Orthology Detection Combining Clustering and Synteny for Very Large Datasets

Simulation of gene family histories

(2014) Maribel Hernandez-Rosales et al.   BMC BIOINFORMATICS

Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq

(2013) Oscar Franzén et al.   PLoS Computational Biology

Roundup 2.0: enabling comparative genomics for over 1800 genomes

(2012) T. F. DeLuca et al.   BIOINFORMATICS

Gene family assignment-free comparative genomics

(2012) Daniel Doerr et al.   BMC BIOINFORMATICS

Orthology relations, symbolic ultrametrics, and cographs

(2012) Marc Hellmuth et al.   JOURNAL OF MATHEMATICAL BIOLOGY

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Development of universal genetic markers based on single-copy orthologous (COSII) genes in Poaceae

(2012) Hailan Liu et al.   PLANT CELL REPORTS

Orthology prediction methods: A quality assessment using curated protein families

(2011) Kalliopi Trachana et al.   BIOESSAYS

Genomic distance under gene substitutions

(2011) Marília D V Braga et al.   BMC BIOINFORMATICS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Positional orthology: putting genomic evolutionary relationships into context

(2011) C. N. Dewey   BRIEFINGS IN BIOINFORMATICS

Computational methods for Gene Orthology inference

(2011) D. M. Kristensen et al.   BRIEFINGS IN BIOINFORMATICS

ALF—A Simulation Framework for Genome Evolution

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

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs

(2011) Khalid Mahmood et al.   NUCLEIC ACIDS RESEARCH

i-ADHoRe 3.0—fast and sensitive detection of genomic homology in extremely large data sets

(2011) Sebastian Proost et al.   NUCLEIC ACIDS RESEARCH

MultiMSOAR 2.0: An Accurate Tool to Identify Ortholog Groups among Multiple Genomes

(2011) Guanqun Shi et al.   PLoS One

Identifying Single Copy Orthologs in Metazoa

(2011) Christopher J. Creevey et al.   PLoS Computational Biology

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

(2010) Guanqun Shi et al.   BMC BIOINFORMATICS

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

OMA 2011: orthology inference among 1000 complete genomes

(2010) A. M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

CYNTENATOR: Progressive Gene Order Alignment of 17 Vertebrate Genomes

(2010) Christian Rödelsperger et al.   PLoS One

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

Biological Sequence Simulation for Testing Complex Evolutionary Hypotheses: indel-Seq-Gen Version 2.0

(2009) Cory L. Strope et al.   MOLECULAR BIOLOGY AND EVOLUTION

Insertion of Horizontally Transferred Genes within Conserved Syntenic Regions of Yeast Genomes

(2009) Thomas Rolland et al.   PLoS One

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

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

SynBlast: Assisting the analysis of conserved synteny information

(2008) Jörg Lehmann et al.   BMC BIOINFORMATICS