Publications

Google Citation Report

Machine Learning Advanced Biological Sequence Analysis and Functional (Gen/Prote)omics Biomolecular Struc- ture and Dynamics Quantum Mechanical Calculations and Molecular Modeling Molecular Dynamics Simulations NMR of Bio- and Small Molecules UV/Vis/CD Optical Spectroscopy Nucleic Acids Proteins Origin of Life


Sahakyan A. B., Chambers V. S., Marsico G., Santner T., Di Antonio M., Balasubramanian S. “Machine Learning Model for Sequence-Driven DNA G-Quadruplex Formation”, Sci. Rep., 7, 14535, 2017. http://dx.doi.org/10.1038/s41598-017-14017-4 • 

quadron toc

Sahakyan A. B., Murat P., Mayer C., Balasubramanian S. “G-Quadruplex Structures within the 3’ UTR of LINE-1 Elements Stimulate Retrotransposition”Nature Str. Mol. Biol., 24, 243-247, 2017http://dx.doi.org/10.1038/nsmb.3367  • •   • Simple summary here.

L1G4

Sahakyan A. B. and Balasubramanian S. “Single Genome Retrieval of Context-Dependent Variability in Mutation Rates for Human Germline”BMC Genomics, 18, 81, 2017http://dx.doi.org/10.1186/s12864-016-3440-5   • • Simple summary here.

Trek summary

Kwok C. K., Marsico G., Sahakyan A. B., Chambers V. S., Balasubramanian S. “rG4-seq Reveals Widespread Formation of G-Quadruplex Structures in the Human Transcriptome”, Nature Methods, 13, 841-844, 2016. http://dx.doi.org/10.1038/nmeth.3965 • 

NatMeth

Kwok C. K., Sahakyan A. B., Balasubramanian S. “Structural Analysis Using SHALiPE to Reveal RNA G-Quadruplex Formation in Human Precursor MicroRNA”, Angew. Chem. Int. Ed., 55, 8958-8961, 2016. http://dx.doi.org/10.1002/anie.201603562

TocAngew

Sahakyan A. B. and Balasubramanian S. “Long Genes and Genes with Multiple Splice Variants are Enriched in Pathways Linked to Cancer and Other Multigenic Diseases”, BMC Genomics, 17, 225, 2016. http://dx.doi.org/10.1186/s12864-016-2582-9 • 

lgenes

Sahakyan A. B. and Balasubramanian S. “Core Variability in Mutation Rates Shapes the Basal Characteristics of the Human Genome”, in press, preprint: BioRxiv, 2015http://dx.doi.org/10.1101/024257   • • 

trek biorxiv

Hardisty R. E., Kawasaki F., Sahakyan A. B., Balasubramanian S. “Selective Chemical Labeling of Natural T Modifications in DNA”, J. Am. Chem. Soc., 137, 9270-9272, 2015http://dx.doi.org/10.1021/jacs.5b03730  •  

toc epigen

Shahkhatuni A. A., Shahkhatuni A. G., Minasyan N. S., Panosyan H. A., Sahakyan A. B. “Revealing the Specific Solute-Solvent Interactions via the Measurements of the NMR Spin-Spin Coupling Constants”, J. Mol. Struct., 1083, 175-178, 2015http://dx.doi.org/10.1016/j.molstruc.2014.11.058 • • 

toc1

Camilloni C., Sahakyan A. B., Holliday M. J., Isern N. G., Zhang F., Eisenmesser E. Z., Vendruscolo M. “Cyclophilin A Catalyzes Proline Isomerization by an Electrostatic Handle Mechanism”, Proc. Natl. Acad. Sci. U. S. A., 111, 10203-10208, 2014http://dx.doi.org/10.1073/pnas.1404220111 • 

pnas

Fu B., Sahakyan A. B., Camilloni C., Tartaglia G. G., Paci E., Caflisch A., Vendruscolo M., Cavalli A. “ALMOST: an All Atom Molecular Simulation Toolkit for Protein Structure Determination”, J. Comput. Chem., 35, 1101-1105, 2014. http://dx.doi.org/10.1002/jcc.23588

almost

Kannan A., Camilloni C., Sahakyan A. B., Cavalli A., Vendruscolo M. “A Conformational Ensemble Derived Using NMR Methyl Chemical Shifts Reveals a Mechanical Clamping Transition that Gates the Binding of the HU Protein to DNA”, J. Am. Chem. Soc., 136, 2204-2207, 2014. http://dx.doi.org/10.1021/ja4105396 • 

