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An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis.
Xiang G, Keller CA, Heuston E, Giardine BM, An L, Wixom AQ, Miller A, Cockburn A, Sauria MEG, Weaver K, Lichtenberg J, Göttgens B, Li Q, Bodine D, Mahony S, Taylor J, Blobel GA, Weiss MJ, Cheng Y, Yue F, Hughes J, Higgs DR, Zhang Y, Hardison RC. Xiang G, et al. Among authors: li q. Genome Res. 2020 Mar;30(3):472-484. doi: 10.1101/gr.255760.119. Epub 2020 Mar 4. Genome Res. 2020. PMID: 32132109 Free PMC article.
Galaxy tools to study genome diversity.
Bedoya-Reina OC, Ratan A, Burhans R, Kim HL, Giardine B, Riemer C, Li Q, Olson TL, Loughran TP Jr, Vonholdt BM, Perry GH, Schuster SC, Miller W. Bedoya-Reina OC, et al. Among authors: li q. Gigascience. 2013 Dec 30;2(1):17. doi: 10.1186/2047-217X-2-17. Gigascience. 2013. PMID: 24377391 Free PMC article.
Measuring the reproducibility and quality of Hi-C data.
Yardımcı GG, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, Taylor J, Yue F, Dekker J, Noble WS. Yardımcı GG, et al. Among authors: li q. Genome Biol. 2019 Mar 19;20(1):57. doi: 10.1186/s13059-019-1658-7. Genome Biol. 2019. PMID: 30890172 Free PMC article.
Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells.
Hardison RC, Zhang Y, Keller CA, Xiang G, Heuston EF, An L, Lichtenberg J, Giardine BM, Bodine D, Mahony S, Li Q, Yue F, Weiss MJ, Blobel GA, Taylor J, Hughes J, Higgs DR, Göttgens B. Hardison RC, et al. Among authors: li q. IUBMB Life. 2020 Jan;72(1):27-38. doi: 10.1002/iub.2195. Epub 2019 Nov 25. IUBMB Life. 2020. PMID: 31769130 Free PMC article. Review.
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes.
Xiang G, He X, Giardine BM, Isaac KJ, Taylor DJ, McCoy RC, Jansen C, Keller CA, Wixom AQ, Cockburn A, Miller A, Qi Q, He Y, Li Y, Lichtenberg J, Heuston EF, Anderson SM, Luan J, Vermunt MW, Yue F, Sauria MEG, Schatz MC, Taylor J, Gottgens B, Hughes JR, Higgs DR, Weiss MJ, Cheng Y, Blobel GA, Bodine DM, Zhang Y, Li Q, Mahony S, Hardison RC. Xiang G, et al. Among authors: li y, li q. bioRxiv [Preprint]. 2024 May 17:2023.04.02.535219. doi: 10.1101/2023.04.02.535219. bioRxiv. 2024. Update in: Genome Res. 2024 Aug 20;34(7):1089-1105. doi: 10.1101/gr.277950.123 PMID: 37066352 Free PMC article. Updated. Preprint.
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