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2,323 results
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TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences.
Harmanci AO, Sharma G, Mathews DH. Harmanci AO, et al. Among authors: sharma g. BMC Bioinformatics. 2011 Apr 20;12:108. doi: 10.1186/1471-2105-12-108. BMC Bioinformatics. 2011. PMID: 21507242 Free PMC article.
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign.
Harmanci AO, Sharma G, Mathews DH. Harmanci AO, et al. Among authors: sharma g. BMC Bioinformatics. 2007 Apr 19;8:130. doi: 10.1186/1471-2105-8-130. BMC Bioinformatics. 2007. PMID: 17445273 Free PMC article.
PARTS: probabilistic alignment for RNA joinT secondary structure prediction.
Harmanci AO, Sharma G, Mathews DH. Harmanci AO, et al. Among authors: sharma g. Nucleic Acids Res. 2008 Apr;36(7):2406-17. doi: 10.1093/nar/gkn043. Epub 2008 Feb 26. Nucleic Acids Res. 2008. PMID: 18304945 Free PMC article.
Stochastic sampling of the RNA structural alignment space.
Harmanci AO, Sharma G, Mathews DH. Harmanci AO, et al. Among authors: sharma g. Nucleic Acids Res. 2009 Jul;37(12):4063-75. doi: 10.1093/nar/gkp276. Epub 2009 May 8. Nucleic Acids Res. 2009. PMID: 19429694 Free PMC article.
SWIFT-scalable clustering for automated identification of rare cell populations in large, high-dimensional flow cytometry datasets, part 1: algorithm design.
Naim I, Datta S, Rebhahn J, Cavenaugh JS, Mosmann TR, Sharma G. Naim I, et al. Among authors: sharma g. Cytometry A. 2014 May;85(5):408-21. doi: 10.1002/cyto.a.22446. Epub 2014 Feb 14. Cytometry A. 2014. PMID: 24677621 Free PMC article.
Dynalign II: common secondary structure prediction for RNA homologs with domain insertions.
Fu Y, Sharma G, Mathews DH. Fu Y, et al. Among authors: sharma g. Nucleic Acids Res. 2014 Dec 16;42(22):13939-48. doi: 10.1093/nar/gku1172. Nucleic Acids Res. 2014. PMID: 25416799 Free PMC article.
Competitive SWIFT cluster templates enhance detection of aging changes.
Rebhahn JA, Roumanes DR, Qi Y, Khan A, Thakar J, Rosenberg A, Lee FE, Quataert SA, Sharma G, Mosmann TR. Rebhahn JA, et al. Among authors: sharma g. Cytometry A. 2016 Jan;89(1):59-70. doi: 10.1002/cyto.a.22740. Epub 2015 Oct 6. Cytometry A. 2016. PMID: 26441030 Free PMC article.
Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data.
Tan Z, Sharma G, Mathews DH. Tan Z, et al. Among authors: sharma g. Biophys J. 2017 Jul 25;113(2):330-338. doi: 10.1016/j.bpj.2017.06.039. Epub 2017 Jul 20. Biophys J. 2017. PMID: 28735622 Free PMC article.
TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.
Tan Z, Fu Y, Sharma G, Mathews DH. Tan Z, et al. Among authors: sharma g. Nucleic Acids Res. 2017 Nov 16;45(20):11570-11581. doi: 10.1093/nar/gkx815. Nucleic Acids Res. 2017. PMID: 29036420 Free PMC article.
Mechanism of HIV-1 RNA dimerization in the central region of the genome and significance for viral evolution.
Piekna-Przybylska D, Sharma G, Bambara RA. Piekna-Przybylska D, et al. Among authors: sharma g. J Biol Chem. 2013 Aug 16;288(33):24140-50. doi: 10.1074/jbc.M113.477265. Epub 2013 Jul 9. J Biol Chem. 2013. PMID: 23839990 Free PMC article.
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