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Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways.
Yin L, Zander M, Huang SC, Xie M, Song L, Saldierna Guzmán JP, Hann E, Shanbhag BK, Ng S, Jain S, Janssen BJ, Clark NM, Walley JW, Beddoe T, Bar-Joseph Z, Lewsey MG, Ecker JR. Yin L, et al. bioRxiv [Preprint]. 2023 Mar 9:2023.03.07.531630. doi: 10.1101/2023.03.07.531630. bioRxiv. 2023. PMID: 36945593 Free PMC article. Preprint.
Clustering short time series gene expression data.
Ernst J, Nau GJ, Bar-Joseph Z. Ernst J, et al. Bioinformatics. 2005 Jun;21 Suppl 1:i159-68. doi: 10.1093/bioinformatics/bti1022. Bioinformatics. 2005. PMID: 15961453
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.
Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP. Peña-Castillo L, et al. Genome Biol. 2008;9 Suppl 1(Suppl 1):S2. doi: 10.1186/gb-2008-9-s1-s2. Epub 2008 Jun 27. Genome Biol. 2008. PMID: 18613946 Free PMC article.
Validation of a 52-gene risk profile for outcome prediction in patients with idiopathic pulmonary fibrosis: an international, multicentre, cohort study.
Herazo-Maya JD, Sun J, Molyneaux PL, Li Q, Villalba JA, Tzouvelekis A, Lynn H, Juan-Guardela BM, Risquez C, Osorio JC, Yan X, Michel G, Aurelien N, Lindell KO, Klesen MJ, Moffatt MF, Cookson WO, Zhang Y, Garcia JGN, Noth I, Prasse A, Bar-Joseph Z, Gibson KF, Zhao H, Herzog EL, Rosas IO, Maher TM, Kaminski N. Herazo-Maya JD, et al. Lancet Respir Med. 2017 Nov;5(11):857-868. doi: 10.1016/S2213-2600(17)30349-1. Epub 2017 Sep 21. Lancet Respir Med. 2017. PMID: 28942086 Free PMC article.
De novo ChIP-seq analysis.
He X, Cicek AE, Wang Y, Schulz MH, Le HS, Bar-Joseph Z. He X, et al. Genome Biol. 2015 Sep 23;16(1):205. doi: 10.1186/s13059-015-0756-4. Genome Biol. 2015. PMID: 26400819 Free PMC article.
151 results