Author

Ruixi Chen

Massachusetts Institute of TechnologyORCID 0000-0002-3663-9768Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Microbiology· 1 Neuroscience· 1

Signature Assays, Organisms & Methods

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Research Focus:differential expression· 3 Approach:statistical model· 3 Research Focus:cell type annotation· 2 Assay:proteomics· 2 Organism:bacteria (other)· 1 Research Focus:benchmarking· 1 Assay:DNA methylation· 1 Approach:experimental assay· 1

Frequent Co-Authors

Peter C. DedoniD· 2 shared Thomas J. BegleyiD· 2 shared Abigail E. McShane· 1 shared Agnieszka DziergowskaiD· 1 shared Andrew EmiliiD· 1 shared Benjamin L. WoloziniD· 1 shared Caleb M. AndersoniD· 1 shared Chi Kong Chan· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

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2 shared papersMicrobiology

Peter C. DedonORCID

Mutual co-authors in cluster

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3 papers

Recent·Most cited

Growth-dependent tRNA Reprogramming and Codon Bias Link Translation to Metabolic State in Enterococcus faecalis

Michelle M. Mitchener, Caleb M. Anderson, Mark Veleba, Kayla Teo, Mélanie Roch, Ruixi Chen, Yifeng Yuan, Isaiah Han, Agnieszka Dziergowska, Kévin Pethe, Thomas J. Begley, Kimberly A. Kline, Peter C. Dedon

This study examines how tRNA reprogramming and codon bias link translation to metabolic state in Enterococcus faecalis across growth phases.

mBio · Aug 31, 2026Peer-reviewedMicrobiology

Distinct age- and pathology-dependent epitranscriptome and translational dysfunction in a tauopathy mouse model

Guangxin Sun, Weiwei Lin, Ruixi Chen, Lulu Jiang, Michael S. DeMott, Abigail E. McShane, Chi Kong Chan, Dylan J. Ehrbar, Xiaoling Zhang, Thomas J. Begley, Andrew Emili, Benjamin L. Wolozin, Peter C. Dedon

This study investigates age- and pathology-dependent changes in the epitranscriptome and translational dysfunction in a tauopathy mouse model, revealing significant alterations in tRNA biology and codon usage patterns.

bioRxiv · May 15, 2025 · PreprintNeuroscience

starTracer: An Accelerated Approach for Precise Marker Gene Identification in Single-Cell RNA-Seq Analysis

Feiyang Zhang, Kaixin Huang, Ruixi Chen, Zechen Liu, Qiongyi Zhao, Shengqun Hou, Wenhao Ma, Yanze Li, Yan Peng, Jincao Chen, Dan Ohtan Wang, Wei Wei, Xiang Li

starTracer improves marker gene identification in single-cell RNA-seq by enhancing specificity and speed compared to Seurat.

Communications Biology · Sep 12, 2024Peer-reviewedBioinformatics