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Procrustes is a machine-learning approach that removes cross-platform batch effects from clinical RNA sequencing data
With the increased use of gene expression profiling for personalized oncology, optimized RNA sequencing (RNA-seq) protocols and algorithms are...
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Effects of Procrustes Superimposition and Semilandmark Sliding on Modularity and Integration: An Investigation Using Simulations of Biological Data
Modularity and integration are fundamental properties of organisms and central to theories of complex adaptation. Modularity and integration of shape...
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Procrustes Shape Cannot be Analyzed, Interpreted or Visualized one Landmark at a Time
Landmark-based geometric morphometrics using the Procrustes approach has become the dominant family of methods in morphometrics. However, the...
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The relationship study among Apis spp. using mitochondrial markers, Procrustes coordinates and residuals of geometric morphometric method
Honeybees are social insects and they have an important role in pollinating plants. The molecular markers provide valuable information on different...
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Dissimilarity in flea and host assemblages and their interaction networks along a spatial distance gradient: different patterns revealed by different network dissimilarity metrics
We investigated the distance-decay pattern (an increase in dissimilarity with increasing geographic distance) in regional assemblages of fleas and...
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Disparity of Structural Variants of the m1 Anterokonid in the Vole Genera Stenocranius and Alexandromys (Arvicolini, Rodentia): Qualitative and Quantitative Approaches
AbstractVariation of anteroconid morphotypes was studied using traditional and GM methods in five vole species: Stenocranius gregalis , Alexandromys middendorffii...
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Does multi-way, long-range chromatin contact data advance 3D genome reconstruction?
BackgroundMethods for inferring the three-dimensional (3D) configuration of chromatin from conformation capture assays that provide strictly pairwise...
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Approaches to studying endocranial morphology in Euarchontoglires: Assessing sources of error for a novel and biologically informative set of landmarks
Despite its importance for making biologically meaningful conclusions in geometric morphometric analyses, landmark error is inconsistently assessed....
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Reworking Geometric Morphometrics into a Methodology of Transformation Grids
Today’s typical application of geometric morphometrics to a quantitative comparison of organismal anatomies begins by standardizing samples of...
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A Graph-Based Mathematical Model for More Efficient Dimensionality Reduction of Landmark Data in Geometric Morphometrics
Geometric Morphometrics can be used to describe morphology as a series of coordinates after the effects of variation in translation, rotation, and...
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Protocol of Geometric Morphometrics for Teratogenicity Testing
Geometric morphometrics (GM) enables a quantitative study of shapes and forms allowing the identification and characterization of teratogenic...
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Exploring motion using geometric morphometrics in microscopic aquatic invertebrates: ‘modes’ and movement patterns during feeding in a bdelloid rotifer model species
BackgroundMovement is a defining aspect of animals, but it is rarely studied using quantitative methods in microscopic invertebrates. Bdelloid...
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Quadratic Trends: A Morphometric Tool Both Old and New
The original exposition of the method of “Cartesian transformations” in D’Arcy Thompson’s On Growth and Form (1917) is still its most cited. But...
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Head geometric morphometrics as a reliable method to discriminate sexes and species of Megalopta, a nocturnal bee genus (Hymenoptera, Apoidea)
Geometric morphometrics is an approach widely used in biological research. For bees, wing landmarks are applied to investigate several questions,...
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Can we Restore Balance to Geometric Morphometrics? A Theoretical Evaluation of how Sample Imbalance Conditions Ordination and Classification
The most common means of performing ordination and classification consist in principal component, canonical variate, and between-group principal...
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Sex Ratio, Sexual Dimorphism, and Wing Geometric Morphometrics in Species of Trypoxylon Latreille, 1796 (Hymenoptera: Crabronidae)
Studying the nesting biology of wasp and bee species provides valuable insights into the ecology and evolution of these insects, shedding light on...
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Morphometric analysis of the size-adjusted linear dimensions of the skull landmarks revealed craniofacial dysmorphology in Mid1-cKO mice
BackgroundThe early craniofacial development is a highly coordinated process involving neural crest cell migration, proliferation, epithelial...
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Dysbiotic microbiome variation in colorectal cancer patients is linked to lifestyles and metabolic diseases
BackgroundDifferences in the composition and diversity of the gut microbial communities among individuals are influenced by environmental factors....
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Evaluating cpn60 for high-resolution profiling of the mammalian skin microbiome and detection of phylosymbiosis
Despite being the most widely used phylogenetic marker for amplicon-based profiling of microbial communities, limited phylogenetic resolution of the...
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Craniofacial Phenomics: Three-Dimensional Assessment of the Size and Shape of Cranial and Dentofacial Structures
Craniofacial phenomics has opened up numerous opportunities to correlate genetic and epigenetic factors to craniofacial phenotypes in order to...