Full Text Journal Articles by
Author Lindi M Wahl

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Estimating the risk of pandemic avian influenza.

Amita Tripathi, Harish Chandra Dhakal, Khagendra Adhikari, Ramesh Chandra Timsina, Lindi M Wahl,

Outbreaks of highly pathogenic strains of avian influenza (HPAI) cause high mortality in avian populations worldwide. When spread from avian reservoirs to humans, HPAI infections cause mortality in about 50% of human infections. Cases of human-to-human transmission of HPAI are relatively rare, and have, to date, only been reported in ... Read more >>

J Biol Dyn (Journal of biological dynamics)
[2021, 15(1):327-341]

Cited: 0 times

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Mosaic vaccination: How distributing different vaccines across a population could improve epidemic control.

David V McLeod, Lindi M Wahl, Nicole Mideo,

Although vaccination has been remarkably effective against some pathogens, for others, rapid antigenic evolution results in vaccination conferring only weak and/or short-lived protection. Consequently, considerable effort has been invested in developing more evolutionarily robust vaccines, either by targeting highly conserved components of the pathogen (universal vaccines) or by including multiple ... Read more >>

Evol Lett (Evolution letters)
[2021, 5(5):458-471]

Cited: 0 times

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Quantifying the forces that maintain prophages in bacterial genomes.

Amjad Khan, Lindi M Wahl,

Genome sequencing has revealed that prophages, viral sequences integrated in a bacterial chromosome, are abundant, accounting for as much as 20% of the bacterial genome. These sequences can confer fitness benefits to the bacterial host, but may also instigate cell death through induction. Several recent investigations have revealed that the ... Read more >>

Theor Popul Biol (Theoretical population biology)
[2020, 133:168-179]

Cited: 1 time

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Evolutionary stability of the lysis-lysogeny decision: Why be virulent?

Lindi M Wahl, Matthew I Betti, David W Dick, Tyler Pattenden, Aaryn J Puccini,

Lytic viruses infect and kill host cells, producing a large number of viral copies. Temperate viruses, in contrast, are able to integrate viral genetic material into the host cell DNA, leaving a viable host cell. The evolutionary advantage of this strategy, lysogeny, has been demonstrated in complex environments that include ... Read more >>

Evolution (Evolution; international journal of organic evolution)
[2019, 73(1):92-98]

Cited: 4 times

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Bee++: An Object-Oriented, Agent-Based Simulator for Honey Bee Colonies.

Matthew Betti, Josh LeClair, Lindi M Wahl, Mair Zamir,

We present a model and associated simulation package (www.beeplusplus.ca) to capture the natural dynamics of a honey bee colony in a spatially-explicit landscape, with temporally-variable, weather-dependent parameters. The simulation tracks bees of different ages and castes, food stores within the colony, pollen and nectar sources and the spatial position of ... Read more >>

Insects (Insects)
[2017, 8(1):]

Cited: 4 times

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Prophage as a genetic reservoir: Promoting diversity and driving innovation in the host community.

A Nadeem, Lindi M Wahl,

Sequencing of bacterial genomes has revealed an abundance of prophage sequences in many bacterial species. Since these sequences are accessible, through recombination, to infecting phages, bacteria carry an arsenal of genetic material that can be used by these viruses. We develop a mathematical model to isolate the effects of this ... Read more >>

Evolution (Evolution; international journal of organic evolution)
[2017, 71(8):2080-2089]

Cited: 7 times

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Mathematical modelling of CRISPR-Cas system effects on biofilm formation.

Qasim Ali, Lindi M Wahl,

Clustered regularly interspaced short palindromic repeats (CRISPR), linked with CRISPR associated (Cas) genes, can confer adaptive immunity to bacteria, against bacteriophage infections. Thus from a therapeutic standpoint, CRISPR immunity increases biofilm resistance to phage therapy. Recently, however, CRISPR-Cas genes have been implicated in reducing biofilm formation in lysogenized cells. Thus ... Read more >>

J Biol Dyn (Journal of biological dynamics)
[2017, 11(sup2):264-284]

Cited: 2 times

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The dynamics of mobile promoters: Enhanced stability in promoter regions.

Mahnaz Rabbani, Lindi M Wahl,

Mobile promoters are emerging as a new class of mobile genetic elements, first identified by examining prokaryote genome sequences, and more recently confirmed by experimental observations in bacteria. Recent datasets have identified over 40,000 putative mobile promoters in sequenced prokaryote genomes, however only one-third of these are in regions of ... Read more >>

J Theor Biol (Journal of theoretical biology)
[2016, 407:401-408]

Cited: 0 times

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Backward bifurcations, turning points and rich dynamics in simple disease models.

