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Synergistic cumulative contagion in epidemic spreadingFeb 08 2018Most epidemic spreading models assume memoryless agents and independent transmissions along different infection channels. Nevertheless, many real-life cases are manifestly time-sensitive and show strong correlations. Although some recent research efforts ... More
Combinatorial views on persistent characters in phylogeneticsFeb 07 2018The so-called binary perfect phylogeny with persistent characters has recently been thoroughly studied in computational biology as it is less restrictive than the well known binary perfect phylogeny. Here, we focus on the notion of (binary) persistent ... More
Maintenance of diversity in a parasite population capable of persistence and reinfectionFeb 07 2018Motivated by observations in DNA data of the human cytomegalovirus, we study the dynamics and the maintenance of diversity in a hierarchical model of a two-type parasite population distributed over its (infected) hosts. The parasite is assumed to be capable ... More
Impact of Land Use on the DOM Composition in Different Seasons in a Subtropical River Flowing through the Region Undergoing Rapid UrbanizationFeb 07 2018The dissolved organic matter (DOM) composition in river ecosystems could reflect the human impacts on the river ecosystem, and plays an important role in the carbon cycling process. We collected water and phytoplankton samples at 107 sites in the Dongjiang ... More
On the role of multiple scales in metapopulations of public good producersFeb 07 2018Multiple scales in metapopulations can give rise to paradoxical behaviour: in a conceptual model for a public goods game, the species associated with a fitness cost due to the public good production can be stabilised in the well-mixed limit due to the ... More
Risk of coinfection outbreaks in temporal networks: a case study of a hospital contact networkFeb 07 2018We study the spreading of cooperative infections in an empirical temporal network of contacts between people, including health care workers and patients, in a hospital. The system exhibits a phase transition leading to one or several endemic branches, ... More
When Acting as a Reproductive Barrier Leading to Sympatric Speciation, Hybrid Sterility Can Only be PrimaryFeb 06 2018Parental gametes unite to form a zygote that develops into an adult with gonads that, in turn, produce gametes. Interruption of this germinal cycle by prezygotic or postzygotic reproductive barriers can result in two independent cycles, each with the ... More
Modeling epidemics on d-cliqued graphsJan 31 2018Since social interactions have been shown to lead to symmetric clusters, we propose here that symmetries play a key role in epidemic modeling. Mathematical models on d-ary tree graphs were recently shown to be particularly effective for modeling epidemics ... More
Ecological invasion in competition-diffusion systems when the exotic species is either very strong or very weakJan 30 2018Reaction-diffusion systems with a Lotka-Volterra-type reaction term, also known as competition-diffusion systems, have been used to investigate the dynamics of the competition among $m$ ecological species for a limited resource necessary to their survival ... More
Parameter Estimation, Sensitivity Analysis and Optimal Control of a Periodic Epidemic Model with Application to HRSV in FloridaJan 29 2018A state wide Human Respiratory Syncytial Virus (HRSV) surveillance system was implemented in Florida in 1999 to support clinical decision-making for prophylaxis of premature infants. The research presented in this paper addresses the problem of fitting ... More
Structural stability of interaction networks against negative external fieldsJan 24 2018We explore structural stability of weighted and unweighted networks of positively interacting agents against a negative external field. We study how the agents support the activity of each other to confront the negative field, which suppresses the activity ... More
Cell adhesion and fluid flow jointly initiate genotype spatial distribution in biofilmsJan 24 2018Biofilms are microbial collectives that occupy a diverse array of surfaces. The function and evolution of biofilms are strongly influenced by the spatial arrangement of different strains and species within them, but how spatiotemporal distributions of ... More
Uniform asymptotic stability of a fractional tuberculosis modelJan 22 2018We propose a Caputo type fractional-order mathematical model for the transmission dynamics of tuberculosis (TB). Uniform asymptotic stability of the unique endemic equilibrium of the fractional-order TB model is proved, for any $\alpha \in (0, 1)$. Numerical ... More
Basic Model of Purposeful KinesisJan 21 2018Feb 01 2018The notions of taxis and kinesis are introduced and used to describe two types of behavior of an organism in non-uniform conditions: (i) Taxis means the guided movement to more favorable conditions; (ii) Kinesis is the non-directional change in space ... More
