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

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1. Mapping Systemic Inflammation and Antibody Responses in Multisystem Inflammatory Syndrome in Children (MIS-C)
   Gruber, Conor N., Patel, Roosheel S., Trachtman, Rebecca, Lepow, Lauren, Amanat, Fatima, Krammer, Florian, Wilson, Karen M., Onel, Kenan, Geanon, Daniel, Tuballes, Kevin et al. · 2020 · Cell
2. Disruption of histone methylation in developing sperm impairs offspring health transgenerationally
   Siklenka, Keith, Erkek, Serap, Godmann, Maren, Lambrot, Romain, McGraw, Serge, Lafleur, Christine, Cohen, Tamara, Xia, Jianguo, Suderman, Matthew, Hallett, Michael et al. · 2015 · Science
3. Predicting drug response and synergy using a deep learning model of human cancer cells
   Kuenzi, Brent M., Park, Jisoo, Fong, Samson H., Sanchez, Kyle S., Lee, John, Kreisberg, Jason F., Ma, Jianzhu, Ideker, Trey · 2020 · Cancer Cell
4. muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data
   Crowell, Helena L., Soneson, Charlotte, Germain, Pierre-Luc, Calini, Daniela, Collin, Ludovic, Raposo, Catarina, Malhotra, Dheeraj, Robinson, Mark D. · 2020 · Nature Communications
5. Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation
   Olson, Calla M, Jiang, Baishan, Erb, Michael A, Liang, Yanke, Doctor, Zainab M, Zhang, Zinan, Zhang, Tinghu, Kwiatkowski, Nicholas, Boukhali, Myriam, Green, Jennifer L et al. · 2018 · Nature Chemical Biology
6. Thalidomide promotes degradation of SALL4, a transcription factor implicated in Duane Radial Ray syndrome
   Donovan, Katherine A, An, Jian, Nowak, Radosław P, Yuan, Jingting C, Fink, Emma C, Berry, Bethany C, Ebert, Benjamin L, Fischer, Eric S · 2018 · eLife
7. Metabolic modeling of single Th17 cells reveals regulators of autoimmunity
   Wagner, Allon, Wang, Chao, Fessler, Johannes, DeTomaso, David, Avila-Pacheco, Julian, Kaminski, James, Zaghouani, Sarah, Christian, Elena, Thakore, Pratiksha, Schellhaass, Brandon et al. · 2021 · Cell
8. Inhibition of dihydroorotate dehydrogenase overcomes differentiation blockade in acute myeloid leukemia
   Sykes, David B., Kfoury, Youmna S., Mercier, François E., Wawer, Mathias J., Law, Jason M., Haynes, Mark K., Lewis, Timothy A., Schajnovitz, Amir, Jain, Esha, Lee, Dongjun et al. · 2016 · Cell
9. Identification of new therapeutic targets for osteoarthritis through genome-wide analyses of UK Biobank data
   arcOGEN Consortium, Tachmazidou, Ioanna, Hatzikotoulas, Konstantinos, Southam, Lorraine, Esparza-Gordillo, Jorge, Haberland, Valeriia, Zheng, Jie, Johnson, Toby, Koprulu, Mine, Zengini, Eleni et al. · 2019 · Nature Genetics
10. Auto-aggressive CXCR6+ CD8 T cells cause liver immune pathology in NASH
    Dudek, Michael, Pfister, Dominik, Donakonda, Sainitin, Filpe, Pamela, Schneider, Annika, Laschinger, Melanie, Hartmann, Daniel, Hüser, Norbert, Meiser, Philippa, Bayerl, Felix et al. · 2021 · Nature
11. Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens
    Nédélec, Yohann, Sanz, Joaquín, Baharian, Golshid, Szpiech, Zachary A., Pacis, Alain, Dumaine, Anne, Grenier, Jean-Christophe, Freiman, Andrew, Sams, Aaron J., Hebert, Steven et al. · 2016 · Cell