Wenjing Zhang, Lindi M Wahl, Pei Yu,

In this paper, dynamical systems theory and bifurcation theory are applied to investigate the rich dynamical behaviours observed in three simple disease models. The 2- and 3-dimensional models we investigate have arisen in previous investigations of epidemiology, in-host disease, and autoimmunity. These closely related models display interesting dynamical behaviors including ... Read more >>

J Math Biol (Journal of mathematical biology)
[2016, 73(4):947-976]

Cited: 3 times

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Extinction probabilities and stationary distributions of mobile genetic elements in prokaryotes: The birth-death-diversification model.

Nicole E Drakos, Lindi M Wahl,

Theoretical approaches are essential to our understanding of the complex dynamics of mobile genetic elements (MGEs) within genomes. Recently, the birth-death-diversification model was developed to describe the dynamics of mobile promoters (MPs), a particular class of MGEs in prokaryotes. A unique feature of this model is that genetic diversification of ... Read more >>

Theor Popul Biol (Theoretical population biology)
[2015, 106:22-31]

Cited: 1 time

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Effects of infection on honey bee population dynamics: a model.

Matt I Betti, Lindi M Wahl, Mair Zamir,

We propose a model that combines the dynamics of the spread of disease within a bee colony with the underlying demographic dynamics of the colony to determine the ultimate fate of the colony under different scenarios. The model suggests that key factors in the survival or collapse of a honey ... Read more >>

PLoS One (PloS one)
[2014, 9(10):e110237]

Cited: 17 times

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Survival probability of beneficial mutations in bacterial batch culture.

Lindi M Wahl, Anna Dai Zhu,

The survival of rare beneficial mutations can be extremely sensitive to the organism's life history and the trait affected by the mutation. Given the tremendous impact of bacteria in batch culture as a model system for the study of adaptation, it is important to understand the survival probability of beneficial ... Read more >>

Genetics (Genetics)
[2015, 200(1):309-320]

Cited: 10 times

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Rates of transposition in Escherichia coli.

Ana Sousa, Ana Sousa, Catarina Bourgard, Lindi M Wahl, Isabel Gordo,

The evolutionary role of transposable elements (TEs) is still highly controversial. Two key parameters, the transposition rate (u and w, for replicative and non-replicative transposition) and the excision rate (e) are fundamental to understanding their evolution and maintenance in populations. We have estimated u, w and e for six families ... Read more >>

Biol Lett (Biology letters)
[2013, 9(6):20130838]

Cited: 27 times

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Birth, death, and diversification of mobile promoters in prokaryotes.

Mark W J van Passel, Harm Nijveen, Lindi M Wahl,

A previous study of prokaryotic genomes identified large reservoirs of putative mobile promoters (PMPs), that is, homologous promoter sequences associated with nonhomologous coding sequences. Here we extend this data set to identify the full complement of mobile promoters in sequenced prokaryotic genomes. The expanded search identifies nearly 40,000 PMP sequences, ... Read more >>

Genetics (Genetics)
[2014, 197(1):291-299]

Cited: 3 times

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The time distribution of sulfadoxine-pyrimethamine protection from malaria.

Samira Akbari, Naveen K Vaidya, Lindi M Wahl,

Sulfadoxine-pyrimethamine (SP) has been one of the most widely used antimalarial treatments world-wide, and is also used prophylactically in vulnerable populations. In this paper, we develop a mathematical model which allows us to infer the time distribution of SP protection from drug-trial data. Fitting our model to data from a ... Read more >>

Bull Math Biol (Bulletin of mathematical biology)
[2012, 74(11):2733-2751]

Cited: 2 times

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Model and test in a fungus of the probability that beneficial mutations survive drift.

Danna R Gifford, J Arjan G M de Visser, Lindi M Wahl,

Determining the probability of fixation of beneficial mutations is critically important for building predictive models of adaptive evolution. Despite considerable theoretical work, models of fixation probability have stood untested for nearly a century. However, recent advances in experimental and theoretical techniques permit the development of models with testable predictions. We ... Read more >>

Biol Lett (Biology letters)
[2013, 9(1):20120310]

Cited: 12 times

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Transmission dynamics of the recently-identified BYD virus causing duck egg-drop syndrome.

Naveen K Vaidya, Feng-bin Wang, Xingfu Zou, Lindi M Wahl,

Baiyangdian (BYD) virus is a recently-identified mosquito-borne flavivirus that causes severe disease in ducks, with extremely rapid transmission, up to 15% mortality within 10 days and 90% reduction in egg production on duck farms within 5 days of infection. Because of the zoonotic nature of flaviviruses, the characterization of BYD ... Read more >>

PLoS One (PloS one)
[2012, 7(4):e35161]

Cited: 5 times

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Estimating the evidence of selection and the reliability of inference in unigenic evolution.

