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An encyclopedia of enhancer-gene regulatory interactions in the human genome.
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.
Item in Clipboard
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.
Item in Clipboard
Chromatin interaction-aware gene regulatory modeling with graph attention networks.
Karbalayghareh A, Sahin M, Leslie CS.
Karbalayghareh A, et al.
Genome Res. 2022 May;32(5):930-944. doi: 10.1101/gr.275870.121. Epub 2022 Apr 8.
Genome Res. 2022.
PMID: 35396274
Free PMC article.
Item in Clipboard
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
Item in Clipboard
Intrinsically Bayesian robust classifier for single-cell gene expression trajectories in gene regulatory networks.
Karbalayghareh A, Braga-Neto U, Dougherty ER.
Karbalayghareh A, et al.
BMC Syst Biol. 2018 Mar 21;12(Suppl 3):23. doi: 10.1186/s12918-018-0549-y.
BMC Syst Biol. 2018.
PMID: 29589564
Free PMC article.
Item in Clipboard
Classification of Single-Cell Gene Expression Trajectories from Incomplete and Noisy Data.
Karbalayghareh A, Braga-Neto U, Dougherty ER.
Karbalayghareh A, et al.
IEEE/ACM Trans Comput Biol Bioinform. 2019 Jan-Feb;16(1):193-207. doi: 10.1109/TCBB.2017.2763946. Epub 2017 Oct 17.
IEEE/ACM Trans Comput Biol Bioinform. 2019.
PMID: 29053466
Item in Clipboard
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
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