Inferring Horizontal Gene Transfer

Supertrees Based on the Subtree Prune-and-Regraft Distance

(2014) Christopher Whidden et al.   SYSTEMATIC BIOLOGY

A Bayesian Method for Analyzing Lateral Gene Transfer

(2014) J. Sjostrand et al.   SYSTEMATIC BIOLOGY

The Inference of Gene Trees with Species Trees

(2014) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Reconciliation and local gene tree rearrangement can be of mutual profit

(2013) Thi Nguyen et al.   Algorithms for Molecular Biology

Systematic inference of highways of horizontal gene transfer in prokaryotes

(2013) Mukul S. Bansal et al.   BIOINFORMATICS

A Pluralistic Account of Homology: Adapting the Models to the Data

(2013) Leanne S. Haggerty et al.   MOLECULAR BIOLOGY AND EVOLUTION

Lateral Gene Transfer from the Dead

(2013) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Efficient Exploration of the Space of Reconciled Gene Trees

(2013) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss

(2012) Mukul S. Bansal et al.   BIOINFORMATICS

Towards a Better Detection of Horizontally Transferred Genes by Combining Unusual Properties Effectively

(2012) Dapeng Xiong et al.   PLoS One

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

(2012) G. J. Szollosi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

(2011) Botond Sipos et al.   BMC BIOINFORMATICS

An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework

(2011) J.-P Doyon et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Detecting Highways of Horizontal Gene Transfer

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

ALF—A Simulation Framework for Genome Evolution

(2011) Daniel A. Dalquen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Towards more robust methods of alien gene detection

(2011) Rajeev K. Azad et al.   NUCLEIC ACIDS RESEARCH

Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments

(2011) Florence Wisniewski-Dyé et al.   PLoS Genetics

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

(2010) Sophie S Abby et al.   BMC BIOINFORMATICS

Inferring Bacterial Genome Flux While Considering Truncated Genes

(2010) Weilong Hao et al.   GENETICS

Rapid evolutionary innovation during an Archaean genetic expansion

(2010) Lawrence A. David et al.   NATURE

Detecting genomic islands using bioinformatics approaches

(2010) Morgan G. I. Langille et al.   NATURE REVIEWS MICROBIOLOGY

A Benchmark of Parametric Methods for Horizontal Transfers Detection

(2010) Jennifer Becq et al.   PLoS One

Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes

(2010) Etienne G. J. Danchin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids

(2010) N. A. Moran et al.   SCIENCE

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model

(2009) M. Csuros et al.   MOLECULAR BIOLOGY AND EVOLUTION

A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes

(2009) Diego Cortez et al.   GENOME BIOLOGY

Uncovering rate variation of lateral gene transfer during bacterial genome evolution

(2008) Weilong Hao et al.   BMC GENOMICS

Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples

(2008) Zhandong Liu et al.   BMC GENOMICS

Resolving the structural features of genomic islands: A machine learning approach

(2007) G. S. Vernikos et al.   GENOME RESEARCH