Andrew D Fernandes, Benjamin P Kleinstiver, David R Edgell, Lindi M Wahl, Gregory B Gloor,

<h4>Background</h4>Unigenic evolution is a large-scale mutagenesis experiment used to identify residues that are potentially important for protein function. Both currently-used methods for the analysis of unigenic evolution data analyze 'windows' of contiguous sites, a strategy that increases statistical power but incorrectly assumes that functionally-critical sites are contiguous. In addition, both ... Read more >>

Algorithms Mol Biol (Algorithms for molecular biology : AMB)
[2010, 5:35]

Cited: 0 times

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Identifying and seeing beyond multiple sequence alignment errors using intra-molecular protein covariation.

Russell J Dickson, Lindi M Wahl, Andrew D Fernandes, Gregory B Gloor,

<h4>Background</h4>There is currently no way to verify the quality of a multiple sequence alignment that is independent of the assumptions used to build it. Sequence alignments are typically evaluated by a number of established criteria: sequence conservation, the number of aligned residues, the frequency of gaps, and the probable correct ... Read more >>

PLoS One (PloS one)
[2010, 5(6):e11082]

Cited: 18 times

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The adaptation rate of asexuals: deleterious mutations, clonal interference and population bottlenecks.

Paulo R A Campos, Lindi M Wahl,

The rate at which a population adapts to its environment is a cornerstone of evolutionary theory, and recent experimental advances in microbial populations have renewed interest in predicting and testing this rate. Efforts to understand the adaptation rate theoretically are complicated by high mutation rates, to both beneficial and deleterious ... Read more >>

Evolution (Evolution; international journal of organic evolution)
[2010, 64(7):1973-1983]

Cited: 15 times

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Adaptation rates of lytic viruses depend critically on whether host cells survive the bottleneck.

Zaheerabbas Patwa, Lindi M Wahl,

We use a branching process approach to estimate the substitution rate, the rate at which beneficial mutations occur and fix, in populations of lytic viruses whose growth is controlled by periodic population bottlenecks. Our model predicts that substitution rates, and by extension adaptation rates, are profoundly affected by the survival ... Read more >>

Evolution (Evolution; international journal of organic evolution)
[2010, 64(4):1166-1172]

Cited: 4 times

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Reproducibility of standardized uptake value measurements determined by 18F-FDG PET in malignant tumors.

Claude Nahmias, Lindi M Wahl,

<h4>Unlabelled</h4>18F-FDG PET is increasingly being used to monitor the early response of malignant tumors to chemotherapy. Understanding the reproducibility of standardized uptake values (SUVs) is an important prerequisite in estimating what constitutes a significant change.<h4>Methods</h4>Twenty-six patients were studied on 2 separate occasions (mean interval +/- SD, 3 +/- 2 d; ... Read more >>

J Nucl Med (Journal of nuclear medicine : official publication, Society of Nuclear Medicine)
[2008, 49(11):1804-1808]

Cited: 114 times

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Time course of early response to chemotherapy in non-small cell lung cancer patients with 18F-FDG PET/CT.

Claude Nahmias, Wahid T Hanna, Lindi M Wahl, Misty J Long, Karl F Hubner, David W Townsend,

<h4>Unlabelled</h4>PET and (18)F-FDG have the potential to follow the early metabolic response to chemotherapy in patients with non-small cell lung cancer and to predict success or failure of the therapy.<h4>Methods</h4>We studied 16 patients with non-small cell lung cancer as they followed 2 courses of docetaxel and carboplatin. Each patient was ... Read more >>

J Nucl Med (Journal of nuclear medicine : official publication, Society of Nuclear Medicine)
[2007, 48(5):744-751]

Cited: 60 times

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Development of an unbiased statistical method for the analysis of unigenic evolution.

Colleen D Behrsin, Chris J Brandl, David W Litchfield, Brian H Shilton, Lindi M Wahl,

<h4>Background</h4>Unigenic evolution is a powerful genetic strategy involving random mutagenesis of a single gene product to delineate functionally important domains of a protein. This method involves selection of variants of the protein which retain function, followed by statistical analysis comparing expected and observed mutation frequencies of each residue. Resultant mutability ... Read more >>

BMC Bioinformatics (BMC bioinformatics)
[2006, 7:150]

Cited: 6 times

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Natural variation in HIV infection: Monte Carlo estimates that include CD8 effector cells.

Jane M Heffernan, Lindi M Wahl,

Viral load and CD4 T-cell counts in patients infected with the human immunodeficiency virus (HIV) are commonly used to guide clinical decisions regarding drug therapy or to assess therapeutic outcomes in clinical trials. However, random fluctuations in these markers of infection can obscure clinically significant change. We employ a Monte ... Read more >>

J Theor Biol (Journal of theoretical biology)
[2006, 243(2):191-204]

Cited: 7 times

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