Inferring synteny between genome assemblies: a systematic evaluation

The genome of Chenopodium quinoa

(2017) David E. Jarvis et al.   NATURE

Reconstructing the genome of the most recent common ancestor of flowering plants

(2017) Florent Murat et al.   NATURE GENETICS

Long-read sequencing improves assembly of Trichinella genomes 10-fold, revealing substantial synteny between lineages diverged over 7 million years

(2017) PETER C. THOMPSON et al.   PARASITOLOGY

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

(2016) Massimo Iorizzo et al.   NATURE GENETICS

The genomic basis of parasitism in the Strongyloides clade of nematodes

(2016) Vicky L Hunt et al.   NATURE GENETICS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Small genome of the fungusEscovopsis weberi, a specialized disease agent of ant agriculture

(2016) Tom J. B. de Man et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts

(2016) Liang Ma et al.   Nature Communications

The genome of Onchocerca volvulus, agent of river blindness

(2016) James A. Cotton et al.   Nature Microbiology

YOC, A new strategy for pairwise alignment of collinear genomes

(2015) Raluca Uricaru et al.   BMC BIOINFORMATICS

Rendering the Intractable More Tractable: Tools from Caenorhabditis elegans Ripe for Import into Parasitic Nematodes

(2015) J. D. Ward   GENETICS

WormBase 2016: expanding to enable helminth genomic research

(2015) Kevin L. Howe et al.   NUCLEIC ACIDS RESEARCH

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

Evaluating synteny for improved comparative studies

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

SynChro: A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes

(2014) Guénola Drillon et al.   PLoS One

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

(2014) James F. Denton et al.   PLoS Computational Biology

Comparative genomic data of the Avian Phylogenomics Project

(2014) Guojie Zhang et al.   GigaScience

FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box genes

(2013) Philip Ruelens et al.   Nature Communications

Screening synteny blocks in pairwise genome comparisons through integer programming

(2011) Haibao Tang et al.   BMC BIOINFORMATICS

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Regulated functional alternative splicing in Drosophila

(2011) J. P. Venables 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

Caenorhabditis briggsae Recombinant Inbred Line Genotypes Reveal Inter-Strain Incompatibility and the Evolution of Recombination

(2011) Joseph A. Ross et al.   PLoS Genetics

Genome-wide synteny through highly sensitive sequence alignment: Satsuma

(2010) M. G. Grabherr et al.   BIOINFORMATICS

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

(2010) Ismael A Vergara et al.   BMC GENOMICS

Cancer: Genomic evolution of metastasis

(2010) E. Georg Luebeck   NATURE

Comparative assessment of methods for aligning multiple genome sequences

(2010) Xiaoyu Chen et al.   NATURE BIOTECHNOLOGY

r2cat: synteny plots and comparative assembly

(2009) P. Husemann et al.   BIOINFORMATICS

ABACAS: algorithm-based automatic contiguation of assembled sequences

(2009) S. Assefa et al.   BIOINFORMATICS

Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution

(2009) Claus Kemkemer et al.   BMC EVOLUTIONARY BIOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Synteny and Collinearity in Plant Genomes

(2008) H. Tang et al.   SCIENCE