Department of Physics and Astronomy
Office: ABB 345
1995-2002 : Lecturer in Bioinformatics at the University of Manchester School of Biological Sciences, UK.
1992-1995 : Royal Society Sorby Research Fellow at the University of Sheffield, UK.
1989-1992 : Post-docs in France at the Service de Physique Théorique (CEA, Saclay) and the Institut Charles Sadron (CNRS, Strasbourg).
1986-1989 : PhD at the Cavendish Laboratory, Cambridge, UK.
I started out as a statistical physicist working on polymers and soft condensed matter. I became interested in applications of statistical mechanics to biological problems. This led me to study RNA folding and various problems in population genetics and evolutionary biology. In recent years I have been working in bioinformatics and molecular evolution. For information on each of the following research areas, please follow the links below:
I am a member of the Origins Institute, which is an interdisciplinary science institute engaged in research in fundamental areas of science linking astronomy, physics, geology, biology and biochemistry. Full details of our activities and our program of speakers and public lecturers can be found here.
Check out the links page to other Canadian Biophysics groups kindly provided by Andrew Rutenberg at Dalhousie.
Together with Cecile Fradin, I am responsible for the Biophysics Specialization in the undergraduate physics program. Students on this specialization take Core Courses in Physics plus a range of courses from Biochemistry, Biology and Genetics. More details of the Biophysics Specialization here.
Courses I Teach or have taught recently:
ORIGINS 1I03 - Introduction to Origins Research - Web Page
PHYSICS 4S03 - Molecular Biophysics - Web Page
BIOCHEMISTRY 4Y03 - Genomes and Evolution - Web Page
PHYSICS 756 - Special Topics in Biophysics - Web Page
Paul G. Higgs and Teresa K. Attwood. (2005) Blackwell, Malden MA
This text, aimed at upper level undergraduates and graduate students, introduces readers to the twin themes of Bioinformatics and Molecular Evolution.
Bioinformatics chapters explain the need for computational methods in the current era of complete genome sequences and high-throughput experiments, introduce the principal biological databases, and discuss methods used to create them and search them. Algorithms for sequence alignment, identification of conserved motifs in protein families, and pattern recognition methods using Hidden Markov Models and neural networks are discussed in detail. A full chapter on data analysis for Microarrays and Proteomics is included.
Evolutionary chapters begin with a brief introduction to population genetics and the study of sequence variation within and between populations, and move on to the description of evolution of DNA and protein sequences. Phylogenetic methods are covered in detail, and examples are given of application of these methods to biological questions. Factors influencing the evolution at the level of whole genomes are also discussed, and methods for the comparison of gene content and gene order between species are presented.
This book explains the theories behind the methods of bioinformatics rather than the technical details of how to use any particular software package. Important mathematical derivations and statistical tests are explained at a level that should be accessible to biological students with perseverance. Muliple-choice ‘self-tests’ are provided, with answers available on an accompanying web site. A section of longer problems is also included. This text will help the next generation of biologists and biochemists gain the confidence with quantitative methods and the specific vocabulary they need to interact with the statisticians, database analysts and software engineers they will encounter in their future careers.
Independent reviews of the book have been published:
Jianzhi Zhang (2005) Evolution 59: 2281-2283
Damien Counsell (2005) Comparative and Functional Genomics 6: 317-319
You can buy it from the Blackwell web site
Ralph Pudritz, Paul Higgs and Jonathon Stone (2007) Cambridge Series in Astrobiology, vol. 3. Cambridge University Press.
Several major breakthroughs in the last decade have helped contribute to the emerging field of Astrobiology. These have ranged from the study of micro-organisms that have adapted to living in extreme environments on Earth, to the discovery of over 200 planets orbiting around other stars, and the ambitious programs for the robotic exploration of Mars and other bodies in our solar system. This book explores some of the most exciting and important problems in this field. Beginning with how planetary systems are discovered, the text examines how these systems formed, and how water and biomolecules necessary for life were produced. It then focuses on how life may have originated and evolved on Earth. The final section takes the reader on an exploration for life elsewhere in the solar system, including Mars, Titan and Europa.
For further information and to order the book, click here
This book arises from the conference on Astrobiology and the Origins of Life that was organized by the Origins Institute at McMaster. The conference program is availavle here