bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling

por Vock, Isaac W., Simon, Matthew D.
Publicado 2023

Solid phase chemistry to covalently and reversibly capture thiolated RNA

por Duffy, Erin E, Canzio, Daniele, Maniatis, Tom, Simon, Matthew D
Publicado 2018

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

por Fang, Rui, Moss, Walter N., Rutenberg-Schoenberg, Michael, Simon, Matthew D.
Publicado 2015

Carbodiimide reagents for the chemical probing of RNA structure in cells

por Wang, Peter Y., Sexton, Alec N., Culligan, William J., Simon, Matthew D.
Publicado 2019

TimeLapse-seq: Adding a temporal dimension to RNA sequencing through nucleoside recoding

por Schofield, Jeremy A., Duffy, Erin E., Kiefer, Lea, Sullivan, Meaghan C., Simon, Matthew D.
Publicado 2018

Improving the study of RNA dynamics through advances in RNA-seq with metabolic labeling and nucleotide-recoding chemistry

por Zimmer, Joshua T., Vock, Isaac W., Schofield, Jeremy A., Kiefer, Lea, Moon, Michelle H., Simon, Matthew D.
Publicado 2023

Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq

por Patel, Shivali, Sexton, Alec N., Strine, Madison S., Wilen, Craig B., Simon, Matthew D., Pyle, Anna Marie
Publicado 2023

Multiplexed Illumina sequencing libraries from picogram quantities of DNA

por Bowman, Sarah K, Simon, Matthew D, Deaton, Aimee M, Tolstorukov, Michael, Borowsky, Mark L, Kingston, Robert E
Publicado 2013

Internally controlled RNA sequencing comparisons using nucleoside recoding chemistry

por Courvan, Meaghan C S, Niederer, Rachel O, Vock, Isaac W, Kiefer, Lea, Gilbert, Wendy V, Simon, Matthew D
Publicado 2022

High-resolution Xist binding maps reveal 2-step spreading during X-inactivation

por Simon, Matthew D., Pinter, Stefan F., Fang, Rui, Sarma, Kavitha, Rutenberg-Schoenberg, Michael, Bowman, Sarah K., Kesner, Barry A., Maier, Verena K., Kingston, Robert E., Lee, Jeannie T.
Publicado 2013

m(6)A mRNA methylation controls T cell homeostasis by targeting IL-7/STAT5/SOCS pathway

por Li, Hua-Bing, Tong, Jiyu, Zhu, Shu, Batista, Pedro J., Duffy, Erin E., Zhao, Jun, Bailis, Will, Cao, Guangchao, Kroehling, Lina, Chen, Yuanyuan, Wang, Geng, Broughton, James P., Chen, Y. Grace, Kluger, Yuval, Simon, Matthew D., Chang, Howard Y., Yin, Zhinan, Flavell, Richard A.
Publicado 2017

ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m(6)A modification-mediated RNA stability control

por Gao, Yimeng, Zimmer, Joshua T., Vasic, Radovan, Liu, Chengyang, Gbyli, Rana, Zheng, Shu-Jian, Patel, Amisha, Liu, Wei, Qi, Zhihong, Li, Yaping, Nelakanti, Raman, Song, Yuanbin, Biancon, Giulia, Xiao, Andrew Z., Slavoff, Sarah, Kibbey, Richard G., Flavell, Richard A., Simon, Matthew D., Tebaldi, Toma, Li, Hua-Bing, Halene, Stephanie
Publicado 2023

Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection

por Wei, Jin, Alfajaro, Mia Madel, Hanna, Ruth E., DeWeirdt, Peter C., Strine, Madison S., Lu-Culligan, William J., Zhang, Shang-Min, Graziano, Vincent R., Schmitz, Cameron O., Chen, Jennifer S., Mankowski, Madeleine C., Filler, Renata B., Gasque, Victor, de Miguel, Fernando, Chen, Huacui, Oguntuyo, Kasopefoluwa, Abriola, Laura, Surovtseva, Yulia V., Orchard, Robert C., Lee, Benhur, Lindenbach, Brett, Politi, Katerina, van Dijk, David, Simon, Matthew D., Yan, Qin, Doench, John G., Wilen, Craig B.
Publicado 2020

Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection

por Wei, Jin, Alfajaro, Mia Madel, DeWeirdt, Peter C., Hanna, Ruth E., Lu-Culligan, William J., Cai, Wesley L., Strine, Madison S., Zhang, Shang-Min, Graziano, Vincent R., Schmitz, Cameron O., Chen, Jennifer S., Mankowski, Madeleine C., Filler, Renata B., Ravindra, Neal G., Gasque, Victor, de Miguel, Fernando J., Patil, Ajinkya, Chen, Huacui, Oguntuyo, Kasopefoluwa Y., Abriola, Laura, Surovtseva, Yulia V., Orchard, Robert C., Lee, Benhur, Lindenbach, Brett D., Politi, Katerina, van Dijk, David, Kadoch, Cigall, Simon, Matthew D., Yan, Qin, Doench, John G., Wilen, Craig B.
Publicado 2021