(Q27319937)

1

0 references

Karl-Magnus Andersson

2

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Eva Friman

3

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Dharmendra Kumar

4

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Dag Ahrén

Creative Commons Attribution 3.0 Unported

6

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language of work or name

English

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publication date

November 2013

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published in

PLOS Genetics

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volume

9

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issue

11

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page(s)

e1003909

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copyright license

start time

14 November 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

DESeq2

object named as

R package DESeq

DESeq

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

The evolutionary origin of orphan genes

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Pathogenicity Determinants in Smut Fungi Revealed by Genome Comparison

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Differential expression analysis for sequence count data

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

The Pfam protein families database

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Evolution of nematode-trapping cells of predatory fungi of the Orbiliaceae based on evidence from rRNA-encoding DNA and multiprotein sequences

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Reconstructing the early evolution of Fungi using a six-gene phylogeny

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

PHI-base: a new database for pathogen host interactions

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Gene identification in novel eukaryotic genomes by self-training algorithm

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

The genome sequence of the rice blast fungus Magnaporthe grisea

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

The COG database: an updated version includes eukaryotes

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

The genome sequence of the filamentous fungus Neurospora crassa

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

21 March 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

21 March 2017

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003909

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Basic local alignment search tool

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

BEAST: Bayesian evolutionary analysis by sampling trees

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Improved prediction of signal peptides: SignalP 3.0

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Tandem repeats finder: a program to analyze DNA sequences

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Phylogeny of nematode-trapping fungi based on 18S rDNA sequences

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Origin and evolution of carnivorism in the Ascomycota (fungi)

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Search and clustering orders of magnitude faster than BLAST

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Fast and accurate long-read alignment with Burrows-Wheeler transform

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

De novo identification of repeat families in large genomes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Genomic perspectives on the evolution of fungal entomopathogenicity in Beauveria bassiana

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Indifferent, affectionate, or deceitful: lifestyles and secretomes of fungi

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Genomic and proteomic analyses of the fungus Arthrobotrys oligospora provide insights into nematode-trap formation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Palaeoanellus dimorphus gen. et sp. nov. (Deuteromycotina): a Cretaceous predatory fungus

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Melanogenesis in dermatophyte species in vitro and during infection

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

How filamentous pathogens co-opt plants: the ins and outs of fungal effectors.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Fungi evolved right on track

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Pep1, a secreted effector protein of Ustilago maydis, is required for successful invasion of plant cells

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Construction, visualisation, and clustering of transcription networks from microarray expression data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

A five-gene phylogeny of Pezizomycotina

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Comparison of transcription of multiple genes at three developmental stages of the plant pathogen Sclerotinia sclerotiorum

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Phylogenetics and evolution of nematode-trapping fungi (Orbiliales) estimated from nuclear and protein coding genes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Fungal Pls1 tetraspanins as key factors of penetration into host plants: a role in re-establishing polarized growth in the appressorium?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Hydrolytic enzymes as virulence factors of Candida albicans

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance gene

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

The contribution of melanin to microbial pathogenesis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Genomics of parasitic and symbiotic fungi

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Two novel fungal virulence genes specifically expressed in appressoria of the rice blast fungus

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Repeat-induced point mutation (RIP) in Magnaporthe grisea: implications for its sexual cycle in the natural field context

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

The role of lineage-specific gene family expansion in the evolution of eukaryotes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Improving the pathogenicity of a nematode-trapping fungus by genetic engineering of a subtilisin with nematotoxic activity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Identification and characterization of TUP1-regulated genes in Candida albicans

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Cloning and characterization of a melanin biosynthetic THR1 reductase gene essential for appressorial penetration of Colletotrichum lagenarium

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Evolution of parasitism in nematode-trapping fungi.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3828140

Comparison of gene expression in trap cells and vegetative hyphae of the nematophagous fungus Monacrosporium haptotylum

31 May 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003909

Paralysis of nematodes: shifts in the transcriptome of the nematode-trapping fungus Monacrosporium haptotylum during infection of Caenorhabditis elegans

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003909

RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003909

Molecular evidence that the extracellular cutinase Pbc1 is required for pathogenicity of Pyrenopeziza brassicae on oilseed rape

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003909

Evolution by gene duplication: an update

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003909

Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003909

Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003909

Fungal Pathogenesis: Gene Clusters Unveiled as Secrets within the Ustilago maydis Code

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003909

Nematophagous fungi: physiological aspects and structure-function relationships

21 January 2018

1 reference

PubMed

12 December 2020

Comparison of the characteristics of fungal and plant tyrosinases

1 reference

PubMed

12 December 2020

Molecular phylogenetics of ascomycotal adhesins--a novel family of putative cell-surface adhesive proteins in fission yeasts

1 reference

PubMed

12 December 2020

1 reference

12 December 2020

10.1371/JOURNAL.PGEN.1003909

Identifiers

DOI

1 reference

release_3kq7w5w535hgvkwnqkwksuwho4

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/3kq7w5w535hgvkwnqkwksuwho4

24 November 2022

mapped directly with Wikidata item

1 reference

1 reference

PubMed publication ID

24244185

1 reference