescu, Lucian Ilie, 2006, Bull. EATCS.

HiTEC: accurate error correction in high-throughput sequencing data

Lucian Ilie, Silvana Ilie, Farideh Fazayeli, 2011, Bioinform..

ALeS: adaptive-length spaced-seed design

Lucian Ilie, Arnab Mallik, Arnab Kumar Mallik, 2020, Bioinform..

SpEED: fast computation of sensitive spaced seeds

Lucian Ilie, Silvana Ilie, Anahita Mansouri Bigvand, 2011, Bioinform..

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

Lucian Ilie, Nilesh Khiste, Lucian Ilie, 2015, Bioinform..

Reducing the Size of NFAs by Using Equivalences and Preorders

Roberto Solis-Oba, Lucian Ilie, Sheng Yu, 2005, CPM.

Predicting Protein-Protein Interactions Using SPRINT

Lucian Ilie, Yiwei Li, Lucian Ilie, 2020, Protein-Protein Interaction Networks.

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

Lucian Ilie, Yiwei Li, G Brian Golding, 2020, Bioinformatics.

Analysis of Maximal Repetitions in Strings

Lucian Ilie, Maxime Crochemore, M. Crochemore, 2007, MFCS.

A simple proof that a word of length n has at most 2n distinct squares

Lucian Ilie, Lucian Ilie, 2005, J. Comb. Theory A.

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

Lucian Ilie, Victor Mitrana, V. Mitrana, 2003, Grammars and Automata for String Processing.

Periods and Binary Words

Tero Harju, Lucian Ilie, Vesa Halava, 2000, J. Comb. Theory A.

Explainable-AI in Automated Medical Report Generation Using Chest X-ray Images

Roberto Solis-Oba, S. Ahmed, Lucian Ilie, 2022, Applied Sciences.

A generalization of repetition threshold

Jeffrey Shallit, Lucian Ilie, Pascal Ochem, 2003, Theoretical Computer Science.

Forbidden subsequences and permutations sortable on two parallel stacks

Tero Harju, Lucian Ilie, T. Harju, 2001, Where Mathematics, Computer Science, Linguistics and Biology Meet.

SAGE2: parallel human genome assembly

Ehsan Haghshenas, Lucian Ilie, Michael Molnar, 2018, Bioinform..

LASER: Large genome ASsembly EvaluatoR

Lucian Ilie, Nilesh Khiste, 2015, BMC Research Notes.

SAGE: String-overlap Assembly of GEnomes

Roberto Solis-Oba, Lucian Ilie, Michael Molnar, 2014, BMC Bioinformatics.

SAGE2: parallel human genome assembly

Lucian Ilie, Michael Molnar, Ehsan Haghshenas, 2018, Bioinform..

LASER: Large genome ASsembly EvaluatoR

Lucian Ilie, Nilesh Khiste, 2015, BMC Research Notes.

HISEA: HIerarchical SEed Aligner for PacBio data

Lucian Ilie, Nilesh Khiste, 2017, BMC Bioinformatics.

The Shortest Common Superstring Problem and Viral Genome Compression

Lucian Ilie, Cristian Popescu, Lucian Ilie, 2006, Fundam. Informaticae.

On Well Quasi Orders of Free Monoids

Lucian Ilie, Arto Salomaa, A. Salomaa, 1998, Theor. Comput. Sci..

On Quasi Orders of Words and the Confluence Property

Tero Harju, Lucian Ilie, T. Harju, 1998, Theor. Comput. Sci..

Generalized Factors of Words

Lucian Ilie, Lucian Ilie, 1998, Fundam. Informaticae.

Uniformly Scattered Factors

Ion Petre, Lucian Ilie, Grzegorz Rozenberg, 2000, Finite Versus Infinite.

Seq-InSite: sequence supersedes structure for protein interaction site prediction

Lucian Ilie, Seyedmohsen Hosseini, G. Golding, 2023, bioRxiv.

Repetitions in strings: Algorithms and combinatorics

Wojciech Rytter, Lucian Ilie, Maxime Crochemore, 2009, Theor. Comput. Sci..

Maximal repetitions in strings

Lucian Ilie, Maxime Crochemore, M. Crochemore, 2008, J. Comput. Syst. Sci..

A note on the number of squares in a word

Lucian Ilie, Lucian Ilie, 2007, Theor. Comput. Sci..

SHRiMP2: Sensitive yet Practical Short Read Mapping

Misko Dzamba, M. Brudno, Lucian Ilie, 2011, Bioinform..

Two-variable word equations

Wojciech Plandowski, Lucian Ilie, Lucian Ilie, 2000, RAIRO Theor. Informatics Appl..

Reducing NFAs by invariant equivalences

Lucian Ilie, Sheng Yu, Sheng Yu, 2003, Theor. Comput. Sci..

Algorithms for Computing Small NFAs

Lucian Ilie, Sheng Yu, Sheng Yu, 2002, MFCS.

Constructing NFA s by Optimal Use of Positions in Regular Expressions

Lucian Ilie, Sheng Yu, Sheng Yu, 2002, CPM.

On NFA Reductions

Lucian Ilie, Gonzalo Navarro, Sheng Yu, 2004, Theory Is Forever.

HISEA: HIerarchical SEed Aligner for PacBio data

Lucian Ilie, Nilesh Khiste, Lucian Ilie, 2017, BMC Bioinformatics.

Some Recent Results on Contextual Languages

Lucian Ilie, Lucian Ilie, 1997, Bull. EATCS.

2-Testability and Relabelings Produce Everything

Lucian Ilie, Arto Salomaa, A. Salomaa, 1998, J. Comput. Syst. Sci..

Multiple spaced seeds for homology search

Lucian Ilie, Silvana Ilie, S. Ilie, 2007, Bioinform..

On the expressiveness of subset-sum representations

Lucian Ilie, Arto Salomaa, A. Salomaa, 2000, Acta Informatica.

On a Geometric Problem of Zigzags

T. Harju, Lucian Ilie, Vesa Halava, 1997, Inf. Process. Lett..

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

Lucian Ilie, Victor Mitrana, V. Mitrana, 1996, German Conference on Bioinformatics.

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

Lucian Ilie, Sorin Constantinescu, Lucian Ilie, 2005, Theor. Comput. Sci..

Repetitions in strings: Algorithms and combinatorics

M. Crochemore, W. Rytter, Lucian Ilie, 2009, Theor. Comput. Sci..

A Simple Algorithm for Computing the Lempel Ziv Factorization

Lucian Ilie, Maxime Crochemore, William F. Smyth, 2008, Data Compression Conference (dcc 2008).

Understanding maximal repetitions in strings

Lucian Ilie, Maxime Crochemore, M. Crochemore, 2008, STACS.

Viral Genome Compression

Lucian Ilie, Cristian Popescu, Kathleen A. Hill, 2006, DNA.

Maximal repetitions in strings ✩

Lucian Ilie, Maxime Crochemore, 2008 .