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Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1016/j.fgb.2012.08.008openalex-snapshot
Reproductive mode and life cycle of the ash dieback pathogen Hymenoscyphus pseudoalbidus
inferredcites →https://doi.org/10.1038/nature08358openalex-snapshot
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
inferredcites →https://doi.org/10.1038/nbt.1621openalex-snapshot
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot
Full-length transcriptome assembly from RNA-Seq data without a reference genome
inferredcites →https://doi.org/10.1038/nprot.2009.2openalex-snapshot
Protein structure prediction on the Web: a case study using the Phyre server
inferredcites →https://doi.org/10.1038/nrmicro2790openalex-snapshot
Genome evolution in filamentous plant pathogens: why bigger can be better
inferredcites →https://doi.org/10.1073/pnas.0902362106openalex-snapshot
A common toxin fold mediates microbial attack and plant defense
inferredcites →https://doi.org/10.1093/bioinformatics/btg316openalex-snapshot
libsequence: a C++ class library for evolutionary genetic analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btm071openalex-snapshot
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btn013openalex-snapshot
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
inferredcites →https://doi.org/10.1093/bioinformatics/btp120openalex-snapshot
TopHat: discovering splice junctions with RNA-Seq
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/nar/gkq1212openalex-snapshot
A new repeat-masking method enables specific detection of homologous sequences
inferredcites →https://doi.org/10.1093/nar/gkt1178openalex-snapshot
The carbohydrate-active enzymes database (CAZy) in 2013
inferredcites →https://doi.org/10.1093/protein/10.1.1openalex-snapshot
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
inferredcites →https://doi.org/10.1094/pd-89-0528copenalex-snapshot
Occurrence of Togninia fraxinopennsylvanica on Esca-Diseased Grapevines (Vitis vinifera) and Declining Ash Trees (Fraxinus latifolia) in California
inferredcites →https://doi.org/10.1094/pd-89-0686bopenalex-snapshot
First Report of Perithecia of Phaeoacremonium viticola on Grapevine (Vitis vinifera) and Ash Tree (Fraxinus latifolia) in California
inferredcites →https://doi.org/10.1101/gr.089532.108openalex-snapshot
ABySS: A parallel assembler for short read sequence data
inferredcites →https://doi.org/10.1101/gr.092759.109openalex-snapshot
Circos: An information aesthetic for comparative genomics
inferredcites →https://doi.org/10.1101/gr.120618.111openalex-snapshot
Integrative analysis of environmental sequences using MEGAN4
inferredcites →https://doi.org/10.1101/gr.1224503openalex-snapshot
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
inferredcites →https://doi.org/10.1101/gr.129684.111openalex-snapshot
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
inferredcites →https://doi.org/10.1101/gr.910003openalex-snapshot
EST Mining and Functional Expression Assays Identify Extracellular Effector Proteins From the Plant PathogenPhytophthora
inferredcites →https://doi.org/10.1111/mpp.12086openalex-snapshot
Out of the woods. Ash dieback and the future of emergent pathogenomics
inferredcites →https://doi.org/10.1126/science.1221748openalex-snapshot
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2164-14-270openalex-snapshot
Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. triticireveal polymorphic and haustorial expressed secreted proteins as candidate effectors
inferredcites →https://doi.org/10.1186/2047-217x-2-10openalex-snapshot
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
inferredcites →https://doi.org/10.1186/2047-217x-2-16openalex-snapshot
EMPeror: a tool for visualizing high-throughput microbial community data
inferredcites →https://doi.org/10.1371/journal.pgen.1002230openalex-snapshot
Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea
inferredcites →https://doi.org/10.3389/fpls.2012.00059openalex-snapshot
Plant Glycosyltransferases Beyond CAZy: A Perspective on DUF Families
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1038/s41559-018-0548-9openalex-snapshot
The ash dieback invasion of Europe was founded by two genetically divergent individuals
inferred← citeshttps://doi.org/10.1101/154492openalex-snapshot
“Genome-wide population diversity in Hymenoscyphus fraxineus points to an eastern Russian origin of European Ash dieback”
inferred← citeshttps://doi.org/10.1186/s12864-016-2690-6openalex-snapshot
Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements
inferred← citeshttps://doi.org/10.3389/fmicb.2019.03088openalex-snapshot
“CATAStrophy,” a Genome-Informed Trophic Classification of Filamentous Plant Pathogens – How Many Different Types of Filamentous Plant Pathogens Are There?
inferred← citeshttps://doi.org/10.3390/f14112151openalex-snapshot
Ash Dieback in Forests and Rural Areas—History and Predictions
inferred← citeshttps://doi.org/10.7554/elife.07460openalex-snapshot
Lessons from Fraxinus, a crowd-sourced citizen science game in genomics
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