Published in Nat Genet on October 31, 2010
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci U S A (2011) 2.97
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics (2011) 2.88
Deep evolutionary comparison of gene expression identifies parallel recruitment of trans-factors in two independent origins of C4 photosynthesis. PLoS Genet (2014) 1.70
A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq. PLoS One (2011) 1.60
Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq. Plant Physiol (2012) 1.58
Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid. BMC Genomics (2011) 1.57
RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing. Plant Physiol (2013) 1.55
Heritable epigenetic variation among maize inbreds. PLoS Genet (2011) 1.54
De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics (2011) 1.45
Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol (2014) 1.45
Retracted Ectopic expression of a maize hybrid down-regulated gene ZmARF25 decreases organ size by affecting cellular proliferation in Arabidopsis. PLoS One (2014) 1.44
Evolution of C4 photosynthesis in the genus Flaveria: how many and which genes does it take to make C4? Plant Cell (2011) 1.43
Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays. PLoS One (2013) 1.40
MaizeGDB: curation and outreach go hand-in-hand. Database (Oxford) (2011) 1.39
Systems analysis of a maize leaf developmental gradient redefines the current C4 model and provides candidates for regulation. Plant Cell (2011) 1.38
Analysis of the Arabidopsis shoot meristem transcriptome during floral transition identifies distinct regulatory patterns and a leucine-rich repeat protein that promotes flowering. Plant Cell (2012) 1.36
RNA structure and the mechanisms of alternative splicing. Curr Opin Genet Dev (2011) 1.35
Ontogeny of the maize shoot apical meristem. Plant Cell (2012) 1.26
Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Res (2012) 1.26
RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug. BMC Genomics (2012) 1.26
Ribulose-1,5-bis-phosphate carboxylase/oxygenase accumulation factor1 is required for holoenzyme assembly in maize. Plant Cell (2012) 1.25
C4 cycles: past, present, and future research on C4 photosynthesis. Plant Cell (2011) 1.24
Dynamic transcriptome landscape of maize embryo and endosperm development. Plant Physiol (2014) 1.24
Characterizing regulatory and functional differentiation between maize mesophyll and bundle sheath cells by transcriptomic analysis. Plant Physiol (2012) 1.18
Transcriptomic profiling of the salt-stress response in the wild recretohalophyte Reaumuria trigyna. BMC Genomics (2013) 1.18
Evolution of C4 photosynthesis in the genus flaveria: establishment of a photorespiratory CO2 pump. Plant Cell (2013) 1.18
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Control of leaf expansion: a developmental switch from metabolics to hydraulics. Plant Physiol (2011) 1.14
De novo sequencing and transcriptome analysis of the desert shrub, Ammopiptanthus mongolicus, during cold acclimation using Illumina/Solexa. BMC Genomics (2013) 1.12
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing. PLoS One (2013) 1.12
Inhibition of tiller bud outgrowth in the tin mutant of wheat is associated with precocious internode development. Plant Physiol (2012) 1.09
Parallel proteomic and phosphoproteomic analyses of successive stages of maize leaf development. Plant Cell (2013) 1.08
Taking the next step: building an Arabidopsis information portal. Plant Cell (2012) 1.06
Genome-wide detection of condition-sensitive alternative splicing in Arabidopsis roots. Plant Physiol (2013) 1.03
ZCN8 encodes a potential orthologue of Arabidopsis FT florigen that integrates both endogenous and photoperiod flowering signals in maize. J Exp Bot (2011) 1.02
Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa. BMC Genomics (2013) 1.00
Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize. Genome Res (2013) 0.99
Mendelian and non-Mendelian regulation of gene expression in maize. PLoS Genet (2013) 0.99
Transcriptome analysis of orange-spotted grouper (Epinephelus coioides) spleen in response to Singapore grouper iridovirus. BMC Genomics (2011) 0.98
Time series expression analyses using RNA-seq: a statistical approach. Biomed Res Int (2013) 0.98
Regulatory modules controlling maize inflorescence architecture. Genome Res (2013) 0.97
Maize centromeres expand and adopt a uniform size in the genetic background of oat. Genome Res (2013) 0.97
De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. BMC Genomics (2013) 0.97
The proteome of copper, iron, zinc, and manganese micronutrient deficiency in Chlamydomonas reinhardtii. Mol Cell Proteomics (2012) 0.97
Developmental dynamics of Kranz cell transcriptional specificity in maize leaf reveals early onset of C4-related processes. J Exp Bot (2014) 0.96
Evolutionary convergence of cell-specific gene expression in independent lineages of C4 grasses. Plant Physiol (2014) 0.95
The differential transcription network between embryo and endosperm in the early developing maize seed. Plant Physiol (2013) 0.95
An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays. Mol Cell Proteomics (2013) 0.95
Anatomical and transcriptional dynamics of maize embryonic leaves during seed germination. Proc Natl Acad Sci U S A (2013) 0.95
High-throughput approaches for plant epigenomic studies. Curr Opin Plant Biol (2011) 0.95
De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. PLoS One (2014) 0.94
Tomato GOLDEN2-LIKE transcription factors reveal molecular gradients that function during fruit development and ripening. Plant Cell (2014) 0.94
In situ hybridization for the precise localization of transcripts in plants. J Vis Exp (2011) 0.93
