Home Page  of  LUCIAN ILIE

LUCIAN ILIE Associate Professor Department of Computer Science University of Western Ontario Middlesex College 368 London, Ontario, N6A 5B7 Canada tel:   519  661 2111  x 86848 fax:  519  661 3515 e-mail:  ilie csd.uwo.ca Information for potential students!!

Curriculum Vitae (includes complete publication list; see also MathSciNet, DBLP)

Research (includes some of my papers)

My research interest is in developing computational methods for the analysis of the high-throughput sequencing data. The next generation sequencing technologies, Illumina's Genome Analyzer, AB's SOLiD, and Roche's 454, produce many GB of data in a single run, with many applications, including whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations, chromosomal rearrangements, etc. The impact of these technologies for everyday life is very far reaching and yet to be understood.
I am currently interested in developing algorithms and software for genome assembly, read correction, read mapping, as well as alignment of biological networks. My work involves tools from algorithms, stringology, combinatorics, graph theory, probability theory and statistics. I am as well interested in fundamental research in stringology, both in algorithms and combinatorics of strings.

Software

• HiTEC: Accurate Error Correction in High-throughput Sequencing Data
• The most performant software for error correction in high-throughput sequencing data
• L. Ilie, F. Fazayeli, S. Ilie. HiTEC: accurate error correction in high-throughput sequencing data, Bioinformatics 27(3) (2011) 295 -- 302
• SpEED: fast computation of sensitive spaced seeds
  • L. Ilie, S. Ilie, A. Mansouri Bigvand, SpEED: fast computation of sensitive spaced seeds, Bioinformatics, to appear.
  • L. Ilie, S. Ilie, Multiple spaced seeds for homology search, Bioinformatics 23(22) (2007) 2969 -- 2977.
• SHRiMP: Accurate Mapping of Short Color-space Reads (SHRiMP2 uses seeds computed by SpEED)
• M. David, M. Dzamba, D. Lister, L. Ilie, M. Brudno, SHRiMP2: Sensitive yet practical short read mapping, Bioinformatics 27(7) (2011) 1011 -- 1012.

Research Group

Teaching

• CS4413a Cryptography and Security
• CS3380/4490/4460z Undergraduate/Bioinformatics Thesis
• CS9601 Biological Sequence Analysis