All Outputs (51)

Investigative power of Genomic Informational Field Theory (GIFT) relative to GWAS for genotype-phenotype mapping (2024)
Journal Article
Kyratzi, P., Matika, O., Brassington, A. H., Clare, C. E., Xu, J., Barrett, D. A., Emes, R. D., Archibald, A. L., Paldi, A., Sinclair, K. D., Wattis, J., & Rauch, C. (2024). Investigative power of Genomic Informational Field Theory (GIFT) relative to GWAS for genotype-phenotype mapping. Physiological Genomics, 56(11), 791-806. https://doi.org/10.1152/physiolgenomics.00049.2024

Identifying associations between phenotype and genotype is the fundamental basis of genetic analyses. Inspired by frequentist probability and the work of R.A. Fisher, genome-wide association studies (GWAS) extract information using averages and varia... Read More about Investigative power of Genomic Informational Field Theory (GIFT) relative to GWAS for genotype-phenotype mapping.

Investigative power of Genomic Informational Field Theory (GIFT) relative to GWAS for genotype-phenotype mapping (2024)
Preprint / Working Paper
Kyratzi, P., Matika, O., Brassington, A. H., Connie, C. E., Xu, J., Barrett, D. A., Emes, R. D., Archibald, A. L., Paldi, A., Sinclair, K. D., Wattis, J., & Rauch, C. Investigative power of Genomic Informational Field Theory (GIFT) relative to GWAS for genotype-phenotype mapping

Identifying associations between phenotype and genotype is the fundamental basis of genetic analyses. Inspired by frequentist probability and the work of R.A. Fisher, genome-wide association studies (GWAS) extract information using averages and varia... Read More about Investigative power of Genomic Informational Field Theory (GIFT) relative to GWAS for genotype-phenotype mapping.

On the Meaning of Averages in Genome-wide Association Studies: What Should Come Next? (2023)
Journal Article
Rauch, C., Wattis, J., & Bray, S. (2023). On the Meaning of Averages in Genome-wide Association Studies: What Should Come Next?. Organisms, 6(1), 7-22. https://doi.org/10.13133/2532-5876/17811

Identifying the association between phenotypes and genotypes is the fundamental basis of genetic analyses. Although genomic technologies used to generate data have rapidly advanced within the last 20 years, the statistical models used in genome-wide... Read More about On the Meaning of Averages in Genome-wide Association Studies: What Should Come Next?.

Mathematical Models of Chiral Symmetry-breaking – A Review of General Theories, and Adiabatic Approximations of the APED System (2022)
Journal Article
Diniz, P. C., Wattis, J. A., & Da Costa, F. P. (2022). Mathematical Models of Chiral Symmetry-breaking – A Review of General Theories, and Adiabatic Approximations of the APED System. Origins of Life and Evolution of Biospheres, 52(4), 183-204. https://doi.org/10.1007/s11084-022-09631-w

We review the literature surrounding chiral symmetry-breaking in chemical systems, with a focus on understanding the mathematical models underlying these chemical processes. We comment in particular on the toy model of Sandars, Viedma’s crystal grind... Read More about Mathematical Models of Chiral Symmetry-breaking – A Review of General Theories, and Adiabatic Approximations of the APED System.

GIFT: New method for the genetic analysis of small gene effects involving small sample sizes (2022)
Journal Article
Rauch, C., Kyratzi, P., Blott, S., Bray, S., & Wattis, J. A. D. (2023). GIFT: New method for the genetic analysis of small gene effects involving small sample sizes. Physical Biology, 20(1), Article 016001. https://doi.org/10.1088/1478-3975/ac99b3

Small gene effects involved in complex/omnigenic traits remain costly to analyse using current genome-wide association methods (GWAS) because of the number of individuals required to return meaningful association(s), a.k.a. study power. Inspired by f... Read More about GIFT: New method for the genetic analysis of small gene effects involving small sample sizes.

Analysis of phenotype-genotype associations using genomic informational field theory (GIFT) (2022)
Journal Article
Wattis, J. A., Bray, S. M., Kyratzi, P., & Rauch, C. (2022). Analysis of phenotype-genotype associations using genomic informational field theory (GIFT). Journal of Theoretical Biology, 548, Article 111198. https://doi.org/10.1016/j.jtbi.2022.111198

We show how field- and information theory can be used to quantify the relationship between genotype and phenotype in cases where phenotype is a continuous variable. Given a sample population of phenotype measurements, from various known genotypes, we... Read More about Analysis of phenotype-genotype associations using genomic informational field theory (GIFT).

