Stanley N - Search Results

1

Dominant CD4⁺ T cell receptors remain stable throughout antiretroviral therapy-mediated immune restoration in people with HIV.

Sponaugle A, Weideman AMK, Ranek J, Atassi G, Kuruc J, Adimora AA, Archin NM, Gay C, Kuritzkes DR, Margolis DM, Vincent BG, Stanley N, Hudgens MG, Eron JJ, Goonetilleke N. Sponaugle A, et al. Among authors: stanley n. Cell Rep Med. 2023 Nov 21;4(11):101268. doi: 10.1016/j.xcrm.2023.101268. Epub 2023 Nov 9. Cell Rep Med. 2023. PMID: 37949070 Free PMC article.

2

Feature selection for preserving biological trajectories in single-cell data.

Ranek JS, Stallaert W, Milner J, Stanley N, Purvis JE. Ranek JS, et al. Among authors: stanley n. bioRxiv [Preprint]. 2023 May 12:2023.05.09.540043. doi: 10.1101/2023.05.09.540043. bioRxiv. 2023. Update in: Nat Commun. 2024 Mar 29;15(1):2765. doi: 10.1038/s41467-024-46773-z. PMID: 37214963 Free PMC article. Updated. Preprint.

3

DELVE: feature selection for preserving biological trajectories in single-cell data.

Ranek JS, Stallaert W, Milner JJ, Redick M, Wolff SC, Beltran AS, Stanley N, Purvis JE. Ranek JS, et al. Among authors: stanley n. Nat Commun. 2024 Mar 29;15(1):2765. doi: 10.1038/s41467-024-46773-z. Nat Commun. 2024. PMID: 38553455 Free PMC article.

4

Benchmarking differential abundance methods for finding condition-specific prototypical cells in multi-sample single-cell datasets.

Yi H, Plotkin A, Stanley N. Yi H, et al. Among authors: stanley n. bioRxiv [Preprint]. 2023 Feb 27:2023.02.24.529894. doi: 10.1101/2023.02.24.529894. bioRxiv. 2023. Update in: Genome Biol. 2024 Jan 3;25(1):9. doi: 10.1186/s13059-023-03143-0. PMID: 36909641 Free PMC article. Updated. Preprint.

5

scLKME: A Landmark-based Approach for Generating Multi-cellular Sample Embeddings from Single-cell Data.

Yi H, Stanley N. Yi H, et al. Among authors: stanley n. bioRxiv [Preprint]. 2023 Nov 15:2023.11.13.566846. doi: 10.1101/2023.11.13.566846. bioRxiv. 2023. PMID: 38014189 Free PMC article. Preprint.

6

A Graph Coarsening Algorithm for Compressing Representations of Single-Cell Data with Clinical or Experimental Attributes.

Chen CJ, Crawford E, Stanley N. Chen CJ, et al. Among authors: stanley n. Pac Symp Biocomput. 2023;28:85-96. Pac Symp Biocomput. 2023. PMID: 36540967 Free article.

7

Cellograph: a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks.

Shahir JA, Stanley N, Purvis JE. Shahir JA, et al. Among authors: stanley n. BMC Bioinformatics. 2024 Jan 15;25(1):25. doi: 10.1186/s12859-024-05641-9. BMC Bioinformatics. 2024. PMID: 38221640 Free PMC article.

8

Benchmarking differential abundance methods for finding condition-specific prototypical cells in multi-sample single-cell datasets.

Yi H, Plotkin A, Stanley N. Yi H, et al. Among authors: stanley n. Genome Biol. 2024 Jan 3;25(1):9. doi: 10.1186/s13059-023-03143-0. Genome Biol. 2024. PMID: 38172966 Free PMC article.

9

Effectiveness of the original monovalent mRNA COVID-19 vaccination series against hospitalization for COVID-19-associated venous thromboembolism.

Hager DN, Zhu Y, Sohn I, Stubblefield WB, Streiff MB, Gaglani M, Steingrub JS, Duggal A, Felzer JR, O'Rourke M, Peltan ID, Mohamed A, Stiller R, Wilson JG, Qadir N, Ginde AA, Zepeski AE, Mallow C, Lauring AS, Johnson NJ, Gibbs KW, Kwon JH, Self WH; Investigating Respiratory Viruses in the Acutely Ill (IVY) Network. Hager DN, et al. J Infect Dis. 2024 Oct 15:jiae502. doi: 10.1093/infdis/jiae502. Online ahead of print. J Infect Dis. 2024. PMID: 39405261

10

Conditional Similarity Triplets Enable Covariate-Informed Representations of Single-Cell Data.

Chen CJ, Yi H, Stanley N. Chen CJ, et al. Among authors: stanley n. Res Sq [Preprint]. 2024 Sep 12:rs.3.rs-4915088. doi: 10.21203/rs.3.rs-4915088/v1. Res Sq. 2024. PMID: 39315265 Free PMC article. Preprint.

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