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
Most 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,
Accurate allocation of multimapped reads enables regulatory element analysis at repeats
Alexis Morrissey, Jeffrey Shi, Daniela Q. James, Shaun Mahony, 2024, Genome Research on p. 937-951
SEM: Size-Based Expectation Maximization for Characterizing Nucleosome Positions and Subtypes
Jianyu Yang, Kuangyu Yen, Shaun Mahony, 2024, on p. 320-323
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles
Jacob Schreiber, Carles Boix, Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun Chieh Chang, Jen Chien Chang, Alex Hawkins-Hooker, Bernhard Schölkopf, Gabriele Schweikert, Mateo Rojas Carulla, Arif Canakoglu, Francesco Guzzo, Luca Nanni, Marco Masseroli, Mark James Carman, Pietro Pinoli, Chenyang Hong, Kevin Y. Yip, Jeffrey P. Spence, Sanjit Singh Batra, Yun S. Song, Shaun Mahony, Zheng Zhang, Wuwei Tan, Yang Shen, Yuanfei Sun, Minyi Shi, Jessika Adrian, Richard Sandstrom, Nina Farrell, Jessica Halow, Kristen Lee, Lixia Jiang, Xinqiong Yang, Charles Epstein, J. Seth Strattan, Bradley Bernstein, Michael Snyder, Manolis Kellis, William Stafford, Anshul Kundaje, 2023, Genome Biology
Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation
S Pinglay, M Bulajić, D Rahe, E Huang, R Brosh, N Mamrak, B King, S German, J Cadley, L Rieber, N Easo, T Lionnet, Shaun Mahony, M Maurano, L Holt, E Mazzoni, J Boeke, 2022, Science on p. eabk2820
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
PEGR: a flexible management platform for reproducible epigenomic and genomic research
D Shao, G Kellogg, A Nematbakhsh, P Kuntala, Shaun Mahony, B Pugh, Lai WKM, William K.M. Lai, 2022, Genome Biology on p. 99
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
K Cochran, D Srivastava, A Shrikumar, A Balsubramani, Ross Hardison, A Kundaje, Shaun Mahony, 2022, Genome Research on p. 512-523
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
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
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
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
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 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
MiniMDS: 3D structural inference from high-resolution Hi-C data
Lila Rieber, Shaun Mahony, 2017, Bioinformatics on p. i261-i266
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
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
Protein-DNA binding in high-resolution
Shaun Mahony, Benjamin Pugh, 2015, Critical Reviews in Biochemistry and Molecular Biology on p. 269-283
News Articles Featuring Shaun Mahony
Sep 10, 2024
Genomic pioneers collaborate to access the inaccessible
A new experimental method allows researchers to dissect how certain proteins, called pioneer factors, can bind to selective regions of the genome that are inaccessible to other DNA binding proteins.
Full Article
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.
Full Article