Evolutionary dynamics of cooperation in neutral populationsDec 06 2017Cooperation is a difficult proposition in the face of Darwinian selection. Those that defect have an evolutionary advantage over cooperators who should therefore die out. However, spatial structure enables cooperators to survive through the formation ... More
Interactions between chronic diseases: asymmetric outcomes of co-infection at individual and population scalesDec 04 2017Co-infecting parasites and pathogens remain a leading challenge for global public health due to their consequences for individual-level infection risk and disease progression. However, a clear understanding of the population-level consequences of co-infection ... More
Deceptiveness of internet data for disease surveillanceNov 16 2017Quantifying how many people are or will be sick, and where, is a critical ingredient in reducing the burden of disease because it helps the public health system plan and implement effective outbreak response. This process of disease surveillance is currently ... More
Survival analysis of DNA mutation motifs with penalized proportional hazardsNov 11 2017Antibodies, an essential part of our immune system, develop in an intricate process to guarantee a broad diversity of antibodies that are able to bind a continually diversifying array of pathogens. This process involves randomly mutating the DNA sequences ... More
Second-order freeriding on antisocial punishment restores the effectiveness of prosocial punishmentOct 12 2017Economic experiments have shown that punishment can increase public goods game contributions over time. However, the effectiveness of punishment is challenged by second-order freeriding and antisocial punishment. The latter implies that non-cooperators ... More
Ancestral distributions in the coalescentMay 26 2017We consider inference about the history of a sample of DNA sequences, conditional upon the haplotype counts and the number of segregating sites observed at the present time. After deriving some theoretical results in the coalescent setting, we implement ... More
Assessing the role of the spatial scale in the analysis of lagoon biodiversity. A case-study on the macrobenthic fauna of the Po River DeltaMay 24 2017The analysis of benthic assemblages is a valuable tool to describe the ecological status of transitional water ecosystems, but species are extremely sensitive and respond to both microhabitat and seasonal differences. The identification of changes in ... More
Statistical physics of human cooperationMay 19 2017Extensive cooperation among unrelated individuals is unique to humans, who often sacrifice personal benefits for the common good and work together to achieve what they are unable to execute alone. The evolutionary success of our species is indeed due, ... More
Role-separating ordering in social dilemmas controlled by topological frustrationFeb 27 2017"Three is a crowd" is an old proverb that applies as much to social interactions, as it does to frustrated configurations in statistical physics models. Accordingly, social relations within a triangle deserve special attention. With this motivation, we ... More
Social learning in a simple task allocation gameFeb 19 2017We investigate the effects of social interactions in task al- location using Evolutionary Game Theory (EGT). We propose a simple task-allocation game and study how different learning mechanisms can give rise to specialised and non- specialised colonies ... More
Population dynamics of synthetic Terraformation motifsDec 30 2016Ecosystems are complex systems, currently experiencing several threats associated with global warming, intensive exploitation, and human-driven habitat degradation. Such threats are pushing ecosystems to the brink of collapse. Because of a general presence ... More
Elusive preferred hosts or nucleic acid level selection? A commentary on: Evolutionary interpretations of mycobacteriophage biodiversity and host-range through the analysis of codon usage bias (Esposito et al. 2016)Dec 06 2016While confirming the long held view that viruses do not closely imitate the use of their host's codon catalogue, Esposito and coworkers nevertheless consider it surprising that, despite having the ability to infect the same host, many mycobacteriophages ... More
Modular knowledge systems accelerate human migration in asymmetric random environmentsDec 06 2016Migration is a key mechanism for expansion of communities. In spatially heterogeneous environments, rapidly gaining knowledge about the local environment is key to the evolutionary success of a migrating population. For historical human migration, environmental ... More
