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

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3. Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago
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4. CDT2‐controlled cell cycle reentry regulates the pathogenesis of Alzheimer's disease
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5. Genome-wide DNA methylation analysis of heavy cannabis exposure in a New Zealand longitudinal cohort
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6. Spliceosome Malfunction Causes Neurodevelopmental Disorders with Overlapping Features
   Li, Dong, Wang, Qin, Bayat, Allan, Battig, Mark R., Zhou, Yijing, Bosch, Daniëlle G.M., van Haaften, Gijs, Granger, Leslie, Petersen, Andrea K., Pérez-Jurado, Luis A. et al. · 2024 · Journal of Clinical Investigation
7. Functional isolation, culture and cryopreservation of adult human primary cardiomyocytes
   Zhou, Bingying, Shi, Xun, Tang, Xiaoli, Zhao, Quanyi, Wang, Le, Yao, Fang, Hou, Yongfeng, Wang, Xianqiang, Feng, Wei, Wang, Liqing et al. · 2022 · Signal Transduction and Targeted Therapy
8. Gene co-expression analysis identifies gene clusters associated with isotropic and polarized growth in Aspergillus fumigatus conidia
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9. Targeting oncoproteins with a positive selection assay for protein degraders
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10. HDAC7-mediated control of tumour microenvironment maintains proliferative and stemness competence of human mammary epithelial cells
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11. EMUDRA: Ensemble of Multiple Drug Repositioning Approaches to improve prediction accuracy
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12. PDE4B inhibition by nerandomilast: Effects on lung fibrosis and transcriptome in fibrotic rats and on biomarkers in human lung epithelial cells
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13. Gbx2 is essential for maintaining thalamic neuron identity and repressing habenular characters in the developing thalamus
    Mallika, Chatterjee, Guo, Qiuxia, Li, James Y.H. · 2015 · Developmental Biology
14. Runx2 (Runt-Related Transcription Factor 2)-Mediated Microcalcification Is a Novel Pathological Characteristic and Potential Mediator of Abdominal Aortic Aneurysm
    Li, Zhiqing, Zhao, Zuoquan, Cai, Zeyu, Sun, Yong, Li, Li, Yao, Fang, Yang, Liu, Zhou, Yuan, Zhu, Haibo, Fu, Yi et al. · 2020 · Arteriosclerosis, Thrombosis, and Vascular Biology
15. The human hepatocyte TXG-MAPr: gene co-expression network modules to support mechanism-based risk assessment
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16. Increased Type I interferon signaling and brain endothelial barrier dysfunction in an experimental model of Alzheimer’s disease
    Jana, Arundhati, Wang, Xinge, Leasure, Joseph W., Magana, Lissette, Wang, Li, Kim, Young-Mee, Dodiya, Hemraj, Toth, Peter T., Sisodia, Sangram S., Rehman, Jalees · 2022 · Scientific Reports
17. A tumor microenvironment-specific gene expression signature predicts chemotherapy resistance in colorectal cancer patients
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18. Differentially expressed genes related to major depressive disorder and antidepressant response: genome-wide gene expression analysis
    Woo, Hye In, Lim, Shinn-Won, Myung, Woojae, Kim, Doh Kwan, Lee, Soo-Youn · 2018 · Experimental & Molecular Medicine
19. Regulation of cell distancing in peri-plaque glial nets by Plexin-B1 affects glial activation and amyloid compaction in Alzheimer’s disease
    Huang, Yong, Wang, Minghui, Ni, Haofei, Zhang, Jinglong, Li, Aiqun, Hu, Bin, Junqueira Alves, Chrystian, Wahane, Shalaka, Rios de Anda, Mitzy, Ho, Lap et al. · 2024 · Nature Neuroscience
20. The HDL lipidome is widely remodeled by fast food versus Mediterranean diet in 4 days
