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atSNP: transcription factor binding affinity testing for regulatory SNP detection.
Zuo C, Shin S, Keleş S. Zuo C, et al. Among authors: keles s. Bioinformatics. 2015 Oct 15;31(20):3353-5. doi: 10.1093/bioinformatics/btv328. Epub 2015 Jun 18. Bioinformatics. 2015. PMID: 26092860 Free PMC article.
RESULTS: We describe A: ffinity T: esting for regulatory SNP: s (atSNP), a computationally efficient R package for identifying rSNPs in silico. atSNP implements an importance sampling algorithm coupled with a first-order Markov model for the background nucleotide sequences …
RESULTS: We describe A: ffinity T: esting for regulatory SNP: s (atSNP), a computationally efficient R package for identifying rSNPs …
Identification of regulatory elements using a feature selection method.
Keleş S, van der Laan M, Eisen MB. Keleş S, et al. Bioinformatics. 2002 Sep;18(9):1167-75. doi: 10.1093/bioinformatics/18.9.1167. Bioinformatics. 2002. PMID: 12217908
We apply this method to a publicly available dataset of the yeast Saccharomyces cerevisiae, focussing on the 800 basepairs immediately upstream of each gene's translation start site (the upstream control region (UCR)). RESULTS: We successfully identify regulatory motifs th …
We apply this method to a publicly available dataset of the yeast Saccharomyces cerevisiae, focussing on the 800 basepairs immediately upstr …
Regulatory motif finding by logic regression.
Keles S, van der Laan MJ, Vulpe C. Keles S, et al. Bioinformatics. 2004 Nov 1;20(16):2799-811. doi: 10.1093/bioinformatics/bth333. Epub 2004 May 27. Bioinformatics. 2004. PMID: 15166027
Statistical analysis of ChIP-seq data with MOSAiCS.
Sun G, Chung D, Liang K, Keleş S. Sun G, et al. Among authors: keles s. Methods Mol Biol. 2013;1038:193-212. doi: 10.1007/978-1-62703-514-9_12. Methods Mol Biol. 2013. PMID: 23872977
A community effort to assess and improve drug sensitivity prediction algorithms.
Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K; NCI DREAM Community; Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G. Costello JC, et al. Nat Biotechnol. 2014 Dec;32(12):1202-12. doi: 10.1038/nbt.2877. Epub 2014 Jun 1. Nat Biotechnol. 2014. PMID: 24880487 Free PMC article.
375 results