Researcher Profile

Researcher Profile

Shaun A. Mahony, PhD

Shaun A. Mahony, PhD

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

Research Interests

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

Recent Publications


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.
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.


Yamada, N, Lai, WKM, Farrell, N, Pugh, BF & Mahony, S 2019, 'Characterizing protein-DNA binding event subtypes in ChIP-exo data', Bioinformatics, vol. 35, no. 6, pp. 903-913.
Zhang, Y & Mahony, S 2019, 'Direct prediction of regulatory elements from partial data without imputation', PLoS computational biology, vol. 15, no. 11, e1007399.
Rieber, L & Mahony, S 2019, 'Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types', Epigenetics and Chromatin, vol. 12, no. 1, 61.
Aydin, B, Kakumanu, A, Rossillo, M, Moreno-Estellés, M, Garipler, G, Ringstad, N, Flames, N, Mahony, S & Mazzoni, EO 2019, 'Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes', Nature Neuroscience, vol. 22, no. 6, pp. 897-908.
Srivastava, D & Mahony, S 2020, 'Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns', Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, vol. 1863, no. 6, 194443.
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 2020, 'Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells', IUBMB Life, vol. 72, no. 1, pp. 27-38.


Yamada, N, Lai, WKM, Farrell, N, Pugh, BF & Mahony, S 2018, Characterizing protein-DNA binding event subtypes in CHIP-exo data. in BJ Raphael (ed.), Research in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 10812 LNBI, Springer Verlag, pp. 291-292, 22nd International Conference on Research in Computational Molecular Biology, RECOMB 2018, Paris, France, 4/21/18.
Vinayachandran, V, Reja, R, Rossi, MJ, Park, B, Rieber, L, Mittal, C, Mahony, S & Pugh, BF 2018, 'Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock', Genome research, vol. 28, no. 3, pp. 357-366.


Velasco, S, Ibrahim, MM, Kakumanu, A, Garipler, G, Aydin, B, Al-Sayegh, MA, Hirsekorn, A, Abdul-Rahman, F, Satija, R, Ohler, U, Mahony, S & Mazzoni, EO 2017, 'A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells', Cell Stem Cell, vol. 20, no. 2, pp. 205-217.e8.
Kakumanu, A, Velasco, S, Mazzoni, E & Mahony, S 2017, 'Deconvolving sequence features that discriminate between overlapping regulatory annotations', PLoS computational biology, vol. 13, no. 10, e1005795.
Rieber, L & Mahony, S 2017, 'MiniMDS: 3D structural inference from high-resolution Hi-C data', Bioinformatics, vol. 33, no. 14, pp. i261-i266.

Clinical Trials Search

Children (age < 18 years)
Adults (age >= 18 years)