Author

Richard E. Baker

University of Massachusetts Chan Medical School

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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Molecular Biology· 2 Bioinformatics· 1 Genetics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Organism:yeast· 3 Research Focus:differential expression· 2 Approach:experimental assay· 2 Organism:bacteria (other)· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Assay:CRISPR screen· 1

Frequent Co-Authors

Christopher M. SassettiiD· 2 shared Munira A. BasraiiD· 2 shared Allan JacobsoniD· 1 shared Ambro van HoofiD· 1 shared Anele GelaiD· 1 shared Anisha ZaveriiD· 1 shared Anita H. CorbettiD· 1 shared Clare M. SmithiD· 1 shared

Activity by Year

2018-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 12 mutual co-author links

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2 shared papersSystems Biology

Christopher M. SassettiORCID

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Author profile →

5 papers

Recent·Most cited

Cross-species blood transcriptional correlates of BCG-mediated protection against tuberculosis include innate and adaptive immune processes

Kate Bridges, Denis Awany, Anele Gela, Temwa-Dango Mwambene, Sherry L. Kurtz, Richard E. Baker, Karen L. Elkins, Christopher M. Sassetti, Thomas J. Scriba, Douglas A. Lauffenburger

This study identifies cross-species blood transcriptional correlates of BCG-mediated protection against tuberculosis using a systems modeling framework, linking innate and adaptive immune processes to vaccine efficacy in humans and non-human primates.

JCI Insight · Nov 11, 2025Peer-reviewedSystems Biology

Progressive polysomal association of Upf1, Upf2, and Upf3 as ribosomes traverse mRNA coding regions

Robin Ganesan, Kotchaphorn Mangkalaphiban, Richard E. Baker, Feng He, Allan Jacobson

The paper investigates the timing and nature of Upf1, Upf2, and Upf3 ribosome association during NMD, revealing progressive polysome association and an early Upf1:80S complex.

bioRxiv · Dec 3, 2021 · PreprintMolecular Biology

A Budding Yeast Model for Human Disease Mutations in the EXOSC2 Cap Subunit of the RNA Exosome

Maria C. Sterrett, Liz Enyenihi, Sara W. Leung, Laurie Hess, Sarah E. Strassler, Daniela Farchi, Richard Sean Lee, Elise S. Withers, Isaac Kremsky, Richard E. Baker, Munira A. Basrai, Ambro van Hoof, Milo B. Fasken, Anita H. Corbett

The paper creates a yeast model of SHRF mutations in EXOSC2 and compares it to an EXOSC3 mutation model, showing distinct RNA exosome functional impacts.

RNA · Jun 23, 2021Peer-reviewedGenetics

Statistical Analysis of Variability in TnSeq Data Across Conditions Using Zero-Inflated Negative Binomial Regression

Siddharth Subramaniyam, Michael A. DeJesus, Anisha Zaveri, Clare M. Smith, Richard E. Baker, Sabine Ehrt, Dirk Schnappinger, Christopher M. Sassetti, Thomas R. Ioerger

This paper introduces a statistical method using Zero-Inflated Negative Binomial regression to identify genes with significant variability in insertion counts across multiple conditions in TnSeq data.

BMC Bioinformatics · Nov 21, 2019Peer-reviewedBioinformatics

N-terminal sumoylation of centromeric histone H3 variant Cse4 regulates its proteolysis to prevent mislocalization to non-centromeric chromatin

Kentaro Ohkuni, Reuben Levy-Myers, Jack Warren, Wei-Chun Au, Yoshimitsu Takahashi, Richard E. Baker, Munira A. Basrai

This study identifies K65 as a SUMO site on Cse4 and shows that sumoylation regulates its ubiquitin-mediated proteolysis to prevent mislocalization and maintain genome stability.

G3 Genes Genomes Genetics · Feb 8, 2018Peer-reviewedMolecular Biology