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Life history traits and dispersal shape neutral genetic diversity in metapopulations
Genetic diversity at population scale, depends on species life-history traits, population dynamics and local and global environmental factors. We...
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Inferring Clusters of Orthologous and Paralogous Transcripts
The alternative processing of eukaryote genes allows producing multiple distinct transcripts from a single gene, thereby contributing to the...
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Inferring Transcript Phylogenies from Transcript Ortholog Clusters
Alternative Splicing (AS) is a mechanism in eukaryotic gene expression by which different combinations of introns are spliced to produce distinct...
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Galled Perfect Transfer Networks
Predicting horizontal gene transfers often requires comparative sequence data, but recent work has shown that character-based approaches could also...
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Reconciliation with Segmental Duplication, Transfer, Loss and Gain
We generalize the reconciliation approach, used for inferring the evolution of a single gene family given a species tree, to groups of co-localized...
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A branching stochastic evolutionary model of the B-cell repertoire
We propose a stochastic framework to describe the evolution of the B-cell repertoire during germinal center (GC) reactions. Our model is formulated...
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Mathematical Modeling of Cancer Signaling Addressing Tumor Heterogeneity
One of the obstacles for cancer therapies is the heterogeneity of cancers. Heterogeneity in signal transduction within the same cell population...
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Applications
After giving a general introduction into the field of tree balance, introducing a variety of different available indices and related tree shape...
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Constrained optimization based adversarial example generation for transfer attacks in network intrusion detection systems
Deep learning has enabled network intrusion detection rates as high as 99.9% for malicious network packets without requiring feature engineering....
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Multiobjective Evolutionary Clustering to Enhance Fault Detection in a PV System
Data clustering combined with multiobjective optimization has become attractive when the structure and the number of clusters in a dataset are...
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Predator–Prey Evolution from an Eco-evolutionary Trade-off Model: The Role of Trait Differentiation
We develop a novel eco-evolutionary modelling framework and demonstrate its efficacy by simulating the evolution of trait distributions in predator...
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Metaheuristics and machine learning: an approach with reinforcement learning assisting neural architecture search
Methaheuristics (MHs) are techniques widely used for solving complex optimization problems. In recent years, the interest in combining MH and machine...
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Stochastic Fluctuations Drive Non-genetic Evolution of Proliferation in Clonal Cancer Cell Populations
Evolutionary dynamics allows us to understand many changes happening in a broad variety of biological systems, ranging from individuals to complete...
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CC-MOEA: A Parallel Multi-objective Evolutionary Algorithm for Recommendation Systems
Recommender systems have nowadays been widely used in a variety of applications such as Amazon and Ebay. Traditional recommendation techniques mainly...
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Percolation in Biological Systems
Most biological systems are so complex that they preclude any reasonable description in terms of the exact interactions among their fundamental...
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Making Your Own Luck: Weak Vertical Swimming Improves Dispersal Success for Coastal Marine Larvae
Dispersive early life stages are common in nature. Although many dispersing organisms (“propagules”) are passively moved by outside forces, some...
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MAGE: Strain Level Profiling of Metagenome Samples
Metagenomic profiling from sequencing data aims to disentangle a microbial sample at lower ranks of taxonomy, such as species and strains. Deep...
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Mathematical Characterization of Private and Public Immune Receptor Sequences
Diverse T and B cell repertoires play an important role in mounting effective immune responses against a wide range of pathogens and malignant cells....
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SIENA: Semi-automatic semantic enhancement of datasets using concept recognition
BackgroundThe amount of available data, which can facilitate answering scientific research questions, is growing. However, the different formats of...
