Published in Plant Physiol on May 01, 2016
Transcriptomic Response of Purple Willow (Salix purpurea) to Arsenic Stress. Front Plant Sci (2017) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol (2010) 53.37
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75
Metagenomic analysis of the human distal gut microbiome. Science (2006) 29.76
The human microbiome project. Nature (2007) 28.53
Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics (2012) 26.90
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci U S A (1990) 24.42
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc (2013) 13.33
How many species are there on Earth and in the ocean? PLoS Biol (2011) 12.80
Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol Biochem (2010) 8.70
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet (2012) 8.55
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res (2012) 7.48
Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol (2003) 6.98
Unsuitability of using ribosomal RNA as loading control for Northern blot analyses related to the imbalance between messenger and ribosomal RNA content in rat mammary tumors. Anal Biochem (2001) 5.12
Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. J Exp Bot (2005) 5.09
Interactive metagenomic visualization in a Web browser. BMC Bioinformatics (2011) 5.03
EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics (2013) 4.79
Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat Genet (2014) 4.45
Validating internal controls for quantitative plant gene expression studies. BMC Plant Biol (2004) 4.45
Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods (2012) 4.43
Correlation of mRNA and protein in complex biological samples. FEBS Lett (2009) 4.38
A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics (2013) 4.36
beta-Actin and GAPDH housekeeping gene expression in asthmatic airways is variable and not suitable for normalising mRNA levels. Thorax (2002) 4.11
A Mutant of Arabidopsis thaliana Which Lacks Activation of RuBP Carboxylase In Vivo. Plant Physiol (1982) 4.08
When defense pathways collide. The response of Arabidopsis to a combination of drought and heat stress. Plant Physiol (2004) 3.80
Ecology drives a global network of gene exchange connecting the human microbiome. Nature (2011) 3.64
Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res (2004) 3.63
The genome of Tetranychus urticae reveals herbivorous pest adaptations. Nature (2011) 3.29
Field and pulping performances of transgenic trees with altered lignification. Nat Biotechnol (2002) 3.24
Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity (Edinb) (2010) 3.22
Identification and validation of reference genes for quantitative RT-PCR normalization in wheat. BMC Mol Biol (2009) 3.04
The splicing factors 9G8 and SRp20 transactivate splicing through different and specific enhancers. RNA (1999) 2.66
Identification of the gene for an Escherichia coli poly(A) polymerase. Proc Natl Acad Sci U S A (1992) 2.22
Development of transgenic yellow poplar for mercury phytoremediation. Nat Biotechnol (1998) 2.04
Differential roles of the universal stress proteins of Escherichia coli in oxidative stress resistance, adhesion, and motility. J Bacteriol (2005) 2.01
Phytoremediation of heavy metal-contaminated land by trees--a review. Environ Int (2003) 2.01
A unified mechanism of action for volatile isoprenoids in plant abiotic stress. Nat Chem Biol (2009) 1.93
Three-dimensional structure of transketolase, a thiamine diphosphate dependent enzyme, at 2.5 A resolution. EMBO J (1992) 1.87
Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions. BMC Mol Biol (2009) 1.75
Polyadenylation and degradation of human mitochondrial RNA: the prokaryotic past leaves its mark. Mol Cell Biol (2005) 1.67
Genome sequencing and population genomics in non-model organisms. Trends Ecol Evol (2013) 1.66
A Rapid and effective method for RNA extraction from different tissues of grapevine and other woody plants. Phytochem Anal (2008) 1.59
The limits of protein sequence comparison? Curr Opin Struct Biol (2005) 1.57
Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes. PLoS Biol (2015) 1.47
Microbiology: Microbiome science needs a healthy dose of scepticism. Nature (2014) 1.47
Antisense inhibition of the photosynthetic antenna proteins CP29 and CP26: implications for the mechanism of protective energy dissipation. Plant Cell (2001) 1.47
Phylogenetic relationships of American willows (Salix L., Salicaceae). PLoS One (2015) 1.45
Phytoremediation: plant-endophyte partnerships take the challenge. Curr Opin Biotechnol (2009) 1.42
Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat Rev Microbiol (2011) 1.39
mRNA decay in prokaryotes and eukaryotes: different approaches to a similar problem. IUBMB Life (2004) 1.38
Validation of endogenous controls for gene expression studies in human adipocytes and preadipocytes. Horm Metab Res (2001) 1.38
Rubisco regulation: a role for inhibitors. J Exp Bot (2008) 1.38
Upgrading root physiology for stress tolerance by ectomycorrhizas: insights from metabolite and transcriptional profiling into reprogramming for stress anticipation. Plant Physiol (2009) 1.37
