De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Genome evolution in the allotetraploid frog Xenopus laevis

(2016) Adam M. Session et al.   NATURE

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity

(2016) Jessen V Bredeson et al.   NATURE BIOTECHNOLOGY

A survey of the sorghum transcriptome using single-molecule long reads

(2016) Salah E. Abdel-Ghany et al.   Nature Communications

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

(2016) Bo Wang et al.   Nature Communications

Transcriptome analyses reveal molecular mechanism underlying tapping panel dryness of rubber tree (Hevea brasiliensis)

(2016) Dejun Li et al.   Scientific Reports

The rubber tree genome shows expansion of gene family associated with rubber biosynthesis

(2016) Nyok-Sean Lau et al.   Scientific Reports

DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

(2016) Chengxi Ye et al.   Scientific Reports

An improved genome reference for the African cichlid, Metriaclima zebra

(2015) Matthew A. Conte et al.   BMC GENOMICS

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

(2015) Fuguang Li et al.   NATURE BIOTECHNOLOGY

Genetic variation and the de novo assembly of human genomes

(2015) Mark J. P. Chaisson et al.   NATURE REVIEWS GENETICS

SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean

(2015) Qijian Song et al.   G3-Genes Genomes Genetics

Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS)

(2015) Wirulda Pootakham et al.   Frontiers in Plant Science

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

(2015) Jarrod A Chapman et al.   GENOME BIOLOGY

The draft genome of Primula veris yields insights into the molecular basis of heterostyly

(2015) Michael D Nowak et al.   GENOME BIOLOGY

SNP Identification from RNA Sequencing and Linkage Map Construction of Rubber Tree for Anchoring the Draft Genome

(2015) Jeremy R. Shearman et al.   PLoS One

The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres

(2015) Daojun Yuan et al.   Scientific Reports

Transcriptional and post-transcriptional regulation of the jasmonate signalling pathway in response to abiotic and harvesting stress in Hevea brasiliensis

(2014) Julien Pirrello et al.   BMC PLANT BIOLOGY

Draft Genome Sequence of Eggplant (Solanum melongena L.): the Representative Solanum Species Indigenous to the Old World

(2014) Hideki Hirakawa et al.   DNA RESEARCH

De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways

(2014) Camila Campos Mantello et al.   PLoS One

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

Cassava genome from a wild ancestor to cultivated varieties

(2014) Wenquan Wang et al.   Nature Communications

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Draft genome sequence of the rubber tree Hevea brasiliensis

(2013) Ahmad Yamin Abdul Rahman et al.   BMC GENOMICS

Natural Pathways to Polyploidy in Plants and Consequences for Genome Reorganization

(2013) A. Tayalé et al.   CYTOGENETIC AND GENOME RESEARCH

ParaAT: A parallel tool for constructing multiple protein-coding DNA alignments

(2012) Zhang Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

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

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

A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome

(2012) Yi Ren et al.   PLoS One

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

(2012) Mark F Rogers et al.   GENOME BIOLOGY

Single nucleotide polymorphism marker development in the rubber tree, Hevea brasiliensis (Euphorbiaceae)

(2011) Wirulda Pootakham et al.   AMERICAN JOURNAL OF BOTANY

Transcriptome Sequencing of Hevea brasiliensis for Development of Microsatellite Markers and Construction of a Genetic Linkage Map

(2011) K. Triwitayakorn et al.   DNA RESEARCH

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis

(2011) Zhihui Xia et al.   PLANT MOLECULAR BIOLOGY

Characterization of a cassiicolin-encoding gene from Corynespora cassiicola, pathogen of rubber tree (Hevea brasiliensis)

(2011) Marine Déon et al.   PLANT SCIENCE

Sequence Analysis of the Genome of an Oil-Bearing Tree, Jatropha curcas L.

(2010) S. Sato et al.   DNA RESEARCH

Draft genome sequence of the oilseed species Ricinus communis

(2010) Agnes P Chan et al.   NATURE BIOTECHNOLOGY

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes

(2009) Patrick P. Edger et al.   CHROMOSOME RESEARCH

Every genome sequence needs a good map

(2009) H. A. Lewin et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

(2008) H. Tang et al.   GENOME RESEARCH

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY