Ye CJ - Search Results

1

Changes in DNA methylation are associated with systemic lupus erythematosus flare remission and clinical subtypes.

Horton MK, Nititham J, Taylor KE, Katz P, Ye CJ, Yazdany J, Dall'Era M, Hurabielle C, Barcellos LF, Criswell LA, Lanata CM. Horton MK, et al. Among authors: ye cj. Clin Epigenetics. 2024 Dec 18;16(1):181. doi: 10.1186/s13148-024-01792-x. Clin Epigenetics. 2024. PMID: 39696438 Free PMC article.

2

Learning antibody sequence constraints from allelic inclusion.

Jagota M, Hsu C, Mazumder T, Sung K, DeWitt WS, Listgarten J, Matsen FA 4th, Ye CJ, Song YS. Jagota M, et al. Among authors: ye cj. bioRxiv [Preprint]. 2024 Oct 25:2024.10.22.619760. doi: 10.1101/2024.10.22.619760. bioRxiv. 2024. PMID: 39484623 Free PMC article. Preprint.

3

Endogenous antigens shape the transcriptome and TCR repertoire in an autoimmune arthritis model.

McCarthy EE, Yu S, Perlmutter N, Nakao Y, Naito R, Lin C, Riekher V, DeRisi J, Ye CJ, Weiss A, Ashouri JF. McCarthy EE, et al. Among authors: ye cj. J Clin Invest. 2024 Nov 26:e174647. doi: 10.1172/JCI174647. Online ahead of print. J Clin Invest. 2024. PMID: 39589811 Free article.

4

Physical inactivity exacerbates pathologic inflammatory signalling at the single cell level in patients with systemic lupus.

Patterson SL, Van Phan H, Ye CJ, Lanata C, González SC, Park J, Criswell LA, Barbour KE, Yazdany J, Dall'Era M, Sirota M, Katz P, Langelier CR. Patterson SL, et al. Among authors: ye cj. EBioMedicine. 2024 Dec;110:105432. doi: 10.1016/j.ebiom.2024.105432. Epub 2024 Nov 11. EBioMedicine. 2024. PMID: 39531917 Free PMC article.

5

Method of moments framework for differential expression analysis of single-cell RNA sequencing data.

Kim MC, Gate R, Lee DS, Tolopko A, Lu A, Gordon E, Shifrut E, Garcia-Nieto PE, Marson A, Ntranos V, Ye CJ. Kim MC, et al. Among authors: ye cj. Cell. 2024 Oct 31;187(22):6393-6410.e16. doi: 10.1016/j.cell.2024.09.044. Epub 2024 Oct 24. Cell. 2024. PMID: 39454576 Free article.

6

Coordinated, multicellular patterns of transcriptional variation that stratify patient cohorts are revealed by tensor decomposition.

Mitchel J, Gordon MG, Perez RK, Biederstedt E, Bueno R, Ye CJ, Kharchenko PV. Mitchel J, et al. Among authors: ye cj. Nat Biotechnol. 2024 Sep 23. doi: 10.1038/s41587-024-02411-z. Online ahead of print. Nat Biotechnol. 2024. PMID: 39313646

7

Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function.

Loeb GB, Kathail P, Shuai RW, Chung R, Grona RJ, Peddada S, Sevim V, Federman S, Mader K, Chu AY, Davitte J, Du J, Gupta AR, Ye CJ, Shafer S, Przybyla L, Rapiteanu R, Ioannidis NM, Reiter JF. Loeb GB, et al. Among authors: ye cj. Nat Genet. 2024 Oct;56(10):2078-2092. doi: 10.1038/s41588-024-01904-6. Epub 2024 Sep 10. Nat Genet. 2024. PMID: 39256582

8

Deciphering the impact of genomic variation on function.

IGVF Consortium. IGVF Consortium. Nature. 2024 Sep;633(8028):47-57. doi: 10.1038/s41586-024-07510-0. Epub 2024 Sep 4. Nature. 2024. PMID: 39232149 Review.

9

Cell-Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes.

Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye CJ, Dall'Era M, Yazdany J, Criswell LA, Fragiadakis GK, Langelier C, Capra JA, Sirota M, Lanata CM. Cutts Z, et al. Among authors: ye cj. ACR Open Rheumatol. 2024 Nov;6(11):769-779. doi: 10.1002/acr2.11713. Epub 2024 Aug 14. ACR Open Rheumatol. 2024. PMID: 39143499 Free PMC article.

10

Current genomic deep learning models display decreased performance in cell type-specific accessible regions.

Kathail P, Shuai RW, Chung R, Ye CJ, Loeb GB, Ioannidis NM. Kathail P, et al. Among authors: ye cj. Genome Biol. 2024 Aug 1;25(1):202. doi: 10.1186/s13059-024-03335-2. Genome Biol. 2024. PMID: 39090688 Free PMC article.

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