jacs toc

Suardiaz R., Sahakyan A. B., Vendruscolo M. “A Geometrical Parametrisation of C1’- C5’ RNA Ribose Chemical Shifts Calculated by Density Functional Theory”, J. Chem. Phys., 139, 034101, 2013. http://dx.doi.org/10.1063/1.4811498 • 

toc

Sahakyan A. B. and Vendruscolo M. “Analysis of Ring Current and Electric Field Effects on the Chemical Shifts of RNA Bases”, J. Phys. Chem. B, 117, 1989-1998, 2013. http://dx.doi.org/10.1021/jp3057306 • 

http://www.cantab.net/users/aleksahak/homepage/Research_files/rna_ring.jpg

Sahakyan A. B. “Computational Studies of Dielectric Permittivity Effects on Chemical Shifts of Alanine Dipeptide”, Chem. Phys. Lett., 547, 66-72, 2012. http://dx.doi.org/10.1016/j. cplett.2012.07.069 • 

Shahkhatuni A. A., Sahakyan A. B., Shahkhatuni A. G., Mamayan S. S., Panosyan H. A. “Correlation of  Spin-Spin Coupling Constants and Their Solvent Sensitivities”, Chem. Phys. Lett., 542, 56-61, 2012. http://dx.doi.org/10.1016/j.cplett.2012.06.010 • 

Sahakyan A. B., Cavalli A., Vranken W. F., Vendruscolo M. “Protein Structure Validation Using Side-Chain Chemical Shifts”, J. Phys. Chem. B, 116, 4754-4759, 2012. http://dx.doi.org/10. 1021/jp2122054 • 

Sahakyan A. B., Vranken W. F., Cavalli A., Vendruscolo M. “Using Side-Chain Aromatic Proton Chemical Shifts for a Quantitative Analysis of Protein Structures”, Angew. Chem. Int. Ed., 50, 9620-9623, 2011. http://dx.doi.org/10.1002/anie.201101641 • Featured in F1000.

F1000prime

Sahakyan A. B., Vranken W. F., Cavalli A., Vendruscolo M. “Structure-Based Prediction of Methyl Chemical Shifts in Proteins”, J. Biomol. NMR, 50, 331-346, 2011. http://dx.doi.org/10.1007/s10858-011-9524-2

Sahakyan A. B., Shahkhatuni A. G., Shahkhatuni A. A., Panosyan H. A. “Electric Field Effects on One-Bond Indirect Spin-Spin Coupling Constants and Possible Biomolecular Perspectives”, J. Phys. Chem. A, 112, 3576-3586, 2008. http://dx.doi.org/10.1021/jp800670y • 

Sahakyan A. B., Shahkhatuni A. G., Shahkhatuni A. A., Panosyan H. A. “Torsion Sensitivity in NMR of Aligned Molecules: Study on Various Substituted Biphenyls”, Magn. Reson. Chem., 46, 144-149, 2008. http://dx.doi.org/10.1002/mrc.2142 • 

Sahakyan A. B., Shahkhatuni A. A., Shahkhatuni A. G., Panosyan H. A. “Dielectric Permittivity and Temperature Effects on Spin-Spin Couplings Studied on Acetonitrile”, Magn. Reson. Chem., 46, 63-68, 2008. http://dx.doi.org/10.1002/mrc.2137 • 

Shahkhatuni A. A., Shahkhatuni A. G., Panosyan H. A., Sahakyan A. B., Byeon I. -J., Gronenborn A. M. “Assessment of Solvent Effects: Do Weak Alignment Media Affect the Structure of the Solute?”, Magn. Reson. Chem., 45, 557-563, 2007. http://dx.doi.org/10.1002/mrc.2004 • 

Sahakyan A. B., Chapter 1.10, “The Principles of Drug Design” in Armenian, “Pharmaceutical Chemistry”, Yerevan, 2008.

http://www.cantab.net/users/aleksahak/homepage/Publications_files/book_cover_pc-filtered.jpg

Sahakyan A. B. and Hakobyan R. H. “The Methodologies of Modern Drug Discovery” in Armenian, In The World of Science, issue X, 2008.

http://www.cantab.net/users/aleksahak/homepage/Publications_files/periodical_cover.jpg