Aleksandr B. Sahakyan (0000-0002-8343-3594)

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My research targets genomics and genome dynamics through the development of highly quantitative methods for describing the structure and dynamics of (epi)genome, gene regulatory pathways, involved macromolecules and their interaction networks. I am interested in combining computational biology, computational chemistry (QM, MD), advanced predictive modelling (a.k.a machine learning) and experimental biophysical techniques to reach a new level of precision in structural systems biology at both genome and proteome levels. Other interests span the origin of life research, prebiotic pathway exploration and weak intermolecular forces.

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University of Oxford: Oxford, Oxfordshire, GB

(RDM Clinical Laboratory Sciences)

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Aleksandr B. Sahakyan

https://orcid.org/0000-0002-8343-3594

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Employment (2)

University of Oxford: Oxford, Oxfordshire, GB

University of Cambridge: Cambridge, Cambridgeshire, GB

Education and qualifications (2)

University of Cambridge: Cambridge, Cambridgeshire, GB

University of Cambridge: Cambridge, Cambridgeshire, GB

Works (40)

Analysis of long-range contacts across cell types outlines a core sequence determinant of 3D genome organisation

Prior knowledge on context-driven DNA fragmentation probabilities can improvede novogenome assembly algorithms

Towards the genomic sequence code of DNA fragility for machine learning

Quantum mechanical electronic and geometric parameters for DNA k-mers as features for machine learning

Generalised interrelations among mutation rates drive the genomic compliance of Chargaff's second parity rule

ROptimus: a parallel general-purpose adaptive optimization engine

Quantum mechanical electronic and geometric parameters for DNA k-mers as features for machine learning

Generalised interrelations among mutation rates drive the genomic compliance of Chargaff’s second parity rule

Optimus: a general purpose adaptive optimisation engine in R

Structure-driven effects on genomic DNA damage propensity at G-quadruplex sites

Thermal and pH Stabilities of i‐DNA: Confronting in vitro Experiments with Models and In‐Cell NMR Data

A Spontaneous Ring‐Opening Reaction Leads to a Repair‐Resistant Thymine Oxidation Product in Genomic DNA

Whole genome experimental maps of DNA G-quadruplexes in multiple species

Structural analysis reveals the formation and role of RNA G-quadruplex structures in human mature microRNAs

Machine learning model for sequence-driven DNA G-quadruplex formation

G-quadruplex structures within the 3′ UTR of LINE-1 elements stimulate retrotransposition

Single genome retrieval of context-dependent variability in mutation rates for human germline.

rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome

Structural Analysis using SHALiPE to Reveal RNA G-Quadruplex Formation in Human Precursor MicroRNA

Long genes and genes with multiple splice variants are enriched in pathways linked to cancer and other multigenic diseases

Core variability in substitution rates and the basal sequence characteristics of the human genome

Selective Chemical Labeling of Natural T Modifications in DNA

Revealing the specific solute–solvent interactions via the measurements of the NMR spin–spin coupling constants

Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism.

ALMOST: An all atom molecular simulation toolkit for protein structure determination

A Conformational Ensemble Derived Using NMR Methyl Chemical Shifts Reveals a Mechanical Clamping Transition That Gates the Binding of the HU Protein to DNA

A geometrical parametrization of C1ʹ-C5ʹ RNA ribose chemical shifts calculated by density functional theory

Analysis of the Contributions of Ring Current and Electric Field Effects to the Chemical Shifts of RNA Bases

Extending the boundaries of the usage of NMR chemical shifts in deciphering biomolecular structure and dynamics

Computational studies of dielectric permittivity effects on chemical shifts of alanine dipeptide

Correlation of 1JCH spin–spin coupling constants and their solvent sensitivities

Protein Structure Validation Using Side-Chain Chemical Shifts

Using side-chain aromatic proton chemical shifts for a quantitative analysis of protein structures.

Using Side-Chain Aromatic Proton Chemical Shifts for a Quantitative Analysis of Protein Structures

Structure-based prediction of methyl chemical shifts in proteins

Water-soluble complexes of cationic (metallo) porphyrins with anionic dye

Electric Field Effects on One-Bond Indirect Spin−Spin Coupling Constants and Possible Biomolecular Perspectives

Torsion sensitivity in NMR of aligned molecules: study on various substituted biphenyls

Dielectric permittivity and temperature effects on spin-spin couplings studied on acetonitrile

Assessment of solvent effects: do weak alignment media affect the structure of the solute?

Peer review (48 reviews for 20 publications/grants)