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Confronting false discoveries in single-cell differential expression

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Cited by:

  1. David G. Coffey & Francesco Maura & Edgar Gonzalez-Kozlova & J. Javier Diaz-Mejia & Ping Luo & Yong Zhang & Yuexin Xu & Edus H. Warren & Travis Dawson & Brian Lee & Hui Xie & Eric Smith & Amanda Ciard, 2023. "Immunophenotypic correlates of sustained MRD negativity in patients with multiple myeloma," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  2. Guillermo Serrano & Nerea Berastegui & Aintzane Díaz-Mazkiaran & Paula García-Olloqui & Carmen Rodriguez-Res & Sofia Huerga-Dominguez & Marina Ainciburu & Amaia Vilas-Zornoza & Patxi San Martin-Uriz &, 2024. "Single-cell transcriptional profile of CD34+ hematopoietic progenitor cells from del(5q) myelodysplastic syndromes and impact of lenalidomide," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  3. Xiaomin Wen & Alex K. Hu & Scott R. Presnell & Emily S. Ford & David M. Koelle & William W. Kwok, 2025. "Longitudinal single cell profiling of epitope specific memory CD4+ T cell responses to recombinant zoster vaccine," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
  4. Eloise Berson & Anjali Sreenivas & Thanaphong Phongpreecha & Amalia Perna & Fiorella C. Grandi & Lei Xue & Neal G. Ravindra & Neelufar Payrovnaziri & Samson Mataraso & Yeasul Kim & Camilo Espinosa & A, 2023. "Whole genome deconvolution unveils Alzheimer’s resilient epigenetic signature," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  5. Suhas V. Vasaikar & Adam K. Savage & Qiuyu Gong & Elliott Swanson & Aarthi Talla & Cara Lord & Alexander T. Heubeck & Julian Reading & Lucas T. Graybuck & Paul Meijer & Troy R. Torgerson & Peter J. Sk, 2023. "A comprehensive platform for analyzing longitudinal multi-omics data," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  6. Jonas Stewen & Kai Kruse & Anca T. Godoi-Filip & Zenia & Hyun-Woo Jeong & Susanne Adams & Frank Berkenfeld & Martin Stehling & Kristy Red-Horse & Ralf H. Adams & Mara E. Pitulescu, 2024. "Eph-ephrin signaling couples endothelial cell sorting and arterial specification," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
  7. Leonardo D. Garma & Lisbeth Harder & Juan M. Barba-Reyes & Sergio Marco Salas & Mónica Díez-Salguero & Mats Nilsson & Alberto Serrano-Pozo & Bradley T. Hyman & Ana B. Muñoz-Manchado, 2024. "Interneuron diversity in the human dorsal striatum," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  8. Allen Yen & Simona Sarafinovska & Xuhua Chen & Dominic D. Skinner & Fatjon Leti & MariaLynn Crosby & Jessica Hoisington-Lopez & Yizhe Wu & Jiayang Chen & Zipeng A. Li & Kevin K. Noguchi & Robi D. Mitr, 2024. "MYT1L deficiency impairs excitatory neuron trajectory during cortical development," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
  9. Jia-Ru Wei & Zhao-Zhe Hao & Chuan Xu & Mengyao Huang & Lei Tang & Nana Xu & Ruifeng Liu & Yuhui Shen & Sarah A. Teichmann & Zhichao Miao & Sheng Liu, 2022. "Identification of visual cortex cell types and species differences using single-cell RNA sequencing," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
  10. T. Hautz & S. Salcher & M. Fodor & G. Sturm & S. Ebner & A. Mair & M. Trebo & G. Untergasser & S. Sopper & B. Cardini & A. Martowicz & J. Hofmann & S. Daum & M. Kalb & T. Resch & F. Krendl & A. Weisse, 2023. "Immune cell dynamics deconvoluted by single-cell RNA sequencing in normothermic machine perfusion of the liver," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  11. Yann Vanrobaeys & Zeru J. Peterson & Emily. N. Walsh & Snehajyoti Chatterjee & Li-Chun Lin & Lisa C. Lyons & Thomas Nickl-Jockschat & Ted Abel, 2023. "Spatial transcriptomics reveals unique gene expression changes in different brain regions after sleep deprivation," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  12. Manvendra Singh & Ying Zhao & Vinicius Daguano Gastaldi & Sonja M. Wojcik & Yasmina Curto & Riki Kawaguchi & Ricardo M. Merino & Laura Fernandez Garcia-Agudo & Holger Taschenberger & Nils Brose & Dani, 2023. "Erythropoietin re-wires cognition-associated transcriptional networks," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  13. Hai C. T. Nguyen & Bukyung Baik & Sora Yoon & Taesung Park & Dougu Nam, 2023. "Benchmarking integration of single-cell differential expression," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  14. Shreya Johri & Kevin Bi & Breanna M. Titchen & Jingxin Fu & Jake Conway & Jett P. Crowdis & Natalie I. Vokes & Zenghua Fan & Lawrence Fong & Jihye Park & David Liu & Meng Xiao He & Eliezer M. Van Alle, 2025. "Dissecting tumor cell programs through group biology estimation in clinical single-cell transcriptomics," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
  15. Haven Tillmon & Breeanne M. Soteros & Liang Shen & Qifei Cong & Mackenna Wollet & Julianne General & Hanna Chin & John Beichen Lee & Flavia R. Carreno & David A. Morilak & Jun Hee Kim & Gek Ming Sia, 2024. "Complement and microglia activation mediate stress-induced synapse loss in layer 2/3 of the medial prefrontal cortex in male mice," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  16. Samir Rachid Zaim & Mark-Phillip Pebworth & Imran McGrath & Lauren Okada & Morgan Weiss & Julian Reading & Julie L. Czartoski & Troy R. Torgerson & M. Juliana McElrath & Thomas F. Bumol & Peter J. Ske, 2024. "MOCHA’s advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts," Nature Communications, Nature, vol. 15(1), pages 1-24, December.
  17. Bing He & Yao Xiao & Haodong Liang & Qianhui Huang & Yuheng Du & Yijun Li & David Garmire & Duxin Sun & Lana X. Garmire, 2023. "ASGARD is A Single-cell Guided Pipeline to Aid Repurposing of Drugs," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  18. Colin Y. C. Lee & Bethany C. Kennedy & Nathan Richoz & Isaac Dean & Zewen K. Tuong & Fabrina Gaspal & Zhi Li & Claire Willis & Tetsuo Hasegawa & Sarah K. Whiteside & David A. Posner & Gianluca Carless, 2024. "Tumour-retained activated CCR7+ dendritic cells are heterogeneous and regulate local anti-tumour cytolytic activity," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  19. Maxime Brunner & David Lopez-Rodriguez & Judith Estrada-Meza & Rafik Dali & Antoine Rohrbach & Tamara Deglise & Andrea Messina & Bernard Thorens & Federico Santoni & Fanny Langlet, 2024. "Fasting induces metabolic switches and spatial redistributions of lipid processing and neuronal interactions in tanycytes," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  20. Alan E. Murphy & Nathan G. Skene, 2022. "A balanced measure shows superior performance of pseudobulk methods in single-cell RNA-sequencing analysis," Nature Communications, Nature, vol. 13(1), pages 1-4, December.
  21. BaDoi N. Phan & Madelyn H. Ray & Xiangning Xue & Chen Fu & Robert J. Fenster & Stephen J. Kohut & Jack Bergman & Suzanne N. Haber & Kenneth M. McCullough & Madeline K. Fish & Jill R. Glausier & Qiao S, 2024. "Single nuclei transcriptomics in human and non-human primate striatum in opioid use disorder," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  22. Alan Yue Yang Teo & Jordan W. Squair & Gregoire Courtine & Michael A. Skinnider, 2024. "Best practices for differential accessibility analysis in single-cell epigenomics," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  23. Ariel Madrigal & Tianyuan Lu & Larisa M. Soto & Hamed S. Najafabadi, 2024. "A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
  24. Chang Su & Dongsoo Lee & Peng Jin & Jingfei Zhang, 2025. "scMultiMap: Cell-type-specific mapping of enhancers and target genes from single-cell multimodal data," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
  25. Özkan İş & Xue Wang & Joseph S. Reddy & Yuhao Min & Elanur Yilmaz & Prabesh Bhattarai & Tulsi Patel & Jeremiah Bergman & Zachary Quicksall & Michael G. Heckman & Frederick Q. Tutor-New & Birsen Can De, 2024. "Gliovascular transcriptional perturbations in Alzheimer’s disease reveal molecular mechanisms of blood brain barrier dysfunction," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
  26. Raymond Hall Yip Louie & Curtis Cai & Jerome Samir & Mandeep Singh & Ira W. Deveson & James M. Ferguson & Timothy G. Amos & Helen Marie McGuire & Kavitha Gowrishankar & Thiruni Adikari & Robert Balder, 2023. "CAR+ and CAR− T cells share a differentiation trajectory into an NK-like subset after CD19 CAR T cell infusion in patients with B cell malignancies," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
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