Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Genomics of the origin and evolution of Citrus

(2018) Guohong Albert Wu et al.   NATURE

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Sugar Transporters in Plants: New Insights and Discoveries

(2017) Benjamin T. Julius et al.   PLANT AND CELL PHYSIOLOGY

A Tonoplast Sugar Transporter Underlies a Sugar Accumulation QTL in Watermelon

(2017) Yi Ren et al.   PLANT PHYSIOLOGY

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Genome diversity of tuber-bearingSolanumuncovers complex evolutionary history and targets of domestication in the cultivated potato

(2017) Michael A. Hardigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

(2017) Raz Avni et al.   SCIENCE

Assemblytics: a web analytics tool for the detection of variants from an assembly

(2016) Maria Nattestad et al.   BIOINFORMATICS

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

(2016) Jessen V Bredeson et al.   NATURE BIOTECHNOLOGY

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

(2016) Jinghua Yang et al.   NATURE GENETICS

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Sucrose Transporter ZmSut1 Expression and Localization Uncover New Insights into Sucrose Phloem Loading

(2016) R. Frank Baker et al.   PLANT PHYSIOLOGY

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Sucrose accumulation in sweet sorghum stems occurs by apoplasmic phloem unloading and does not involve differential Sucrose transporter expression

(2015) Saadia Bihmidine et al.   BMC PLANT BIOLOGY

SWEETs, transporters for intracellular and intercellular sugar translocation

(2015) Joon-Seob Eom et al.   CURRENT OPINION IN PLANT BIOLOGY

De Novo Plant Genome Assembly Based on Chromatin Interactions: A Case Study of Arabidopsis thaliana

(2015) Ting Xie et al.   Molecular Plant

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

(2015) Robert VanBuren et al.   NATURE

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Tissue-specific transcriptome analysis within the maturing sugarcane stalk reveals spatial regulation in the expression of cellulose synthase and sucrose transporter gene families

(2015) Rosanne E. Casu et al.   PLANT MOLECULAR BIOLOGY

Identification of the transporter responsible for sucrose accumulation in sugar beet taproots

(2015) Benjamin Jung et al.   Nature Plants

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum and interspecific G. hirsutum × G. barbadense populations

(2014) Joseph I. Said et al.   MOLECULAR GENETICS AND GENOMICS

Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice

(2014) Lin Wang et al.   NATURE BIOTECHNOLOGY

Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates

(2014) C. Kim et al.   PLANT CELL

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

(2014) et al.   SCIENCE

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

(2014) B. Chalhoub et al.   SCIENCE

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Regulation of assimilate import into sink organs: update on molecular drivers of sink strength

(2013) Saadia Bihmidine et al.   Frontiers in Plant Science

A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy

(2012) Kankshita Swaminathan et al.   BMC GENOMICS

Genome size variation in three Saccharum species

(2012) Jisen Zhang et al.   EUPHYTICA

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

Metabolic engineering of sugars and simple sugar derivatives in plants

(2012) John W. Patrick et al.   PLANT BIOTECHNOLOGY JOURNAL

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) Xiyin Wang et al.   PLANT CELL

Genetic structure and domestication history of the grape

(2011) Sean Myles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sucrose Efflux Mediated by SWEET Proteins as a Key Step for Phloem Transport

(2011) L.-Q. Chen et al.   SCIENCE

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A genomic analysis of disease-resistance genes encoding nucleotide binding sites in Sorghum bicolor

(2010) Xiao Cheng et al.   GENETICS AND MOLECULAR BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane

(2010) Olivier Garsmeur et al.   NEW PHYTOLOGIST

Current perspectives on the regulation of whole-plant carbohydrate partitioning

(2010) Thomas L. Slewinski et al.   PLANT SCIENCE

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TEclass--a tool for automated classification of unknown eukaryotic transposable elements

(2009) G. Abrusan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution

(2008) J. Salse et al.   PLANT CELL