12. Reliability of human cortical organoid generation
    Yoon, Se-Jin, Elahi, Lubayna S., Pașca, Anca M., Marton, Rebecca M., Gordon, Aaron, Revah, Omer, Miura, Yuki, Walczak, Elisabeth M., Holdgate, Gwendolyn M., Fan, H. Christina et al. · 2019 · Nature Methods
13. Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex
    Hrvatin, Sinisa, Hochbaum, Daniel R., Nagy, M. Aurel, Cicconet, Marcelo, Robertson, Keiramarie, Cheadle, Lucas, Zilionis, Rapolas, Ratner, Alex, Borges-Monroy, Rebeca, Klein, Allon M. et al. · 2018 · Nature Neuroscience
14. Efficacy of faecal microbiota transplantation for patients with irritable bowel syndrome in a randomised, double-blind, placebo-controlled study
    El-Salhy, Magdy, Hatlebakk, Jan Gunnar, Gilja, Odd Helge, Bråthen Kristoffersen, Anja, Hausken, Trygve · 2020 · Gut
15. Controlling Bias and inflation in epigenome- and transcriptome-wide association studies using the empirical null distribution
    the BIOS Consortium, van Iterson, Maarten, van Zwet, Erik W., Heijmans, Bastiaan T. · 2017 · Genome biology
16. Atopic Dermatitis Is an IL-13–Dominant Disease with Greater Molecular Heterogeneity Compared to Psoriasis
    Tsoi, Lam C., Rodriguez, Elke, Degenhardt, Frauke, Baurecht, Hansjörg, Wehkamp, Ulrike, Volks, Natalie, Szymczak, Silke, Swindell, William R., Sarkar, Mrinal K., Raja, Kalpana et al. · 2019 · Journal of Investigative Dermatology
17. Transcriptomic profiling across the nonalcoholic fatty liver disease spectrum reveals gene signatures for steatohepatitis and fibrosis
    Govaere, Olivier, Cockell, Simon, Tiniakos, Dina, Queen, Rachel, Younes, Ramy, Vacca, Michele, Alexander, Leigh, Ravaioli, Federico, Palmer, Jeremy, Petta, Salvatore et al. · 2020 · Science Translational Medicine
18. Single-nucleus transcriptome analysis reveals dysregulation of angiogenic endothelial cells and neuroprotective glia in Alzheimer’s disease
    Lau, Shun-Fat, Cao, Han, Fu, Amy K. Y., Ip, Nancy Y. · 2020 · Proceedings of the National Academy of Sciences
19. Computational principles and challenges in single-cell data integration
    Argelaguet, Ricard, Cuomo, Anna S. E., Stegle, Oliver, Marioni, John C. · 2021 · Nature Biotechnology
20. Acceleration of β Cell Aging Determines Diabetes and Senolysis Improves Disease Outcomes
    Aguayo-Mazzucato, Cristina, Andle, Joshua, Lee, Terrence B., Midha, Ayush, Talemal, Lindsay, Chipashvili, Vaja, Hollister-Lock, Jennifer, van Deursen, Jan, Weir, Gordon, Bonner-Weir, Susan · 2019 · Cell Metabolism
21. Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma
    Lee, Karla A., Thomas, Andrew Maltez, Bolte, Laura A., Björk, Johannes R., de Ruijter, Laura Kist, Armanini, Federica, Asnicar, Francesco, Blanco-Miguez, Aitor, Board, Ruth, Calbet-Llopart, Neus et al. · 2022 · Nature Medicine
22. WRN helicase is a synthetic lethal target in microsatellite unstable cancers
    Chan, Edmond M., Shibue, Tsukasa, McFarland, James M., Gaeta, Benjamin, Ghandi, Mahmoud, Dumont, Nancy, Gonzalez, Alfredo, McPartlan, Justine S., Li, Tianxia, Zhang, Yanxi et al. · 2019 · Nature