Is nestedness in mutualistic networks an evolutionary spandrel?Dec 06 2016Mutualistic networks have been shown to involve complex patterns of interactions among animal and plant species. The architecture of these webs seems to pervade some of their robust and fragile behaviour. Recent work indicates that there is a strong correlation ... More
Zipf's law, unbounded complexity and open-ended evolutionDec 06 2016A major problem for evolutionary theory is understanding the so called {\em open-ended} nature of evolutionary change. Open-ended evolution (OEE) refers to the unbounded increase in complexity that seems to characterise evolution on multiple scales. This ... More
Species tree estimation using Neighbor JoiningDec 06 2016Recent theoretical work has demonstrated that Neighbor Joining applied to concatenated DNA sequences is a statistically consistent method of species tree reconstruction. This brief note compares the accuracy of this approach to other popular statistically ... More
Mathematical model of plant-virus interactions mediated by RNA interferenceDec 05 2016Cross-protection, which refers to a process whereby artificially inoculating a plant with a mild strain provides protection against a more aggressive isolate of the virus, is known to be an effective tool of disease control in plants. In this paper we ... More
WKB theory of large deviations in stochastic populationsDec 05 2016Dec 06 2016Stochasticity can play an important role in the dynamics of biologically relevant populations. These span a broad range of scales: from intra-cellular populations of molecules to population of cells and then to groups of plants, animals and people. Large ... More
WKB theory of large deviations in stochastic populationsDec 05 2016Stochasticity can play an important role in the dynamics of biologically relevant populations. These span a broad range of scales: from intra-cellular populations of molecules to population of cells and then to groups of plants, animals and people. Large ... More
A continuum approximation to the population dynamics of periodical cicadasDec 05 2016In addition to their unusually long life cycle, periodical cicadas, Magicicada spp., provide an exceptional example of spatially synchronized life stage phenology in nature. Within regions (broods) spanning 50,000 to 500,000 km^2, adults emerge synchronously ... More
Universality of the SIS prevalence in networksDec 05 2016Epidemic models are increasingly used in real-world networks to understand diffusion phenomena (such as the spread of diseases, emotions, innovations, failures) or the transport of information (such as news, memes in social on-line networks). A new analysis ... More
Primordial Sex Facilitates the Emergence of EvolutionDec 02 2016Compartments are ubiquitous throughout biology, yet their importance stretches back to the origin of cells. In the context of origin of life, we assume that a protocell, a compartment enclosing functional components, requires $N$ components to be evolvable. ... More
A SICA compartmental model in epidemiology with application to HIV/AIDS in Cape VerdeDec 02 2016We propose a new mathematical model for the transmission dynamics of the human immunodeficiency virus (HIV). Global stability of the unique endemic equilibrium is proved. Then, based on data provided by the "Progress Report on the AIDS response in Cape ... More
Universal statistics of selected valuesDec 02 2016Selection, the tendency of some traits to become more frequent than others in a population under the influence of some (natural or artificial) agency, is a key component of Darwinian evolution and countless other natural and social phenomena. Yet a general ... More
Chaos in the Y-chromosome evolution?Dec 01 2016The Y-chromosome degeneration is still an intriguing mechanism and comprises the very origin of sex. We present a coupled version of the well known logistic map and the logistic equation describing the evolution of XY chromosomes. Although chaos was found ... More
A dynamic stress model explains the delayed drug effect in artemisinin treatment of Plasmodium falciparumDec 01 2016Artemisinin resistance constitutes a major threat to the continued success of control programs for malaria. With alternative antimalarial drugs not yet available, improving our understanding of how artemisinin-based drugs act and how resistance manifests ... More
Assessing the impacts of time to detection distribution assumptions on detection probability estimationDec 01 2016Abundance estimates from animal point-count surveys require accurate estimates of detection probabilities. The standard model for estimating detection from removal-sampled point-count surveys assumes that organisms at a survey site are detected at a constant ... More
More than trees, do we need a complex perspective for sustainable forest management?Nov 30 2016Forests are complex systems, and it is necessary to include this characteristic in every forest definition, in order to consider the restriction that this imposes in terms of prediction and control. This lost of predictability and controllability should ... More
