Differential expression analysis for sequence count data

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Items 101–200 of 402

1. Adaptive Chromatin Remodeling Drives Glioblastoma Stem Cell Plasticity and Drug Tolerance
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2. The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans
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3. Enhancer loops appear stable during development and are associated with paused polymerase
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4. A deep learning model to predict RNA-Seq expression of tumours from whole-slide images
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5. From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing
   Marinov, Georgi K., Williams, Brian A., McCue, Ken, Schroth, Gary P., Gertz, Jason, Myers, Richard M., Wold, Barbara J. · 2014 · Genome Research
6. Normalizing single-cell RNA sequencing data: challenges and opportunities
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7. Benchmarking of cell type deconvolution pipelines for transcriptomics data
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8. Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals
   Vernot, Benjamin, Tucci, Serena, Kelso, Janet, Schraiber, Joshua G., Wolf, Aaron B., Gittelman, Rachel M., Dannemann, Michael, Grote, Steffi, McCoy, Rajiv C., Norton, Heather et al. · 2016 · Science
9. Competition between DNA methylation and transcription factors determines binding of NRF1
   Domcke, Silvia, Bardet, Anaïs Flore, Adrian Ginno, Paul, Hartl, Dominik, Burger, Lukas, Schübeler, Dirk · 2015 · Nature
10. Mutant p53 Drives Pancreatic Cancer Metastasis through Cell-Autonomous PDGF Receptor β Signaling
    Weissmueller, Susann, Manchado, Eusebio, Saborowski, Michael, Morris, John P., Wagenblast, Elvin, Davis, Carrie A., Moon, Sung-Hwan, Pfister, Neil T., Tschaharganeh, Darjus F., Kitzing, Thomas et al. · 2014 · Cell
11. Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl
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12. Comparison of software packages for detecting differential expression in RNA-seq studies
    Seyednasrollah, F., Laiho, A., Elo, L. L. · 2015 · Briefings in Bioinformatics
13. Non-classical Immunity Controls Microbiota Impact on Skin Immunity and Tissue Repair
    Linehan, Jonathan L., Harrison, Oliver J., Han, Seong-Ji, Byrd, Allyson L., Vujkovic-Cvijin, Ivan, Villarino, Alejandro V., Sen, Shurjo K., Shaik, Jahangheer, Smelkinson, Margery, Tamoutounour, Samira et al. · 2018 · Cell
14. Induction and transcriptional regulation of the co-inhibitory gene module in T cells
    Chihara, Norio, Madi, Asaf, Kondo, Takaaki, Zhang, Huiyuan, Acharya, Nandini, Singer, Meromit, Nyman, Jackson, Marjanovic, Nemanja D., Kowalczyk, Monika S., Wang, Chao et al. · 2018 · Nature
15. The R882H DNMT3A mutation associated with AML dominantly inhibits wild-type DNMT3A by blocking its ability to form active tetramers
    Russler-Germain, David A., Spencer, David H., Young, Margaret A., Lamprecht, Tamara L., Miller, Christopher A., Fulton, Robert, Meyer, Matthew R., Erdmann-Gilmore, Petra, Townsend, R. Reid, Wilson, Richard K. et al. · 2014 · Cancer Cell
16. Senolysis by glutaminolysis inhibition ameliorates various age-associated disorders
    Johmura, Yoshikazu, Yamanaka, Takehiro, Omori, Satotaka, Wang, Teh-Wei, Sugiura, Yuki, Matsumoto, Masaki, Suzuki, Narumi, Kumamoto, Soichiro, Yamaguchi, Kiyoshi, Hatakeyama, Seira et al. · 2021 · Science
17. Mapping microglia states in the human brain through the integration of high-dimensional techniques
    Sankowski, Roman, Böttcher, Chotima, Masuda, Takahiro, Geirsdottir, Laufey, Sagar, Sindram, Elena, Seredenina, Tamara, Muhs, Andreas, Scheiwe, Christian, Shah, Mukesch Johannes et al. · 2019 · Nature Neuroscience
18. Essential genome of <i>Pseudomonas aeruginosa</i> in cystic fibrosis sputum
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19. Impaired insulin/IGF1 signaling extends life span by promoting mitochondrial L-proline catabolism to induce a transient ROS signal
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20. Fasting Activates Fatty Acid Oxidation to Enhance Intestinal Stem Cell Function during Homeostasis and Aging
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21. CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
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22. YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers
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23. Members of the human gut microbiota involved in recovery from Vibrio cholerae infection
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24. Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues
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25. Normalization, testing, and false discovery rate estimation for RNA-sequencing data
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26. Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors
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27. Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin
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28. Robustly detecting differential expression in RNA sequencing data using observation weights
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29. Improved Survival with T Cell Clonotype Stability After Anti–CTLA-4 Treatment in Cancer Patients
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30. Analysis of microbial compositions: a review of normalization and differential abundance analysis
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31. Extensive Variation in Chromatin States Across Humans
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32. Biomarkers of NAFLD progression: a lipidomics approach to an epidemic
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33. Complement Component 3 adapts the cerebrospinal fluid for leptomeningeal metastasis.
