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Epilogos: information-theoretic navigation of multi-tissue functional genomic annotations
Jacob Quon, Alex Reynolds, Nalu Tripician, Eric Rynes, Athanasios Teodosiadis, Manolis Kellis, Wouter Meuleman
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Iterative deep learning-design of human enhancers exploits condensed sequence grammar to achieve cell type-specificity
Christopher Yin, Sebastian Castillo Hair, Gun Woo Byeon, Peter Bromley, Wouter Meuleman, Georg Seelig
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DNA-Diffusion: Leveraging Generative Models for Controlling Chromatin Accessibility and Gene Expression via Synthetic Regulatory Elements

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Lucas Ferreira DaSilva, Simon Senan, Zain Munir Patel, Aniketh Janardhan Reddy, Sameer Gabbita, Zach Nussbaum, César Miguel Valdez Córdova, Aaron Wenteler, Noah Weber, Tin M Tunjic, Others
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Automated sequence-based annotation and interpretation of the human genome

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Anshul Kundaje, Wouter Meuleman
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Regulatory genomic circuitry of human disease loci by integrative epigenomics

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Carles a Boix, Benjamin T James, Yongjin P Park, Wouter Meuleman, Manolis Kellis
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Index and biological spectrum of human DNase I hypersensitive sites
Wouter Meuleman, Alexander Muratov, Eric Rynes, Jessica Halow, Kristen Lee, Daniel Bates, Morgan Diegel, Douglas Dunn, Fidencio Neri, Athanasios Teodosiadis, Alex, Reynolds, Eric Haugen, Jemma Nelson, Audra Johnson, Mark Frerker, Michael Buckley, Richard Sandstrom, Jeff Vierstra, Rajinder Kaul, John Stamatoyannopoulos
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Global reference mapping of human transcription factor footprints
Jeff Vierstra, John Lazar, Richard Sandstrom, Jessica Halow, Kristen Lee, Daniel Bates, Morgan Diegel, Douglas Dunn, Fidencio Neri, Eric Haugen, Eric Rynes, Alex, Reynolds, Jemma Nelson, Audra Johnson, Mark Frerker, Michael Buckley, Rajinder Kaul, Wouter Meuleman, John Stamatoyannopoulos
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Expanded encyclopaedias of DNA elements in the human and mouse genomes

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Jill E Moore, Michael J Purcaro, Henry E Pratt, Charles B Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie a Davis, Alexander Dobin, Others
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Multi-scale chromatin state annotation using a hierarchical hidden Markov model
Eugenio Marco, Wouter Meuleman, Jialiang Huang, Kimberly Glass, Luca Pinello, Jianrong Wang, Manolis Kellis, Guo-Cheng Yuan
Small chromosomal regions position themselves autonomously according to their chromatin class
Harmen JG Van De Werken, Josien C Haan, Yana Feodorova, Dominika Bijos, An Weuts, Koen Theunis, Sjoerd JB Holwerda, Wouter Meuleman, Ludo Pagie, Katharina Thanisch, Others