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Predicting lung aging using scRNA-Seq data.
Song Q, Singh A, McDonough JE, Adams TS, Vos R, De Man R, Myers G, Ceulemans LJ, Vanaudenaerde BM, Wuyts WA, Yan X, Schuppe J, Hagood JS, Kaminski N, Bar-Joseph Z. Song Q, et al. Among authors: bar joseph z. PLoS Comput Biol. 2024 Dec 19;20(12):e1012632. doi: 10.1371/journal.pcbi.1012632. Online ahead of print. PLoS Comput Biol. 2024. PMID: 39700255 Free article.
scDOT: optimal transport for mapping senescent cells in spatial transcriptomics.
Nguyen ND, Rosas L, Khaliullin T, Jiang P, Hasanaj E, Ovando-Ricardez JA, Bueno M, Rahman I, Pryhuber GS, Li D, Ma Q, Finkel T, Königshoff M, Eickelberg O, Rojas M, Mora AL, Lugo-Martinez J, Bar-Joseph Z. Nguyen ND, et al. Among authors: bar joseph z. Genome Biol. 2024 Nov 8;25(1):288. doi: 10.1186/s13059-024-03426-0. Genome Biol. 2024. PMID: 39516853 Free PMC article.
Identifying indications for novel drugs using electronic health records.
Adamek L, Padiasek G, Zhang C, O'Dwyer I, Capit N, Dormont F, Hernandez R, Bar-Joseph Z, Rufino B. Adamek L, et al. Among authors: bar joseph z. Comput Biol Med. 2024 Dec;183:109158. doi: 10.1016/j.compbiomed.2024.109158. Epub 2024 Oct 23. Comput Biol Med. 2024. PMID: 39437603 Free article.
Proxy endpoints - bridging clinical trials and real world data.
Kryukov M, Moriarty KP, Villamea M, O'Dwyer I, Chow O, Dormont F, Hernandez R, Bar-Joseph Z, Rufino B. Kryukov M, et al. Among authors: bar joseph z. J Biomed Inform. 2024 Oct;158:104723. doi: 10.1016/j.jbi.2024.104723. Epub 2024 Sep 17. J Biomed Inform. 2024. PMID: 39299565 Free article.
SpatialOne: end-to-end analysis of visium data at scale.
Kamel M, Sarangi A, Senin P, Villordo S, Sunaal M, Barot H, Wang S, Solbas A, Cano L, Classe M, Bar-Joseph Z, Pla Planas A. Kamel M, et al. Among authors: bar joseph z. Bioinformatics. 2024 Sep 2;40(9):btae509. doi: 10.1093/bioinformatics/btae509. Bioinformatics. 2024. PMID: 39152991 Free PMC article.
Constrained Pseudo-time Ordering for Clinical Transcriptomics Data.
Mathur S, Mattoo H, Bar-Joseph Z. Mathur S, et al. Among authors: bar joseph z. IEEE/ACM Trans Comput Biol Bioinform. 2024 Aug 13;PP. doi: 10.1109/TCBB.2024.3442669. Online ahead of print. IEEE/ACM Trans Comput Biol Bioinform. 2024. PMID: 39137087
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.
182 results