Author

M. D. Simon

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Cancer Biology· 2 Biochemistry· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Assay:bulk RNA-seq· 2 Research Focus:gene regulatory network inference· 2 Organism:human· 2 Research Focus:cancer & tumor microenvironment· 1 Research Focus:cell signaling & trafficking· 1 Research Focus:cell type annotation· 1 Assay:ChIP-seq· 1

Frequent Co-Authors

J. T. Zimmer· 3 shared H. Lin· 2 shared K. M. Neugebauer· 2 shared L. Kiefer· 2 shared N. Neuenkirchen· 2 shared A. E. Barentine· 1 shared A. K. Gupta· 1 shared A. K. Verma· 1 shared

Activity by Year

2021-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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3 shared papersCancer Biology

J. T. Zimmer

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Author profile →

3 papers

Recent·Most cited

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

J. T. Zimmer, I. W. Vock, J. A. Schofield, L. Kiefer, M. H. Moon, M. D. Simon

This paper identifies and mitigates dropout in RNA metabolic labeling and NR-seq experiments through optimized protocols and improved alignment pipelines.

bioRxiv · May 24, 2023 · PreprintBiochemistry

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

P. C. Boddu, A. K. Gupta, R. Roy, B. De La Pena Avalos, A. Olazabal Herrero, N. Neuenkirchen, J. T. Zimmer, N. S. Chandhok, D. King, Y. Nannya, S. Ogawa, H. Lin, M. D. Simon, E. Dray, G. Kupfer, , M. M. Pillai

This paper shows that mutations in SF3B1 and U2AF1 cause transcription elongation defects leading to chromatin changes and identifies targeting the Sin3/HDAC complex as a potential therapy.

bioRxiv · Feb 25, 2023Cancer Biology

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

G. Biancon, P. Joshi, J. T. Zimmer, T. Hunck, Y. Gao, M. D. Lessard, E. Courchaine, A. E. Barentine, M. Machyna, V. Botti, A. Qin, R. Gbyli, A. Patel, Y. Song, L. Kiefer, , S. Halene

This study uses multi-omics profiling to analyze U2AF1 mutations in myeloid malignancies, revealing altered RNA binding, splicing, and stress granule formation.

bioRxiv · Apr 22, 2021Cancer Biology