Arya G - Search Results

1

Computational prediction of efficient splice sites for trans-splicing ribozymes.

Meluzzi D, Olson KE, Dolan GF, Arya G, Müller UF. Meluzzi D, et al. Among authors: arya g. RNA. 2012 Mar;18(3):590-602. doi: 10.1261/rna.029884.111. Epub 2012 Jan 24. RNA. 2012. PMID: 22274956 Free PMC article.

2

Biophysics of knotting.

Meluzzi D, Smith DE, Arya G. Meluzzi D, et al. Among authors: arya g. Annu Rev Biophys. 2010;39:349-66. doi: 10.1146/annurev.biophys.093008.131412. Annu Rev Biophys. 2010. PMID: 20192771 Review.

3

Recovering ensembles of chromatin conformations from contact probabilities.

Meluzzi D, Arya G. Meluzzi D, et al. Among authors: arya g. Nucleic Acids Res. 2013 Jan 7;41(1):63-75. doi: 10.1093/nar/gks1029. Epub 2012 Nov 11. Nucleic Acids Res. 2013. PMID: 23143266 Free PMC article.

4

Efficient estimation of contact probabilities from inter-bead distance distributions in simulated polymer chains.

Meluzzi D, Arya G. Meluzzi D, et al. Among authors: arya g. J Phys Condens Matter. 2015 Feb 18;27(6):064120. doi: 10.1088/0953-8984/27/6/064120. Epub 2015 Jan 7. J Phys Condens Matter. 2015. PMID: 25563926

5

Quantification of DNA cleavage specificity in Hi-C experiments.

Meluzzi D, Arya G. Meluzzi D, et al. Among authors: arya g. Nucleic Acids Res. 2016 Jan 8;44(1):e4. doi: 10.1093/nar/gkv820. Epub 2015 Aug 11. Nucleic Acids Res. 2016. PMID: 26264668 Free PMC article.

6

Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data.

Meluzzi D, Arya G. Meluzzi D, et al. Among authors: arya g. Methods. 2020 Oct 1;181-182:24-34. doi: 10.1016/j.ymeth.2019.08.008. Epub 2019 Aug 27. Methods. 2020. PMID: 31470090 Free PMC article. Review.

7

Zinc finger protein binding to DNA: an energy perspective using molecular dynamics simulation and free energy calculations on mutants of both zinc finger domains and their specific DNA bases.

Hamed MY, Arya G. Hamed MY, et al. Among authors: arya g. J Biomol Struct Dyn. 2016 May;34(5):919-34. doi: 10.1080/07391102.2015.1068224. Epub 2016 Feb 2. J Biomol Struct Dyn. 2016. PMID: 26196228

8

Dynamics of forced nucleosome unraveling and role of nonuniform histone-DNA interactions.

Dobrovolskaia IV, Arya G. Dobrovolskaia IV, et al. Among authors: arya g. Biophys J. 2012 Sep 5;103(5):989-98. doi: 10.1016/j.bpj.2012.07.043. Biophys J. 2012. PMID: 23009848 Free PMC article.

9

Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

Migliori AD, Smith DE, Arya G. Migliori AD, et al. Among authors: arya g. J Mol Biol. 2014 Dec 12;426(24):4002-4017. doi: 10.1016/j.jmb.2014.09.023. Epub 2014 Oct 13. J Mol Biol. 2014. PMID: 25311860 Free PMC article.

10

Cation-Activated Avidity for Rapid Reconfiguration of DNA Nanodevices.

Marras AE, Shi Z, Lindell MG 3rd, Patton RA, Huang CM, Zhou L, Su HJ, Arya G, Castro CE. Marras AE, et al. Among authors: arya g. ACS Nano. 2018 Sep 25;12(9):9484-9494. doi: 10.1021/acsnano.8b04817. Epub 2018 Sep 4. ACS Nano. 2018. PMID: 30169013

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