Publications by our group

As applied mathematicians, we are fortunate to be able to collaborate with experimentalists in a wide range of research areas in biology. The publications by my group are listed below by topic:

Experimental Evolution
- van Passel, M.W.J., Nijveen, H. and Wahl, L.M. "The birth, death and diversification of mobile promoters in prokaryotes", Genetics, submitted.
- Sousa, A., Bourgard, C., Wahl, L.M. and Gordo, I. (2013) "Rates of transposition in Escherichia coli", Biology Letters, in press.
- Gifford, D.R, de Visser, J.A.G.M. and Wahl, L.M. (2012) "Model and test in a fungus of the probability that beneficial mutations survive drift", Biology Letters, doi:10.1098/rsbl.2012.0310.
- Wahl, L.M. (2011) "Fixation when N and s vary: classical approaches give elegant new results", Genetics, 188: 783-785.
- Campos, P.R.A. and Wahl, L.M. (2010) "The adaptation rate of asexuals: deleterious mutations, clonal interference and population bottlenecks", Evolution, 64 (7): 1973-1983.
- Patwa, Z. and Wahl, L.M. (2010) "Adaptation rates of lytic viruses depend critically on whether host cells survive the bottleneck", Evolution, 64: 1166-1172.
- Patwa, Z. and Wahl, L.M. (2009) "The impact of host-cell dynamics on the fixation probability for lytic viruses", Journal of Theoretical Biology, 259: 799-810.
- Campos, P.R.A. and Wahl, L.M. (2009) "The effects of population bottlenecks on clonal interference, and the adaptation effective population size", Evolution, 63 (4): 950-958.
- Patwa, Z. and Wahl, L.M. (2008) "Fixation probabilities for lytic viruses: the attachment-lysis model", Genetics, 180: 459-470.
- Patwa, Z. and Wahl, L.M. (2008) "The fixation probability of beneficial mutations.", Journal of the Royal Society Interface, 5: 1279-1289.
- Alexander, H.K. and Wahl, L.M. (2008) "Fixation probabilities depend on life history: fecundity, generation time and survival in a burst-death model", Evolution, 62 (7): 1600-1609.
- Hubbarde, J.E. and Wahl, L.M. (2008) "Estimating the optimal bottleneck ratio for experimental evolution: the burst-death model", Mathematical Biosciences, 213: 113-118.
- Hubbarde, J.E., Wild, G. and Wahl, L.M. (2007) "Fixation probabilities when generation times are variable: the burst-death model", Genetics, 176: 1703-1712.
- Wahl, L.M. and DeHaan, C.S. (2004) "Fixation probability favors increased fecundity over reduced generation time.", Genetics, 168: 1009-1018.
- Heffernan, J. M. and Wahl, L. M. (2002) "The effects of genetic drift in experimental evolution.", Theoretical Population Biology, 62: 349-356
- Wahl, L. M., Gerrish, P. J. and Saika-Voivod, I. (2002) "Evaluating the impact of population bottlenecks in experimental evolution.", Genetics, 162:961-971.
- Wahl, L. M. and Gerrish, P. J. (2001) "Fixation probability in populations with periodic bottlenecks." Evolution, 55 (12): 2606-2610.
- Wahl, L. M. (2001) "Experimental evolution: analytical approaches and the need for a specific, integrated theory." Comments on Theoretical Biology, 6: 189-204.
- Wahl, L. M. and Krakauer, D. C. (2000), "Models of experimental evolution: The role of genetic chance and selective necessity." Genetics, 156: 1437-1448.
HIV Dynamics
- Zhang, W.J., Wahl, L.M. and Yu, P. "Viral blips may not need a trigger: How transient viremia can arise in deterministic in-host models", SIAM Review, to appear.
- Zhang, W.J., Wahl, L.M. and Yu, P. (2013) "Conditions for transient viremia in deterministic in-host models: viral blips need no exogenous trigger", SIAM Journal of Applied Mathematics,73 (2): 853–881.
- van Gaalen, R. and Wahl, L.M. (2009) "Reconciling conflicting clinical studies of antioxidant supplementation as HIV therapy: a mathematical approach", BMC Public Health, 9, S12 (18 pages).
