Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

Marbach, Daniel, Lamparter, David, Quon, Gerald, Kellis, Manolis, Kutalik, Zoltán, Bergmann, Sven·2016·Nature Methods

Cited by (346)

Items 101–200 of 346

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    Patrice Delaney, Anjana Ramdas Nair, Catherine Palmer, Nouf Khan, Kirsten C. Sadler · 2020 · Toxicology and Applied Pharmacology
  2. Inference of cell type specific regulatory networks on mammalian lineages
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  3. Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro
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  8. Inferring Gene Regulatory Networks From Single-Cell Transcriptomic Data Using Bidirectional RNN
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  10. Integrating comprehensive functional annotations to boost power and accuracy in gene-based association analysis
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  17. RegEnrich gene regulator enrichment analysis reveals a key role of the ETS transcription factor family in interferon signaling
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  18. Contextualized Protein-Protein Interactions
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  19. A systematic comparison of computational methods for expression forecasting
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    Rosie Griffiths, Woods Jon S, Aixin Cheng, Ping Wang, Sam Griffiths‐Jones, Matthew Ronshaugen, Susan J. Kimber · 2020 · Scientific Reports
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  28. Comparison of confound adjustment methods in the construction of gene co-expression networks
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  29. Socioeconomic inequalities in early adulthood disrupt the immune transcriptomic landscape via upstream regulators
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  31. Current Advances of Hollow Capsules as Controlled Drug Delivery Systems
    Huy Quang Tran, Mrinal R. Bhave, Aimin Yu · 2020 · ChemistrySelect
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  84. Applying Systems Medicine in the clinic
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  92. Measuring cynicism toward organizational change--one dimension or two?
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