23. Epigenetic regulation of brain region-specific microglia clearance activity
    Ayata, Pinar, Badimon, Ana, Strasburger, Hayley J., Duff, Mary Kaye, Montgomery, Sarah E., Loh, Yong-Hwee E., Ebert, Anja, Pimenova, Anna A., Ramirez, Brianna R., Chan, Andrew T. et al. · 2018 · Nature Neuroscience
24. Transgenerational transmission of environmental information in C. elegans
    Klosin, Adam, Casas, Eduard, Hidalgo-Carcedo, Cristina, Vavouri, Tanya, Lehner, Ben · 2017 · Science
25. Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity
    Pillon, Nicolas J., Gabriel, Brendan M., Dollet, Lucile, Smith, Jonathon A. B., Sardón Puig, Laura, Botella, Javier, Bishop, David J., Krook, Anna, Zierath, Juleen R. · 2020 · Nature Communications
26. NOX4 inhibition potentiates immunotherapy by overcoming cancer-associated fibroblast-mediated CD8 T-cell exclusion from tumors
    Ford, Kirsty, Hanley, Christopher J., Mellone, Massimiliano, Szyndralewiez, Cedric, Heitz, Freddy, Wiesel, Philippe, Wood, Oliver, Machado, Maria, Lopez, Maria-Antoinette, Ganesan, Anusha-Preethi et al. · 2020 · Cancer Research
27. Human cardiac organoids for the modelling of myocardial infarction and drug cardiotoxicity
    Richards, Dylan J., Li, Yang, Kerr, Charles M., Yao, Jenny, Beeson, Gyda C., Coyle, Robert C., Chen, Xun, Jia, Jia, Damon, Brooke, Wilson, Robert et al. · 2020 · Nature Biomedical Engineering
28. Spatially confined sub-tumor microenvironments in pancreatic cancer
    Grünwald, Barbara T., Devisme, Antoine, Andrieux, Geoffroy, Vyas, Foram, Aliar, Kazeera, McCloskey, Curtis W., Macklin, Andrew, Jang, Gun Ho, Denroche, Robert, Romero, Joan Miguel et al. · 2021 · Cell
29. Massively multiplex chemical transcriptomics at single-cell resolution
    Srivatsan, Sanjay R., McFaline-Figueroa, José L., Ramani, Vijay, Saunders, Lauren, Cao, Junyue, Packer, Jonathan, Pliner, Hannah A., Jackson, Dana L., Daza, Riza M., Christiansen, Lena et al. · 2020 · Science
30. The mammalian ribo-interactome reveals ribosome functional diversity and heterogeneity
    Simsek, Deniz, Tiu, Gerald C., Flynn, Ryan A., Byeon, Gun W., Leppek, Kathrin, Xu, Adele F., Chang, Howard Y., Barna, Maria · 2017 · Cell
31. Autism genes converge on asynchronous development of shared neuron classes
    Paulsen, Bruna, Velasco, Silvia, Kedaigle, Amanda J., Pigoni, Martina, Quadrato, Giorgia, Deo, Anthony J., Adiconis, Xian, Uzquiano, Ana, Sartore, Rafaela, Yang, Sung Min et al. · 2022 · Nature
32. A Chemoproteomic Approach to Query the Degradable Kinome Using a Multi-kinase Degrader
    Huang, Hai-Tsang, Dobrovolsky, Dennis, Paulk, Joshiawa, Yang, Guang, Weisberg, Ellen L., Doctor, Zainab M., Buckley, Dennis L., Cho, Joong-Heui, Ko, Eunhwa, Jang, Jaebong et al. · 2018 · Cell Chemical Biology
33. Effects of microbiota-directed foods in gnotobiotic animals and undernourished children
    Gehrig, Jeanette L., Venkatesh, Siddarth, Chang, Hao-Wei, Hibberd, Matthew C., Kung, Vanderlene L., Cheng, Jiye, Chen, Robert Y., Subramanian, Sathish, Cowardin, Carrie A., Meier, Martin F. et al. · 2019 · Science
