Sparse and compositionally robust inference of microbial ecological networks. by Zachary D Kurtz, Christian L Müller, Emily R Miraldi, Dan R Littman, Martin J Blaser, Richard A Bonneau

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Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration by Andrea Toth, Paranthaman Kannan, John Snowball, Matthew Kofron, Joseph A. Wayman, James P. Bridges, Emily R. Miraldi, Daniel Swarr, William J. Zacharias

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Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate by Ramya Raviram, Pedro P. Rocha, Vincent M. Luo, Emily Swanzey, Emily R. Miraldi, Edward B. Chuong, Cédric Feschotte, Richard Bonneau, Jane A. Skok

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4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments. by Ramya Raviram, Pedro P Rocha, Christian L Müller, Emily R Miraldi, Sana Badri, Yi Fu, Emily Swanzey, Charlotte Proudhon, Valentina Snetkova, Richard Bonneau, Jane A Skok

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maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. by Tareian A Cazares, Faiz W Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T Bejjani, Joseph A Wayman, Omer Donmez, Benjamin Wronowski, Sreeja Parameswaran, Leah C Kottyan, Artem Barski, Matthew T Weirauch, V B Surya Prasath, Emily R Miraldi

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Global discovery of lupus genetic risk variant allelic enhancer activity by Xiaoming Lu, Xiaoting Chen, Carmy Forney, Omer Donmez, Daniel Miller, Sreeja Parameswaran, Ted Hong, Yongbo Huang, Mario Pujato, Tareian Cazares, Emily R. Miraldi, John P. Ray, Carl G. de Boer, John B. Harley, Matthew T. Weirauch, Leah C. Kottyan

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