SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes
Brannan, Kristopher W., Jin, Wenhao, Huelga, Stephanie C., Banks, Charles A.S., Gilmore, Joshua M., Florens, Laurence, Washburn, Michael P., Van Nostrand, Eric L., Pratt, Gabriel A., Schwinn, Marie K., Daniels, Danette L., Yeo, Gene W.
Published in Molecular cell (20.10.2016)
Published in Molecular cell (20.10.2016)
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Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes
Brannan, Kristopher W., Chaim, Isaac A., Marina, Ryan J., Yee, Brian A., Kofman, Eric R., Lorenz, Daniel A., Jagannatha, Pratibha, Dong, Kevin D., Madrigal, Assael A., Underwood, Jason G., Yeo, Gene W.
Published in Nature methods (01.05.2021)
Published in Nature methods (01.05.2021)
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Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a “Sitting Duck Torpedo” Mechanism
Cortazar, Michael A., Sheridan, Ryan M., Erickson, Benjamin, Fong, Nova, Glover-Cutter, Kira, Brannan, Kristopher, Bentley, David L.
Published in Molecular cell (19.12.2019)
Published in Molecular cell (19.12.2019)
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A relay velocity model infers cell-dependent RNA velocity
Li, Shengyu, Zhang, Pengzhi, Chen, Weiqing, Ye, Lingqun, Brannan, Kristopher W., Le, Nhat-Tu, Abe, Jun-ichi, Cooke, John P., Wang, Guangyu
Published in Nature biotechnology (01.01.2024)
Published in Nature biotechnology (01.01.2024)
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Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition
Fong, Nova, Brannan, Kristopher, Erickson, Benjamin, Kim, Hyunmin, Cortazar, Michael A., Sheridan, Ryan M., Nguyen, Tram, Karp, Shai, Bentley, David L.
Published in Molecular cell (15.10.2015)
Published in Molecular cell (15.10.2015)
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Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing
Marina, Ryan J., Brannan, Kristopher W., Dong, Kevin D., Yee, Brian A., Yeo, Gene W.
Published in Cell reports (Cambridge) (03.11.2020)
Published in Cell reports (Cambridge) (03.11.2020)
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HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence
Jin, Wenhao, Brannan, Kristopher W., Kapeli, Katannya, Park, Samuel S., Tan, Hui Qing, Gosztyla, Maya L., Mujumdar, Mayuresh, Ahdout, Joshua, Henroid, Bryce, Rothamel, Katherine, Xiang, Joy S., Wong, Limsoon, Yeo, Gene W.
Published in Molecular cell (20.07.2023)
Published in Molecular cell (20.07.2023)
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Large-scale map of RNA-binding protein interactomes across the mRNA life cycle
Street, Lena A., Rothamel, Katherine L., Brannan, Kristopher W., Jin, Wenhao, Bokor, Benjamin J., Dong, Kevin, Rhine, Kevin, Madrigal, Assael, Al-Azzam, Norah, Kim, Jenny Kim, Ma, Yanzhe, Gorhe, Darvesh, Abdou, Ahmed, Wolin, Erica, Mizrahi, Orel, Ahdout, Joshua, Mujumdar, Mayuresh, Doron-Mandel, Ella, Jovanovic, Marko, Yeo, Gene W.
Published in Molecular cell (03.10.2024)
Published in Molecular cell (03.10.2024)
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Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution
Jagannatha, Pratibha, Tankka, Alexandra T, Lorenz, Daniel A, Yu, Tao, Yee, Brian A, Brannan, Kristopher W, Zhou, Catherine Jiarui, Underwood, Jason G, Yeo, Gene W
Published in Genome research (21.06.2024)
Published in Genome research (21.06.2024)
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Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions
Xiang, Joy S, Mueller, Jasmine R, Luo, En-Ching, Yee, Brian A, Schafer, Danielle, Schmok, Jonathan C, Tan, Frederick E, Rothamel, Katherine, McVicar, Rachael N, Kwong, Elizabeth M, Jones, Krysten L, Her, Hsuan-Lin, Chen, Chun-Yuan, Vu, Anthony Q, Jin, Wenhao, Park, Samuel S, Le, Phuong, Brannan, Kristopher W, Kofman, Eric R, Li, Yanhua, Tankka, Alexandra T, Dong, Kevin D, Song, Yan, Carlin, Aaron F, Van Nostrand, Eric L, Leibel, Sandra L, Yeo, Gene W
Published in bioRxiv (23.02.2022)
Published in bioRxiv (23.02.2022)
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Paper
Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions
Yeo, Gene, Xiang, Joy, Mueller, Jasmine, Luo, En-Ching, Yee, Brian, Schafer, Danielle, Schmok, Jonathan, Tan, Frederick, Rothamel, Katherine, McVicar, Rachael, Kwong, Elizabeth, Croker, Ben, Jones, Krysten, Her, Hsuan-Lin, Chen, Chun-Yuan, Vu, Anthony, Jin, Wenhao, Park, Samuel, Le, Phuong, Brennan, Kristopher, Kofman, Eric, Li, Yanhua, Tankka, Alexandra, Dong, Kevin, Song, Yan, Clark, Alex, Carlin, Aaron, Nostrand, Eric Van, Leibel, Sandra
Published in Research square (17.03.2022)
Published in Research square (17.03.2022)
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Abstract 1558: Deciphering the role of ribosomal paralogs RPL39/RPL39L in metaplastic breast cancer
Chervo, Maria F., li, Main, Mancino, Chiara, Martinez, Karina A. Ortega, Shah, Vrutant V., Qian, Wei, Zhou, Jianying, Guzman-Rojas, Liliana, Matre, Polina, Taraballi, Francesca, Brannan, Kristopher W., Chang, Jenny C.
Published in Cancer research (Chicago, Ill.) (22.03.2024)
Published in Cancer research (Chicago, Ill.) (22.03.2024)
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Large-scale map of RNA binding protein interactomes across the mRNA life-cycle
Street, Lena, Rothamel, Katherine, Brannan, Kristopher, Jin, Wenhao, Bokor, Benjamin, Dong, Kevin, Rhine, Kevin, Madrigal, Assael, Al-Azzam, Norah, Kim, Jenny Kim, Ma, Yanzhe, Abdou, Ahmed, Wolin, Erica, Doron-Mandel, Ella, Ahdout, Joshua, Mujumdar, Mayuresh, Jovanovic, Marko, Yeo, Gene W
Published in bioRxiv (08.06.2023)
Published in bioRxiv (08.06.2023)
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