Research into the Potential to Adapt and Establish of the invasive Asian Tiger Mosquito Aedes (Stegomyia) albopictus (SKUSE)Nov 30 2016There is general agreement that the former (breeding) macrohabitat of the Asian tiger mosquito, Aedes albopictus (synonym: Stegomyia albopicta) has been described as phytotelmata in the forested areas of Southeast Asia, however, this has changed in the ... More
A rare mutation model in a spatial heterogeneous environment: the Hawk and Dove gameNov 30 2016We propose a stochastic model in evolutionary game theory where individuals (or subpopulations) can mutate changing their strategies randomly (but rarely) and explore the external environment. This environment affects the selective pressure by modifying ... More
Invasive competition with Fokker-Planck diffusion and noiseNov 30 2016Defeat and success of the competitive invasion of a populated area is described with a standard Lotka-Volterra competition model. The resident is adapted to the heterogeneous living conditions, i.e., its motion is modelled as space-dependent, so-called ... More
The optimal rate for resolving a near-polytomy in a phylogenyNov 30 2016The reconstruction of phylogenetic trees from discrete character data is typically relies on models that assume the characters evolve under a continuous-time Markov process operating at some overall rate $\lambda$. When $\lambda$ is too high or too low, ... More
Spatial organization, grouping strategies and cyclic dominance in asymmetric predator-prey gamesNov 29 2016Predators may attack isolated or grouped preys in a cooperative, collective way. Whether a gregarious behavior is advantageous to each species depends on several conditions and game theory is a useful tool to deal with such a problem. We here extend the ... More
Stability of two-species communities: drift, environmental stochasticity, storage effect and selectionNov 29 2016The dynamics of two competing species in a finite size community is one of the most studied problems in population genetics and community ecology. Stochastic fluctuations lead, inevitably, to the extinction of one of the species, but the relevant timescale ... More
The spatial dynamics of ecosystem engineersNov 28 2016The changes on abiotic features of ecosystems have rarely been taken into account by population dynamics models, which typically focus on trophic and competitive interactions between species. However, understanding the population dynamics of organisms ... More
Dynamic landscape models of coevolutionary gamesNov 28 2016Players of coevolutionary games may update not only their strategies but also their networks of interaction. Based on interpreting the payoff of players as fitness, dynamic landscape models are proposed. The modeling procedure is carried out for Prisoner's ... More
Energy intake functions of ectotherms and endotherms derived from their body mass growthNov 28 2016How animals allocate energy to different body functions is still not completely understood and a challenging topic until recently. Here, we investigate in more detail the allocation of energy intake to growth, reproduction or heat production by developing ... More
Stegosaurus chiralityNov 26 2016We explain that Stegosaurus exhibited exterior chirality and observe that the largest plate in particular of USNM 4394, USNM 4714, DMNS 2818 and NHMUK R36730 appears to have tilted to the right rather than to the left in each case. Several instances in ... More
Epidemic spreading and bond percolation in multilayer networksNov 26 2016The Susceptible-Infected-Recovered (SIR) model is studied in multilayer networks with arbitrary number of links across the layers. By following the mapping to bond percolation we give the exact expression for the epidemic threshold and the fraction of ... More
The Phillip Island penguin parade (a mathematical treatment)Nov 26 2016We present a simple mathematical formulation to describe the little penguins parade in Phillip Island. We observed that penguins have the tendency to waddle back and forth on the shore to create a sufficiently large group and then walk home compactly ... More
The Phillip Island penguin parade (a mathematical treatment)Nov 26 2016Dec 02 2016Penguins are flightless, so they are forced to walk while on land. In particular, they show rather specific behaviors in their homecoming, which are interesting to observe and to describe analytically. In this paper, we present a simple mathematical formulation ... More
A Comparison Between the Stability Properties in a DDE Model for Leukemia and the Modified Fractional CounterpartNov 24 2016In this paper, a delay differential equations (DDEs) model of leukemia is introduced and its dynamical properties are investigated in comparison with the modified fractional-order system where the Caputo's derivative is used. The model takes into account ... More
