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simuPOP: a forward-time population genetics simulation environment.
Peng B, Kimmel M. Peng B, et al. Bioinformatics. 2005 Sep 15;21(18):3686-7. doi: 10.1093/bioinformatics/bti584. Epub 2005 Jul 14. Bioinformatics. 2005. PMID: 16020469
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.
Kristensen DM, Ward RM, Lisewski AM, Erdin S, Chen BY, Fofanov VY, Kimmel M, Kavraki LE, Lichtarge O. Kristensen DM, et al. BMC Bioinformatics. 2008 Jan 11;9:17. doi: 10.1186/1471-2105-9-17. BMC Bioinformatics. 2008. PMID: 18190718 Free PMC article.
Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity.
Kristensen DM, Chen BY, Fofanov VY, Ward RM, Lisewski AM, Kimmel M, Kavraki LE, Lichtarge O. Kristensen DM, et al. Protein Sci. 2006 Jun;15(6):1530-6. doi: 10.1110/ps.062152706. Epub 2006 May 2. Protein Sci. 2006. PMID: 16672239 Free PMC article.
Cavity-aware motifs reduce false positives in protein function prediction.
Chen BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE. Chen BY, et al. Comput Syst Bioinformatics Conf. 2006:311-23. Comput Syst Bioinformatics Conf. 2006. PMID: 17369649
ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data.
Rustagi N, Hampton OA, Li J, Xi L, Gibbs RA, Plon SE, Kimmel M, Wheeler DA. Rustagi N, et al. BMC Bioinformatics. 2016 Apr 27;17:188. doi: 10.1186/s12859-016-1031-8. BMC Bioinformatics. 2016. PMID: 27121965 Free PMC article.
Forward-time simulations of human populations with complex diseases.
Peng B, Amos CI, Kimmel M. Peng B, et al. PLoS Genet. 2007 Mar 23;3(3):e47. doi: 10.1371/journal.pgen.0030047. Epub 2007 Feb 15. PLoS Genet. 2007. PMID: 17381243 Free PMC article.
Simulations provide support for the common disease-common variant hypothesis.
Peng B, Kimmel M. Peng B, et al. Genetics. 2007 Feb;175(2):763-76. doi: 10.1534/genetics.106.058164. Epub 2006 Dec 6. Genetics. 2007. PMID: 17151262 Free PMC article.
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