Paul G. Higgs - Publications

Jia WL, Higgs PG (2007) Codon usage in mitochondrial genomes: distinguishing context-depenedent mutation from tranlsational selection. Mol. Biol. Evol. (in press).

Higgs PG (2007) Linking population genetics to phylogenetics. Banach Center Publications (in press)

Higgs, P.G. & Pudritz, R.E. (2007) From protoplanetary disks to prebiotic amino acids and the origin of the genetic code. In "Planetary systems and the origins of life", Cambridge Series in Astrobiology, vol 3. Eds. Pudritz, R.E., Higgs, P.G. & Stone, J. Cambridge University Press.

Thorne JL, Choi SC, Yu J, Higgs PG, Kishino H. (2007) Population genetics without intraspecific data. Mol. Biol. Evol. 24: 1667-1677.

Higgs, P.G., Hao, W., & Golding, G.B. (2007) Identification of selective effects on highly expressed genes. Evolutionary Bioinformatics. 2: 1-13.

Sengupta, S., Yang, X., & Higgs, P.G. (2007) The mechanisms of codon reassignments in mitochondrial genetic codes. J. Mol. Evol. 64: 662-688.

Xu, W., Jameson, D., Tang, B., Higgs, P.G. (2006) The relationship between the rate of molecular evolution and the rate of genome rearrangement in animal mitochondrial genomes. J. Mol. Evol. 63, 375-392.

Urbina, D., Tang, B. & Higgs, P.G. (2006) The response of amino acid frequencies to directional mutational pressure in mitochondrial genome sequences is related to the physical properties of the amino acids and to the structure of the genetic code. J. Mol. Evol. 62, 340-361.

Sengupta, S. & Higgs, P.G. (2005) A Unified Theory of Codon Reassignment in Alternative Genetic Codes. Genetics 170, 831-840.

Rattray, M. & Higgs, P.G. (2005) RNA-based Phylogenetic Methods. In Probabilistic Modeling in Bioinformatics and Medical Informatics. Husmeier, D., Dybowski, R., Roberts, S. (Eds). Springer Verlag. pp191-210.

Quince, C., Higgs, P.G. & McKane, A.J. (2005) Topological structure and interaction strengths in model food webs. Ecological Modelling 187, 389-412.

Quince, C., Higgs, P.G. & McKane, A.J. (2005) Deleting species from model food webs. Oikos 110, 283-296.

Gibson, A. Gowri-Shankar, V., Higgs, P.G. & Rattray, M. (2005) A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods. Mol. Biol. Evol. 22, 251-264.

Higgs, P.G., Jameson, D., Jow, H. & Rattray, M. (2003) The evolution of tRNA-Leucine genes in animal mitochondrial genomes. J. Mol. Evol. 57, 435-445.

Hudelot, C., Gowri-Shankar, V., Jow, H., Rattray, M. & Higgs, P.G. (2003) RNA-based Phylogenetic Methods: Application to Mammalian Mitochondrial RNA Sequences. Mol. Phyl. Evol. 28, 241-252.

Jameson, D., Gibson, A.P., Hudelot, C. & Higgs, P.G. (2003) OGRe: a relational database for comparative analysis of mitochondrial genomes. Nucl. Acids. Res. 31, 202-206.

Hoyle, D.C. & Higgs, P.G. (2003) Factors affecting the errors in estimation of evolutionary distances between sequences. Mol. Biol. Evol. 20, 1-9.

Jow, H., Hudelot, C., Rattray, M. & Higgs, P.G. (2002) Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Mol. Biol. Evol. 19, 1591-1601.

Quince, C., Higgs, P.G. & McKane, A.J. (2002) Food Web Structures and the Evolution of Biological Communities. In Biological Evolution and Statistical Physics. Eds. Lässig, M. & Valleriani, A. Lecture Notes in Physics 585, 281-298. Springer Verlag.

Tyler, K.M, Higgs, P.G., Matthews, K.R. & Gull, K. (2001) Limitation of Trypanosoma brucei parasitaemia is best described by a combination of density dependent parasite differentiation and parasite killing by the host immune response. Proc. Roy. Soc. Lond. Ser B 268, 2235-2243.

