Moderated statistical tests for assessing differences in tag abundance

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3. Transcriptome profiling of brown adipose tissue during cold exposure reveals extensive regulation of glucose metabolism
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4. Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments
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5. Adaptive Modifications of Muscle Phenotype in High-Altitude Deer Mice Are Associated with Evolved Changes in Gene Regulation
   Graham R. Scott, Todd S. Elogio, Mikaela A. Lui, Jay F. Storz, Zachary A. Cheviron · 2015 · Molecular Biology and Evolution
6. NanoStringDiff: a novel statistical method for differential expression analysis based on NanoString nCounter data
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7. Loss of RNA–Dependent RNA Polymerase 2 (RDR2) Function Causes Widespread and Unexpected Changes in the Expression of Transposons, Genes, and 24-nt Small RNAs
   Yi Jia, Damon R. Lisch, Kazuhiro Ohtsu, Michael J. Scanlon, Dan S. Nettleton, Patrick S. Schnable · 2009 · PLoS Genetics
8. Transcriptional responses of three model diatoms to nitrate limitation of growth
   Sara J. Bender, Colleen A. Durkin, Chris T. Berthiaume, Rhonda L. Morales, E. Virginia Armbrust · 2014 · Frontiers in Marine Science
9. Mutant U2AF1-expressing cells are sensitive to pharmacological modulation of the spliceosome
   Cara Lunn Shirai, Brian S. White, Manorama Tripathi, ROBERTO C. TAPIA-CONYER, James N. Ley, Matthew Ndonwi, Sanghyun Peter Kim, Jin Shao, Alexa Carver, Borja Sáez et al. · 2017 · Nature Communications
10. bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data
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11. Dual regulation by microRNA-200b-3p and microRNA-200b-5p in the inhibition of epithelial-to-mesenchymal transition in triple-negative breast cancer
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12. De Novo Assembly of the Manila Clam Ruditapes philippinarum Transcriptome Provides New Insights into Expression Bias, Mitochondrial Doubly Uniparental Inheritance and Sex Determination
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14. Normalization, bias correction, and peak calling for ChIP-seq
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15. Induction of fibroblast senescence generates a non-fibrogenic myofibroblast phenotype that differentially impacts on cancer prognosis
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16. Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis
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17. DiMSum: an error model and pipeline for analyzing deep mutational scanning data and diagnosing common experimental pathologies
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18. Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR
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19. High-Throughput RNA Sequencing of Pseudomonas-Infected Arabidopsis Reveals Hidden Transcriptome Complexity and Novel Splice Variants
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20. A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data
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21. FUNCTIONAL GENOMICS OF ADAPTATION TO HYPOXIC COLD-STRESS IN HIGH-ALTITUDE DEER MICE: TRANSCRIPTOMIC PLASTICITY AND THERMOGENIC PERFORMANCE
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22. Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain
    Courtney C. Babbitt, Olivier D. Fedrigo, Adam D. Pfefferle, Alan P. Boyle, Julie E. Horvath, Terrence S. Furey, Gregory A. Wray · 2010 · Genome Biology and Evolution
23. Functional genomics analysis of vitamin D effects on CD4+ T cells in vivo in experimental autoimmune encephalomyelitis
    Manuel Zeitelhofer, Milena Z. Adzemovic, David Gómez-Cabrero, Petra Bergman, Sonja Hochmeister, Marie N’diaye, Atul Paulson, Sabrina Ruhrmann, Malin Almgren, Jesper N. Tegner et al. · 2017 · Proceedings of the National Academy of Sciences
24. Transcriptomic Analyses of Sexual Dimorphism of the Zebrafish Liver and the Effect of Sex Hormones
    Weiling Zheng, Hongyan Xu, Siew Hong Lam, Huaien Luo, Radha Krishna Murthy Karuturi, Zhiyuan Gong · 2013 · PLoS ONE
25. Single-cell transcriptomics unveils xylem cell development and evolution
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26. Off-Target Effect of doublecortin Family shRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation
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27. RnaSeqSampleSize: real data based sample size estimation for RNA sequencing
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28. Differentially Expressed Transcripts and Dysregulated Signaling Pathways and Networks in African American Breast Cancer
    Paul A. Stewart, Jennifer Luks, Mark D. Roycik, Qing‐Xiang Amy Sang, Jinfeng Zhang · 2013 · PLoS ONE
29. Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training
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30. DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics
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31. The transcriptional signature of human ovarian carcinoma macrophages is associated with extracellular matrix reorganization
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32. Proteome profiling in IL-1β and VEGF-activated human umbilical vein endothelial cells delineates the interlink between inflammation and angiogenesis
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33. Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing
    Peter L. Chang, Joseph P. Dunham, Sergey V. Nuzhdin, Michelle N Arbeitman · 2011 · BMC Genomics
34. In-Depth Transcriptome Analysis of the Red Swamp Crayfish Procambarus clarkii
    Huaishun Shen, Yacheng Hu, Yuanchao Ma, X. Edward Zhou, Zenghong Xu, Yan Shui, Chunyan Li, Peng Xu, Xiaowen Sun · 2014 · PLoS ONE
35. SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence
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36. Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models
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37. Identification of genes and pathways involved in kidney renal clear cell carcinoma
    William E. Yang, Kenji Yoshigoe, Xiang Qin, Jun S. Liu, Jack Y. Yang, Andrzej Niemierko, Youping Deng, Yunlong Liu, A. Keith Dunker, Zhongxue Chen et al. · 2014 · BMC Bioinformatics
38. Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata
    Eshita Sharma, Axel Künstner, Bonnie A. Fraser, Gideon Zipprich, Verena A. Kottler, Stefan R. Henz, Detlef Weigel, Christine Dreyer · 2014 · BMC Genomics
39. Digital Gene Expression Signatures for Maize Development
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40. Transcriptomic analysis by RNA sequencing reveals that hepatic interferon-induced genes may be associated with feed efficiency in beef heifers1
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41. multiHiCcompare: joint normalization and comparative analysis of complex Hi-C experiments
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42. Differential protein occupancy profiling of the mRNA transcriptome
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43. EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments
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44. Genome-wide identification of neuronal activity-regulated genes in Drosophila
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45. Identification of small RNAs in extracellular vesicles from the commensal yeast Malassezia sympodialis
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46. Effect of Doxorubicin/Pluronic SP1049C on Tumorigenicity, Aggressiveness, DNA Methylation and Stem Cell Markers in Murine Leukemia
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47. Altered gene expression and repressed markers of autophagy in skeletal muscle of insulin resistant patients with type 2 diabetes
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48. Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis
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49. Transcription factor protein interactomes reveal genetic determinants in heart disease
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50. Visual and statistical comparison of metagenomes
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51. A cis-carotene derived apocarotenoid regulates etioplast and chloroplast development
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52. Genetically Encoded Fragment-Based Discovery from Phage-Displayed Macrocyclic Libraries with Genetically Encoded Unnatural Pharmacophores
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53. Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves
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54. Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research
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55. RUNX1 positively regulates a cell adhesion and migration program in murine hemogenic endothelium prior to blood emergence
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56. Grapevine (Vitis vinifera) Crown Galls Host Distinct Microbiota
    H. Faist, Alexander Keller, U. Hentschel, R. Deeken · 2016 · Applied and Environmental Microbiology
57. The salivary microbiome of diabetic and non‐diabetic adults with periodontal disease
    Amarpreet Sabharwal, Kevin Ganley, Jeffrey C. Miecznikowski, Elaine M. Haase, Virginia Monsul Barnes, Frank Andrew Scannapieco · 2018 · Journal of Periodontology
58. Very-low-protein diets lead to reduced food intake and weight loss, linked to inhibition of hypothalamic mTOR signaling, in mice
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59. Loss of Dnmt3b function upregulates the tumor modifier Ment and accelerates mouse lymphomagenesis
    Ryan A. Hlady, Slavomíra Nováková, Jana Opavska, David L. Klinkebiel, Staci L. Peters, Juraj Bies, J Dickson Hannah, Javeed Iqbal, Kristi M. Anderson, Hollie M. Siebler et al. · 2011 · Journal of Clinical Investigation
60. Mediator subunit 16 functions in the regulation of iron uptake gene expression in Arabidopsis
    Yue Zhang, Huilan Wu, Ning Wang, Huajie Fan, Chunlin Chen, Yan Cui, Hongfei Liu, Hong‐Qing Ling · 2014 · New Phytologist
61. Physiological and genomic evidence that selection on the transcription factor Epas1 has altered cardiovascular function in high-altitude deer mice
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62. Kruppel-like Factor-9 (KLF9) Inhibits Glioblastoma Stemness through Global Transcription Repression and Integrin α6 Inhibition
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63. Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing
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64. Windshield splatter analysis with the Galaxy metagenomic pipeline
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65. Genetically encoded multivalent liquid glycan array displayed on M13 bacteriophage
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66. Dual RNA-seq of Parasite and Host Reveals Gene Expression Dynamics during Filarial Worm–Mosquito Interactions
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67. Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife
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68. Distinct Exosomal miRNA Profiles from BALF and Lung Tissue of COPD and IPF Patients
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69. FUS-ALS hiPSC-derived astrocytes impair human motor units through both gain-of-toxicity and loss-of-support mechanisms
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70. Novel Data Transformations for RNA-seq Differential Expression Analysis
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71. GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences
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72. JUM is a computational method for comprehensive annotation-free analysis of alternative pre-mRNA splicing patterns
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73. Gene Regulation by CcpA and Catabolite Repression Explored by RNA-Seq in Streptococcus mutans
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74. Single cell transcriptome atlas of mouse mammary epithelial cells across development
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75. Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing
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76. Longitudinal RNA sequencing of the deep transcriptome during neurogenesis of cortical glutamatergic neurons from murine ESCs
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77. Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline
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78. The WRKY45-Dependent Signaling Pathway Is Required For Resistance against Striga hermonthica Parasitism
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80. SPARSim single cell: a count data simulator for scRNA-seq data
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81. Single cell transcriptomics reveals lineage trajectory of retinal ganglion cells in wild-type and Atoh7-null retinas
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84. Dynamics of Wolbachia pipientis Gene Expression Across the Drosophila melanogaster Life Cycle
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85. Epiregulin is a dendritic cell–derived EGFR ligand that maintains skin and lung fibrosis
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87. De novo characterization of the gene-rich transcriptomes of two color-polymorphic spiders, Theridion grallator and T. californicum (Araneae: Theridiidae), with special reference to pigment genes
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88. Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria
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89. Identification of Differentially Expressed Genes in RNA-seq Data of Arabidopsis thaliana : A Compound Distribution Approach
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90. Transcriptomic responses to environmental temperature by turtles with temperature-dependent and genotypic sex determination assessed by RNAseq inform the genetic architecture of embryonic gonadal development
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91. Maladaptive phenotypic plasticity in cardiac muscle growth is suppressed in high‐altitude deer mice
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92. Essential Role for Dnmt1 in the Prevention and Maintenance of MYC-Induced T-Cell Lymphomas
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93. Error estimates for the analysis of differential expression from RNA-seq count data
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94. Identification of recurrent FHL2-GLI2 oncogenic fusion in sclerosing stromal tumors of the ovary
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95. The Impact of Normalization Approaches to Automatically Detect Radiogenomic Phenotypes Characterizing Breast Cancer Receptors Status
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96. Statistical methods for identifying differentially expressed genes in RNA-Seq experiments
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97. Catalase deletion promotes prediabetic phenotype in mice
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98. RNA-seq based transcriptional analysis of Saccharomyces cerevisiae and Lachancea thermotolerans in mixed-culture fermentations under anaerobic conditions
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99. Lycium barbarum Glycopeptide prevents the development and progression of acute colitis by regulating the composition and diversity of the gut microbiota in mice
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100. Reactive Glia-Derived Neuroinflammation: a Novel Hallmark in Lafora Progressive Myoclonus Epilepsy That Progresses with Age
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