Further Simulations and Analyses Demonstrate Open Problems of Phylostratigraphy

Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution

(2016) Bryan A. Moyers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Open questions in the study of de novo genes: what, how and why

(2016) Aoife McLysaght et al.   NATURE REVIEWS GENETICS

Determinants of the rate of protein sequence evolution

(2015) Jianzhi Zhang et al.   NATURE REVIEWS GENETICS

Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution

(2014) B. A. Moyers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution

(2013) Rafik Neme et al.   BMC GENOMICS

Phylostratigraphic profiles reveal a deep evolutionary history of the vertebrate head sensory systems

(2013) Martin Sebastijan Šestak et al.   Frontiers in Zoology

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa

(2010) Tomislav Domazet-Lošo et al.   BMC BIOLOGY

Large-Scale Analysis of Orthologs and Paralogs under Covarion-Like and Constant-but-Different Models of Amino Acid Evolution

(2010) R. A. Studer et al.   MOLECULAR BIOLOGY AND EVOLUTION

A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns

(2010) Tomislav Domazet-Lošo et al.   NATURE

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis

(2009) Huai-Chun Wang et al.   BMC EVOLUTIONARY BIOLOGY

Recent de novo origin of human protein-coding genes

(2009) D. G. Knowles et al.   GENOME RESEARCH

A Dirichlet Process Covarion Mixture Model and Its Assessments Using Posterior Predictive Discrepancy Tests

(2009) Yan Zhou et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Ancient Evolutionary Origin of Genes Associated with Human Genetic Diseases

(2008) T. Domazet-Loso et al.   MOLECULAR BIOLOGY AND EVOLUTION