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Genome annotation

RNA-Seq differential expression analysis: An extended review and a software tool

Juliana Costa-Silva, Douglas Domingues, Fabricio Martins Lopes

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

Shanrong Zhao, Wai-Ping Fung-Leung, [ ... ], Xuejun Liu

The Evolution of Mammalian Gene Families

Jeffery P. Demuth, Tijl De Bie, [ ... ], Matthew W. Hahn

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

Adam C. English, Stephen Richards, [ ... ], Richard A. Gibbs

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

Daniel R. Mende, Alison S. Waller, [ ... ], Peer Bork

BBMerge – Accurate paired shotgun read merging via overlap

Brian Bushnell, Jonathan Rood, Esther Singer

DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing

Fabienne Brenet, Michelle Moh, [ ... ], Joseph M. Scandura

Distinct Gene Number-Genome Size Relationships for Eukaryotes and Non-Eukaryotes: Gene Content Estimation for Dinoflagellate Genomes

Yubo Hou, Senjie Lin

Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles

David Vallenet, Patrice Nordmann, [ ... ], Stéphane Cruveiller

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

Ramy K. Aziz, Scott Devoid, [ ... ], Fangfang Xia

Considering Transposable Element Diversification in De Novo Annotation Approaches

Timothée Flutre, Elodie Duprat, Catherine Feuillet, Hadi Quesneville

Tn-Seq Explorer: A Tool for Analysis of High-Throughput Sequencing Data of Transposon Mutant Libraries

Sina Solaimanpour, Felipe Sarmiento, Jan Mrázek

Evaluation of Three Automated Genome Annotations for Halorhabdus utahensis

Peter Bakke, Nick Carney, [ ... ], A. Malcolm Campbell

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