How does cell size regulation affect population growth?Nov 23 2016The proliferation of a growing microbial colony is well characterized by the population growth rate. However, at the single-cell level, isogenic cells often exhibit different cell-cycle durations. For evolutionary dynamics, it is thus important to establish ... More
The effects of stochasticity at the single-cell level and cell size control on the population growthNov 23 2016Sep 18 2017Establishing a quantitative connection between the population growth rate and the generation times of single cells is a prerequisite for understanding evolutionary dynamics of microbes. However, existing theories fail to account for the experimentally ... More
Solving multi-objective optimization problems in conservation with the reference point methodNov 23 2016Managing biodiversity extinction crisis requires wise decision-making processes able to account for the limited of resources available. In most decision problems in conservation biology, several conflicting objectives have to be taken into account. Most ... More
A model of the best-of-N nest-site selection process in honeybeesNov 22 2016The ability of a honeybee swarm to select the best nest site plays a fundamental role in determining the future colony's fitness. To date, the nest-site selection process has mostly been modelled and theoretically analysed for the case of binary decisions. ... More
Modeling contact networks of patients and MRSA spread in Swedish hospitalsNov 21 2016Methicillin-resistant Staphylococcus aureus (MRSA) is a difficult-to-treat infection that only in the European Union affects about 150,000 patients and causes extra costs of 380 million Euros annually to the health-care systems. Increasing efforts have ... More
Numerical optimal control for HIV prevention with dynamic budget allocationNov 21 2016This paper is about numerical control of HIV propagation. The contribution of the paper is threefold: first, a novel model of HIV propagation is proposed; second, the methods from numerical optimal control are successfully applied to the developed model ... More
Evaluating genetic drift in time-series evolutionary analysisNov 18 2016The Wright-Fisher model is the most popular population model for describing the behaviour of evolutionary systems with a finite population size. Approximations to the model have commonly been used for the analysis of time-resolved genome sequence data, ... More
Quantifying gender preferences across humans lifespanNov 18 2016In human relations individuals' gender and age play a key role in the structures and dynamics of their social arrangements. In order to analyze the gender preferences of individuals in interaction with others at different stages of their lives we study ... More
Biodiversity in models of cyclic dominance is preserved by heterogeneity in site-specific invasion ratesNov 17 2016Global, population-wide oscillations in models of cyclic dominance may result in the collapse of biodiversity due to the accidental extinction of one species in the loop. Previous research has shown that such oscillations can emerge if the interaction ... More
Phylogenetic treesNov 17 2016We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees ... More
Estimation of reproduction number and non stationary spectral analysis of Dengue epidemicNov 16 2016In this work we analyze the post monsoon Dengue outbreaks by analyzing the transient and long term dynamics of Dengue incidences and its environmental correlates in Ahmedabad city in western India from 2005-2012. We calculate the reproduction number $R_p$ ... More
Influence of awareness that results from direct experience on the spread of epidemicsNov 15 2016Here we study ODE epidemic models with spread of awareness, assuming that a certain proportion of the hosts will become aware of the ongoing outbreak upon recovery. This study builds on W. Just and J. Saldana's work in [1], and is conducted under the ... More
Evaluation of vaccination strategies for SIR epidemics on random networks incorporating household structureNov 15 2016This paper is concerned with the analysis of vaccination strategies in a stochastic SIR (susceptible $\to$ infected $\to$ removed) model for the spread of an epidemic amongst a population of individuals with a random network of social contacts that is ... More
Modelling the proliferation of transposable elements in populations under environmental stressNov 15 2016In this article, we investigate the evolution of sexual diploid populations which are hosts for active TE families. Our purpose is to explore the relationship between the environmental change, that influences such population and activity of those TEs ... More
Modeling disease spread in populations with birth, death, and concurrencyNov 15 2016The existence of sexual partnerships that overlap in time (concurrent relationships) is believed by some to be a significant contributing factor to the spread of HIV, although this is controversial. We derive an analytic model which allows us to investigate ... More
