limma powers differential expression analyses for RNA-sequencing and microarray studies

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Items 301–400 of 649

1. Development of an in vitro human liver system for interrogating nonalcoholic steatohepatitis
   Feaver, Ryan E., Cole, Banumathi K., Lawson, Mark J., Hoang, Stephen A., Marukian, Svetlana, Blackman, Brett R., Figler, Robert A., Sanyal, Arun J., Wamhoff, Brian R., Dash, Ajit · 2016 · JCI Insight
2. powsimR: power analysis for bulk and single cell RNA-seq experiments
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3. Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses
   Dugourd, Aurelien, Kuppe, Christoph, Sciacovelli, Marco, Gjerga, Enio, Gabor, Attila, Emdal, Kristina B., Vieira, Vitor, Bekker‐Jensen, Dorte B., Kranz, Jennifer, Bindels, Eric.M.J. et al. · 2021 · Molecular Systems Biology
4. 11-Ketotestosterone is the Dominant Circulating Bioactive Androgen During Normal and Premature Adrenarche
   Rege, Juilee, Turcu, Adina, Kasa-Vubu, Josephine Z, Lerario, Antonio M, Auchus, Gabriela C, Auchus, Richard J, Smith, Joshua M, White, Perrin C, Rainey, William E · 2018 · The Journal of Clinical Endocrinology & Metabolism
5. A Transcriptomic Method to Determine Airway Immune Dysfunction in T2-High and T2-Low Asthma
   Peters, Michael C., Ringel, Lando, Dyjack, Nathan, Herrin, Rachelle, Woodruff, Prescott G., Rios, Cydney, O’Connor, Brian, Fahy, John V., Seibold, Max A. · 2019 · American Journal of Respiratory and Critical Care Medicine
6. Integrative epigenetic taxonomy of primary prostate cancer
   Stelloo, Suzan, Nevedomskaya, Ekaterina, Kim, Yongsoo, Schuurman, Karianne, Valle-Encinas, Eider, Lobo, João, Krijgsman, Oscar, Peeper, Daniel Simon, Chang, Seiwon Laura, Feng, Felix Yi-Chung et al. · 2018 · Nature Communications
7. Human gut microbiome composition and tryptophan metabolites were changed differently by fast food and Mediterranean diet in 4 days: a pilot study
   Zhu, Chenghao, Sawrey-Kubicek, Lisa, Beals, Elizabeth, Rhodes, Chris H., Houts, Hannah Eve, Sacchi, Romina, Zivkovic, Angela M. · 2020 · Nutrition Research
8. Abnormal brain cholesterol homeostasis in Alzheimer’s disease-a targeted metabolomic and transcriptomic study
   Varma, Vijay R., Büşra Lüleci, H., Oommen, Anup M., Varma, Sudhir, Blackshear, Chad T., Griswold, Michael E., An, Yang, Roberts, Jackson A., O’Brien, Richard, Pletnikova, Olga et al. · 2021 · npj Aging and Mechanisms of Disease
9. An epigenome-wide association study of sex-specific chronological ageing
   McCartney, Daniel L., Zhang, Futao, Hillary, Robert F., Zhang, Qian, Stevenson, Anna J., Walker, Rosie M., Bermingham, Mairead L., Boutin, Thibaud, Morris, Stewart W., Campbell, Archie et al. · 2020 · Genome Medicine
10. Neuropilin-1 is a T cell memory checkpoint limiting long-term antitumor immunity
    Liu, Chang, Somasundaram, Ashwin, Manne, Sasikanth, Gocher, Angela M., Szymczak-Workman, Andrea L., Vignali, Kate M., Scott, Ellen N., Normolle, Daniel P., John Wherry, E., Lipson, Evan J. et al. · 2020 · Nature Immunology
11. T _H 17 cells require ongoing classic IL-6 receptor signaling to retain transcriptional and functional identity
    Harbour, Stacey N., DiToro, Daniel F., Witte, Steven J., Zindl, Carlene L., Gao, Min, Schoeb, Trenton R., Jones, Gareth W., Jones, Simon A., Hatton, Robin D., Weaver, Casey T. · 2020 · Science Immunology
12. Gut Microbiota Dysbiosis Is Associated with Elevated Bile Acids in Parkinson’s Disease
    Li, Peipei, Killinger, Bryan A., Ensink, Elizabeth, Beddows, Ian, Yilmaz, Ali, Lubben, Noah, Lamp, Jared, Schilthuis, Meghan, Vega, Irving E., Woltjer, Randy et al. · 2021 · Metabolites