    Zhu, Chenghao, Sawrey-Kubicek, Lisa, Beals, Elizabeth, Hughes, Riley L., Rhodes, Chris H., Sacchi, Romina, Zivkovic, Angela M. · 2019 · Metabolomics
21. Transcriptome Analysis Uncovers a Link Between Copper Metabolism, and Both Fungal Fitness and Antifungal Sensitivity in the Opportunistic Yeast Candida albicans
    Khemiri, Inès, Tebbji, Faiza, Sellam, Adnane · 2020 · Frontiers in Microbiology
22. Multi-omics network analysis reveals distinct stages in the human aging progression in epidermal tissue
    Holzscheck, Nicholas, Söhle, Jörn, Kristof, Boris, Grönniger, Elke, Gallinat, Stefan, Wenck, Horst, Winnefeld, Marc, Falckenhayn, Cassandra, Kaderali, Lars · 2020 · Aging
23. Methylome-wide association study of antidepressant use in Generation Scotland and the Netherlands Twin Register implicates the innate immune system
    Barbu, Miruna C., Huider, Floris, Campbell, Archie, Amador, Carmen, Adams, Mark J., Lynall, Mary-Ellen, Howard, David M., Walker, Rosie M., Morris, Stewart W., Van Dongen, Jenny et al. · 2022 · Molecular Psychiatry
24. Integrated Identification and Quantification Error Probabilities for Shotgun Proteomics
    The, Matthew, Käll, Lukas · 2019 · Molecular & Cellular Proteomics
25. miR-146a-5p impairs melanoma resistance to kinase inhibitors by targeting COX2 and regulating NFkB-mediated inflammatory mediators
    Vergani, Elisabetta, Dugo, Matteo, Cossa, Mara, Frigerio, Simona, Di Guardo, Lorenza, Gallino, Gianfrancesco, Mattavelli, Ilaria, Vergani, Barbara, Lalli, Luca, Tamborini, Elena et al. · 2020 · Cell Communication and Signaling
26. Integrated biology approach reveals molecular and pathological interactions among Alzheimer’s Aβ42, Tau, TREM2, and TYROBP in Drosophila models
    Sekiya, Michiko, Wang, Minghui, Fujisaki, Naoki, Sakakibara, Yasufumi, Quan, Xiuming, Ehrlich, Michelle E., De Jager, Philip L., Bennett, David A., Schadt, Eric E., Gandy, Sam et al. · 2018 · Genome Medicine
27. Pharmacological inhibition of LSD1 triggers myeloid differentiation by targeting GSE1 oncogenic functions in AML
    Nicosia, Luciano, Boffo, Francesca Ludovica, Ceccacci, Elena, Conforti, Fabio, Pallavicini, Isabella, Bedin, Fabio, Ravasio, Roberto, Massignani, Enrico, Somervaille, Tim C. P., Minucci, Saverio et al. · 2022 · Oncogene
28. Gene expression in cord blood links genetic risk for neurodevelopmental disorders with maternal psychological distress and adverse childhood outcomes
    Breen, Michael S., Wingo, Aliza P., Koen, Nastassja, Donald, Kirsten A., Nicol, Mark, Zar, Heather J., Ressler, Kerry J., Buxbaum, Joseph D., Stein, Dan J. · 2018 · Brain, Behavior, and Immunity
29. meQTL and ncRNA functional analyses of 102 GWAS-SNPs associated with depression implicate HACE1 and SHANK2 genes
    Ciuculete, Diana M., Voisin, Sarah, Kular, Lara, Jonsson, Jörgen, Rask-Andersen, Mathias, Mwinyi, Jessica, Schiöth, Helgi B. · 2020 · Clinical Epigenetics
30. A network of paralogous stress response transcription factors in the human pathogen Candida glabrata
    Merhej, Jawad, Thiebaut, Antonin, Blugeon, Corinne, Pouch, Juliette, Ali Chaouche, Mohammed El Amine, Camadro, Jean-Michel, Le Crom, Stéphane, Lelandais, Gaëlle, Devaux, Frédéric · 2016 · Frontiers in Microbiology
31. Inducible knock-out of BCL6 in lymphoma cells results in tumor stasis
    Schlager, Stefanie, Salomon, Carina, Olt, Sabine, Albrecht, Christoph, Ebert, Anja, Bergner, Oliver, Wachter, Johannes, Trapani, Francesca, Gerlach, Daniel, Voss, Tilman et al. · 2020 · Oncotarget
32. Blood DNA methylation signatures to detect dementia prior to overt clinical symptoms
    Fransquet, Peter Daniel, Lacaze, Paul, Saffery, Richard, Phung, James, Parker, Emily, Shah, Raj, Murray, Anne, Woods, Robyn L., Ryan, Joanne · 2020 · Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring
33. AKT3 expression in mesenchymal colorectal cancer cells drives growth and is associated with epithelial-mesenchymal transition
    Buikhuisen, Joyce Y., Gomez Barila, Patricia M., Torang, Arezo, Dekker, Daniëlle, de Jong, Joan H., Cameron, Kate, Vitale, Sara, Stassi, Giorgio, van Hooff, Sander R., Castro, Mauro A. A. et al. · 2021 · Cancers
34. Sex-specific cell types and molecular pathways indicate fibro-calcific aortic valve stenosis
    Myasoedova, Veronika A., Massaiu, Ilaria, Moschetta, Donato, Chiesa, Mattia, Songia, Paola, Valerio, Vincenza, Alfieri, Valentina, Capoulade, Romain, Trabattoni, Daniela, Andreini, Daniele et al. · 2022 · Frontiers in Immunology
35. Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003
    Bottacini, Francesca, Zomer, Aldert, Milani, Christian, Ferrario, Chiara, Lugli, Gabriele Andrea, Egan, Muireann, Ventura, Marco, van Sinderen, Douwe · 2017 · BMC Genomics
36. A Comprehensive Survey of Statistical Approaches for Differential Expression Analysis in Single-Cell RNA Sequencing Studies
    Das, Samarendra, Rai, Anil, Merchant, Michael L., Cave, Matthew C., Rai, Shesh N. · 2021 · Genes
37. Leukocyte Methylomic Imprints of Exposure to the Genocide against the Tutsi in Rwanda: a Pilot Epigenome-Wide Analysis
    Musanabaganwa, Clarisse, Wani, Agaz H, Donglasan, Janelle, Fatumo, Segun, Jansen, Stefan, Mutabaruka, Jean, Rutembesa, Eugene, Uwineza, Annette, Hermans, Erno J, Roozendaal, Benno et al. · 2022 · Epigenomics
38. Identification of novel diagnostic panel for mild cognitive impairment and Alzheimer’s disease: findings based on urine proteomics and machine learning
    Wang, Yuye, Sun, Yu, Wang, Yu, Jia, Shuhong, Qiao, Yanan, Zhou, Zhi, Shao, Wen, Zhang, Xiangfei, Guo, Jing, Zhang, Bin et al. · 2023 · Alzheimer's Research & Therapy
39. Correction of Biochemical Abnormalities and Improved Muscle Function in a Phase I/II Clinical Trial of Clenbuterol in Pompe Disease
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40. X chromosome dosage and the genetic impact across human tissues
    Viuff, Mette, Skakkebæk, Anne, Johannsen, Emma B., Chang, Simon, Pedersen, Steen Bønlykke, Lauritsen, Katrine Meyer, Pedersen, Mette Glavind Bülow, Trolle, Christian, Just, Jesper, Gravholt, Claus H. · 2023 · Genome Medicine
41. Neutral or Detrimental Effects of TREM2 Agonist Antibodies in Preclinical Models of Alzheimer’s Disease and Multiple Sclerosis
    Etxeberria, Ainhoa, Shen, Yun-An A., Vito, Stephen, Silverman, Sean M., Imperio, Jose, Lalehzadeh, Guita, Soung, Allison L., Du, Changchun, Xie, Luke, Choy, Man Kin et al. · 2024 · The Journal of Neuroscience
42. Distinct sex-specific DNA methylation differences in Alzheimer’s disease
    C. Silva, Tiago, Zhang, Wei, Young, Juan I., Gomez, Lissette, Schmidt, Michael A., Varma, Achintya, Chen, X. Steven, Martin, Eden R., Wang, Lily · 2022 · Alzheimer's Research & Therapy
43. A Clinical Outcome of the Anti-PD-1 Therapy of Melanoma in Polish Patients Is Mediated by Population-Specific Gut Microbiome Composition
    Pietrzak, Bernadeta, Tomela, Katarzyna, Olejnik-Schmidt, Agnieszka, Galus, Łukasz, Mackiewicz, Jacek, Kaczmarek, Mariusz, Mackiewicz, Andrzej, Schmidt, Marcin · 2022 · Cancers
44. Untitled work
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45. Phenotypic and Clonal Stability of Antigen-Inexperienced Memory-like T Cells across the Genetic Background, Hygienic Status, and Aging
    Moudra, Alena, Niederlova, Veronika, Novotny, Jiri, Schmiedova, Lucie, Kubovciak, Jan, Matejkova, Tereza, Drobek, Ales, Pribikova, Michaela, Stopkova, Romana, Cizkova, Dagmar et al. · 2021 · The Journal of Immunology
46. Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge
    Zhang, Runzhi, Walker, Alejandro R., Datta, Susmita · 2021 · Biology Direct
