limma: Linear Models for Microarray Data

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7. A Novel Genomic Signature with Translational Significance for Human Idiopathic Pulmonary Fibrosis
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12. Double-Stranded RNA Induces an Antiviral Defense Status in Epidermal Keratinocytes through TLR3-, PKR-, and MDA5/RIG-I-Mediated Differential Signaling
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13. Integrated MicroRNA and mRNA Signatures Associated with Survival in Triple Negative Breast Cancer
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14. TRAIL induces apoptosis in triple-negative breast cancer cells with a mesenchymal phenotype
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15. Reduced Oct4 Expression Directs a Robust Pluripotent State with Distinct Signaling Activity and Increased Enhancer Occupancy by Oct4 and Nanog
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17. Epigenetic Regulator miRNA Pattern Differences Among SARS-CoV, SARS-CoV-2, and SARS-CoV-2 World-Wide Isolates Delineated the Mystery Behind the Epic Pathogenicity and Distinct Clinical Characteristics of Pandemic COVID-19
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18. Aberrant DNA methylation patterns of spermatozoa in men with unexplained infertility
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19. MicroRNA Expression Levels Are Altered in the Cerebrospinal Fluid of Patients with Young-Onset Alzheimer’s Disease
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20. Endometrial-Peritoneal Interactions during Endometriotic Lesion Establishment
    Mary Louise Hull, Claudia Rangel‐Escareño, Jane M. Godsland, John R. Doig, Claire M. Johnson, Stephen C. Phillips, S. Kaye Smith, Simon Tavaré, Cristin Gregor Print, David S. Jones · 2008 · American Journal Of Pathology
21. HDAC inhibitors attenuate the development of hypersensitivity in models of neuropathic pain
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22. Rescued Tolerant CD8 T Cells Are Preprogrammed to Reestablish the Tolerant State
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23. Using transcriptomics to identify and validate novel biomarkers of human skeletal muscle cancer cachexia
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24. Temporal Expression Patterns of Hormone Metabolism Genes during Imbibition of Arabidopsis thaliana Seeds: A Comparative Study on Dormant and Non-Dormant Accessions
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25. The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing
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26. Nuclear factor I/B is an oncogene in small cell lung cancer
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27. MicroRNA profiling of adrenocortical tumors reveals miR-483 as a marker of malignancy
    Patterson, Erin E., Holloway, Alisha K., Weng, Julie, Fojo, Tito, Kebebew, Electron · 2011 · Cancer
28. Anatomical and Transcriptomic Studies of the Coleorhiza Reveal the Importance of This Tissue in Regulating Dormancy in Barley
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29. Metabolic and Innate Immune Cues Merge into a Specific Inflammatory Response via the UPR
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30. The F-Box Protein ACRE189/ACIF1 Regulates Cell Death and Defense Responses Activated during Pathogen Recognition in Tobacco and Tomato
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31. Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells
    Patrício Godoy, Wolfgang Schmidt‐Heck, Karthick Natarajan, Baltasar Lucendo‐Villarin, Dagmara Szkolnicka, Annika Asplund, Petter Björquist, Agata Widera, Regina M. Stöber, Gisela Campos et al. · 2015 · Journal of Hepatology
32. IL-15 Regulates Homeostasis and Terminal Maturation of NKT Cells
    Laura E. Gordy, Jelena S. Bezbradica, Andrew I. Flyak, Charles T. Spencer, Alexis D. Dunkle, Jingchun Sun, Aleksandar K. Stanic, Mark Robin Boothby, You-Wen He, Zhongming Zhao et al. · 2011 · The Journal of Immunology
33. Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster
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34. Epidermal cell differentiation in cotton mediated by the homeodomain leucine zipper gene, GhHD‐1
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35. Severe Preeclampsia-Related Changes in Gene Expression at the Maternal-Fetal Interface Include Sialic Acid-Binding Immunoglobulin-Like Lectin-6 and Pappalysin-2
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36. The effects of long-term daily folic acid and vitamin B12 supplementation on genome-wide DNA methylation in elderly subjects
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37. The Human Cytomegalovirus–Encoded Chemokine Receptor US28 Promotes Angiogenesis and Tumor Formation via Cyclooxygenase-2
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38. microRNA Profiles in Parkinson's Disease Prefrontal Cortex
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39. Analysis of Global and Absorption, Distribution, Metabolism, and Elimination Gene Expression in the Progressive Stages of Human Nonalcoholic Fatty Liver Disease
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40. Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory
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41. Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree
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42. Human bronchial epithelial cells exposed in vitro to cigarette smoke at the air-liquid interface resemble bronchial epithelium from human smokers
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43. Comparative Analysis of the σB-Dependent Stress Responses inListeria monocytogenesandListeria innocuaStrains Exposed to Selected Stress Conditions
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44. A framework for understanding gene expression plasticity and its influence on stress tolerance
