Predictive Biophysical Neural Network Modeling of a Compendium of in vivo Transcription Factor DNA Binding Profiles for Escherichia coli
Patrick Lally, Laura Gómez-Romero, Víctor H. Tierrafría, Patricia Aquino, Claire Rioualen, Xiaoman Zhang, Sunyoung Kim, Gabriele Baniulyte, Jonathan Plitnick, Carol Smith, Mohan Babu, Julio Collado‐Vides, Joseph T. Wade, James E. Galagan
The paper maps DNA binding of 139 E. coli TFs using ChIP-Seq and trains BoltzNet, a neural network that predicts TF binding energy from DNA sequence, validated with biophysical experiments.
Nature Communications · May 7, 2025Peer-reviewedBioinformatics