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De novo discovery of structured ncRNA motifs in genomic sequences.
Ruzzo WL, Gorodkin J. Ruzzo WL, et al. Methods Mol Biol. 2014;1097:303-18. doi: 10.1007/978-1-62703-709-9_15. Methods Mol Biol. 2014. PMID: 24639166 Review.
Pre-mRNA secondary structure prediction aids splice site prediction.
Patterson DJ, Yasuhara K, Ruzzo WL. Patterson DJ, et al. Pac Symp Biocomput. 2002:223-34. Pac Symp Biocomput. 2002. PMID: 11928478
Sequence-based heuristics for faster annotation of non-coding RNA families.
Weinberg Z, Ruzzo WL. Weinberg Z, et al. Bioinformatics. 2006 Jan 1;22(1):35-9. doi: 10.1093/bioinformatics/bti743. Epub 2005 Nov 2. Bioinformatics. 2006. PMID: 16267089
CMfinder--a covariance model based RNA motif finding algorithm.
Yao Z, Weinberg Z, Ruzzo WL. Yao Z, et al. Bioinformatics. 2006 Feb 15;22(4):445-52. doi: 10.1093/bioinformatics/btk008. Epub 2005 Dec 15. Bioinformatics. 2006. PMID: 16357030
How accurately is ncRNA aligned within whole-genome multiple alignments?
Wang AX, Ruzzo WL, Tompa M. Wang AX, et al. BMC Bioinformatics. 2007 Oct 26;8:417. doi: 10.1186/1471-2105-8-417. BMC Bioinformatics. 2007. PMID: 17963514 Free PMC article.
MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries.
Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, Bendoraite A, Mitchell PS, Nelson AM, Ruzzo WL, Ware C, Radich JP, Gentleman R, Ruohola-Baker H, Tewari M. Bar M, et al. Stem Cells. 2008 Oct;26(10):2496-505. doi: 10.1634/stemcells.2008-0356. Epub 2008 Jun 26. Stem Cells. 2008. PMID: 18583537 Free PMC article.
Finding non-coding RNAs through genome-scale clustering.
Tseng HH, Weinberg Z, Gore J, Breaker RR, Ruzzo WL. Tseng HH, et al. J Bioinform Comput Biol. 2009 Apr;7(2):373-88. doi: 10.1142/s0219720009004126. J Bioinform Comput Biol. 2009. PMID: 19340921 Free PMC article.
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