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Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference.
Genome Biol. 2024 Jan 18;25(1):24. doi: 10.1186/s13059-023-03134-1.
Genome Biol. 2024.
PMID: 38238840
Free PMC article.
Structure primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference.
Tjärnberg A, Beheler-Amass M, Jackson CA, Christiaen LA, Gresham D, Bonneau R.
Tjärnberg A, et al. Among authors: christiaen la.
bioRxiv [Preprint]. 2023 Feb 3:2023.02.02.526909. doi: 10.1101/2023.02.02.526909.
bioRxiv. 2023.
PMID: 36778259
Free PMC article.
Updated.
Preprint.
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Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data.
Tjärnberg A, Mahmood O, Jackson CA, Saldi GA, Cho K, Christiaen LA, Bonneau RA.
Tjärnberg A, et al. Among authors: christiaen la.
PLoS Comput Biol. 2021 Jan 7;17(1):e1008569. doi: 10.1371/journal.pcbi.1008569. eCollection 2021 Jan.
PLoS Comput Biol. 2021.
PMID: 33411784
Free PMC article.
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Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes.
Burguera D, Marquez Y, Racioppi C, Permanyer J, Torres-Méndez A, Esposito R, Albuixech-Crespo B, Fanlo L, D'Agostino Y, Gohr A, Navas-Perez E, Riesgo A, Cuomo C, Benvenuto G, Christiaen LA, Martí E, D'Aniello S, Spagnuolo A, Ristoratore F, Arnone MI, Garcia-Fernàndez J, Irimia M.
Burguera D, et al. Among authors: christiaen la.
Nat Commun. 2017 Nov 27;8(1):1799. doi: 10.1038/s41467-017-01961-y.
Nat Commun. 2017.
PMID: 29180615
Free PMC article.
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Fibroblast growth factor signalling controls nervous system patterning and pigment cell formation in Ciona intestinalis.
Racioppi C, Kamal AK, Razy-Krajka F, Gambardella G, Zanetti L, di Bernardo D, Sanges R, Christiaen LA, Ristoratore F.
Racioppi C, et al. Among authors: christiaen la.
Nat Commun. 2014 Sep 5;5:4830. doi: 10.1038/ncomms5830.
Nat Commun. 2014.
PMID: 25189217
Free PMC article.
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