Higgs, P.G. & Ungar, G. (2001) The dilution wave in polymer crystallization is described by Fisher’s reaction-diffusion equation. J. Chem. Phys. 114, 6958-9.

Drossel, B., Higgs, P.G. & McKane (2001) The influence of predator-prey population dynamics on the long-term evolution of food web structure. J. Theor. Biol. 208, 91-107.

Savill, N.J., Hoyle, D.C. & Higgs, P.G. (2001) RNA sequence evolution with secondary structure constraints: Comparison of substitution rate models using maximum likelihood methods. Genetics 157, 399-411.

Higgs, P.G. (2000a) RNA Secondary Structure: Physical and Computational Aspects. Quart. Rev. Biophys. 33, 199-253.

Higgs, P.G. (2000b) The Mimetic Transition: A simulation study of the evolution of learning by imitation. Proc. Roy. Soc. Lond. Ser. B 276, 1355-1361.

Ungar, G., Mandal, P.K., Higgs, P.G., de Silva, D.S.M., Boda, E. and Chen, C.M. (2000) Dilution wave and negative-order crystallization kinetics of chain molecules. Phys. Rev. Lett. 85, 4397-4400.

Savill, N.J. & Higgs, P.G. (2000) Redundant and non-functional guide RNAs in Trypanosoma brucei are a consequence of multiple genes per minicircle. Gene 256, 245-252.

Taylor, C.F. & Higgs, P.G. (2000). A population genetics model for multiple quantitative traits exhibiting pleiotropy and epistasis. J. Theor. Biol. 203, 419-437.

Caldarelli, G., Drossel, B., Higgs, P.G. & McKane, A.J. (2000) Using stochastic dynamics to model multispecies communities, in Stochastic and Chaotic Dynamics in the Lakes, D. S. Broomhead, E. A. Luchinskaya, P. V. E. McClintock and T. Mullin (eds), (American Institute of Physics, Melville, NY) pp 226-231.

Yong, C.W. & Higgs, P.G. (1999). Chain Orientation in Polymer Networks: Computer Simulation Using the Bond Fluctuation Model. Macromolecules 32, 5062-5071.

Savill, N.J. & Higgs, P.G. (1999). A theoretical study of random segregation of minicircles in trypanosomatids. Proc. R. Soc. Lond. B 266, 611-620.

Caldarelli, G., Higgs, P.G. & McKane, A.J. (1998). Modelling Coevolution in Multi-species Communities. J. Theor. Biol. 193, 345-358.

Morgan, S.R. & Higgs, P.G. (1998). Barrier heights between groundstates in a model of RNA secondary structure. J. Phys A (Math. & Gen.) 31, 3153-3170.

Chen, C.M. & Higgs, P.G. (1998). Monte-Carlo simulation of polymer crystallisation in dilute solution. J. Chem. Phys. 108, 4305-4314.

Higgs, P.G. (1998). Compensatory Neutral Mutations and the Evolution of RNA. Genetica 102/103 91-101. Special issue published in book form as Mutation and Evolution. Eds. Woodruff, R.C., Thompson, J.N. Kluwer Academic Publishers, Dordrecht, Netherlands.

Chen, C.M., Higgs, P.G. & MacKintosh, F.C. (1997). Theory of Fission for Two-component Lipid Vesicles. Phys. Rev. Lett. 79, 1579-82.

Higgs, P.G. (1996). Overlaps Between RNA Secondary Structures. Phys. Rev. Lett. 76, 704-707.

Morgan, S.R. & Higgs, P.G. (1996). Evidence for Kinetic Effects in the Folding of Large RNA Molecules. J. Chem. Phys. 105, 7152-7157.

Woodcock, G. & Higgs, P.G. (1996). Population Evolution on a Multiplicative Single-Peak Fitness Landscape. J. Theor. Biol. 179, 61-73.

Sotta, P., Higgs, P.G., Depner, M. & Deloche, B. (1995). Monte Carlo simulations of the orientational order in a strained polymer network - effect of density. Macromolecules 28, 7208-14.

Higgs, P.G. (1995a). Thermodynamic properties of transfer RNA: a computational study. J. Chem. Soc. Faraday Transactions 91, 2531-40.

Higgs, P.G. (1995b). Frequency Distributions in Population Genetics Parallel those in Statistical Physics. Phys. Rev. E 51, 95-101.

Higgs, P.G. & Woodcock, G. (1995). The Accumulation of Mutations in Asexual Populations, and the Structure of Genealogical Trees in the Presence of Selection. J. Math. Biol. 33, 677-702.

Higgs, P.G. & Morgan, S.R. (1995) Thermodynamics of RNA folding : When is an RNA molecule in equilibrium? In "Advances in Artificial Life" Eds. F.Moran et al. Lecture Notes in Artificial Intelligence no. 929, p 852, Springer, 1995. Proceedings of the European Conference on Artificial Life, Granada 1995.

Woodcock, G. & Higgs, P.G. (1995). Evolution on a Multiplicative Single-Peak Fitness Landscape. "Advances in Artificial Life" Eds. F.Moran et al Lecture Notes in Artificial Intelligence no. 929, p 148, Springer, 1995. Proceedings of the European Conference on Artificial Life, Granada 1995.

Derrida, B. & Higgs, P.G. (1994). Low Temperature Properties of Directed Walks with Random Self-Interactions. J. Phys. A (Math. & Gen.) 27, 5485-93.

Higgs, P.G. (1994). Error Thresholds and Stationary Mutant Distributions in Multi-locus Diploid genetics models. Genet. Res. Camb. 63, 63-78.

Higgs, P.G. & Ungar, G. (1994). The growth of Polymer Crystals at the transition from Extended chains to Folded chains. J. Chem. Phys. 100, 640-648.

Higgs, P.G. (1993). RNA Secondary Structure: A Comparison of Real and Random Sequences. J. Phys. I 3, 43-59.

Higgs, P.G. & Derrida, B. (1992). Genetic Distance and Species Formation in Evolving Populations. J. Molecular Evolution 35, 454-65.

Derrida, B., Griffiths, R.B. & and Higgs, P.G. (1992). A Model of Directed Walks with Random Self Interaction. Europhys. Lett. 18, 361-5.

Higgs, P.G. & Derrida, B. (1991). Stochastic Models for Species Formation in Evolving Populations. J.Phys.A (Math. & Gen.) 24, L985-L991.

Higgs, P.G. & Orland, H. (1991). Scaling Behaviour of Polyelectrolytes and Polyampholytes - Simulation by an Ensemble Growth Method. J. Chem. Phys. 95, 4506-18.

Higgs, P.G. & Raphael, E. (1991). Conformational changes of a polyelectrolyte in a poor solvent. J.Phys. I 1, 1-7.

Higgs, P.G. & Joanny, J.F. (1991). Theory of polyampholyte solutions. J.Chem.Phys. 94, 1543-54.

Higgs, P.G. & and Joanny, J.F. (1990). Enhanced membrane rigidity in charged lamellar phases. J.Phys.(France). 51, 2307-20.

Higgs, P.G. & Ross-Murphy, S.B. (1990). Creep measurements in Gelatin gels. Int. J. Biol. Macromol. 12, 233-239.

Higgs, P.G. & Ball, R.C. (1990). A 'reel-chain' model for the elasticity of biopolymer networks, and its relationship to slip-link models for entanglements. In Physical Networks. Eds. W.Burchard and S.B.Ross-Murphy (proceedings of Networks 88, Freiburg, Germany). Elsevier Applied Science.

Higgs, P.G. & Ball, R.C. (1989). Formation of gels and complexes by pairwise polymer interactions. J.Phys.(France). 50, 3285-3308.

Higgs, P.G. & Gaylord, R.J. (1990). Slip-links, hoops and tubes - Tests of entanglement models of rubber elasticity. Polymer 31, 70-77.

Higgs, P.G. & Ball, R.C. (1989a). Trapped entanglements in rubbers - A unification of models. Europhys. Lett. 8, 357-360.

Higgs, P.G. & Ball, R.C. (1989b). Some ideas concerning the elasticity of biopolymer networks. Macromolecules 22, 2432-37.

Higgs, P.G. & Ball, R.C. (1988). Polydisperse polymer networks: elasticity, orientational properties, and small angle neutron scattering. J.Phys.(France) 49, 1785-1811.