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635 results

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Mixture model for sub-phenotyping in GWAS.
Warde-Farley D, Brudno M, Morris Q, Goldenberg A. Warde-Farley D, et al. Among authors: goldenberg a. Pac Symp Biocomput. 2012:363-74. Pac Symp Biocomput. 2012. PMID: 22174291 Free 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.
Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.
Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellón V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C; Members of the Rheumatoid Arthritis Challenge Consortium; Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TWJ, Kurreeman F, Allaart CF, Louis Bridges S Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM. Sieberts SK, et al. Among authors: goldenberg a. Nat Commun. 2016 Aug 23;7:12460. doi: 10.1038/ncomms12460. Nat Commun. 2016. PMID: 27549343 Free PMC article.
Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.
Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellón V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C; Members of the Rheumatoid Arthritis Challenge Consortium; Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TWJ, Kurreeman F, Allaart CF, Bridges SL Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM. Sieberts SK, et al. Among authors: goldenberg a. Nat Commun. 2016 Oct 10;7:13205. doi: 10.1038/ncomms13205. Nat Commun. 2016. PMID: 27721464 Free PMC article. 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):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.
635 results