Nadia Tahiri
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View article: aPhyloGeo: a Python application for correlating genetic and climatic conditions
aPhyloGeo: a Python application for correlating genetic and climatic conditions Open
Motivation Environmental variation and its influence on genetic diversity is a central topic in evolutionary biology and phylogeography. Accurate correlations between genetic and climatic datasets to understand the genetic adaptations of d…
View article: Finding maximum common contractions between phylogenetic networks
Finding maximum common contractions between phylogenetic networks Open
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations co…
View article: Graph-based method for constructing consensus trees
Graph-based method for constructing consensus trees Open
A consensus tree is a phylogenetic tree that synthesizes a given collection of phylogenetic trees, all of which share the same leaf labels but may have different topologies, typically obtained through bootstrapping. Our research focuses on…
View article: Comparison of phylogenetic trees defined on different but mutually overlapping sets of taxa: A review
Comparison of phylogenetic trees defined on different but mutually overlapping sets of taxa: A review Open
Phylogenetic trees represent the evolutionary relationships and ancestry of various species or groups of organisms. Comparing these trees by measuring the distance between them is essential for applications such as tree clustering and the …
View article: Host–Virus Cophylogenetic Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts
Host–Virus Cophylogenetic Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts Open
Bats, with their virus tolerance, social behaviors, and mobility, are reservoirs for emerging viruses, including coronaviruses (CoVs) known for genetic flexibility. Studying the cophylogenetic link between bats and CoVs provides vital insi…
View article: Ecological and Spatial Influences on the Genetics of Cumacea (Crustacea: Peracarida) in the Northern North Atlantic
Ecological and Spatial Influences on the Genetics of Cumacea (Crustacea: Peracarida) in the Northern North Atlantic Open
The peracarid taxon Cumacea is an essential indicator of benthic quality in marine ecosystems. This study investigated the influence of environmental (i.e., biological or ecosystemic), climatic (i.e., meteorological or atmospheric), and sp…
View article: Novel Algorithm for Comparing Phylogenetic Trees with Different but Overlapping Taxa
Novel Algorithm for Comparing Phylogenetic Trees with Different but Overlapping Taxa Open
Comparing phylogenetic trees is a prominent problem widely used in applications such as clustering and building the Tree of Life. While there are many well-developed distance measures for phylogenetic trees defined on the same set of taxa,…
View article: Finding Maximum Common Contractions Between Phylogenetic Networks
Finding Maximum Common Contractions Between Phylogenetic Networks Open
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations co…
View article: Review of: "Micro- and Macroevolution: A Continuum or Two Distinct Types of Change?"
Review of: "Micro- and Macroevolution: A Continuum or Two Distinct Types of Change?" Open
Potential competing interests: No potential competing interests to declare.This article thoroughly examines the relationship between microevolution and macroevolution, proposing a distinction between first-order evolution (microevolution) …
View article: Host-Virus Cophylogeny Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts
Host-Virus Cophylogeny Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts Open
Background: Bats, with their virus tolerance, social behaviors, and mobility, are reservoirs for emerging viruses, including coronaviruses (CoVs) known for genetic flexibility. Studying the cophylogenetic link between bats and CoVs provide…
View article: A new machine learning workflow to create an optimal waiting list in hospitals
A new machine learning workflow to create an optimal waiting list in hospitals Open
Hospital emergency departments treat a variety of illnesses and injuries, improve important prognoses, prevent sequelae and relieve pain, especially for patients who visit the emergency room. These departments accept all types of medical p…
View article: aPhyloGeo-Covid: A Web Interface for Reproducible Phylogeographic Analysis of SARS-CoV-2 Variation using Neo4j and Snakemake
aPhyloGeo-Covid: A Web Interface for Reproducible Phylogeographic Analysis of SARS-CoV-2 Variation using Neo4j and Snakemake Open
The gene sequencing data, along with the associated lineage tracing and research data generated throughout the Coronavirus disease 2019 (COVID-19) pandemic, constitute invaluable resources that profoundly empower phylogeography research. T…
View article: Inferring multiple consensus trees and supertrees using clustering: a review
Inferring multiple consensus trees and supertrees using clustering: a review Open
Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species phylogene…
View article: GPTree Cluster: phylogenetic tree cluster generator in the context of supertree inference
GPTree Cluster: phylogenetic tree cluster generator in the context of supertree inference Open
