@article{b8609a4e955c42788eac15886917be5c,
title = "Modeling transcriptional regulation of model species with deep learning",
abstract = "To enable large-scale analyses of transcription regulation in model species, we developed DeepArk, a set of deep learning models of the cis-regulatory activities for four widely studied species: Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, and Mus musculus. DeepArk accurately predicts the presence of thousands of different context-specific regulatory features, including chromatin states, histone marks, and transcription factors. In vivo studies show that DeepArk can predict the regulatory impact of any genomic variant (including rare or not previously observed) and enables the regulatory annotation of understudied model species.",
author = "Cofer, {Evan M.} and Jo{\~a}o Raimundo and Alicja Tadych and Yuji Yamazaki and Wong, {Aaron K.} and Theesfeld, {Chandra L.} and Levine, {Michael S.} and Troyanskaya, {Olga G.}",
note = "Funding Information: We acknowledge all members of the Troyanskaya and Levine laboratories for their helpful discussions, as well as the SCC center at the Flatiron Institute. We thank Beryl M. Jones, Siena Dumas Ang, and Rachel Kaletsky for their feedback regarding the DeepArk web server. We also thank Teka H. Nicholas for proofreading the manuscript. We acknowledge that this work was performed using the high-performance computing resources at the Simons Foundation and the TIGRESS computer center at Princeton University. E.M.C. was supported by National Institutes of Health (NIH) grant T32 HG003284 and the National Science Foundation Graduate Research Fellowship Program (NSF-GRFP). This work was supported by NIH grant R01 GM071966 (O.G.T.) and R35 GM118147 (M.S.L.). Publisher Copyright: {\textcopyright} 2021 Cofer et al.",
year = "2021",
month = jun,
doi = "10.1101/gr.266171.120",
language = "English (US)",
volume = "31",
pages = "1097--1105",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "6",
}