| scholarly article | Q13442814 |
| P50 | author | Thomas Brutnell | Q37624264 |
| P2093 | author name string | Lin Wang | |
| Pinghua Li | |||
| P2860 | cites work | Transcript length bias in RNA-seq data confounds systems biology | Q21093194 |
| Ultrafast and memory-efficient alignment of short DNA sequences to the human genome | Q21183894 | ||
| The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants | Q22065864 | ||
| The B73 Maize Genome: Complexity, Diversity, and Dynamics | Q22065899 | ||
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| RNA-Seq: a revolutionary tool for transcriptomics | Q24596169 | ||
| Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage | Q24616834 | ||
| The transcriptional landscape of the yeast genome defined by RNA sequencing | Q24633693 | ||
| Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening | Q24642779 | ||
| Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development | Q48064547 | ||
| Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing | Q48080987 | ||
| PASS: a program to align short sequences | Q51851743 | ||
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| Fast and accurate short read alignment with Burrows-Wheeler transform | Q24653853 | ||
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| Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing | Q29547470 | ||
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| Highly integrated single-base resolution maps of the epigenome in Arabidopsis | Q29616098 | ||
| Complementary DNA sequencing: expressed sequence tags and human genome project | Q29618255 | ||
| MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes | Q30004199 | ||
| Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis | Q30358980 | ||
| Single-molecule sequencing of an individual human genome | Q30434015 | ||
| Initial assessment of gene diversity for the oomycete pathogen Phytophthora infestans based on expressed sequences | Q30823597 | ||
| Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis | Q31095568 | ||
| Structure and architecture of the maize genome. | Q33229027 | ||
| Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology | Q33261408 | ||
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| Using quality scores and longer reads improves accuracy of Solexa read mapping | Q33321695 | ||
| Microarray analysis of vegetative phase change in maize | Q33345976 | ||
| Big impacts by small RNAs in plant development | Q33346279 | ||
| Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules | Q33347859 | ||
| Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats | Q33381867 | ||
| High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families | Q33391570 | ||
| Small RNA deep sequencing reveals role for Arabidopsis thaliana RNA-dependent RNA polymerases in viral siRNA biogenesis | Q33420820 | ||
| Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array | Q33456179 | ||
| Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data | Q33485579 | ||
| Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response | Q33493210 | ||
| Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response | Q33505863 | ||
| Navigating gene expression using microarrays--a technology review | Q34325306 | ||
| Comprehensive gene expression analysis by transcript profiling | Q34541419 | ||
| Genomewide comparative analysis of alternative splicing in plants | Q34598692 | ||
| Next-generation DNA sequencing techniques | Q34607452 | ||
| Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution | Q34779368 | ||
| Genetic properties of the maize nested association mapping population | Q34996053 | ||
| Direct RNA sequencing | Q35004834 | ||
| A pathway-specific microarray analysis highlights the complex and co-ordinated transcriptional networks of the developing grain of field-grown barley | Q35819928 | ||
| Profiling a plant: expression analysis in Arabidopsis | Q36732894 | ||
| Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant | Q36937105 | ||
| Epigenetic reprogramming and small RNA silencing of transposable elements in pollen | Q37142129 | ||
| Statistical inferences for isoform expression in RNA-Seq | Q37153258 | ||
| Computational and analytical framework for small RNA profiling by high-throughput sequencing | Q37168949 | ||
| A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level | Q37215414 | ||
| Genome-wide analyses of alternative splicing in plants: opportunities and challenges. | Q37231296 | ||
| Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing. | Q37293358 | ||
| Roles of plant small RNAs in biotic stress responses | Q37515393 | ||
| Short-read sequencing technologies for transcriptional analyses. | Q37539957 | ||
| Expression profiling of rice segregating for drought tolerance QTLs using a rice genome array | Q39060537 | ||
| Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa | Q39630513 | ||
| Quantification of the yeast transcriptome by single-molecule sequencing | Q39892179 | ||
| Deep sequencing of the zebrafish transcriptome response to mycobacterium infection. | Q39894345 | ||
| Rapid whole-genome mutational profiling using next-generation sequencing technologies | Q43012575 | ||
| A PCR-based platform for microRNA expression profiling studies | Q43155279 | ||
| Transcription profiling of soybean nodulation by Bradyrhizobium japonicum | Q44831797 | ||
| Trends in microarray analysis | Q46121545 | ||
| Microarray analysis of the interaction between the aphid Rhopalosiphum padi and host plants reveals both differences and similarities between susceptible and partially resistant barley lines. | Q46196909 | ||
| Gene expression analysis of light-modulated germination in tomato seeds. | Q46224941 | ||
| P433 | issue | 2 | |
| P921 | main subject | transcriptome | Q252857 |
| high-throughput sequencing | Q112147935 | ||
| P304 | page(s) | 118-128 | |
| P577 | publication date | 2010-02-03 | |
| P13046 | publication type of scholarly work | review article | Q7318358 |
| P1433 | published in | Briefings in functional genomics | Q26841935 |
| P1476 | title | Exploring plant transcriptomes using ultra high-throughput sequencing | |
