相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes
Joelle Amselem et al.
BMC GENOMICS (2015)
Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi
Eric Fontanillas et al.
MOLECULAR BIOLOGY AND EVOLUTION (2015)
Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment
Claire Veneault-Fourrey et al.
FUNGAL GENETICS AND BIOLOGY (2014)
Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes
Pierre Gladieux et al.
MOLECULAR ECOLOGY (2014)
The carbohydrate-active enzymes database (CAZy) in 2013
Vincent Lombard et al.
NUCLEIC ACIDS RESEARCH (2014)
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi
Robert Riley et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum
Sarah M. Schmidt et al.
BMC GENOMICS (2013)
Extensive Divergence Between Mating-Type Chromosomes of the Anther-Smut Fungus
Michael E. Hood et al.
GENETICS (2013)
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Brian J. Haas et al.
NATURE PROTOCOLS (2013)
Loss and Retention of RNA Interference in Fungi and Parasites
Francisco E. Nicolas et al.
PLOS PATHOGENS (2013)
A normalization strategy for comparing tag count data
Koji Kadota et al.
ALGORITHMS FOR MOLECULAR BIOLOGY (2012)
LINKAGE TO THE MATING-TYPE LOCUS ACROSS THE GENUS MICROBOTRYUM: INSIGHTS INTO NONRECOMBINING CHROMOSOMES
Elsa Petit et al.
EVOLUTION (2012)
SIBLING COMPETITION ARENA: SELFING AND A COMPETITION ARENA CAN COMBINE TO CONSTITUTE A BARRIER TO GENE FLOW IN SYMPATRY
A. K. Gibson et al.
EVOLUTION (2012)
Patterns of Repeat-Induced Point Mutation in Transposable Elements of Basidiomycete Fungi
Felix Horns et al.
GENOME BIOLOGY AND EVOLUTION (2012)
Sex, outcrossing and mating types: unsolved questions in fungi and beyond
S. Billiard et al.
JOURNAL OF EVOLUTIONARY BIOLOGY (2012)
Reorganizing the protein space at the Universal Protein Resource (UniProt)
Rolf Apweiler et al.
NUCLEIC ACIDS RESEARCH (2012)
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
Dimitrios Floudas et al.
SCIENCE (2012)
Does diacylglycerol serve as a signaling molecule in plants?
Wei Dong et al.
PLANT SIGNALING & BEHAVIOR (2012)
Assigning duplication events to relative temporal scales in genome-wide studies
Jaime Huerta-Cepas et al.
BIOINFORMATICS (2011)
Having sex, yes, but with whom? Inferences from fungi on the evolution of anisogamy and mating types
Sylvain Billiard et al.
BIOLOGICAL REVIEWS (2011)
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Bo Li et al.
BMC BIOINFORMATICS (2011)
Degeneration in Codon Usage within the Region of Suppressed Recombination in the Mating-Type Chromosomes of Neurospora tetrasperma
C. A. Whittle et al.
EUKARYOTIC CELL (2011)
Evidence of the accumulation of allele-specific non-synonymous substitutions in the young region of recombination suppression within the mating-type chromosomes of Neurospora tetrasperma
C. A. Whittle et al.
HEREDITY (2011)
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred G. Grabherr et al.
NATURE BIOTECHNOLOGY (2011)
SignalP 4.0: discriminating signal peptides from transmembrane regions
Thomas Nordahl Petersen et al.
NATURE METHODS (2011)
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
Jaime Huerta-Cepas et al.
NUCLEIC ACIDS RESEARCH (2011)
Ongoing and future developments at the Universal Protein Resource
Rolf Apweiler et al.
NUCLEIC ACIDS RESEARCH (2011)
Considering Transposable Element Diversification in De Novo Annotation Approaches
Timothee Flutre et al.
PLOS ONE (2011)
S-MART, A Software Toolbox to Aid RNA-seq Data Analysis
Matthias Zytnicki et al.
PLOS ONE (2011)
Obligate biotrophy features unraveled by the genomic analysis of rust fungi
Sebastien Duplessis et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
About PAR: The distinct evolutionary dynamics of the pseudoautosomal region
Sarah P. Otto et al.
TRENDS IN GENETICS (2011)
Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations
Thierry Rouxel et al.
NATURE COMMUNICATIONS (2011)
Polyamines: ubiquitous polycations with unique roles in growth and stress responses
Taku Takahashi et al.
ANNALS OF BOTANY (2010)
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Mark D. Robinson et al.
