Improving Genome-Wide Scans of Positive Selection by Using Protein Isoforms of Similar Length

Evidence for Widespread Positive and Purifying Selection Across the European Rabbit (Oryctolagus cuniculus) Genome

(2012) M. Carneiro et al.   MOLECULAR BIOLOGY AND EVOLUTION

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Sequence shortening in the rodent ancestor

(2011) S. Laurie et al.   GENOME RESEARCH

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes

(2011) P. Markova-Raina et al.   GENOME RESEARCH

The Relationships Among MicroRNA Regulation, Intrinsically Disordered Regions, and Other Indicators of Protein Evolutionary Rate

(2011) S. C.-C. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Performance of Positive Selection Inference by Filtering Unreliable Alignment Regions

(2011) Eyal Privman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Assessment of orthologous splicing isoforms in human and mouse orthologous genes

(2010) Federico Zambelli et al.   BMC GENOMICS

Lineage-Specific Variation in Intensity of Natural Selection in Mammals

(2010) M. Toll-Riera et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment

(2009) Adrian Schneider et al.   Genome Biology and Evolution

The difficulty of avoiding false positives in genome scans for natural selection

(2009) S. Mallick et al.   GENOME RESEARCH

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics