Shaun Mahony
Associate Professor of Biochemistry & Molecular Biology
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404 Frear South
University Park, PA - sam77@psu.edu
- 814-865-3008
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 Genes Genomics Genome Proteins Motor Neurons Dna Gene Expression Nucleosomes Experiment Embryonic Stem Cells Chromatin Immunoprecipitation Sequencing Chromatin Assembly And Disassembly Biochemistry Quality Control Modeling Regulator Genes Experiments Epigenetics Neural Networks Stomach Neurotransmitter Agents H3k4me3 ChipMost Recent Publications
PEGR: a flexible management platform for reproducible epigenomic and genomic research
Danying Shao, G Kellogg, Ali Nematbakhsh, Prashant Kuntala, Shaun Mahony, B. Pugh, W Lai,
Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation
Sudarshan Pinglay, Milica Bulajić, Dylan Rahe, Emily Huang, Ran Brosh, Sergei German, John Cadley, Lila Rieber, Nicole Easo, Shaun Mahony, Matthew Maurano, Liam Holt, Esteban Mazzoni, Jef Boeke,
PEGR: a flexible management platform for reproducible epigenomic and genomic research
Danying Shao, Gretta D. Kellogg, Ali Nematbakhsh, Prashant K. Kuntala, Shaun Mahony, B. Franklin Pugh, William K.M. Lai, 2022, Genome Biology
Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation
Sudarshan Pinglay, Milica Bulajić, Dylan P. Rahe, Emily Huang, Ran Brosh, Nicholas E. Mamrak, Benjamin R. King, Sergei German, John A. Cadley, Lila Rieber, Nicole Easo, Timothée Lionnet, Shaun Mahony, Matthew T. Maurano, Liam J. Holt, Esteban O. Mazzoni, Jef D. Boeke, 2022, Science
Foxa2 and Pet1 Direct and Indirect Synergy Drive Serotonergic Neuronal Differentiation
Begüm Aydin, Michael Sierk, Mireia Moreno-Estelles, Link Tejavibulya, Nikathan Kumar, Nuria Flames, Shaun Mahony, Esteban O. Mazzoni, 2022, Frontiers in Neuroscience
The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes
Görkem Garipler, Congyi Lu, Alexis Morrissey, Lorena S. Lopez-Zepeda, Yingzhen Pei, Simon E. Vidal, Ana Paula Zen Petisco Fiore, Begüm Aydin, Matthias Stadtfeld, Uwe Ohler, Shaun Mahony, Neville E. Sanjana, Esteban O. Mazzoni, 2022, Cell Reports
Domain-adaptive neural networks improve cross-species prediction of transcription factor binding
Kelly Cochran, Divyanshi Srivastava, Avanti Shrikumar, Akshay Balsubramani, Ross C. Hardison, Anshul Kundaje, Shaun Mahony, 2022, Genome Research on p. 512-523
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
Assessing relationships between chromatin interactions and regulatory genomic activities using the self-organizing map.
T Kunz, L Rieber, Shaun Mahony, 2021, Methods on p. 12-21
Most-Cited Papers
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
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
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
Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes
Begüm Aydin, Akshay Kakumanu, Mary Rossillo, Mireia Moreno-Estellés, Görkem Garipler, Niels Ringstad, Nuria Flames, Shaun Mahony, Esteban O. Mazzoni, 2019, Nature Neuroscience on p. 897-908
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
Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock
Vinesh Vinayachandran, Rohit Reja, Matthew J. Rossi, Bongsoo Park, Lila Rieber, Chitvan Mittal, Shaun Mahony, B. Franklin Pugh, 2018, Genome Research on p. 357-366
News Articles Featuring Shaun Mahony
Mar 11, 2021
Biochemistry and molecular biology professor receives NSF CAREER Award
Shaun Mahony, assistant professor of biochemistry and molecular biology, has been honored with a Faculty Early Career Development (CAREER) award from the National Science Foundation (NSF).
Full Article
May 18, 2019
Shaun Mahony employs machine learning to study gene regulation
Once the fodder of science fiction books and movies, Artificial intelligence -- AI -- and machine learning are making an impact on nearly every facet of society. Penn State’s Institute for CyberScience are among Penn State’s research leaders who are both using AI in their work and studying ways to make sure that the technology’s societal impact is as safe and as beneficial as possible.
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