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deepTools2: a next generation web server for deep-sequencing data analysis.
Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, Richter AS, Heyne S, Dündar F, Manke T. Ramírez F, et al. Among authors: ryan dp. Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5. doi: 10.1093/nar/gkw257. Epub 2016 Apr 13. Nucleic Acids Res. 2016. PMID: 27079975 Free PMC article.
Community-Driven Data Analysis Training for Biology.
Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz HR, Houwaart T, Jagtap P, Larivière D, Le Corguillé G, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D; Galaxy Training Network; Taylor J, Backofen R, Nekrutenko A, Grüning B. Batut B, et al. Cell Syst. 2018 Jun 27;6(6):752-758.e1. doi: 10.1016/j.cels.2018.05.012. Cell Syst. 2018. PMID: 29953864 Free PMC article.
RELACS nuclei barcoding enables high-throughput ChIP-seq.
Arrigoni L, Al-Hasani H, Ramírez F, Panzeri I, Ryan DP, Santacruz D, Kress N, Pospisilik JA, Bönisch U, Manke T. Arrigoni L, et al. Among authors: ryan dp. Commun Biol. 2018 Dec 5;1:214. doi: 10.1038/s42003-018-0219-z. eCollection 2018. Commun Biol. 2018. PMID: 30534606 Free PMC article.
Hypofractionated Radiotherapy-Related Lymphopenia Is Associated With Worse Survival in Unresectable Intrahepatic Cholangiocarcinoma.
Lee G, Kim DW, Smart AC, Horick NK, Eyler CE, Roberts HJ, Pathak P, Goyal L, Franses J, Heather JM, Hwang WL, Grassberger C, Klempner SJ, Drapek LC, Allen JN, Blaszkowsky LS, Parikh AR, Ryan DP, Clark JW, Hong TS, Wo JY. Lee G, et al. Among authors: ryan dp. Am J Clin Oncol. 2024 May 20. doi: 10.1097/COC.0000000000001108. Online ahead of print. Am J Clin Oncol. 2024. PMID: 38767086
Transfer Learning Reveals Cancer-Associated Fibroblasts Are Associated with Epithelial-Mesenchymal Transition and Inflammation in Cancer Cells in Pancreatic Ductal Adenocarcinoma.
Guinn S, Kinny-Köster B, Tandurella JA, Mitchell JT, Sidiropoulos DN, Loth M, Lyman MR, Pucsek AB, Zabransky DJ, Lee JW, Kartalia E, Ramani M, Seppälä TT, Cherry C, Suri R, Zlomke H, Patel J, He J, Wolfgang CL, Yu J, Zheng L, Ryan DP, Ting DT, Kimmelman A, Gupta A, Danilova L, Elisseeff JH, Wood LD, Stein-O'Brien G, Kagohara LT, Jaffee EM, Burkhart RA, Fertig EJ, Zimmerman JW. Guinn S, et al. Among authors: ryan dp. Cancer Res. 2024 May 2;84(9):1517-1533. doi: 10.1158/0008-5472.CAN-23-1660. Cancer Res. 2024. PMID: 38587552
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