BIOINFORMATICS (2010)
The illustrated life cycle of Microbotryum on the host plant Silene latifolia
Angela Maria Schaefer et al.
BOTANY (2010)
A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution
Christian Biemont
GENETICS (2010)
The mutational spectrum of non-CpG DNA varies with CpG content
Jean-Claude Walser et al.
GENOME RESEARCH (2010)
Comprehensive comparative analysis of strand-specific RNA sequencing methods
Joshua Z. Levin et al.
NATURE METHODS (2010)
PROSITE, a protein domain database for functional characterization and annotation
Christian J. A. Sigrist et al.
NUCLEIC ACIDS RESEARCH (2010)
Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation
Assaf Zemach et al.
SCIENCE (2010)
A Novel High-Affinity Sucrose Transporter Is Required for Virulence of the Plant Pathogen Ustilago maydis
Ramon Wahl et al.
PLOS BIOLOGY (2010)
Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes
Laurent Duret et al.
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS (2009)
Fungal Effector Proteins
Ioannis Stergiopoulos et al.
Annual Review of Phytopathology (2009)
A White Campion (Silene latifolia) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping
Maria Domenica Moccia et al.
BMC GENOMICS (2009)
Ancient Trans-specific Polymorphism at Pheromone Receptor Genes in Basidiomycetes
Benjamin Devier et al.
GENETICS (2009)
Evolutionary Strata in a Small Mating-Type-Specific Region of the Smut Fungus Microbotryum violaceum
Antonina A. Votintseva et al.
GENETICS (2009)
Hybrid sterility and inviability in the parasitic fungal species complex Microbotryum
D. M. De Vienne et al.
JOURNAL OF EVOLUTIONARY BIOLOGY (2009)
Phylogenetic determinants of potential host shifts in fungal pathogens
D. M. de Vienne et al.
JOURNAL OF EVOLUTIONARY BIOLOGY (2009)
Can GC Content at Third-Codon Positions Be Used as a Proxy for Isochore Composition?
Eran Elhaik et al.
MOLECULAR BIOLOGY AND EVOLUTION (2009)
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
Brian J. Haas et al.
NATURE (2009)
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
Brandi L. Cantarel et al.
NUCLEIC ACIDS RESEARCH (2009)
Transcriptome analysis by strand-specific sequencing of complementary DNA
Dmitri Parkhomchuk et al.
NUCLEIC ACIDS RESEARCH (2009)
Hidden diversity in the non-caryophyllaceous plant-parasitic members of Microbotryum (Pucciniomycotina: Microbotryales)
Martin Kemler et al.
SYSTEMATICS AND BIODIVERSITY (2009)
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead et al.
GENOME BIOLOGY (2009)
RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences
James K. Hane et al.
BMC BIOINFORMATICS (2008)
PredGPI: a GPI-anchor predictor
Andrea Pierleoni et al.
BMC BIOINFORMATICS (2008)
Cophylogeny of the anther smut fungi and their caryophyllaceous hosts:: Prevalence of host shifts and importance of delimiting parasite species for inferring cospeciation
Guislaine Refregier et al.
BMC EVOLUTIONARY BIOLOGY (2008)
Mating system of the anther smut fungus Microbotryum violaceum:: Selfing under heterothallism
Tatiana Giraud et al.
EUKARYOTIC CELL (2008)
The mating-type chromosome in the filamentous ascomycete Neurospora tetrasperma represents a model for early evolution of sex chromosomes
Audrius Menkis et al.
PLOS GENETICS (2008)
Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments
Brian J. Haas et al.
GENOME BIOLOGY (2008)
Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes
Roxana Yockteng et al.
BMC GENOMICS (2007)
Evolution of reproductive isolation within a parasitic fungal species complex
Mickael Le Gac et al.
EVOLUTION (2007)
Advantages of combined transmembrane topology and signal peptide prediction -: the Phobius web server
Lukas Kaell et al.
NUCLEIC ACIDS RESEARCH (2007)
WoLF PSORT: protein localization predictor
Paul Horton et al.
NUCLEIC ACIDS RESEARCH (2007)
NucPred - Predicting nuclear localization of proteins
Markus Brameier et al.
BIOINFORMATICS (2007)
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genornes
Genis Parra et al.
BIOINFORMATICS (2007)
Functional genomic analysis supports conservation of function among cellulose synthase-like a gene family members and suggests diverse roles of mannans in plants
Aaron H. Liepman et al.
