GENESPACE tracks regions of interest and gene copy number variation across multiple genomes

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Platypus and echidna genomes reveal mammalian biology and evolution

(2021) Yang Zhou et al.   NATURE

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

(2021) John T. Lovell et al.   NATURE

Towards complete and error-free genome assemblies of all vertebrate species

(2021) Arang Rhie et al.   NATURE

Sensitive protein alignments at tree-of-life scale using DIAMOND

(2021) Benjamin Buchfink et al.   NATURE METHODS

Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly

(2021) Tingting Zhu et al.   PLANT JOURNAL

Sex chromosome evolution among amniotes: is the origin of sex chromosomes non-random?

(2021) Lukáš Kratochvíl et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

(2021) Matthew B. Hufford et al.   SCIENCE

Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding

(2021) John T. Lovell et al.   Nature Communications

Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome

(2021) Vidhya Jagannathan et al.   Genes

Phylogenetic reconstruction based on synteny block and gene adjacencies

(2020) Guénola Drillon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

(2020) Z. Jeffrey Chen et al.   NATURE GENETICS

Deeply conserved synteny resolves early events in vertebrate evolution

(2020) Oleg Simakov et al.   Nature Ecology & Evolution

A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci

(2020) Sujan Mamidi et al.   NATURE BIOTECHNOLOGY

Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes

(2019) Tao Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome sequence of the model rice variety KitaakeX

(2019) Rashmi Jain et al.   BMC GENOMICS

One thousand plant transcriptomes and the phylogenomics of green plants

(2019)   NATURE

Components of the ribosome biogenesis pathway underlie establishment of telomere length set point in Arabidopsis

(2019) Liliia R. Abdulkina et al.   Nature Communications

Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions

(2018) Matthew Haas et al.   Journal of Integrative Plant Biology

The genomic landscape of molecular responses to natural drought stress in Panicum hallii

(2018) John T. Lovell et al.   Nature Communications

Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations

(2016) Chunhui Li et al.   BMC GENOMICS

On the relative abundance of autopolyploids and allopolyploids

(2015) Michael S. Barker et al.   NEW PHYTOLOGIST

Identification of Photosynthesis-Associated C4 Candidate Genes through Comparative Leaf Gradient Transcriptome in Multiple Lineages of C3 and C4 Species

(2015) Zehong Ding et al.   PLoS One

Integrated Syntenic and Phylogenomic Analyses Reveal an Ancient Genome Duplication in Monocots

(2014) Yuannian Jiao et al.   PLANT CELL

Complex evolutionary trajectories of sex chromosomes across bird taxa

(2014) Q. Zhou et al.   SCIENCE

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

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

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Seventy Million Years of Concerted Evolution of a Homoeologous Chromosome Pair, in Parallel, in Major Poaceae Lineages

(2011) Xiyin Wang et al.   PLANT CELL

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

MADS-box gene expression and implications for developmental origins of the grass spikelet

(2009) Jill C. Preston et al.   AMERICAN JOURNAL OF BOTANY

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

The Preferential Retention of Starch Synthesis Genes Reveals the Impact of Whole-Genome Duplication on Grass Evolution

(2008) Y. Wu et al.   MOLECULAR BIOLOGY AND EVOLUTION