34. The plastisphere in marine ecosystem hosts potential specific microbial degraders including alcanivorax borkumensis as a key player for the low-density polyethylene degradation
    Delacuvellerie, Alice, Cyriaque, Valentine, Gobert, Sylvie, Benali, Samira, Wattiez, Ruddy · 2019 · Journal of Hazardous Materials
35. Comprehensive Multi-omics Analysis Reveals Mitochondrial Stress as a Central Biological Hub for Spaceflight Impact
    da Silveira, Willian A., Fazelinia, Hossein, Rosenthal, Sara Brin, Laiakis, Evagelia C., Kim, Man S., Meydan, Cem, Kidane, Yared, Rathi, Komal S., Smith, Scott M., Stear, Benjamin et al. · 2020 · Cell
36. A multidimensional systems biology analysis of cellular senescence in aging and disease
    Avelar, Roberto A., Ortega, Javier Gómez, Tacutu, Robi, Tyler, Eleanor J., Bennett, Dominic, Binetti, Paolo, Budovsky, Arie, Chatsirisupachai, Kasit, Johnson, Emily, Murray, Alex et al. · 2020 · Genome Biology
37. Microbial signals drive pre-leukaemic myeloproliferation in a Tet2-deficient host
    Meisel, Marlies, Hinterleitner, Reinhard, Pacis, Alain, Chen, Li, Earley, Zachary M., Mayassi, Toufic, Pierre, Joseph F., Ernest, Jordan D., Galipeau, Heather J., Thuille, Nikolaus et al. · 2018 · Nature
38. Distinct descending motor cortex pathways and their roles in movement
    Economo, Michael N., Viswanathan, Sarada, Tasic, Bosiljka, Bas, Erhan, Winnubst, Johan, Menon, Vilas, Graybuck, Lucas T., Nguyen, Thuc Nghi, Smith, Kimberly A., Yao, Zizhen et al. · 2018 · Nature
39. Sex differences in nucleus accumbens transcriptome profiles associated with susceptibility versus resilience to subchronic variable stress
    Hodes, Georgia E., Pfau, Madeline L., Purushothaman, Immanuel, Ahn, H. Francisca, Golden, Sam A., Christoffel, Daniel J., Magida, Jane, Brancato, Anna, Takahashi, Aki, Flanigan, Meghan E. et al. · 2015 · The Journal of Neuroscience
40. Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia
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41. Association of inflammatory biomarkers with clinical outcomes in nivolumab-treated patients with advanced hepatocellular carcinoma
    Sangro, Bruno, Melero, Ignacio, Wadhawan, Samir, Finn, Richard S., Abou-Alfa, Ghassan K., Cheng, Ann-Lii, Yau, Thomas, Furuse, Junji, Park, Joong-Won, Boyd, Zachary et al. · 2020 · Journal of Hepatology
42. Necroptosis microenvironment directs lineage commitment in liver cancer
    Seehawer, Marco, Heinzmann, Florian, D’Artista, Luana, Harbig, Jule, Roux, Pierre-François, Hoenicke, Lisa, Dang, Hien, Klotz, Sabrina, Robinson, Lucas, Doré, Grégory et al. · 2018 · Nature
43. Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia
    Giustacchini, Alice, Thongjuea, Supat, Barkas, Nikolaos, Woll, Petter S, Povinelli, Benjamin J, Booth, Christopher A G, Sopp, Paul, Norfo, Ruggiero, Rodriguez-Meira, Alba, Ashley, Neil et al. · 2017 · Nature Medicine
44. Human neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions for optimal therapeutic protection
