Manuscripts under review or in preparation (copies available by request):
- Yu P., Pooladvand P., Tanaka M.M. and Wahl L.M. "Extinctions caused by host-range expansion", SIAM J. Applied Dynamical Systems, under review.
- Gonçalves-Oliveira J., Pattenden T., Nachum-Biala Y., Carstens M. de Sousa K., Wahl L.M., Harrus S. "Exploring the diversity and evolutionary strategies of prophages in Hyphomicrobiales, comparing animal-associated with non-animal-associated bacteria", BMC Microbiology, under review.
- Wahl L.M. and Tanaka M.M. "Predation as the driver of bacterial extinction", under review.
- Morales D.T., Kushnir A. and Wahl L.M. "Adaptation re-shapes the distribution of fitness effects", in preparation.
- Tuffaha M., Castellano D., Gutenkunst R.N., and Wahl L.M. "Non-hypermutator cancers access driver mutations through
reversals in germline mutational bias", in preparation
- Ezadian M. and Wahl L.M. "Correcting for selection in mutation accumulation experiments", in preparation.
- Cho G.H., Wahl L.M., Roberts W.A. and Sherry D.F. "Dominance and cognitive ability in black-capped chickadees", Animal Cognition, in revision.
Papers in refereed journals:
- Vázquez-Mendoza I., Rodríguez-Torres E.E., Ezadian M., Wahl L.M. and Gerrish P.J. (2024) "Estimating the rate of mutation to a mutator phenotype", Axioms, 13: 117.
- Korosec C., Wahl L.M. and Heffernan J.M. (2024) "Within-host evolution of SARS-CoV-2: how often are de novo mutations transmitted?", Virus Evolution, in press.
- Sane, M., Diwan, G.D., Bhat, B.A., Wahl, L.M. and Agashe D. (2023) "Shifts in mutation spectra enhance access to beneficial mutations", Proc Natl Acad Sci USA 120 (22): e2207355120.
- Wahl, L.M. and Campos, P.R.A. (2023) "Evolutionary rescue on genotypic fitness landscapes", Interface, 20: 20230424.
- Tuffaha, M., Varakunan, S., Castellano, D., Gutenkunst, R.N. and Wahl, L.M. (2023) "Shifts in mutation bias promote mutators by altering the distribution of fitness effects", American Naturalist, 202 (4): online.
- Korosec, C.S., Betti, M.I., Dick, D.W., Ooi, H.K., Moyles, I.R., Wahl, L.M. and Heffernan, J.M. (2023) "Multiple cohort study of hospitalized SARS-CoV-2 in-host infection dynamics: parameter estimates, identifiability, sensitivity and the eclipse phase profile", Journal of Theoretical Biology, 564: 111449.
- Tanaka, M.M. and Wahl, L.M. (2022) "Surviving environmental change: when increasing population size can increase extinction risk", Proc. Roy. Soc. B, 289: 20220439.
- Wahl, L.M. and Agashe, D. (2022) "Selection bias in mutation accumulation", Evolution, 76(3): 528-540.
- Wahl, L.M. and Tanaka, M.M. (2022) "Hazardous loss of variation through selective sweeps in asexual populations", American Naturalist, 199(3): 313-329.
- Pattenden, T., Eagles, C. and Wahl, L.M. (2021) "Host life-history traits influence the distribution of prophages and the genes they carry", Phil. Trans. Roy. Soc. London B, 377: 20200465.
- Tripathi, A., Dhakal, H.C., Adhikari, K., Timsina, R.C. and Wahl, L.M. (2021) "Estimating the risk of pandemic avian influenza", Journal of Biological Dynamics, 15(1): 327-341.
- McLeod, D.V., Wahl, L.M., and Mideo, N. (2021) "Mosaic vaccination: how distributing different vaccines across a population could improve epidemic control", Evolution Letters 5(5): 458-471. Preprint.
- Freitas, O., Campos, P.R.A. and Wahl, L.M. (2021) "Robustness and predictability of evolution in bottlenecked populations", Phys. Rev. E, 103: 042415.
- Khan, A., Burmeister, A.L. and Wahl, L.M. (2020) "Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages", PLOS Computational Biology, e1008482.
- Hanna-Benson, C., Kroeze, S., Gandhi, R., Haffie, T. and Wahl, L.M. (2020) "Students as partners in collaborative course design and educational research", International Journal of Students as Partners, 4(2): 61-80. DOI:10.15173/ijsap.v4i2.4237.
- Khan, A. and Wahl, L.M. (2020) "Quantifying the forces that maintain prophages in bacterial genomes", Theoretical Population Biology, 133: 168-179
- Wahl, L.M., Betti, M.I., Dick, D.W., Pattenden, T. and Puccini, A. (2019) "Evolutionary stability of the lysis-lysogeny decision: why be virulent?", Evolution, 73(1): 92-98.
- Chabas, H., Lion, S., Nicot, A., Meaden, S., van Houte, S., Moineau, S., Wahl, L.M., Westra, E.R. and Gandon, S. (2018) "Evolutionary emergence of infectious diseases in heterogeneous host populations", PLOS Biology, 16(9):e2006738.
- Sigal, D., Reid, J. and Wahl, L.M. (2018) "Effects of Transmission Bottlenecks on the Diversity of Influenza A Virus", Genetics, 210: 1075-1088.
- LeClair, J.S. and Wahl, L.M. (2017) "The impact of population bottlenecks on microbial adaptation", J. Stat. Phys., 172 (1): 114-125.
