Selected papers (feel free to ask for copies)

Bioinformatics

• S. Ashrafzadeh, G.B. Golding, S. Ilie, L. Ilie, Scoring alignments by embedding vector similarity, Briefings in Bioinformatics, 2024, to appear.
• S. Hosseini, G.B. Golding, L. Ilie, Seq-InSite: sequence supersedes structure for protein inter- action site prediction, Bioinformatics 24(1) (2024) btad738.
• S. Hosseini, L. Ilie, PITHIA: protein interaction site prediction using multiple sequence alignments and attention, International Journal of Molecular Sciences 23(21) (2022) 12814.
• A, Mallik, L, Ilie, ALeS: Adaptive-length spaced-seed design, Bioinformatics 37(9) (2021) 1206 -- 1210.
• Y. Li, G.B. Golding, L. Ilie, DELPHI: accurate deep ensemble model for protein interaction sites prediction, Bioinformatics 37(7) (2021) 896 -- 904.
• Y. Li, L. Ilie, Predicting Protein–Protein Interactions Using SPRINT, Protein-Protein Interaction Networks, Humana, New York, NY 2020 1-11
• M. Molnar, E. Haghshenas, L. Ilie, SAGE2: Parallel Human Genome Assembly, Bioinformatics 34(4) (2018) 678 -- 680.
• N. Khiste, L. Ilie, HISEA: HIerarchical SEed Aligner for PacBio data, BMC Bioinformatics 18(1) (2017) 564.
• Y. Li, L. Ilie, SPRINT: Ultrafast protein-protein interaction prediction of the entire human interactome, BMC Bioinformatics 18 (2017) 485.
• N. Khiste, L. Ilie, LASER: Large genome ASsembly EvaluatoR, BMC Research Notes 8 (2015) 709.
• M. Molnar, L. Ilie, Correcting Illumina data, Briefings in Bioinformatics 16(4) (2015) 588 – 599.
• N. Khiste, L. Ilie, E-MEM: Efficient computation of Maximal Exact Matches for very large genomes, Bioinformatics 31(4) (2015) 509 -- 514.
• L. Ilie, B. Haider, M. Molnar, R. Solis-Oba, SAGE: String-graph Assembly of GEnomes, BMC Bioinformatics 15 (2014) 302.
• L. Ilie, H. Mohamadi, G.B. Golding, W.F. Smyth, BOND: Basic OligoNucleotide Design, BMC Bioinformatics 14 (2013) 69.
• L. Ilie, M. Molnar, RACER: Rapid and Accurate Correction of Errors in Reads, Bioinformatics 29 (2013) 2490 -- 2493.
• L. Ilie, S. Ilie, and A. Mansouri Bigvand, SpEED: fast computation of sensitive spaced seeds, Bioinformatics 27(17) (2011) 2433 -- 2434.
• L. Ilie, S. Ilie, S. Khoshraftar, and A. Mansouri-Bigvand, Seeds for effective oligonucleotide design, BMC Genomics 12 (2011) 280.
• M. David, M. Dzamba, D. Lister, L. Ilie, and M. Brudno, SHRiMP2: Sensitive yet practical short read mapping, Bioinformatics 27(7) (2011) 1011 -- 1012.
• L. Ilie, F. Fazayeli, and S. Ilie, HiTEC: accurate error correction in high-throughput sequencing data, Bioinformatics 27(3) (2011) 295 -- 302.
• L. Ilie and S. Ilie, Fast computation of neighbor seeds, Bioinformatics 25(6) (2009) 822 -- 823.
• L. Ilie and S. Ilie, Multiple spaced seeds for homology search, Bioinformatics 23(22) (2007) 2969 -- 2977.
• L. Ilie and S. Ilie, Fast computation of multiple spaced seeds for homology search, in: R. Giancarlo, S. Hannenhalli, eds., Proc. of the 7th Workshop on Algorithms in Bioinformatics (WABI'07) (Philadelphia, 2007), Lecture Notes in Bioinformatics 4645, Springer, Berlin, 2007, 346 -- 358.

