Differential expression analysis for sequence count data

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Items 301–400 of 402

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7. Detecting ancient positive selection in humans using extended lineage sorting
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8. Succinylation of H3K122 destabilizes nucleosomes and enhances transcription
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10. An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets
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12. Sex‐biased hippocampal pathology in the 5XFAD mouse model of Alzheimer's disease: A multi‐omic analysis
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13. Immune correlates of tuberculosis disease and risk translate across species
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14. Modeling alcohol-associated liver disease in a human Liver-Chip
    Nawroth, Janna C., Petropolis, Debora B., Manatakis, Dimitris V., Maulana, Tengku Ibrahim, Burchett, Gabriel, Schlünder, Katharina, Witt, Anke, Shukla, Abhishek, Kodella, Konstantia, Ronxhi, Janey et al. · 2021 · Cell Reports
15. Neural progenitors adopt specific identities by directly repressing all alternative progenitor transcriptional programs
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16. ROTS: reproducible RNA-seq biomarker detector—prognostic markers for clear cell renal cell cancer
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17. Impact of low dose oral exposure to bisphenol A (BPA) on the neonatal rat hypothalamic and hippocampal transcriptome: a clarity-BPA consortium study
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18. Maternal separation with early weaning: a rodent model providing novel insights into neglect associated developmental deficits
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19. Comparison of methods to detect differentially expressed genes between single-cell populations
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20. Comparative assessment of differential network analysis methods
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21. Meta-omics uncover temporal regulation of pathways across oral microbiome genera during <i>in vitro</i> sugar metabolism
    Edlund, Anna, Yang, Youngik, Yooseph, Shibu, Hall, Adam P, Nguyen, Don D, Dorrestein, Pieter C, Nelson, Karen E, He, Xuesong, Lux, Renate, Shi, Wenyuan et al. · 2015 · The ISME Journal
22. Multi-metal restriction by calprotectin impacts de novo flavin biosynthesis in Acinetobacter baumannii
    Wang, Jiefei, Lonergan, Zachery R., Gonzalez-Gutierrez, Giovanni, Nairn, Brittany L., Maxwell, Christina N., Zhang, Yixiang, Andreini, Claudia, Karty, Jonathan A., Chazin, Walter J., Trinidad, Jonathan C. et al. · 2019 · Cell chemical biology
23. Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer
    Wyatt, Alexander W, Mo, Fan, Wang, Kendric, McConeghy, Brian, Brahmbhatt, Sonal, Jong, Lina, Mitchell, Devon M, Johnston, Rebecca L, Haegert, Anne, Li, Estelle et al. · 2014 · Genome Biology
24. Activation of endogenous retroviruses during brain development causes an inflammatory response
    Jönsson, Marie E, Garza, Raquel, Sharma, Yogita, Petri, Rebecca, Södersten, Erik, Johansson, Jenny G, Johansson, Pia A, Atacho, Diahann AM, Pircs, Karolina, Madsen, Sofia et al. · 2021 · The EMBO Journal
25. Interplay among transcription factors Ets21c, Fos and Ftz-F1 drives JNK-mediated tumor malignancy
    Külshammer, Eva, Mundorf, Juliane, Kilinc, Merve, Frommolt, Peter, Wagle, Prerana, Uhlirova, Mirka · 2015 · Disease Models &amp; Mechanisms
26. Caloric restriction promotes functional changes involving short-chain fatty acid biosynthesis in the rat gut microbiota
    Tanca, Alessandro, Abbondio, Marcello, Palomba, Antonio, Fraumene, Cristina, Marongiu, Fabio, Serra, Monica, Pagnozzi, Daniela, Laconi, Ezio, Uzzau, Sergio · 2018 · Scientific Reports
27. Transcriptome changes induced by abiotic stresses in Artemisia annua
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28. Mice deficient in NRROS show abnormal microglial development and neurological disorders
    Wong, Kit, Noubade, Rajkumar, Manzanillo, Paolo, Ota, Naruhisa, Foreman, Oded, Hackney, Jason A, Friedman, Brad A, Pappu, Rajita, Scearce-Levie, Kimberly, Ouyang, Wenjun · 2017 · Nature Immunology