- Betti, M., Wahl, L.M. and Zamir, M. (2017) "Reproduction number and asymptotic stability for a model of honey bee dynamics with continuous age structure", Bull. Math. Biol., 79 (7): 1586-1611.
- Nadeem, A. and Wahl, L.M. (2017) "Prophage as a genetic reservoir: Promoting diversity and driving innovation in the host communityt", Evolution, 71 (8): 2080-2089.
- Ali, Q. and Wahl, L.M. (2017) "Mathematical modeling of CRISPR-CAS system effects on biofilm formation", J. Biol. Dyn., 11: 264-284.
- Betti, M., LeClair, J., Wahl, L.M. and Zamir, M. (2017) "Bee++: An object-oriented agent-based simulator for honey bee colonies", Insects, 8(1): 31, doi:10.3390/insects8010031.
- Wahl, L.M. and Pattenden, T. (2017) "Prophage provide a safe haven for adaptive exploration in temperate viruses", Genetics, 206: 407-416.
- Yu, P., Nadeem, A. and Wahl, L.M. (2017) "The impact of prophage on the equilibria and stability of phage and host", Journal of Nonlinear Science, 27: 817-846.
- Betti, M., Wahl, L.M. and Zamir, M. (2016) "Age structure is critical to the population dynamics and survival of honey bee colonies", Roy. Soc. Open Science, 3:160444.
- Zhang, W., Yu, P. and Wahl, L.M. (2016) "Backward bifurcations, turning points and rich dynamics in simple disease models", J. Math. Bio., 73(4): 947-976.
- Rabbani, M. and Wahl, L.M. (2016) "The dynamics of mobile promoters: enhanced stability in promoter regions", J. Theor. Biol., 407: 401-408.
- Ruiz Vargas, E., Mitchell, D.G.V., Greening, S.G. and Wahl, L.M. (2016) "Network analysis of human fMRI data suggests modular restructuring after simulated acquired brain injury", Med. Biol. Eng. Comp., 54 (1):235-248.
- Yu, P., Zhang, W. and Wahl, L.M. (2016) "Dynamical analysis and simulation of a 2-dimensional disease model with convex incidence", Comm. Nonlin. Sci. Num. Comp., 37: 163-192.
- Drakos, N.E. and Wahl, L.M. (2015) "Extinction probabilities and stationary distributions of mobile genetic elements in prokaryotes: the birth-death-diversification model", Theor. Pop. Bio., 106: 22-31.
- Wahl, L.M. and Zhu, A.D. (2015) "Survival probability of beneficial mutations in bacteria", Genetics, 200: 309-320.
- Vaidya, N. and Wahl, L.M. (2015) "Avian influenza dynamics under periodic environmental conditions", SIAM J. Appl. Math, 75 (2): 443-467.
- Zhang, W., Wahl, L.M. and Yu, P. (2014) "Modelling and analysis of recurrent autoimmune disease", SIAM J. Appl. Math, 74: 1998-2025.
- Betti M.I., Wahl, L.M. and Zamir, M. (2014) "Effects of infection on honey bee population dynamics: A model" PLoS One, 9 (10), e110237.
- Ruiz Vargas, E. and Wahl, L.M. (2014) "The gateway coefficient: a novel metric for identifying critical connections in modular networks", Eur. Phys. J. B, 87: 161 (10 pages).
- Ruiz Vargas, E., Greening, S.G., Mitchell, D.G.V. and Wahl, L.M. (2014) "Topology of whole brain functional MRI networks: Improving the truncated scale-free model", Physica A: Statistical Mechanics and its Applications, 405: 151-158.
- van Passel, M.W.J., Nijveen, H. and Wahl, L.M. (2014) "Birth,
death and diversification of mobile promoters in prokaryotes", Genetics, 197: 291-299.
- Zhang, W.J., Wahl, L.M. and Yu, P. (2014) "Viral blips may not need a trigger: How transient viremia can arise in deterministic in-host models", SIAM Review, 56 (1): 127-155.
- Sousa, A., Bourgard, C., Wahl, L.M. and Gordo, I. (2013) "Rates of transposition in Escherichia coli", Biology Letters, 9 (6): 20130838, doi:10.1098/rsbl.2013.0838.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Neff, B.D. and Wahl, L.M. (2004) "Mechanisms of sperm
competition: testing the fair raffle.", Evolution, 58 (8): 1846-1851.
- Wahl, L.M. and DeHaan, C.S. (2004) "Fixation probability favors
increased fecundity over reduced generation time.", Genetics, 168: 1009-1018.
- 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.
- 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.
- 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. (2002) "Evolving the division of labour:
Generalists, specialists and task allocation.", Journal of Theoretical Biology
, 219: 371-388.
- 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.
- Wahl, L. M. (2002) "The division of labour:
Genotypic versus phenotypic specialization." American Naturalist,
160 (1): 135-145.
- 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.
- 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 Krakauer, D. C. (2000), "Models of experimental evolution: The role of genetic chance and selective necessity." Genetics, 156: 1437-1448.
- Wahl, L. M., and Bittner, B. (2000) "Immunological transitions in response to antigenic mutation during viral infection." International Immunology, 12: 1371-1380.
- 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. and Nowak, M. A.. (2000), "Adherence and resistance: Predictions for therapy outcome", Proceedings of the Royal Society, Biological, 267: 835-843.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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. 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.
- 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.
- 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.
- 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.
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