Research map: Emerging Principles in Spatial Functional Genomics

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Papers in this map

  1. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9 · John G. Doench · 2016 · 5174 citations · Cited by this paper
  2. Decoding the complexity of intestinal immunity with spatial transcriptomics · 2026 · Related
  3. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens · Atray C. Dixit · 2016 · 2027 citations · Cited by this paper
  4. Understanding antiphospholipid syndrome clinical phenotypes with the guidance of antiphospholipid antibody-related pathogenic mechanisms · 2026 · Related
  5. A molecular cell atlas of the human lung from single-cell RNA sequencing · Kyle J. Travaglini · 2020 · 1901 citations · Cited by this paper
  6. Functional interactions of Kv1.3 channels in microglia and T cells and their implications in neurodegeneration · 2026 · Related
  7. High-throughput functional genomics using CRISPR–Cas9 · Ophir Shalem · 2015 · 1296 citations · Cited by this paper
  8. A critical look at disease classification/diagnosis criteria in rheumatology · 2026 · Related
  9. Pooled CRISPR screening with single-cell transcriptome readout · Paul Datlinger · 2017 · 1199 citations · Cited by this paper
  10. Mapping antibody sequences and effector functions across spatial niches · 2026 · Related
  11. Optical Pooled Screens in Human Cells · David Feldman · 2019 · 343 citations · Cited by this paper
  12. Why we need to maintain a critical view on big data and artificial intelligence predictions · 2026 · Related
  13. Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer · Jia‐Ren Lin · 2023 · 310 citations · Cited by this paper
  14. From disease to syndrome: the evolution of Parkinson’s as a heterogeneous entity · 2026 · Related
  15. Spatial CRISPR genomics identifies regulators of the tumor microenvironment · Maxime Dhainaut · 2022 · 300 citations · Cited by this paper
  16. Recurrent pericarditis in children: evidence, controversies, and emerging perspectives · 2026 · Related
  17. Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion · Chris J. Frangieh · 2021 · 290 citations · Cited by this paper
  18. Next-generation CRISPR screens enable causal systems immunology · 2026 · Related
  19. In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer · Juan Dubrot · 2022 · 233 citations · Cited by this paper
  20. Spatial metabolic heterogeneity shapes CD8+ T cell function in cancer · 2026 · Related
  21. A Tunable Diffusion-Consumption Mechanism of Cytokine Propagation Enables Plasticity in Cell-to-Cell Communication in the Immune System · Alon Oyler‐Yaniv · 2017 · 219 citations · Cited by this paper
  22. SpatialData: an open and universal data framework for spatial omics · Luca Marconato · 2024 · 211 citations · Cited by this paper
  23. The phenotypic landscape of essential human genes · Luke Funk · 2022 · 183 citations · Cited by this paper
  24. Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens · Aleksandra Wroblewska · 2018 · 181 citations · Cited by this paper
  25. Genetic screens in isogenic mammalian cell lines without single cell cloning · Peter C. DeWeirdt · 2020 · 160 citations · Cited by this paper
  26. Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows · Sergio Marco Salas · 2025 · 120 citations · Cited by this paper
  27. Ovarian cancer-derived IL-4 promotes immunotherapy resistance · Gürkan Mollaoglu · 2024 · 118 citations · Cited by this paper
  28. Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits · Loïc Binan · 2025 · 108 citations · Cited by this paper
  29. In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription · Amjad Askary · 2019 · 104 citations · Cited by this paper
  30. Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues · Zhiliang Bai · 2024 · 104 citations · Cited by this paper
  31. Chemotherapy induces myeloid-driven spatially confined T cell exhaustion in ovarian cancer · Inga-Maria Launonen · 2024 · 81 citations · Cited by this paper
  32. A multimodal atlas of tumour metabolism reveals the architecture of gene–metabolite covariation · Elisa Benedetti · 2023 · 75 citations · Cited by this paper
  33. Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView · Takamasa Kudo · 2024 · 62 citations · Cited by this paper
  34. Perturb-Multimodal: A platform for pooled genetic screens with imaging and sequencing in intact mammalian tissue · Reuben A. Saunders · 2025 · 58 citations · Cited by this paper
  35. Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap · Jiacheng Gu · 2024 · 55 citations · Cited by this paper
  36. Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma · Tanjina Kader · 2024 · 51 citations · Cited by this paper
  37. High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer · Luke W. Koblan · 2025 · 36 citations · Cited by this paper
  38. Machine Learning–Assisted Recurrence Prediction for Patients With Early-Stage Non–Small-Cell Lung Cancer · Adrianna Janik · 2023 · 29 citations · Cited by this paper
  39. Integrating cross-sample and cross-modal data for spatial transcriptomics and metabolomics with SpatialMETA · Ruonan Tian · 2025 · 29 citations · Cited by this paper

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