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45. Human Monocyte Subsets Are Transcriptionally and Functionally Altered in Aging in Response to Pattern Recognition Receptor Agonists
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46. Improved biclustering of microarray data demonstrated through systematic performance tests
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47. Annotating Genes of Known and Unknown Function by Large-Scale Coexpression Analysis
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48. Gene Expression Profiling of the Human Maternal-Fetal Interface Reveals Dramatic Changes between Midgestation and Term
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50. In Vivo Interference with AtTCP20 Function Induces Severe Plant Growth Alterations and Deregulates the Expression of Many Genes Important for Development
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52. Gene set enrichment analysis for genome-wide DNA methylation data
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57. A panel of genes methylated with high frequency in colorectal cancer
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58. MicroRNA-145 Targets YES and STAT1 in Colon Cancer Cells
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60. Osteoactivin Promotes Breast Cancer Metastasis to Bone
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61. Transcriptional responses of Arabidopsis thaliana ecotypes with different glucosinolate profiles after attack by polyphagous Myzus persicae and oligophagous Brevicoryne brassicae
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63. Association of PD-1/PD-L axis expression with cytolytic activity, mutational load, and prognosis in melanoma and other solid tumors
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64. MED18 interaction with distinct transcription factors regulates multiple plant functions
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66. Human Papillomavirus Deregulates the Response of a Cellular Network Comprising of Chemotactic and Proinflammatory Genes
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67. Identification of novel markers in rheumatoid arthritis through integrated analysis of DNA methylation and microRNA expression
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70. Evidence of Chronic Allograft Injury in Liver Biopsies From Long-term Pediatric Recipients of Liver Transplants
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71. DNA hypermethylation and DNA hypomethylation is present at different loci in chronic kidney disease
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72. Gene expression profiling–based dissection of MLL translocated and MLL germline acute lymphoblastic leukemia in infants
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76. Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells
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77. Soybean Homologs of MPK4 Negatively Regulate Defense Responses and Positively Regulate Growth and Development
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78. Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana
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79. Transcription profiling of a recently colonised pyrethroid resistant Anopheles gambiae strain from Ghana
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80. Obesity impairs short-term and working memory through gut microbial metabolism of aromatic amino acids
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81. Specific promoter methylation identifies different subgroups of MLL-rearranged infant acute lymphoblastic leukemia, influences clinical outcome, and provides therapeutic options
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82. PLZF expression maps the early stages of ILC1 lineage development
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83. Estrogen induces apoptosis in estrogen deprivation-resistant breast cancer through stress responses as identified by global gene expression across time
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84. Molecular Distinctions between Stasis and Telomere Attrition Senescence Barriers Shown by Long-term Culture of Normal Human Mammary Epithelial Cells
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85. Development and clinical validity of a novel blood-based molecular biomarker for subclinical acute rejection following kidney transplant
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86. Time of day shapes Arabidopsis drought transcriptomes
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87. Long-term in vitro culture of grape berries and its application to assess the effects of sugar supply on anthocyanin accumulation
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88. Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells
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89. A Variant in the Neuropeptide Receptor npr-1 is a Major Determinant of Caenorhabditis elegans Growth and Physiology
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90. Down-weighting overlapping genes improves gene set analysis
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91. Deep sequencing reveals complex mechanisms of diapause preparation in the invasive mosquito, Aedes albopictus
    Monica F. Poelchau, Julie A. Reynolds, Christine G. Elsik, David L. Denlinger, Peter Armbruster · 2013 · Proceedings of the Royal Society B Biological Sciences
92. A chloroplast retrograde signal, 3’-phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination
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93. The Mouse Cytosine-5 RNA Methyltransferase NSun2 Is a Component of the Chromatoid Body and Required for Testis Differentiation
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