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
  • DNA
  • Chromatin
  • Datasets
  • Motor Neurons
  • Binding Sites
  • Nucleotide Motifs
  • Chromatin Immunoprecipitation
  • Embryonic Stem Cells

Recent Publications


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.
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.


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.


Han, GC, Vinayachandran, V, Bataille, AR, Park, B, Chan-Salis, KY, Keller, CA, Long, M, Mahony, S, Hardison, RC & Pugh, BF 2016, 'Genome-wide organization of GATA1 and TAL1 determined at high resolution', Molecular and cellular biology, vol. 36, no. 1, pp. 157-172.
Verma, SS, Frase, AT, Verma, A, Pendergrass, SA, Mahony, S, Haas, DW & Ritchie, MD 2016, 'Phenome-wide interaction study (PheWIS) in aids clinical trials group data (ACTG)', Pacific Symposium on Biocomputing, pp. 57-68.
Ariyachet, C, Tovaglieri, A, Xiang, G, Lu, J, Shah, MS, Richmond, CA, Verbeke, C, Melton, DA, Stanger, BZ, Mooney, D, Shivdasani, RA, Mahony, S, Xia, Q, Breault, DT & Zhou, Q 2016, 'Reprogrammed Stomach Tissue as a Renewable Source of Functional β Cells for Blood Glucose Regulation', Cell Stem Cell, vol. 18, no. 3, pp. 410-421.
Iwafuchi-Doi, M, Donahue, G, Kakumanu, A, Watts, JA, Mahony, S, Pugh, BF, Lee, D, Kaestner, KH & Zaret, KS 2016, 'The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation', Molecular cell, vol. 62, no. 1, pp. 79-91.

Clinical Trials Search

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