RNA-Seq: a revolutionary tool for transcriptomics

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2. Transcriptomic characterization of cold acclimation in larval zebrafish
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3. Full‐length de novo assembly of RNA‐seq data in pea ( P isum sativum L.) provides a gene expression atlas and gives insights into root nodulation in this species
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4. Zebrafish Get Connected: Investigating Neurotransmission Targets and Alterations in Chemical Toxicity
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5. Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis
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6. A meta-analysis of gene expression-based biomarkers predicting outcome after tamoxifen treatment in breast cancer
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7. Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
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8. Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library
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9. Platforms for Investigating LncRNA Functions
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10. Classification and clustering of sequencing data using a Poisson model
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11. Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa
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12. Bipartite graphs in systems biology and medicine: a survey of methods and applications
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13. Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing
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14. Gene expression profiling by mRNA sequencing reveals increased expression of immune/inflammation-related genes in the hippocampus of individuals with schizophrenia
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15. Arabidopsis Floral Initiator SKB1 Confers High Salt Tolerance by Regulating Transcription and Pre-mRNA Splicing through Altering Histone H4R3 and Small Nuclear Ribonucleoprotein LSM4 Methylation
    Zhaoliang Zhang, Shupei Zhang, Ya Zhang, Xin Wang, Dan Li, Qiuling Li, Minghui Yue, Qun Li, Yue Zhang, Yunyuan Xu et al. · 2011 · The Plant Cell
16. An Overview of Machine Learning and Big Data for Drug Toxicity Evaluation
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17. Applied Genetics and Genomics in Alfalfa Breeding
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18. Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types
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19. Interplay between Biomaterials and the Immune System: Perspective on Challenges and Opportunities in Regenerative Medicine
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20. Proteomics in evolutionary ecology: linking the genotype with the phenotype
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21. The Past and Future of Tuberculosis Research
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22. Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science
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23. Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data
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24. Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant (Camellia sinensis)
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25. From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites
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26. Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets
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27. A model based criterion for gene expression calls using RNA-seq data
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28. Zinc Oxide Nanoparticles Cause Inhibition of Microbial Denitrification by Affecting Transcriptional Regulation and Enzyme Activity
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29. Environmental RNA: A Revolution in Ecological Resolution?
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30. Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next‐gen approaches
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31. Integrating transcriptome and proteome profiling: Strategies and applications
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32. Recommendation on Design, Execution, and Reporting of Animal Atherosclerosis Studies: A Scientific Statement From the American Heart Association
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33. De Novo Origin of Human Protein-Coding Genes
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34. Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics
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35. Circular RNAs in Brain and Other Tissues: A Functional Enigma
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36. Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique
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37. Garbage in, garbage out: A critical evaluation of strategies used for validation of immunohistochemical biomarkers
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38. Non-model organisms, a species endangered by proteogenomics
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39. Conserved developmental transcriptomes in evolutionarily divergent species
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40. READemption—a tool for the computational analysis of deep-sequencing–based transcriptome data
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41. Self-Amplifying mRNA Vaccines
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42. Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling
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43. Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers
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44. PANOMICS meets germplasm
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45. Advances in AI and machine learning for predictive medicine
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46. An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era
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47. Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay
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48. NGS Technologies as a Turning Point in Rare Disease Research , Diagnosis and Treatment
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49. Genome-wide Transcriptional Profiling of Appressorium Development by the Rice Blast Fungus Magnaporthe oryzae
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50. Next-generation sequencing and its applications in molecular diagnostics
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51. Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants
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52. Estimation of alternative splicing isoform frequencies from RNA-Seq data
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53. A single molecule view of gene expression
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54. Old Trade, New Tricks: Insights into the Spontaneous Mutation Process from the Partnering of Classical Mutation Accumulation Experiments with High-Throughput Genomic Approaches
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55. Creating reference gene annotation for the mouse C57BL6/J genome assembly
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56. A simple guide to de novo transcriptome assembly and annotation
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57. Differential Expression Analysis of Complex RNA-seq Experiments Using edgeR
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58. Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution
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59. Bioinformatics analysis of mass spectrometry‐based proteomics data sets
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60. Heart Failure–Associated Changes in RNA Splicing of Sarcomere Genes
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61. TU-tagging: cell type–specific RNA isolation from intact complex tissues
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62. Speciation genetics: current status and evolving approaches
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63. Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation
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64. Genome-wide identification, phylogeny, and expression analysis of the SWEET gene family in tomato
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65. Cell‐type specific analysis of translating RNAs in developing flowers reveals new levels of control
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66. RNA-Seq Analysis of Human Trigeminal and Dorsal Root Ganglia with a Focus on Chemoreceptors
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67. De novo derivation of proteomes from transcriptomes for transcript and protein identification
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68. Comparative Transcriptome Analyses Indicate Molecular Homology of Zebrafish Swimbladder and Mammalian Lung
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69. MicroRNAs in adipose tissue: their role in adipogenesis and obesity
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70. Investigating the molecular basis of local adaptation to thermal stress: population differences in gene expression across the transcriptome of the copepod Tigriopus californicus
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71. Global Analysis of the Transcriptional Response of Whitefly to Tomato Yellow Leaf Curl China Virus Reveals the Relationship of Coevolved Adaptations
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72. Practical low‐coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species
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73. A four‐gene‐based prognostic model predicts overall survival in patients with hepatocellular carcinoma
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74. Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data
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75. Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application
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76. Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis
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77. Cis and Trans Acting Factors Involved in Human Cytomegalovirus Experimental and Natural Latent Infection of CD14 (+) Monocytes and CD34 (+) Cells
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78. Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish
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79. Plant-associated fungal communities in the light of meta’omics
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80. Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
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83. Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.]
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84. Controlling false discoveries in high-dimensional situations: boosting with stability selection
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85. Comparative Evolutionary and Developmental Dynamics of the Cotton (Gossypium hirsutum) Fiber Transcriptome
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86. Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing
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87. Transforming RNA-Seq Data to Improve the Performance of Prognostic Gene Signatures
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88. Catalyzing plant science research with RNA-seq
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89. Cryptosporidium: parasite and disease
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90. Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis
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91. Deep sequencing the circadian and diurnal transcriptome ofDrosophilabrain
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92. AutoImpute: Autoencoder based imputation of single-cell RNA-seq data
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93. Understanding transcriptional regulation by integrative analysis of transcription factor binding data
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94. Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes
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95. Transcriptome Dynamics of the Stomatal Lineage: Birth, Amplification, and Termination of a Self-Renewing Population
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96. Generating and navigating proteome maps using mass spectrometry
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97. Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples
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99. What triggers grass endophytes to switch from mutualism to pathogenism?
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100. Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money
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