Bioinformatics software -- the most recent version of the source code is available on GitHub: https://github.com/lucian-ilie
Protein-protein interaction prediction
Sequence similarity search
- ALeS: Adaptive-length spaced-seed design
- A, Mallik, L, Ilie, ALeS: Adaptive-length spaced-seed design,
Bioinformatics, Bioinformatics (2020) btaa945.
- E-MEM: Efficient Computation of Maximal Exact Maches
- N. Khiste, L. Ilie, E-MEM: Efficient computation of Maximal Exact Matches for very large genomes, Bioinformatics 31(4) (2015) 509 -- 514.
- SpEED: Spaced SEEDs
- Fast computation of highly sensitive spaced seeds for effective local similarity detection
- L. Ilie, S. Ilie, and A. Mansouri Bigvand, SpEED: fast computation of sensitive spaced seeds, Bioinformatics 27(17) (2011) 2433 -- 2434.
- L. Ilie and S. Ilie, Multiple spaced seeds for homology search, Bioinformatics 23(22) (2007) 2969 -- 2977.
Error correction in DNA sequencing data
- Correcting Illumina Data
- New methods and tools for thorough evaluation of error correcting performance
- M. Molnar, L. Ilie, Correcting Illumina data, Briefings in Bioinformatics (2014), bbu029.
- RACER: Rapid and Accurate Correction of Errors in Reads
- Accurate and efficient correction of errors in NGS data
- L. Ilie, M. Molnar, RACER: Rapid and Accurate Correction of Errors in Reads, Bioinformatics 29 (2013) 2490 -- 2493.
- HiTEC: High-Throughput Error Correction
- Accurate error correction in NGS data
- L. Ilie, F. Fazayeli, and S. Ilie, HiTEC: accurate error correction in high-throughput sequencing data, Bioinformatics 27(3) (2011) 295 -- 302.
- SAGE: String Graph Assembly of GEnomes
- A genome assembler that is based on the overlap graph and that works well on short and medium-size genomes.
- L. Ilie, B. Haider, M. Molnar, R. Solis-Oba, SAGE: String-graph Assembly of GEnomes, BMC Bioinformatics 15 (2014) 302.
- LASER: Large genome ASsembly EvaluatoR
- A tool for genome assembly evaluation based on E-MEM and Quast; it produces the same evaluation as Quast but is 5.6 times faster and use half the memory.
- N. Khiste, L. Ilie, LASER: Large genome ASsembly EvaluatoR, BMC Research Notes 8 (2015) 709.
- SAGE2: String Graph Assembly of GEnomes 2
- An improved parallel algorithm and implementation of SAGE that works well on Illumina data for human genomes.
- M. Molnar, E. Haghshenas, L. Ilie, SAGE2: Parallel Human Genome Assembly, Bioinformatics (2017) btx648.
- HISEA: HIerarchical SEed Aligner
- A read overlapper for PacBio data that has higher sensitivity and precision than the state-of-the-art. It produces the best PacBio assemblies in the Canu assembly pipeline.
- N. Khiste, L. Ilie, HISEA: HIerarchical SEed Aligner for PacBio data, BMC Bioinformatics (2017), to appear.
DNA Oligonucleotide design
Short read mapping
- SHRiMP: Short Read Mapping Program
- Accurate mapping of short color-space reads
- SHRiMP2 uses seeds computed by SpEED
- M. David, M. Dzamba, D. Lister, L. Ilie, and M. Brudno, SHRiMP2: Sensitive yet practical short read mapping, Bioinformatics 27(7) (2011) 1011 -- 1012.