    Winkler, Emma S., Gilchuk, Pavlo, Yu, Jinsheng, Bailey, Adam L., Chen, Rita E., Chong, Zhenlu, Zost, Seth J., Jang, Hyesun, Huang, Ying, Allen, James D. et al. · 2021 · Cell
45. Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA
    Abbosh, Christopher, Frankell, Alexander M., Harrison, Thomas, Kisistok, Judit, Garnett, Aaron, Johnson, Laura, Veeriah, Selvaraju, Moreau, Mike, Chesh, Adrian, Chaunzwa, Tafadzwa L. et al. · 2023 · Nature
46. Dynamic shifts in the composition of resident and recruited macrophages influence tissue remodeling in NASH
    Daemen, Sabine, Gainullina, Anastasiia, Kalugotla, Gowri, He, Li, Chan, Mandy M., Beals, Joseph W., Liss, Kim H., Klein, Samuel, Feldstein, Ariel E., Finck, Brian N. et al. · 2021 · Cell Reports
47. Batch effects and the effective design of single-cell gene expression studies
    Tung, Po-Yuan, Blischak, John D., Hsiao, Chiaowen Joyce, Knowles, David A., Burnett, Jonathan E., Pritchard, Jonathan K., Gilad, Yoav · 2017 · Scientific Reports
48. Rational discovery of molecular glue degraders via scalable chemical profiling
    Mayor-Ruiz, Cristina, Bauer, Sophie, Brand, Matthias, Kozicka, Zuzanna, Siklos, Marton, Imrichova, Hana, Kaltheuner, Ines H., Hahn, Elisa, Seiler, Kristina, Koren, Anna et al. · 2020 · Nature Chemical Biology
49. Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis
    Sahraeian, Sayed Mohammad Ebrahim, Mohiyuddin, Marghoob, Sebra, Robert, Tilgner, Hagen, Afshar, Pegah T., Au, Kin Fai, Bani Asadi, Narges, Gerstein, Mark B., Wong, Wing Hung, Snyder, Michael P. et al. · 2017 · Nature Communications
50. Impaired Mitochondrial Biogenesis in Adipose Tissue in Acquired Obesity
    Heinonen, Sini, Buzkova, Jana, Muniandy, Maheswary, Kaksonen, Risto, Ollikainen, Miina, Ismail, Khadeeja, Hakkarainen, Antti, Lundbom, Jesse, Lundbom, Nina, Vuolteenaho, Katriina et al. · 2015 · Diabetes
51. Neoadjuvant cabozantinib and nivolumab convert locally advanced hepatocellular carcinoma into resectable disease with enhanced antitumor immunity
    Ho, Won Jin, Zhu, Qingfeng, Durham, Jennifer, Popovic, Aleksandra, Xavier, Stephanie, Leatherman, James, Mohan, Aditya, Mo, Guanglan, Zhang, Shu, Gross, Nicole et al. · 2021 · Nature Cancer
52. A systematic evaluation of normalization methods in quantitative label-free proteomics
    Välikangas, Tommi, Suomi, Tomi, Elo, Laura L. · 2016 · Briefings in Bioinformatics
53. From cohorts to molecules: adverse impacts of endocrine disrupting mixtures
    Caporale, Nicolò, Leemans, Michelle, Birgersson, Lina, Germain, Pierre-Luc, Cheroni, Cristina, Borbély, Gábor, Engdahl, Elin, Lindh, Christian, Bressan, Raul Bardini, Cavallo, Francesca et al. · 2022 · Science
54. FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data
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55. Mitochondrial DNA drives abscopal responses to radiation that are inhibited by autophagy
    Yamazaki, Takahiro, Kirchmair, Alexander, Sato, Ai, Buqué, Aitziber, Rybstein, Marissa, Petroni, Giulia, Bloy, Norma, Finotello, Francesca, Stafford, Lena, Navarro Manzano, Esther et al. · 2020 · Nature Immunology
56. Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration
    Ratnapriya, Rinki, Sosina, Olukayode A., Starostik, Margaret R., Kwicklis, Madeline, Kapphahn, Rebecca J., Fritsche, Lars G., Walton, Ashley, Arvanitis, Marios, Gieser, Linn, Pietraszkiewicz, Alexandra et al. · 2019 · Nature Genetics
57. Mapping the Degradable Kinome Provides a Resource for Expedited Degrader Development
    Donovan, Katherine A., Ferguson, Fleur M., Bushman, Jonathan W., Eleuteri, Nicholas A., Bhunia, Debabrata, Ryu, SeongShick, Tan, Li, Shi, Kun, Yue, Hong, Liu, Xiaoxi et al. · 2020 · Cell
58. Host-Protozoan Interactions Protect from Mucosal Infections through Activation of the Inflammasome
    Chudnovskiy, Aleksey, Mortha, Arthur, Kana, Veronika, Kennard, Andrea, Ramirez, Juan David, Rahman, Adeeb, Remark, Romain, Mogno, Ilaria, Ng, Ruby, Gnjatic, Sasha et al. · 2016 · Cell
59. Transcriptional signature in microglia associated with Aβ plaque phagocytosis
    Grubman, Alexandra, Choo, Xin Yi, Chew, Gabriel, Ouyang, John F., Sun, Guizhi, Croft, Nathan P., Rossello, Fernando J., Simmons, Rebecca, Buckberry, Sam, Landin, Dulce Vargas et al. · 2021 · Nature Communications
60. Joint analysis of heterogeneous single-cell RNA-seq dataset collections
    Barkas, Nikolas, Petukhov, Viktor, Nikolaeva, Daria, Lozinsky, Yaroslav, Demharter, Samuel, Khodosevich, Konstantin, Kharchenko, Peter V. · 2019 · Nature Methods
61. Deleting DNMT3A in CAR T cells prevents exhaustion and enhances antitumor activity
    Prinzing, Brooke, Zebley, Caitlin C., Petersen, Christopher T., Fan, Yiping, Anido, Alejandro Allo, Yi, Zhongzhen, Nguyen, Phuong, Houke, Haley, Bell, Matthew, Haydar, Dalia et al. · 2021 · Science Translational Medicine
62. A blood atlas of COVID-19 defines hallmarks of disease severity and specificity
    Ahern, David J., Ai, Zhichao, Ainsworth, Mark, Allan, Chris, Allcock, Alice, Angus, Brian, Ansari, M. Azim, Arancibia-Cárcamo, Carolina V., Aschenbrenner, Dominik, Attar, Moustafa et al. · 2022 · Cell
63. Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data
    Wang, Tianyu, Li, Boyang, Nelson, Craig E., Nabavi, Sheida · 2019 · BMC Bioinformatics
64. The enteric nervous system relays psychological stress to intestinal inflammation
    Schneider, Kai Markus, Blank, Niklas, Alvarez, Yelina, Thum, Katharina, Lundgren, Patrick, Litichevskiy, Lev, Sleeman, Madeleine, Bahnsen, Klaas, Kim, Jihee, Kardo, Simon et al. · 2023 · Cell
65. Combined Social and Spatial Coding in a Descending Projection from the Prefrontal Cortex
    Murugan, Malavika, Jang, Hee Jae, Park, Michelle, Miller, Ellia M., Cox, Julia, Taliaferro, Joshua P., Parker, Nathan F., Bhave, Varun, Hur, Hong, Liang, Yupu et al. · 2017 · Cell
66. LC3-Associated Phagocytosis in Myeloid Cells Promotes Tumor Immune Tolerance
    Cunha, Larissa D., Yang, Mao, Carter, Robert, Guy, Clifford, Harris, Lacie, Crawford, Jeremy C., Quarato, Giovanni, Boada-Romero, Emilio, Kalkavan, Halime, Johnson, Michael D.L. et al. · 2018 · Cell
67. Microglial NF-κB drives tau spreading and toxicity in a mouse model of tauopathy