Breather modes of fully nonlinear mass-in-mass chains (2022)
Journal Article
Wattis, J. A. (2022). Breather modes of fully nonlinear mass-in-mass chains. Physical Review E, 105(5), Article 054212. https://doi.org/10.1103/PhysRevE.105.054212

We propose a model for a chain of particles coupled by nonlinear springs in which each mass has an internal mass and all interactions are assumed to be nonlinear. We show how to construct an asymptotic solution of this system using multiple timescale... Read More about Breather modes of fully nonlinear mass-in-mass chains.

Solution classes of the matrix second Painlevé hierarchy (2022)
Journal Article
Gordoa, P. R., Pickering, A., & Wattis, J. (2022). Solution classes of the matrix second Painlevé hierarchy. Physica D: Nonlinear Phenomena, 435, Article 133295. https://doi.org/10.1016/j.physd.2022.133295

We explore the generation of classes of solutions of the matrix second Painlevé hierarchy. This involves the consideration of the application of compositions of auto-Bäcklund transformations to different initial solutions, with the number of distinct... Read More about Solution classes of the matrix second Painlevé hierarchy.

Mathematical modelling of earlier stages of COVID-19 transmission dynamics in Ghana (2022)
Journal Article
Acheampong, E., Okyere, E., Iddi, S., Bonney, J. H., Wattis, J. A., Gomes, R. L., & Asamoah, J. K. K. (2022). Mathematical modelling of earlier stages of COVID-19 transmission dynamics in Ghana. Results in Physics, 34, Article 105193. https://doi.org/10.1016/j.rinp.2022.105193

In late 2019, a novel coronavirus, the SARS-CoV-2 outbreak was identified in Wuhan, China and later spread to every corner of the globe. Whilst the number of infection-induced deaths in Ghana, West Africa are minimal when compared with the rest of th... Read More about Mathematical modelling of earlier stages of COVID-19 transmission dynamics in Ghana.

Stochastic fractal and Noether's theorem (2021)
Journal Article
Rahman, R., Nowrin, F., Rahman, M. S., Wattis, J. A. D., & Hassan, M. K. (2021). Stochastic fractal and Noether's theorem. Physical Review E, 103(2), Article 022106. https://doi.org/10.1103/physreve.103.022106

We consider the binary fragmentation problem in which, at any breakup event, one of the daughter segments either survives with probability p or disappears with probability 1 − p. It describes a stochastic dyadic Cantor set that evolves in time, and e... Read More about Stochastic fractal and Noether's theorem.

Integrability and asymptotic behaviour of a differential-difference matrix equation (2020)
Journal Article
Gordoa, P. R., Pickering, A., & Wattis, J. A. (2021). Integrability and asymptotic behaviour of a differential-difference matrix equation. Physica D: Nonlinear Phenomena, 415, Article 132754. https://doi.org/10.1016/j.physd.2020.132754

In this paper we consider the matrix lattice equation U_{n,t} (U_{n+1} − U_{n−1} ) = g(n)I, in both its autonomous (g(n) = 2) and nonautonomous (g(n) = 2n − 1) forms. We show that each of these two matrix lattice equations are integrable. In addition... Read More about Integrability and asymptotic behaviour of a differential-difference matrix equation.

Monte–Carlo simulation of crystallization in single‐chain square‐well homopolymers (2020)
Journal Article
Wicks, T. J., Wattis, J. A. D., & Graham, R. S. (2021). Monte–Carlo simulation of crystallization in single‐chain square‐well homopolymers. Polymer Crystallization, 4(1), Article e10146. https://doi.org/10.1002/pcr2.10146

© 2020 Wiley Periodicals LLC We present Monte–Carlo (MC) simulations of the crystallization transition of single-chain square-well homopolymers, with a continuous description of monomer positions. For long chains with short-ranged interactions this s... Read More about Monte–Carlo simulation of crystallization in single‐chain square‐well homopolymers.

Mathematical modelling of telomere length dynamics (2019)
Journal Article
Wattis, J. A., Qi, Q., & Byrne, H. M. (2019). Mathematical modelling of telomere length dynamics. Journal of Mathematical Biology, 1-38. https://doi.org/10.1007/s00285-019-01448-y

© 2019, The Author(s). Telomeres are repetitive DNA sequences located at the ends of chromosomes. During cell division, an incomplete copy of each chromosome’s DNA is made, causing telomeres to shorten on successive generations. When a threshold leng... Read More about Mathematical modelling of telomere length dynamics.

Asymptotic analysis of breather modes in a two-dimensional mechanical lattice (2019)
Journal Article
Wattis, J., & Alzaidi, A. (2020). Asymptotic analysis of breather modes in a two-dimensional mechanical lattice. Physica D: Nonlinear Phenomena, 401, Article 132207. https://doi.org/10.1016/j.physd.2019.132207

We consider a two-dimensional square lattice in which each node is restricted to the plane of the lattice, but is permitted to move in both directions of the lattice. We assume nodes are connected to nearest neighbours along the lattice directions wi... Read More about Asymptotic analysis of breather modes in a two-dimensional mechanical lattice.