Summary For many years, evolutionary and molecular biologists have been working with phylogenetic supertrees, which are oriented acyclic graph structures. In the standard approaches, supertrees are obtained by concatenating a set of phylog…
View article: New Metrics for Classifying Phylogenetic Trees Using K-means and the Symmetric Difference Metric
New Metrics for Classifying Phylogenetic Trees Using K-means and the Symmetric Difference Metric Open
The k -means method can be adapted to any type of metric space and is sometimes linked to the median procedures. This is the case for symmetric difference metric (or Robinson and Foulds) distance in phylogeny, where it can lead to median t…
View article: aPhyloGeo-Covid: A Web Interface for Reproducible Phylogeographic Analysis of SARS-CoV-2 Variation using Neo4j and Snakemake
aPhyloGeo-Covid: A Web Interface for Reproducible Phylogeographic Analysis of SARS-CoV-2 Variation using Neo4j and Snakemake Open
The gene sequencing data, along with the associated lineage tracing and research data generated throughout the Coronavirus disease 2019 (COVID-19) pandemic, constitute invaluable resources that profoundly empower phylogeography research. T…
View article: Using Clustering and Machine Learning Methods to Provide Intelligent Grocery Shopping Recommendations
Using Clustering and Machine Learning Methods to Provide Intelligent Grocery Shopping Recommendations Open
Nowadays, grocery lists make part of shopping habits of many customers. With the popularity of e-commerce and plethora of products and promotions available on online stores, it can become increasingly difficult for customers to identify. p…
View article: Intelligent personalized shopping recommendation using clustering and supervised machine learning algorithms
Intelligent personalized shopping recommendation using clustering and supervised machine learning algorithms Open
Next basket recommendation is a critical task in market basket data analysis. It is particularly important in grocery shopping, where grocery lists are an essential part of shopping habits of many customers. In this work, we first present …
View article: Phylogeography: Analysis of genetic and climatic data of SARS-CoV-2
Phylogeography: Analysis of genetic and climatic data of SARS-CoV-2 Open
Due to the fact that the SARS-CoV-2 pandemic reaches its peak, researchers around the globe are combining efforts to investigate the genetics of different variants to better deal with its distribution. This paper discusses phylogeographic …
View article: Phylogeography: Analysis of genetic and climatic data of SARS-CoV-2
Phylogeography: Analysis of genetic and climatic data of SARS-CoV-2 Open
Due to the fact that the SARS-CoV-2 pandemic reaches its peak, researchers around the globe are combining efforts to investigate the genetics of different variants to better deal with its distribution. This paper discusses phylogeographic …
View article: Quantitative Structure-Activity Relationship (QSAR) modeling to predict the transfer of environmental chemicals across the placenta
Quantitative Structure-Activity Relationship (QSAR) modeling to predict the transfer of environmental chemicals across the placenta Open
The increasing diversity of environmental chemicals in the environment, some of which may be developmental toxicants, is a public health concern. The aim of this work was to contribute to the development of rapid and effective methods to a…
View article: Building alternative consensus trees and supertrees using<i>k</i>-means and Robinson and Foulds distance
Building alternative consensus trees and supertrees using<i>k</i>-means and Robinson and Foulds distance Open
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination …
View article: Building alternative consensus trees and supertrees using k-means and Robinson and Foulds distance
Building alternative consensus trees and supertrees using k-means and Robinson and Foulds distance Open
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination …
View article: A deep learning approach for building multiple trees classification
A deep learning approach for building multiple trees classification Open
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer or hybridization e…
View article: An intelligent shopping list based on the application of partitioning and machine learning algorithms
An intelligent shopping list based on the application of partitioning and machine learning algorithms Open
A grocery list is an integral part of the shopping experience of many consumers. First, we propose a new machine learning model written in Python 3 that predicts which grocery products the consumer will buy again or will try to buy for the…
View article: An intelligent shopping list based on the application of partitioning and machine learning algorithms
An intelligent shopping list based on the application of partitioning and machine learning algorithms Open
A grocery list is an integral part of the shopping experience of many consumers. Several mobile retail studies of grocery apps indicate that potential customers place the highest priority on features that help them to create and manage per…
View article: A New Fast Method For Inferring Multiple Consensus Trees Using K-Medoids
A New Fast Method For Inferring Multiple Consensus Trees Using K-Medoids Open
Department of computer science, Université du Québec à Montréal, Case postale 8888, Succursale Centre-ville, H3C 3P8 Montréal, CA