Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton

Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits

(2018) Xiongming Du et al.   NATURE GENETICS

Centromeric DNA characterization in the model grass Brachypodium distachyon provides insights on the evolution of the genus

(2018) Yinjia Li et al.   PLANT JOURNAL

The maize W22 genome provides a foundation for functional genomics and transposon biology

(2018) Nathan M. Springer et al.   NATURE GENETICS

Shifting the limits in wheat research and breeding using a fully annotated reference genome

(2018) et al.   SCIENCE

The opium poppy genome and morphinan production

(2018) Li Guo et al.   SCIENCE

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

(2017) Ming-Cheng Luo et al.   NATURE

Dynamic location changes of Bub1-phosphorylated-H2AThr133 with CENH3 nucleosome in maize centromeric regions

(2017) Handong Su et al.   NEW PHYTOLOGIST

Suppressing a Putative Sterol Carrier Gene Reduces Plasmodesmal Permeability and Activates Sucrose Transporter Genes during Cotton Fiber Elongation

(2017) Zhiyuan Zhang et al.   PLANT CELL

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

(2017) Raz Avni et al.   SCIENCE

The NnCenH3 protein and centromeric DNA sequence profiles ofNelumbo nuciferaGaertn. (sacred lotus) reveal the DNA structures and dynamics of centromeres in basal eudicots

(2016) Zhixuan Zhu et al.   PLANT JOURNAL

Rapid proliferation and nucleolar organizer targeting centromeric retrotransposons in cotton

(2016) Jinlei Han et al.   PLANT JOURNAL

Inbreeding drives maize centromere evolution

(2016) Kevin L. Schneider et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

(2016) Eric Talevich et al.   PLoS Computational Biology

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Sugar transport across the plant vacuolar membrane: nature and regulation of carrier proteins

(2015) Rainer Hedrich 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

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

(2015) Fuguang Li et al.   NATURE BIOTECHNOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

(2015) Tianzhen Zhang et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

GbEXPATR, a species-specific expansin, enhances cotton fibre elongation through cell wall restructuring

(2015) Yang Li et al.   PLANT BIOTECHNOLOGY JOURNAL

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Genome sequence of the cultivated cotton Gossypium arboreum

(2014) Fuguang Li et al.   NATURE GENETICS

Silencing the vacuolar invertase geneGhVIN1blocks cotton fiber initiation from the ovule epidermis, probably by suppressing a cohort of regulatory genes via sugar signaling

(2014) Lu Wang et al.   PLANT JOURNAL

Control of vacuolar dynamics and regulation of stomatal aperture by tonoplast potassium uptake

(2014) Z. Andres et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Maize centromeres expand and adopt a uniform size in the genetic background of oat

(2013) K. Wang et al.   GENOME RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Dual Functions of WLIM1a in Cell Elongation and Secondary Wall Formation in Developing Cotton Fibers

(2013) L.-B. Han et al.   PLANT CELL

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

(2012) Andrew H. Paterson et al.   NATURE

Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research

(2012) Meiping Zhang et al.   Nature Protocols

MIPS PlantsDB: a database framework for comparative plant genome research

(2012) Thomas Nussbaumer et al.   NUCLEIC ACIDS RESEARCH

Repeatless and Repeat-Based Centromeres in Potato: Implications for Centromere Evolution

(2012) Z. Gong et al.   PLANT CELL

Ion Exchangers NHX1 and NHX2 Mediate Active Potassium Uptake into Vacuoles to Regulate Cell Turgor and Stomatal Function in Arabidopsis

(2012) V. Barragan et al.   PLANT CELL

The Cotton Centromere Contains a Ty3-gypsy-like LTR Retroelement

(2012) Song Luo et al.   PLoS One

How do plants feel the heat?

(2012) Ron Mittler et al.   TRENDS IN BIOCHEMICAL SCIENCES

Phytozome: a comparative platform for green plant genomics

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

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

TheArabidopsisNa+/H+Antiporters NHX1 and NHX2 Control Vacuolar pH and K+Homeostasis to Regulate Growth, Flower Development, and Reproduction

(2011) Elias Bassil et al.   PLANT CELL

Malate transport by the vacuolar AtALMT6 channel in guard cells is subject to multiple regulation

(2011) Stefan Meyer et al.   PLANT JOURNAL

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

(2010) A. McKenna et al.   GENOME RESEARCH

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

The genome of Theobroma cacao

(2010) Xavier Argout et al.   NATURE GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Evidence That High Activity of Vacuolar Invertase Is Required for Cotton Fiber and Arabidopsis Root Elongation through Osmotic Dependent and Independent Pathways, Respectively

(2010) L. Wang et al.   PLANT PHYSIOLOGY

ADP-ribosylation factor machinery mediates endocytosis in plant cells

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

ABA perception and signalling

(2010) Agepati S. Raghavendra et al.   TRENDS IN PLANT SCIENCE

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki 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

Developmental and molecular physiological evidence for the role of phosphoenolpyruvate carboxylase in rapid cotton fibre elongation

(2009) Xiao-Rong Li et al.   JOURNAL OF EXPERIMENTAL BOTANY

Intra- and extra-cellular excretion of carboxylates

(2009) Stefan Meyer et al.   TRENDS IN PLANT SCIENCE

Ethylene signaling: new levels of complexity and regulation

(2008) Mandy D Kendrick et al.   CURRENT OPINION IN PLANT BIOLOGY

genBlastA: Enabling BLAST to identify homologous gene sequences

(2008) R. She et al.   GENOME RESEARCH

Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph

(2008) Yonghui Wu et al.   PLoS Genetics