Paul Higgs - McMaster Experts

Affiliations

Faculty of Science, McMaster University
Joint Appointment, Biochemistry & Biomedical Sciences, Faculty of Health Sciences
Director, Origins Institute, Faculty of Science
Associate Member, Biology, Faculty of Science
Professor, Physics & Astronomy, Faculty of Science
Senior Lecturer in Bioinformatics, School of Biological Sciences, University of Manchester
Lecturer in Bioinformatics, School of Biological Sciences, University of Manchester

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selected scholarly activity

books
chapters
- Three Ways to Make an RNA Sequence Steps from Chemistry to the RNA World. 395-407. 2019
- Origin of Life, RNA World and. 175-180. 2016
- From protoplanetary disks to prebiotic amino acids and the origin of the genetic code. 62-88. 2007
- RNA-Based Phylogenetic Methods. Advanced Information and Knowledge Processing. 191-210. 2005
- Compensatory neutral mutations and the evolution of RNA. 91-101. 1998
conferences
- Using stochastic dynamics to model multispecies communities. AIP Conference Proceedings. 226-231. 2000
- Population evolution in a single peak fitness landscape how high are the clouds?. Lecture Notes in Computer Science. 148-157. 1995
- Thermodynamics of RNA folding. When is an RNA molecule in equilibrium?. Lecture Notes in Computer Science. 852-861. 1995
- LOW-TEMPERATURE PROPERTIES OF DIRECTED WALKS WITH RANDOM SELF-INTERACTIONS. SURFACE DISORDERING : GROWTH, ROUGHENING, AND PHASE TRANSITIONS. 243-252. 1992
- ENHANCED MEMBRANE RIGIDITY IN CHARGED LAMELLAR PHASES. LARGE-SCALE MOLECULAR SYSTEMS. 583-586. 1991
journal articles
- Evolution of RNA Viruses: Reasons for the Existence of Separate Plus, Minus, and Double-Strand Replication Strategies. Viruses. 16:1081-1081. 2024
- Equilibrium and Non‐equilibrium Reaction Schemes for Prebiotic Polymerization of Ribonucleotides. ChemSystemsChem. 6. 2024
- Evolution of Bipartite and Segmented Viruses from Monopartite Viruses. Viruses. 15:1135-1135. 2023
- Rolling Circles as a Means of Encoding Genes in the RNA World. Life. 12:1373-1373. 2022
- Computer simulations of Template-Directed RNA Synthesis driven by temperature cycling in diverse sequence mixtures. PLoS Computational Biology. 18:e1010458-e1010458. 2022
- Rolling-circle and strand-displacement mechanisms for non-enzymatic RNA replication at the time of the origin of life. Journal of Theoretical Biology. 527:110822-110822. 2021
- When Is a Reaction Network a Metabolism? Criteria for Simple Metabolisms That Support Growth and Division of Protocells. Life. 11:966-966. 2021
- Can the RNA World Still Function without Cytidine?. Molecular Biology and Evolution (MBE). 37:71-83. 2020
- Survival of RNA Replicators Is Much Easier in Protocells Than in Surface-Based, Spatial Systems. Life. 9:65-65. 2019
- Evolution of protein interfaces in multimers and fibrils. Journal of Chemical Physics. 150:225102. 2019
- Constraining the Time Interval for the Origin of Life on Earth. Astrobiology. 18:343-364. 2018
- The evolution of antibiotic production rate in a spatial model of bacterial competition. PLoS ONE. 13:e0205202-e0205202. 2018
- The Role of Templating in the Emergence of RNA from the Prebiotic Chemical Mixture. Life. 7:41-41. 2017
- Error thresholds for RNA replication in the presence of both point mutations and premature termination errors. Journal of Theoretical Biology. 428:34-42. 2017
- Chemical Evolution and the Evolutionary Definition of Life. Journal of Molecular Evolution. 84:225-235. 2017
- Co-operation between Polymerases and Nucleotide Synthetases in the RNA World. PLoS Computational Biology. 12:e1005161-e1005161. 2016
- Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss. Molecular Biology and Evolution (MBE). 33:1843-1857. 2016
- The Effect of Limited Diffusion and Wet–Dry Cycling on Reversible Polymerization Reactions: Implications for Prebiotic Synthesis of Nucleic Acids. Life. 6:24-24. 2016
- Pathways of Genetic Code Evolution in Ancient and Modern Organisms. Journal of Molecular Evolution. 80:229-243. 2015
- The RNA World: molecular cooperation at the origins of life. Nature Reviews Genetics. 16:7-17. 2015
- The origin and spread of a cooperative replicase in a prebiotic chemical system. Journal of Theoretical Biology. 364:249-259. 2015
- Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome. Molecular Biology and Evolution (MBE). 29:3413-3425. 2012
- Comment on 'How does Biology emerge from Chemistry?'. Origins of Life and Evolution of Biospheres. 42:436-438. 2012
- Comment: Creating Many Identical Copies of a Macromolecular Sequence. Origins of Life and Evolution of Biospheres. 42:416-419. 2012
- The Importance of Stochastic Transitions for the Origin of Life. Origins of Life and Evolution of Biospheres. 42:453-457. 2012