PLANT PHYSIOLOGY (2007)
Locating proteins in the cell using TargetP, SignalP and related tools
Olof Emanuelsson et al.
NATURE PROTOCOLS (2007)
Phylogenetic evidence of host-specific cryptic species in the anther smut fungus
Mickael Le Gac et al.
EVOLUTION (2007)
Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome
Cizhong Jiang et al.
BMC GENOMICS (2006)
Fungal laccases - occurrence and properties
P Baldrian
FEMS MICROBIOLOGY REVIEWS (2006)
Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition
BR Morton et al.
GENETICS (2006)
Cuticular lipid composition, surface structure, and gene expression in Arabidopsis stem epidermis
MC Suh et al.
PLANT PHYSIOLOGY (2005)
Blast2GO:: a universal tool for annotation, visualization and analysis in functional genomics research
A Conesa et al.
BIOINFORMATICS (2005)
Combined evidence annotation of transposable elements in genome sequences
H Quesneville et al.
PLOS COMPUTATIONAL BIOLOGY (2005)
Repeat-induced point mutation and the population structure of transposable elements in Microbotryum violaceum
ME Hood et al.
GENETICS (2005)
PILER: identification and classification of genomic repeats
RC Edgar et al.
BIOINFORMATICS (2005)
Expression of the floral B-function gene SLM2 in female flowers of Silene latifolia infected with the smut fungus Microbotryum violaceum
Y Kazama et al.
PLANT AND CELL PHYSIOLOGY (2005)
Differential expression of mepA, mepC and smtE during growth and development of Microbotryum violaceum
CF Hughes et al.
MYCOLOGIA (2005)
Repetitive DNA in the automictic fungus Microbotryum violaceum
ME Hood
GENETICA (2005)
CpG mutation rates in the human genome are highly dependent on local GC content
KJ Fryxell et al.
MOLECULAR BIOLOGY AND EVOLUTION (2005)
Repbase update, a database of eukaryotic repetitive elements
J Jurka et al.
CYTOGENETIC AND GENOME RESEARCH (2005)
Lipid-induced filamentous growth in Ustilago maydis
J Klose et al.
MOLECULAR MICROBIOLOGY (2004)
Shared forces of sex chromosome evolution in haploid-mating and diploid-mating organisms:: Microbotryum violaceum and other model organisms
ME Hood et al.
GENETICS (2004)
Improved prediction of signal peptides: SignalP 3.0
JD Bendtsen et al.
JOURNAL OF MOLECULAR BIOLOGY (2004)
AUGUSTUS: a web server for gene finding in eukaryotes
M Stanke et al.
NUCLEIC ACIDS RESEARCH (2004)
Evolution of fungal sex chromosomes
JA Fraser et al.
MOLECULAR MICROBIOLOGY (2004)
TigrScan and GlimmerHMM:: two open source ab initio eukaryotic gene-finders
WH Majoros et al.
BIOINFORMATICS (2004)
Divergent and convergent signaling by the diacylglycerol second messenger pathway in mammals
N Brose et al.
CURRENT OPINION IN NEUROBIOLOGY (2004)
GeneWise and genomewise
E Birney et al.
GENOME RESEARCH (2004)
OrthoMCL: Identification of ortholog groups for eukaryotic genomes
L Li et al.
GENOME RESEARCH (2003)
Atypical laccase isoenzymes from copper supplemented Pleurotus ostreatus cultures
G Palmieri et al.
ENZYME AND MICROBIAL TECHNOLOGY (2003)
Accumulation of Spock and Worf, two novel non-LTR retrotransposons, on the neo-Y chromosome of Drosophila miranda
D Bachtrog
MOLECULAR BIOLOGY AND EVOLUTION (2003)
The ecology and genetics of a host shift:: Microbotryum as a model system
J Antonovics et al.
AMERICAN NATURALIST (2002)
Automated de novo identification of repeat sequence families in sequenced genomes
ZR Bao et al.
GENOME RESEARCH (2002)
Rolling-circle transposons in eukaryotes
VV Kapitonov et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
The role of haustoria in sugar supply during infection of broad bean by the rust fungus Uromyces fabae
RT Voegele et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2001)
Purification, characterization, and functional role of a novel extracellular protease from Pleurotus ostreatus
G Palmieri et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2001)
Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
A Krogh et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)
Intratetrad mating, heterozygosity, and the maintenance of deleterious alleles in Microbotryum violaceum (=Ustilago violacea)
ME Hood et al.
HEREDITY (2000)