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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: gresham d. 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.
mRNA condensation fluidizes the cytoplasm.
Xie Y, Liu T, Gresham D, Holt LJ. Xie Y, et al. Among authors: gresham d. bioRxiv [Preprint]. 2023 Jul 15:2023.05.30.542963. doi: 10.1101/2023.05.30.542963. bioRxiv. 2023. PMID: 37398029 Free PMC article. Preprint.
Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data.
Roder AE, Johnson K, Knoll M, Khalfan M, Wang B, Schultz-Cherry S, Banakis S, Kreitman A, Mederos C, Youn JH, Mercado R, Wang W, Ruchnewitz D, Samanovic MI, Mulligan MJ, Lassig M, Åuksza M, Das S, Gresham D, Ghedin E. Roder AE, et al. Among authors: gresham d. bioRxiv [Preprint]. 2022 Aug 16:2021.05.05.442873. doi: 10.1101/2021.05.05.442873. bioRxiv. 2022. Update in: mBio. 2023 Aug 31;14(4):e0104623. doi: 10.1128/mbio.01046-23. PMID: 36656775 Free PMC article. Updated. Preprint.
Influenza A virus reassortment is strain dependent.
Taylor KY, Agu I, José I, Mäntynen S, Campbell AJ, Mattson C, Chou TW, Zhou B, Gresham D, Ghedin E, Díaz Muñoz SL. Taylor KY, et al. Among authors: gresham d. PLoS Pathog. 2023 Mar 1;19(3):e1011155. doi: 10.1371/journal.ppat.1011155. eCollection 2023 Mar. PLoS Pathog. 2023. PMID: 36857394 Free PMC article.
95 results