A Limited Role for Carbonic Anhydrase in C4 Photosynthesis as Revealed by a ca1ca2 Double Mutant in Maize. Plant Physiol (2014) 0.92
RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications. BMC Plant Biol (2014) 0.92
Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model. Plant Physiol (2014) 0.92
Arabidopsis and maize RidA proteins preempt reactive enamine/imine damage to branched-chain amino acid biosynthesis in plastids. Plant Cell (2014) 0.92
Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize. Plant Cell (2014) 0.91
Transcriptome sequencing and comparative analysis of Saccharina japonica (Laminariales, Phaeophyceae) under blue light induction. PLoS One (2012) 0.91
Adaptation of maize source leaf metabolism to stress related disturbances in carbon, nitrogen and phosphorus balance. BMC Genomics (2013) 0.91
The ZmASR1 protein influences branched-chain amino acid biosynthesis and maintains kernel yield in maize under water-limited conditions. Plant Physiol (2011) 0.91
Cellulose Synthase-Like D1 is integral to normal cell division, expansion, and leaf development in maize. Plant Physiol (2011) 0.90
Transcriptome profiling of the cold response and signaling pathways in Lilium lancifolium. BMC Genomics (2014) 0.89
Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population. Genome Biol (2015) 0.89
Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population. Plant Physiol (2014) 0.89
Mechanism of cytoplasmic mRNA translation. Arabidopsis Book (2015) 0.89
Engineering crassulacean acid metabolism to improve water-use efficiency. Trends Plant Sci (2014) 0.88
Heterosis in early maize ear inflorescence development: a genome-wide transcription analysis for two maize inbred lines and their hybrid. Int J Mol Sci (2014) 0.88
New approaches to Prunus transcriptome analysis. Genetica (2011) 0.88
Functional genomics of a generalist parasitic plant: laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression. BMC Plant Biol (2013) 0.88
Pyrosequencing of the Camptotheca acuminata transcriptome reveals putative genes involved in camptothecin biosynthesis and transport. BMC Genomics (2011) 0.88
Identification of PAN2 by quantitative proteomics as a leucine-rich repeat-receptor-like kinase acting upstream of PAN1 to polarize cell division in maize. Plant Cell (2012) 0.88
Dynamic transcriptomic profiles between tomato and a wild relative reflect distinct developmental architectures. Plant Physiol (2013) 0.88
The maize glossy13 gene, cloned via BSR-Seq and Seq-walking encodes a putative ABC transporter required for the normal accumulation of epicuticular waxes. PLoS One (2013) 0.88
Parallel recruitment of multiple genes into c4 photosynthesis. Genome Biol Evol (2013) 0.88
Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species. J Exp Bot (2014) 0.87
Dynamics of Chloroplast Translation during Chloroplast Differentiation in Maize. PLoS Genet (2016) 0.87
Genetic and genomic toolbox of Zea mays. Genetics (2015) 0.86
A Secreted Effector Protein of Ustilago maydis Guides Maize Leaf Cells to Form Tumors. Plant Cell (2015) 0.86
Identification of Photosynthesis-Associated C4 Candidate Genes through Comparative Leaf Gradient Transcriptome in Multiple Lineages of C3 and C4 Species. PLoS One (2015) 0.86
Comparative genomic analysis of the R2R3 MYB secondary cell wall regulators of Arabidopsis, poplar, rice, maize, and switchgrass. BMC Plant Biol (2014) 0.86
Regulation of the photorespiratory GLDPA gene in C(4) flaveria: an intricate interplay of transcriptional and posttranscriptional processes. Plant Cell (2012) 0.86
Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species. Plant Cell (2014) 0.86
Function of PPR proteins in plastid gene expression. RNA Biol (2013) 0.85
An overview of gene expression dynamics during early ovarian folliculogenesis: specificity of follicular compartments and bi-directional dialog. BMC Genomics (2013) 0.85
The tomato genome: implications for plant breeding, genomics and evolution. Genome Biol (2012) 0.85
Drought Induces Distinct Growth Response, Protection, and Recovery Mechanisms in the Maize Leaf Growth Zone. Plant Physiol (2015) 0.85
A novel RNA binding protein affects rbcL gene expression and is specific to bundle sheath chloroplasts in C4 plants. BMC Plant Biol (2013) 0.85
A thylakoid membrane protein harboring a DnaJ-type zinc finger domain is required for photosystem I accumulation in plants. J Biol Chem (2014) 0.85
Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maize. BMC Genomics (2015) 0.85
Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit. J Exp Bot (2015) 0.84
DEXUS: identifying differential expression in RNA-Seq studies with unknown conditions. Nucleic Acids Res (2013) 0.84
Transcriptome dynamics of a desert poplar (Populus pruinosa) in response to continuous salinity stress. Plant Cell Rep (2014) 0.84
Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome. PLoS One (2016) 0.84
Transcriptome analysis of embryo maturation in maize. BMC Plant Biol (2013) 0.84
Towards an improved apple reference transcriptome using RNA-seq. Mol Genet Genomics (2014) 0.84
Genome-wide identification, evolution and expression analysis of mTERF gene family in maize. PLoS One (2014) 0.84
Reactive oxygen species regulate leaf pulvinus abscission zone cell separation in response to water-deficit stress in cassava. Sci Rep (2016) 0.84
ZmbZIP60 mRNA is spliced in maize in response to ER stress. BMC Res Notes (2012) 0.84
Pistillody mutant reveals key insights into stamen and pistil development in wheat (Triticum aestivum L.). BMC Genomics (2015) 0.84
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