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Researcher Profile

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Shaun A. Mahony, PhD

Shaun A. Mahony, PhD

Associate Professor, Biochemistry & Molecular Biology
Scientific Program:Mechanisms of Carcinogenesis
Disease Teams:
Institute for CyberScience (ICS) - Associate

Research Interests

  • Transcription Factors
  • Genome
  • Genes
  • Proteins
  • Chromatin
  • DNA
  • Chromatin Immunoprecipitation Sequencing
  • Datasets
  • Motor Neurons
  • Binding Sites
  • Nucleotide Motifs
  • Epigenomics

Recent Publications


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.


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.


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.
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.
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.
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.


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.
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.
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.
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.


Yamada, N, Rossi, MJ, Farrell, N, Pugh, BF & Mahony, S 2020, 'Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes', Nucleic acids research, vol. 48, no. 20, pp. 11215-11226.
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 2020, 'An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis', Genome research, vol. 30, no. 3, pp. 472-484.
Kunz, T, Rieber, L & Mahony, S 2020, 'Assessing relationships between chromatin interactions and regulatory genomic activities using the self-organizing map', Methods.
Yamada, N, Kuntala, PK, Pugh, BF & Mahony, S 2020, 'ChExMix: A Method for Identifying and Classifying Protein-DNA Interaction Subtypes', Journal of Computational Biology, vol. 27, no. 3, pp. 429-435.
Bulajić, M, Srivastava, D, Dasen, JS, Wichterle, H, Mahony, S & Mazzoni, EO 2020, 'Differential abilities to engage inaccessible chromatin diversify vertebrate Hox binding patterns', Development (Cambridge), vol. 147, no. 22, dev194761.
Shao, D, Kellogg, G, Mahony, S, Lai, W & Pugh, BF 2020, PEGR: A management platform for ChIP-based next generation sequencing pipelines. in PEARC 2020 - Practice and Experience in Advanced Research Computing 2020: Catch the Wave. ACM International Conference Proceeding Series, Association for Computing Machinery, pp. 285-292, 2020 Conference on Practice and Experience in Advanced Research Computing: Catch the Wave, PEARC 2020, Virtual, Online, United States, 7/27/20.