String algorithms

• M. Crochemore, L. Ilie, C. Iliopoulos, M. Kubica, W. Rytter, and T. Walen, Computing the Longest Previous Factor, European Journal of Combinatorics 34(1) (2013) 15 -- 26.
• A. Al-Hafeedh, M. Crochemore, L. Ilie, J. Kopylov, W.F. Smyth, G. Tischler, and M. Yusufu, A comparison of Lempel-Ziv LZ77 factorization algorithms, ACM Computing Surveys 45(1) (2012) 5.
• L. Ilie, G. Navarro, and L. Tinta, The Longest Common Extension problem revisited and an application to approximate string searching, Journal of Discrete Algorithms 8(4) (2010) 418 -- 428.
• L. Ilie and W.F. Smyth, Minimum unique substrings and maximal repeats, Fundamenta Informaticae 110 (1-4) (2011) 183 -- 195.
• M. Crochemore, L. Ilie, and L. Tinta, The "runs" conjecture, Theoretical Computer Science 412(27) (2011) 2931 -- 2941.
• M. Crochemore, L. Ilie, and W. Rytter, Repetitions in strings: algorithms and combinatorics, Theoretical Computer Science 410(50) (2009) 5227 -- 5235.
• L. Ilie and L. Tinta, Practical algorithms for the longest common extension problem, Proc. of the 16th International Symposium on String Processing and Information Retrieval (SPIRE'09), Lecture Notes in Computer Science 5721, Springer, Heidelberg, 2009, 302 -- 309.
• M. Crochemore, L. Ilie, C. Iliopoulos, M. Kubica, W. Rytter, and T. Walen, LPF computation revisited, Proc. of 20th IWOCA, Lecture Notes in Computer Science 5874, Springer, Heidelberg, 2009, 158--169.
• L. Ilie, G. Navarro, and L. Tinta, The Longest Common Extension problem revisited and an application to approximate string searching, Journal of Discrete Algorithms 8(4) (2010) 418 -- 428.
• M. Crochemore, L. Ilie, and W. F. Smyth, A simple algorithm for computing the Lempel--Ziv factorization, Proc. of 17th Data Compression Conference (DCC'08) (Snowbird, Utah, USA), IEEE Computer Society, Los Alamitos, CA, 2008, 482 -- 488.
  
• M. Crochemore and L. Ilie, Computing Longest Previous Factor in linear time and applications, Information Processing Letters 106 (2008) 75 –- 80.
• M. Crochemore, L. Ilie, and L. Tinta, Towards a solution to the "runs" conjecture, in: P. Ferragina and G. Landau (eds.), Proc. of the 19th Annual Symposium on Combinatorial Pattern Matching (CPM'08) (Pisa, Italy), Lecture Notes in Computer Science 5029, Springer, Berlin, 2008, 290 -- 302.
• M. Crochemore, L. Ilie, and Emine Seid-Hilmi, The structure of factor oracles, International Journal of Foundations of Computer Science 18(4) (2007) 781 -- 797.
• L. Ilie, R. Solis-Oba, and S. Yu, Reducing NFAs by equivalences and preorders, in: A. Apostolico, M. Crochemore, K. Park, eds., Proc. of 16th Annual Symposium on Combinatorial Pattern Matching (CPM'05) (Jeju island, Korea, 2005), Lecture Notes in Computer Science 3537, Springer, Berlin, 2005, 310 -- 321.
• L. Ilie, G. Navarro, and S. Yu On NFA reductions, in: J. Karhumaki, H. Maurer, G. Paun, G.Rozenberg, eds., Theory is Forever (Salomaa Festschrift), Lecture Notes in Computer Science 3113, Springer-Verlag, Berlin, Heidelberg, 2004, 112 -- 124.
• L. Ilie and S. Yu, Follow automata, Information and Computation 186 (1)) (2003) 1 -- 162.
• L. Ilie and S. Yu, Reducing NFAs by invariant equivalences, Theoretical Computer Science 306(1-3) (2003) 373 -- 390.

String combinatorics

• M. Crochemore and L. Ilie, Maximal repetitions in strings, Journal of Computer and System Sciences 74 (2008) 796 –- 807.
  
• L. Ilie, A note on the number of squares in a word, Theoretical Computer Science 380(3) (2007) 373 -- 376.
• L. Ilie, A simple proof that a word of length n has at most 2n distinct squares, Journal of Combinatorial Theory, Ser. A, 112(1) (2005) 163 -- 164.
• L. Ilie, P. Ochem, and J. Shallit, A generalization of repetition threshold, Theoretical Computer Science, 345(2-3) (2005) 359 -- 369.
• S. Constantinescu and L. Ilie, Generalized Fine and Wilf's theorem for arbitrary number of periods, Theoretical Computer Science 339(1) (2005) 49 -- 60.
• S. Constantinescu and L. Ilie, The Lempel--Ziv complexity of fixed points of morphisms, SIAM Journal on Discrete Mathematics 21(2) (2007) 466 -- 481.
• L. Ilie, S. Yu, and K. Zhang, Word complexity and repetitions in words, International Journal of Foundations of Computer Science, 15(1) (2004) 41 -- 55.
• V. Halava, T. Harju, and L. Ilie, Periods and binary words, Journal of Combinatorial Theory, Ser. A, 89 (2000) 298 -- 308.