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gkmSVM: an R package for gapped-kmer SVM.
Ghandi M, Mohammad-Noori M, Ghareghani N, Lee D, Garraway L, Beer MA. Ghandi M, et al. Among authors: beer ma. Bioinformatics. 2016 Jul 15;32(14):2205-7. doi: 10.1093/bioinformatics/btw203. Epub 2016 Apr 19. Bioinformatics. 2016. PMID: 27153639 Free PMC article.
Group normalization for genomic data.
Ghandi M, Beer MA. Ghandi M, et al. Among authors: beer ma. PLoS One. 2012;7(8):e38695. doi: 10.1371/journal.pone.0038695. Epub 2012 Aug 13. PLoS One. 2012. PMID: 22912661 Free PMC article.
Robust k-mer frequency estimation using gapped k-mers.
Ghandi M, Mohammad-Noori M, Beer MA. Ghandi M, et al. Among authors: beer ma. J Math Biol. 2014 Aug;69(2):469-500. doi: 10.1007/s00285-013-0705-3. Epub 2013 Jul 17. J Math Biol. 2014. PMID: 23861010 Free PMC article.
Enhanced regulatory sequence prediction using gapped k-mer features.
Ghandi M, Lee D, Mohammad-Noori M, Beer MA. Ghandi M, et al. Among authors: beer ma. PLoS Comput Biol. 2014 Jul 17;10(7):e1003711. doi: 10.1371/journal.pcbi.1003711. eCollection 2014 Jul. PLoS Comput Biol. 2014. PMID: 25033408 Free PMC article.
A comparative encyclopedia of DNA elements in the mouse genome.
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treu… See abstract for full author list ➔ Yue F, et al. Among authors: beer ma, ma z. Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992. Nature. 2014. PMID: 25409824 Free PMC article.
72 results