47. Ceramides and phospholipids are downregulated with liraglutide treatment: results from the LiraFlame randomized controlled trial
    Zobel, Emilie H, Wretlind, Asger, Ripa, Rasmus S, Rotbain Curovic, Viktor, von Scholten, Bernt J, Suvitaival, Tommi, Hansen, Tine W, Kjær, Andreas, Legido-Quigley, Cristina, Rossing, Peter · 2021 · BMJ Open Diabetes Research & Care
48. Violent aggression predicted by multiple pre-adult environmental hits
    Mitjans, Marina, Seidel, Jan, Begemann, Martin, Bockhop, Fabian, Moya-Higueras, Jorge, Bansal, Vikas, Wesolowski, Janina, Seelbach, Anna, Ibáñez, Manuel Ignacio, Kovacevic, Fatka et al. · 2019 · Molecular Psychiatry
49. A model for predicting prognosis in patients with esophageal squamous cell carcinoma based on joint representation learning
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50. Targeting eIF4A triggers an interferon response to synergize with chemotherapy and suppress triple-negative breast cancer
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51. Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma
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52. Lymphoid gene expression supports neuroprotective microglia function
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53. Evolution of reduced co-activator dependence led to target expansion of a starvation response pathway
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55. Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement
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56. Polarized Entry of Human Parechoviruses in the Airway Epithelium
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57. HDACi delivery reprograms tumor-infiltrating myeloid cells to eliminate antigen-loss variants
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58. Using Machine Learning to Measure Relatedness Between Genes: A Multi-Features Model
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59. Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib
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60. Effects of SPI1-mediated transcriptome remodeling on Alzheimer's disease-related phenotypes in mouse models of Aβ amyloidosis
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61. Osteoblast differentiation profiles define sex specific gene expression patterns in craniosynostosis
    Park, Sarah S., Beyer, Richard P., Smyth, Matthew D., Clarke, Christine M., Timms, Andrew E., Bammler, Theo K., Stamper, Brendan D., Mecham, Brigham H., Gustafson, Jennifer A., Cunningham, Michael L. · 2015 · Bone
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63. Single-cell multi-omics map of human fetal blood in Down syndrome
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64. Single-cell RNA sequencing reveals maturation trajectory in human pluripotent stem cell-derived cardiomyocytes in engineered tissues
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65. RNA-seq analysis of gene expression, viral pathogen, and B-cell/T-cell receptor signatures in complex chronic disease
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66. Phenotypic flexibility in respiratory traits is associated with improved aerial respiration in an amphibious fish out of water
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67. Locus-specific induction of gene expression from heterochromatin loci during cellular senescence
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68. DeepMF: deciphering the latent patterns in omics profiles with a deep learning method
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69. Loss of succinyl-CoA synthetase in mouse forebrain results in hypersuccinylation with perturbed neuronal transcription and metabolism
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70. Patients with schizophrenia and bipolar disorder display a similar global gene expression signature in whole blood that reflects elevated proportion of immature neutrophil cells with association to lipid changes
