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Effective cluster-based seed design for cross-species sequence comparisons.
Zhou L, Mihai I, Florea L. Zhou L, et al. Bioinformatics. 2008 Dec 15;24(24):2926-7. doi: 10.1093/bioinformatics/btn547. Epub 2008 Oct 20. Bioinformatics. 2008. PMID: 18940827
Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.
Afsari B, Guo T, Considine M, Florea L, Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Zambo KD, Ha PK, Geman D, Ochs MF, Califano JA, Gaykalova DA, Favorov AV, Fertig EJ. Afsari B, et al. Bioinformatics. 2018 Jun 1;34(11):1859-1867. doi: 10.1093/bioinformatics/bty004. Bioinformatics. 2018. PMID: 29342249 Free PMC article.
Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing.
Walenz B, Florea L. Walenz B, et al. Bioinformatics. 2011 Jul 1;27(13):1869-70. doi: 10.1093/bioinformatics/btr285. Epub 2011 May 6. Bioinformatics. 2011. PMID: 21551146 Free PMC article.
Bioinformatics of alternative splicing and its regulation.
Florea L. Florea L. Brief Bioinform. 2006 Mar;7(1):55-69. doi: 10.1093/bib/bbk005. Brief Bioinform. 2006. PMID: 16761365 Review.
A method for identifying alternative or cryptic donor splice sites within gene and mRNA sequences. Comparisons among sequences from vertebrates, echinoderms and other groups.
Buckley KM, Florea LD, Smith LC. Buckley KM, et al. BMC Genomics. 2009 Jul 16;10:318. doi: 10.1186/1471-2164-10-318. BMC Genomics. 2009. PMID: 19607703 Free PMC article.
Finding anchors for genomic sequence comparison.
Lippert RA, Zhao X, Florea L, Mobarry C, Istrail S. Lippert RA, et al. J Comput Biol. 2005 Jul-Aug;12(6):762-76. doi: 10.1089/cmb.2005.12.762. J Comput Biol. 2005. PMID: 16108715
Sim4cc: a cross-species spliced alignment program.
Zhou L, Pertea M, Delcher AL, Florea L. Zhou L, et al. Nucleic Acids Res. 2009 Jun;37(11):e80. doi: 10.1093/nar/gkp319. Epub 2009 May 8. Nucleic Acids Res. 2009. PMID: 19429899 Free PMC article.
Universal seeds for cDNA-to-genome comparison.
Zhou L, Stanton J, Florea L. Zhou L, et al. BMC Bioinformatics. 2008 Jan 23;9:36. doi: 10.1186/1471-2105-9-36. BMC Bioinformatics. 2008. PMID: 18215286 Free PMC article.
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