CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts

SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models

(2014) Ian Reid et al.   BMC BIOINFORMATICS

OMIGA: Optimized Maker-Based Insect Genome Annotation

(2014) Jinding Liu et al.   MOLECULAR GENETICS AND GENOMICS

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

(2014) Alexandre Lomsadze et al.   NUCLEIC ACIDS RESEARCH

3′ Untranslated Regions Mediate Transcriptional Interference between Convergent Genes Both Locally and Ectopically in Saccharomyces cerevisiae

(2014) Luwen Wang et al.   PLoS Genetics

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

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

RNA-Seq analysis reveals new gene models and alternative splicing in the fungal pathogen Fusarium graminearum

(2013) Chunzhao Zhao et al.   BMC GENOMICS

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes

(2013) K. J. Hoff et al.   NUCLEIC ACIDS RESEARCH

TheAspergillusGenome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations

(2013) Gustavo C. Cerqueira et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Evolution of three Pyrenophora cereal pathogens: Recent divergence, speciation and evolution of non-coding DNA

(2012) Simon R. Ellwood et al.   FUNGAL GENETICS AND BIOLOGY

Fungal Bioconversion of Lignocellulosic Residues; Opportunities & Perspectives

(2012) Mehdi Dashtban et al.   International Journal of Biological Sciences

The Top 10 fungal pathogens in molecular plant pathology

(2012) RALPH DEAN et al.   MOLECULAR PLANT PATHOLOGY

Update on activities at the Universal Protein Resource (UniProt) in 2013

(2012)   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2012)   NUCLEIC ACIDS RESEARCH

AntiFam: a tool to help identify spurious ORFs in protein annotation

(2012) R. Y. Eberhardt et al.   Database-The Journal of Biological Databases and Curation

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis

(2011) Alessandro Guida et al.   BMC GENOMICS

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Comparative Functional Genomics of the Fission Yeasts

(2011) N. Rhind et al.   SCIENCE

New developments in pathogenicity and virulence of necrotrophs

(2010) Richard P Oliver et al.   CURRENT OPINION IN PLANT BIOLOGY

Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq

(2010) V. M. Bruno et al.   GENOME RESEARCH

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

An Overview of Nested Genes in Eukaryotic Genomes

(2009) Anuj Kumar   EUKARYOTIC CELL

Acquisition of prokaryotic genes by fungal genomes

(2009) Marina Marcet-Houben et al.   TRENDS IN GENETICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

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

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

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

(2008) Diego Martinez et al.   NATURE BIOTECHNOLOGY

Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum

(2008) Marco A van den Berg et al.   NATURE BIOTECHNOLOGY

Cross-kingdom patterns of alternative splicing and splice recognition

(2008) Abigail M McGuire et al.   GENOME BIOLOGY

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY