Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research (Q38114153)

29 August 2017

Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research (English)

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29 August 2017

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29 August 2017

5

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29 August 2017

S Papakostas

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author name string

E H Leder

series ordinal

3

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PubMed ID

23763602

29 August 2017

M J Davis

series ordinal

4

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29 August 2017

1 June 2013

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29 August 2017

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29 August 2017

22

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29 August 2017

12

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29 August 2017

3216-3241

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PubMed ID

23763602

maintained by WikiProject

29 August 2017

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Domain-based and family-specific sequence identity thresholds increase the levels of reliable protein function transfer

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Genes under positive selection in a model plant pathogenic fungus, Botrytis

21 January 2018

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Phylogenetic and functional assessment of orthologs inference projects and methods

21 January 2018

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Inferring orthology and paralogy

21 January 2018

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Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs

21 January 2018

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Basic local alignment search tool

21 January 2018

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

21 January 2018

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Gene duplication and environmental adaptation within yeast populations

21 January 2018

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Natural variation, functional pleiotropy and transcriptional contexts of odorant binding protein genes in Drosophila melanogaster

21 January 2018

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An ontology for cell types

21 January 2018

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Pathway databases and tools for their exploitation: benefits, current limitations and challenges

21 January 2018

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ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

21 January 2018

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QuickGO: a web-based tool for Gene Ontology searching

21 January 2018

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Logical properties of foundational relations in bio-ontologies.

21 January 2018

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Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

21 January 2018

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SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar).

21 January 2018

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Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach

21 January 2018

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Gene loss and evolutionary rates following whole-genome duplication in teleost fishes

21 January 2018

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Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer

21 January 2018

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OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups

21 January 2018

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Assessing performance of orthology detection strategies applied to eukaryotic genomes

21 January 2018

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The ecoresponsive genome of Daphnia pulex

21 January 2018

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Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles

21 January 2018

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Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research

21 January 2018

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Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered European eel

21 January 2018

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Automatic, context-specific generation of Gene Ontology slims

21 January 2018

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Genome duplication and the origin of angiosperms

21 January 2018

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Transcriptional plasticity of a soil arthropod across different ecological conditions.

21 January 2018

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The simple fool's guide to population genomics via RNA-Seq: an introduction to high-throughput sequencing data analysis

21 January 2018

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Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development

21 January 2018

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Proteomics in evolutionary ecology: linking the genotype with the phenotype

21 January 2018

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Sperm proteomics reveals intensified selection on mouse sperm membrane and acrosome genes

21 January 2018

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G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery

21 January 2018

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agriGO: a GO analysis toolkit for the agricultural community

21 January 2018

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GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

21 January 2018

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A transcriptional network associated with natural variation in Drosophila aggressive behavior

21 January 2018

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Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.

21 January 2018

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A review of modern multiple hypothesis testing, with particular attention to the false discovery proportion.

21 January 2018

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Distinguishing Homologous from Analogous Proteins

21 January 2018

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Aspects of molecular evolution

21 January 2018

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Fish proteome analysis: model organisms and non-sequenced species

21 January 2018

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Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

21 January 2018

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Bioconductor: open software development for computational biology and bioinformatics

21 January 2018

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Population transcriptomics of life-history variation in the genus Salmo

21 January 2018

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Toward principles for the design of ontologies used for knowledge sharing?

21 January 2018

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Protein dispensability and rate of evolution

21 January 2018

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Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags

21 January 2018

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Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

21 January 2018

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PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

21 January 2018

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GO Trimming: Systematically reducing redundancy in large Gene Ontology datasets

21 January 2018

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Characterization of common carp transcriptome: sequencing, de novo assembly, annotation and comparative genomics

21 January 2018

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Ancestral polyploidy in seed plants and angiosperms

21 January 2018

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Molecular cloning and characterization of spiggin. An androgen-regulated extraorganismal adhesive with structural similarities to von Willebrand Factor-related proteins.

21 January 2018

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Estimating the annotation error rate of curated GO database sequence annotations

21 January 2018

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Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish

21 January 2018

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Ten years of pathway analysis: current approaches and outstanding challenges

21 January 2018

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Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection

21 January 2018

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Emergence and evolution of modern molecular functions inferred from phylogenomic analysis of ontological data

21 January 2018

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Computational methods for Gene Orthology inference

21 January 2018

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Taxonomy-based partitioning of the Gene Ontology

21 January 2018

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Ecological and evolutionary genomics of Saccharomyces cerevisiae

21 January 2018

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Female-biased expression on the X chromosome as a key step in sex chromosome evolution in threespine sticklebacks.

21 January 2018

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Environmental adaptation contributes to gene polymorphism across the Arabidopsis thaliana genome

21 January 2018

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A functional phylogenomic view of the seed plants

21 January 2018

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OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

21 January 2018

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Comparative and demographic analysis of orang-utan genomes

21 January 2018

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A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions

21 January 2018

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Three periods of regulatory innovation during vertebrate evolution

21 January 2018

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BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks

21 January 2018

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Using Gene Ontology and genomic controlled vocabularies to analyze high-throughput gene lists: three tool comparison

21 January 2018

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Structural variants in the soybean genome localize to clusters of biotic stress-response genes

21 January 2018

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A minimal gene set for cellular life derived by comparison of complete bacterial genomes

21 January 2018

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Additional gene ontology structure for improved biological reasoning

21 January 2018

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Testing the ortholog conjecture with comparative functional genomic data from mammals

21 January 2018

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Population-specific gene expression responses to hybridization between farm and wild Atlantic salmon

21 January 2018

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InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

21 January 2018

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Six quantitative trait loci influence task thresholds for hygienic behaviour in honeybees (Apis mellifera).

21 January 2018

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Proteomic profiling of early life stages of European grayling (Thymallus thymallus).

21 January 2018

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A proteomics approach reveals divergent molecular responses to salinity in populations of European whitefish (Coregonus lavaretus).

21 January 2018

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What is needed for next-generation ecological and evolutionary genomics?

21 January 2018

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Genomics. Ecological genomics gets down to genes--and function.

21 January 2018

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21 January 2018

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Transcriptome profiles link environmental variation and physiological response of Mytilus californianus between Pacific tides

21 January 2018

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The what, where, how and why of gene ontology--a primer for bioinformaticians

21 January 2018

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InterProScan: protein domains identifier

21 January 2018

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g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments

21 January 2018

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Automatic clustering of orthologs and in-paralogs from pairwise species comparisons

21 January 2018

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Transcriptome-wide signature of hybrid breakdown associated with intrinsic reproductive isolation in lake whitefish species pairs (Coregonus spp. Salmonidae).

21 January 2018

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Use and misuse of the gene ontology annotations

21 January 2018

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Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics

21 January 2018

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Enrichment or depletion of a GO category within a class of genes: which test?

21 January 2018

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Genomic evidence for two functionally distinct gene classes.

21 January 2018

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The use of gene ontology evidence codes in preventing classifier assessment bias

21 January 2018

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21 January 2018

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Database resources of the National Center for Biotechnology Information

21 January 2018

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Cytoscape: a software environment for integrated models of biomolecular interaction networks

21 January 2018

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Towards the mammalian interactome: Inference of a core mammalian interaction set in mouse

21 January 2018

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Quality of computationally inferred gene ontology annotations

21 January 2018

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The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

21 January 2018

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The genome sequence of Atlantic cod reveals a unique immune system

21 January 2018

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REVIGO summarizes and visualizes long lists of gene ontology terms

21 January 2018

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Gene expression analyses of immune responses in Atlantic salmon during early stages of infection by salmon louse (Lepeophtheirus salmonis) revealed bi-phasic responses coinciding with the copepod-chalimus transition

21 January 2018

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A genomic perspective on protein families

21 January 2018

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The COG database: new developments in phylogenetic classification of proteins from complete genomes

21 January 2018

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The COG database: an updated version includes eukaryotes

21 January 2018

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Gene ontology: tool for the unification of biology

21 January 2018

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The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species

21 January 2018

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Ontology annotation: mapping genomic regions to biological function

21 January 2018

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Orthology prediction methods: a quality assessment using curated protein families

21 January 2018

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Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing.

21 January 2018

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Ortholog detection using the reciprocal smallest distance algorithm.

21 January 2018

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Automatic genome-wide reconstruction of phylogenetic gene trees.

21 January 2018

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Green systems biology - From single genomes, proteomes and metabolomes to ecosystems research and biotechnology

21 January 2018

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Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee.

21 January 2018

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Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life

21 January 2018

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The preferential retention of starch synthesis genes reveals the impact of whole-genome duplication on grass evolution.

21 January 2018

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Integrated network analysis platform for protein-protein interactions

21 January 2018

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Changes in reproductive roles are associated with changes in gene expression in fire ant queens.

21 January 2018

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The genome of the fire ant Solenopsis invicta

21 January 2018

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A beginner's guide to eukaryotic genome annotation

21 January 2018

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RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis

21 January 2018

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The Schistosoma japonicum genome reveals features of host-parasite interplay

21 January 2018

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Non-orthologous gene displacement

21 January 2018

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Variation in gene expression ofAndropogon gerardiiin response to altered environmental conditions associated with climate change

21 January 2018

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The proteomics of feather development in pied flycatchers (Ficedula hypoleuca) with different plumage coloration

21 January 2018

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21 January 2018

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21 January 2018

Identifiers

DOI

10.1111/MEC.12309

1 reference

29 August 2017

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PubMed ID

23763602