- Krakovska, O. and Wahl, L.M. (2007) "Drug-sparing regimens for HIV combination therapy: benefits predicted for drug coasting", Bulletin of Mathematical Biology, 69: 2627-2647.
- Krakovska, O. and Wahl, L.M. (2007) "Optimal drug treatment regimens for HIV depend on adherence.", Journal of Theoretical Biology , 246: 499-509.
- Krakovska, O. and Wahl, L.M. (2007) "Costs versus Benefits: Best possible and best practical treatment strategies for HIV", Journal of Mathematical Biology, 54: 385-406.
- Heffernan, J.M. and Wahl, L.M. (2006) "Natural variation in HIV infection: Monte Carlo estimates that include CD8 effector cells.", Journal of Theoretical Biology, 243: 191-204.
- Heffernan, J.M. and Wahl, L.M. (2005) "Monte Carlo estimates of natural variation in HIV infection.", Journal of Theoretical Biology, 236 (2): 137-153.
- Smith, R.J. and Wahl, L.M. (2005) "Drug resistance in an immunological model of HIV-1 infection with impulsive drug effects.", Bulletin of Mathematical Biology, 67 (4): 783-813.
- Smith, R.J. and Wahl, L.M. (2004) "Distinct effects of protease and reverse transcriptase inhibition in an immunological model of HIV-1 infection with impulsive drug effects.", Bulletin of Mathematical Biology, 66 (5): 1259-1283.
- Wahl, L. M., and Bittner, B. (2000) "Immunological transitions in response to antigenic mutation during viral infection." International Immunology, 12: 1371-1380.
- Bittner, B. and Wahl, L. M. (2000), "Immune responses against conserved and variable viral epitopes", Journal of Theoretical Medicine, 3: 37-49.
- Wahl, L. M. and Nowak, M. A.. (2000), "Adherence and resistance: Predictions for therapy outcome", Proceedings of the Royal Society, Biological, 267: 835-843.
- Nowak, M. A., Lloyd, A. L., Vasquez, G., Wiltrout, T. A., Wahl, L. M., Bischofberger, N., Williams, J., Kinter, A., Fauci, A. S., Hirsch, V. M. and Lifson, J. D. (1997), "Viral dynamics of primary viremia and antiretroviral therapy in simian immunodeficiency virus infection", Journal of Virology, 71: 7518-7525.
- Lifson, J. D., Nowak, M. A., Goldstein, C., Rossio, J. L., Kinter, A., Vasquez, G., Wiltrout, T. A., Brown, C., Schneider, D., Wahl, L. M., Lloyd, A. L., Williams, J., Elkins, W. R., Fauci, A. S. and Hirsch, V. M. (1997), "The extent of early viral replication is a critical determinant of the natural history of simian immunodeficiency virus (SIV) infection", Journal of Virology, 71: 9508-9514.
- Klenerman, P., Phillips, R. E., Rinaldo, C. R., Wahl, L. M., Ogg, G., May, R. M., McMicheal, A. J. and Nowak, M. A. (1996), "Cytotoxic T lymphocytes and viral turnover in HIV type 1 infection", Proc. Natl. Acad. Sci. USA, 93: 15323-15328.
Bioinformatics and Biochemistry
- Fernandes, A.D., Kleinstiver, B.P., Edgell, D.R., Wahl, L.M. and Gloor, G.B. (2010) "Estimating the evidence of selection and the reliability of inference in unigenic evolution", Algorithms in Molecular Biology, 5:35.
- Dickson, R.J., Wahl, L.M., Fernandes, A.D. and Gloor, G.B. (2010) "Identifying and seeing beyond multiple sequence alignment errors using intra-molecular protein covariation", PLoS One, 5 (6): e11082.
- Dunn, S.D., Wahl, L.M. and Gloor, G.B. (2008) "Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction", Bioinformatics, 24: 333-340.
- Behrsin, C.D., Bateman, K.S., Hamilton, K.S., Wahl, L.M., Brandl, C.J., Shilton, B.H. and Litchfield, D.W. (2007) "Functionally important residues in the peptidyl-prolyl isomerase Pin1 revealed by unigenic evolution", Journal of Molecular Biology, 365: 1143-1162.
