ORFcor: Identifying and Accommodating ORF Prediction Inconsistencies for Phylogenetic Analysis

Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation

(2012) Jonathan L Klassen et al.   BMC GENOMICS

The SAR11 Group of Alpha-Proteobacteria Is Not Related to the Origin of Mitochondria

(2012) Naiara Rodríguez-Ezpeleta et al.   PLoS One

Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling

(2012) John J. Wiens et al.   PLoS One

Consistency of gene starts among Burkholderia genomes

(2011) John Dunbar et al.   BMC GENOMICS

Computational methods for Gene Orthology inference

(2011) D. M. Kristensen et al.   BRIEFINGS IN BIOINFORMATICS

An Integrative Method for Identifying the Over-Annotated Protein-Coding Genes in Microbial Genomes

(2011) J.-F. Yu et al.   DNA RESEARCH

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Independent Genome Reduction and Phylogenetic Reclassification of the Oceanic SAR11 Clade

(2011) J. Viklund et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Gene Ontology: enhancements for 2011

(2011)   NUCLEIC ACIDS RESEARCH

Genome Majority Vote Improves Gene Predictions

(2011) Michael E. Wall et al.   PLoS Computational Biology

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

A computational genomics pipeline for prokaryotic sequencing projects

(2010) Andrey O. Kislyuk et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes

(2010) Amrita Pati et al.   NATURE METHODS

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Getting Started in Gene Orthology and Functional Analysis

(2010) Gang Fang et al.   PLoS Computational Biology

MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction

(2009) Gang-Qing Hu et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The effect of sequencing errors on metagenomic gene prediction

(2009) Katharina J Hoff   BMC GENOMICS

Evaluation of Three Automated Genome Annotations for Halorhabdus utahensis

(2009) Peter Bakke et al.   PLoS One

The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

(2009) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

MicroScope: a platform for microbial genome annotation and comparative genomics

(2009) D. Vallenet et al.   Database-The Journal of Biological Databases and Curation

Genomics and Evolution of Heritable Bacterial Symbionts

(2008) Nancy A. Moran et al.   Annual Review of Genetics

Prediction of translation initiation site for microbial genomes with TriTISA

(2008) Gang-Qing Hu et al.   BIOINFORMATICS

Computational evaluation of TIS annotation for prokaryotic genomes

(2008) Gang-Qing Hu et al.   BMC BIOINFORMATICS

Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?

(2008) Albert Pallejà et al.   BMC GENOMICS