Ilie, Lucian

SHRiMP2: Sensitive yet Practical Short Read Mapping

David, M., Dzamba, M., Lister, D., Ilie, L., & Brudno, M. (2011) · Bioinformatics

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

Cited by 348

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

Hosseini, S., Golding, G. B., & Ilie, L. (2024) · Bioinformatics

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 26

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

Hosseini, S., Golding, G. B., & Ilie, L. (2023) · Bioinformatics

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 26

Scoring alignments by embedding vector similarity

Ashrafzadeh, S., Golding, G. B., Ilie, S., & Ilie, L. (2023) · Briefings in Bioinformatics

Machine Learning in BioinformaticsGenomics and Phylogenetic Studies

Cited by 8

Protein embeddings and local alignments

Malec, J., Golding, G. B., & Ilie, L. (2026) · Computational and Structural Biotechnology Journal

Genomics and Phylogenetic StudiesMachine Learning in Bioinformatics

Cited by 5

Protein Embeddings and Local Alignments

Malec, J., Golding, G. B., & Ilie, L. (2025) · Computational and Structural Biotechnology Journal

Genomics and Phylogenetic StudiesMachine Learning in Bioinformatics

Cited by 5

Ankh-score produces better sequence alignments than AlphaFold3

Malec, J., Rusen, K., Golding, G. B., & Ilie, L. (2025) · Proteins Structure Function and Bioinformatics

Genomics and Phylogenetic StudiesMachine Learning in Bioinformatics

Cited by 1

Ankh‐Score Produces Better Sequence Alignments Than AlphaFold3

Malec, J., Rusen, K., Golding, G. B., & Ilie, L. (2026) · Proteins: Structure, Function, and Bioinformatics

Genomics and Phylogenetic StudiesMachine Learning in Bioinformatics

Cited by 1