Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks. - Bowen Yu 004; Harish Doraiswamy; Xi Chen; Emily R. Miraldi; Mario Luis Arrieta-Ortiz; Christoph Hafemeister; Aviv Madar; Richard Bonneau; Cláudio T. Silva (IEEE Trans. Vis. Comput. Graph., 2014)

Sparse and Compositionally Robust Inference of Microbial Ecological Networks. - Zachary D. Kurtz; Christian L. Müller; Emily R. Miraldi; Dan R. Littman; Martin J. Blaser; Richard A. Bonneau (PLoS Comput. Biol., 2015)

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments. - 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 (PLoS Comput. Biol., 2016)

Multi-study inference of regulatory networks for more accurate models of gene regulation. - Dayanne M. Castro; Nicholas R. de Veaux; Emily R. Miraldi; Richard Bonneau (PLoS Comput. Biol., 2019)

High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0. - Claudia Skok Gibbs; Christopher A. Jackson; Giuseppe-Antonio Saldi; Andreas Tjärnberg; Aashna Shah; Aaron Watters; Nicholas De Veaux; Konstantine Tchourine; Ren Yi; Tymor Hamamsy; Dayanne M. Castro; Nicholas Carriero; et al. (Bioinform., 2022)

maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. - 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; et al. (PLoS Comput. Biol., 2023)