A survey of genome-wide single nucleotide polymorphisms through genome resequencing in the Périgord black truffle (Tuber melanosporum Vittad.)

Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8

(2014) James K. Hane et al.   PLoS Genetics

Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus

(2014) Kui Lin et al.   PLoS Genetics

Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors

(2014) Antoine Persoons et al.   Frontiers in Plant Science

Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors

(2013) Dario Cantu et al.   BMC GENOMICS

Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

(2013) Matteo Fumagalli et al.   GENETICS

Single-nucleotide polymorphism discovery inLeptographium longiclavatum, a mountain pine beetle-associated symbiotic fungus, using whole-genome resequencing

(2013) Dario I. Ojeda et al.   Molecular Ecology Resources

Population genetics of the westernmost distribution of the glaciations-surviving black truffle Tuber melanosporum

(2013) Iván García-Cunchillos et al.   MYCORRHIZA

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

(2013) Thomas Wicker et al.   NATURE GENETICS

Fine-scale spatial genetic structure of the black truffle (Tuber melanosporum) investigated with neutral microsatellites and functional mating type genes

(2013) Claude Murat et al.   NEW PHYTOLOGIST

Historical Biogeography and Diversification of Truffles in the Tuberaceae and Their Newly Identified Southern Hemisphere Sister Lineage

(2013) Gregory Bonito et al.   PLoS One

Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts

(2013) S. Hacquard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis , Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

(2013) Viola A. Manning et al.   G3-Genes Genomes Genetics

EggLib: processing, analysis and simulation tools for population genetics and genomics

(2012) Stéphane De Mita et al.   BMC GENETICS

Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping

(2011) Bujie Zhan et al.   BMC GENOMICS

Transposable element origins of epigenetic gene regulation

(2011) Damon Lisch et al.   CURRENT OPINION IN PLANT BIOLOGY

On the road to understanding truffles in the underground

(2011) Ursula Kües et al.   FUNGAL GENETICS AND BIOLOGY

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Sequencing the fungal tree of life

(2011) F. Martin et al.   NEW PHYTOLOGIST

Deep RNA sequencing improved the structural annotation of the Tuber melanosporum transcriptome

(2011) E. Tisserant et al.   NEW PHYTOLOGIST

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

(2011) S. Duplessis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

(2011) C. E. Ellison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes

(2010) A. John Clutterbuck   FUNGAL GENETICS AND BIOLOGY

Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control

(2010) D. E. Neafsey et al.   GENOME RESEARCH

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

(2010) Francis Martin et al.   NATURE

Isolation and characterization of MAT genes in the symbiotic ascomycete Tuber melanosporum

(2010) Andrea Rubini et al.   NEW PHYTOLOGIST

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Detecting signatures of balancing selection to identify targets of anti-parasite immunity

(2010) Gareth D. Weedall et al.   TRENDS IN PARASITOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

SNP identification in crop plants

(2009) Martin W Ganal et al.   CURRENT OPINION IN PLANT BIOLOGY

Tuber melanosporumoutcrosses: analysis of the genetic diversity within and among its natural populations under this new scenario

(2008) Claudia Riccioni et al.   NEW PHYTOLOGIST