Inferring horizontal gene transferResolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogsTowards practical, high-capacity, low-maintenance information storage in synthesized DNAThe what, where, how and why of gene ontology--a primer for bioinformaticiansOMA 2011: orthology inference among 1000 complete genomesConceptual framework and pilot study to benchmark phylogenomic databases based on reference gene treesHomoeologs: What Are They and How Do We Infer Them?The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory diseaseAn expanded evaluation of protein function prediction methods shows an improvement in accuracyBig data and other challenges in the quest for orthologsToward community standards in the quest for orthologsStandardized benchmarking in the quest for orthologsWho watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.Phylogenetic profiling: how much input data is enough?Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences.Covariance of maximum likelihood evolutionary distances between sequences aligned pairwiseSWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2Algorithm of OMA for large-scale orthology inference.Phylogenetic and functional assessment of orthologs inference projects and methodsGlobal regulatory architecture of human, mouse and rat tissue transcriptomes.Comparative genomics reveals contraction in olfactory receptor genes in batsiTRAQ-based analysis of changes in the cassava root proteome reveals pathways associated with post-harvest physiological deterioration.ALF--a simulation framework for genome evolution.Inferring orthology and paralogy.Quality of computationally inferred gene ontology annotations.A transcriptomic-phylogenomic analysis of the evolutionary relationships of flatworms.Inferring hierarchical orthologous groups from orthologous gene pairs.The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation studySurvey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes.The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.A Gene Ontology Tutorial in Python.Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast.Compensation of Dosage-Sensitive Genes on the Chicken Z Chromosome.Clustering Genes of Common Evolutionary History.Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of LifeBase-calling for next-generation sequencing platformsGene Ontology: Pitfalls, Biases, and Remedies.Primer on the Gene Ontology.The Microbe browser for comparative genomics.
P50
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P50
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