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Transparency and reproducibility in artificial intelligence.
Haibe-Kains B, Adam GA, Hosny A, Khodakarami F; Massive Analysis Quality Control (MAQC) Society Board of Directors; Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T, Hoffman MM, Leek JT, Korthauer K, Huber W, Brazma A, Pineau J, Tibshirani R, Hastie T, Ioannidis JPA, Quackenbush J, Aerts HJWL. Haibe-Kains B, et al. Among authors: goldenberg a. Nature. 2020 Oct;586(7829):E14-E16. doi: 10.1038/s41586-020-2766-y. Epub 2020 Oct 14. Nature. 2020. PMID: 33057217 Free PMC article.
Identifying cancer specific functionally relevant miRNAs from gene expression and miRNA-to-gene networks using regularized regression.
Mezlini AM, Wang B, Deshwar A, Morris Q, Goldenberg A. Mezlini AM, et al. Among authors: goldenberg a. PLoS One. 2013 Oct 2;8(10):e73168. doi: 10.1371/journal.pone.0073168. eCollection 2013. PLoS One. 2013. PMID: 24098326 Free PMC article.
Our method is based on a linear regression with an elastic net regularization. Our simulations show that, with our method, the active miRNAs can be detected with high accuracy and our approach is robust to high levels of noise and missing information. ...The code is availa …
Our method is based on a linear regression with an elastic net regularization. Our simulations show that, with our method, the active …
PharmacoGx: an R package for analysis of large pharmacogenomic datasets.
Smirnov P, Safikhani Z, El-Hachem N, Wang D, She A, Olsen C, Freeman M, Selby H, Gendoo DM, Grossmann P, Beck AH, Aerts HJ, Lupien M, Goldenberg A, Haibe-Kains B. Smirnov P, et al. Among authors: goldenberg a. Bioinformatics. 2016 Apr 15;32(8):1244-6. doi: 10.1093/bioinformatics/btv723. Epub 2015 Dec 9. Bioinformatics. 2016. PMID: 26656004
Assessment of pharmacogenomic agreement.
Safikhani Z, El-Hachem N, Quevedo R, Smirnov P, Goldenberg A, Juul Birkbak N, Mason C, Hatzis C, Shi L, Aerts HJ, Quackenbush J, Haibe-Kains B. Safikhani Z, et al. Among authors: goldenberg a. F1000Res. 2016 May 9;5:825. doi: 10.12688/f1000research.8705.1. eCollection 2016. F1000Res. 2016. PMID: 27408686 Free PMC article.
Safikhani et al. reply.
Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B. Safikhani Z, et al. Among authors: goldenberg a. Nature. 2016 Nov 30;540(7631):E6-E8. doi: 10.1038/nature20172. Nature. 2016. PMID: 27905416 No abstract available.
Safikhani et al. reply.
Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B. Safikhani Z, et al. Among authors: goldenberg a. Nature. 2016 Nov 30;540(7631):E11-E12. doi: 10.1038/nature20581. Nature. 2016. PMID: 27905423 No abstract available.
Safikhani et al. reply.
Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B. Safikhani Z, et al. Among authors: goldenberg a. Nature. 2016 Nov 30;540(7631):E2-E4. doi: 10.1038/nature19839. Nature. 2016. PMID: 27905430 No abstract available.
Revisiting inconsistency in large pharmacogenomic studies.
Safikhani Z, Smirnov P, Freeman M, El-Hachem N, She A, Rene Q, Goldenberg A, Birkbak NJ, Hatzis C, Shi L, Beck AH, Aerts HJWL, Quackenbush J, Haibe-Kains B. Safikhani Z, et al. Among authors: goldenberg a. F1000Res. 2016 Sep 16;5:2333. doi: 10.12688/f1000research.9611.3. eCollection 2016. F1000Res. 2016. PMID: 28928933 Free PMC article.
660 results