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
Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles (Genome Biology, (2023), 24, 1, (79), 10.1186/s13059-023-02915-y)
Jacob Matthew Schreiber, Carles A. 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, Jefrey P. Spence, Sanjit Singh Batra, Yun S. Song, Shaun Mahony, Zheng Zhang, Wuwei Tan, Yang Shen, Yuanfei Sun, Minyi Shi, Jessika Adrian, Richard S. Sandstrom, Nina P. Farrell, Jessica M. Halow, Kristen Lee, Lixia Jiang, Xinqiong Yang, Charles B. Epstein, J. Seth Strattan, Bradley E. Bernstein, Michael P. Snyder, Manolis Kellis, William S. Noble, Anshul Bharat Kundaje, 2025, Genome Biology
DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum
Victoria A. Bonnell, Yuning Zhang, Alan S. Brown, John Horton, Gabrielle A. Josling, Tsu Pei Chiu, Remo Rohs, Shaun Mahony, Raluca Gordân, Manuel Llinás, 2024, Nucleic Acids Research on p. 10161-10179
Size-based expectation maximization for characterizing nucleosome positions and subtypes
Jianyu Yang, Kuangyu Yen, Shaun Mahony, 2024, Genome Research on p. 1334-1343
Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1
Cheng Xu, Holly Kleinschmidt, Jianyu Yang, Erik M. Leith, Jenna Johnson, Song Tan, Shaun Mahony, Lu Bai, 2024, Molecular Cell on p. 2838-2855.e10
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
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
Guanjue Xiang, Xi He, Belinda M. Giardine, Kathryn J. Isaac, Kathryn Weaver, Dylan J. Taylor, Rajiv C. McCoy, Camden Jansen, Cheryl A. Keller, Alexander Q. Wixom, April Cockburn, Amber Reese Miller, Qian Qi, Yanghua He, Yichao Li, Jens Lichtenberg, Elisabeth F. Heuston, Stacie M. Anderson, Jing Luan, Marit W. Vermunt, Feng Yue, Michael E.G. Sauria, Michael C. Schatz, James Taylor, Berthold Göttgens, Berthoid Gottgens, Jim R. Hughes, Douglas R. Higgs, Mitchell J. Weiss, Yong Cheng, Gerd A. Blobel, David M. Bodine, Yu Zhang, Qunhua Li, Shaun Mahony, Ross C. Hardison, 2024, Genome Research on p. 1089-1105
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
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
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
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
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
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
Genome-wide organization of GATA1 and TAL1 determined at high resolution
G. Celine Han, Vinesh Vinayachandran, Alain R. Bataille, Bongsoo Park, Ka Yim Chan-Salis, Cheryl A. Keller, Maria Long, Shaun Mahony, Ross C. Hardison, B. Franklin Pugh, 2016, Molecular and Cellular Biology on p. 157-172
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
News Articles Featuring Shaun Mahony
Jun 20, 2025
How a genetic tug-of-war decides the fate of a honey bee
Despite having identical genetic instructions, female honey bee larvae can develop into either long-lived reproductive queens or short-lived sterile workers who help rear their sisters rather than laying their own eggs. Now, an interdisciplinary team led by researchers at Penn State has uncovered the molecular mechanisms that control how the conflict between genes inherited from the father and the mother determine the larva’s fate.
Full Article
Apr 09, 2025
NCEMS working groups to answer molecular and cellular bioscience questions
The U.S. National Science Foundation National Synthesis Center for Emergence in the Molecular and Cellular Sciences at Penn State aims to drive multidisciplinary collaboration utilizing publicly available research data.
Full Article
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