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Finding motifs using random projections.
Buhler J, Tompa M. Buhler J, et al. J Comput Biol. 2002;9(2):225-42. doi: 10.1089/10665270252935430. J Comput Biol. 2002. PMID: 12015879
Efficient large-scale sequence comparison by locality-sensitive hashing.
Buhler J. Buhler J. Bioinformatics. 2001 May;17(5):419-28. doi: 10.1093/bioinformatics/17.5.419. Bioinformatics. 2001. PMID: 11331236
Fast, sensitive discovery of conserved genome-wide motifs.
Ihuegbu NE, Stormo GD, Buhler J. Ihuegbu NE, et al. J Comput Biol. 2012 Feb;19(2):139-47. doi: 10.1089/cmb.2011.0249. J Comput Biol. 2012. PMID: 22300316 Free PMC article.
Designing secondary structure profiles for fast ncRNA identification.
Sun Y, Buhler J. Sun Y, et al. Comput Syst Bioinformatics Conf. 2008;7:145-56. Comput Syst Bioinformatics Conf. 2008. PMID: 19642276
Designing patterns and profiles for faster HMM search.
Sun Y, Buhler J. Sun Y, et al. IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):232-43. doi: 10.1109/TCBB.2008.14. IEEE/ACM Trans Comput Biol Bioinform. 2009. PMID: 19407348
An iterative method for selecting degenerate multiplex PCR primers.
Souvenir R, Buhler J, Stormo G, Zhang W. Souvenir R, et al. Methods Mol Biol. 2007;402:245-68. doi: 10.1007/978-1-59745-528-2_12. Methods Mol Biol. 2007. PMID: 17951799 Review.
Designing patterns for profile HMM search.
Sun Y, Buhler J. Sun Y, et al. Bioinformatics. 2007 Jan 15;23(2):e36-43. doi: 10.1093/bioinformatics/btl323. Bioinformatics. 2007. PMID: 17237102
Designing multiple simultaneous seeds for DNA similarity search.
Sun Y, Buhler J. Sun Y, et al. J Comput Biol. 2005 Jul-Aug;12(6):847-61. doi: 10.1089/cmb.2005.12.847. J Comput Biol. 2005. PMID: 16108721
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