Matthew D. Simon

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 31 papers. Top paper: “Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection”.

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

Cell(2020)10.1016/j.cell.2020.10.028

N/A

0.955DataRank · unranked

580 citations

Mia Madel Alfajaro, Peter C. DeWeirdt, Ruth E. Hanna, William J. Lu-Culligan, Wesley L. Cai +26 more

Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies

Molecular Cell(2022)10.1016/j.molcel.2022.02.025

N/A

0.665DataRank · unranked

83 citations

Poorval Joshi, Joshua T. Zimmer, Torben Hunck, Yimeng Gao, Mark D. Lessard +18 more

STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts

Molecular Cell(2021)10.1016/j.molcel.2021.08.019

N/A

0.581DataRank · unranked

47 citations

Nicolle A. Rosa-Mercado, Daniele Canzio, Joan A. Steitz, Matthew D. Simon, Joshua T. Zimmer

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

Nature Communications(2023)10.1038/s41467-023-38623-1

N/A

0.530DataRank · unranked

11 citations

Alec N. Sexton, Madison S. Strine, Craig B. Wilen, Matthew D. Simon, Anna Marie Pyle +1 more

Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis

Molecular Cell(2025)10.1016/j.molcel.2025.02.025

N/A

0.396DataRank · unranked

13 citations

Isaac W. Vock, Matthew D. Simon, Karla M. Neugebauer, Leonard Schärfen

Phosphorylation of the nuclear poly(A) binding protein (PABPN1) during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics

Nucleic Acids Research(2024)10.1093/nar/gkae562

N/A

0.381DataRank · unranked

7 citations

David V. Phizicky, Leonard Schärfen, Courtney L Brown, Dahyana Arias Escayola, Jean Kanyo +4 more

RBM15-MKL1 fusion protein promotes leukemia via m6A methylation and Wnt pathway activation

Blood(2025)10.1182/blood.2024027712

N/A

0.360DataRank · unranked

10 citations

Giulia Biancon, Manyi Wei, Christian Ramirez, Irene Moratti, Andreas P. Pintado-Urbanc +10 more

Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination

Molecular Cell(2025)10.1016/j.molcel.2025.02.007

N/A

0.345DataRank · unranked

9 citations

Anurupa Devi Yadavalli, Filip Šenigl, Gabriel Matos‐Rodrigues, Dijin Xu, Andreas P. Pintado-Urbanc +5 more

Internally controlled RNA sequencing comparisons using nucleoside recoding chemistry

Nucleic Acids Research(2022)10.1093/nar/gkac693

N/A

0.329DataRank · unranked

5 citations

Rachel O. Niederer, Isaac W. Vock, Lea Kiefer, W Gilbert, Matthew D. Simon +1 more

Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite

PLoS Computational Biology(2025)10.1371/journal.pcbi.1013179

N/A

0.312DataRank · unranked

7 citations

Justin W. Mabin, Martin Machyna, Alexandra Zhang, J. Robert Hogg, Matthew D. Simon +1 more

RNADecayCafe, a uniformly processed atlas of RNA half-life estimates across multiple human cell lines

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.19.671151

N/A

0.165DataRank · unranked

2 citations

Dié Tang, Antonio J. Giráldez, Matthew D. Simon, Isaac W. Vock

ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m6A modification-mediated RNA stability control

Cell Reports(2023)10.1016/j.celrep.2023.113163

N/A

0DataRank · unranked

43 citations

Joshua T. Zimmer, Radovan Vasic, Chengyang Liu, Rana Gbyli, Shu-Jian Zheng +16 more

Acetyl-methyllysine marks chromatin at active transcription start sites

Nature(2023)10.1038/s41586-023-06565-9

N/A

0DataRank · unranked

32 citations

Leah J. Connor, Yixuan Xie, Babatunde Ekundayo, Brendan T Rose, Martin Machyna +9 more

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

RNA(2023)10.1261/rna.079451.122

N/A

0DataRank · unranked

29 citations

Matthew D. Simon, Isaac W. Vock

Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1

Molecular Cell(2023)10.1016/j.molcel.2023.07.020

N/A

0DataRank · unranked

18 citations

Kristjan H. Gretarsson, Rochelle M. Shih, Laura J Hsieh, Tracy Lou, Pablo De Ioannes +11 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.24.542133

N/A

0DataRank · unranked

5 citations

Isaac W. Vock, Jeremy A. Schofield, Lea Kiefer, Michelle H. Moon, Matthew D. Simon +1 more

Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape

Molecular Cell(2024)10.1016/j.molcel.2024.02.032

N/A

0DataRank · unranked

38 citations

Abhishek Gupta, Rahul Roy, Bárbara de la Peña Avalos, Anne Olazabal‐Herrero, Nils Neuenkirchen +13 more

Disulfide Tethering to Map Small Molecule Binding Sites Transcriptome-wide

ACS Chemical Biology(2024)10.1021/acschembio.4c00538

N/A

0DataRank · unranked

4 citations

Isaac W. Vock, Andrew D. Streit, Leah J. Connor, Julia Senkina, Jonathan A. Ellman +2 more

Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.09.24.614732

N/A

0DataRank · unranked

1 citations

Anurupa Devi Yadavalli, Gabriel Matos‐Rodrigues, Dijin Xu, Andreas P. Pintado-Urbanc, Matthew D. Simon +4 more

Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.10.14.617411

N/A

0DataRank · unranked

1 citations

Justin W. Mabin, Martin Machyna, Alexandra Zhang, J. Robert Hogg, Matthew D. Simon +1 more

MYOD represses gene expression from non-E-box motifs

Genes & Development(2025)10.1101/gad.352708.125

N/A

0DataRank · unranked

1 citations

Jimmy Massenet, Andreas P. Pintado-Urbanc, Leah J. Connor, Monica Nicolau, Swetha J. Sundar +12 more

p53 Activates the Long Noncoding RNA Pvt1b to Inhibit Myc and Suppress Tumorigenesis

Molecular Cell(2020)10.1016/j.molcel.2019.12.014

N/A

0DataRank · unranked

156 citations

Elena Martínez‐Terroba, Joshua T. Zimmer, Clara Liao, Ephrath Tesfaye, Nima Hooshdaran +7 more

Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitor

Cell chemical biology(2020)10.1016/j.chembiol.2020.12.003

N/A

0DataRank · unranked

20 citations

Jeremy A. Schofield, Zhenkun Na, Tanja Hann, Matthew D. Simon, Sarah A. Slavoff +1 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.16.155101

N/A

0DataRank · unranked

70 citations

Mia Madel Alfajaro, Ruth E. Hanna, Peter C. DeWeirdt, Madison S. Strine, William J. Lu-Culligan +22 more

Hyperosmotic stress induces downstream-of-gene transcription and alters the RNA Polymerase II interactome despite widespread transcriptional repression

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.30.178103

N/A

0DataRank · unranked

0 citations

Joshua T. Zimmer, Maria Apostolidi, Jesse Rinehart, Matthew D. Simon, Joan A. Steitz +1 more

Discovery of cellular substrates of human RNA decapping enzyme Dcp2 using a stapled bicyclic peptide inhibitor

ChemRxiv(2020)10.26434/chemrxiv.12233102

N/A

0DataRank · unranked

0 citations

Zhenkun Na, Sarah A. Slavoff, Matthew D. Simon, Jeremy A. Schofield, Tanja Hann +1 more

Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression

Molecular Cell(2021)10.1016/j.molcel.2020.12.002

N/A

0DataRank · unranked

105 citations

Joshua T. Zimmer, Maria Apostolidi, Jesse Rinehart, Matthew D. Simon, Joan A. Steitz +1 more

Multi-omics profiling of U2AF1 mutants dissects pathogenic mechanisms affecting RNA granules in myeloid malignancies

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.22.441020

N/A

0DataRank · unranked

3 citations

Poorval Joshi, Joshua T. Zimmer, Torben Hunck, Yimeng Gao, Mark D. Lessard +18 more

Functional elements of the cis-regulatory lincRNA-p21

Cell Reports(2022)10.1016/j.celrep.2022.110687

N/A

0DataRank · unranked

37 citations

M. Ángeles Jiménez, Joshua T. Zimmer, Adam Williams, Matthew D. Simon, Nadya Dimitrova +1 more

Targeted Degradation of mRNA Decapping Enzyme DcpS by a VHL-Recruiting PROTAC

ACS Chemical Biology(2022)10.1021/acschembio.2c00145

N/A

0DataRank · unranked

15 citations

Michael J. Bond, Andreas P. Pintado-Urbanc, Mehana Daftary, Mackenzie W. Krone, Todd Douglas +6 more

Differential kinetic analysis using nucleotide recoding RNA-seq and bakR

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.02.505697

N/A

0DataRank · unranked

0 citations

Matthew D. Simon, Isaac W. Vock