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
sam77@psu.edu

Research Interests

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

Recent Publications

2021

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
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. https://doi.org/10.1111/mmi.14676

2020

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. https://doi.org/10.1093/nar/gkaa618
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. https://doi.org/10.1101/gr.255760.119
Kunz, T, Rieber, L & Mahony, S 2020, 'Assessing relationships between chromatin interactions and regulatory genomic activities using the self-organizing map', Methods. https://doi.org/10.1016/j.ymeth.2020.07.002
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. https://doi.org/10.1089/cmb.2019.0466
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. https://doi.org/10.1242/dev.194761
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. https://doi.org/10.1145/3311790.3396621

2019

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. https://doi.org/10.1093/bioinformatics/bty703
Zhang, Y & Mahony, S 2019, 'Direct prediction of regulatory elements from partial data without imputation', PLoS computational biology, vol. 15, no. 11, e1007399. https://doi.org/10.1371/journal.pcbi.1007399
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. https://doi.org/10.1186/s13072-019-0308-3
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. https://doi.org/10.1038/s41593-019-0399-y
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. https://doi.org/10.1016/j.bbagrm.2019.194443
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. https://doi.org/10.1002/iub.2195

2018

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. https://doi.org/10.1101/gr.226761.117

2017

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. https://doi.org/10.1016/j.stem.2016.11.006
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. https://doi.org/10.1371/journal.pcbi.1005795
Rieber, L & Mahony, S 2017, 'MiniMDS: 3D structural inference from high-resolution Hi-C data', Bioinformatics, vol. 33, no. 14, pp. i261-i266. https://doi.org/10.1093/bioinformatics/btx271

Clinical Trials Search


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