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Transcriptional regulatory model of fibrosis progression in the human lung.
McDonough JE, Ahangari F, Li Q, Jain S, Verleden SE, Herazo-Maya J, Vukmirovic M, DeIuliis G, Tzouvelekis A, Tanabe N, Chu F, Yan X, Verschakelen J, Homer RJ, Manatakis DV, Zhang J, Ding J, Maes K, De Sadeleer L, Vos R, Neyrinck A, Benos PV, Bar-Joseph Z, Tantin D, Hogg JC, Vanaudenaerde BM, Wuyts WA, Kaminski N. McDonough JE, et al. JCI Insight. 2019 Nov 14;4(22):e131597. doi: 10.1172/jci.insight.131597. JCI Insight. 2019. PMID: 31600171 Free PMC article.
CodonBERT large language model for mRNA vaccines.
Li S, Moayedpour S, Li R, Bailey M, Riahi S, Kogler-Anele L, Miladi M, Miner J, Pertuy F, Zheng D, Wang J, Balsubramani A, Tran K, Zacharia M, Wu M, Gu X, Clinton R, Asquith C, Skaleski J, Boeglin L, Chivukula S, Dias A, Strugnell T, Montoya FU, Agarwal V, Bar-Joseph Z, Jager S. Li S, et al. Among authors: bar joseph z. Genome Res. 2024 Aug 20;34(7):1027-1035. doi: 10.1101/gr.278870.123. Genome Res. 2024. PMID: 38951026 Free PMC article.
Combined analysis reveals a core set of cycling genes.
Lu Y, Mahony S, Benos PV, Rosenfeld R, Simon I, Breeden LL, Bar-Joseph Z. Lu Y, et al. Genome Biol. 2007;8(7):R146. doi: 10.1186/gb-2007-8-7-r146. Genome Biol. 2007. PMID: 17650318 Free PMC article.
Reconstructing dynamic microRNA-regulated interaction networks.
Schulz MH, Pandit KV, Lino Cardenas CL, Ambalavanan N, Kaminski N, Bar-Joseph Z. Schulz MH, et al. Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15686-91. doi: 10.1073/pnas.1303236110. Epub 2013 Aug 28. Proc Natl Acad Sci U S A. 2013. PMID: 23986498 Free PMC article.
162 results