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Deep embedding and alignment of protein sequences.
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
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CASMAP: detection of statistically significant combinations of SNPs in association mapping.
Llinares-López F, Papaxanthos L, Roqueiro D, Bodenham D, Borgwardt K.
Llinares-López F, et al.
Bioinformatics. 2019 Aug 1;35(15):2680-2682. doi: 10.1093/bioinformatics/bty1020.
Bioinformatics. 2019.
PMID: 30541062
Free PMC article.
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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.
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Network-assisted analysis of GWAS data identifies a functionally-relevant gene module for childhood-onset asthma.
Liu Y, Brossard M, Sarnowski C, Vaysse A, Moffatt M, Margaritte-Jeannin P, Llinares-López F, Dizier MH, Lathrop M, Cookson W, Bouzigon E, Demenais F.
Liu Y, et al. Among authors: llinares lopez f.
Sci Rep. 2017 Apr 20;7(1):938. doi: 10.1038/s41598-017-01058-y.
Sci Rep. 2017.
PMID: 28428554
Free PMC article.
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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.
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Genome-wide detection of intervals of genetic heterogeneity associated with complex traits.
Llinares-López F, Grimm DG, Bodenham DA, Gieraths U, Sugiyama M, Rowan B, Borgwardt K.
Llinares-López F, et al.
Bioinformatics. 2015 Jun 15;31(12):i240-9. doi: 10.1093/bioinformatics/btv263.
Bioinformatics. 2015.
PMID: 26072488
Free PMC article.
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