Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types af Lila Rieber, Shaun Mahony

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High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. af Yuchun Guo, Shaun Mahony, David K Gifford

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DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. af Shaun Mahony, Philip E Auron, Panayiotis V Benos

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An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding af Divyanshi Srivastava, Begüm Aydin, Esteban O. Mazzoni, Shaun Mahony

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PEGR: a flexible management platform for reproducible epigenomic and genomic research af Danying Shao, Gretta D. Kellogg, Ali Nematbakhsh, Prashant K. Kuntala, Shaun Mahony, B. Franklin Pugh, William K. M. Lai

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An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding. af Shaun Mahony, Matthew D Edwards, Esteban O Mazzoni, Richard I Sherwood, Akshay Kakumanu, Carolyn A Morrison, Hynek Wichterle, David K Gifford

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Foxa2 and Pet1 Direct and Indirect Synergy Drive Serotonergic Neuronal Differentiation af Begüm Aydin, Michael Sierk, Mireia Moreno-Estelles, Mireia Moreno-Estelles, Link Tejavibulya, Nikathan Kumar, Nuria Flames, Shaun Mahony, Esteban O. Mazzoni

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Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque. af Guy Zinman, Rachel Brower-Sinning, Chineye H Emeche, Jason Ernst, Grace Tzu-Wei Huang, Shaun Mahony, Amy J Myers, Dawn M O'Dee, JoAnne L Flynn, Gerard J Nau, Ted M Ross, Russell D Salter, Panayiotis V Benos, Ziv Bar Joseph, Penelope A Morel

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Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. af Katherine Belov, Janine E Deakin, Anthony T Papenfuss, Michelle L Baker, Sandra D Melman, Hannah V Siddle, Nicolas Gouin, David L Goode, Tobias J Sargeant, Mark D Robinson, Matthew J Wakefield, Shaun Mahony, Joseph G R Cross, Panayiotis V Benos, Paul B Samollow, Terence P Speed, Jennifer A Marshall Graves, Robert D Miller

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Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles af 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, ENCODE Imputation Challenge Participants

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The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles af 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, ENCODE Imputation Challenge Participants

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