Abstract:
:Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set X of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate processes (for example, hybrid evolution, endosymbiosis, and lateral gene transfer). A major goal in systematic biology is to infer evolutionary relationships, and while phylogenetic trees can be uniquely determined from various simple combinatorial data on X, for networks the reconstruction question is much more subtle. Here we ask when can a network be uniquely reconstructed from its 'ancestral profile' (the number of paths from each ancestral vertex to each element in X). We show that reconstruction holds (even within the class of all networks) for a class of networks we call 'orchard networks', and we provide a polynomial-time algorithm for reconstructing any orchard network from its ancestral profile. Our approach relies on establishing a structural theorem for orchard networks, which also provides for a fast (polynomial-time) algorithm to test if any given network is of orchard type. Since the class of orchard networks includes tree-sibling tree-consistent networks and tree-child networks, our result generalise reconstruction results from 2008 and 2009. Orchard networks allow for an unbounded number k of reticulation vertices, in contrast to tree-sibling tree-consistent networks and tree-child networks for which k is at most 2|X|-4 and |X|-1, respectively.
journal_name
Math Bioscijournal_title
Mathematical biosciencesauthors
Erdős PL,Semple C,Steel Mdoi
10.1016/j.mbs.2019.04.009subject
Has Abstractpub_date
2019-07-01 00:00:00pages
33-40eissn
0025-5564issn
1879-3134pii
S0025-5564(19)30023-9journal_volume
313pub_type
杂志文章abstract::On the basis of this study, it is concluded that within physiological limits the minimum value for the mean capture time of LDL receptors by coated pits must be induced fundamentally by an optimal characterization of their insertion rate function. The corresponding steady-state surface aggregation patterns for the unb...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/s0025-5564(99)00043-7
更新日期:1999-11-01 00:00:00
abstract::The transmission dynamics of a communicable disease in a subdivided population where the spread among groups follows the proportionate mixing model while the within-group transmission can correspond to preferred mixing, proportionate mixing among subgroups, or mixing between social and nonsocial subgroups, is analyzed...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/0025-5564(89)90061-8
更新日期:1989-10-01 00:00:00
abstract::A Gompertz-type diffusion process characterized by the presence of exogenous factors in the drift term is considered. Such a process is able to describe the dynamics of populations in which both the intrinsic rates are modified by means of time-dependent terms. In order to quantify the effect of such terms the evaluat...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2013.01.001
更新日期:2013-09-01 00:00:00
abstract::The two methods available for analyzing the global structural identifiability of the parameters of a nonlinear system with a specified input function, the Taylor series approach and the similarity transformation approach, are compared and contrasted through application to three examples. It is shown that, as for linea...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/0025-5564(90)90055-4
更新日期:1990-11-01 00:00:00
abstract::The results of recent experimental and epidemiological studies provide evidence on the connection between carcinogenesis, cancer progression, and aging. Existing models, however, are traditionally focused only on one of these aspects of health deterioration. In this paper, we derive a new model of cancer, which descri...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2008.12.007
更新日期:2009-04-01 00:00:00
abstract::A stochastic model for hospital infection incorporating both direct transmission and indirect transmission via free-living bacteria in the environment is investigated. We examine the long term behavior of the model by calculating a stationary distribution and normal approximation of the distribution. The quasi-station...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2012.10.002
更新日期:2013-01-01 00:00:00
abstract::During normal, voluntary movements, skeletal muscles typically contract in a highly dynamic manner; the length of the muscle and the speed of contraction change continuously. In this study, we present an approach to predict the accurate behavior of muscles for such dynamic contractions using Huxley's cross-bridge mode...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/s0025-5564(96)00115-0
更新日期:1997-01-01 00:00:00
abstract::Malaria is an infectious disease present all around the globe and responsible for half a million deaths per year. A within-host model of this infection requires a framework capable of properly approximating not only the blood stage of the infection but also the erythropoietic process that is in charge of overcoming th...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2015.08.020
更新日期:2015-12-01 00:00:00
abstract::A new epidemic model is developed that describes the spread of an infectious disease with fatal risk. The model includes as extreme cases the standard general epidemic process (for diseases that confer immunity after infection) and the fatal epidemic process (for diseases that lead inevitably to death). Both determini...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/0025-5564(93)90019-7
更新日期:1993-09-01 00:00:00
abstract::General nonstationary birth-death process with possible catastrophes on finite state space is studied. The approach for obtaining the bounds on the rates of convergence to the limiting characteristics is outlined. Method for construction of the limiting characteristics is proposed. We also show that, as a rule, the in...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2013.02.009
更新日期:2013-09-01 00:00:00
abstract::When comparing the performance of a stochastic model of an epidemic at two points in a parameter space, a threshold is said to have been crossed when at one point an epidemic develops with positive probability; while at the other there is a tendency for an epidemic to become extinct. The approach used to find threshol...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/s0025-5564(01)00093-1
更新日期:2002-05-01 00:00:00
abstract::We numerically investigate the influence of intrinsic channel noise on the dynamical response of delay-coupling in neuronal systems. The stochastic dynamics of the spiking is modeled within a stochastic modification of the standard Hodgkin-Huxley model wherein the delay-coupling accounts for the finite propagation tim...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2013.02.007
更新日期:2013-09-01 00:00:00
abstract::We investigate a mathematical model of tumor-immune interactions with chemotherapy, and strategies for optimally administering treatment. In this paper we analyze the dynamics of this model, characterize the optimal controls related to drug therapy, and discuss numerical results of the optimal strategies. The form of ...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2006.05.003
更新日期:2007-09-01 00:00:00
