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Network enrichment analysis in complex experiments.
Shojaie A, Michailidis G. Shojaie A, et al. Stat Appl Genet Mol Biol. 2010;9(1):Article22. doi: 10.2202/1544-6115.1483. Epub 2010 May 22. Stat Appl Genet Mol Biol. 2010. PMID: 20597848 Free PMC article.
Discovering graphical Granger causality using the truncating lasso penalty.
Shojaie A, Michailidis G. Shojaie A, et al. Bioinformatics. 2010 Sep 15;26(18):i517-23. doi: 10.1093/bioinformatics/btq377. Bioinformatics. 2010. PMID: 20823316 Free PMC article.
AVAILABILITY: The proposed truncating lasso method is implemented in the R-package 'grangerTlasso' and is freely available at http://www.stat.lsa.umich.edu/~shojaie/....
AVAILABILITY: The proposed truncating lasso method is implemented in the R-package 'grangerTlasso' and is freely available at http://www.sta …
Network-based pathway enrichment analysis with incomplete network information.
Ma J, Shojaie A, Michailidis G. Ma J, et al. Among authors: Shojaie A. Bioinformatics. 2016 Oct 15;32(20):3165-3174. doi: 10.1093/bioinformatics/btw410. Epub 2016 Jun 29. Bioinformatics. 2016. PMID: 27357170 Free PMC article.
Combining Supervised and Unsupervised Learning for Improved miRNA Target Prediction.
Sedaghat N, Fathy M, Modarressi MH, Shojaie A. Sedaghat N, et al. Among authors: Shojaie A. IEEE/ACM Trans Comput Biol Bioinform. 2018 Sep-Oct;15(5):1594-1604. doi: 10.1109/TCBB.2017.2727042. Epub 2017 Jul 13. IEEE/ACM Trans Comput Biol Bioinform. 2018. PMID: 28715336 Free PMC article.
Gene set analysis methods: a systematic comparison.
Mathur R, Rotroff D, Ma J, Shojaie A, Motsinger-Reif A. Mathur R, et al. Among authors: Shojaie A. BioData Min. 2018 May 31;11:8. doi: 10.1186/s13040-018-0166-8. eCollection 2018. BioData Min. 2018. PMID: 29881462 Free PMC article.
Graph Estimation with Joint Additive Models.
Voorman A, Shojaie A, Witten D. Voorman A, et al. Among authors: Shojaie A. Biometrika. 2014 Mar 1;101(1):85-101. doi: 10.1093/biomet/ast053. Biometrika. 2014. PMID: 25013234 Free PMC article.
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