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

These publication tags are generated from the output of this researcher. Click any tag below to view other Huck researchers working on the same topic.

Transcription Factors Genes Chromatin Genomics Genome Proteins Dna Experiments Nucleosomes Experiment Gene Expression Data Storage Equipment Chromatin Immunoprecipitation Sequencing Embryonic Stem Cells Motor Neurons Datasets Protein Biochemistry Quality Control Chromatin Immunoprecipitation Modeling Regulator Genes Heat Shock Response Neural Networks Stomach

Most Recent Publications

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,

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

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

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

Begüm Aydin, Michael Sierk, Mireia Moreno-Estelles, Link Tejavibulya, Nikathan Kumar, Nuria Flames, Shaun Mahony, Esteban O. Mazzoni, 2022, Frontiers in Neuroscience

D Shao, G Kellogg, A Nematbakhsh, P Kuntala, Shaun Mahony, B Pugh, Lai WKM, William K.M. Lai, 2022, Genome Biology on p. 99

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

K Cochran, D Srivastava, A Shrikumar, A Balsubramani, Ross Hardison, A Kundaje, Shaun Mahony, 2022, Genome Research on p. 512-523

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

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

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

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

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

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

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

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

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

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

Shaun Mahony, Benjamin Pugh, 2015, Critical Reviews in Biochemistry and Molecular Biology on p. 269-283