    Wang, Chao, Fan, Li, Khawaja, Rabia R., Liu, Bangyan, Zhan, Lihong, Kodama, Lay, Chin, Marcus, Li, Yaqiao, Le, David, Zhou, Yungui et al. · 2022 · Nature Communications
68. Mesenchymal inflammation drives genotoxic stress in hematopoietic stem cells and predicts disease evolution in human pre-leukemia
    Zambetti, Noemi A., Ping, Zhen, Chen, Si, Kenswil, Keane J.G., Mylona, Maria A., Sanders, Mathijs A., Hoogenboezem, Remco M., Bindels, Eric M.J., Adisty, Maria N., Van Strien, Paulina M.H. et al. · 2016 · Cell stem cell
69. Commensal bacteria promote endocrine resistance in prostate cancer through androgen biosynthesis
    Pernigoni, Nicolò, Zagato, Elena, Calcinotto, Arianna, Troiani, Martina, Mestre, Ricardo Pereira, Calì, Bianca, Attanasio, Giuseppe, Troisi, Jacopo, Minini, Mirko, Mosole, Simone et al. · 2021 · Science
70. Two subsets of stem-like CD8+ memory T cell progenitors with distinct fate commitments in humans
    Galletti, Giovanni, De Simone, Gabriele, Mazza, Emilia M. C., Puccio, Simone, Mezzanotte, Claudia, Bi, Timothy M., Davydov, Alexey N., Metsger, Maria, Scamardella, Eloise, Alvisi, Giorgia et al. · 2020 · Nature Immunology
71. Exaggerated false positives by popular differential expression methods when analyzing human population samples
    Li, Yumei, Ge, Xinzhou, Peng, Fanglue, Li, Wei, Li, Jingyi Jessica · 2022 · Genome Biology
72. Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type
    Boldog, Eszter, Bakken, Trygve E., Hodge, Rebecca D., Novotny, Mark, Aevermann, Brian D., Baka, Judith, Bordé, Sándor, Close, Jennie L., Diez-Fuertes, Francisco, Ding, Song-Lin et al. · 2018 · Nature Neuroscience
73. The Intestine Harbors Functionally Distinct Homeostatic Tissue-Resident and Inflammatory Th17 Cells
    Omenetti, Sara, Bussi, Claudio, Metidji, Amina, Iseppon, Andrea, Lee, Sunjae, Tolaini, Mauro, Li, Ying, Kelly, Gavin, Chakravarty, Probir, Shoaie, Saeed et al. · 2019 · Immunity
74. Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans
    Patnode, Michael L., Beller, Zachary W., Han, Nathan D., Cheng, Jiye, Peters, Samantha L., Terrapon, Nicolas, Henrissat, Bernard, Le Gall, Sophie, Saulnier, Luc, Hayashi, David K. et al. · 2019 · Cell
75. Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data
    Holland, Christian H., Tanevski, Jovan, Perales-Patón, Javier, Gleixner, Jan, Kumar, Manu P., Mereu, Elisabetta, Joughin, Brian A., Stegle, Oliver, Lauffenburger, Douglas A., Heyn, Holger et al. · 2020 · Genome Biology
76. Monoterpenes Support Systemic Acquired Resistance within and between Plants
    Riedlmeier, Marlies, Ghirardo, Andrea, Wenig, Marion, Knappe, Claudia, Koch, Kerstin, Georgii, Elisabeth, Dey, Sanjukta, Parker, Jane E., Schnitzler, Jörg-Peter, Vlot, A. Corina · 2017 · The Plant Cell
77. Caloric restriction in humans reveals immunometabolic regulators of health span
    Spadaro, O., Youm, Y., Shchukina, I., Ryu, S., Sidorov, S., Ravussin, A., Nguyen, K., Aladyeva, E., Predeus, A. N., Smith, S. R. et al. · 2022 · Science
78. Regulatory T Cell Specificity Directs Tolerance versus Allergy against Aeroantigens in Humans