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34. Effector T-cell trafficking between the leptomeninges and the cerebrospinal fluid
    Schläger, Christian, Körner, Henrike, Krueger, Martin, Vidoli, Stefano, Haberl, Michael, Mielke, Dorothee, Brylla, Elke, Issekutz, Thomas, Cabañas, Carlos, Nelson, Peter J. et al. · 2016 · Nature
35. <i>Polyester</i> : simulating RNA-seq datasets with differential transcript expression
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36. FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data
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37. <i>CHD8</i> regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors
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38. Calculating Sample Size Estimates for RNA Sequencing Data
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39. Inflammatory fibroblasts mediate resistance to neoadjuvant therapy in rectal cancer
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40. Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
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41. Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data
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42. Activation of PKA leads to mesenchymal-to-epithelial transition and loss of tumor-initiating ability
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43. Single-cell analysis defines a pancreatic fibroblast lineage that supports anti-tumor immunity
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44. Resolving early mesoderm diversification through single-cell expression profiling
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45. A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae
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46. Autism-like behaviours and germline transmission in transgenic monkeys overexpressing MeCP2
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47. CDK12 regulates DNA repair genes by suppressing intronic polyadenylation
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48. Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
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49. Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice
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50. Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation
    Gaidatzis, Dimos, Burger, Lukas, Florescu, Maria, Stadler, Michael B · 2015 · Nature Biotechnology
51. Simultaneous profiling of transcriptome and DNA methylome from a single cell
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52. Genome-wide Mapping of Transcriptional Start Sites Defines an Extensive Leaderless Transcriptome in Mycobacterium tuberculosis
    Cortes, Teresa, Schubert, Olga T., Rose, Graham, Arnvig, Kristine B., Comas, Iñaki, Aebersold, Ruedi, Young, Douglas B. · 2013 · Cell Reports
53. BASiCS: Bayesian Analysis of Single-Cell Sequencing Data
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54. Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells
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55. RNA-seq: technical variability and sampling
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56. The transcriptional landscape of mouse beta cells compared to human beta cells reveals notable species differences in long non-coding RNA and protein-coding gene expression
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57. Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes
    Solomon, Kevin V., Haitjema, Charles H., Henske, John K., Gilmore, Sean P., Borges-Rivera, Diego, Lipzen, Anna, Brewer, Heather M., Purvine, Samuel O., Wright, Aaron T., Theodorou, Michael K. et al. · 2016 · Science
58. Adaptive Immune Resistance Emerges from Tumor-Initiating Stem Cells
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59. Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue
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60. Disentangling neural cell diversity using single-cell transcriptomics
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61. Power analysis and sample size estimation for RNA-Seq differential expression
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62. QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments
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63. Oncogenic collagen I homotrimers from cancer cells bind to α3β1 integrin and impact tumor microbiome and immunity to promote pancreatic cancer
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64. Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads
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65. Role of DNA Methylation in Modulating Transcription Factor Occupancy
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66. Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo
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67. SCnorm: robust normalization of single-cell RNA-seq data
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68. A comparison of statistical methods for detecting differentially expressed genes from RNA‐seq data
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69. Molecular and cellular reorganization of neural circuits in the human lineage
