The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies

An RNA-Seq based gene expression atlas of the common bean

(2014) Jamie A O’Rourke et al.   BMC GENOMICS

De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification

(2014) Steven A Yates et al.   BMC GENOMICS

Cold acclimation, de-acclimation and re-acclimation of spring canola, winter canola and winter wheat: The role of carbohydrates, cold-induced stress proteins and vernalization

(2014) Russell G. Trischuk et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

A reference genome for common bean and genome-wide analysis of dual domestications

(2014) Jeremy Schmutz et al.   NATURE GENETICS

A plant-specificHUA2-LIKE(HULK) gene family inArabidopsis thalianais essential for development

(2014) Sathya S. Jali et al.   PLANT JOURNAL

Development of an Alfalfa SNP Array and Its Use to Evaluate Patterns of Population Structure and Linkage Disequilibrium

(2014) Xuehui Li et al.   PLoS One

A Saturated Genetic Linkage Map of Autotetraploid Alfalfa ( Medicago sativa L.) Developed Using Genotyping-by-Sequencing Is Highly Syntenous with the Medicago truncatula Genome

(2014) Xuehui Li et al.   G3-Genes Genomes Genetics

Characterization of a novel Medicago sativa NAC transcription factor gene involved in response to drought stress

(2013) Yong Xin Wang   MOLECULAR BIOLOGY REPORTS

Increased β-Cyanoalanine Nitrilase Activity Improves Cyanide Tolerance and Assimilation in Arabidopsis

(2013) Brendan O'Leary et al.   Molecular Plant

Analysis of the Alfalfa Root Transcriptome in Response to Salinity Stress

(2013) Olga A. Postnikova et al.   PLANT AND CELL PHYSIOLOGY

Replication protein A subunit 3 and the iron efficiency response in soybean

(2013) SARAH E. ATWOOD et al.   PLANT CELL AND ENVIRONMENT

Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants

(2013) W.-k. Jiang et al.   PLANT PHYSIOLOGY

Nod factor perception protein carries weight in biotic interactions

(2013) Clare Gough et al.   TRENDS IN PLANT SCIENCE

ATAF1 transcription factor directly regulates abscisic acid biosynthetic gene NCED3 in Arabidopsis thaliana

(2013) Michael Krogh Jensen et al.   FEBS Open Bio

Control ofArabidopsisRoot Development

(2012) Jalean J. Petricka et al.   Annual Review of Plant Biology

Phosphoinositide Signaling

(2012) Wendy F. Boss et al.   Annual Review of Plant Biology

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

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

(2012) Limin Fu et al.   BIOINFORMATICS

Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing

(2012) Xuehui Li et al.   BMC GENOMICS

Deep Sequencing Identifies Viral and Wasp Genes with Potential Roles in Replication of Microplitis demolitor Bracovirus

(2012) G. R. Burke et al.   JOURNAL OF VIROLOGY

Understanding plant cold hardiness: an opinion

(2012) Lawrence V. Gusta et al.   PHYSIOLOGIA PLANTARUM

An RNA-Seq Transcriptome Analysis of Orthophosphate-Deficient White Lupin Reveals Novel Insights into Phosphorus Acclimation in Plants

(2012) J. A. O'Rourke et al.   PLANT PHYSIOLOGY

The Cassava Genome: Current Progress, Future Directions

(2012) Simon Prochnik et al.   Tropical Plant Biology

Applied Genetics and Genomics in Alfalfa Breeding

(2012) Xuehui Li et al.   Agronomy-Basel

Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing

(2011) Susanne U Franssen et al.   BMC GENOMICS

Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis

(2011) Yuanhong Han et al.   BMC GENOMICS

Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery

(2011) Sukhjiwan Kaur et al.   BMC GENOMICS

Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

(2011) S Samuel Yang et al.   BMC GENOMICS

SND2, a NAC transcription factor gene, regulates genes involved in secondary cell wall development in Arabidopsis fibres and increases fibre cell area in Eucalyptus

(2011) Steven G Hussey et al.   BMC PLANT BIOLOGY

Defining the Transcriptome Assembly and Its Use for Genome Dynamics and Transcriptome Profiling Studies in Pigeonpea (Cajanus cajan L.)

(2011) A. Dubey et al.   DNA RESEARCH

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway

(2011) Imène Hichri et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes

(2011) J. Li et al.   NUCLEIC ACIDS RESEARCH

The effects of phenotypic plasticity on photosynthetic performance in winter rye, winter wheat and Brassica napus

(2011) Keshav Dahal et al.   PHYSIOLOGIA PLANTARUM

Never too many? How legumes control nodule numbers

(2011) VIRGINIE MORTIER et al.   PLANT CELL AND ENVIRONMENT

Downregulation of putative UDP-glucose: flavonoid 3-O-glucosyltransferase gene alters flower coloring in Phalaenopsis

(2011) Wen-Huei Chen et al.   PLANT CELL REPORTS

System responses to long-term drought and re-watering of two contrasting alfalfa varieties

(2011) Yun Kang et al.   PLANT JOURNAL

The Soybean Rhg1 Locus for Resistance to the Soybean Cyst Nematode Heterodera glycines Regulates the Expression of a Large Number of Stress- and Defense-Related Genes in Degenerating Feeding Cells

(2011) P. K. Kandoth et al.   PLANT PHYSIOLOGY

Comparative studies on tolerance of Medicago truncatula and Medicago falcata to freezing

(2011) Li-Li Zhang et al.   PLANTA

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

Protection of Sinorhizobium against Host Cysteine-Rich Antimicrobial Peptides Is Critical for Symbiosis

(2011) Andreas F. Haag et al.   PLOS BIOLOGY

The regulation of carotenoid pigmentation in flowers

(2010) Changfu Zhu et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

(2010) Andrew J Severin et al.   BMC PLANT BIOLOGY

Power of Deep Sequencing and Agilent Microarray for Gene Expression Profiling Study

(2010) Lin Feng et al.   MOLECULAR BIOTECHNOLOGY

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Asparagine as a major factor in the N-feedback regulation of N2 fixation in Medicago truncatula

(2010) Saad Sulieman et al.   PHYSIOLOGIA PLANTARUM

How Many Peas in a Pod? Legume Genes Responsible for Mutualistic Symbioses Underground

(2010) H. Kouchi et al.   PLANT AND CELL PHYSIOLOGY

VND-INTERACTING2, a NAC Domain Transcription Factor, Negatively Regulates Xylem Vessel Formation inArabidopsis

(2010) Masatoshi Yamaguchi et al.   PLANT CELL

Walls are thin 1 (WAT1), an Arabidopsis homolog of Medicago truncatula NODULIN21, is a tonoplast-localized protein required for secondary wall formation in fibers

(2010) Philippe Ranocha et al.   PLANT JOURNAL

Plant Peptides Govern Terminal Differentiation of Bacteria in Symbiosis

(2010) W. Van de Velde et al.   SCIENCE

Single-Feature Polymorphism Discovery in the Transcriptome of Tetraploid Alfalfa

(2009) S. Samuel Yang et al.   Plant Genome

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

A gene expression atlas of the model legumeMedicago truncatula

(2008) Vagner A. Benedito et al.   PLANT JOURNAL

Comparative Genomic Sequence and Expression Analyses of Medicago truncatula and Alfalfa Subspecies falcata COLD-ACCLIMATION-SPECIFIC Genes

(2008) J. C. Pennycooke et al.   PLANT PHYSIOLOGY

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE