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Page 1
An encyclopedia of enhancer-gene regulatory interactions in the human genome.
Gschwind AR, Mualim KS, Karbalayghareh A, Sheth MU, Dey KK, Jagoda E, Nurtdinov RN, Xi W, Tan AS, Jones H, Ma XR, Yao D, Nasser J, Avsec Ž, James BT, Shamim MS, Durand NC, Rao SSP, Mahajan R, Doughty BR, Andreeva K, Ulirsch JC, Fan K, Perez EM, Nguyen TC, Kelley DR, Finucane HK, Moore JE, Weng Z, Kellis M, Bassik MC, Price AL, Beer MA, Guigó R, Stamatoyannopoulos JA, Lieberman Aiden E, Greenleaf WJ, Leslie CS, Steinmetz LM, Kundaje A, Engreitz JM. Gschwind AR, et al. Among authors: karbalayghareh a. bioRxiv [Preprint]. 2023 Nov 13:2023.11.09.563812. doi: 10.1101/2023.11.09.563812. bioRxiv. 2023. PMID: 38014075 Free PMC article. Preprint.
ChromaFold predicts the 3D contact map from single-cell chromatin accessibility.
Gao VR, Yang R, Das A, Luo R, Luo H, McNally DR, Karagiannidis I, Rivas MA, Wang ZM, Barisic D, Karbalayghareh A, Wong W, Zhan YA, Chin CR, Noble W, Bilmes JA, Apostolou E, Kharas MG, Béguelin W, Viny AD, Huangfu D, Rudensky AY, Melnick AM, Leslie CS. Gao VR, et al. Among authors: karbalayghareh a. bioRxiv [Preprint]. 2023 Jul 28:2023.07.27.550836. doi: 10.1101/2023.07.27.550836. bioRxiv. 2023. PMID: 37546906 Free PMC article. Preprint.
Optimal Bayesian Transfer Learning for Count Data.
Karbalayghareh A, Qian X, Dougherty ER. Karbalayghareh A, et al. IEEE/ACM Trans Comput Biol Bioinform. 2021 Mar-Apr;18(2):644-655. doi: 10.1109/TCBB.2019.2920981. Epub 2021 Apr 8. IEEE/ACM Trans Comput Biol Bioinform. 2021. PMID: 31180899
Classification of State Trajectories in Gene Regulatory Networks.
Karbalayghareh A, Braga-Neto U, Hua J, Dougherty ER. Karbalayghareh A, et al. IEEE/ACM Trans Comput Biol Bioinform. 2018 Jan-Feb;15(1):68-82. doi: 10.1109/TCBB.2016.2616470. Epub 2016 Oct 11. IEEE/ACM Trans Comput Biol Bioinform. 2018. PMID: 27740496
Epiphany: predicting Hi-C contact maps from 1D epigenomic signals.
Yang R, Das A, Gao VR, Karbalayghareh A, Noble WS, Bilmes JA, Leslie CS. Yang R, et al. Among authors: karbalayghareh a. Genome Biol. 2023 Jun 6;24(1):134. doi: 10.1186/s13059-023-02934-9. Genome Biol. 2023. PMID: 37280678 Free PMC article.