2023
Wenhao Jin, Kristopher W. Brannan (co-first), Katannya Kapeli, Samuel S. Park, Hui Qing Tan, Maya L. Gosztyla, Mayuresh Mujumdar, Joshua Ahdout, Bryce Henroid, Katherine Rothamel, Joy S. Xiang, Limsoon Wong, and Gene W. Yeo “HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence.” Molecular Cell. 2023. Epub 2023/07/09. doi: https://doi.org/10.1016/j.molcel.2023.06.019
Shengyu Li, Pengzhi Zhang, Weiqing Chen, Lingqun Ye, Kristopher W. Brannan, Nhat-Tu Le, Jun-ichi Abe, John P. Cooke & Guangyu Wang “A relay velocity model infers cell-dependent RNA velocity.” Nature Biotechnology. 2023. Epub 2023/04/04. doi: https://doi.org/10.1038/s41587-023-01728-5
2021
Kristopher Brannan, Isaac Chaim, Ryan Marina, Brian Yee, Eric Kofman, Daniel Lorenz, Pratibha Jagannatha, Kevin Dong, Assael Madrigal, Jason Underwood, Gene Yeo “Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes” Nature Methods (2021) https://doi.org/10.1038/s41592-021-01128-0
2020
Ryan Marina, Kristopher Brannan (co-first), Kevin Dong, Brian Yee, Gene W. Yeo “Evaluation of RNA-targeting CRISPR/Cas systems for site-specific A-to-I RNA editing” Cell Reports (2020) doi:10.1016/j.celrep.2020.108350
2019
Michael Cortazar, Ryan Sheridan, Benjamin Erickson, Nova Fong, Kira Glover-Cutter, Kristopher Brannan, David L Bentley “Control of RNA pol II speed by PNUTS-PP1 and Spt5 dephosphorylation facilitates termination by a “sitting duck torpedo” mechanism” Molecular Cell (2019) doi:10.1016/j.molcel.2019.09.031
2016
Kristopher Brannan, Gene W. Yeo “From a Protein-RNA Predictions toward a Peptide-RNA code” Molecular Cell (2016). doi:10.1016/j.molcel.2016.10.023
Kristopher Brannan, Wenhao Jin, Stephanie C. Huelga, Charles A.S. Banks, Joshua M. Gilmore, Laurence Florens, Michael P. Washburn, Eric L. Van Nostrand, Gabriel A. Pratt, Marie K. Schwinn, Danette L. Daniels, and Gene W. Yeo ”SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes” Molecular Cell. (2016);64(2):282-293. doi: 10.1016/j.molcel.2016.09.003.
2015
Nova Fong, Kristopher Brannan, Benjamin Erickson, Hyunmin Kim, Michael A. Cortazar, Ryan M. Sheridan, Tram Nguyen, Shai Karp, and David L. Bentley “Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition” Molecular Cell (2015) doi:10.1016/j.molcel.2015.09.026
2012
Kris Brannan, David L Bentley “Control of Transcriptional Elongation by RNA Polymerase II: A Retrospective.” Genetics research international (2012) doi:10.1155/2012/170173
Kris Brannan, Hyunmin Kim, Benjamin Erickson, Kira Glover-Cutter, Soojin Kim, Nova Fong, Lauren Kiemele, Kirk Hansen, Richard Davis, Jens Lykke-Andersen, David L Bentley “mRNA Decapping Factors and the Exonuclease Xrn2 Function in Widespread Premature Termination of RNA Polymerase II Transcription.” Molecular Cell (2012) doi:10.1016/j.molcel.2012.03.006