Shaun Mahony

Associate Professor of Biochemistry & Molecular Biology

Shaun Mahony

Research Summary

We apply neural networks and other machine learning approaches to understand how transcription factors control cellular identity

Huck Graduate Students

Huck Affiliations

Links

Publication Tags

Transcription Factors Chromatin Genome Dna Proteins Genes Motor Neurons Genomics Chip Embryonic Stem Cells Binding Sites Experiments Neurogenesis Nucleosomes Ligands Experiment Protein Neurons Retinoic Acid Receptors Cells Visualization Chromatin Assembly And Disassembly Gene Expression Transcription Factor High Resolution

Most Recent Papers

An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding

Divyanshi Srivastava, Begüm Aydin, Esteban O. Mazzoni, Shaun Mahony, 2021, Genome Biology

The PfAP2-G2 transcription factor is a critical regulator of gametocyte maturation

Suprita Singh, Joana M. Santos, Lindsey M. Orchard, Naomi Yamada, Riëtte van Biljon, Heather J. Painter, Shaun Mahony, Manuel Llinás, 2021, Molecular Microbiology on p. 1005-1024

A high-resolution protein architecture of the budding yeast genome

Matthew J. Rossi, Prashant K. Kuntala, William K.M. Lai, Naomi Yamada, Nitika Badjatia, Chitvan Mittal, Guray Kuzu, Kylie Bocklund, Nina P. Farrell, Thomas R. Blanda, Joshua D. Mairose, Ann V. Basting, Katelyn S. Mistretta, David J. Rocco, Emily S. Perkinson, Gretta D. Kellogg, Shaun Mahony, B. Franklin Pugh, 2021, Nature on p. 309-314

Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes

Naomi Yamada, Matthew J. Rossi, Nina Farrell, B. Franklin Pugh, Shaun Mahony, 2020, Nucleic Acids Research on p. 11215-11226

Differential abilities to engage inaccessible chromatin diversify vertebrate Hox binding patterns

Milica Bulajić, Divyanshi Srivastava, Jeremy S. Dasen, Hynek Wichterle, Shaun Mahony, Esteban O. Mazzoni, 2020, Journal of Embryology and Experimental Morphology

PEGR

Danying Shao, Gretta Kellogg, Shaun Mahony, William Lai, B. Franklin Pugh, 2020, on p. 285-292

Assessing relationships between chromatin interactions and regulatory genomic activities using the self-organizing map

Timothy Kunz, Lila Rieber, Shaun Mahony, 2020, ImmunoMethods

Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns

Divyanshi Srivastava, Shaun Mahony, 2020, Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

ChExMix

Naomi Yamada, Prashant Kumar Kuntala, B. Franklin Pugh, Shaun Mahony, 2020, Journal of Computational Biology on p. 429-435

PEGR: a management platform for ChIP-based next generation sequencing pipelines

Danying Shao, Gretta Kellogg, Shaun Mahony, William Lai, B Pugh, 2020, on p. 285-292

Most-Cited Papers

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

Yuchun Guo, Shaun A. Mahony, David K. Gifford, 2012, PLoS Computational Biology

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

Makiko Iwafuchi-Doi, Greg Donahue, Akshay Kakumanu, Jason A. Watts, Shaun Mahony, B. Franklin Pugh, Dolim Lee, Klaus H. Kaestner, Kenneth S. Zaret, 2016, Molecular Cell on p. 79-91

Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity

Esteban O. Mazzoni, Shaun Mahony, Michael Closser, Carolyn A. Morrison, Stephane Nedelec, Damian J. Williams, Disi An, David K. Gifford, Hynek Wichterle, 2013, Nature Neuroscience on p. 1219-1227

Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis

Shaun A. Mahony, Esteban O. Mazzoni, Scott McCuine, Richard A. Young, Hynek Wichterle, David K. Gifford, 2011, Genome Biology

Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals

Esteban O. Mazzoni, Shaun Mahony, Mirza Peljto, Tulsi Patel, Seraphim R. Thornton, Scott McCuine, Christopher Reeder, Laurie A. Boyer, Richard A. Young, David K. Gifford, Hynek Wichterle, 2013, Nature Neuroscience on p. 1191-1198

Reprogrammed stomach tissue as a renewable source of functional β cells for blood glucose regulation

Chaiyaboot Ariyachet, Alessio Tovaglieri, Guanjue Xiang, Jiaqi Lu, Manasvi S. Shah, Camilla A. Richmond, Catia Verbeke, Douglas A. Melton, Ben Z. Stanger, David Mooney, Ramesh A. Shivdasani, Shaun Mahony, Qing Xia, David T. Breault, Qiao Zhou, 2016, Cell Stem Cell on p. 410-421

Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons

Simona Lodato, Bradley J. Molyneaux, Emanuela Zuccaro, Loyal A. Goff, Hsu Hsin Chen, Wen Yuan, Alyssa Meleski, Emi Takahashi, Shaun Mahony, John L. Rinn, David K. Gifford, Paola Arlotta, 2014, Nature Neuroscience on p. 1046-1054

Embryonic stem cell-based mapping of developmental transcriptional programs

Esteban O. Mazzoni, Shaun A. Mahony, Michelina Iacovino, Carolyn A. Morrison, George Mountoufaris, Michael Closser, Warren A. Whyte, Richard A. Young, Michael Kyba, David K. Gifford, Hynek Wichterle, 2011, Nature Methods on p. 1056-1060

A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells

Silvia Velasco, Mahmoud M. Ibrahim, Akshay Kakumanu, Görkem Garipler, Begüm Aydin, Mohamed Ahmed Al-Sayegh, Antje Hirsekorn, Farah Abdul-Rahman, Rahul Satija, Uwe Ohler, Shaun Mahony, Esteban O. Mazzoni, 2017, Cell Stem Cell on p. 205-217.e8

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford, 2014, PLoS Computational Biology