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

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Publication Tags

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Transcription Factors Chromatin Genes Genomics Motor Neurons Genome Experiments Experiment Dna Proteins Nucleosomes Data Storage Equipment Gene Expression Embryonic Stem Cells Chromatin Assembly And Disassembly Datasets Chromatin Immunoprecipitation Sequencing Biochemistry Quality Control Modeling Regulator Genes Partition Neural Networks Chip Multidimensional Scaling

Most Recent Publications

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, G Kellogg, Ali Nematbakhsh, Prashant Kuntala, Shaun Mahony, B. Pugh, W Lai,

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

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

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 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

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

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

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

MiniMDS: 3D structural inference from high-resolution Hi-C data

Lila Rieber, Shaun Mahony, 2017, Bioinformatics on p. i261-i266