abstract::Quantitative models for characterising the detailed branching patterns of dendritic trees aim to explain these patterns either in terms of growth models based on principles of dendritic development or reconstruction models that describe an existing structure by means of a canonical set of elementary properties of dend...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2006.08.005
更新日期:2007-02-01 00:00:00
abstract::In 1992, Watts and May introduced a simple dynamical systems model of the spread of HIV based on disease transmission per partnership including the length of partnership duration. This model allowed for the treatment of concurrent partnerships, although it was hampered by the assumption of an important latent phase wh...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2016.09.009
更新日期:2016-12-01 00:00:00
abstract::In a random walk (RW) in Z an individual starts at 0 and moves at discrete unitary steps to the right or left with respective probabilities p and 1-p. Assuming p > 1/2 and finite a, a > 1, the probability that state a will be reached before -a is Q(a, p) where Q(a, p) > p. Here we introduce the cooperative random walk...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2016.06.011
更新日期:2016-09-01 00:00:00
abstract::An optimal parameter selection model of cancer chemotherapy is presented which describes the treatment of a tumor over a fixed period of time by the repeated administration of a single drug. The drug is delivered at evenly spaced intervals over the treatment period at doses to be selected by the model. The model const...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/0025-5564(90)90005-j
更新日期:1990-05-01 00:00:00
abstract::This paper considers complex models arising in sociobiology. These combine genetic and strategic aspects to model the effect of gene-linked strategies on the ability of individuals to survive to maturity, mate and produce offspring. Several important models considered in the literature are generalised and extended to ...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/s0025-5564(98)10011-1
更新日期:1998-08-01 00:00:00
abstract::In this paper, we investigate the effects of recurring mass gathering event on the spread of an epidemic. Mass gatherings take place when a large number of people from different locations visit a particular region during a short time period. Such activity plays a crucial role in the epidemic spread as traveling facili...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2019.03.006
更新日期:2019-06-01 00:00:00
abstract:OBJECTIVE:Biological processes actually are a dynamic molecular process over time. Time course gene expression experiments provide opportunities to explore patterns of gene expression change over a time and understand the dynamic behavior of gene expression, which is crucial for study on development and progression of ...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2016.08.012
更新日期:2016-11-01 00:00:00
abstract::When ionizing radiation strikes a cell it induces DNA double strand breaks (DSBs). Subsequently, some of the DSBs misrejoin and thus cause alterations in the size distribution of the DNA fragments. We derive a system of non-linear integro-differential equations describing the misrejoining interactions of five classes ...
journal_title:Mathematical biosciences
pub_type: 杂志文章,评审
doi:10.1016/s0025-5564(98)00006-6
更新日期:1998-05-01 00:00:00
abstract::Recent experimental data have shown that HIV-specific CD4 T cells provide a very important target for HIV replication. We use mathematical models to explore the effect of specific CD4 T cell infection on the dynamics of virus spread and immune responses. Infected CD4 T cells can provide antigen for their own stimulati...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2007.01.007
更新日期:2007-09-01 00:00:00
abstract::Many situations in population biology involve a rate--typically a contact or recruitment rate--which increases linearly for small populations but reaches a maximum value (saturates) for large populations. Models for populations of variable size need to incorporate both characteristics to predict behavior accurately. T...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2004.11.001
更新日期:2004-12-01 00:00:00
abstract::In linear, stochastic dynamics it is shown that the quasideterministic population size is equivalent to the mean population size. The quasideterministic dynamics are defined by the conditional infinitesimal mean of the process. The stochastic component of the dynamics includes both Gaussian and Poisson white noise, wi...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/0025-5564(89)90010-2
更新日期:1989-03-01 00:00:00
abstract::In this paper we compare foraging strategies that might be used by predators seeking prey in a patchy environment. The strategies differ in the extent to which predators aggregate in response to prey density. The approach to the comparison is suggested by the idea of evolutionarily stable strategies. A strategy is sai...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/s0025-5564(99)00027-9
更新日期:1999-08-01 00:00:00
abstract::A non-traditional approach of fitting dynamic resource biomass models to data is developed in this paper. A variational adjoint technique is used for dynamic parameter estimation. In the variational formulation, a cost function measuring the distance between the model solution and the observations is minimized. The da...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/s0025-5564(02)00178-5
更新日期:2003-03-01 00:00:00
abstract::Half-sib, first cousin, half nth cousin, and nth cousin mating systems are robust in that small deviations from the mating structure will not significantly alter the levels of genetic identity or effect qualitative distinctions between the models. Substitution of nearest kin in matings may either increase or decrease ...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/0025-5564(91)90026-f
更新日期:1991-04-01 00:00:00
abstract::A mathematical model of the T-lymphocyte proliferation process (in vivo and in vitro) is presented. This model takes into account cell-cycle progression and the regulation by lymphokines (lymphocyte activating factor interleukin 1 and T-cell growth factor interleukin 2). Using data on the generalized picture of the sh...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/0025-5564(93)90071-h
更新日期:1993-06-01 00:00:00
abstract::The spread of the human immunodeficiency virus (HIV) depends prominently on the migration of people between different regions. An important consequence of this population mobility is that HIV control strategies that are optimal in a regional sense may not be optimal in a national sense. We formulate various mathematic...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2008.03.003
更新日期:2008-06-01 00:00:00
abstract::This paper deals with numerical modeling and simulation of heat transfer in skin tissues using non-linear dual-phase-lag (DPL) bioheat transfer model under periodic heat flux boundary condition. The blood perfusion is assumed temperature-dependent which results in non-linear DPL bioheat transfer model in order to pred...
journal_title:Mathematical biosciences
pub_type: 杂志文章
doi:10.1016/j.mbs.2017.08.009
更新日期:2017-11-01 00:00:00