| P478 | volume | 9 |
| Q34315594 | A bi-Poisson model for clustering gene expression profiles by RNA-seq |
| Q26822918 | A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data |
| Q44766747 | A guideline to family-wide comparative state-of-the-art quantitative RT-PCR analysis exemplified with a Brassicaceae cross-species seed germination case study |
| Q30000938 | A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq |
| Q38040652 | Accessing complex crop genomes with next-generation sequencing |
| Q30657447 | An optimal test with maximum average power while controlling FDR with application to RNA-seq data |
| Q38440087 | Analysis of de novo sequencing and transcriptome assembly and lignocellulolytic enzymes gene expression of Coriolopsis gallica HTC. |
| Q38465350 | Analysis of the tomato leaf transcriptome during successive hemibiotrophic stages of a compatible interaction with the oomycete pathogen Phytophthora infestans |
| Q36055863 | Application of Genomic Tools in Plant Breeding |
| Q33353249 | Cell type‐specific transcriptional profiling: implications for metabolite profiling |
| Q28703615 | Comparative transcriptome analysis to investigate the high starch accumulation of duckweed (Landoltia punctata) under nutrient starvation |
| Q35439677 | Comparative transcriptomic analysis of the response to cold acclimation in Eucalyptus dunnii |
| Q38444278 | Comparative transcriptomics of rice plants under cold, iron, and salt stresses. |
| Q36446217 | Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents |
| Q28534334 | Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data |
| Q60048475 | DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq Data |
| Q30830052 | De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification |
| Q34257320 | Digital gene expression analysis based on integrated de novo transcriptome assembly of sweet potato [Ipomoea batatas (L.) Lam]. |
| Q30717777 | Dispersion estimation and its effect on test performance in RNA-seq data analysis: a simulation-based comparison of methods |
| Q28485226 | Ectopic Overexpression of SlHsfA3, a Heat Stress Transcription Factor from Tomato, Confers Increased Thermotolerance and Salt Hypersensitivity in Germination in Transgenic Arabidopsis |
| Q28533610 | Ectopic Overexpression of SsCBF1, a CRT/DRE-Binding Factor from the Nightshade Plant Solanum lycopersicoides, Confers Freezing and Salt Tolerance in Transgenic Arabidopsis |
| Q28730848 | Exploring the Switchgrass Transcriptome Using Second-Generation Sequencing Technology |
| Q30938549 | From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data |
| Q27023985 | Frontiers in metabolic reconstruction and modeling of plant genomes |
| Q92236256 | Fully Bayesian analysis of RNA-seq counts for the detection of gene expression heterosis |
| Q37828623 | Gene expression analysis for the identification of selection and local adaptation in fishes |
| Q36939230 | Genome-Wide Transcriptome Profiling of Mycobacterium smegmatis MC² 155 Cultivated in Minimal Media Supplemented with Cholesterol, Androstenedione or Glycerol |
| Q92344173 | Gibberellin causes wide transcriptional modifications in the early stage of grape cluster development |
| Q36030800 | GpDSR7, a Novel E3 Ubiquitin Ligase Gene in Grimmia pilifera Is Involved in Tolerance to Drought Stress in Arabidopsis |
| Q33975961 | Green systems biology — From single genomes, proteomes and metabolomes to ecosystems research and biotechnology |
| Q41911239 | High throughput RNA sequencing of a hybrid maize and its parents shows different mechanisms responsive to nitrogen limitation |
| Q34416461 | High-throughput sequencing of black pepper root transcriptome |
| Q45012492 | Identifying differentially expressed genes under heat stress and developing molecular markers in orchardgrass (Dactylis glomerata L.) through transcriptome analysis |
| Q26849760 | Legume genomics: understanding biology through DNA and RNA sequencing |
| Q37512758 | Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos |
| Q35761806 | NGS technologies for analyzing germplasm diversity in genebanks. |
| Q45009119 | New approaches to Prunus transcriptome analysis |
| Q43017993 | Next-generation sequencing-based transcriptome profiling analysis of Pohlia nutans reveals insight into the stress-relevant genes in Antarctic moss |
| Q38199642 | Plant systems biology: insights, advances and challenges. |
| Q33631740 | RNA sequencing analysis of the gametophyte transcriptome from the liverwort, Marchantia polymorpha |
| Q37836977 | Regulatory mechanisms underlying C4 photosynthesis |
| Q28608474 | Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution |
| Q64054099 | Selection of reference genes for the quantitative real-time PCR normalization of gene expression in Isatis indigotica fortune |
| Q37860746 | Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses |
| Q24598955 | Setaria viridis: a model for C4 photosynthesis |
| Q38167317 | The transcriptomics of secondary growth and wood formation in conifers |
| Q35138984 | Transcriptome analysis of methyl jasmonate-elicited Panax ginseng adventitious roots to discover putative ginsenoside biosynthesis and transport genes |
| Q38248415 | Transcriptome characteristics of filamentous fungi deduced using high-throughput analytical technologies. |
| Q61798266 | Transcriptome-based identification and validation of reference genes for plant-bacteria interaction studies using Nicotiana benthamiana |
| Q34277521 | Transcriptome-wide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO2-concentrating mechanism regulator CIA5/CCM1. |
| Q34466870 | Transcriptomic analysis reveals tomato genes whose expression is induced specifically during effector-triggered immunity and identifies the Epk1 protein kinase which is required for the host response to three bacterial effector proteins |
| Q36314305 | Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato-Pseudomonas pathosystem |
| Q31050282 | What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment |
| Q33565173 | Why assembling plant genome sequences is so challenging |
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