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70. Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors
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71. A statistical approach for identifying differential distributions in single-cell RNA-seq experiments
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72. Peroxisome Proliferator-Activated Receptor γ and C/EBPα Synergistically Activate Key Metabolic Adipocyte Genes by Assisted Loading
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73. A Transcriptome-wide RNAi Screen in the Drosophila Ovary Reveals Factors of the Germline piRNA Pathway
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74. Complete cardiac regeneration in a mouse model of myocardial infarction
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75. Intersection of population variation and autoimmunity genetics in human T cell activation
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76. A two-part mixed-effects model for analyzing longitudinal microbiome compositional data
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77. A systematic evaluation of single cell RNA-seq analysis pipelines
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78. BET bromodomain inhibition suppresses innate inflammatory and profibrotic transcriptional networks in heart failure
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79. Commensal Microbes and Hair Follicle Morphogenesis Coordinately Drive Treg Migration into Neonatal Skin
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80. A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers
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81. Sodium butyrate attenuates social behavior deficits and modifies the transcription of inhibitory/excitatory genes in the frontal cortex of an autism model
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82. A broken promise: microbiome differential abundance methods do not control the false discovery rate
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83. PRC2 Facilitates the Regulatory Topology Required for Poised Enhancer Function during Pluripotent Stem Cell Differentiation
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84. Role of sirtuins in lifespan regulation is linked to methylation of nicotinamide
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85. Peripheral benzodiazepine receptor/translocator protein global knock-out mice are viable with no effects on steroid hormone biosynthesis
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86. Transcription Factor Cooperativity in Early Adipogenic Hotspots and Super-Enhancers
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87. A marine fungus Alternaria alternata FB1 efficiently degrades polyethylene
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88. Microbes &amp; neurodevelopment – Absence of microbiota during early life increases activity-related transcriptional pathways in the amygdala
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89. Activating hotspot L205R mutation in <i>PRKACA</i> and adrenal Cushing’s syndrome
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90. Intrinsic Immunogenicity of Small Cell Lung Carcinoma Revealed by Its Cellular Plasticity
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91. Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function
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92. Alzheimer’s disease is associated with altered expression of genes involved in immune response and mitochondrial processes in astrocytes
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93. Transcription in Living Cells: Molecular Mechanisms of Bursting
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94. Evolution of resistance to a last-resort antibiotic in Staphylococcus aureus via bacterial competition
    Koch, Gudrun, Yepes, Ana, Förstner, Konrad U., Wermser, Charlotte, Stengel, Stephanie T., Modamio, Jennifer, Ohlsen, Knut, Foster, Kevin R., Lopez, Daniel · 2014 · Cell
95. MEF2C regulates cortical inhibitory and excitatory synapses and behaviors relevant to neurodevelopmental disorders
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96. Transcriptome Analysis of the Human Striatum in Tourette Syndrome
    Lennington, Jessica B., Coppola, Gianfilippo, Kataoka-Sasaki, Yuko, Fernandez, Thomas V., Palejev, Dean, Li, Yifan, Huttner, Anita, Pletikos, Mihovil, Sestan, Nenad, Leckman, James F. et al. · 2016 · Biological Psychiatry
97. Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies
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98. Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data
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99. RBFOX1 regulates both splicing and transcriptional networks in human neuronal development
    Fogel, Brent L., Wexler, Eric, Wahnich, Amanda, Friedrich, Tara, Vijayendran, Chandran, Gao, Fuying, Parikshak, Neelroop, Konopka, Genevieve, Geschwind, Daniel H. · 2012 · Human Molecular Genetics
100. Identification of differentially expressed microRNAs across the developing human brain
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