13. Apoptotic caspases inhibit abscopal responses to radiation and identify a new prognostic biomarker for breast cancer patients
    Rodriguez-Ruiz, Maria Esperanza, Buqué, Aitziber, Hensler, Michal, Chen, Jonathan, Bloy, Norma, Petroni, Giulia, Sato, Ai, Yamazaki, Takahiro, Fucikova, Jitka, Galluzzi, Lorenzo · 2019 · OncoImmunology
14. KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors
    Feng, Chenchen, Song, Chao, Liu, Yuejuan, Qian, Fengcui, Gao, Yu, Ning, Ziyu, Wang, Qiuyu, Jiang, Yong, Li, Yanyu, Li, Meng et al. · 2020 · Nucleic Acids Research
15. Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency
    Yang, Pengyi, Humphrey, Sean J., Cinghu, Senthilkumar, Pathania, Rajneesh, Oldfield, Andrew J., Kumar, Dhirendra, Perera, Dinuka, Yang, Jean Y.H., James, David E., Mann, Matthias et al. · 2019 · Cell Systems
16. BI 456906: Discovery and preclinical pharmacology of a novel GCGR/GLP-1R dual agonist with robust anti-obesity efficacy
    Zimmermann, Tina, Thomas, Leo, Baader-Pagler, Tamara, Haebel, Peter, Simon, Eric, Reindl, Wolfgang, Bajrami, Besnik, Rist, Wolfgang, Uphues, Ingo, Drucker, Daniel J. et al. · 2022 · Molecular Metabolism
17. Combined mutation in Vhl, Trp53 and Rb1 causes clear cell renal cell carcinoma in mice
    Harlander, Sabine, Schönenberger, Désirée, Toussaint, Nora C, Prummer, Michael, Catalano, Antonella, Brandt, Laura, Moch, Holger, Wild, Peter J, Frew, Ian J · 2017 · Nature Medicine
18. MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts
    Abernathy, Daniel G., Kim, Woo Kyung, McCoy, Matthew J., Lake, Allison M., Ouwenga, Rebecca, Lee, Seong Won, Xing, Xiaoyun, Li, Daofeng, Lee, Hyung Joo, Heuckeroth, Robert O. et al. · 2017 · Cell Stem Cell
19. Inferring relevant cell types for complex traits by using single-cell gene expression
    Calderon, Diego, Bhaskar, Anand, Knowles, David A., Golan, David, Raj, Towfique, Fu, Audrey Q., Pritchard, Jonathan K. · 2017 · The American Journal of Human Genetics
20. Progranulin deficiency causes impairment of autophagy and TDP-43 accumulation
    Chang, Michael C., Srinivasan, Karpagam, Friedman, Brad A., Suto, Eric, Modrusan, Zora, Lee, Wyne P., Kaminker, Joshua S., Hansen, David V., Sheng, Morgan · 2017 · Journal of Experimental Medicine
21. Regulation of tumor angiogenesis and mesenchymal–endothelial transition by p38α through TGF-β and JNK signaling
    Batlle, Raquel, Andrés, Eva, Gonzalez, Lorena, Llonch, Elisabet, Igea, Ana, Gutierrez-Prat, Núria, Berenguer-Llergo, Antoni, Nebreda, Angel R. · 2019 · Nature Communications
22. Immunoprophylactic and immunotherapeutic control of hormone receptor-positive breast cancer
    Buqué, Aitziber, Bloy, Norma, Perez-Lanzón, Maria, Iribarren, Kristina, Humeau, Juliette, Pol, Jonathan G., Levesque, Sarah, Mondragon, Laura, Yamazaki, Takahiro, Sato, Ai et al. · 2020 · Nature Communications
23. Gene expression links functional networks across cortex and striatum
    Anderson, Kevin M., Krienen, Fenna M., Choi, Eun Young, Reinen, Jenna M., Yeo, B. T. Thomas, Holmes, Avram J. · 2018 · Nature Communications
24. Mechanistic evaluation of primary human hepatocyte culture using global proteomic analysis reveals a selective dedifferentiation profile
    Heslop, James A., Rowe, Cliff, Walsh, Joanne, Sison-Young, Rowena, Jenkins, Roz, Kamalian, Laleh, Kia, Richard, Hay, David, Jones, Robert P., Malik, Hassan Z. et al. · 2017 · Archives of Toxicology
25. Ketolysis drives CD8+ T cell effector function through effects on histone acetylation
    Luda, Katarzyna M., Longo, Joseph, Kitchen-Goosen, Susan M., Duimstra, Lauren R., Ma, Eric H., Watson, McLane J., Oswald, Brandon M., Fu, Zhen, Madaj, Zachary, Kupai, Ariana et al. · 2023 · Immunity
26. Large Scale Gene Expression Meta-Analysis Reveals Tissue-Specific, Sex-Biased Gene Expression in Humans
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27. Therapeutic responses to <i>Roseomonas mucosa</i> in atopic dermatitis may involve lipid-mediated TNF-related epithelial repair
    Myles, Ian A., Castillo, Carlo R., Barbian, Kent D., Kanakabandi, Kishore, Virtaneva, Kimmo, Fitzmeyer, Emily, Paneru, Monica, Otaizo-Carrasquero, Francisco, Myers, Timothy G., Markowitz, Tovah E. et al. · 2020 · Science Translational Medicine
28. Antitumor effect of oncolytic virus and paclitaxel encapsulated in extracellular vesicles for lung cancer treatment
    Garofalo, M., Saari, H., Somersalo, P., Crescenti, D., Kuryk, L., Aksela, L., Capasso, C., Madetoja, M., Koskinen, K., Oksanen, T. et al. · 2018 · Journal of Controlled Release
29. A cell identity switch allows residual BCC to survive Hedgehog pathway inhibition
    Biehs, Brian, Dijkgraaf, Gerrit J. P., Piskol, Robert, Alicke, Bruno, Boumahdi, Soufiane, Peale, Franklin, Gould, Stephen E., de Sauvage, Frederic J. · 2018 · Nature
30. Disturbed glucose and pyruvate metabolism in glaucoma with neuroprotection by pyruvate or rapamycin
    Harder, Jeffrey M., Guymer, Chelsea, Wood, John P. M., Daskalaki, Evangelia, Chidlow, Glyn, Zhang, Chi, Balasubramanian, Revathi, Cardozo, Brynn H., Foxworth, Nicole E., Deering, Kelly E. et al. · 2020 · Proceedings of the National Academy of Sciences
31. An RNA-Seq atlas of gene expression in mouse and rat normal tissues
    Söllner, Julia F., Leparc, German, Hildebrandt, Tobias, Klein, Holger, Thomas, Leo, Stupka, Elia, Simon, Eric · 2017 · Scientific Data
32. Early stem cell aging in the mature brain
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33. Kupffer-cell-derived IL-6 is repurposed for hepatocyte dedifferentiation via activating progenitor genes from injury-specific enhancers
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34. Osteocyte transcriptome mapping identifies a molecular landscape controlling skeletal homeostasis and susceptibility to skeletal disease
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35. Neuropathological and transcriptomic characteristics of the aged brain
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36. Preoperative stimulation of resolution and inflammation blockade eradicates micrometastases
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37. The gut microbiota promotes distal tissue regeneration via RORγ+ regulatory T cell emissaries
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38. Multi‐omic rejuvenation of naturally aged tissues by a single cycle of transient reprogramming
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39. Chromatin remodelling drives immune cell–fibroblast communication in heart failure
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40. Deficiency of TYROBP, an adapter protein for TREM2 and CR3 receptors, is neuroprotective in a mouse model of early Alzheimer’s pathology
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41. Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype
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42. DNA Methylation Patterns Separate Senescence from Transformation Potential and Indicate Cancer Risk
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43. Selective USP7 inhibition elicits cancer cell killing through a p53-dependent mechanism.
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44. Human germline heterozygous gain-of-function <i>STAT6</i> variants cause severe allergic disease
    Sharma, Mehul, Leung, Daniel, Momenilandi, Mana, Jones, Lauren C.W., Pacillo, Lucia, James, Alyssa E., Murrell, Jill R., Delafontaine, Selket, Maimaris, Jesmeen, Vaseghi-Shanjani, Maryam et al. · 2023 · Journal of Experimental Medicine
45. Agonist immunotherapy restores T cell function following MEK inhibition improving efficacy in breast cancer
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46. Transcription factor PU.1 represses and activates gene expression in early T cells by redirecting partner transcription factor binding
    Hosokawa, Hiroyuki, Ungerbäck, Jonas, Wang, Xun, Matsumoto, Masaki, Nakayama, Keiichi I., Cohen, Sarah M., Tanaka, Tomoaki, Rothenberg, Ellen V. · 2018 · Immunity
47. Gut microbiota composition during infancy and subsequent behavioural outcomes
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48. dmrff: identifying differentially methylated regions efficiently with power and control
    Suderman, Matthew, Staley, James R, French, Robert, Arathimos, Ryan, Simpkin, Andrew, Tilling, Kate · 2018
49. Fecal transplant prevents gut dysbiosis and anxiety-like behaviour after spinal cord injury in rats
    Schmidt, Emma K. A., Torres-Espin, Abel, Raposo, Pamela J. F., Madsen, Karen L., Kigerl, Kristina A., Popovich, Phillip G., Fenrich, Keith K., Fouad, Karim · 2020 · PLoS ONE
50. Acute pharmacological degradation of Helios destabilizes regulatory T cells
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51. Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF
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52. A mouse tissue atlas of small noncoding RNA
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53. Therapeutic targeting of the RB1 pathway in retinoblastoma with the oncolytic adenovirus VCN-01
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54. Functional Genomics Identify Distinct and Overlapping Genes Mediating Resistance to Different Classes of Heterobifunctional Degraders of Oncoproteins
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55. Niche stiffening compromises hair follicle stem cell potential during ageing by reducing bivalent promoter accessibility
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56. A genetic link between risk for Alzheimer's disease and severe COVID-19 outcomes via the <i>OAS1</i> gene
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57. Distinct initiating events underpin the immune and metabolic heterogeneity of KRAS-mutant lung adenocarcinoma
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58. Identity domains capture individual differences from across the behavioral repertoire
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59. Peptide-level Robust Ridge Regression Improves Estimation, Sensitivity, and Specificity in Data-dependent Quantitative Label-free Shotgun Proteomics
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60. A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples
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61. SREBP1c-PARP1 axis tunes anti-senescence activity of adipocytes and ameliorates metabolic imbalance in obesity
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62. DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing
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63. Discrete Distributional Differential Expression (D ³ E) - A Tool for Gene Expression Analysis of Single-cell RNA-seq Data
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64. VGF-derived peptide TLQP-21 modulates microglial function through C3aR1 signaling pathways and reduces neuropathology in 5xFAD mice
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65. Cell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape
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66. scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies
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67. Extensive remodeling of the extracellular matrix during aging contributes to age-dependent impairments of muscle stem cell functionality
    Schüler, Svenja C., Kirkpatrick, Joanna M., Schmidt, Manuel, Santinha, Deolinda, Koch, Philipp, Di Sanzo, Simone, Cirri, Emilio, Hemberg, Martin, Ori, Alessandro, von Maltzahn, Julia · 2021 · Cell Reports
68. Autoreactive CD8+ T cells are restrained by an exhaustion-like program that is maintained by LAG3
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69. Autophagy protein NRBF2 has reduced expression in Alzheimer’s brains and modulates memory and amyloid-beta homeostasis in mice
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70. Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease
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71. Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability
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72. Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data
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73. Differential Content of Proteins, mRNAs, and miRNAs Suggests that MDSC and Their Exosomes May Mediate Distinct Immune Suppressive Functions
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74. Transcription Factor PU.1 Promotes Conventional Dendritic Cell Identity and Function via Induction of Transcriptional Regulator DC-SCRIPT
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75. MTOR signaling orchestrates stress-induced mutagenesis, facilitating adaptive evolution in cancer
    Cipponi, Arcadi, Goode, David L., Bedo, Justin, McCabe, Mark J., Pajic, Marina, Croucher, David R., Rajal, Alvaro Gonzalez, Junankar, Simon R., Saunders, Darren N., Lobachevsky, Pavel et al. · 2020 · Science
76. Estrogen receptor α drives pro-resilient transcription in mouse models of depression
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77. Identification of Alzheimer's disease–associated long noncoding RNAs
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78. Myofibroblast YAP/TAZ activation is a key step in organ fibrogenesis
    He, Xiaolin, Tolosa, Monica F., Zhang, Tianzhou, Goru, Santosh Kumar, Ulloa Severino, Luisa, Misra, Paraish S., McEvoy, Caitríona M., Caldwell, Lauren, Szeto, Stephen G., Gao, Feng et al. · 2022 · JCI Insight
79. Genome-wide CRISPR screen for PARKIN regulators reveals transcriptional repression as a determinant of mitophagy
    Potting, Christoph, Crochemore, Christophe, Moretti, Francesca, Nigsch, Florian, Schmidt, Isabel, Manneville, Carole, Carbone, Walter, Knehr, Judith, DeJesus, Rowena, Lindeman, Alicia et al. · 2018 · Proceedings of the National Academy of Sciences
80. Healthy aging and muscle function are positively associated with NAD+ abundance in humans
    Janssens, Georges E., Grevendonk, Lotte, Perez, Ruben Zapata, Schomakers, Bauke V., de Vogel-van den Bosch, Johan, Geurts, Jan M. W., van Weeghel, Michel, Schrauwen, Patrick, Houtkooper, Riekelt H., Hoeks, Joris · 2022 · Nature Aging
81. GAM: a web-service for integrated transcriptional and metabolic network analysis
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82. Biologically informed deep learning to query gene programs in single-cell atlases
    Lotfollahi, Mohammad, Rybakov, Sergei, Hrovatin, Karin, Hediyeh-zadeh, Soroor, Talavera-López, Carlos, Misharin, Alexander V., Theis, Fabian J. · 2023 · Nature Cell Biology
83. Rapid idiosyncratic mechanisms of clinical resistance to KRAS G12C inhibition
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84. Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition
    Deliu, Elena, Arecco, Niccolò, Morandell, Jasmin, Dotter, Christoph P., Contreras, Ximena, Girardot, Charles, Käsper, Eva-Lotta, Kozlova, Alena, Kishi, Kasumi, Chiaradia, Ilaria et al. · 2018 · Nature Neuroscience
85. Grandmaternal stress during pregnancy and DNA methylation of the third generation: an epigenome-wide association study
    Serpeloni, F, Radtke, K, de Assis, S G, Henning, F, Nätt, D, Elbert, T · 2017 · Translational Psychiatry
86. Harnessing peripheral DNA methylation differences in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) to reveal novel biomarkers of disease
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