Research map: The next-generation virtual cell: From spatiotemporal transcriptomic modeling to closed-loop target discovery in complex diseases

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  1. GRADE: an emerging consensus on rating quality of evidence and strength of recommendations · Gordon Henry Guyatt · 2008 · 23433 citations · Cited by this paper
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  15. The false hope of current approaches to explainable artificial intelligence in health care · Marzyeh Ghassemi · 2021 · 1654 citations · Cited by this paper
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  17. The Missing Diversity in Human Genetic Studies · Giorgio Sirugo · 2019 · 1625 citations · Cited by this paper
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  19. Green AI · Roy Schwartz · 2020 · 1536 citations · Cited by this paper
  20. Benchmarking atlas-level data integration in single-cell genomics · Malte D. Luecken · 2021 · 1535 citations · Cited by this paper
  21. Effective gene expression prediction from sequence by integrating long-range interactions · Žiga Avsec · 2021 · 1422 citations · Cited by this paper
  22. A Whole-Cell Computational Model Predicts Phenotype from Genotype · Jonathan R. Karr · 2012 · 1354 citations · Cited by this paper
  23. Transfer learning enables predictions in network biology · Christina V. Theodoris · 2023 · 1207 citations · Cited by this paper
  24. MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data · Ricard Argelaguet · 2020 · 1146 citations · Cited by this paper
  25. The Clinician and Dataset Shift in Artificial Intelligence · Samuel G. Finlayson · 2021 · 806 citations · Cited by this paper
  26. Multi-omics single-cell data integration and regulatory inference with graph-linked embedding · Zhi‐Jie Cao · 2022 · 654 citations · Cited by this paper
  27. Deep Visual Proteomics defines single-cell identity and heterogeneity · Andreas Mund · 2022 · 586 citations · Cited by this paper
  28. Large-scale foundation model on single-cell transcriptomics · Minsheng Hao · 2024 · 561 citations · Cited by this paper
  29. Gene‐specific correlation of RNA and protein levels in human cells and tissues · Fredrik Edfors · 2016 · 534 citations · Cited by this paper
  30. Transparency and reproducibility in artificial intelligence · Benjamin Haibe‐Kains · 2020 · 534 citations · Cited by this paper
  31. Metabolic modeling of single Th17 cells reveals regulators of autoimmunity · Allon Wagner · 2021 · 530 citations · Cited by this paper
  32. How to build the virtual cell with artificial intelligence: Priorities and opportunities · Charlotte Bunne · 2024 · 385 citations · Cited by this paper
  33. Predicting transcriptional outcomes of novel multigene perturbations with GEARS · Yusuf Roohani · 2023 · 357 citations · Cited by this paper
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  36. A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data · Norah Alghamdi · 2021 · 257 citations · Cited by this paper
  37. Advancing regulatory variant effect prediction with AlphaGenome · Natasha S. Latysheva · 2026 · 236 citations · Cited by this paper
  38. Network-based machine learning in colorectal and bladder organoid models predicts anti-cancer drug efficacy in patients · JungHo Kong · 2020 · 216 citations · Cited by this paper
  39. Tackling algorithmic bias and promoting transparency in health datasets: the STANDING Together consensus recommendations · Joseph Edward Alderman · 2024 · 168 citations · Cited by this paper

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