Street K - Search Results

1

Progressive immune dysfunction with advancing disease stage in renal cell carcinoma.

Braun DA, Street K, Burke KP, Cookmeyer DL, Denize T, Pedersen CB, Gohil SH, Schindler N, Pomerance L, Hirsch L, Bakouny Z, Hou Y, Forman J, Huang T, Li S, Cui A, Keskin DB, Steinharter J, Bouchard G, Sun M, Pimenta EM, Xu W, Mahoney KM, McGregor BA, Hirsch MS, Chang SL, Livak KJ, McDermott DF, Shukla SA, Olsen LR, Signoretti S, Sharpe AH, Irizarry RA, Choueiri TK, Wu CJ. Braun DA, et al. Among authors: street k. Cancer Cell. 2021 May 10;39(5):632-648.e8. doi: 10.1016/j.ccell.2021.02.013. Epub 2021 Mar 11. Cancer Cell. 2021. PMID: 33711273 Free PMC article.

2

Significance analysis for clustering with single-cell RNA-sequencing data.

Grabski IN, Street K, Irizarry RA. Grabski IN, et al. Among authors: street k. Nat Methods. 2023 Aug;20(8):1196-1202. doi: 10.1038/s41592-023-01933-9. Epub 2023 Jul 10. Nat Methods. 2023. PMID: 37429993

3

MUC1-C Dictates JUN and BAF-Mediated Chromatin Remodeling at Enhancer Signatures in Cancer Stem Cells.

Bhattacharya A, Fushimi A, Yamashita N, Hagiwara M, Morimoto Y, Rajabi H, Long MD, Abdulla M, Ahmad R, Street K, Liu S, Liu T, Kufe D. Bhattacharya A, et al. Among authors: street k. Mol Cancer Res. 2022 Apr 1;20(4):556-567. doi: 10.1158/1541-7786.MCR-21-0672. Mol Cancer Res. 2022. PMID: 35022313 Free PMC article.

4

Trajectory-based differential expression analysis for single-cell sequencing data.

Van den Berge K, Roux de Bézieux H, Street K, Saelens W, Cannoodt R, Saeys Y, Dudoit S, Clement L. Van den Berge K, et al. Among authors: street k. Nat Commun. 2020 Mar 5;11(1):1201. doi: 10.1038/s41467-020-14766-3. Nat Commun. 2020. PMID: 32139671 Free PMC article.

5

Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects.

Van den Berge K, Chou HJ, Roux de Bézieux H, Street K, Risso D, Ngai J, Dudoit S. Van den Berge K, et al. Among authors: street k. Cell Rep Methods. 2022 Nov 1;2(11):100321. doi: 10.1016/j.crmeth.2022.100321. eCollection 2022 Nov 21. Cell Rep Methods. 2022. PMID: 36452861 Free PMC article.

6

A Guide to Trajectory Inference and RNA Velocity.

Weiler P, Van den Berge K, Street K, Tiberi S. Weiler P, et al. Among authors: street k. Methods Mol Biol. 2023;2584:269-292. doi: 10.1007/978-1-0716-2756-3_14. Methods Mol Biol. 2023. PMID: 36495456

7

Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution.

Fletcher RB, Das D, Gadye L, Street KN, Baudhuin A, Wagner A, Cole MB, Flores Q, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J. Fletcher RB, et al. Cell Stem Cell. 2017 Jun 1;20(6):817-830.e8. doi: 10.1016/j.stem.2017.04.003. Epub 2017 May 11. Cell Stem Cell. 2017. PMID: 28506465 Free PMC article.

8

Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference.

Perraudeau F, Risso D, Street K, Purdom E, Dudoit S. Perraudeau F, et al. Among authors: street k. F1000Res. 2017 Jul 21;6:1158. doi: 10.12688/f1000research.12122.1. eCollection 2017. F1000Res. 2017. PMID: 28868140 Free PMC article.

9

Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities.

Gadye L, Das D, Sanchez MA, Street K, Baudhuin A, Wagner A, Cole MB, Choi YG, Yosef N, Purdom E, Dudoit S, Risso D, Ngai J, Fletcher RB. Gadye L, et al. Among authors: street k. Cell Stem Cell. 2017 Dec 7;21(6):775-790.e9. doi: 10.1016/j.stem.2017.10.014. Epub 2017 Nov 22. Cell Stem Cell. 2017. PMID: 29174333 Free PMC article.

10

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

Street K, Risso D, Fletcher RB, Das D, Ngai J, Yosef N, Purdom E, Dudoit S. Street K, et al. BMC Genomics. 2018 Jun 19;19(1):477. doi: 10.1186/s12864-018-4772-0. BMC Genomics. 2018. PMID: 29914354 Free PMC article.

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