TY - JOUR T1 - BindSpace: decoding transcription factor binding signals by large-scale joint embedding JF - bioRxiv DO - 10.1101/359539 SP - 359539 AU - Han Yuan AU - Meghana Kshirsagar AU - Lee Zamparo AU - Yuheng Lu AU - Christina S. Leslie Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/06/29/359539.abstract N2 - Decoding transcription factor (TF) binding signals in genomic DNA is a fundamental problem. Here we present a prediction model called BindSpace that learns to embed DNA sequences and TF class/family labels into the same space. By training on binding data for hundreds of TFs and embedding over 1M DNA sequences, BindSpace achieves state-of-the-art multiclass binding prediction performance, in vitro and in vivo, and can distinguish signals of closely related TFs. ER -