- Behrsin, C.D., Brandl, C.J., Litchfield, D.W., Shilton, B.H. and Wahl, L.M. (2006) "Development of an unbiased statistical method for the analysis of unigenic evolution", BMC Bioinformatics, 7:150 (11 pages) download here .
- Martin, L.C., Gloor, G.B., Dunn, S.D. and Wahl, L.M. (2005) "Using information theory to search for functional domains in proteins.", Bioinformatics, 21 (22): 4116-4124.
- Gloor, G.B., Wahl, L.M., Martin, L.C. and Dunn, S.D. (2005) "Mutual Information in Protein Multiple Sequence Alignments Reveals Two Classes of Coevolving Positions", Biochemistry, 44 (19): 7156-7165.
Positron Tomography
- Nahmias, C. and Wahl, L.M. (2008) "Reproducibility of Standardized Uptake Value measurements determined by 18F-FDG PET in malignant tumors", Journal of Nuclear Medicine, 49 (11): 1804-1808.
- Nahmias, C., Hanna, W.T., Wahl, L.M., Long, M.J., Hubner, K.F. and Townsend, D.W. (2007) "Time course of early response to chemotherapy in non-small cell lung cancer patients with 18-F-FDG-PET/CT", Journal of Nuclear Medicine, 48: 744-751.
- Asselin, M.-C., Wahl, L. M., Amano, S. and Nahmias, C. (2002) "Compartmental model for the in vivo metabolism and partitioning of 6-[18F]fluoro-L-meta-tyrosine in whole blood.", Physics in Medicine and Biology, 47 (11): 1961-1977.
- Nahmias, C., Wahl, L. M., Amano, S., Asselin, M.-C. and Chirakal, R. (2000), "The equilibration of [18F]6-fluoro-L-m-tyrosine between plasma and erythrocytes", Journal of Nuclear Medicine, 41: 1636-1641.
- Wahl, L. M., Chen, J. J., Thompson, M., Chirakal, R. and Nahmias, C. (1999), "The time course of metabolites in human plasma after 6-[18F]fluoro-L-m-tyrosine administration", European Journal of Nuclear Medicine, 26: 1407-1412.
- Wahl, L. M., Asselin, M.-C. and Nahmias, C. (1999), "Regions of interest in the venous sinuses as input functions for quantitative PET", Journal of Nuclear Medicine, 40: 1666-1675.
- Fallen, E. L., Coates, G., Nahmias, C., Chirakal, R., Beanlands, R., Wahl, L. M., Woodcock, G., Thompson, M. and Kamath, M. (1999), "Recovery rates of regional sympathetic reinnervation and myocardial blood flow after acute myocardial infarction", American Heart Journal, 137: 863-869.
- Wahl, L. M. and Nahmias, C. (1998), "Statistical power analysis for positron tomographic studies in humans", Journal of Nuclear Medicine, 39: 1826-1829.
- Wahl, L. M. and Nahmias, C. (1997), "Controversies arising from recent FDOPA articles -- Reply", Journal of Nuclear Medicine, 38: 1270.
- Bartolucci, G., Wahl, L. M., Thompson, M. and Nahmias, C. (1997), "Patterns of cerebral glucose metabolism correlate with clinical manifestations in acquired brain injuries", Brain and Cognition, 35: 418-420.
- Wahl, L. M. and Nahmias, C. (1996a), "Modelling of fluorine-18-6-fluoro-L-dopa in humans", Journal of Nuclear Medicine, 37: 432-437.
- Wahl, L. M. and Nahmias, C. (1996b), "Quantification of dopamine metabolism in man: a mathematically justifiable approach", Physics in Medicine and Biology, 41: 963-978.
- Nahmias, C., Wahl, L. M., Chirakal, R., Firnau, G. and Garnett, E. S. (1995), "A probe for intracellular aromatic amino-acid decarboxylase activity: Distribution and kinetics of [F-18]6-fluoro-L-m-tyrosine in the human brain", Movement Disorders, 10 (3): 298-304.
- Wahl, L. M., Chirakal, R., Firnau, G., Garnett, E. S. and Nahmias, C. (1994), "The distribution and kinetics of [F-18]6-fluoro-3-O-methyl-L-dopa in the human brain", Journal of Cerebral Blood Flow and Metabolism, 14: 664-670.