    Bacher, Petra, Heinrich, Frederik, Stervbo, Ulrik, Nienen, Mikalai, Vahldieck, Marco, Iwert, Christina, Vogt, Katrin, Kollet, Jutta, Babel, Nina, Sawitzki, Birgit et al. · 2016 · Cell
79. Dream: powerful differential expression analysis for repeated measures designs
    Hoffman, Gabriel E, Roussos, Panos · 2021 · Bioinformatics
80. Tau induces blood vessel abnormalities and angiogenesis-related gene expression in P301L transgenic mice and human Alzheimer’s disease
    Bennett, Rachel E., Robbins, Ashley B., Hu, Miwei, Cao, Xinrui, Betensky, Rebecca A., Clark, Tim, Das, Sudeshna, Hyman, Bradley T. · 2018 · Proceedings of the National Academy of Sciences
81. Social status alters immune regulation and response to infection in macaques
    Snyder-Mackler, Noah, Sanz, Joaquín, Kohn, Jordan N., Brinkworth, Jessica F., Morrow, Shauna, Shaver, Amanda O., Grenier, Jean-Christophe, Pique-Regi, Roger, Johnson, Zachary P., Wilson, Mark E. et al. · 2016 · Science
82. In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes
    Jin, Xin, Simmons, Sean K., Guo, Amy, Shetty, Ashwin S., Ko, Michelle, Nguyen, Lan, Jokhi, Vahbiz, Robinson, Elise, Oyler, Paul, Curry, Nathan et al. · 2020 · Science
83. Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines
    Cano-Gamez, Kiki, Soskic, Blagoje, Roumeliotis, Theodoros I., So, Ernest, Smyth, Deborah J., Baldrighi, Marta, Willé, David, Nakic, Nikolina, Esparza-Gordillo, Jorge, Larminie, Christopher G. C. et al. · 2020 · Nature Communications
84. Interleukin-11 is a therapeutic target in idiopathic pulmonary fibrosis
    Ng, Benjamin, Dong, Jinrui, D’Agostino, Giuseppe, Viswanathan, Sivakumar, Widjaja, Anissa A., Lim, Wei-Wen, Ko, Nicole S. J., Tan, Jessie, Chothani, Sonia P., Huang, Benjamin et al. · 2019 · Science Translational Medicine
85. γδ T cells are effectors of immunotherapy in cancers with HLA class I defects
    de Vries, Natasja L., van de Haar, Joris, Veninga, Vivien, Chalabi, Myriam, Ijsselsteijn, Marieke E., van der Ploeg, Manon, van den Bulk, Jitske, Ruano, Dina, van den Berg, Jose G., Haanen, John B. et al. · 2023 · Nature
86. The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice
    Kindt, Alida, Liebisch, Gerhard, Clavel, Thomas, Haller, Dirk, Hörmannsperger, Gabriele, Yoon, Hongsup, Kolmeder, Daniela, Sigruener, Alexander, Krautbauer, Sabrina, Seeliger, Claudine et al. · 2018 · Nature Communications
87. Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation
    Lee, Hyeseung, Fenster, Robert J., Pineda, S. Sebastian, Gibbs, Whitney S., Mohammadi, Shahin, Davila-Velderrain, Jose, Garcia, Francisco J., Therrien, Martine, Novis, Hailey S., Gao, Fan et al. · 2020 · Neuron
88. A bacterial bile acid metabolite modulates Treg activity through the nuclear hormone receptor NR4A1
    Li, Wei, Hang, Saiyu, Fang, Yuan, Bae, Sena, Zhang, Yancong, Zhang, Minghao, Wang, Gang, McCurry, Megan D., Bae, Munhyung, Paik, Donggi et al. · 2021 · Cell Host & Microbe
89. Making sense of the ageing methylome
    Seale, Kirsten, Horvath, Steve, Teschendorff, Andrew, Eynon, Nir, Voisin, Sarah · 2022 · Nature Reviews Genetics
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