Shaun A. Mahony, PhD - Penn State Cancer Institute
Researcher Profile
Shaun A. Mahony, PhD
Associate Professor, Biochemistry & Molecular Biology
Scientific Program:Mechanisms of Carcinogenesis
Recent Publications
2025
ENCODE Imputation Challenge Participants 2025, 'Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles (Genome Biology, (2023), 24, 1, (79), 10.1186/s13059-023-02915-y)', Genome biology, vol. 26, no. 1, 31. https://doi.org/10.1186/s13059-025-03494-w
2024
Morrissey, A, Shi, J, James, DQ & Mahony, S 2024, 'Accurate allocation of multimapped reads enables regulatory element analysis at repeats', Genome research, vol. 34, no. 6, pp. 937-951. https://doi.org/10.1101/gr.278638.123
Bonnell, VA, Zhang, Y, Brown, AS, Horton, J, Josling, GA, Chiu, TP, Rohs, R, Mahony, S, Gordân, R & Llinás, M 2024, 'DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum', Nucleic acids research, vol. 52, no. 17, pp. 10161-10179. https://doi.org/10.1093/nar/gkae585
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, Göttgens, B, Hughes, JR, Higgs, DR, Weiss, MJ, Cheng, Y, Blobel, GA, Bodine, DM, Zhang, Y, Li, Q, Mahony, S & Hardison, RC 2024, 'Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes', Genome research, vol. 34, no. 7, pp. 1089-1105. https://doi.org/10.1101/gr.277950.123
Yang, J, Yen, K & Mahony, S 2024, SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes. in J Ma (ed.), Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 14758 LNCS, Springer Science and Business Media Deutschland GmbH, pp. 320-323, 28th International Conference on Research in Computational Molecular Biology, RECOMB 2024, Cambridge, United States, 4/29/24. https://doi.org/10.1007/978-1-0716-3989-4_21
Yang, J, Yen, K & Mahony, S 2024, 'Size-based expectation maximization for characterizing nucleosome positions and subtypes', Genome research, vol. 34, no. 9, pp. 1334-1343. https://doi.org/10.1101/gr.279138.124
Xu, C, Kleinschmidt, H, Yang, J, Leith, EM, Johnson, J, Tan, S, Mahony, S & Bai, L 2024, 'Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1', Molecular cell, vol. 84, no. 15, pp. 2838-2855.e10. https://doi.org/10.1016/j.molcel.2024.06.022
2023
ENCODE Imputation Challenge Participants 2023, 'The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles', Genome biology, vol. 24, no. 1, 79. https://doi.org/10.1186/s13059-023-02915-y
2022
Cochran, K, Srivastava, D, Shrikumar, A, Balsubramani, A, Hardison, RC, Kundaje, A & Mahony, S 2022, 'Domain-adaptive neural networks improve cross-species prediction of transcription factor binding', Genome research, vol. 32, no. 3, pp. 512-523. https://doi.org/10.1101/GR.275394.121
Aydin, B, Sierk, M, Moreno-Estelles, M, Tejavibulya, L, Kumar, N, Flames, N, Mahony, S & Mazzoni, EO 2022, 'Foxa2 and Pet1 Direct and Indirect Synergy Drive Serotonergic Neuronal Differentiation', Frontiers in Neuroscience, vol. 16, 903881. https://doi.org/10.3389/fnins.2022.903881
Pinglay, S, Bulajić, M, Rahe, DP, Huang, E, Brosh, R, Mamrak, NE, King, BR, German, S, Cadley, JA, Rieber, L, Easo, N, Lionnet, T, Mahony, S, Maurano, MT, Holt, LJ, Mazzoni, EO & Boeke, JD 2022, 'Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation', Science, vol. 377, no. 6601, eabk2820. https://doi.org/10.1126/science.abk2820
Garipler, G, Lu, C, Morrissey, A, Lopez-Zepeda, LS, Pei, Y, Vidal, SE, Zen Petisco Fiore, AP, Aydin, B, Stadtfeld, M, Ohler, U, Mahony, S, Sanjana, NE & Mazzoni, EO 2022, 'The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes', Cell Reports, vol. 38, no. 11, 110524. https://doi.org/10.1016/j.celrep.2022.110524
2021
Rossi, MJ, Kuntala, PK, Lai, WKM, Yamada, N, Badjatia, N, Mittal, C, Kuzu, G, Bocklund, K, Farrell, NP, Blanda, TR, Mairose, JD, Basting, AV, Mistretta, KS, Rocco, DJ, Perkinson, ES, Kellogg, GD, Mahony, S & Pugh, BF 2021, 'A high-resolution protein architecture of the budding yeast genome', Nature, vol. 592, no. 7853, pp. 309-314. https://doi.org/10.1038/s41586-021-03314-8
Srivastava, D, Aydin, B, Mazzoni, EO & Mahony, S 2021, 'An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding', Genome biology, vol. 22, no. 1, 20. https://doi.org/10.1186/s13059-020-02218-6
Xiang, G, Giardine, BM, Mahony, S, Zhang, Y & Hardison, RC 2021, 'S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types', Bioinformatics, vol. 37, no. 18, pp. 3011-3013. https://doi.org/10.1093/bioinformatics/btab148
Singh, S, Santos, JM, Orchard, LM, Yamada, N, van Biljon, R, Painter, HJ, Mahony, S & Llinás, M 2021, 'The PfAP2-G2 transcription factor is a critical regulator of gametocyte maturation', Molecular Microbiology, vol. 115, no. 5, pp. 1005-1024. https://doi.org/10.1111/mmi.14676