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Deep Learning Models for LC-MS Untargeted Metabolomics Data Analysis
Metabolomics, the measurement of all metabolites in a given system, is a growing research field with great potential and manifold applications in...
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NIAID/SMB Workshop on Multiscale Modeling of Infectious and Immune-Mediated Diseases
On July 19th, 2023, the National Institute of Allergy and Infectious Diseases co-organized a workshop with the Society of Mathematical Biology, with...
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Distance-Based Regression Analysis for Measuring Associations
Distance-based regression model, as a nonparametric multivariate method, has been widely used to detect the association between variations in a...
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Network-Based Computational Modeling to Unravel Gene Essentiality
Essential genes are reductively defined as those fundamental for an organism’s reproductive success and growth. Still, the so-called essentiality of...
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A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
BackgroundThe current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health...
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Poisson Distribution
After finishing the chapter, readers will be able to …...
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On a Third-Order Singular Arc of Optimal Control in a Minimization Problem for a Mathematical Model of Psoriasis Treatment
We consider a mathematical model of psoriasis treatment on a given time interval. The model consists of three nonlinear differential equations that...
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MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions
BackgroundMicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components),...
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Multidimensional Scaling for Genomic Data
Scientists working with genomic data face challenges to analyze and understand an ever-increasing amount of data. Multidimensional scaling (MDS)...
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DecontaMiner: A Pipeline for the Detection and Analysis of Contaminating Sequences in Human NGS Sequencing Data
Reads alignment is an essential step of next generation sequencing) data analyses. One challenging issue is represented by unmapped reads that are...
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OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data
As a special class of non-coding RNAs (ncRNAs), microRNAs (miRNAs) perform important roles in numerous biological and pathological processes. The...
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Predicting the Metagenomics Content with Multiple CART Trees
Metagenomics is a technique for the characterization and identification of microbial genomes using direct isolation of genomic DNA from the...
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On using physico-chemical properties of amino acids in string kernels for protein classification via support vector machines
String kernels are popular tools for analyzing protein sequence data and they have been successfully applied to many computational biology problems....
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Ontology-based representation and analysis of host-Brucella interactions
BackgroundBiomedical ontologies are representations of classes of entities in the biomedical domain and how these classes are related in computer-...
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An Integrated Method for Functional Analysis of Microbial Communities by Gene Ontology Based on 16S miRNA Gene
The environment and human serve as elaborate hosts of microbes, including a diversity of commensal and pathogenic bacteria that contribute to both...
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A New Algorithm for Inferring Hybridization Events Based on the Detection of Horizontal Gene Transfers
Hybridization and horizontal gene transfer are two major mechanisms of reticulate evolution. Both of them allow for a creation of new species by...
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The environment ontology: contextualising biological and biomedical entities
As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for...
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Mining semantic networks of bioinformatics e-resources from the literature
BackgroundThere have been a number of recent efforts (e.g. BioCatalogue, BioMoby) to systematically catalogue bioinformatics tools, services and...
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Modeling of a multifactor therapeutic effect on a biosystem
This paper considers topical issues of enhancing the effectiveness of diagnostic and therapeutic processes based on ecobionics, including the...