Author

C. J. Ye

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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Immunology· 6 Cell Biology· 2

Signature Assays, Organisms & Methods

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Organism:human· 7 Research Focus:cell type annotation· 5 Approach:experimental assay· 5 Research Focus:differential expression· 4 Assay:scRNA-seq· 4 Research Focus:drug response / drug discovery· 3 Approach:statistical model· 3 Assay:CRISPR screen· 2

Frequent Co-Authors

Y. Sun· 4 shared A. Marson· 2 shared B. Hwang· 2 shared C. Wibrand· 2 shared D. B. Goodman· 2 shared E. Flynn· 2 shared G. K. Fragiadakis· 2 shared J. Eyquem· 2 shared

Activity by Year

2020-2023 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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4 shared papersImmunology

Y. Sun

Mutual co-authors in cluster

Author profile →

8 papers

Recent·Most cited

ADPKD-Causing Missense Variants in Polycystin-1 Disrupt Cell Surface Localization or Polycystin Channel Function

K. Ha, G. B. Loeb, M. Park, M. Gupta, Y. Akiyama, J. Argiris, A. Pinedo, C. H. Park, N. Brandes, F. Ritu, C. J. Ye, J. F. Reiter, M. Delling

This study classifies ADPKD-causing missense variants in polycystin-1 into two categories based on their effects on cell surface localization or ion channel function and suggests small-molecule therapies.

bioRxiv · Dec 4, 2023Cell Biology

Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics

G. Rabadam, C. Wibrand, E. Flynn, G. C. Hartoularos, Y. Sun, C. J. Ye, S. Kim, Z. J. Gartner, M. Sirota, J. Neely

This study uses single-cell transcriptomics to identify immune dysregulation in JDM, revealing coordinated type I interferon activity and B cell abnormalities.

bioRxiv · Nov 7, 2023Immunology

Deciphering Cell-types and Gene Signatures Associated with Disease Activity in Rheumatoid Arthritis using Single Cell RNA-sequencing

M. Binvignat, B. Miao, C. Wibrand, M. Yang, D. Rychkov, E. Flynn, J. Nititham, W. Tamaki, U. Khan, A. Carvidi, M. Krueger, E. Niemi, Y. Sun, G. K. Fragiadakis, J. Sellam, , M. Sirota

This study uses single-cell RNA sequencing of PBMCs from RA patients and controls to identify disease-associated cell subsets and gene signatures linked to RA disease activity.

bioRxiv · Oct 5, 2023 · PreprintImmunology

Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells

C. A. Tsuchida, N. Brandes, R. Bueno, M. Trinidad, T. Mazumder, B. Yu, B. Hwang, C. Chang, J. Liu, Y. Sun, C. R. Hopkins, K. R. Parker, Y. Qi, A. Satpathy, E. Stadtmauer, , J. A. Doudna

This study investigates chromosome loss in CRISPR-Cas9-engineered T cells and shows a modified manufacturing process reduces it while preserving editing efficacy.

bioRxiv · Mar 22, 2023Cell Biology

Modular Pooled Discovery of Synthetic Knockin Sequences to Program Durable Cell Therapies

F. Blaeschke, Y. Y. Chen, R. Apathy, Z. Li, C. T. Mowery, W. A. Nyberg, A. To, R. Yu, R. Bueno, M. C. Kim, R. Schmidt, D. B. Goodman, T. Feuchtinger, J. Eyquem, C. J. Ye, , A. Marson

The paper develops ModPoKI, a platform for modular construction of DNA knockin libraries to identify gene constructs that enhance T cell function and persistence.

bioRxiv · Jul 27, 2022Immunology

Naive arthritogenic SKG T cells have a defect in anergy and a repertoire pruned by superantigen

J. F. Ashouri, E. McCarthy, S. Yu, N. Perlmutter, C. Lin, J. DeRisi, C. J. Ye, A. Weiss

This study identifies a defect in anergy and a biased TCR repertoire in naive arthritogenic SKG CD4 T cells, driven by endogenous viral superantigens, leading to autoimmune arthritis.

bioRxiv · Jan 13, 2022 · PreprintImmunology

Pooled screening of CAR T cells identifies non-native signaling domains for next- generation immunotherapies

D. B. Goodman, C. S. Azimi, K. Kearns, K. Garakani, J. Garcia, N. Patel, B. Hwang, D. Lee, E. Park, C. J. Ye, A. Marson, J. Bluestone, K. Roybal

This study identifies non-native signaling domains in CAR T cells that enhance proliferation or cytotoxicity, offering improved designs for immunotherapies.

bioRxiv · Jul 11, 2021 · PreprintImmunology

Global Absence and Targeting of Protective Immune States in Severe COVID-19.

A. J. Combes, T. Courau, N. F. Kuhn, K. H. Hu, A. Ray, W. S. Chen, S. J. Clearly, N. W. Chew, D. Kushnoor, G. C. Reeder, A. Shen, J. Tsui, K. J. Hiam-Galvez, P. Munoz-Sandoval, W. S. Zhu, , M. F. Krummel

The paper identifies that severe COVID-19 patients lack ISG-expressing cells and have antibodies that block their production, contrasting with mild cases.

bioRxiv · Oct 28, 2020Immunology