Evolutionary Game Theory
- Wahl, L. M. (2002) "Evolving the division of labour: Generalists, specialists and task allocation.", Journal of Theoretical Biology , 219: 371-388.
- Wahl, L. M. (2002) "The division of labour: Genotypic versus phenotypic specialization." American Naturalist, 160 (1): 135-145.
- Wahl, L. M. and Nowak, M. A. (1999), "The continuous prisoner's dilemma. I. Linear reactive strategies", Journal of Theoretical Biology, 200: 307-322.
- Wahl, L. M. and Nowak, M. A. (1999), "The continuous prisoner's dilemma. II. Linear reactive strategies with noise", Journal of Theoretical Biology, 200: 323-338.
Theoretical Neuroscience
- Ruiz Vargas, E., Greening, S.G., Mitchell, D.G.V. and Wahl, L.M. "Topology of whole brain functional MRI networks: Improving the truncated scale-free model", submitted.
- Ruiz Vargas, E., Mitchell, D.G.V., Greening, S.G. and Wahl, L.M. "Network analysis of human fMRI data suggests modular restructuring after simulated acquired brain injury", submitted.
- Ruiz Vargas, E. and Wahl, L.M. "The gateway coefficient: a novel metric for identifying critical connections in modular networks ", submitted.
- Wahl, L. M., Jack, J. J. B., Larkman, A. U. and Stratford, K. J. (1997), "The effects of synaptic noise on measurements of evoked excitatory postsynaptic response amplitudes", Biophysical Journal, 73: 205-219.
- Wahl, L. M., Pouzat, C. and Stratford, K. J. (1996), "Monte Carlo simulation of fast excitatory synaptic transmission at a hippocampal synapse", Journal of Neurophysiology, 75: 597-608.
- Wahl, L. M., Stratford, K. J., Larkman, A. U. and Jack, J. J. B. (1995), "The variance of successive peaks in synaptic amplitude histograms: effects of inter-site differences in quantal size", Proceedings of the Royal Society B, 262: 77-85.
Other areas (theoretical immunology, epidemiology, bone physiology...)
- Vaidya, N. and Wahl, L.M. "The sensitivity of avian influenza dynamics in wild birds to time-varying environmental temperature", submitted.
- Chan, B.S. and Wahl, L.M. (2013) "The Scholarship of Teaching and Learning in Canadian Post-Secondary Mathematics: 2000-2010", The Canadian Journal for the Scholarship of Teaching and Learning 4 (1): Article 3.
- Akbari, S., Vaidya, N. and Wahl, L.M. (2012) "The time distribution of sulfadoxine-pyrimethamine protection from malaria", Bulletin of Mathematical Biology, 74: 2733-2751.
- Vaidya, N., Wang, F.-B., Zou, X, and Wahl, L.M. (2012) "Transmission dynamics of the recently-identified BYD virus causing duck egg-drop syndrome", PLoS ONE, 7(4): e35161.
- Alexander, H.K. and Wahl, L.M. (2011) "Self-tolerance and autoimmunity in a regulatory T cell model", Bulletin of Mathematical Biology, 73: 33-71.
- Yao, W., Hertel, L. and Wahl, L.M. (2006) "Dynamics of recurrent viral infection.", Proceedings of the Royal Society, Biological, 273 (1598): 2193-2199.
- Heffernan, J.M. and Wahl, L.M. (2006) "Improving estimates of the basic reproductive ratio: Using both the mean and the dispersal of transition times", Theoretical Population Biology, 70: 135-145.
- Heffernan, J.M., Smith, R.J. and Wahl, L.M. (2005) "Perspectives on the basic reproductive ratio.", Journal of the Royal Society Interface, 2 (4): 281-293, download here.
- Neff, B.D. and Wahl, L.M. (2004) "Mechanisms of sperm competition: testing the fair raffle.", Evolution, 58 (8): 1846-1851.
- Komarova, S.V., Smith, R.J., Dixon, S.J., Sims S.M. and Wahl, L.M. (2003) "Mathematical model predicts a critical role for osteoblast autocrine regulation in the control of bone remodeling.", Bone, 33: 206-215.
- Heppler, G. R. and Wahl, L. M., (1992), "Finite Element Analysis of Free-Free Shells of Revolution", Journal of Sound and Vibration, 152: 263-283.

Complete publication list
Back to homepage