Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees

Unified modeling of gene duplication, loss, and coalescence using a locus tree

(2012) M. D. Rasmussen et al.   GENOME RESEARCH

The origin of multicellularity in cyanobacteria

(2011) Bettina E Schirrmeister et al.   BMC EVOLUTIONARY BIOLOGY

Models, algorithms and programs for phylogeny reconciliation

(2011) J.-P. Doyon et al.   BRIEFINGS IN BIOINFORMATICS

Lateral gene transfer

(2011) Olga Zhaxybayeva et al.   CURRENT BIOLOGY

From Gene Trees to Species Trees II: Species Tree Inference by Minimizing Deep Coalescence Events

(2011) Louxin Zhang   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Detecting Highways of Horizontal Gene Transfer

(2011) Mukul S. Bansal et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting

(2011) Yun Yu et al.   SYSTEMATIC BIOLOGY

A Survey of Combinatorial Methods for Phylogenetic Networks

(2010) Daniel H. Huson et al.   Genome Biology and Evolution

Rapid evolutionary innovation during an Archaean genetic expansion

(2010) Lawrence A. David et al.   NATURE

2× genomes - depth does matter

(2010) Michel C Milinkovitch et al.   GENOME BIOLOGY

Evolution by leaps: gene duplication in bacteria

(2009) Margrethe H Serres et al.   Biology Direct

Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus

(2009) Olga Zhaxybayeva et al.   Genome Biology and Evolution

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

Species Tree Inference by Minimizing Deep Coalescences

(2009) Cuong Than et al.   PLoS Computational Biology

Reconciliation with Non-Binary Species Trees

(2008) Benjamin Vernot et al.   JOURNAL OF COMPUTATIONAL BIOLOGY