29. A functional genetic screen defines the AKT-induced senescence signaling network
    Chan, Keefe T., Blake, Shaun, Zhu, Haoran, Kang, Jian, Trigos, Anna S., Madhamshettiwar, Piyush B., Diesch, Jeannine, Paavolainen, Lassi, Horvath, Peter, Hannan, Ross D. et al. · 2020 · Cell Death &amp; Differentiation
30. Taxa of the nasal microbiome are associated with influenza-specific IgA response to live attenuated influenza vaccine
    Salk, Hannah M., Simon, Whitney L., Lambert, Nathaniel D., Kennedy, Richard B., Grill, Diane E., Kabat, Brian F., Poland, Gregory A. · 2016 · PLoS ONE
31. A Cancer-Specific Ubiquitin Ligase Drives mRNA Alternative Polyadenylation by Ubiquitinating the mRNA 3′ End Processing Complex
    Yang, Seung Wook, Li, Lei, Connelly, Jon P., Porter, Shaina N., Kodali, Kiran, Gan, Haiyun, Park, Jung Mi, Tacer, Klementina Fon, Tillman, Heather, Peng, Junmin et al. · 2020 · Molecular Cell
32. Repression of p63 and induction of EMT by mutant Ras in mammary epithelial cells
    Yoh, Kathryn E., Regunath, Kausik, Guzman, Asja, Lee, Seung-Min, Pfister, Neil T., Akanni, Olutosin, Kaufman, Laura J., Prives, Carol, Prywes, Ron · 2016 · Proceedings of the National Academy of Sciences
33. Monitoring of Technical Variation in Quantitative High-Throughput Datasets
    Lauss, Martin, Visne, Ilhami, Kriegner, Albert, Ringnér, Markus, Jönsson, Göran, Höglund, Mattias · 2013 · Cancer Informatics
34. Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency
    Pękowska, Aleksandra, Klaus, Bernd, Xiang, Wanqing, Severino, Jacqueline, Daigle, Nathalie, Klein, Felix A., Oleś, Małgorzata, Casellas, Rafael, Ellenberg, Jan, Steinmetz, Lars M. et al. · 2018 · Cell Systems
35. Regulation of early T-lineage gene expression and developmental progression by the progenitor cell transcription factor PU.1
    Champhekar, Ameya, Damle, Sagar S., Freedman, George, Carotta, Sebastian, Nutt, Stephen L., Rothenberg, Ellen V. · 2015 · Genes &amp; Development
36. Foxp1 in Forebrain Pyramidal Neurons Controls Gene Expression Required for Spatial Learning and Synaptic Plasticity
    Araujo, Daniel J., Toriumi, Kazuya, Escamilla, Christine O., Kulkarni, Ashwinikumar, Anderson, Ashley G., Harper, Matthew, Usui, Noriyoshi, Ellegood, Jacob, Lerch, Jason P., Birnbaum, Shari G. et al. · 2017 · The Journal of Neuroscience
37. RNA Sequencing and Proteogenomics Reveal the Importance of Leaderless mRNAs in the Radiation-Tolerant Bacterium Deinococcus deserti
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38. Calcium Signaling Pathway Genes <i>RUNX2</i> and <i>CACNA1C</i> Are Associated With Calcific Aortic Valve Disease
    Guauque-Olarte, Sandra, Messika-Zeitoun, David, Droit, Arnaud, Lamontagne, Maxime, Tremblay-Marchand, Joël, Lavoie-Charland, Emilie, Gaudreault, Nathalie, Arsenault, Benoit J., Dubé, Marie-Pierre, Tardif, Jean-Claude et al. · 2015 · Circulation: Cardiovascular Genetics
39. Mutational signatures reveal the role of RAD52 in p53-independent p21-driven genomic instability
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40. Zinc Finger Transcription Factors Displaced SREBP Proteins as the Major Sterol Regulators during Saccharomycotina Evolution
    Maguire, Sarah L., Wang, Can, Holland, Linda M., Brunel, François, Neuvéglise, Cécile, Nicaud, Jean-Marc, Zavrel, Martin, White, Theodore C., Wolfe, Kenneth H., Butler, Geraldine · 2014 · PLoS Genetics
41. Immune Quiescence of the Brain Is Set by Astroglial Connexin 43
    Boulay, Anne-Cécile, Mazeraud, Aurélien, Cisternino, Salvatore, Saubaméa, Bruno, Mailly, Phillipe, Jourdren, Laurent, Blugeon, Corinne, Mignon, Virginie, Smirnova, Maria, Cavallo, Alessia et al. · 2015 · The Journal of Neuroscience
42. UBR5 forms ligand-dependent complexes on chromatin to regulate nuclear hormone receptor stability
    Tsai, Jonathan M., Aguirre, Jacob D., Li, Yen-Der, Brown, Jared, Focht, Vivian, Kater, Lukas, Kempf, Georg, Sandoval, Brittany, Schmitt, Stefan, Rutter, Justine C. et al. · 2023 · Molecular Cell
43. Chronic LSD alters gene expression profiles in the mPFC relevant to schizophrenia
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44. The genomic landscape of 8-oxodG reveals enrichment at specific inherently fragile promoters
    Gorini, Francesca, Scala, Giovanni, Di Palo, Giacomo, Dellino, Gaetano Ivan, Cocozza, Sergio, Pelicci, Pier Giuseppe, Lania, Luigi, Majello, Barbara, Amente, Stefano · 2020 · Nucleic Acids Research
45. Modulation of potential respiratory pathogens by pH1N1 viral infection.
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46. Rbpj expression in regulatory T cells is critical for restraining TH2 responses
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47. Proteasome subunit PSMC3 variants cause neurosensory syndrome combining deafness and cataract due to proteotoxic stress
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48. Calcareous sponge genomes reveal complex evolution of α-carbonic anhydrases and two key biomineralization enzymes
    Voigt, Oliver, Adamski, Marcin, Sluzek, Kasia, Adamska, Maja · 2014 · BMC Evolutionary Biology
49. subSeq: Determining Appropriate Sequencing Depth Through Efficient Read Subsampling
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50. The MazF-regulon: a toolbox for the post-transcriptional stress response in<i>Escherichia coli</i>
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51. Uncovering a Predictive Molecular Signature for the Onset of NASH-Related Fibrosis in a Translational NASH Mouse Model
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52. Serotonergic neuron regulation informed by <i>in vivo</i> single‐cell transcriptomics
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53. Conserved Translatome Remodeling in Nematode Species Executing a Shared Developmental Transition
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54. Cross-Comparison of Human iPSC Motor Neuron Models of Familial and Sporadic ALS Reveals Early and Convergent Transcriptomic Disease Signatures
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55. Identification and Functional Characterization of Rca1, a Transcription Factor Involved in both Antifungal Susceptibility and Host Response in Candida albicans
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56. Similarities in Gene Expression Profiles during<i>In Vitro</i>Aging of Primary Human Embryonic Lung and Foreskin Fibroblasts
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57. Time-Course Analysis of Gene Expression During the<i>Saccharomyces cerevisiae</i>Hypoxic Response
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58. Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks
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59. Sex-Specific Neurodevelopmental Programming by Placental Insulin Receptors on Stress Reactivity and Sensorimotor Gating
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60. A Uniform Computational Approach Improved on Existing Pipelines to Reveal Microbiome Biomarkers of Nonresponse to Immune Checkpoint Inhibitors
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61. Genetic modifications associated with ketogenic diet treatment in the BTBR^T+Tf/J mouse model of autism spectrum disorder
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62. Atf3 links loss of epithelial polarity to defects in cell differentiation and cytoarchitecture
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63. Transcriptome analysis of genetically matched human induced pluripotent stem cells disomic or trisomic for chromosome 21
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64. Fungal acetylome comparative analysis identifies an essential role of acetylation in human fungal pathogen virulence
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65. Integrative RNA-seq and microarray data analysis reveals GC content and gene length biases in the psoriasis transcriptome
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66. The RUNX1/IL-34/CSF-1R axis is an autocrinally regulated modulator of resistance to BRAF-V600E inhibition in melanoma
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68. Cell Contact–Dependent Priming and Fc Interaction with CD32+ Immune Cells Contribute to the TGN1412-Triggered Cytokine Response
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69. Antifungal activity of vitamin D3 against Candida albicans in vitro and in vivo
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70. Conserved genes and pathways in primary human fibroblast strains undergoing replicative and radiation induced senescence
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72. Dnmt3a Regulates Global Gene Expression in Olfactory Sensory Neurons and Enables Odorant-Induced Transcription
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76. Mammary-specific gene activation is defined by progressive recruitment of STAT5 during pregnancy and the establishment of H3K4me3 marks
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77. A Comprehensive Survey of Statistical Approaches for Differential Expression Analysis in Single-Cell RNA Sequencing Studies
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78. NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data
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79. Angiopoietin–TIE2 feedforward circuit promotes PIK3CA-driven venous malformations
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80. Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer
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81. RNAseq based transcriptomics study of SMCs from carotid atherosclerotic plaque: BMP2 and IDs proteins are crucial regulators of plaque stability
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82. Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data
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83. Cardiovascular Risk and Resilience Among Black Adults: Rationale and Design of the MECA Study
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84. The effect of GLP-1 receptor agonist lixisenatide on experimental diabetic retinopathy
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85. Polymerization of ZBTB transcription factors regulates chromatin occupancy
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86. Chronic Psychological Stress Alters Gene Expression in Rat Colon Epithelial Cells Promoting Chromatin Remodeling, Barrier Dysfunction and Inflammation
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87. Differential contribution of cis and trans gene transcription regulatory mechanisms in amygdala and prefrontal cortex and modulation by social stress
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88. The stress-responsive gene<i>GDPGP1/mcp-1</i>regulates neuronal glycogen metabolism and survival
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89. Dissecting miRNA gene repression on single cell level with an advanced fluorescent reporter system
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90. Ubiquitin proteolysis of a CDK-related kinase regulates titan cell formation and virulence in the fungal pathogen Cryptococcus neoformans
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91. Comparative transcriptome profiling of <i>Kappaphycus alvarezii</i> (Rhodophyta, Gigartinales) in response to two extreme temperature treatments: an RNA-seq-based resource for photosynthesis research
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92. Multi‐Omics Analysis of Experimentally Evolved <i>Candida auris</i> Isolates Reveals Modulation of Sterols, Sphingolipids, and Oxidative Stress in Acquired Amphotericin B Resistance
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93. Transcriptional and proteomic characterization of telomere-induced senescence in a human alveolar epithelial cell line
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