Positional orthology: putting genomic evolutionary relationships into context

DRIMM-Synteny: decomposing genomes into evolutionary conserved segments

(2010) Son K. Pham et al.   BIOINFORMATICS

EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes

(2010) Khalid Mahmood et al.   BIOINFORMATICS

MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement

(2010) Guanqun Shi et al.   BMC BIOINFORMATICS

Noncoding Sequences Near Duplicated Genes Evolve Rapidly

(2010) Dennis Kostka et al.   Genome Biology and Evolution

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Accurate identification of orthologous segments among multiple genomes

(2009) Tsuyoshi Hachiya et al.   BIOINFORMATICS

Identification of mammalian orthologs using local synteny

(2009) Jin Jun et al.   BMC GENOMICS

Evolutionarily Stable Association of Intronic snoRNAs and microRNAs with Their Host Genes

(2009) Marc P. Hoeppner et al.   Genome Biology and Evolution

Multiple whole-genome alignments without a reference organism

(2009) I. Dubchak et al.   GENOME RESEARCH

Adaptive evolution of young gene duplicates in mammals

(2009) M. V. Han et al.   GENOME RESEARCH

Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans

(2009) A. P. Jackson et al.   GENOME RESEARCH

Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria

(2009) Kevin Penn et al.   ISME Journal

Duplication Mechanism and Disruptions in Flanking Regions Determine the Fate of Mammalian Gene Duplicates

(2009) Jin Jun et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Divergent Evolution of Duplicate Genes Leads to Genetic Incompatibilities Within A. thaliana

(2009) D. Bikard et al.   SCIENCE

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

(2009) Adrian M. Altenhoff et al.   PLoS Computational Biology

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

Syntenator: Multiple gene order alignments with a gene-specific scoring function

(2008) Christian Rödelsperger et al.   Algorithms for Molecular Biology

Precise detection of rearrangement breakpoints in mammalian chromosomes

(2008) Claire Lemaitre et al.   BMC BIOINFORMATICS

SynBlast: Assisting the analysis of conserved synteny information

(2008) Jörg Lehmann et al.   BMC BIOINFORMATICS

SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes

(2008) Frédéric Lemoine et al.   BMC BIOINFORMATICS

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH

The quest for orthologs: finding the corresponding gene across genomes

(2008) Arnold Kuzniar et al.   TRENDS IN GENETICS

Asymmetric histone modifications between the original and derived loci of human segmental duplications

(2008) Deyou Zheng   GENOME BIOLOGY

CLUSTERING OF MAIN ORTHOLOGS FOR MULTIPLE GENOMES

(2008) ZHENG FU et al.   Journal of Bioinformatics and Computational Biology