SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand

Genome Evolution in Maize: From Genomes Back to Genes

(2015) James C. Schnable   Annual Review of Plant Biology

Evaluating synteny for improved comparative studies

(2014) C. G. Ghiurcuta et al.   BIOINFORMATICS

Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes

(2014) MeiYee Law et al.   PLANT PHYSIOLOGY

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

(2014) B. Chalhoub et al.   SCIENCE

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

(2014) R. E. Green et al.   SCIENCE

Whole Genome and Tandem Duplicate Retention Facilitated Glucosinolate Pathway Diversification in the Mustard Family

(2013) Johannes A. Hofberger et al.   Genome Biology and Evolution

Architecture and evolution of a minute plant genome

(2013) Enrique Ibarra-Laclette et al.   NATURE

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

(2013) Annabelle Haudry et al.   NATURE GENETICS

Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species

(2013) A. J. Waters et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Amborella Genome and the Evolution of Flowering Plants

(2013) et al.   SCIENCE

A web-based multi-genome synteny viewer for customized data

(2012) Kashi V Revanna et al.   BMC BIOINFORMATICS

Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses

(2012) James C. Schnable et al.   Genome Biology and Evolution

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

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

Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants

(2012) Laura Baxter et al.   PLANT CELL

Unleashing the Genome of Brassica Rapa

(2012) Haibao Tang et al.   Frontiers in Plant Science

Screening synteny blocks in pairwise genome comparisons through integer programming

(2011) Haibao Tang et al.   BMC BIOINFORMATICS

MicroSyn: A user friendly tool for detection of microsynteny in a gene family

(2011) Bin Cai et al.   BMC BIOINFORMATICS

Positional orthology: putting genomic evolutionary relationships into context

(2011) C. N. Dewey   BRIEFINGS IN BIOINFORMATICS

Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize

(2011) A. M. Barbaglia et al.   GENETICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME 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

SyMAP v3.4: a turnkey synteny system with application to plant genomes

(2011) Carol Soderlund et al.   NUCLEIC ACIDS RESEARCH

Different Gene Families in Arabidopsis thaliana Transposed in Different Epochs and at Different Frequencies throughout the Rosids

(2011) M. R. Woodhouse et al.   PLANT CELL

Genes Identified by Visible Mutant Phenotypes Show Increased Bias toward One of Two Subgenomes of Maize

(2011) James C. Schnable et al.   PLoS One

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

(2011) Stephen A. Goff et al.   Frontiers in Plant Science

Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster

(2010) Ismael A Vergara et al.   BMC GENOMICS

CYNTENATOR: Progressive Gene Order Alignment of 17 Vertebrate Genomes

(2010) Christian Rödelsperger et al.   PLoS One

Transposed Genes in Arabidopsis Are Often Associated with Flanking Repeats

(2010) Margaret R. Woodhouse et al.   PLoS Genetics

Detecting gene clusters under evolutionary constraint in a large number of genomes

(2009) Xu Ling et al.   BIOINFORMATICS

OrthoClusterDB: an online platform for synteny blocks

(2009) Man-Ping Ng et al.   BMC BIOINFORMATICS

Sixty Million Years in Evolution of Soft Grain Trait in Grasses: Emergence of the Softness Locus in the Common Ancestor of Pooideae and Ehrhartoideae, after their Divergence from Panicoideae

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

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes

(2009) Xianjun Dong et al.   GENOME BIOLOGY

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

(2008) H. Tang et al.   GENOME RESEARCH

Many or most genes in Arabidopsis transposed after the origin of the order Brassicales

(2008) M. Freeling et al.   GENOME RESEARCH

How to usefully compare homologous plant genes and chromosomes as DNA sequences

(2008) Eric Lyons et al.   PLANT JOURNAL

Synteny and Collinearity in Plant Genomes

(2008) H. Tang et al.   SCIENCE

The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids

(2008) Eric Lyons et al.   Tropical Plant Biology