On the Need for Mechanistic Models in Computational Genomics and Metagenomics

Probing Allostery Through DNA

(2013) S. Kim et al.   SCIENCE

Evolution of transcriptional regulation in closely related bacteria

(2012) Olga V Tsoy et al.   BMC EVOLUTIONARY BIOLOGY

The interface of protein structure, protein biophysics, and molecular evolution

(2012) David A. Liberles et al.   PROTEIN SCIENCE

Whole-Genome Sequencing: The New Standard of Care?

(2012) L. R. Brunham et al.   SCIENCE

Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants

(2012) A. Keinan et al.   SCIENCE

Tempo and Mode in Evolution of Transcriptional Regulation

(2012) Kacy L. Gordon et al.   PLoS Genetics

The public goods hypothesis for the evolution of life on Earth

(2011) James O McInerney et al.   Biology Direct

Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids

(2011) Shinichiro Maruyama et al.   BMC EVOLUTIONARY BIOLOGY

PROGRESS TOWARD A GENERAL SPECIES CONCEPT

(2011) Bernhard Hausdorf   EVOLUTION

Estimating the Distribution of Selection Coefficients from Phylogenetic Data Using Sitewise Mutation-Selection Models

(2011) A. U. Tamuri et al.   GENETICS

Toward a General Model for the Evolutionary Dynamics of Gene Duplicates

(2011) Anke Konrad et al.   Genome Biology and Evolution

Antibiotic Production by Myxobacteria Plays a Role in Predation

(2011) Y. Xiao et al.   JOURNAL OF BACTERIOLOGY

Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?

(2011) Asli I. Özen et al.   MICROBIAL ECOLOGY

The Evolution of Protein Structures and Structural Ensembles Under Functional Constraint

(2011) Jessica Siltberg-Liberles et al.   Genes

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

Mechanistic revisions of phenomenological modeling strategies in molecular evolution

(2010) Nicolas Rodrigue et al.   TRENDS IN GENETICS

Intrinsically bent DNA in replication origins and gene promoters

(2009) F. Gimenes et al.   GENETICS AND MOLECULAR RESEARCH

The gene evolution model and computing its associated probabilities

(2009) Lars Arvestad et al.   JOURNAL OF THE ACM

On incomplete sampling under birth–death models and connections to the sampling-based coalescent

(2009) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian statistical methods for genetic association studies

(2009) Matthew Stephens et al.   NATURE REVIEWS GENETICS

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

An introduced and a native vertebrate hybridize to form a genetic bridge to a second native species

(2008) D. B. McDonald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA