Publications by authors named "Matthew D Simon"

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Investigation of TRMT61B methyltransferase activity on mRNA and its effects on translation.
Dorthy Fang, John M Babich, Ryan Stanton, Isaac W Vock, Kyrillos Abdallah, Matthew D Simon

bioRxiv· December 2025

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MYOD represses gene expression from non-E-box motifs.
Chiara Nicoletti, Jimmy Massenet, Andreas P Pintado-Urbanc, Leah J Connor, Monica Nicolau, Matthew D Simon

Genes Dev· November 2025

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RBM15-MKL1 fusion protein promotes leukemia via m6A methylation and Wnt pathway activation.
Madeline Y Mayday, Giulia Biancon, Manyi Wei, Christian Ramirez, Irene Moratti, Matthew D Simon

Blood· August 2025

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RNADecayCafe, a uniformly processed atlas of RNA half-life estimates across multiple human cell lines.
Isaac W Vock, Dié Tang, Antonio J Giraldez, Matthew D Simon

bioRxiv· August 2025

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Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite.
Isaac W Vock, Justin W Mabin, Martin Machyna, Alexandra Zhang, J Robert Hogg, Matthew D Simon

PLoS Comput Biol· July 2025

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Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.
Lizhen Wu, Anurupa Devi Yadavalli, Filip Senigl, Gabriel Matos-Rodrigues, Dijin Xu, Matthew D Simon

Mol Cell· April 2025

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Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis.
Leonard Schärfen, Isaac W Vock, Matthew D Simon, Karla M Neugebauer

Mol Cell· April 2025

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Uncovering the isoform-resolution kinetic landscape of nonsense-mediated mRNA decay with EZbakR.
Justin W Mabin, Isaac W Vock, Martin Machyna, Nazmul Haque, Poonam Thakran, Matthew D Simon

bioRxiv· March 2025

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RBM15-MKL1 fusion protein promotes leukemia via m6A methylation and WNT pathway activation.
Madeline Y Mayday, Giulia Biancon, Manyi Wei, Christian Ramirez, Irene Moratti, Matthew D Simon

bioRxiv· February 2025

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E-box independent chromatin recruitment turns MYOD into a transcriptional repressor.
Chiara Nicoletti, Jimmy Massenet, Andreas P Pintado-Urbanc, Leah J Connor, Monica Nicolau, Matthew D Simon

bioRxiv· December 2024

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Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis.
Leonard Schärfen, Isaac W Vock, Matthew D Simon, Karla M Neugebauer

bioRxiv· November 2024

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Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite.
Isaac W Vock, Justin W Mabin, Martin Machyna, Alexandra Zhang, J Robert Hogg, Matthew D Simon

bioRxiv· October 2024

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Phosphorylation of the nuclear poly(A) binding protein (PABPN1) during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics.
Jackson M Gordon, David V Phizicky, Leonard Schärfen, Courtney L Brown, Dahyana Arias Escayola, Matthew D Simon

Nucleic Acids Res· September 2024

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Disulfide Tethering to Map Small Molecule Binding Sites Transcriptome-wide.
Michelle H Moon, Isaac W Vock, Andrew D Streit, Leah J Connor, Julia Senkina, Matthew D Simon

ACS Chem Biol· September 2024

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Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.
Lizhen Wu, Anurupa Devi Yadavalli, Gabriel Matos-Rodrigues, Dijin Xu, Andreas P Pintado-Urbanc, Matthew D Simon

bioRxiv· September 2024

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Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape.
Prajwal C Boddu, Abhishek K Gupta, Rahul Roy, Bárbara De La Peña Avalos, Anne Olazabal-Herrero, Matthew D Simon

Mol Cell· April 2024

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Acetyl-methyllysine marks chromatin at active transcription start sites.
William J Lu-Culligan, Leah J Connor, Yixuan Xie, Babatunde E Ekundayo, Brendan T Rose, Matthew D Simon

Nature· October 2023

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ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through mA modification-mediated RNA stability control.
Yimeng Gao, Joshua T Zimmer, Radovan Vasic, Chengyang Liu, Rana Gbyli, Matthew D Simon

Cell Rep· October 2023

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Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1.
Stephen Abini-Agbomson, Kristjan Gretarsson, Rochelle M Shih, Laura Hsieh, Tracy Lou, Matthew D Simon

Mol Cell· August 2023

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bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling.
Isaac W Vock, Matthew D Simon

RNA· July 2023

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Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq.
Shivali Patel, Alec N Sexton, Madison S Strine, Craig B Wilen, Matthew D Simon

Nat Commun· June 2023

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Improving the study of RNA dynamics through advances in RNA-seq with metabolic labeling and nucleotide-recoding chemistry.
Joshua T Zimmer, Isaac W Vock, Jeremy A Schofield, Lea Kiefer, Michelle H Moon, Matthew D Simon

bioRxiv· May 2023

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Internally controlled RNA sequencing comparisons using nucleoside recoding chemistry.
Meaghan C S Courvan, Rachel O Niederer, Isaac W Vock, Lea Kiefer, Wendy V Gilbert, Matthew D Simon

Nucleic Acids Res· October 2022

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Targeted Degradation of mRNA Decapping Enzyme DcpS by a VHL-Recruiting PROTAC.
Jake C Swartzel, Michael J Bond, Andreas P Pintado-Urbanc, Mehana Daftary, Mackenzie W Krone, Matthew D Simon

ACS Chem Biol· July 2022

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Functional elements of the cis-regulatory lincRNA-p21.
Lauren Winkler, Maria Jimenez, Joshua T Zimmer, Adam Williams, Matthew D Simon

Cell Rep· April 2022

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