An Epidemiological Model of Malaria Accounting for Asymptomatic CarriersNov 15 2016Asymptomatic individuals in the context of malarial disease refers to subjects who carry a parasite load but do not show clinical symptoms. A correct understanding of the influence of asymptomatic individuals on transmission dynamics will provide a comprehensive ... More
Critical Population Size for Branching Process Approximation of Probability of Disease ExtinctionNov 14 2016Deterministicmodelstostudythedynamicsofinfectiousdiseaseshavebeenan effective tool for prediction of the persistence of infection. The basic reproduction number R0 has been shown to be a threshold in such models with R0 > 1 a sufficient condition for ... More
Asymptotically Optimal Amplifiers for the Moran ProcessNov 13 2016Dec 05 2017We study the Moran process as adapted by Lieberman, Hauert and Nowak. This is a model of an evolving population on a graph where certain individuals, called "mutants" have fitness r and other individuals, called "non-mutants" have fitness 1. We focus ... More
Asymptotically Optimal Amplifiers for the Moran ProcessNov 13 2016We study the Moran process as adapted by Lieberman, Hauert and Nowak. A family of directed graphs is said to be strongly amplifying if the extinction probability tends to 0 when the Moran process is run on graphs in this family. The most-amplifying known ... More
Asymptotically Optimal Amplifiers for the Moran ProcessNov 13 2016Nov 23 2016We study the Moran process as adapted by Lieberman, Hauert and Nowak. This is a model of an evolving population on a graph where certain individuals, called "mutants" have fitness r and other individuals, called "non-mutants" have fitness 1. We focus ... More
Coupled, multi-strain SIS, SIR and SIRS epidemic modelsNov 13 2016We introduce and analyze coupled, multi-strain SIS, SIR and SIRS epidemic models designed to simulate the emergence and dissemination of drug-resistant pathogen strains. In particular, we provide a detailed investigation of the connection between the ... More
The Reasonable Effectiveness of Agent-Based Simulations in Evolutionary Game TheoryNov 13 2016This is a Reply to comments published in Physics of Life Reviews, on our article "Evolutionary game theory using agent-based methods" (Physics of Life Reviews, 2016, arXiv:1404.0994).
Mean-field models for non-Markovian epidemics on networks: from edge-based compartmental to pairwise modelsNov 12 2016This paper presents a novel extension of the edge-based compartmental model for epidemics with arbitrary distributions of transmission and recovery times. Using the message passing approach we also derive a new pairwise-like model for epidemics with Markovian ... More
Shared information between residues is sufficient to detect pair-wise epistasis in a proteinNov 12 2016In a comment on our manuscript "Strong selection significantly increases epistatic interactions in the long-term evolution of a protein", Dr. Crona challenges our assertion that shared entropy (that is, information) between two residues implies epistasis ... More
The Neural Basis and Evolution of Divergent and Convergent ThoughtNov 11 2016This chapter takes as its departure point a neural level theory of insight that arose from studies of the sparse, distributed, content-addressable architecture of associative memory. It is argued that convergent thought is most fruitfully characterized ... More
Uncertainty in phylogenetic tree estimatesNov 10 2016Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly model the multivariate ... More
Mouse T cell repertoires as statistical ensembles: overall characterization and age dependenceNov 09 2016The ability of the adaptive immune system to respond to arbitrary pathogens stems from the broad diversity of immune cell surface receptors (TCRs). This diversity originates in a stochastic DNA editing process (VDJ recombination) that acts each time a ... More
Turbulence as a problem in non-equilibrium statistical mechanicsNov 09 2016The transitional and well-developed regimes of turbulent shear flows exhibit a variety of remarkable scaling laws that are only now beginning to be systematically studied and understood. In the first part of this article, we summarize recent progress ... More
Turbulence as a problem in non-equilibrium statistical mechanicsNov 09 2016Nov 15 2016The transitional and well-developed regimes of turbulent shear flows exhibit a variety of remarkable scaling laws that are only now beginning to be systematically studied and understood. In the first part of this article, we summarize recent progress ... More
Human mobility networks and persistence of rapidly mutating pathogensNov 08 2016Rapidly mutating pathogens may be able to persist in the population and reach an endemic equilibrium by escaping hosts' acquired immunity. For such diseases, multiple biological, environmental and population-level mechanisms determine the dynamics of ... More