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71. The role of miR-106p-5p in cervical cancer: from expression to molecular mechanism
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72. A probiotic has differential effects on allergic airway inflammation in A/J and C57BL/6 mice and is correlated with the gut microbiome
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73. A Fibrosis-Independent hepatic transcriptomic signature identifies drivers of disease progression in primary sclerosing cholangitis
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74. Multiomics of Colorectal Cancer Organoids Reveals Putative Mediators of Cancer Progression Resulting from SMAD4 Inactivation
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75. Transcriptome Analysis of CHO Cell Size Increase During a Fed-Batch Process
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76. Construction of genetic classification model for coronary atherosclerosis heart disease using three machine learning methods
    Peng, Wenjuan, Sun, Yuan, Zhang, Ling · 2022 · BMC Cardiovascular Disorders
77. LKB1 drives stasis and C/EBP-mediated reprogramming to an alveolar type II fate in lung cancer
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78. COPD patients with chronic bronchitis and higher sputum eosinophil counts show increased type‐2 and PDE4 gene expression in sputum
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79. Dual-Targeted Magnetic Mesoporous Silica Nanoparticles Reduce Brain Amyloid-β Burden via Depolymerization and Intestinal Metabolism
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80. Complement factor B is critical for sub-RPE deposit accumulation in a model of Doyne honeycomb retinal dystrophy with features of age-related macular degeneration
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81. Sex‐specific peripheral and central responses to stress‐induced depression and treatment in a mouse model
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82. Consequences of VHL Loss on Global DNA Methylome
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83. Molecular Landscape of Sex- and Modality-Specific Exercise Adaptation in Human Skeletal Muscle through Large-Scale Multi-Omics Integration
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84. Identification and Validation of the Prognostic Panel in Clear Cell Renal Cell Carcinoma Based on Resting Mast Cells for Prediction of Distant Metastasis and Immunotherapy Response
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85. Evaluation of exploratory fluid biomarkers from a phase 1 senolytic trial in mild Alzheimer's disease
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86. Machine Learning of Hematopoietic Stem Cell Divisions from Paired Daughter Cell Expression Profiles Reveals Effects of Aging on Self-Renewal
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87. ADAMTS12 acts as a tumor microenvironment related cancer promoter in gastric cancer
    Hou, Yangming, Xu, Yingjuan, Wu, Dequan · 2021 · Scientific Reports
88. Genomic and physiological mechanisms underlying skin plasticity during water to air transition in an amphibious fish
    Dong, Yun-wei, Blanchard, Tessa S., Noll, Angela, Vasquez, Picasso, Schmitz, Juergen, Kelly, Scott P., Wright, Patricia A., Whitehead, Andrew · 2020 · Journal of Experimental Biology
89. Skin metatranscriptomics reveals a landscape of variation in microbial activity and gene expression across the human body
    Chia, Minghao, Ng, Amanda Hui Qi, Ravikrishnan, Aarthi, Mohamed Naim, Ahmad Nazri, Wearne, Stephen, Common, John, Nagarajan, Niranjan · 2026 · Nature Biotechnology
90. Impact of aging on meningeal gene expression
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