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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 …
CNV-guided multi-read allocation for ChIP-seq.
Zhang Q, Keleş S. Zhang Q, et al. Among authors: keles s. Bioinformatics. 2014 Oct 15;30(20):2860-7. doi: 10.1093/bioinformatics/btu402. Epub 2014 Jun 24. Bioinformatics. 2014. PMID: 24966364 Free PMC article.
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 …
GLANET: genomic loci annotation and enrichment tool.
Otlu B, Firtina C, Keles S, Tastan O. Otlu B, et al. Among authors: keles s. Bioinformatics. 2017 Sep 15;33(18):2818-2828. doi: 10.1093/bioinformatics/btx326. Bioinformatics. 2017. PMID: 28541490 Free PMC article.
400 results