Search results for "Computational Mathematic"
showing 10 items of 987 documents
MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems
2016
This is a pre-copyedited, author-produced version of an article accepted for publication in Bioinformatics following peer review. The version of recordJorge González-Domínguez, Yongchao Liu, Juan Touriño, Bertil Schmidt; MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems, Bioinformatics, Volume 32, Issue 24, 15 December 2016, Pages 3826–3828, https://doi.org/10.1093/bioinformatics/btw558is available online at: https://doi.org/10.1093/bioinformatics/btw558 [Abstracts] MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-sca…
Simulation-based estimation of branching models for LTR retrotransposons
2017
Abstract Motivation LTR retrotransposons are mobile elements that are able, like retroviruses, to copy and move inside eukaryotic genomes. In the present work, we propose a branching model for studying the propagation of LTR retrotransposons in these genomes. This model allows us to take into account both the positions and the degradation level of LTR retrotransposons copies. In our model, the duplication rate is also allowed to vary with the degradation level. Results Various functions have been implemented in order to simulate their spread and visualization tools are proposed. Based on these simulation tools, we have developed a first method to evaluate the parameters of this propagation …
REGGAE : a novel approach for the identification of key transcriptional regulators
2019
Abstract Motivation Transcriptional regulators play a major role in most biological processes. Alterations in their activities are associated with a variety of diseases and in particular with tumor development and progression. Hence, it is important to assess the effects of deregulated regulators on pathological processes. Results Here, we present REGulator-Gene Association Enrichment (REGGAE), a novel method for the identification of key transcriptional regulators that have a significant effect on the expression of a given set of genes, e.g. genes that are differentially expressed between two sample groups. REGGAE uses a Kolmogorov–Smirnov-like test statistic that implicitly combines assoc…
In vitro versus in vivo compositional landscapes of histone sequence preferences in eucaryotic genomes
2018
Abstract Motivation Although the nucleosome occupancy along a genome can be in part predicted by in vitro experiments, it has been recently observed that the chromatin organization presents important differences in vitro with respect to in vivo. Such differences mainly regard the hierarchical and regular structures of the nucleosome fiber, whose existence has long been assumed, and in part also observed in vitro, but that does not apparently occur in vivo. It is also well known that the DNA sequence has a role in determining the nucleosome occupancy. Therefore, an important issue is to understand if, and to what extent, the structural differences in the chromatin organization between in vit…
Stability of stationary solutions in models of the Calvin cycle
2017
Abstract In this paper results are obtained concerning the number of positive stationary solutions in simple models of the Calvin cycle of photosynthesis and the stability of these solutions. It is proved that there are open sets of parameters in the model of Zhu et al. (2009) for which there exist two positive stationary solutions. There are never more than two isolated positive stationary solutions but under certain explicit special conditions on the parameters there is a whole continuum of positive stationary solutions. It is also shown that in the set of parameter values for which two isolated positive stationary solutions exist there is an open subset where one of the solutions is asym…
A study on time discretization and adaptive mesh refinement methods for the simulation of cancer invasion: The urokinase model
2016
In the present work we investigate a model that describes the chemotactically and proteolytically driven tissue invasion by cancer cells. The model is a system of advection-reaction-diffusion equations that takes into account the role of the serine protease urokinase-type plasminogen activator. The analytical and numerical study of such a system constitutes a challenge due to the merging, emerging, and traveling concentrations that the solutions exhibit. Classical numerical methods applied to this system necessitate very fine discretization grids to resolve these dynamics in an accurate way. To reduce the computational cost without sacrificing the accuracy of the solution, we apply adaptive…
GIS Infomobility for Travellers
2016
Geographical Information Systems (GIS) are essential systems to support decisions on territorial and environmental aspects. But they not always have been properly used for this purpose. Only in recent years GIS have been getting better used for the planning, management and control of the territory. The application of GIS to the transport sector has become relevant both for management and decision-making in support of Public Administration (PA) and citizens. GIS are particularly useful for roads and routing graphs management capabilities as well as for searching the most suitable path. The results achieved in this research activity aimed to evaluate different road graphs, proprietary and fre…
A stochastic dynamical social model involving a human happiness index
2018
[EN] This paper presents a new human happiness index built through five dimensions: development, freedom, solidarity, justice and peace. These five dimensions are evaluated through quantitative variables obtained from the Human Development Reports, World Data Bank and Eurostat. The new happiness index has been built following the guidelines set by the Human Development Reports of the UN for the construction of quality indices, and it has been compared on a set of 13 EU countries with the Overall Life Satisfaction Index, which is used by the UN. Moreover, the new index has been included in a dynamic mathematical model through the demographic rates to study the evolution of the population. Th…
Packing colorings of subcubic outerplanar graphs
2018
Given a graph $G$ and a nondecreasing sequence $S=(s_1,\ldots,s_k)$ of positive integers, the mapping $c:V(G)\longrightarrow \{1,\ldots,k\}$ is called an $S$-packing coloring of $G$ if for any two distinct vertices $x$ and $y$ in $c^{-1}(i)$, the distance between $x$ and $y$ is greater than $s_i$. The smallest integer $k$ such that there exists a $(1,2,\ldots,k)$-packing coloring of a graph $G$ is called the packing chromatic number of $G$, denoted $\chi_{\rho}(G)$. The question of boundedness of the packing chromatic number in the class of subcubic (planar) graphs was investigated in several earlier papers; recently it was established that the invariant is unbounded in the class of all sub…
Miscellaneous Graph Preliminaries
2020
Summary This article contains many auxiliary theorems which were missing in the Mizar Mathematical Library [2] to the best of the author’s knowledge. Most of them regard graph theory as formalized in the GLIB series (cf. [8]) and most of them are preliminaries needed in [7] or other forthcoming articles.