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Enhancer Dynamics and Spatial Organization Drive Anatomically Restricted Cellular States in the Human Spinal Cord.
Kandror EK, Wang A, Carriere M, Peterson A, Liao W, Tjärnberg A, Fung JH, Mahbubani KT, Loper J, Pangburn W, Xu Y, Saeb-Parsy K, Rabadan R, Maniatis T, Rizvi AH. Kandror EK, et al. Among authors: tjarnberg a. bioRxiv [Preprint]. 2025 Jan 11:2025.01.10.632483. doi: 10.1101/2025.01.10.632483. bioRxiv. 2025. PMID: 39829819 Free PMC article. Preprint.
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. bioRxiv [Preprint]. 2023 Feb 3:2023.02.02.526909. doi: 10.1101/2023.02.02.526909. bioRxiv. 2023. Update in: Genome Biol. 2024 Jan 18;25(1):24. doi: 10.1186/s13059-023-03134-1 PMID: 36778259 Free PMC article. Updated. Preprint.
High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0.
Skok Gibbs C, Jackson CA, Saldi GA, Tjärnberg A, Shah A, Watters A, De Veaux N, Tchourine K, Yi R, Hamamsy T, Castro DM, Carriero N, Gorissen BL, Gresham D, Miraldi ER, Bonneau R. Skok Gibbs C, et al. Among authors: tjarnberg a. Bioinformatics. 2022 Apr 28;38(9):2519-2528. doi: 10.1093/bioinformatics/btac117. Bioinformatics. 2022. PMID: 35188184 Free PMC article.
22 results