Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly ofMalassezia sympodialis

The diversity of fungal genome

(2015) Tapan Kumar Mohanta et al.   BIOLOGICAL PROCEDURES ONLINE

Proteogenomic Discovery of a Small, Novel Protein in Yeast Reveals a Strategy for the Detection of Unannotated Short Open Reading Frames

(2015) Daniel Yagoub et al.   JOURNAL OF PROTEOME RESEARCH

Regional centromeres in the yeastCandida lusitaniaelack pericentromeric heterochromatin

(2015) Shivali Kapoor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome

(2015) Luigi Faino et al.   mBio

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin

(2015) Guangxi Wu et al.   PLoS Genetics

Analysis of stranded information using an automated procedure for strand specific RNA sequencing

(2014) Benjamín Sigurgeirsson et al.   BMC GENOMICS

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh et al.   NATURE

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

(2014) Guilhem Janbon et al.   PLoS Genetics

Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions

(2013) Jainab Khatun et al.   BMC GENOMICS

The 135 kbp mitochondrial genome of Agaricus bisporus is the largest known eukaryotic reservoir of group I introns and plasmid-related sequences

(2013) Cyril Férandon et al.   FUNGAL GENETICS AND BIOLOGY

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations

(2013) Gordon Gremme et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq

(2013) Gloria M. Sheynkman et al.   MOLECULAR & CELLULAR PROTEOMICS

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of fungal sexual reproduction

(2013) Joseph Heitman et al.   MYCOLOGIA

Topographic diversity of fungal and bacterial communities in human skin

(2013) Keisha Findley et al.   NATURE

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics

(2013) Rui M M Branca et al.   NATURE METHODS

Genomic Insights into the Atopic Eczema-Associated Skin Commensal Yeast Malassezia sympodialis

(2013) A. Gioti et al.   mBio

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Web Apollo: a web-based genomic annotation editing platform

(2013) Eduardo Lee et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

ParsEval: parallel comparison and analysis of gene structure annotations

(2012) Daniel S Standage et al.   BMC BIOINFORMATICS

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

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

Mitochondrial genome variability within the Candida parapsilosis species complex

(2012) Matus Valach et al.   MITOCHONDRION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Gene Conversion Occurs within the Mating-Type Locus of Cryptococcus neoformans during Sexual Reproduction

(2012) Sheng Sun et al.   PLoS Genetics

Malassezia Fungi Are Specialized to Live on Skin and Associated with Dandruff, Eczema, and Other Skin Diseases

(2012) Charles W. Saunders et al.   PLoS Pathogens

Sex in Fungi

(2011) Min Ni et al.   Annual Review of Genetics

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Diversity in Requirement of Genetic and Epigenetic Factors for Centromere Function in Fungi

(2011) Babhrubahan Roy et al.   EUKARYOTIC CELL

The discovery of novel protein-coding features in mouse genome based on mass spectrometry data

(2011) Xiao-Bin Xing et al.   GENOMICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Evolution of linear chromosomes and multipartite genomes in yeast mitochondria

(2011) Matus Valach et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Nanovesicles from Malassezia sympodialis and Host Exosomes Induce Cytokine Responses – Novel Mechanisms for Host-Microbe Interactions in Atopic Eczema

(2011) Ulf Gehrmann et al.   PLoS One

Sequencing and Validation of the Genome of a Campylobacter concisus Reveals Intra-Species Diversity

(2011) Nandan P. Deshpande et al.   PLoS One

Scalable Transcriptome Preparation for Massive Parallel Sequencing

(2011) Henrik Stranneheim et al.   PLoS One

Chromosomal G + C Content Evolution in Yeasts: Systematic Interspecies Differences, and GC-Poor Troughs at Centromeres

(2010) Denise B. Lynch et al.   Genome Biology and Evolution

Centromere identity: a challenge to be faced

(2010) Gunjan D. Mehta et al.   MOLECULAR GENETICS AND GENOMICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

A Deviation from the Bipolar-Tetrapolar Mating Paradigm in an Early Diverged Basidiomycete

(2010) Marco A. Coelho et al.   PLoS Genetics

r2cat: synteny plots and comparative assembly

(2009) P. Husemann et al.   BIOINFORMATICS

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

(2009) Geraldine Butler et al.   NATURE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

(2008) K. Baerenfaller et al.   SCIENCE

The Agrocybe aegerita mitochondrial genome contains two inverted repeats of the nad4 gene arisen by duplication on both sides of a linear plasmid integration site

(2007) C. Ferandon et al.   FUNGAL GENETICS AND BIOLOGY