Nuclear poly(A) tail size is regulated by Cnot1 during the serum response (2019)
Other
Singhania, R., Thorn, G. J., Williams, K., Gandhi, R. D., Daher, C., Barthet-Barateig, A., …de Moor, C. H. (2019). Nuclear poly(A) tail size is regulated by Cnot1 during the serum response

The poly(A) tail removal from mRNAs introduces a delay between mRNA synthesis and decay. We measured levels and poly(A) tail sizes of serum-induced mRNAs and used mathematical modelling to compare their deadenylation time with the delay in decay and... Read More about Nuclear poly(A) tail size is regulated by Cnot1 during the serum response.

Modelling Emerging Pollutants in Wastewater Treatment: A Case Study using the Pharmaceutical 17α−ethinylestradiol (2019)
Journal Article
Acheampong, E., Dryden, I. L., Wattis, J. A., Twycross, J., Scrimshaw, M. D., & Gomes, R. L. (2019). Modelling Emerging Pollutants in Wastewater Treatment: A Case Study using the Pharmaceutical 17α−ethinylestradiol. Computers and Chemical Engineering, 128, 477-487. https://doi.org/10.1016/j.compchemeng.2019.06.020

Mathematical modelling can play a key role in understanding as well as quantifying uncertainties surrounding the presence and fate of emerging pollutants in wastewater treatment processes (WWTPs). This paper presents for the first time a simplified e... Read More about Modelling Emerging Pollutants in Wastewater Treatment: A Case Study using the Pharmaceutical 17α−ethinylestradiol.

Effects of competition between random sequential nucleation of point-sized seeds and island growth by adsorption of finite-sized grains (2019)
Journal Article
Khanam, A., Wattis, J. A., & Hassan, M. K. (2019). Effects of competition between random sequential nucleation of point-sized seeds and island growth by adsorption of finite-sized grains. Physical Review E, 99(4), Article 042110. https://doi.org/10.1103/PhysRevE.99.042110

We study random sequential adsorption of particles from a pool onto a one-dimensional substrate following ballistic deposition rules with separate nucleation and growth processes occurring simultaneously. Nucleation describes the formation of point-s... Read More about Effects of competition between random sequential nucleation of point-sized seeds and island growth by adsorption of finite-sized grains.

Asymptotic approximations to travelling waves in the diatomic Fermi-Pasta-Ulam lattice (2019)
Journal Article
Wattis, J. A. (2019). Asymptotic approximations to travelling waves in the diatomic Fermi-Pasta-Ulam lattice. Mathematics in Engineering, 1(2), 327-342. https://doi.org/10.3934/mine.2019.2.327

We construct high-order approximate travelling waves solutions of the diatomic Fermi-Pasta-Ulam lattice using asymptotic techniques which are valid for arbitrary mass ratios. Separately small amplitude ansatzs are made for the motion of the lighter a... Read More about Asymptotic approximations to travelling waves in the diatomic Fermi-Pasta-Ulam lattice.

The second Painlevé equation, a related nonautonomous semidiscrete equation, and a limit to the first Painlevé equation: scalar and matrix cases (2018)
Journal Article
Pickering, A., Gordoa, P. R., & Wattis, J. A. (2019). The second Painlevé equation, a related nonautonomous semidiscrete equation, and a limit to the first Painlevé equation: scalar and matrix cases. Physica D: Nonlinear Phenomena, 391, 72-86. https://doi.org/10.1016/j.physd.2018.12.001

In this paper we consider the matrix nonautonomous semidiscrete (or lattice) equation D dtUn = (2n − 1)(Un+1 − Un−1)−1, as well as the scalar case thereof. This equation was recently derived in the context of auto-Bäcklund transformations for a matri... Read More about The second Painlevé equation, a related nonautonomous semidiscrete equation, and a limit to the first Painlevé equation: scalar and matrix cases.

Behaviour of the extended modified Volterra lattice --reductions to generalised mKdV and NLS equations (2018)
Journal Article
Wattis, J. A., Gordoa, P., & Pickering, A. (2018). Behaviour of the extended modified Volterra lattice --reductions to generalised mKdV and NLS equations. Communications in Nonlinear Science and Numerical Simulation, 65, 98-110. https://doi.org/10.1016/j.cnsns.2018.05.016

We consider the first member of an extended modified Volterra lattice hierarchy. This system of equations is differential with respect to one independent variable and differential-delay with respect to a second independent variable. We use asymptot... Read More about Behaviour of the extended modified Volterra lattice --reductions to generalised mKdV and NLS equations.