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CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.
Parra G, Bradnam K, Korf I. Parra G, et al. Bioinformatics. 2007 May 1;23(9):1061-7. doi: 10.1093/bioinformatics/btm071. Epub 2007 Mar 1. Bioinformatics. 2007. PMID: 17332020
GC skew is a conserved property of unmethylated CpG island promoters across vertebrates.
Hartono SR, Korf IF, Chédin F. Hartono SR, et al. Nucleic Acids Res. 2015 Nov 16;43(20):9729-41. doi: 10.1093/nar/gkv811. Epub 2015 Aug 7. Nucleic Acids Res. 2015. PMID: 26253743 Free PMC article.
Applying word-based algorithms: the IMEter.
Korf IF, Rose AB. Korf IF, et al. Methods Mol Biol. 2009;553:287-301. doi: 10.1007/978-1-60327-563-7_14. Methods Mol Biol. 2009. PMID: 19588111 Review.
R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters.
Ginno PA, Lott PL, Christensen HC, Korf I, Chédin F. Ginno PA, et al. Mol Cell. 2012 Mar 30;45(6):814-25. doi: 10.1016/j.molcel.2012.01.017. Epub 2012 Mar 1. Mol Cell. 2012. PMID: 22387027 Free PMC article.
Large-scale methylation domains mark a functional subset of neuronally expressed genes.
Schroeder DI, Lott P, Korf I, LaSalle JM. Schroeder DI, et al. Genome Res. 2011 Oct;21(10):1583-91. doi: 10.1101/gr.119131.110. Epub 2011 Jul 22. Genome Res. 2011. PMID: 21784875 Free PMC article.
StochHMM: a flexible hidden Markov model tool and C++ library.
Lott PC, Korf I. Lott PC, et al. Bioinformatics. 2014 Jun 1;30(11):1625-6. doi: 10.1093/bioinformatics/btu057. Epub 2014 Jan 30. Bioinformatics. 2014. PMID: 24489371 Free PMC article.
SAMSA: a comprehensive metatranscriptome analysis pipeline.
Westreich ST, Korf I, Mills DA, Lemay DG. Westreich ST, et al. BMC Bioinformatics. 2016 Sep 29;17(1):399. doi: 10.1186/s12859-016-1270-8. BMC Bioinformatics. 2016. PMID: 27687690 Free PMC article.
SAMSA2: a standalone metatranscriptome analysis pipeline.
Westreich ST, Treiber ML, Mills DA, Korf I, Lemay DG. Westreich ST, et al. Among authors: korf i. BMC Bioinformatics. 2018 May 21;19(1):175. doi: 10.1186/s12859-018-2189-z. BMC Bioinformatics. 2018. PMID: 29783945 Free PMC article.
Longer first introns are a general property of eukaryotic gene structure.
Bradnam KR, Korf I. Bradnam KR, et al. PLoS One. 2008 Aug 29;3(8):e3093. doi: 10.1371/journal.pone.0003093. PLoS One. 2008. PMID: 18769727 Free PMC article.
Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species.
Kern C, Wang Y, Chitwood J, Korf I, Delany M, Cheng H, Medrano JF, Van Eenennaam AL, Ernst C, Ross P, Zhou H. Kern C, et al. Among authors: korf i. BMC Genomics. 2018 Sep 18;19(1):684. doi: 10.1186/s12864-018-5037-7. BMC Genomics. 2018. PMID: 30227846 Free PMC article.
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