RNAi-mediated suppression of p-coumaroyl-CoA 3'-hydroxylase in hybrid poplar impacts lignin deposition and soluble secondary metabolism. Proc Natl Acad Sci U S A (2008) 1.35
Metaorganisms as the new frontier. Zoology (Jena) (2011) 1.33
CP12 provides a new mode of light regulation of Calvin cycle activity in higher plants. Proc Natl Acad Sci U S A (1997) 1.33
Agriculture: Beyond food versus fuel. Nature (2011) 1.26
Transcript profiling of poplar leaves upon infection with compatible and incompatible strains of the foliar rust Melampsora larici-populina. Plant Physiol (2007) 1.24
The structure of photosystem II in Arabidopsis: localization of the CP26 and CP29 antenna complexes. Biochemistry (2003) 1.23
Evaluation of control transcripts in real-time RT-PCR expression analysis during maritime pine embryogenesis. Planta (2005) 1.21
De novo assembly of bacterial transcriptomes from RNA-seq data. Genome Biol (2015) 1.18
Having a BLAST with bioinformatics (and avoiding BLASTphemy). Genome Biol (2001) 1.15
Polyadenylation of mRNA in bacteria. Microbiology (1996) 1.13
De novo sequencing and transcriptome analysis of the desert shrub, Ammopiptanthus mongolicus, during cold acclimation using Illumina/Solexa. BMC Genomics (2013) 1.12
Single cystathionine β-synthase domain-containing proteins modulate development by regulating the thioredoxin system in Arabidopsis. Plant Cell (2011) 1.12
Thiamine in plants: aspects of its metabolism and functions. Phytochemistry (2010) 1.12
Selection of optimal reference genes for normalization in quantitative RT-PCR. BMC Bioinformatics (2010) 1.11
Evaluation of reference genes for gene expression studies in radish (Raphanus sativus L.) using quantitative real-time PCR. Biochem Biophys Res Commun (2012) 1.11
Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes. Proc Natl Acad Sci U S A (2012) 1.10
A role for SR proteins in plant stress responses. Plant Signal Behav (2011) 1.08
E6AP-dependent degradation of DLG4/PSD95 by high-risk human papillomavirus type 18 E6 protein. J Virol (2006) 1.08
Selection of housekeeping genes for normalization by real-time RT-PCR: analysis of Or-MYB1 gene expression in Orobanche ramosa development. Anal Biochem (2008) 1.06
Proteome analysis of cold stress response in Arabidopsis thaliana using DIGE-technology. J Exp Bot (2006) 1.06
Redox regulation of the Calvin-Benson cycle: something old, something new. Front Plant Sci (2013) 1.05
The upregulation of thiamine (vitamin B1) biosynthesis in Arabidopsis thaliana seedlings under salt and osmotic stress conditions is mediated by abscisic acid at the early stages of this stress response. BMC Plant Biol (2012) 1.04
Beyond transcription: RNA-binding proteins as emerging regulators of plant response to environmental constraints. Plant Sci (2011) 1.04
Light-harvesting chlorophyll a/b-binding proteins are required for stomatal response to abscisic acid in Arabidopsis. J Exp Bot (2011) 1.03
SpUSP, an annexin-interacting universal stress protein, enhances drought tolerance in tomato. J Exp Bot (2012) 1.02
Increasing phytoremediation efficiency and reliability using novel omics approaches. Trends Biotechnol (2014) 1.02
Microbial expression profiles in the rhizosphere of willows depend on soil contamination. ISME J (2013) 1.00
Enhancing phytoremediation through the use of transgenics and endophytes. New Phytol (2008) 1.00
Bacterial/archaeal/organellar polyadenylation. Wiley Interdiscip Rev RNA (2011) 1.00
Analysis of RNA decay, processing, and polyadenylation in Escherichia coli and other prokaryotes. Methods Enzymol (2008) 1.00
A transcriptomic network underlies microstructural and physiological responses to cadmium in Populus x canescens. Plant Physiol (2013) 0.99
Linkage between bacterial and fungal rhizosphere communities in hydrocarbon-contaminated soils is related to plant phylogeny. ISME J (2013) 0.99
Modulation of thiamine metabolism in Zea mays seedlings under conditions of abiotic stress. J Exp Bot (2008) 0.98
Increased fructose 1,6-bisphosphate aldolase in plastids enhances growth and photosynthesis of tobacco plants. J Exp Bot (2012) 0.98
Selection of suitable reference genes for qPCR normalization under abiotic stresses in Oenanthe javanica (BI.) DC. PLoS One (2014) 0.98
Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle. ISME J (2013) 0.97
Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences. Open Biol (2013) 0.96
Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic. Cell Rep (2015) 0.96
Metagenome analyses of corroded concrete wastewater pipe biofilms reveal a complex microbial system. BMC Microbiol (2012) 0.96
Tracking the best reference genes for RT-qPCR data normalization in filamentous fungi. BMC Genomics (2015) 0.93
Next Generation Sequencing Technologies: The Doorway to the Unexplored Genomics of Non-Model Plants. Front Plant Sci (2015) 0.90
Stress responses to polycyclic aromatic hydrocarbons in Arabidopsis include growth inhibition and hypersensitive response-like symptoms. J Exp Bot (2005) 0.90
Enhanced salt tolerance of transgenic poplar plants expressing a manganese superoxide dismutase from Tamarix androssowii. Mol Biol Rep (2010) 0.89