- Autocatalytic Replication and Homochirality in Biopolymers: Is Homochirality a Requirement of Life or a Result of It?. Astrobiology. 12:818-829. 2012
- Comments on “Evolutionary dynamics of RNA-like replicator systems”. Physics of Life Reviews. 9:270-271. 2012
- Contributions of Speed and Accuracy to Translational Selection in Bacteria. PLoS ONE. 7:e51652-e51652. 2012
- The origin of life is a spatially localized stochastic transition. Biology Direct. 7:42-42. 2012
- Origin and evolution of gene families in Bacteria and Archaea. BMC Bioinformatics. 12:S14. 2011
- Comparison of the Roles of Nucleotide Synthesis, Polymerization, and Recombination in the Origin of Autocatalytic Sets of RNAs. Astrobiology. 11:895-906. 2011
- The advantages and disadvantages of horizontal gene transfer and the emergence of the first species. Biology Direct. 6:1-1. 2011
- The Influence of Anticodon-Codon Interactions and Modified Bases on Codon Usage Bias in Bacteria. Molecular Biology and Evolution (MBE). 27:2129-2140. 2010
- Origin of Self-Replicating Biopolymers: Autocatalytic Feedback Can Jump-Start the RNA World. Journal of Molecular Evolution. 69:541-554. 2009
- A Thermodynamic Basis for Prebiotic Amino Acid Synthesis and the Nature of the First Genetic Code. Astrobiology. 9:483-490. 2009
- A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code. Biology Direct. 4:16-16. 2009
- Coevolution of Codon Usage and tRNA Genes Leads to Alternative Stable States of Biased Codon Usage. Molecular Biology and Evolution (MBE). 25:2279-2291. 2008
- Compositional Inheritance: Comparison of Self-assembly and Catalysis. Origins of Life and Evolution of Biospheres. 38:399-418. 2008
- Codon Usage in Mitochondrial Genomes: Distinguishing Context-Dependent Mutation from Translational Selection. Molecular Biology and Evolution (MBE). 25:339-351. 2008
- Population Genetics Without Intraspecific Data. Molecular Biology and Evolution (MBE). 24:1667-1677. 2007
- The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes. Journal of Molecular Evolution. 64:662-688. 2007
- Identification of Conflicting Selective Effects on Highly Expressed Genes. Evolutionary Bioinformatics. 3:117693430700300-117693430700300. 2007
- The Relationship Between the Rate of Molecular Evolution and the Rate of Genome Rearrangement in Animal Mitochondrial Genomes. Journal of Molecular Evolution. 63:375-392. 2006
- The Response of Amino Acid Frequencies to Directional Mutation Pressure in Mitochondrial Genome Sequences Is Related to the Physical Properties of the Amino Acids and to the Structure of the Genetic Code. Journal of Molecular Evolution. 62:340-361. 2006
- Topological structure and interaction strengths in model food webs. Ecological Modelling. 187:389-412. 2005
- Deleting species from model food webs. Oikos. 110:283-296. 2005
- A Unified Model of Codon Reassignment in Alternative Genetic Codes. Genetics. 170:831-840. 2005
- A Comprehensive Analysis of Mammalian Mitochondrial Genome Base Composition and Improved Phylogenetic Methods. Molecular Biology and Evolution (MBE). 22:251-264. 2005
- Comparison of tRNA and rRNA Phylogenies in Proteobacteria: Implications for the Frequency of Horizontal Gene Transfer 2004
- The Evolution of tRNA-Leu Genes in Animal Mitochondrial Genomes. Journal of Molecular Evolution. 57:435-445. 2003
- The evolution of tRNA-Leu genes in animal mitochondrial genomes. Journal of Molecular Evolution. 57:435-445. 2003
- RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences. Molecular Phylogenetics and Evolution. 28:241-252. 2003
- Factors Affecting the Errors in the Estimation of Evolutionary Distances Between Sequences. Molecular Biology and Evolution (MBE). 20:1-9. 2003
- OGRe: a relational database for comparative analysis of mitochondrial genomes. Nucleic Acids Research (NAR). 31:202-206. 2003
- Bayesian Phylogenetics Using an RNA Substitution Model Applied to Early Mammalian Evolution. Molecular Biology and Evolution (MBE). 19:1591-1601. 2002
- Limitation ofTrypanosoma bruceiparasitaemia results from density-dependent parasite differentiation and parasite killing by the host immune response. Proceedings of the Royal Society of London. Biological Sciences. 268:2235-2243. 2001
- The dilution wave in polymer crystallization is described by Fisher’s reaction-diffusion equation. Journal of Chemical Physics. 114:6958-6959. 2001
- RNA Sequence Evolution With Secondary Structure Constraints: Comparison of Substitution Rate Models Using Maximum-Likelihood Methods. Genetics. 157:399-411. 2001
- The Influence of Predator–Prey Population Dynamics on the Long-term Evolution of Food Web Structure. Journal of Theoretical Biology. 208:91-107. 2001
- Dilution Wave and Negative-Order Crystallization Kinetics of Chain Molecules. Physical Review Letters. 85:4397-4400. 2000
