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Article
Open AccessAirborne DNA reveals predictable spatial and seasonal dynamics of fungi
Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions1,2. ...
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Article
Open AccessGlobal Spore Sampling Project: A global, standardized dataset of airborne fungal DNA
Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of...
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Article
Open AccessGlobal arthropod beta-diversity is spatially and temporally structured by latitude
Global biodiversity gradients are generally expected to reflect greater species replacement closer to the equator. However, empirical validation of global biodiversity gradients largely relies on vertebrates, ...
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Article
Open AccessSpatial cumulant models enable spatially informed treatment strategies and analysis of local interactions in cancer systems
Theoretical and applied cancer studies that use individual-based models (IBMs) have been limited by the lack of a mathematical formulation that enables rigorous analysis of these models. However, spatial cumul...
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Article
Open AccessHigh resolution DNA barcode library for European butterflies reveals continental patterns of mitochondrial genetic diversity
The study of global biodiversity will greatly benefit from access to comprehensive DNA barcode libraries at continental scale, but such datasets are still very rare. Here, we assemble the first high-resolution...
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Article
Open AccessA unified framework for analysis of individual-based models in ecology and beyond
Individual-based models, ‘IBMs’, describe naturally the dynamics of interacting organisms or social or financial agents. They are considered too complex for mathematical analysis, but computer simulations of t...
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Article
Open AccessEffect of wet storage conditions on potato tuber transcriptome, phytohormones and growth
Stored potato (Solanum tuberosum L.) tubers are sensitive to wet conditions that can cause rotting in long-term storage. To study the effect of water on the tuber surface during storage, microarray analysis, RNA-...
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Article
Open AccessBARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing
Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each ...
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Article
Open AccessPhytotoxin produced by the netted scab pathogen, Streptomyces turgidiscabies strain 65, isolated in Sweden
Streptomyces spp. are a highly diverse group of bacteria most of which are soil-inhabiting saprophytes. A few are plant pathogens that produce a family of phytotoxins called thaxtomins and cause significant econo...
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Article
Open AccessThe Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera
Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanv...
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Chapter
Optimal Designs for Microarray Experiments with Biological and Technical Replicates
Microarrays are powerful tools for global monitoring of gene expressions in many areas of biomedical research (Brown and Botstein (1999)). Since the first publication on the statistical analysis of data from m...
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Article
Speech Dimensionality Analysis on Hypercubical Self-Organizing Maps
The problem of finding the intrinsic dimension of speech is addressed in this paper. Astructured vector quantization lattice, Self-Organizing Map (SOM), is used as a projection space for the data. The goal is ...
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Chapter and Conference Paper
Clustering and Visualization of Large Protein Sequence Databases by Means of an Extension of the Self-Organizing Map
New, more effective software tools are needed for the analysis and organization of the continually growing biological databases. An extension of the Self-Organizing Map (SOM) is used in this work for the clust...
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Article
Self-Organizing Maps and Learning Vector Quantization for Feature Sequences
The Self-Organizing Map (SOM) and Learning Vector Quantization (LVQ) algorithms are constructed in this work for variable-length and warped feature sequences. The novelty is to associate an entire feature vect...
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Article
Redundant Hash Addressing of Feature Sequences Using the Self-Organizing Map
Kohonen's Self-Organizing Map (SOM) is combined with the Redundant Hash Addressing (RHA) principle. The SOM encodes the input feature vector sequence into the sequence of best-matching unit (BMU) indices and t...
