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Page 1
InterPro: the protein sequence classification resource in 2025.
Blum M, Andreeva A, Florentino LC, Chuguransky SR, Grego T, Hobbs E, Pinto BL, Orr A, Paysan-Lafosse T, Ponamareva I, Salazar GA, Bordin N, Bork P, Bridge A, Colwell L, Gough J, Haft DH, Letunic I, Llinares-López F, Marchler-Bauer A, Meng-Papaxanthos L, Mi H, Natale DA, Orengo CA, Pandurangan AP, Piovesan D, Rivoire C, Sigrist CJA, Thanki N, Thibaud-Nissen F, Thomas PD, Tosatto SCE, Wu CH, Bateman A. Blum M, et al. Among authors: llinares lopez f. Nucleic Acids Res. 2025 Jan 6;53(D1):D444-D456. doi: 10.1093/nar/gkae1082. Nucleic Acids Res. 2025. PMID: 39565202 Free PMC article.
The Pfam protein families database: embracing AI/ML.
Paysan-Lafosse T, Andreeva A, Blum M, Chuguransky SR, Grego T, Pinto BL, Salazar GA, Bileschi ML, Llinares-López F, Meng-Papaxanthos L, Colwell LJ, Grishin NV, Schaeffer RD, Clementel D, Tosatto SCE, Sonnhammer E, Wood V, Bateman A. Paysan-Lafosse T, et al. Among authors: llinares lopez f. Nucleic Acids Res. 2025 Jan 6;53(D1):D523-D534. doi: 10.1093/nar/gkae997. Nucleic Acids Res. 2025. PMID: 39540428 Free PMC article.
Deep embedding and alignment of protein sequences.
Llinares-López F, Berthet Q, Blondel M, Teboul O, Vert JP. Llinares-López F, et al. Nat Methods. 2023 Jan;20(1):104-111. doi: 10.1038/s41592-022-01700-2. Epub 2022 Dec 15. Nat Methods. 2023. PMID: 36522501
DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer.
Baid G, Cook DE, Shafin K, Yun T, Llinares-López F, Berthet Q, Belyaeva A, Töpfer A, Wenger AM, Rowell WJ, Yang H, Kolesnikov A, Ammar W, Vert JP, Vaswani A, McLean CY, Nattestad M, Chang PC, Carroll A. Baid G, et al. Among authors: llinares lopez f. Nat Biotechnol. 2023 Feb;41(2):232-238. doi: 10.1038/s41587-022-01435-7. Epub 2022 Sep 1. Nat Biotechnol. 2023. PMID: 36050551
graphkernels: R and Python packages for graph comparison.
Sugiyama M, Ghisu ME, Llinares-López F, Borgwardt K. Sugiyama M, et al. Among authors: llinares lopez f. Bioinformatics. 2018 Feb 1;34(3):530-532. doi: 10.1093/bioinformatics/btx602. Bioinformatics. 2018. PMID: 29028902 Free PMC article.
Genome-wide genetic heterogeneity discovery with categorical covariates.
Llinares-López F, Papaxanthos L, Bodenham D, Roqueiro D; COPDGene Investigators; Borgwardt K. Llinares-López F, et al. Bioinformatics. 2017 Jun 15;33(12):1820-1828. doi: 10.1093/bioinformatics/btx071. Bioinformatics. 2017. PMID: 28200033 Free PMC article.