- RNA Sequence Evolution with Secondary Structure Constraints. Biochemical Society Transactions. 28:A185-A185. 2000
- Redundant and non-functional guide RNA genes in Trypanosoma brucei are a consequence of multiple genes per minicircle. Gene. 256:245-252. 2000
- The evolution of minicircles and guide RNAs in Trypanosomes. Biochemical Society Transactions. 28:A481-A481. 2000
- RNA secondary structure: physical and computational aspects. Quarterly Reviews of Biophysics. 33:199-253. 2000
- The mimetic transition: a simulation study of the evolution of learning by imitation. Proceedings of the Royal Society of London. Biological Sciences. 267:1355-1361. 2000
- A Population Genetics Model for Multiple Quantitative Traits Exhibiting Pleiotropy and Epistasis. Journal of Theoretical Biology. 203:419-437. 2000
- Chain Orientation in Polymer Networks: Computer Simulations Using the Bond Fluctuation Model. Macromolecules. 32:5062-5071. 1999
- A theoretical study of random segregation of minicircles in trypanosomatids. Proceedings of the Royal Society of London. Biological Sciences. 266:611-620. 1999
- Modelling Coevolution in Multispecies Communities. Journal of Theoretical Biology. 193:345-358. 1998
- Barrier heights between ground states in a model of RNA secondary structure. Journal of Physics A: Mathematical and Theoretical. 31:3153-3170. 1998
- Monte-Carlo simulations of polymer crystallization in dilute solution. Journal of Chemical Physics. 108:4305-4314. 1998
- Compensatory neutral mutations and the evolution of RNA.. Genetica. 102/103:91-101. 1998
- Theory of Fission for Two-Component Lipid Vesicles. Physical Review Letters. 79:1579-1582. 1997
- Evidence for kinetic effects in the folding of large RNA molecules. Journal of Chemical Physics. 105:7152-7157. 1996
- Population Evolution on a Multiplicative Single-Peak Fitness Landscape. Journal of Theoretical Biology. 179:61-73. 1996
- Overlaps between RNA Secondary Structures. Physical Review Letters. 76:704-707. 1996
- Monte Carlo Simulations of the Orientational Order in a Strained Polymer Network: Effect of Density. Macromolecules. 28:7208-7214. 1995
- The accumulation of mutations in asexual populations and the structure of genealogical trees in the presence of selection. Journal of Mathematical Biology. 33:677-702. 1995
- Frequency distributions in population genetics parallel those in statistical physics. Physical Review E. 51:95-101. 1995
- Thermodynamic properties of transfer RNA: a computational study. Journal of the Chemical Society - Faraday Transactions. 91:2531-2531. 1995
- NATURAL-SELECTION AT THE CLASS-II MAJOR HISTOCOMPATIBILITY COMPLEX LOCI OF MAMMALS - DISCUSSION. Philosophical Transactions of the Royal Society of London. Biological Sciences. 346:366-367. 1994
- SELECTION BY PARASITES FOR CLONAL DIVERSITY AND MIXED MATING - DISCUSSION. Philosophical Transactions of the Royal Society of London. Biological Sciences. 346:280-281. 1994
- Low-temperature properties of directed walks with random self interactions. Journal of Physics A: Mathematical and Theoretical. 27:5485-5493. 1994
- Error thresholds and stationary mutant distributions in multi-locus diploid genetics models. Genetical Research. 63:63-78. 1994
- The growth of polymer crystals at the transition from extended chains to folded chains. Journal of Chemical Physics. 100:640-648. 1994
- General discussion. Faraday Discussions. 95:145-145. 1993
- General discussion. Faraday Discussions. 95:367-367. 1993
- RNA secondary structure: a comparison of real and random sequences. Journal de Physique, I. 3:43-59. 1993
- Genetic distance and species formation in evolving populations. Journal of Molecular Evolution. 35:454-465. 1992
- A Model of Directed Walks with Random Self-Interactions. Europhysics Letters. 18:361-366. 1992
- Scaling behavior of polyelectrolytes and polyampholytes: Simulation by an ensemble growth method. Journal of Chemical Physics. 95:4506-4518. 1991
- Stochastic models for species formation in evolving populations. Journal of Physics A: Mathematical and Theoretical. 24:L985-L991. 1991
- Theory of polyampholyte solutions. Journal of Chemical Physics. 94:1543-1554. 1991
- Conformation changes of a polyelectrolyte chain in a poor solvent. Journal de Physique, I. 1:1-7. 1991
- Creep measurements on gelatin gels. International Journal of Biological Macromolecules. 12:233-240. 1990
- Slip-links, hoops and tubes: tests of entanglement models of rubber elasticity. Polymer. 31:70-74. 1990
- Some ideas concerning the elasticity of biopolymer networks. Macromolecules. 22:2432-2437. 1989
- Trapped Entanglements in Rubbers. A Unification of Models. Europhysics Letters. 8:357-361. 1989
- Polydisperse polymer networks : elasticity, orientational properties, and small angle neutron scattering. Journal de Physique. 49:1785-1811. 1988
preprints