Application of SIR epidemiological model: new trendsNov 08 2016The simplest epidemiologic model composed by mutually exclusive compartments SIR (susceptible-infected-susceptible) is presented to describe a reality. From health concerns to situations related with marketing, informatics or even sociology, several are ... More
Lightweight Interactions for Reciprocal Cooperation in a Social Network GameNov 08 2016The construction of reciprocal relationships requires cooperative interactions during the initial meetings. However, cooperative behavior with strangers is risky because the strangers may be exploiters. In this study, we show that people increase the ... More
Modularity promotes epidemic recurrenceNov 08 2016The long-term evolution of epidemic processes depends crucially on the structure of contact networks. As empirical evidence indicates that human populations exhibit strong community organization, we investigate here how such mesoscopic configurations ... More
An epidemic model for cholera with optimal control treatmentNov 07 2016We propose a mathematical model for cholera with treatment through quarantine. The model is shown to be both epidemiologically and mathematically well posed. In particular, we prove that all solutions of the model are positive and bounded; and that every ... More
An epidemic model for cholera with optimal control treatmentNov 07 2016Dec 01 2016We propose a mathematical model for cholera with treatment through quarantine. The model is shown to be both epidemiologically and mathematically well posed. In particular, we prove that all solutions of the model are positive and bounded; and that every ... More
Minimal-assumption inference from population-genomic dataNov 06 2016Samples of multiple complete genome sequences contain vast amounts of information about the evolutionary history of populations, much of it in the associations among polymorphisms at different loci. Current methods that take advantage of this linkage ... More
Ancestry in adapting, spatially-extended populationsNov 06 2016Selective sweeps affect neutral genetic diversity through hitchhiking. While this effect is limited to the local genomic region of the sweep in panmictic populations, we find that in spatially-extended populations the combined effects of many unlinked ... More
Reverse vaccinology in Plasmodium falciparum 3D7Nov 05 2016A timely immunization can be effective against certain diseases and can save thousands of lives. However, for some diseases it has been difficult, so far, to develop an efficient vaccine. Malaria, a tropical disease caused by a parasite of the genus Plasmodium, ... More
Network model of human aging: frailty limits and information measuresNov 05 2016Aging is associated with the accumulation of damage throughout a persons life. Individual health can be assessed by the Frailty Index (FI). The FI is calculated simply as the proportion $f$ of accumulated age related deficits relative to the total, leading ... More
Amplifiers and Suppressors of Selection for the Moran Process on Undirected GraphsNov 05 2016We consider the classic Moran process modeling the spread of genetic mutations, as extended to structured populations by Lieberman et al.\ (Nature, 2005). In this process, individuals are the vertices of a connected graph $G$. Initially, there is a single ... More
Recovering the Brownian Coalescent Point Process from the Kingman Coalescent by Conditional SamplingNov 04 2016We consider a continuous population whose dynamics is described by the standard stationary Fleming-Viot process, so that the genealogy of $n$ uniformly sampled individuals is distributed as the Kingman $n$-coalescent. In this note, we study some genealogical ... More
Can we 'future-proof' consensus trees?Nov 03 2016Consensus methods are widely used for combining phylogenetic trees into a single estimate of the evolutionary tree for a group of species. As more taxa are added, the new source trees may begin to tell a different evolutionary story when restricted to ... More
From degree-correlated to payoff-correlated activity for an optimal resolution of social dilemmasNov 03 2016An active participation of players in evolutionary games depends on several factors, ranging from personal stakes to the properties of the interaction network. Diverse activity patterns thus have to be taken into account when studying the evolution of ... More
Reproduction Number And Asymptotic Stability For The Dynamics of a Honey Bee Colony with Continuous Age StructureNov 02 2016A system of partial differential equations is derived as a model for the dynamics of a honey bee colony with a continuous age distribution, and the system is then extended to include the effects of a simplified infectious disease. In the disease-free ... More