Publications

Publications

• Cation valence dependence of hydrogen bond and stacking potentials in DNA mesoscopic models

  • Biophysical Chemistry January 2023

  • parameters in TfReg

• Mesoscopic model confirms strong hydrogen bonding metal mediation for T-Hg2+-T and weaker for C-Ag+-C

  • Chemical Physics Letters July 2022

  • parameters in TfReg

• Complete mesoscopic parameterization of single LNA modifications in DNA applied to oncogene probe design

  • Journal of Chemical Information and Modeling July 2021

  • parameters in TfReg

• Mesoscopic Evaluation of DNA Mismatches in PCR Primer-Target Hybridisation to Detect SARS-CoV-2 Variants of Concern

  • Brazilian Symposium on Bioinformatics. Cham: Springer International Publishing, 2021.

• Thermodynamic evaluation of the impact of DNA mismatches in PCR-type SARS-CoV-2 primers and probes

  • Molecular and Cellular Probes April 2021

  • BioRxiv November 2020

• Salt dependent mesoscopic model for RNA with multiple strand concentrations

  • Biophysical Chemistry April 2021

  • ChemRxiv November 2020

  • parameters in Tfreg

• Melting Temperature Measurement and Mesoscopic Evaluation of Single, Double and Triple DNA Mismatches.

  • Chemical Science August 2020

  • ChemRxiv March 2020

  • parameters in Tfreg

• Sharp DNA denaturation in a helicoidal mesoscopic model

  • Chemical Physics Letters September 2020

  • arXiv 

• Optical and theoretical study of strand recognition by nucleic acid probes

  • Communications Chemistry 2020

  • parameters in TfReg

• DNA/TNA Mesoscopic Modeling of Melting Temperatures Suggest Weaker Hydrogen Bonding of CG than in DNA/RNA

  • Chemical Physics Letters

  • ChemRxiv March 2020

  • parameters in TfReg

• Replacing salt correction factors with optimized RNA nearest-neighbour enthalpy and entropy parameters

  • Chemical Physics 2019

  • parameters in VarGibbs

• Nearest-neighbour parameters optimized for melting temperature prediction of DNA/RNA hybrids at high and low salt concentrations

  • Biophysical Chemistry 2019

  • parameters in VarGibbs

• DNA/RNA hybrid mesoscopic model shows strong stability dependence with deoxypyrimidine content and stacking interactions similar to RNA/RNA,

  • Chemical Physics Letters 2018

  • parameters in TfReg

• [PDF] An asymmetric mesoscopic model for single bulges in RNA (October 2017)

• Mesoscopic modelling of Cy3 and Cy5 dyes attached to DNA duplexes

  • Biophysical Chemistry 2017

  • parameters in Tfreg

• [PDF] Evaluating Hydrogen Bonds and Base Stacking of Single, Tandem and Terminal GU Mismatches in RNA with a Mesoscopic Model (December 2015)

• [PDF] DNA terminal base pairs have weaker hydrogen bonds especially for AT under low salt concentration (November 2015)

• New parameters for inosine:

• [PDF] Deoxyinosine mismatch parameters calculated with a mesoscopic model result in uniform hydrogen bonding and strongly variable stacking interactions (May 2015)

• This article describes the VarGibbs software hosted here.

• Optimization method for obtaining nearest-neighbour DNA entropies and enthalpies directly from melting temperatures (November 2014)

• Here we show some problematic aspects of network topology studies of biological databases.

• Detection of construction biases in biological databases: the case of miRBase (July 2014)

• Here we derive a new 2D Peyrard-Bishop Hamiltonian from a 3D equivalent and use it to model a structural parameter for DNA.

• Analysing DNA structural parameters using a mesoscopic model (2014)

• This is the article describing the TfReg software package hosted here.

• [PDF] TfReg: Calculating DNA and RNA melting temperatures and opening profiles with mesoscopic models (March 2013) 

• We show that mirtrons do have some curious properties if we analyse their CG content, quite different from normal miRNAs.

• CG-content log-ratio distributions of Caenorhabditis elegans and Drosophila melanogaster mirtrons (January 2013)

• Here we obtain the Peyrard-Bishop model parameters for RNA. One interesting finding is that the hydrogen bond for CG base pairs is identical to that of DNA, even though we use completely different data. The other finding is that AU base pairs in RNA have a stronger hydrogen bond than AT in DNA.

• Mesoscopic model parametrization of hydrogen bonds and stacking interactions of RNA from melting temperatures (October 2012)

• [PDF] Finite-enthalpy model parameters from DNA melting temperatures (December 2011) 

• [PDF] Wavelet coefficients as a guide to DNA phase transitions (August 2009)

• [PDF] Sharp DNA denaturation due to solvent interaction (March 2006)

All publications

You can see my publications at ResearchGate, Google Scholar or at Researcher ID. If there is anything you can not access from your site, please feel free to sent me an email.