Matthew D Simon (Matthew Simon)

ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 19

Top Venues

bioRxiv : the preprint server for biology

Biochemistry

Nucleic acids research

ACS chemical biology

Yale University

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Yale University

United States

Associate Professor :: Molecular Biophysics and Biochemistry

Publications

Jackson M Gordon, David V Phizicky, Leonard Schärfen, Courtney L Brown, Dahyana Arias Escayola, Jean Kanyo, Tukiet T Lam, Matthew D Simon, Karla M Neugebauer
Phosphorylation of the nuclear poly(A) binding protein (PABPN1) during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics. Nucleic acids research (2024)
Jackson M Gordon, David V Phizicky, Leonard Schärfen, Courtney L Brown, Dahyana Arias Escayola, Jean Kanyo, Tukiet T Lam, Matthew D Simon, Karla M Neugebauer
Phosphorylation of the nuclear poly(A) binding protein (PABPN1) during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics. Nucleic acids research (2024)
Michelle H Moon, Isaac W Vock, Andrew D Streit, Leah J Connor, Julia Senkina, Jonathan A Ellman, Matthew D Simon
Disulfide Tethering to Map Small Molecule Binding Sites Transcriptome-wide. ACS chemical biology (2024)
Stephen Abini-Agbomson, Kristjan Gretarsson, Rochelle M Shih, Laura Hsieh, Tracy Lou, Pablo De Ioannes, Nikita Vasilyev, Rachel Lee, Miao Wang, Matthew D Simon, Jean-Paul Armache, Evgeny Nudler, Geeta Narlikar, Shixin Liu, Chao Lu, Karim-Jean Armache
Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. bioRxiv : the preprint server for biology (2023)
Prajwal C Boddu, Abhishek Gupta, Rahul Roy, Barbara De La Pena Avalos, Ane Olazabal Herrero, Nils Neuenkirchen, Josh Zimmer, Namrata Chandhok, Darren King, Yashuhito Nannya, Seishi Ogawa, Haifan Lin, Matthew D Simon, Eloise Dray, Gary Kupfer, Amit K Verma, Karla M Neugebauer, Manoj M Pillai
Transcription elongation defects link oncogenic splicing factor mutations to targetable alterations in chromatin landscape. bioRxiv : the preprint server for biology (2023)
William J Lu-Culligan, Leah J Connor, Yixuan Xie, Babatunde E Ekundayo, Brendan T Rose, Martin Machyna, Andreas P Pintado-Urbanc, Joshua T Zimmer, Isaac W Vock, Natarajan V Bhanu, Megan C King, Benjamin A Garcia, Franziska Bleichert, Matthew D Simon
Acetyl-methyllysine marks chromatin at active transcription start sites. Nature (2023)
Joshua T Zimmer, Isaac W Vock, Jeremy A Schofield, Lea Kiefer, Michelle H Moon, Matthew D Simon
Improving the study of RNA dynamics through advances in RNA-seq with metabolic labeling and nucleotide-recoding chemistry. bioRxiv : the preprint server for biology (2023)
Shivali Patel, Alec N Sexton, Madison S Strine, Craig B Wilen, Matthew D Simon, Anna Marie Pyle
Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq. Nature communications 14 (1) (2023)
Prajwal C Boddu, Abhishek Gupta, Rahul Roy, Barbara De La Pena Avalos, Ane Olazabal Herrero, Nils Neuenkirchen, Josh Zimmer, Namrata Chandhok, Darren King, Yashuhito Nannya, Seishi Ogawa, Haifan Lin, Matthew D Simon, Eloise Dray, Gary Kupfer, Amit K Verma, Karla M Neugebauer, Manoj M Pillai
Transcription elongation defects link oncogenic splicing factor mutations to targetable alterations in chromatin landscape. bioRxiv : the preprint server for biology (2023)
Isaac W Vock, Matthew D Simon
bakR: Uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian Hierarchical modeling. RNA (New York, N.Y.) (2023)
Jake C Swartzel, Michael J Bond, Andreas P Pintado-Urbanc, Mehana Daftary, Mackenzie W Krone, Todd Douglas, Evan J Carder, Joshua T Zimmer, Takahiro Maeda, Matthew D Simon, Craig M Crews
Targeted Degradation of mRNA Decapping Enzyme DcpS by a VHL-Recruiting PROTAC. ACS chemical biology 17 (7) (2022)
Meaghan C S Courvan, Rachel O Niederer, Isaac W Vock, Lea Kiefer, Wendy V Gilbert, Matthew D Simon
Internally controlled RNA sequencing comparisons using nucleoside recoding chemistry. Nucleic acids research 50 (19) (2022)
Zhenkun Na, Yang Luo, Jeremy A Schofield, Stephanie Smelyansky, Alexandra Khitun, Sowndarya Muthukumar, Eugene Valkov, Matthew D Simon, Sarah A Slavoff
The NBDY Microprotein Regulates Cellular RNA Decapping. Biochemistry 59 (42) (2020)
Yang Luo, Jeremy A Schofield, Matthew D Simon, Sarah A Slavoff
Global Profiling of Cellular Substrates of Human Dcp2. Biochemistry 59 (43) (2020)
Martin Machyna, Lea Kiefer, Matthew D Simon
Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin. Nature structural & molecular biology 27 (3) (2020)
Lea Kiefer, Matthew D Simon
Stella's Role in Oocyte DNA Methylation Suggests Additional Activities of DNMT1. Biochemistry 58 (14) (2019)
Tyler S Smith, Madeline A Zoltek, Matthew D Simon
Reengineering a tRNA Methyltransferase To Covalently Capture New RNA Substrates. Journal of the American Chemical Society 141 (44) (2019)
Jeremy A Schofield, Erin E Duffy, Lea Kiefer, Meaghan C Sullivan, Matthew D Simon
TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding. Nature methods 15 (3) (2018)
Lea Kiefer, Jeremy A Schofield, Matthew D Simon
Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-Thioguanosine. Journal of the American Chemical Society 140 (44) (2018)

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Publication Activity (10 Years)

Top Topics

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Matthew D Simon (Matthew Simon)