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Journal Articles
- 2023
[j6]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:
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS Comput. Biol. 19(1) (2023)- 2022
- [j5]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, Bram L. Gorissen, David Gresham, Emily R. Miraldi, Richard Bonneau:
High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0. Bioinform. 38(9): 2519-2528 (2022) - 2019
- [j4]Dayanne M. Castro, Nicholas R. de Veaux, Emily R. Miraldi, Richard Bonneau:
Multi-study inference of regulatory networks for more accurate models of gene regulation. PLoS Comput. Biol. 15(1) (2019) - 2016
- [j3]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:
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments. PLoS Comput. Biol. 12(3) (2016) - 2015
- [j2]Zachary D. Kurtz, Christian L. Müller, Emily R. Miraldi, Dan R. Littman, Martin J. Blaser, Richard A. Bonneau:
Sparse and Compositionally Robust Inference of Microbial Ecological Networks. PLoS Comput. Biol. 11(5) (2015) - 2014
- [j1]Bowen Yu, Harish Doraiswamy, Xi Chen, Emily R. Miraldi, Mario Luis Arrieta-Ortiz, Christoph Hafemeister, Aviv Madar, Richard Bonneau, Cláudio T. Silva:
Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks. IEEE Trans. Vis. Comput. Graph. 20(12): 1903-1912 (2014)
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